To cite ChIP-Atlas in your publication:

• Paper
  • Zou, Z., Ohta, T., Oki, S. ChIP-Atlas 3.0: a data-mining suite to explore chromosome architecture together with large-scale regulome data. Nucleic Acids Res. 52(W1), W45-W53, 2024. http://dx.doi.org/10.1093/nar/gkae358
  • Zou, Z., Ohta, T., Miura, F., Oki, S. ChIP-Atlas 2021 update: a data-mining suite for exploring epigenomic landscapes by fully integrating ChIP-seq, ATAC-seq and Bisulfite-seq data. Nucleic Acids Res. 50(W1), W175-W182, 2022. http://dx.doi.org/10.1093/nar/gkac199
  • Oki, S., Ohta, T., Shioi, G., Hatanaka, H., Ogasawara, O., Okuda, Y., Kawaji, H., Nakaki, R., Sese, J., Meno, C. ChIP-Atlas: a data-mining suite powered by full integration of public ChIP-seq data. EMBO Rep. 19(12), e46255, 2018. http://dx.doi.org/10.15252/embr.201846255
• Web tool
  • Oki, S; Ohta, T (2015): ChIP-Atlas. https://chip-atlas.org

Publications citing ChIP-Atlas:

1. Abudahab, S., et al. Genome-wide analysis of hepatic DNA methylation reveals impact of epigenetic aging on xenobiotic metabolism and transport genes in an aged mouse model. Geroscience (2024). Link.
2. Adams, M., et al. Generation and analysis of a mouse multi-tissue genome annotation atlas. bioRxiv (2024). Link.
3. Agostino, SD., et al. The Strong Activation of p53 Tumor Suppressor Drives the Synthesis of the Enigmatic Isoform of DUSP13 Protein. Biomedicines (2024). Link.
4. Ahn, JY., et al. Dual function of PHF16 in reinstating homeostasis of murine intestinal epithelium after crypt regeneration. Dev Cell (2024). Link.
5. Al-Hadeethi, T., et al. Association Between Periodontitis and COVID-19. Curr Oral Health Rep (2024). Link.
6. Ali, S., et al. BATF controls IFN I production via DC-SCRIPT in plasmacytoid dendritic cells. bioRxiv (2024). Link.
7. Arimura, Y., et al. MagIC-Cryo-EM: Structural determination on magnetic beads for scarce macromolecules in heterogeneous samples. bioRxiv (2024). Link.
8. Balachandra, V., et al. DNAJC9 prevents CENP-A mislocalization and chromosomal instability by maintaining the fidelity of histone supply chains. EMBO J (2024). Link.
9. Barnes, PE., et al. Differential gene expression in cells with different p53 mutations identifies genome-wide p53 targets and shows distinct modulation of cellular pathways in response to DNA damage. bioRxiv (2024). Link.
10. Beknazarov, N., et al. Z-DNA formation in promoters conserved between human and mouse are associated with increased transcription reinitiation rates. Sci Rep (2024). Link.
11. Bergin, CJ.., et al. The dopamine transporter antagonist vanoxerine inhibits G9a and suppresses cancer stem cell functions in colon tumors. Nat Cancer (2024). Link.
12. Bhattacharyya, S., et al. Identifying genetic variants associated with chromatin looping and genome function. Nat Commun (2024). Link.
13. Brown, M., et al. Concordant B and T Cell Heterogeneity Inferred from the Multiomic Landscape of Peripheral Blood Mononuclear Cells in a Crohn's Disease Cohort. J Crohns Colitis (2024). Link.
14. Bryce-Smith, S., et al. TDP-43 loss induces extensive cryptic polyadenylation in ALS/FTD. bioRxiv (2024). Link.
15. Chandra, O., et al. Explainable models using transcription factor binding and epigenome patterns at promoters reveal disease-associated genes and their regulators in the context of cell-types. bioRxiv (2024). Link.
16. Chang, YH., et al. SETDB1 suppresses NK cell-mediated immunosurveillance in acute myeloid leukemia with granulo-monocytic differentiation. Cell Rep (2024). Link.
17. Chen, B., et al. LINC02454-CCT complex interaction is essential for telomerase activity and cell proliferation in head and neck squamous cell carcinoma. Cancer Lett (2024). Link.
18. Chen, H., et al. MiR-375 impairs breast cancer cell stemness by targeting the KLF5/G6PD signaling axis. Environ Toxicol (2024). Link.
19. Cheng, S., et al. Review and Evaluate the Bioinformatics Analysis Strategies of ATAC-seq and CUT&Tag Data. Genomics Proteomics Bioinformatics (2024). Link.
20. Christensen, LM.., et al. T-regulatory cells require Sin3a for stable expression of Foxp3. Front Immunol (2024). Link.
21. Cinquin, O. ChIP-GPT: a managed large language model for robust data extraction from biomedical database records. Brief Bioinform (2024). Link.
22. Cisneros-Soberanis, F., et al. Near millimolar concentration of nucleosomes in mitotic chromosomes from late prometaphase into anaphase. J Cell Biol (2024). Link.
23. Corton, J.C., et al. A 50-gene biomarker identifies estrogen receptor-modulating chemicals in a microarray compendium. Chem Biol Interact (2024). Link.
24. Cui, M., et al. HKDC1, a target of TFEB, is essential to maintain both mitochondrial and lysosomal homeostasis, preventing cellular senescence. Proc Natl Acad Sci U S A (2024). Link.
25. Cui, W., et al. Gut microbial metabolite facilitates colorectal cancer development via ferroptosis inhibition. Nat Cell Biol (2024). Link.
26. De Paolis, V., et al. Unconventional p65/p52 NF-κB module regulates key tumor microenvironment-related genes in breast tumor-associated macrophages (TAMs). C R Acad Sci III (2024). Link.
27. Deng, Q., et al. SMARCA4 is a haploinsufficient B cell lymphoma tumor suppressor that fine-tunes centrocyte cell fate decisions. Cancer Cell (2024). Link.
28. Dennis, M., et al. Her2 amplification, Rel-A, and Bach1 can influence APOBEC3A expression in breast cancer cells. PLoS Genet (2024). Link.
29. Diawara, M., et al. The transcription factors NR5A1 and JUNB cooperate to activate the Axl promoter in mouse Sertoli cell lines. Mol Biol Rep (2024). Link.
30. Ding, L., et al. Maternal high fat diet induces circadian clock-independent endocrine alterations impacting the metabolism of the offspring. iScience (2024). Link.
31. Du, Z., et al. RRM2 Promotes Liver Metastasis of Pancreatic Cancer by Stabilizing YBX1 and Activating the TGF-beta Pathway. iScience (2024). Link.
32. Ekstrom, TL.., et al. USP44 overexpression drives a MYC-like gene expression program in neuroblastoma through epigenetic reprogramming. Mol Cancer Res (2024). Link.
33. Fernández-Ginés, R., et al. Specific targeting of the NRF2/β-TrCP axis promotes beneficial effects in NASH. Redox Biol (2024). Link.
34. Franco Acevedo, A., et al. The transcriptional repressor BCL6 regulates CXCR3 chemokine and HLA II expression in endothelial cells. Am J Transplant (2024). Link.
35. Frenkel, M., et al. Large-scale discovery of chromatin dysregulation induced by oncofusions and other protein-coding variants. Nat Biotechnol (2024). Link.
36. Gan, Y., et al. Inferring gene regulatory networks from single-cell transcriptomics based on graph embedding. Bioinformatics (2024). Link.
37. Gancedo, S.N.., et al. The xenobiotic transporter ABCC4/MRP4 promotes epithelial mesenchymal transition in pancreatic cancer. Front Pharmacol (2024). Link.
38. Gao, L., et al. Caffeine upregulates SIRT3 expression to ameliorate astrocytes-mediated HIV-1 Tat neurotoxicity via suppression of EGR1 signaling pathway. J Neurovirol (2024). Link.
39. Garg, S., et al. BRD9 regulates normal human hematopoietic stem cell function and lineage differentiation. Cell Death Differ (2024). Link.
40. Grześ, M., et al. A common druggable signature of oncogenic c-Myc, mutant KRAS and mutant p53 reveals functional redundancy and competition among oncogenes in cancer. Cell Death Dis (2024). Link.
41. Gu, J., et al. Noncanonical functions of microRNAs in the nucleus. Sheng Wu Hua Xue Yu Sheng Wu Wu Li Xue Bao (Shanghai) (2024). Link.
42. Gualdrini, F., et al. An integrative epigenome-based strategy for unbiased functional profiling of clinical kinase inhibitors. Mol Syst Biol (2024). Link.
43. Guo, H., et al. Sp1 Regulates the M1 Polarization of Microglia Through the HuR/NF-κB Axis after Spinal Cord Injury. Int J Neurosci (2024). Link.
44. Han, S., et al. E2F1 modulates RCCD1 expression to participate in the initiation and progression of EMT in colorectal cancer. Pathol Res Pract (2024). Link.
45. Hara, T., et al. High N6-methyladenosine-activated TCEAL8 mRNA is a novel pancreatic cancer marker. Cancer Sci (2024). Link.
46. He, H., et al. GINS2 regulates temozolomide chemosensitivity via the EGR1/ECT2 axis in gliomas. Cell Death Dis (2024). Link.
47. He, W., et al. Npy transcription is regulated by noncanonical STAT3 signaling in hypothalamic neurons: Implication with lipotoxicity and obesity. Molec Cell Endocr (2024). Link.
48. Hosoi, H., et al. IGLL5 controlled by super-enhancer affects cell survival and MYC expression in mature B-cell lymphoma. Leuk Res Rep (2024). Link.
49. Iida, M., et al. Dysregulated synaptic gene expression in oligodendrocytes of spinal and bulbar muscular atrophy. bioRxiv (2024). Link.
50. Inoue, T., et al. The c.1617del variant of TMEM260 is identified as the most frequent single gene determinant for Japanese patients with a specific type of congenital heart disease. J Hum Genet (2024). Link.
51. Ito, M., et al. Protein acylations induced by a ketogenic diet demonstrate diverse patterns depending on organs and differ between histones and global proteins. Biochem Biophys Res Commun (2024). Link.
52. Iyer, P., et al. MGA deletion leads to Richter's transformation by modulating mitochondrial OXPHOS. Sci Transl Med (2024). Link.
53. Jabeen, S., et al. A Comprehensive Evaluation of Self Attention for Detecting Feature Interactions. bioRxiv (2024). Link.
54. Jones, AG.., et al. Biological sex affects functional variation across the human genome. medRxiv (2024). Link.
55. Kaizuka, T., et al. Remodeling of the postsynaptic proteome in male mice and marmosets during synapse development. Nat Commun (2024). Link.
56. Kalyanaraman, H., et al. A plasma membrane-associated form of the androgen receptor enhances nuclear androgen signaling in osteoblasts and prostate cancer cells. Sci Signal (2024). Link.
57. Kano, N., et al. Identification and characterization of putative enhancer regions that direct Il6 transcription in murine macrophages. Int Immunol (2024). Link.
58. Karkoutly, S., et al. FoxO transcription factors regulate urea cycle through Ass1. Biochem Biophys Res Commun (2024). Link.
59. Katagiri, M., et al. NR4A3 deficiency ameliorates contact hypersensitivity and exacerbates psoriasis by regulating gene expression in dendritic cells. bioRxiv (2024). Link.
60. Kawakatsu, R., et al. Venetoclax efficacy on acute myeloid leukemia is enhanced by the combination with butyrate. Sci Rep (2024). Link.
61. Kim, GD., et al. Cell Type- and Age-Specific Expression of lncRNAs across Kidney Cell Types. J Am Soc Nephrol (2024). Link.
62. Kirtana, R., et al. Modulation of H3K4 trimethylation by KDM5A and MLLs impacts metabolic adaptability in prostate and cervical cancer cells. bioRxiv (2024). Link.
63. Kohnke, T., et al. Human ASXL1-mutant hematopoiesis is driven by a truncated protein associated with aberrant de-ubiquitination of H2AK119. Blood Cancer Discov (2024). Link.
64. Kuga, T., et al. Enhanced GATA4 expression in senescent systemic lupus erythematosus monocytes promotes high levels of IFNα production. Front Immunol (2024). Link.
65. Lambourne, L., et al. Widespread variation in molecular interactions and regulatory properties among transcription factor isoforms. bioRxiv (2024). Link.
66. Lee, PW.T.., et al. Hypoxia- and Postirradiation reoxygenation-induced HMHA1/ARHGAP45 expression contributes to cancer cell invasion in a HIF-dependent manner. Br J Cancer (2024). Link.
67. Li, C., et al. Mi-2β promotes immune evasion in melanoma by activating EZH2 methylation. Nat Commun (2024). Link.
68. Li, J., et al. Stabilization of KPNB1 by deubiquitinase USP7 promotes glioblastoma progression through the YBX1-NLGN3 axis. J Exp Clin Cancer Res (2024). Link.
69. Li, JN., et al. SnoRNA U50A mediates everolimus resistance in breast cancer through mTOR downregulation. Transl Oncol (2024). Link.
70. Li, X., et al. LINE-1 transcription activates long-range gene expression. Nat Genet (2024). Link.
71. Li, XC., et al. TF-High-Evolutionary: in vivo mutagenesis of gene regulatory networks for the study of the genetics and evolution of the Drosophila regulatory genome. Mol Biol Evol (2024). Link.
72. Li-Bao, L., et al. Regulation of Myc transcription by an enhancer cluster dedicated to pluripotency and early embryonic expression. Nat Commun (2024). Link.
73. Liao, TT., et al. Hypoxia-induced long non-coding RNA HIF1A‑AS2 regulates stability of MHC class I protein in head and neck cancer. Cancer Immunol Res (2024). Link.
74. Liguoro, D., et al. The MITF/mir-579-3p regulatory axis dictates BRAF-mutated melanoma cell fate in response to MAPK inhibitors. Cell Death Dis (2024). Link.
75. Lim, CH., et al. ER Stress-Activated HSF1 Governs Cancer Cell Resistance to USP7 Inhibitor-Based Chemotherapy through the PERK Pathway. Int J Mol Sci (2024). Link.
76. Lin, HY., et al. The TLK-ASF1 histone chaperone pathway plays a critical role in IL-1b-mediated AML progression. Blood (2024). Link.
77. Lin, SC., et al. Un-methylation of NUDT21 represses docosahexaenoic acid biosynthesis contributing to enzalutamide resistance in prostate cancer. Drug Resist Update (2024). Link.
78. Lin, YS., et al. Overexpression of NUDT16L1 sustains proper function of mitochondria and leads to ferroptosis insensitivity in colorectal cancer. Redox Biol (2024). Link.
79. Liu, K., et al. HMGA2 overexpression activates IGF2BP2 to stabilize APLP2 via m6A modification and promote pancreatic cancer progression. Heliyon (2024). Link.
80. Liu, N., et al. RBM39 enhances cholangiocarcinoma growth through EZH2-mediated WNT7B/β-catenin pathway. Cell Mol Gastroenterol Hepatol (2024). Link.
81. Liu, X., et al. Discovering common pathogenetic processes between tuberculosis and COVID-19 by bioinformatics and system biology approach. Heliyon (2024). Link.
82. Liu, Y., et al. ETS1-mediated Regulation of SOAT1 Enhances the Malignant Phenotype of Oral Squamous Cell Carcinoma and Induces Tumor-associated Macrophages M2-like Polarization. Int J Biol Sci (2024). Link.
83. Lodi, MK., et al. COFFEE: Consensus Single Cell-Type Specific Inference for Gene Regulatory Networks. bioRxiv (2024). Link.
84. Lorenzo, J.P., et al. APOBEC2 safeguards skeletal muscle cell fate through binding chromatin and regulating transcription of non-muscle genes during myoblast differentiation. Proc Natl Acad Sci U S A (2024). Link.
85. Loupe, JM.., et al. Multiomic profiling of transcription factor binding and function in human brain. Nat Neurosci (2024). Link.
86. Lu, F., et al. Oncogenic Gene CNOT7 Promotes Progression and Induces Poor Prognosis of Glioma. Mol Biotechnol (2024). Link.
87. Lu, Z., et al. Assessing NGS-based computational methods for predicting transcriptional regulators with query gene sets. bioRxiv (2024). Link.
88. Lu, Z., et al. Assessing next-generation sequencing-based computational methods for predicting transcriptional regulators with query gene sets. Brief Bioinform (2024). Link.
89. Lu, Z., et al. BIT: Bayesian Identification of Transcriptional Regulators. bioRxiv (2024). Link.
90. M, A., et al. Chem-CRISPR/dCas9FCPF: a platform for chemically induced epigenome editing. Nucleic Acids Res (2024). Link.
91. M, SP., et al. Genomic profiling of six human somatic histone H1 variants denotes that H1X accumulates at recently incorporated transposable elements. Nucleic Acids Res (2024). Link.
92. Ma, W., et al. Orphan Nuclear Receptor NR4A3 Promotes Vascular Calcification via Histone Lactylation. Circ Res (2024). Link.
93. MacFawn, I., et al. Grainyhead-like-2, an epithelial master programmer, promotes interferon induction and suppresses breast cancer recurrence. Mol Immunol (2024). Link.
94. Mahmood, N., et al. Methyl-CpG binding domain protein 2 (Mbd2) drives breast cancer progression through the modulation of epithelial-to-mesenchymal transition. Exp Mol Med (2024). Link.
95. Mahmood, N., et al. The ISR downstream target ATF4 represses long-term memory in a cell type-specific manner. Proc Natl Acad Sci U S A (2024). Link.
96. Malekpour, SA., et al. Single-cell multi-omics analysis identifies context-specific gene regulatory gates and mechanisms. Brief Bioinform (2024). Link.
97. Mannens, CC.A.., et al. Chromatin accessibility during human first-trimester neurodevelopment. Nature (2024). Link.
98. Mannion, AJ.., et al. Regulation of YAP Promotor Accessibility in Endothelial Mechanotransduction. Arterioscler Thromb Vasc Biol (2024). Link.
99. Miao, M., et al. IL-13 facilitates ferroptotic death in asthmatic epithelial cells via SOCS1-mediated ubiquitinated degradation of SLC7A11. Redox Biol (2024). Link.
100. Minaeva, M., et al. Specifying cellular context of transcription factor regulons for exploring context-specific gene regulation programs. bioRxiv (2024). Link.
101. Montero-Hidalgo, AJ.., et al. SRSF6 modulates histone-chaperone HIRA splicing to orchestrate AR and E2F activity in prostate cancer. Sci Adv (2024). Link.
102. Moreira, P., et al. Nuclear factor Y, a key player in neuronal gene regulation. Sci Prog (2024). Link.
103. Murao, N., et al. The Derlin-1-Stat5b axis maintains homeostasis of adult hippocampal neurogenesis. EMBO Rep (2024). Link.
104. Nakamura, T., et al. Topologically associating domains define the impact of de novo promoter variants on autism spectrum disorder risk. Cell Genom (2024). Link.
105. Nakanishi, T., et al. Complex intrinsic abnormalities in osteoblast lineage cells of X-linked hypophosphatemia: Analysis of human iPS cell models generated by CRISPR/Cas9-mediated gene ablation. Bone (2024). Link.
106. Nguyen, A., et al. Jumonji histone demethylases are therapeutic targets in small cell lung cancer. Oncogene (2024). Link.
107. Niimi, K., et al. Macrophages play a crucial role in vascular smooth muscle cell coverage. Development (2024). Link.
108. Nornes, S., et al. A catalogue of verified and characterized arterial enhancers for key arterial identity genes. bioRxiv (2024). Link.
109. Oguchi, A., et al. An atlas of transcribed enhancers across helper T cell diversity for decoding human diseases. Science (2024). Link.
110. Olszewska, A.M.., et al. Genomic and non-genomic action of vitamin D on ion channels - Targeting mitochondria. Mitochondrion (2024). Link.
111. Pandey, A., et al. CTCF and BORIS-mediated Autophagy regulation via Alternative splicing of BNIP3L in Breast Cancer. J Biol Chem (2024). Link.
112. Peng, G., et al. TSCRE: a comprehensive database for tumor-specific cis-regulatory elements. NAR Cancer (2024). Link.
113. Peng, Q., et al. Analysis of blood methylation quantitative trait loci in East Asians reveals ancestry-specific impacts on complex traits. Nat Genet (2024). Link.
114. Petersen, RM.., et al. Uncovering methylation-dependent genetic effects on regulatory element function in diverse genomes. bioRxiv (2024). Link.
115. Peña-Martínez, EG.., et al. Cardiovascular Disease-Associated Non-Coding Variants Disrupt GATA4-DNA Binding and Regulatory Functions. bioRxiv (2024). Link.
116. Pollin, G., et al. Ehmt2 inactivation in pancreatic epithelial cells shapes the transcriptional landscape and inflammation response of the whole pancreas. Front Genet (2024). Link.
117. Rachid Zaim, S., et al. MOCHA's advanced statistical modeling of scATAC-seq data enables functional genomic inference in large human cohorts. Nat Commun (2024). Link.
118. Rajendra, KC., et al. Evidence of RNA polymerase III recruitment and transcription at protein-coding gene promoters. bioRxiv (2024). Link.
119. Ramirez, JM., et al. The molecular impact of cigarette smoking resembles aging across tissues. bioRxiv (2024). Link.
120. Refael, T., et al. An i-motif-regulated enhancer, eRNA and adjacent lncRNA affect Lhb expression through distinct mechanisms in a sex-specific context. Cell Mol Life Sci (2024). Link.
121. Ren, Y., et al. Hyper-methylation and DNMT3A mediated LTC4S downregulation promoted lung adenocarcinoma tumorigenesis via mTORC1 signaling pathway. Heliyon (2024). Link.
122. Rhizobium, GE. The 22nd annual Nucleic Acids Research Web Server Issue 2024. Nucleic Acids Res (2024). Link.
123. Ribeiro, JH., et al. A human-specific, concerted repression of microcephaly genes contributes to radiation-induced growth defects in forebrain organoids. bioRxiv (2024). Link.
124. Ruscitti, C., et al. Recruited atypical Ly6G+ macrophages license alveolar regeneration after lung injury. Sci Immunol (2024). Link.
125. Ryu, JE., et al. Circadian regulation of endoplasmic reticulum calcium response in mouse cultured astrocytes. bioRxiv (2024). Link.
126. Safaeesirat, A., et al. Inference of Transcriptional Regulation From STARR-seq Data. bioRxiv (2024). Link.
127. Sakai, S., et al. In vivo transition in chromatin accessibility during differentiation of deep-layer excitatory neurons in the neocortex. bioRxiv (2024). Link.
128. Sarott, RC., et al. Relocalizing transcriptional kinases to activate apoptosis. Science (2024). Link.
129. Sato, Y., et al. Calcineurin/NFATc1 pathway represses cellular cytotoxicity by modulating histone H3 expression. Sci Rep (2024). Link.
130. Sergi, B., et al. Epidrug Screening Identifies Type I PRMT Inhibitors as Modulators of Lysosomal Exocytosis and Drug Sensitivity in Cancers. bioRxiv (2024). Link.
131. Shen, X., et al. TRIM33 plays a critical role in regulating dendritic cell differentiation and homeostasis by modulating Irf8 and Bcl2l11 transcription. Cell Mol Immunol (2024). Link.
132. Shrestha, R., et al. An Atlas of Accessible Chromatin in Advanced Prostate Cancer Reveals the Epigenetic Evolution during Tumor Progression. Cancer Res (2024). Link.
133. Singh, DK.., et al. MANCR lncRNA Modulates Cell-Cycle Progression and Metastasis by Cis-Regulation of Nuclear Rho-GEF. Mol Cell Biol (2024). Link.
134. Siraj, L., et al. Functional dissection of complex and molecular trait variants at single nucleotide resolution. bioRxiv (2024). Link.
135. Sizer, RE., et al. Selective Occupation by E2F and RB of Loci Expressed by RNA Polymerase III. Cancers (2024). Link.
136. Sonnemann, HM.., et al. Placental co-transcriptional activator Vestigial-like 1 (VGLL1) drives tumorigenesis via increasing transcription of proliferation and invasion genes. Front Oncol (2024). Link.
137. Stadler, M., et al. asteRIa enables robust interaction modeling between chromatin modifications and epigenetic readers. bioRxiv (2024). Link.
138. Statello, L., et al. The chromatin-associated lncREST ensures effective replication stress response by promoting the assembly of fork signaling factors. Nat Commun (2024). Link.
139. Su, G., et al. Inferring gene regulatory networks by hypergraph variational autoencoder. bioRxiv (2024). Link.
140. Suzuki, H., et al. Mutant α-synuclein causes death of human cortical neurons via ERK1/2 and JNK activation. Mol Brain (2024). Link.
141. Tabata, S., et al. NFκB dynamics-dependent epigenetic changes modulate inflammatory gene expression and induce cellular senescence. FEBS J (2024). Link.
142. Takasugi, M., et al. An atlas of the aging mouse proteome reveals the features of age-related post-transcriptional dysregulation. Nat Commun (2024). Link.
143. Takhaveev, V., et al. Click-chemistry-aided quantitation and sequencing of oxidized guanines and apurinic sites uncovers their transcription-linked strand bias in human cells. bioRxiv (2024). Link.
144. Tan, H., et al. TSPYL1 as a Critical Regulator of TGFβ Signaling through Repression of TGFBR1 and TSPYL2. Adv Sci (2024). Link.
145. Tang, L., et al. Targeting autophagy overcomes cancer-intrinsic resistance to CAR-T immunotherapy in B-cell malignancies. Cancer Commun (2024). Link.
146. Thapa, R., et al. The Long Non-Coding RNA Gene AC027288.3 Plays a Role in Human Endometrial Stromal Fibroblast Decidualization. Cells (2024). Link.
147. Tomita-Naito, S., et al. Insidious chromatin change with a propensity to exhaust intestinal stem cells during aging. iScience (2024). Link.
148. Tomiyasu, H., et al. FOXO1 promotes cancer cell growth through MDM2-mediated p53 degradation. J Biol Chem (2024). Link.
149. Ueno, T., et al. Myc upregulates Ggct, γ-glutamylcyclotransferase to promote development of p53-deficient osteosarcoma. bioRxiv (2024). Link.
150. Ulfig, A., et al. Redox heterogeneity in mouse embryonic stem cells individualizes cell fate decisions. Dev Cell (2024). Link.
151. Umhoefer, JM.., et al. Deciphering regulation of FOXP3 expression in human conventional T cells. bioRxiv (2024). Link.
152. Vishnevsky, OV.., et al. Peak Scores Significantly Depend on the Relationships between Contextual Signals in ChIP-Seq Peaks. Int J Mol Sci (2024). Link.
153. Wan, L., et al. Identification of a molecular network regulated by multiple ASD high risk genes. Hum Mol Genet (2024). Link.
154. Wan, R., et al. Unveiling gene regulatory networks during cellular state transitions without linkage across time points. Sci Rep (2024). Link.
155. Wan, Y., et al. Brusatol induces ferroptosis to inhibit hepatocellular carcinoma progression by targeting ATF3. Chem Biol Drug Des (2024). Link.
156. Wang, C., et al. The Oncogenic Role of TNFRSF12A in Colorectal Cancer and Pan-Cancer Bioinformatics Analysis. Cancer Res Treat (2024). Link.
157. Wang, J. TFTF: An R-Based Integrative Tool for Decoding Human Transcription Factor–Target Interactions. Biomolecules (2024). Link.
158. Wang, W., et al. Scalable identification of lineage-specific gene regulatory networks from metacells with NetID. bioRxiv (2024). Link.
159. Wei, T., et al. FOXM1/DEPDC1 feedback loop promotes hepatocarcinogenesis and represents promising targets for cancer therapy. Cancer Sci (2024). Link.
160. Wei, X., et al. Competitive-like binding between carbon black and CTNNB1 to ΔNp63 interpreting the abnormal respiratory epithelial repair after injury. Sci Total Environ (2024). Link.
161. Wu, B., et al. Overloading And unpacKing (OAK) - droplet-based combinatorial indexing for ultra-high throughput single-cell multiomic profiling. bioRxiv (2024). Link.
162. Wu, F., et al. NUP43 promotes PD-L1/nPD-L1/PD-L1 feedback loop via TM4SF1/JAK/STAT3 pathway in colorectal cancer progression and metastatsis. Cell Death Discov (2024). Link.
163. YOSHIZAWA, MASATO., et al. Depletion of DNTTIP2 Induces Cell Cycle Arrest in Pancreatic Cancer Cells. Cancer Genomics Proteomics (2024). Link.
164. Ye, P., et al. Genomics-FM: Universal Foundation Model for Versatile and Data-Efficient Functional Genomic Analysis. bioRxiv (2024). Link.
165. Yi, W., et al. Molecular Signatures of CB-6644 Inhibition of the RUVBL1/2 Complex in Multiple Myeloma. Int J Mol Sci (2024). Link.
166. Yoshioka, H., et al. Alteration of Gene Expression in Pathological Keratinization of the Ocular Surface. Invest Ophthalmol Vis Sci (2024). Link.
167. Yu, X., et al. Time-course swRNA-seq uncovers a hierarchical gene regulatory network in controlling the response-repair-remodeling after wounding. Commun Biol (2024). Link.
168. Z, Z., et al. ChIP-Atlas 3.0: a data-mining suite to explore chromosome architecture together with large-scale regulome data. Nucleic Acids Res (2024). Link.
169. Zandigohar, M., et al. Transcription Factor Activity Regulating Macrophage Heterogeneity during Skin Wound Healing. J Immunol (2024). Link.
170. Zeng, Y., et al. CellFM: a large-scale foundation model pre-trained on transcriptomics of 100 million human cells. bioRxiv (2024). Link.
171. Zhang, D., et al. LogicGep: Boolean networks inference using symbolic regression from time-series transcriptomic profiling data. Brief Bioinform (2024). Link.
172. Zhang, G., et al. TRAPT: A multi-stage fused deep learning framework for transcriptional regulators prediction via integrating large-scale epigenomic data. bioRxiv (2024). Link.
173. Zhang, Q., et al. ZDHHC1 downregulates LIPG and inhibits colorectal cancer growth via IGF2BP1 Palmitoylation. Cancer Gene Ther (2024). Link.
174. Zhang, S., et al. Endogenous sulfur dioxide deficiency as a driver of cardiomyocyte senescence through abolishing sulphenylation of STAT3 at cysteine 259. Redox Biol (2024). Link.
175. Zhang, W., et al. HDAC7 is a potential therapeutic target in acute erythroid leukemia. Leukemia (2024). Link.
176. Zhao, X., et al. Identification the immune related marker genes and transcription-factor network in ruptured cerebral aneurysms using bioinformatics analysis and machine-learning strategies. Biomed Signal Process Control (2024). Link.
177. Zhou, X., et al. TFTG: A comprehensive database for human transcription factors and their targets. Comput Struct Biotechnol J (2024). Link.
178. Zhou, Z., et al. FBW7/GSK3β mediated degradation of IGF2BP2 inhibits IGF2BP2-SLC7A5 positive feedback loop and radioresistance in lung cancer. J Exp Clin Cancer Res (2024). Link.
179. Zhu, X., et al. Genomic and transcriptomic features of androgen receptor signaling inhibitor resistance in metastatic castration-resistant prostate cancer. J Clin Invest (2024). Link.
180. da Silva, JéEH.., et al. A Data-Distribution and Successive Spline Points based discretization approach for evolving gene regulatory networks from scRNA-Seq time-series data using Cartesian Genetic Programming. Biosystems (2024). Link.
181. Łasut-Szyszka, B., et al. Transcriptomic and proteomic study of cancer cell lines exposed to actinomycin D and nutlin-3a reveals numerous, novel candidates for p53-regulated genes. Chem Biol Interact (2024). Link.
182. Abashkin, DA.., et al. ASCL1 Is Involved in the Pathogenesis of Schizophrenia by Regulation of Genes Related to Cell Proliferation, Neuronal Signature Formation, and Neuroplasticity. Int J Mol Sci (2023). Link.
183. Anzawa, H., et al. C4S DB: Comprehensive Collection and Comparison for ChIP-Seq Database. J Mol Biol (2023). Link.
184. Arimoto, K., et al. Expansion of interferon inducible gene pool via USP18 inhibition promotes cancer cell pyroptosis. Nat Commun (2023). Link.
185. Armaos, A., et al. The PENGUIN approach to reconstruct protein interactions at enhancer-promoter regions and its application to prostate cancer. Nat Commun (2023). Link.
186. Arriojas, A., et al. A Bayesian Noisy Logic Model for Inference of Transcription Factor Activity from Single Cell and Bulk Transcriptomic Data. bioRxiv (2023). Link.
187. Asavasupreechar, T., et al. PRB inhibited cell proliferation through let-7b-E2F1 in breast cancer. Endocr Relat Cancer (2023). Link.
188. Azzi, A., et al. The circadian clock protein Cryptochrome 1 is a direct target and feedback regulator of the Hippo pathway. iScience (2023). Link.
189. BP, P., et al. Pcgf1 gene disruption reveals primary involvement of epigenetic mechanism in neuronal subtype specification in the enteric nervous system. Dev Growth Differ (2023). Link.
190. Badia-i-Mompel, P., et al. Gene regulatory network inference in the era of single-cell multi-omics. Nat Rev Genet (2023). Link.
191. Bai, Y., et al. Trans-omic analysis reveals opposite metabolic dysregulation between feeding and fasting in liver associated with obesity. bioRxiv (2023). Link.
192. Barvaux, S., et al. SinCMat: A single-cell-based method for predicting functional maturation transcription factors. Stem Cell Rep (2023). Link.
193. Beknazarov, N., et al. Z-Flipons conserved between human and mouse are associated with increased transcription initiation rates. bioRxiv (2023). Link.
194. Bertonnier-Brouty, L., et al. E2F transcription factors promote tumorigenicity in pancreatic ductal adenocarcinoma. bioRxiv (2023). Link.
195. Bhardwaj, V., et al. HIV-1 Vpr induces ciTRAN to prevent transcriptional repression of the provirus. Sci Adv (2023). Link.
196. Bhin, J., et al. MYC is a clinically significant driver of mTOR inhibitor resistance in breast cancer. J Exp Med (2023). Link.
197. Bi, X., et al. Pan-cancer analyses reveal multi-omic signatures and clinical implementations of the forkhead-box gene family. Cancer Med (2023). Link.
198. Bossardi Ramos, R., et al. Shock drives a STAT3 and JunB-mediated coordinated transcriptional and DNA methylation response in the endothelium. J Cell Sci (2023). Link.
199. Bu, Q., et al. STC2 is a potential biomarker of hepatocellular carcinoma with its expression being upregulated in Nrf1α-deficient cells, but downregulated in Nrf2-deficient cells. Int J Biol Macromol (2023). Link.
200. Bu, Q., et al. Stanniocalcin 2 (STC2) is a potent biomarker of hepatocellular carcinoma with its expression being augmented in Nrf1α-deficient cells, but diminished in Nrf2-deficient cells. bioRxiv (2023). Link.
201. Bustin, KA.., et al. Phenelzine-based probes reveal Secernin-3 is involved in thermal nociception. bioRxiv (2023). Link.
202. Büchel, J., et al. Single-nucleotide-resolution genomic maps of O6-methylguanine from the glioblastoma drug temozolomide. bioRxiv (2023). Link.
203. C, B., et al. Transmicron: accurate prediction of insertion probabilities improves detection of cancer driver genes from transposon mutagenesis screens. Nucleic Acids Res (2023). Link.
204. CN, C., et al. PlantPAN 4.0: updated database for identifying conserved non-coding sequences and exploring dynamic transcriptional regulation in plant promoters. Nucleic Acids Res (2023). Link.
205. Castillo, Hé., et al. Architecture and evolutionary conservation of Xenopus tropicalis osteoblast-specific regulatory regions shed light on bone diseases and early skeletal evolution. bioRxiv (2023). Link.
206. Chandra, A., et al. Quantitative control of Ets1 dosage by a multi-enhancer hub promotes Th1 cell differentiation and protects from allergic inflammation. Immunity (2023). Link.
207. Chandra, O., et al. Patterns of transcription factor binding and epigenome at promoters allow interpretable predictability of multiple functions of non-coding and coding genes. Comput Struct Biotechnol J (2023). Link.
208. Chen, L., et al. NPM3 as an unfavorable prognostic biomarker involved in oncogenic pathways of lung adenocarcinoma via MYC translational activation. Comb Chem High Throughput Screen (2023). Link.
209. Chen, W., et al. Mechanic Insight into the Distinct and Common Roles of Ovariectomy Versus Adrenalectomy on Adipose Tissue Remodeling in Female Mice. Int J Mol Sci (2023). Link.
210. Chen, WC., et al. Genome-wide association study of esophageal squamous cell cancer identifies shared and distinct risk variants in African and Chinese populations. Am J Hum Genet (2023). Link.
211. Chen, Y., et al. Canonical and nuclear mTOR specify distinct transcriptional programs in androgen-dependent prostate cancer cells. Mol Cancer Res (2023). Link.
212. Cheng, R., et al. A Combinatorial Regulatory Platform Determines Expression of RNA Polymerase III Subunit RPC7α ( POLR3G) in Cancer. Cancers (2023). Link.
213. Chow, CC.T.., et al. ZBTB2 is Recruited to a Specific Subset of HIF-1 Target Loci to Facilitate Full Gene Expression Under Hypoxia. J Mol Biol (2023). Link.
214. Chow, CN., et al. Databases and prospects of dynamic gene regulation in eukaryotes: A mini review. Comput Struct Biotechnol J (2023). Link.
215. Dai, C., et al. Comprehensive analysis of the diagnostic and therapeutic value of the hypoxia-related gene PLAUR in the progression of atherosclerosis. Sci Rep (2023). Link.
216. Diawara, M., et al. Regulatory mechanisms of SoxD transcription factors and their influences on male fertility. Reprod Biol (2023). Link.
217. Dong, L., et al. A functional crosstalk between the H3K9 methylation writers and their reader HP1 in safeguarding embryonic stem cell identity. Stem Cell Rep (2023). Link.
218. Escalante-Covarrubias, Q., et al. Time-of-day defines NAD+ efficacy to treat diet-induced metabolic disease by synchronizing the hepatic clock in mice. Nat Commun (2023). Link.
219. Etoh, K., et al. A web-based integrative transcriptome analysis, RNAseqChef, uncovers cell/tissue type-dependent action of sulforaphane. J Biol Chem (2023). Link.
220. FC, Q., et al. SEanalysis 2.0: a comprehensive super-enhancer regulatory network analysis tool for human and mouse. Nucleic Acids Res (2023). Link.
221. Fajac, A., et al. Mutant mice lacking alternatively spliced p53 isoforms unveil Ackr4 as a male-specific prognostic factor in Myc-driven B-cell lymphomas. bioRxiv (2023). Link.
222. Feng, G., et al. CellPolaris: Decoding Cell Fate through Generalization Transfer Learning of Gene Regulatory Networks. bioRxiv (2023). Link.
223. Feng, K., et al. Gene regulatory network inference based on causal discovery integrating with graph neural network. Quant Biol (2023). Link.
224. Filipovic, D., et al. Interpretable predictive models of genome-wide aryl hydrocarbon receptor-DNA binding reveal tissue specific binding determinants. Toxicol Sci (2023). Link.
225. Francia, MG., et al. AKT1 induces Nanog promoter in a SUMOylation-dependent manner in different pluripotent contexts. BMC Res Notes (2023). Link.
226. Freeman, TF.., et al. Ribosome biogenesis disruption mediated chromatin structure changes revealed by SRAtac, a customizable end to end analysis pipeline for ATAC-seq. BMC Genomics (2023). Link.
227. Frenkel, M., et al. Discovering chromatin dysregulation induced by protein-coding perturbations at scale. bioRxiv (2023). Link.
228. Fu, Y., et al. Fam72a functions as a cell-cycle-controlled gene during proliferation and antagonizes apoptosis through reprogramming PP2A substrates. Dev Cell (2023). Link.
229. Gao, Z., et al. Phase Separation Modulates the Formation and Stabilities of DNA Guanine Quadruplex. JACS Au (2023). Link.
230. García‐Hernández, V., et al. β-Catenin activity induces an RNA biosynthesis program promoting therapy resistance in T-cell acute lymphoblastic leukemia. EMBO Mol Med (2023). Link.
231. Ghaibour, K., et al. An Efficient Protocol for CUT&RUN Analysis of FACS-Isolated Mouse Satellite Cells. J Vis Exp (2023). Link.
232. Goncalves, TM., et al. Unsupervised Machine Learning Identify Cis-Regulatory Network Involved in Neurodegeneration. Alzheimers Dement (2023). Link.
233. Gong, B., et al. Epigenetic and transcriptional activation of the secretory kinase FAM20C as an oncogene in glioma. J Genet Genom (2023). Link.
234. Grey, W., et al. The CKS1/CKS2 Proteostasis Axis Is Crucial to Maintain Hematopoietic Stem Cell Function. Hemasphere (2023). Link.
235. Hagemann, S., et al. IGF2BP1 induces high-risk neuroblastoma and forms a druggable feedforward loop with MYCN promoting 17q oncogene expression. bioRxiv (2023). Link.
236. Hagemann, S., et al. IGF2BP1 induces neuroblastoma via a druggable feedforward loop with MYCN promoting 17q oncogene expression. Mol Cancer (2023). Link.
237. Hamba, Y., et al. Topologically associating domain underlies tissue specific expression of long intergenic non-coding RNAs. iScience (2023). Link.
238. Hanaki, S., et al. Impact of FKBP52 on cell proliferation and hormone-dependent cancers. Cancer Sci (2023). Link.
239. Harada, S., et al. The Lysophospholipase PNPLA7 Controls Hepatic Choline and Methionine Metabolism. Biomolecules (2023). Link.
240. Herbert, A. Flipons and small RNAs accentuate the asymmetries of pervasive transcription by the reset and sequence-specific microcoding of promoter conformation. J Biol Chem (2023). Link.
241. Hino, S., et al. Chromatin Immunoprecipitation Sequencing (ChIP-seq) for Detecting Histone Modifications and Modifiers. Methods Mol Biol (2023). Link.
242. Hou, Y., et al. Transcriptome sequencing analysis reveals a potential role of lncRNA NONMMUT058932.2 and NONMMUT029203.2 in abnormal myelin development of male offspring following prenatal PM2.5 exposure. Sci Total Environ (2023). Link.
243. Hsieh, Y‐T., et al. IFN-stimulated metabolite transporter ENT3 facilitates viral genome release. EMBO Rep (2023). Link.
244. Hu, Q., et al. GPX3 expression was down-regulated but positively correlated with poor outcome in human cancers. Front Oncol (2023). Link.
245. Huang, D., et al. MAX transcriptionally enhances PD-L1 to inhibit CD8+ T cell-mediated killing of lung adenocarcinoma cells. Cell Immunol (2023). Link.
246. Huang, W., et al. NFAT and NF-κB dynamically co-regulate TCR and CAR signaling responses in human T cells. Cell Rep (2023). Link.
247. Hughes, LA.., et al. Copy number variation in tRNA isodecoder genes impairs mammalian development and balanced translation. Nat Commun (2023). Link.
248. Huo, S., et al. ATF3/SPI1/SLC31A1 Signaling Promotes Cuproptosis Induced by Advanced Glycosylation End Products in Diabetic Myocardial Injury. Int J Mol Sci (2023). Link.
249. Inagaki, T., et al. Prolonged Kaposi’s Sarcoma-associated Herpesvirus vIL-6 Exposure Enhances Inflammatory Responses by Epigenetic Reprogramming. bioRxiv (2023). Link.
250. Inubushi, T., et al. On-demand chlorine dioxide solution enhances odontoblast differentiation through desulfation of cell surface heparan sulfate proteoglycan and subsequent activation of canonical Wnt signaling. Front Cell Dev Biol (2023). Link.
251. Ishikawa, M., et al. Inference of gene regulatory networks using time-series single-cell RNA-seq data with CRISPR perturbations. bioRxiv (2023). Link.
252. Isobe, S., et al. Reduced FOXF1 links unrepaired DNA damage to pulmonary arterial hypertension. Nat Commun (2023). Link.
253. Itakura, H., et al. Tumor-suppressive role of the musculoaponeurotic fibrosarcoma gene in colorectal cancer. iScience (2023). Link.
254. Ito, S., et al. Androgen receptor binding sites enabling genetic prediction of mortality due to prostate cancer in cancer-free subjects. Nat Commun (2023). Link.
255. Iyer, DR.., et al. Cyclic-AMP response element binding protein (CREB) and microRNA miR-29b regulate renalase gene expression under catecholamine excess conditions. Life Sci (2023). Link.
256. Iyer, P., et al. MGA deletion leads to Richter’s transformation via modulation of mitochondrial OXPHOS. bioRxiv (2023). Link.
257. J, M., et al. Genetic variation is a key determinant of chromatin accessibility and drives differences in the regulatory landscape of C57BL/6J and 129S1/SvImJ mice. Nucleic Acids Res (2023). Link.
258. Jain, L., et al. The growth hormone receptor interacts with transcriptional regulator HMGN1 upon GH-induced nuclear translocation. J Cell Commun Signal (2023). Link.
259. Janacova, L., et al. Catechol-O-methyl transferase suppresses cell invasion and interplays with MET signaling in estrogen dependent breast cancer. Sci Rep (2023). Link.
260. Kaller, M., et al. c-MYC-Induced AP4 Attenuates DREAM-Mediated Repression by p53. Cancers (2023). Link.
261. Kamimoto, K., et al. Dissecting cell identity via network inference and in silico gene perturbation. Nature (2023). Link.
262. Kartiganer, Z., et al. Improved Cell-Type Identification and Comprehensive Mapping of Regulatory Features with Spatial Epigenomics 96-Channel Microfluidic Platform. GEN Biotech (2023). Link.
263. Kawamura, G., et al. Optogenetic decoding of Akt2-regulated metabolic signaling pathways in skeletal muscle cells using transomics analysis. Sci Signal (2023). Link.
264. Kernfeld, E., et al. Model-X knockoffs reveal data-dependent limits on regulatory network identification. bioRxiv (2023). Link.
265. Kirtana, R.., et al. KDM5A noncanonically binds antagonists MLL1/2 to mediate gene regulation and promotes epithelial to mesenchymal transition. Biochim Biophys Acta (2023). Link.
266. Kobayashi, H., et al. Post-fertilization transcription initiation in an ancestral LTR retrotransposon drives lineage-specific genomic imprinting of ZDBF2. bioRxiv (2023). Link.
267. Kojima, H., et al. MEF2C/p300-mediated epigenetic remodeling promotes the maturation of induced cardiomyocytes. Stem Cell Rep (2023). Link.
268. Koyama, Y., et al. Increased RUNX3 expression mediates tumor-promoting ability of human breast cancer-associated fibroblasts. Cancer Med (2023). Link.
269. Kubo, A., et al. Protective effects of Mkl1/2 against lipodystrophy and muscle atrophy via PI3K/AKT-independent FoxO repression. bioRxiv (2023). Link.
270. Kumegawa, K., et al. Chromatin profile-based identification of a novel ER-positive breast cancer subgroup with reduced ER-responsive element accessibility. Br J Cancer (2023). Link.
271. Kurosawa, K., et al. ncBAF enhances PXR-mediated transcriptional activation in the human and mouse liver. Biochem Pharmacol (2023). Link.
272. Kurosawa, K., et al. ncBAF, a chromatin remodeler, enhances PXR-mediated transcriptional activation in the human and mouse liver. bioRxiv (2023). Link.
273. L, M., et al. Detecting and dissecting signaling crosstalk via the multilayer network integration of signaling and regulatory interactions. Nucleic Acids Res (2023). Link.
274. Lacher, SE.., et al. An antioxidant response element regulates the HIF1α axis in breast cancer cells. Free Radic Biol Med (2023). Link.
275. Ladias, P., et al. Cancer Associated PRDM9: Implications for Linking Genomic Instability and Meiotic Recombination. Int J Mol Sci (2023). Link.
276. Latyshev, P., et al. Unsupervised domain adaptation methods for cross-species transfer of regulatory code signals. Front Big Data (2023). Link.
277. Le Ciclé, C., et al. The Neurod1/4-Ntrk3-Src pathway regulates gonadotrope cell adhesion and motility. Cell Death Discov (2023). Link.
278. Lee, J., et al. Dnmt1/Tet2-mediated changes in Cmip methylation regulate the development of nonalcoholic fatty liver disease by controlling the Gbp2-Pparγ-CD36 axis. Exp Mol Med (2023). Link.
279. Lee, SA., et al. FUS Facilitates Gene Body Export from Nuclear Condensates. bioRxiv (2023). Link.
280. Li, C., et al. Gp78 deficiency in hepatocytes alleviates hepatic ischemia-reperfusion injury via suppressing ACSL4-mediated ferroptosis. Cell Death Dis (2023). Link.
281. Li, F., et al. VGLL4 and MENIN function as TEAD1 corepressors to block pancreatic β cell proliferation. Cell Rep (2023). Link.
282. Li, J., et al. Overexpression of Ultrabithorax Changes the Development of Silk Gland and the Expression of Fibroin Genes in Bombyx mori. Int J Mol Sci (2023). Link.
283. Li, J., et al. The Recurrent-Specific Regulation Network of Prognostic Stemness-Related Signatures in Low-Grade Glioma. Dis Markers (2023). Link.
284. Liang, H., et al. Targeting CBX3 with a Dual BET/PLK1 Inhibitor Enhances the Antitumor Efficacy of CDK4/6 Inhibitors in Prostate Cancer. Adv Sci (2023). Link.
285. Lim, JM., et al. CREB-Regulated Transcriptional Coactivator 2 Proteome Landscape is Modulated by SREBF1. Mol Cell Proteom (2023). Link.
286. Lin, SC., et al. Targeting YAP1 ameliorates progesterone resistance in endometriosis. Hum Reprod (2023). Link.
287. Ling, YH., et al. Cell cycle regulation of the psoriasis associated gene CCHCR1 by transcription factor E2F1. PLoS One (2023). Link.
288. Liu, R., et al. Nuclear respiratory factor 1 drives hepatocellular carcinoma progression by activating LPCAT1-ERK1/2-CREB axis. Biol Direct (2023). Link.
289. Liu, Z., et al. NFYC-37 promotes tumor growth by activating the mevalonate pathway in bladder cancer. Cell Rep (2023). Link.
290. Lu, J., et al. DPM2 serve as novel oncogene and prognostic marker transactivated by ESR1 in breast cancer. Environ Toxicol (2023). Link.
291. Lu, Y., et al. ER stress mediates Angiotensin II-augmented innate immunity memory and facilitates distinct susceptibilities of thoracic from abdominal aorta to aneurysm development. Front Immunol (2023). Link.
292. Lu-Culligan, WJ.., et al. Acetyl-methyllysine marks chromatin at active transcription start sites. Nature (2023). Link.
293. Ma, C., et al. Super Enhancer-Associated Circular RNA-CircKrt4 Regulates Hypoxic Pulmonary Artery Endothelial Cell Dysfunction in Mice. Arterioscler Thromb Vasc Biol (2023). Link.
294. Maehara, H., et al. DNA hypomethylation characterizes genes encoding tissue-dominant functional proteins in liver and skeletal muscle. Sci Rep (2023). Link.
295. Mangoni, D., et al. LINE-1 regulates cortical development by acting as long non-coding RNAs. Nat Commun (2023). Link.
296. Mannion, AJ.., et al. The junctional mechanosensor AmotL2 regulates YAP promotor accessibility. bioRxiv (2023). Link.
297. Mao, G., et al. Gene Regulatory Network Inference Using Convolutional Neural Networks from scRNA-seq Data. J Comput Biol (2023). Link.
298. Marku, M., et al. From time-series transcriptomics to gene regulatory networks: A review on inference methods. PLoS Comput Biol (2023). Link.
299. Martins, KM.., et al. Prevalent and Disseminated Recombinant and Wild-Type Adeno-Associated Virus Integration in Macaques and Humans. Hum Gene Ther (2023). Link.
300. Mbebi, AJ.., et al. Gene regulatory network inference using mixed-norms regularized multivariate model with covariance selection. PLoS Comput Biol (2023). Link.
301. Medina-Jover, F., et al. A rise in double-strand breaks sensitizes tumours to oxidative metabolism inhibitors. bioRxiv (2023). Link.
302. Meng, Q., et al. Consensus peaks of chromatin accessibility in the human genome. bioRxiv (2023). Link.
303. Miyazawa, K., et al. Cross-ancestry genome-wide analysis of atrial fibrillation unveils disease biology and enables cardioembolic risk prediction. Nat Genet (2023). Link.
304. Moreira, P., et al. Nuclear Factor-Y is a Pervasive Regulator of Neuronal Gene Expression. bioRxiv (2023). Link.
305. Morita, T., et al. Actin-related protein 5 suppresses the cooperative activation of cardiac gene transcription by myocardin and MEF2. FEBS Open Bio (2023). Link.
306. Mu, Q., et al. Identifying predictors of glioma evolution from longitudinal sequencing. Sci Transl Med (2023). Link.
307. Murakami, T., et al. HOXA10 promotes Gdf5 expression in articular chondrocytes. Sci Rep (2023). Link.
308. Murao, N., et al. Homeostatic Regulation of Seizure Susceptibility and Cognitive Function by ER Quality Controller Derlin-1 through Maintenance of Adult Neurogenesis. bioRxiv (2023). Link.
309. Nagao, S., et al. Reduced DEFA5 Expression and STAT3 Activation Underlie the Submucosal Invasion of Early Gastric Cancers. Digestion (2023). Link.
310. Nakamura, J., et al. TFEB-mediated lysosomal exocytosis alleviates high fat diet-induced lipotoxicity in the kidney. JCI Insight (2023). Link.
311. Navarrete-López, P., et al. Loss of the importin Kpna2 causes infertility in male mice by disrupting the translocation of testis-specific transcription factors. iScience (2023). Link.
312. Nethander, M., et al. An atlas of genetic determinants of forearm fracture. Nat Genet (2023). Link.
313. Neu, D., et al. Oncogenic reactivation of young L1s is a hallmark of colon cancer. bioRxiv (2023). Link.
314. Noh, M., et al. Particulate matter-induced metabolic recoding of epigenetics in macrophages drives pathogenesis of chronic obstructive pulmonary disease. J Hazard Mater (2023). Link.
315. Odongoo, R., et al. Overlapping role of c-Jun N-terminal kinase (JNK) 1 and 2 in imidazole ketone erastin-induced ferroptosis. Gene Rep (2023). Link.
316. Oey, NE.., et al. A Proteome-Wide Effect of PHF8 Knockdown on Cortical Neurons Shows Downregulation of Parkinson’s Disease-Associated Protein Alpha-Synuclein and Its Interactors. Biomedicines (2023). Link.
317. Ohata, H., et al. PROX1 induction by autolysosomal activity stabilizes persister-like state of colon cancer via feedback repression of the NOX1-mTORC1 pathway. Cell Rep (2023). Link.
318. Ohishi, H., et al. Transcription-coupled changes in higher-order genomic structure and transcription hub viscosity prolong enhancer-promoter connectivity. bioRxiv (2023). Link.
319. Ojewunmi, OO.., et al. The genetic dissection of fetal haemoglobin persistence in sickle cell disease in Nigeria. medRxiv (2023). Link.
320. Oliveros, W., et al. Systematic characterization of regulatory variants of blood pressure genes ll Systematic characterization of regulatory variants of blood pressure genes. Cell Genom (2023). Link.
321. Onodera, T., et al. Protective roles of adiponectin and molecular signatures of HNF4α and PPARα as downstream targets of adiponectin in pancreatic β cells. Mol Metab (2023). Link.
322. Osada, N., et al. c-FOS is an integral component of the IKZF1 transactivator complex and mediates lenalidomide resistance in multiple myeloma. Clin Transl Med (2023). Link.
323. Ota, H., et al. Switching mechanism from AR to EGFR signaling via 3-O-sulfated heparan sulfate in castration-resistant prostate cancer. Sci Rep (2023). Link.
324. Pan, H., et al. A nutrient-deficient microenvironment facilitates ferroptosis resistance via the FAM60A-PPAR axis in pancreatic ductal adenocarcinoma. Research (Lambertville) (2023). Link.
325. Peña-Martínez, EG.., et al. Prioritizing Cardiovascular Disease-Associated Variants Altering NKX2-5 Binding through an Integrative Computational Approach. medRxiv (2023). Link.
326. Peña-Martínez, EG.., et al. Prioritizing Cardiovascular Disease-Associated Variants Altering NKX2-5 and TBX5 Binding through an Integrative Computational Approach. J Biol Chem (2023). Link.
327. Peñuelas‐Haro, I., et al. A novel empeROR of pancreatic malignancy. EMBO J (2023). Link.
328. Pinton, A., et al. PHF6-altered T-ALL harbor epigenetic repressive switch at bivalent promoters and respond to 5-azacitidine and venetoclax. Clin Cancer Res (2023). Link.
329. Po, A., et al. An econometric lens resolves cell-state parallax. bioRxiv (2023). Link.
330. Rader, AE.., et al. Combined inactivation of RB and Hippo converts differentiating Drosophila photoreceptors into eye progenitor cells through derepression of homothorax. Dev Cell (2023). Link.
331. Raicu, AM., et al. Retinoblastoma protein activity revealed by CRISPRi study of divergent Rbf1 and Rbf2 paralogs. bioRxiv (2023). Link.
332. Rakotopare, J., et al. A systematic approach identifies p53-DREAM pathway target genes associated with blood or brain abnormalities. Dis Model Mech (2023). Link.
333. Rakotopare, J., et al. p53 in the Molecular Circuitry of Bone Marrow Failure Syndromes. Int J Mol Sci (2023). Link.
334. Rojas-Quintero, J., et al. Spatial Transcriptomics Resolve an Emphysema-specific Lymphoid Follicle B Cell Signature in COPD. Am J Respir Crit Care Med (2023). Link.
335. Rommelfanger, MK.., et al. Gene regulatory network inference with popInfer reveals dynamic regulation of hematopoietic stem cell quiescence upon diet restriction and aging. bioRxiv (2023). Link.
336. Ross, MO., et al. PTPN2 copper-sensing rapidly relays copper level fluctuations into EGFR/CREB activation and associated CTR1 transcriptional repression. bioRxiv (2023). Link.
337. Ryan, TA.J.., et al. Dimethyl fumarate and 4-octyl itaconate are anticoagulants that suppress Tissue Factor in macrophages via inhibition of Type I Interferon. Nat Commun (2023). Link.
338. Rymuza, J., et al. Methods for constructing and evaluating consensus genomic interval sets. bioRxiv (2023). Link.
339. Sakai, K., et al. Testicular histone hyperacetylation in mice by valproic acid administration affects the next generation by changes in sperm DNA methylation. PLoS One (2023). Link.
340. Sakai, S., et al. d-Alanine Affects the Circadian Clock to Regulate Glucose Metabolism in Kidney. Kidney360 (2023). Link.
341. Sanchez-Hernandez, ES;., et al. Glucocorticoid Receptor Regulates and Interacts with LEDGF/p75 to Promote Docetaxel Resistance in Prostate Cancer Cells. Cells (2023). Link.
342. Sarott, R., et al. Borrowing Transcriptional Kinases to Activate Apoptosis. bioRxiv (2023). Link.
343. Sekine, K., et al. Transposons contribute to the acquisition of cell type-specific cis-elements in the brain. Commun Biol (2023). Link.
344. Shan, W., et al. Identification of canonical pyroptosis-related genes, associated regulation axis, and related traditional Chinese medicine in spinal cord injury. Front Aging Neurosci (2023). Link.
345. Shen, J., et al. Current insights into the oncogenic roles of lncRNA LINC00355. Cancer Innov (2023). Link.
346. Shimoda, M., et al. KSHV uses viral IL6 to expand infected immunosuppressive macrophages. bioRxiv (2023). Link.
347. Shimoda, M., et al. Virally encoded interleukin-6 facilitates KSHV replication in monocytes and induction of dysfunctional macrophages. PLoS Pathog (2023). Link.
348. Shinzawa, K., et al. GREB1 isoform 4 is specifically transcribed by MITF and required for melanoma proliferation. Oncogene (2023). Link.
349. Shojaee, A., et al. Robust discovery of gene regulatory networks from single-cell gene expression data by Causal Inference Using Composition of Transactions. Brief Bioinform (2023). Link.
350. Silva-Llanes, I., et al. The Transcription Factor NRF2 Has Epigenetic Regulatory Functions Modulating HDACs, DNMTs, and miRNA Biogenesis. Antioxidants (2023). Link.
351. Sokolov, DK.., et al. Dexamethasone Inhibits Heparan Sulfate Biosynthetic System and Decreases Heparan Sulfate Content in Orthotopic Glioblastoma Tumors in Mice. Int J Mol Sci (2023). Link.
352. Sugimoto, H., et al. iTraNet: A Web-Based Platform for integrated Trans-Omics Network Visualization and Analysis. bioRxiv (2023). Link.
353. Sugimoto, J., et al. Controlling Trophoblast Cell Fusion in the Human Placenta—Transcriptional Regulation of Suppressyn, an Endogenous Inhibitor of Syncytin-1. Biomolecules (2023). Link.
354. Sun, W., et al. Catalytic domain-dependent and -independent transcriptional activities of the tumour suppressor histone H3K27 demethylase UTX/KDM6A in specific cancer types. Epigenetics (2023). Link.
355. Suzuki, A., et al. Ablation of Max expression induces meiotic onset in sexually undifferentiated germ cells. bioRxiv (2023). Link.
356. Tabata, S., et al. NFκB nuclear dynamics orchestrate inflammatory aging. bioRxiv (2023). Link.
357. Tabe-Bordbar, S., et al. Integrative modeling of lncRNA-chromatin interaction maps reveals diverse mechanisms of nuclear retention. BMC Genomics (2023). Link.
358. Tagore, M., et al. GABA regulates electrical activity and tumor initiation in melanoma. Cancer Discov (2023). Link.
359. Tahara, S., et al. Transcription factor-binding k-mer analysis clarifies the cell type dependency of binding specificities and cis-regulatory SNPs in humans. BMC Genomics (2023). Link.
360. Taing, L., et al. Cistrome Data Browser: integrated search, analysis and visualization of chromatin data. Nucleic Acids Res (2023). Link.
361. Tamura, I., et al. Genome-wide analysis of histone modifications that underlie the dynamic changes in gene expression during decidualization in human endometrial stromal cells. Mol Hum Reprod (2023). Link.
362. Tanaka, Y., et al. Ror1 promotes PPARα-mediated fatty acid metabolism in astrocytes. Genes Cells (2023). Link.
363. Tang, Y., et al. "Meiosis arrester" C-natriuretic peptide directly stimulates oocyte mtDNA accumulation and is implicated in aging-associated oocyte mtDNA loss. FASEB J (2023). Link.
364. Toyoda, K., et al. HTLV-1 bZIP factor-induced reprogramming of lactate metabolism and epigenetic status promote leukemic cell expansion. Blood Cancer Discov (2023). Link.
365. Trovato, M., et al. Histone H3.3 lysine 9 and 27 control repressive chromatin states at cryptic cis-regulatory elements and bivalent promoters in mouse embryonic stem cells. bioRxiv (2023). Link.
366. Tzani, A., et al. FAM222A, Part of the BET-Regulated Basal Endothelial Transcriptome, Is a Novel Determinant of Endothelial Biology and Angiogenesis. Arterioscler Thromb Vasc Biol (2023). Link.
367. Vahab, N., et al. Uncovering Co-regulatory Modules and Gene Regulatory Networks in the Heart through Machine Learning-based Analysis of Large-scale Epigenomic Data. bioRxiv (2023). Link.
368. Vičić Bočkor, V., et al. Transcription Factors HNF1A, HNF4A, and FOXA2 Regulate Hepatic Cell Protein N-Glycosylation. Engineering (Beijing) (2023). Link.
369. Waisman, A., et al. The transcription factor OCT6 promotes the dissolution of the naïve pluripotent state by repressing Nanog and activating a formative state gene regulatory network. bioRxiv (2023). Link.
370. Wang, J., et al. Inferring gene regulatory network from single-cell transcriptomes with graph autoencoder model. PLoS Genet (2023). Link.
371. Wang, M., et al. Deletions of singular U1 snRNA gene significantly interfere with transcription and 3'-end mRNA formation. PLoS Genet (2023). Link.
372. Wang, X., et al. Decoding key cell sub-populations and molecular alterations in glioblastoma at recurrence by single-cell analysis. Acta Neuropathol Commun (2023). Link.
373. Wang, Y., et al. Large-scale loss-of-function perturbations reveal a comprehensive epigenetic regulatory network in breast cancer. Cancer Biol Med (2023). Link.
374. Watabe, S., et al. Regulation of 4-HNE via SMARCA4 Is Associated with Worse Clinical Outcomes in Hepatocellular Carcinoma. Biomedicines (2023). Link.
375. Watanabe, M., et al. The kinetics of signaling through the common FcRγ chain determine cytokine profiles in dendritic cells. Sci Signal (2023). Link.
376. Weinstock, JS.., et al. Gene regulatory network inference from CRISPR perturbations in primary CD4+ T cells elucidates the genomic basis of immune disease. bioRxiv (2023). Link.
377. Wen, L., et al. Tubular aryl hydratocarbon receptor upregulates EZH2 to promote cellular senescence in cisplatin-induced acute kidney injury. Cell Death Dis (2023). Link.
378. Wernig-Zorc, S., et al. The long non-coding RNA MALAT1 modulates NR4A1 expression through a downstream regulatory element in specific cancer-cell-types. bioRxiv (2023). Link.
379. Włodarczyk, T., et al. Epiregulon: Inference of single-cell transcription factor activity to dissect mechanisms of lineage plasticity and drug response. bioRxiv (2023). Link.
380. Xiang, J., et al. ATF4 May Be Essential for Adaption of the Ocular Lens to Its Avascular Environment. Cells (2023). Link.
381. Xu, H., et al. Inferring CTCF binding patterns and anchored loops across human tissues and cell types. bioRxiv (2023). Link.
382. Xu, J., et al. STGRNS: an interpretable transformer-based method for inferring gene regulatory networks from single-cell transcriptomic data. Bioinformatics (2023). Link.
383. Xue, B., et al. Opportunities and challenges in sharing and reusing genomic interval data. Front Genet (2023). Link.
384. Y, D., et al. SCAN: Spatiotemporal Cloud Atlas for Neural cells. Nucleic Acids Res (2023). Link.
385. Yadav, P., et al. Hypoxia-induced loss of SRSF2-dependent DNA methylation promotes CTCF-mediated alternative splicing of VEGFA in breast cancer. iScience (2023). Link.
386. Yamakado, N., et al. Chemical inhibition of LSD1 leads to epithelial to mesenchymal transition in vitro of an oral squamous cell carcinoma OM-1 cell line via release from LSD1-dependent suppression of ZEB1. Biochem Biophys Res Commun (2023). Link.
387. Yamamoto, R., et al. Computer model of IL-6 dependent rheumatoid arthritis in F759 mice. Int Immunol (2023). Link.
388. Yamazaki, M., et al. YAP/BRD4-controlled ROR1 promotes tumor-initiating cells and hyperproliferation in pancreatic cancer. EMBO J (2023). Link.
389. Yan, Q., et al. LINC00941: a novel player involved in the progression of human cancers. Hum Cell (2023). Link.
390. Yang, C., et al. TRIM15 forms a regulatory loop with the AKT/FOXO1 axis and LASP1 to modulate the sensitivity of HCC cells to TKIs. Cell Death Dis (2023). Link.
391. Yari, S., et al. JAK inhibition ameliorates bone destruction by simultaneously targeting mature osteoclasts and their precursors. Inflamm Regen (2023). Link.
392. Yonezawa, S., et al. Meta-analysis of heat-stressed transcriptomes using the public gene expression database from human and mouse samples. bioRxiv (2023). Link.
393. Yumimoto, K., et al. Molecular evolution of Keap1 was essential for adaptation of vertebrates to terrestrial life. Sci Adv (2023). Link.
394. Z, Z., et al. MethMarkerDB: a comprehensive cancer DNA methylation biomarker database. Nucleic Acids Res (2023). Link.
395. Zhang, N., et al. CRISPR screening reveals gleason score and castration resistance related oncodriver ring finger protein 19 A (RNF19A) in prostate cancer. Drug Resist Update (2023). Link.
396. Zhang, R., et al. G-Quadruplex Structures Are Key Modulators of Somatic Structural Variants in Cancers. Cancer Res (2023). Link.
397. Zhang, W., et al. FOXP3 recognizes microsatellites and bridges DNA through multimerization. Nature (2023). Link.
398. Zhang, Z., et al. Therapeutic potency of compound RMY-205 for pulmonary fibrosis induced by SARS-CoV-2 nucleocapsid protein. Cell Chem Biol (2023). Link.
399. Zhao, W., et al. Progesterone activates histone lactylation-Hif1α-glycolysis feedback loop to promote decidualization. Endocrinology (2023). Link.
400. Zimmermann, B., et al. Topological structures and syntenic conservation in sea anemone genomes. Nat Commun (2023). Link.
401. Zou, Z., et al. Elucidating disease-associated mechanisms triggered by pollutants via the epigenetic landscape using large-scale ChIP-Seq data. bioRxiv (2023). Link.
402. Abdelfattah, N., et al. Sex-biased Yap1 oncogene function. bioRxiv (2022). Link.
403. Acevedo, AF., et al. BCL6 regulates the endothelial pro-immunogenic phenotype relevant to organ transplant rejection. bioRxiv (2022). Link.
404. Acevedo, AF., et al. The DNA binding protein BCL6 regulates NFκB-controlled endothelial inflammatory gene expression. bioRxiv (2022). Link.
405. Ambrosini, G., et al. The Breast Cancer Epigenomics Track Hub. bioRxiv (2022). Link.
406. Anderson, CJ.., et al. Strand-resolved mutagenicity of DNA damage and repair. bioRxiv (2022). Link.
407. Anerillas, C., et al. A BDNF-TrkB autocrine loop enhances senescent cell viability. Nat Commun (2022). Link.
408. Atindaana, E., et al. Bimodal Expression Patterns, and Not Viral Burst Sizes, Predict the Effects of Vpr on HIV-1 Proviral Populations in Jurkat Cells. mBio (2022). Link.
409. Awamleh, Z., et al. DNA methylation signature associated with Bohring-Opitz syndrome: a new tool for functional classification of variants in ASXL genes. Eur J Hum Genet (2022). Link.
410. Baessler, A., et al. Tet2 coordinates with Foxo1 and Runx1 to balance T follicular helper cell and T helper 1 cell differentiation. Sci Adv (2022). Link.
411. Barlier, Cé., et al. RNetDys: identification of disease-related impaired regulatory interactions due to SNPs. bioRxiv (2022). Link.
412. Bideyan, L., et al. Hepatic GATA4 regulates cholesterol and triglyceride homeostasis in collaboration with LXRs. Genes Dev (2022). Link.
413. Bideyan, L., et al. Integrative analysis reveals multiple modes of LXR transcriptional regulation in liver. Proc Natl Acad Sci U S A (2022). Link.
414. Booth, LN.., et al. Males induce premature demise of the opposite sex by multifaceted strategies. Nat Aging (2022). Link.
415. Bujnicki, J., et al. Editorial: the 20th annual Nucleic Acids Research Web Server Issue 2022. Nucleic Acids Res (2022). Link.
416. Butera, A., et al. p53-driven lipidome influences non-cell-autonomous lysophospholipids in pancreatic cancer. Biol Direct (2022). Link.
417. Cao, M., et al. The synergistic interaction landscape of chromatin regulators reveals their epigenetic regulation mechanisms across five cancer cell lines. Comput Struct Biotechnol J (2022). Link.
418. Chai, G., et al. Sevoflurane inhibits histone acetylation and contributes to cognitive dysfunction by enhancing the expression of ANP32A in aging mice. Behav Brain Res (2022). Link.
419. Chandra, O., et al. Inferring functions of coding and non-coding genes using epigenomic patterns and deciphering the effect of combinatorics of transcription factors binding at promoters. bioRxiv (2022). Link.
420. Chauvistré, H., et al. Persister state-directed transitioning and vulnerability in melanoma. Nat Commun (2022). Link.
421. Chen, F., et al. Placental DNA methylation changes in gestational diabetes mellitus. Epigenetics (2022). Link.
422. Chen, G., et al. Graph attention network for link prediction of gene regulations from single cell RNA-sequencing data. Bioinformatics (2022). Link.
423. Chen, H., et al. BET Inhibitors Target the SCLC-N subtype of Small Cell Lung Cancer by Blocking NEUROD1 Transactivation. Mol Cancer Res (2022). Link.
424. Chen, J., et al. MYT1L is required for suppressing earlier neuronal development programs in the adult mouse brain. bioRxiv (2022). Link.
425. Chen, KY., et al. Adipocyte-Specific Ablation of PU.1 Promotes Energy Expenditure and Ameliorates Metabolic Syndrome in Aging Mice. Front Aging (2022). Link.
426. Chen, M., et al. Integrative analyses for the identification of idiopathic pulmonary fibrosis-associated genes and shared loci with other diseases. Thorax (2022). Link.
427. Chen, T., et al. GSTM3 deficiency impedes DNA mismatch repair to promote gastric tumorigenesis via CAND1/NRF2-KEAP1 signaling. Cancer Lett (2022). Link.
428. Chirichella, M., et al. RFX transcription factors control a miR-150/PDAP1 axis that restrains the proliferation of human T cells. PLoS Biol (2022). Link.
429. Corleone, G., et al. Enhancer plasticity sustains oncogenic transformation and progression of B-Cell Acute Lymphoblastic leukemia. bioRxiv (2022). Link.
430. Del Giudice, M., et al. FOXA1 regulates alternative splicing in prostate cancer. Cell Rep (2022). Link.
431. Dong, C., et al. Curcumin Attenuates Hydrocephalus via Activation of E2F Transcription Factor 4. Cerebrovasc Dis (2022). Link.
432. Dufour, CR.., et al. The mTOR chromatin-bound interactome in prostate cancer. Cell Rep (2022). Link.
433. Eguchi, R., et al. TRANSDIRE: data-driven direct reprogramming by a pioneer factor-guided trans-omics approach. Bioinformatics (2022). Link.
434. Escalante-Covarrubias, Q., et al. Time-of-day defines the efficacy of NAD+ to treat diet-induced metabolic disease by adjusting oscillations of the hepatic circadian clock. bioRxiv (2022). Link.
435. Eustice, M., et al. Nutrient sensing pathways regulating adult reproductive diapause in C. elegans. PLoS One (2022). Link.
436. Fang, XQ., et al. PGC1α Cooperates with FOXA1 to Regulate Epithelial Mesenchymal Transition through the TCF4-TWIST1. Int J Mol Sci (2022). Link.
437. Feng, C., et al. Arborinine from Glycosmis parva leaf extract inhibits clear-cell renal cell carcinoma by inhibiting KDM1A/UBE2O signaling. Food Nutr Res (2022). Link.
438. Filipovic, D., et al. Predictive Models of Genome-wide Aryl Hydrocarbon Receptor DNA Binding Reveal Tissue Specific Binding Determinants. bioRxiv (2022). Link.
439. Freimer, JW.., et al. Systematic discovery and perturbation of regulatory genes in human T cells reveals the architecture of immune networks. Nat Genet (2022). Link.
440. Fu, LY., et al. ChIP-Hub provides an integrative platform for exploring plant regulome. Nat Commun (2022). Link.
441. Gao, Y., et al. TRmir: A Comprehensive Resource for Human Transcriptional Regulatory Information of MiRNAs. Front Genet (2022). Link.
442. Gourisankar, S., et al. Rewiring Cancer Drivers to Activate Apoptosis. bioRxiv (2022). Link.
443. Guan, J., et al. SRGS: sparse partial least squares-based recursive gene selection for gene regulatory network inference. BMC Genomics (2022). Link.
444. Gupta, A., et al. Dynamic Control Balancing Cell Proliferation and Inflammation is Crucial for an Effective Immune Response to Malaria. Front Mol Biosci (2022). Link.
445. Habano, W., et al. Aryl hydrocarbon receptor as a DNA methylation reader in the stress response pathway. CRC Crit Rev Toxicol (2022). Link.
446. Harada, T., et al. Novel antimyeloma therapeutic option with inhibition of the HDAC1-IRF4 axis and PIM kinase. Blood Adv (2022). Link.
447. Hasegawa, A., et al. Heterozygous variants in GATA2 contribute to DCML deficiency in mice by disrupting tandem protein binding. Commun Biol (2022). Link.
448. Hassan, HM.., et al. Regulation of Chromatin Accessibility by the Farnesoid X Receptor Is Essential for Circadian and Bile Acid Homeostasis In Vivo. Cancers (2022). Link.
449. He, S., et al. The Role of the SOX9/lncRNA ANXA2P2/miR-361-3p/SOX9 Regulatory Loop in Cervical Cancer Cell Growth and Resistance to Cisplatin. Front Oncol (2022). Link.
450. He, X., et al. PBRM1 presents a potential prognostic marker and therapeutic target in duodenal papillary carcinoma. Clin Transl Med (2022). Link.
451. Hersbach, BA., et al. Probing cell identity hierarchies by fate titration and collision during direct reprogramming. Mol Syst Biol (2022). Link.
452. Hinton, A., et al. OPA1 Downregulation in Skeletal Muscle Induces MERC formation in an ATF4-Dependent Manner. bioRxiv (2022). Link.
453. Hirata, H., et al. A novel role of helix-loop-helix transcriptional factor Bhlhe40 in osteoclast activation. J Cell Physiol (2022). Link.
454. Hoffmann, M., et al. TF-Prioritizer: a java pipeline to prioritize condition-specific transcription factors. bioRxiv (2022). Link.
455. Hsieh, YT., et al. Equilibrative Nucleoside Transporter 3 is an IFN-stimulated Gene that Facilitates Viral Genome Release. bioRxiv (2022). Link.
456. Hu, X., et al. Aryl hydrocarbon receptor utilises cellular zinc signals to maintain the gut epithelial barrier. bioRxiv (2022). Link.
457. Hu, Y., et al. RUNX1 inhibits the antiviral immune response against influenza A virus through attenuating type I interferon signaling. Virol J (2022). Link.
458. Huang, T., et al. Identification of upstream transcription factor binding sites in orthologous genes using mixed Student's t-test statistics. PLoS Comput Biol (2022). Link.
459. Ideno, H., et al. Human PSCs determine the competency of cerebral organoid differentiation via FGF signaling and epigenetic mechanisms. iScience (2022). Link.
460. Ito, N., et al. The Ccl17 gene encoding TARC is synergistically transactivated by PU.1 and IRF4 driven by the mammalian common promoter in dendritic cells. Allergy (2022). Link.
461. Itokazu, M., et al. Adipose-derived exosomes block muscular stem cell proliferation in aged mouse by delivering miRNA Let-7d-3p that targets transcription factor HMGA2. J Biol Chem (2022). Link.
462. Iwata, M., et al. Regulome-based characterization of drug activity across the human diseasome. NPJ Syst Biol Appl (2022). Link.
463. J, H., et al. ChIPBase v3.0: the encyclopedia of transcriptional regulations of non-coding RNAs and protein-coding genes. Nucleic Acids Res (2022). Link.
464. J, W., et al. CohesinDB: a comprehensive database for decoding cohesin-related epigenomes, 3D genomes and transcriptomes in human cells. Nucleic Acids Res (2022). Link.
465. Jiang, J., et al. IReNA: Integrated regulatory network analysis of single-cell transcriptomes and chromatin accessibility profiles. iScience (2022). Link.
466. Jing, F., et al. Prediction of the transcription factor binding sites with meta-learning. Methods (2022). Link.
467. Kaizuka, T., et al. Developmental dynamics of the postsynaptic proteome to understand synaptic maturation and dysmaturation. bioRxiv (2022). Link.
468. Kanemoto, Y., et al. A long non-coding RNA as a direct vitamin D target transcribed from the anti-sense strand of the human HSD17B2 locus. Biosci Rep (2022). Link.
469. Kim, DK., et al. Aβ-induced mitochondrial dysfunction in neural progenitors controls KDM5A to influence neuronal differentiation. Exp Mol Med (2022). Link.
470. Kim, I., et al. AURKB, in concert with REST, acts as an oxygen-sensitive epigenetic regulator of the hypoxic induction of MDM2. BMB Rep (2022). Link.
471. Kitami, K., et al. Peritoneal restoration by repurposing vitamin D inhibits ovarian cancer dissemination via blockade of the TGF-β1/thrombospondin-1 axis. Matrix Biol (2022). Link.
472. Kobelyatskaya, AA.., et al. ALDH3A2, ODF2, QSOX2, and MicroRNA-503-5p Expression to Forecast Recurrence in TMPRSS2-ERG-Positive Prostate Cancer. Int J Mol Sci (2022). Link.
473. Kojima, S., et al. Epigenome editing reveals core DNA methylation for imprinting control in the Dlk1-Dio3 imprinted domain. Nucleic Acids Res (2022). Link.
474. Kokaji, T., et al. Construction of an inter-organ transomic network for whole-body metabolism. Curr Opin Endocr Metab Res (2022). Link.
475. Kokaji, T., et al. In vivo transomic analyses of glucose-responsive metabolism in skeletal muscle reveal core differences between the healthy and obese states. bioRxiv (2022). Link.
476. Kondo, J., et al. Transcription factor SP1 regulates haptoglobin fucosylation via induction of GDP-fucose transporter 1 in the hepatoma cell line HepG2. Biochem Biophys Rep (2022). Link.
477. Kong, S., et al. Nucleosome-Omics: A Perspective on the Epigenetic Code and 3D Genome Landscape. Genes (2022). Link.
478. Kozlova, AA.., et al. Assessment of DDAH1 and DDAH2 Contributions to Psychiatric Disorders via In Silico Methods. Int J Mol Sci (2022). Link.
479. Kreiß, M., et al. Human 5-lipoxygenase regulates transcription by association to euchromatin. Biochem Pharmacol (2022). Link.
480. Labaf, M., et al. Increased AR expression in castration-resistant prostate cancer rapidly induces AR signaling reprogramming with the collaboration of EZH2. Front Oncol (2022). Link.
481. Larsen, EG.., et al. Transmembrane protein TMEM184B is necessary for interleukin-31-induced itch. Pain (2022). Link.
482. Lavrekha, VV.., et al. CisCross: A gene list enrichment analysis to predict upstream regulators in Arabidopsis thaliana. Front Plant Sci (2022). Link.
483. Lee, SH., et al. Activation function 1 of progesterone receptor is required for progesterone antagonism of oestrogen action in the uterus. BMC Biol (2022). Link.
484. Letson, CT.., et al. Targeting BET Proteins downregulates miR-33a to promote synergy with PIM inhibitors in CMML. bioRxiv (2022). Link.
485. Li, F., et al. TEAD1 regulates cell proliferation through a pocket-independent transcription repression mechanism. Nucleic Acids Res (2022). Link.
486. Li, R., et al. Elucidation of an mTORC2-PKC-NRF2 pathway that sustains the ATF4 stress response and identification of Sirt5 as a key ATF4 effector. Cell Death Discov (2022). Link.
487. Li, W., et al. YTHDC1 is downregulated by the YY1/HDAC2 complex and controls the sensitivity of ccRCC to sunitinib by targeting the ANXA1-MAPK pathway. J Exp Clin Cancer Res (2022). Link.
488. Li, Y., et al. ARID3A promotes the chemosensitivity of colon cancer by inhibiting AKR1C3. Cell Biol Int (2022). Link.
489. Li, Y., et al. Immunoglobulin superfamily 9 (IGSF9) is trans-activated by p53, inhibits breast cancer metastasis via FAK. Oncogene (2022). Link.
490. Liao, Y., et al. Downregulation of LNMAS orchestrates partial EMT and immune escape from macrophage phagocytosis to promote lymph node metastasis of cervical cancer. Oncogene (2022). Link.
491. Lisacek, F., et al. Worldwide Glycoscience Informatics Infrastructure: The GlySpace Alliance. JACS Au (2022). Link.
492. Liu, T., et al. Computational identification of preneoplastic cells displaying high stemness and risk of cancer progression. Cancer Res (2022). Link.
493. Liu, W., et al. A novel FBW7/NFAT1 axis regulates cancer immunity in sunitinib-resistant renal cancer by inducing PD-L1 expression. J Exp Clin Cancer Res (2022). Link.
494. Liu, Z., et al. JAK2/STAT3 inhibition attenuates intestinal ischemia-reperfusion injury via promoting autophagy: in vitro and in vivo study. Mol Biol Rep (2022). Link.
495. Lu, Y., et al. Thioredoxin-interacting protein-activated intracellular potassium deprivation mediates the anti-tumour effect of a novel histone acetylation inhibitor HL23, a fangchinoline derivative, in human hepatocellular carcinoma. J Adv Res (2022). Link.
496. Lyu, Q., et al. A small proportion of X-linked genes contribute to X chromosome upregulation in early embryos via BRD4-mediated transcriptional activation. Curr Biol (2022). Link.
497. M, W., et al. Hexokinase 2 is a transcriptional target and a positive modulator of AHR signalling. Nucleic Acids Res (2022). Link.
498. M, Z., et al. MethBank 4.0: an updated database of DNA methylation across a variety of species. Nucleic Acids Res (2022). Link.
499. Ma, X., et al. Single-cell RNA sequencing reveals B cell-T cell interactions in vascular adventitia of hyperhomocysteinemia-accelerated atherosclerosis. Protein Cell (2022). Link.
500. MacKay, H., et al. Sex-specific epigenetic development in the mouse hypothalamic arcuate nucleus pinpoints human genomic regions associated with body mass index. Sci Adv (2022). Link.
501. Maity, AK.., et al. Inference of age-associated transcription factor regulatory activity changes in single cells. Nat Aging (2022). Link.
502. Maixner, N., et al. Visceral Adipose Tissue E2F1-miRNA206/210 Pathway Associates with Type 2 Diabetes in Humans with Extreme Obesity. Cells (2022). Link.
503. Mamivand, A., et al. Data mining of bulk and single-cell RNA sequencing introduces OBI1-AS1 as an astrocyte marker with possible role in glioma recurrence and progression. Clin Epigenetics (2022). Link.
504. Marques, IJ.., et al. Wt1 transcription factor impairs cardiomyocyte specification and drives a phenotypic switch from myocardium to epicardium. Development (2022). Link.
505. Martínez Corrales, G., et al. Transcriptional memory of dFOXO activation in youth curtails later-life mortality through chromatin remodeling and Xbp1. Nat Aging (2022). Link.
506. Masamoto, Y., et al. EVI1 exerts distinct roles in AML via ERG and cyclin D1 promoting a chemoresistance and immune-suppressive environment. Blood Adv (2022). Link.
507. Matsumoto, A., et al. C11orf21, a novel RUNX1 target gene, is down-regulated by RUNX1-ETO. BBA Adv (2022). Link.
508. Mbebi, AJ.., et al. Gene regulatory network inference using mixed-norms regularized multivariate model with covariance selection. bioRxiv (2022). Link.
509. McKowen, JK., et al. The Drosophila BEAF Insulator Protein Interacts with the Polybromo Subunit of the PBAP Chromatin Remodeling Complex. Genes Genomes Genet (2022). Link.
510. Mei, H., et al. Autophagy Facilitates Cancer-Intrinsic Evasion of CAR T Cell-Mediated Cytotoxicity in B-Cell Malignancies. Blood (2022). Link.
511. Meller, A., et al. Mining Proteomics Datasets to Uncover Functional Pseudogenes. Methods Mol Biol (2022). Link.
512. Metcalf, MG.., et al. Cell non-autonomous control of autophagy and metabolism by glial cells. bioRxiv (2022). Link.
513. Miao, J., et al. Sp1 Inhibits PGC-1α via HDAC2-Catalyzed Histone Deacetylation in Chronic Constriction Injury-Induced Neuropathic Pain. ACS Chem Neurosci (2022). Link.
514. Migdał, M., et al. xcore: an R package for inference of gene expression regulators. bioRxiv (2022). Link.
515. Mori, J., et al. Identification of cell cycle-associated and -unassociated regulators for expression of a hepatocellular carcinoma oncogene cyclin-dependent kinase inhibitor 3. Biochem Biophys Res Commun (2022). Link.
516. Mori, T., et al. Depletion of NIMA-related kinase Nek2 induces aberrant self-renewal and apoptosis in stem/progenitor cells of aged muscular tissues. Mech Ageing Dev (2022). Link.
517. Morin, A., et al. Characterizing the targets of transcription regulators by aggregating ChIP-seq and perturbation expression data sets. bioRxiv (2022). Link.
518. Morita, T., et al. Actin-related protein 5 functions as a novel modulator of MyoD and MyoG in skeletal muscle and in rhabdomyosarcoma. Elife (2022). Link.
519. Mouri, K., et al. Prioritization of autoimmune disease-associated genetic variants that perturb regulatory element activity in T cells. Nat Genet (2022). Link.
520. Muromoto, R., et al. Regulation of NFKBIZ gene promoter activity by STAT3, C/EBPβ, and STAT1. Biochem Biophys Res Commun (2022). Link.
521. Nair, PR.., et al. MLL1 regulates cytokine-driven cell migration and metastasis. bioRxiv (2022). Link.
522. Nakamura, H., et al. Hypoxia-inducible factor-1α and poly [ADP ribose] polymerase 1 cooperatively regulate Notch3 expression under hypoxia via a noncanonical mechanism. J Biol Chem (2022). Link.
523. Neal, A., et al. Finding and Verifying Enhancers for Endothelial-Expressed Genes. Methods Mol Biol (2022). Link.
524. Ng, KJ., et al. Sox2 in the dermal papilla regulates hair follicle pigmentation. Cell Rep (2022). Link.
525. Nie, M., et al. Targeting acetylcholine signaling modulates persistent drug tolerance in EGFR-mutant lung cancer and impedes tumor relapse. J Clin Invest (2022). Link.
526. Nishi, K., et al. Novel estrogen-responsive genes (ERGs) for the evaluation of estrogenic activity. PLoS One (2022). Link.
527. Ochsner, SA.., et al. Transcriptional regulatory networks of circulating immune cells in type 1 diabetes: A community knowledgebase. iScience (2022). Link.
528. Ohnishi, T., et al. Periodontitis promotes the expression of gingival transmembrane serine protease 2 (TMPRSS2), a priming protease for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). J Oral Biosci (2022). Link.
529. Ono, K., et al. Congenital sideroblastic anemia model due to ALAS2 mutation is susceptible to ferroptosis. Sci Rep (2022). Link.
530. Panatta, E., et al. Metabolic regulation by p53 prevents R-loop-associated genomic instability. Cell Rep (2022). Link.
531. Panatta, E., et al. p53 regulates expression of nuclear envelope components in cancer cells. Biol Direct (2022). Link.
532. Peng, L., et al. Bombesin receptor-activated protein exacerbates cisplatin-induced AKI by regulating the degradation of SIRT2. Nephrol Dial Transplant (2022). Link.
533. Pontis, J., et al. Primate-specific transposable elements shape transcriptional networks during human development. Nat Commun (2022). Link.
534. Q, Z., et al. ChromLoops: a comprehensive database for specific protein-mediated chromatin loops in diverse organisms. Nucleic Acids Res (2022). Link.
535. Reagor, CC.., et al. Depicting pseudotime-lagged causality across single-cell trajectories for accurate gene-regulatory inference. bioRxiv (2022). Link.
536. Ren, J., et al. Downregulation of CBX7 induced by EZH2 upregulates FGFR3 expression to reduce sensitivity to cisplatin in bladder cancer. Br J Cancer (2022). Link.
537. Rhizobium, GE. TFSyntax: a database of transcription factors binding syntax in mammalian genomes. Nucleic Acids Res (2022). Link.
538. Richard, D., et al. Intronic regulation of SARS-CoV-2 receptor (ACE2) expression mediated by immune signaling and oxidative stress pathways. iScience (2022). Link.
539. Richard, D., et al. Lineage-Specific Differences and Regulatory Networks Governing Human Chondrocyte Development. bioRxiv (2022). Link.
540. Rykaczewska, U., et al. Plaque Evaluation by Ultrasound and Transcriptomics Reveals BCLAF1 as a Regulator of Smooth Muscle Cell Lipid Transdifferentiation in Atherosclerosis. Arterioscler Thromb Vasc Biol (2022). Link.
541. Saadey, AA.., et al. Rebalancing TGFβ1/BMP signals in exhausted T cells unlocks responsiveness to immune checkpoint blockade therapy. Nat Immunol (2022). Link.
542. Sakai, H., et al. Uhrf1 governs the proliferation and differentiation of muscle satellite cells. iScience (2022). Link.
543. Samelson, AJ.., et al. BRD2 inhibition blocks SARS-CoV-2 infection by reducing transcription of the host cell receptor ACE2. Nat Cell Biol (2022). Link.
544. Sasaki, N., et al. Gp130-Mediated STAT3 Activation Contributes to the Aggressiveness of Pancreatic Cancer through H19 Long Non-Coding RNA Expression. Cancers (2022). Link.
545. Sasaki, N., et al. PRC2-dependent regulation of ganglioside expression during dedifferentiation contributes to the proliferation and migration of vascular smooth muscle cells. Front Cell Dev Biol (2022). Link.
546. Sato, F., et al. COL8A1 facilitates the growth of triple-negative breast cancer via FAK/Src activation. Breast Cancer Res Treat (2022). Link.
547. Sawada, T., et al. Antagonistic action of a synthetic androgen ligand mediated by chromatin remodeling in a human prostate cancer cell line. Biochem Biophys Res Commun (2022). Link.
548. Schihada, H., et al. Isoforms of GPR35 have distinct extracellular N-termini that allosterically modify receptor-transducer coupling and mediate intracellular pathway bias. J Biol Chem (2022). Link.
549. Schuhwerk, H., et al. The EMT transcription factor ZEB1 governs a fitness-promoting but vulnerable DNA replication stress response. Cell Rep (2022). Link.
550. Serrano-Zayas, C., et al. Regulation of cellular LDL uptake by PROX1 and CHD7. bioRxiv (2022). Link.
551. Shen, SH., et al. Bromodomain-containing protein 4 activates cardiotrophin-like cytokine factor 1, an unfavorable prognostic biomarker, and promotes glioblastoma in vitro. Ann Transl Med (2022). Link.
552. Shin, J., et al. SARS-CoV-2 infection impairs the insulin/IGF signaling pathway in the lung, liver, adipose tissue, and pancreatic cells via IRF1. Metabolism (2022). Link.
553. Silvennoinen, K., et al. SCN1A overexpression, associated with a genomic region marked by a risk variant for a common epilepsy, raises seizure susceptibility. Acta Neuropathol (2022). Link.
554. Singh, A., et al. Conserved neuropeptidergic regulation of intestinal integrity in invertebrate models of aging. bioRxiv (2022). Link.
555. Siswanto, FM., et al. Chlorogenic acid activates Nrf2/SKN-1 and prolongs the lifespan of Caenorhabditis elegans via the Akt-FOXO3/DAF16a-DDB1 pathway and activation of DAF16f. J Gerontol A Biol Sci Med Sci (2022). Link.
556. Smirnov, D., et al. SIRT6 is a key regulator of mitochondrial function in the brain. bioRxiv (2022). Link.
557. Sokolowska, KE., et al. Identified in blood diet-related methylation changes stratify liver biopsies of NAFLD patients according to fibrosis grade. Clin Epigenetics (2022). Link.
558. Sokolowski, DJ.., et al. Differential Expression Enrichment Tool (DEET): An interactive atlas of human differential gene expression. bioRxiv (2022). Link.
559. Su, Y., et al. Epigenetic histone acetylation modulating prenatal Poly I:C induced neuroinflammation in the prefrontal cortex of rats: a study in a maternal immune activation model. Front Cell Neurosci (2022). Link.
560. Sugawara, S., et al. RNaseH2A downregulation drives inflammatory gene expression via genomic DNA fragmentation in senescent and cancer cells. Commun Biol (2022). Link.
561. Sun, J., et al. The lncRNA CASC2 Modulates Hepatocellular Carcinoma Cell Sensitivity and Resistance to TRAIL Through Apoptotic and Non-Apoptotic Signaling. Front Oncol (2022). Link.
562. Tahara, S., et al. MOCCS profile analysis clarifies the cell type dependency of transcription factor-binding sequences and cis-regulatory SNPs in humans. bioRxiv (2022). Link.
563. Takayama, S., et al. GATA6 regulates expression of annexin A10 (ANXA10) associated with epithelial-mesenchymal transition of oral squamous cell carcinoma. Arch Oral Biol (2022). Link.
564. Takeuchi, C., et al. Mod(mdg4) variants repress telomeric retrotransposon HeT-A by blocking subtelomeric enhancers. bioRxiv (2022). Link.
565. Talamanca, L., et al. Sex-dimorphic and age-dependent organization of 24 hour gene expression rhythms in human. bioRxiv (2022). Link.
566. Tanigawa, Y., et al. WhichTF is functionally important in your open chromatin data?. PLoS Comput Biol (2022). Link.
567. Terakawa, A., et al. Trans-omics analysis of insulin action reveals a cell growth subnetwork which co-regulates anabolic processes. iScience (2022). Link.
568. Toyoda, K., et al. Reprogramming of lactate metabolism is linked to the oncogenesis of the virus-induced leukemia. bioRxiv (2022). Link.
569. Tsujino, T., et al. CRISPR screens reveal genetic determinants of PARP inhibitor sensitivity and resistance in prostate cancer. bioRxiv (2022). Link.
570. Vorontsova, JE.., et al. A new insight into the aryl hydrocarbon receptor/cytochrome 450 signaling pathway in MG63, HOS, SAOS2, and U2OS cell lines. Biochimie (2022). Link.
571. Wang, Y., et al. NetREX-CF integrates incomplete transcription factor data with gene expression to reconstruct gene regulatory networks. Commun Biol (2022). Link.
572. Wang, Z., et al. Towards a better understanding of TF-DNA binding prediction from genomic features. Comput Biol Med (2022). Link.
573. Woogeng, IN., et al. Inducing human retinal pigment epithelium-like cells from somatic tissue. Stem Cell Rep (2022). Link.
574. Wu, B., et al. ORAI1 Limits SARS-CoV-2 Infection by Regulating Tonic Type I IFN Signaling. J Immunol (2022). Link.
575. Wu, L., et al. Natural Coevolution of Tumor and Immunoenvironment in Glioblastoma. Cancer Discov (2022). Link.
576. Wu, S., et al. Bromodomain containing 4 transcriptionally activated Deltex E3 ubiquitin ligase 2 contributes to glioma progression and predicts an unfavorable prognosis. Ann Transl Med (2022). Link.
577. Y, H., et al. Mitochondrial stress induces AREG expression and epigenomic remodeling through c-JUN and YAP-mediated enhancer activation. Nucleic Acids Res (2022). Link.
578. Yamada, M., et al. KLF5-regulated extracellular matrix remodeling secures biliary epithelial tissue integrity against cholestatic liver injury. bioRxiv (2022). Link.
579. Yamamoto-Imoto, H., et al. Age-associated decline of MondoA drives cellular senescence through impaired autophagy and mitochondrial homeostasis. Cell Rep (2022). Link.
580. Yamashita, Y., et al. Osteoblast lineage cells-derived Sema3A regulates bone homeostasis independently of androgens. Endocrinology (2022). Link.
581. Yamazaki, M., et al. ROR1 plays a critical role in pancreatic tumor-initiating cells with a partial EMT signature. bioRxiv (2022). Link.
582. Yan, B., et al. A comprehensive single cell data analysis of in lymphoblastoid cells reveals the role of Super-enhancers in maintaining EBV latency. bioRxiv (2022). Link.
583. Yang, K., et al. Prognostic and Immunotherapeutic Roles of KRAS in Pan-Cancer. Cells (2022). Link.
584. Yang, L., et al. Sevoflurane Offers Neuroprotection in a Cerebral Ischemia/Reperfusion Injury Rat Model Through the E2F1/EZH2/TIMP2 Regulatory Axis. Mol Neurobiol (2022). Link.
585. Yashar, WM.., et al. GoPeaks: histone modification peak calling for CUT&Tag. Genome Biol (2022). Link.
586. Yheskel, M., et al. Proximity labeling reveals a new in vivo network of interactors for the histone demethylase KDM5. bioRxiv (2022). Link.
587. Yonezawa, Y., et al. Identification of a Functional Susceptibility Variant for Adolescent Idiopathic Scoliosis that Upregulates Early Growth Response 1 (EGR1)-Mediated UNCX Expression. J Bone Miner Res (2022). Link.
588. Zelenka, T., et al. The 3D enhancer network of the developing T cell genome is shaped by SATB1. Nat Commun (2022). Link.
589. Zhang, H., et al. CBX3 Regulated By YBX1 Promotes Smoking-induced Pancreatic Cancer Progression via Inhibiting SMURF2 Expression. Int J Biol Sci (2022). Link.
590. Zhang, L., et al. STAT3 is a biologically relevant therapeutic target in H3K27M-mutant diffuse midline glioma. Neuro Oncol (2022). Link.
591. Zhang, T., et al. ADAR1 masks the cancer immunotherapeutic promise of ZBP1-driven necroptosis. Nature (2022). Link.
592. Zhang, Y., et al. Fusion prior gene network for high reliable single-cell gene regulatory network inference. Comput Biol Med (2022). Link.
593. Zhao, J., et al. CanMethdb: a database for genome-wide DNA methylation annotation in cancers. Bioinformatics (2022). Link.
594. Zhao, M., et al. A hybrid deep learning framework for gene regulatory network inference from single-cell transcriptomic data. Brief Bioinform (2022). Link.
595. Zheng, X., et al. Downregulation of HINFP induces senescence-associated secretory phenotype to promote metastasis in a non-cell-autonomous manner in bladder cancer. Oncogene (2022). Link.
596. Zhong, X., et al. CBX3 is associated with metastasis and glutathione/ glycosphingolipid metabolism in colon adenocarcinoma. J Gerontol A Biol Sci Med Sci (2022). Link).
597. Zhu, T., et al. A pan-tissue DNA methylation atlas enables in silico decomposition of human tissue methylomes at cell-type resolution. Nat Methods (2022). Link.
598. Zou, Z., et al. Epigenetic landscape of drug responses revealed through large-scale ChIP-seq data analyses. BMC Bioinformatics (2022). Link.
599. A, M., et al. AnnoMiner is a new web-tool to integrate epigenetics, transcription factor occupancy and transcriptomics data to predict transcriptional regulators. Sci Rep (2021). Link.
600. A, M., et al. Integrative Bioinformatics and Experimental Investigation Introduces OBI1-AS1 as a Key LncRNA in the Progression of Low-grade Glioma to Glioblastoma. Research Square (2021). Link.
601. A, N., et al. Hyperleptinemia in obese state renders luminal breast cancers refractory to tamoxifen by coordinating a crosstalk between Med1, miR205 and ErbB. NPJ Breast Cancer (2021). Link.
602. A, W., et al. E-cadherin is regulated by GATA-2 and marks the early commitment of mouse hematopoietic progenitors to the basophil and mast cell fates. Sci Immunol (2021). Link.
603. AP, W., et al. Bayesian information sharing enhances detection of regulatory associations in rare cell types. Bioinformatics (2021). Link.
604. Agudelo, LZ.., et al. Metabolic resilience is encoded in genome plasticity. bioRxiv (2021). Link.
605. Aizawa, S., et al. Early reactivation of clustered genes on the inactive X chromosome during somatic cell reprogramming. Stem Cell Rep (2021). Link.
606. Alfeghaly, C., et al. Implication of repeat insertion domains in the trans -activity of the long non-coding RNA ANRIL . Nucleic Acids Res (2021). Link.
607. Astudillo, P. Analysis in silico of the functional interaction between WNT5A and YAP/TEAD signaling in cancer. PeerJ (2021). Link.
608. B. Tóth, Bá., et al. Regulatory modules of human thermogenic adipocytes: functional genomics of large cohort and Meta-analysis derived marker-genes. BMC Genomics (2021). Link.
609. Bang, J., et al. Identification of Signaling Pathways for Early Embryonic Lethality and Developmental Retardation in Sephs1 -/- Mice. Int J Mol Sci (2021). Link.
610. Biani, M.C.., et al. Small extracellular vesicles from iPSC-MSC lose their regenerative potential upon UV-C irradiation. bioRxiv (2021). Link.
611. Bono, H. Meta-analysis of oxidative transcriptomes in insects. Antioxidants (2021). Link.
612. C, F., et al. PFKFB4 is overexpressed in clear-cell renal cell carcinoma promoting pentose phosphate pathway that mediates Sunitinib resistance. J Exp Clin Cancer Res (2021). Link.
613. CA, A., et al. ACSNI: An unsupervised machine-learning tool for prediction of tissue-specific pathway components using gene expression profiles. Patterns (2021). Link.
614. Centenera, MM.., et al. ELOVL5 is a critical and targetable fatty acid elongase in prostate cancer. Cancer Res (2021). Link.
615. Cerase, A., et al. Chd8 regulates X chromosome inactivation in mouse through fine-tuning control of Xist expression. Commun Biol (2021). Link.
616. Chen, H., et al. BET Bromodomain Inhibitors Target the NEUROD1-subtype SCLC by Blocking NEUROD1 Transactivation. bioRxiv (2021). Link.
617. Chen, M., et al. Integrative Analyses Reveal Novel Disease-associated Loci and Genes for Idiopathic Pulmonary Fibrosis. medRxiv (2021). Link.
618. Choi, S., et al. Identification of a Putative Enhancer RNA for EGFR in Hyper-Accessible Regions in Esophageal Squamous Cell Carcinoma Cells by Analysis of Chromatin Accessibility Landscapes. Front Oncol (2021). Link.
619. Cofer, EM.., et al. Modeling transcriptional regulation of model species with deep learning. Genome Res (2021). Link.
620. De Smedt, J., et al. PU.1 drives specification of pluripotent stem cell-derived endothelial cells to LSEC-like cells. Cell Death Dis (2021). Link.
621. Dhaka, B., et al. Differential chromatin accessibility landscape of gain-of-function mutant p53 tumours. BMC Cancer (2021). Link.
622. Doi, H., et al. Early-life midazolam exposure persistently changes chromatin accessibility to impair adult hippocampal neurogenesis and cognition. Proc Natl Acad Sci U S A (2021). Link.
623. Droin, C., et al. Space-time logic of liver gene expression at sub-lobular scale. Nat Metab (2021). Link.
624. Durand, Sé., et al. RSL24D1 sustains steady-state ribosome biogenesis and pluripotency translational programs in embryonic stem cells. bioRxiv (2021). Link.
625. E, M., et al. NUAK2 and RCan2 participate in the p53 mutant pro-tumorigenic network. Biol Direct (2021). Link.
626. Feng, H., et al. Identification of core miRNAs and regulatory pathways in breast cancer by integrated bioinformatics analysis. Mol Omics (2021). Link.
627. Feng, L., et al. Comprehensive Analysis of E3 Ubiquitin Ligases Reveals Ring Finger Protein 223 as a Novel Oncogene Activated by KLF4 in Pancreatic Cancer. Front Cell Dev Biol (2021). Link.
628. Feng, P., et al. A machine learning-based framework for modeling transcription elongation. Proc Natl Acad Sci U S A (2021). Link.
629. Fernandez Lahore, G., et al. Polymorphic estrogen receptor binding site causes Cd2-dependent sex bias in the susceptibility to autoimmune diseases. Nat Commun (2021). Link.
630. Franco, ED., et al. Primate-specific ZNF808 is essential for pancreatic development in humans. medRxiv (2021). Link.
631. Fujino, K., et al. A human endogenous bornavirus-like nucleoprotein encodes a mitochondrial protein associated with cell viability. J Virol (2021). Link.
632. Fujino, S., et al. HNF1A regulates colorectal cancer progression and drug resistance as a downstream of POU5F1. Sci Rep (2021). Link.
633. G, D., et al. Comprehensive analysis of epigenetic signatures of human transcription control. Mol Omics (2021). Link.
634. Gallo, A., et al. NF-Y subunits overexpression in gastric adenocarcinomas (STAD). Sci Rep (2021). Link.
635. Gharavi, E., et al. Embeddings of genomic region sets capture rich biological associations in lower dimensions. Bioinformatics (2021). Link.
636. H, D., et al. Early-life midazolam exposure persistently changes chromatin accessibility to impair adult hippocampal neurogenesis and cognition. Proc Natl Acad Sci U S A (2021). Link.
637. H, M., et al. Evi1 upregulates Fbp1 and supports progression of acute myeloid leukemia through pentose phosphate pathway activation. Cancer Sci (2021). Link.
638. H, O., et al. Lysine Demethylase 5A is Required for MYC Driven Transcription in Multiple Myeloma. Blood Cancer Discov (2021). Link.
639. Hamano, M., et al. Prediction of single-cell mechanisms for disease progression in hypertrophic remodelling by a trans-omics approach. Sci Rep (2021). Link.
640. Hammal, F., et al. ReMap 2022: a database of Human, Mouse, Drosophila and Arabidopsis regulatory regions from an integrative analysis of DNA-binding sequencing experiments. Nucleic Acids Res (2021). Link.
641. Hanaki, S., et al. PP1 regulatory subunit NIPP1 regulates transcription of E2F1 target genes following DNA damage. Cancer Sci (2021). Link.
642. Harada, Y., et al. ETS‐dependent enhancers for endothelial‐specific expression of serum/glucocorticoid‐regulated kinase 1 during mouse embryo development. Genes Cells (2021). Link.
643. He, L., et al. An optimized two-step chromatin immunoprecipitation protocol to quantify the associations of two separate proteins and their common target DNA. STAR Protoc (2021). Link.
644. Hernández-Nava, E., et al. Transcriptional and Epigenetic Bioinformatic Analysis of Claudin-9 Regulation in Gastric Cancer. J Oncol (2021). Link.
645. Hiebert, P. The Nrf2 transcription factor: A multifaceted regulator of the extracellular matrix. Matrix Biol Plus (2021). Link.
646. Hisamatsu, Y., et al. Matrix Metalloproteinases in Human Decidualized Endometrial Stromal Cells. Curr Issues Mol Biol (2021). Link.
647. Hisano, O., et al. Short single-stranded DNAs with putative non-canonical structures comprise a new class of plasma cell-free DNA. BMC Biol (2021). Link.
648. Hosoi, H., et al. Super-enhancers for RUNX3 are required for cell proliferation in EBV-infected B cell lines. Gene (2021). Link.
649. Hosoya, T., et al. Chondroprotective effects of CDK4/6 inhibition via enhanced ubiquitin-dependent degradation of JUN in synovial fibroblasts. Baillieres Clin Rheumatol (2021). Link.
650. Hossain, SMM., et al. Discovering key transcriptomic regulators in pancreatic ductal adenocarcinoma using Dirichlet process Gaussian mixture model. Sci Rep (2021). Link.
651. Huang, CCF., et al. Functional mapping of androgen receptor enhancer activity. Genome Biol (2021). Link.
652. Hudecova, I., et al. Characteristics, origin, and potential for cancer diagnostics of ultrashort plasma cell-free DNA. Genome Res (2021). Link.
653. Inazumi, H., et al. NRSF-GNAO1 Pathway Contributes to the Regulation of Cardiac Ca 2+ Homeostasis. Circ Res (2021). Link.
654. J, D., et al. Systematic identification of genomic elements that regulate FCGR2A expression and harbor variants linked with autoimmune disease. Hum Mol Genet (2021). Link.
655. J, S., et al. Cancer drivers and clonal dynamics in acute lymphoblastic leukaemia subtypes. Research Square (2021). Link.
656. J, W., et al. JUNB suppresses distant metastasis by influencing the initial metastatic stage. Clin Exp Metastasis (2021). Link.
657. Jang, M., et al. Matrix stiffness epigenetically regulates the oncogenic activation of the Yes-associated protein in gastric cancer. Nat Biomed Eng (2021). Link.
658. Jarvis, LB.., et al. Therapeutically expanded human regulatory T-cells are super-suppressive due to HIF1A induced expression of CD73. Commun Biol (2021). Link.
659. Jia, Y., et al. Super enhancer-mediated upregulation of HJURP promotes growth and survival of t(4;14)-positive multiple myeloma. Cancer Res (2021). Link.
660. Jiang, JC., et al. Integrated transcription factor profiling with transcriptome analysis identifies L1PA2 transposons as global regulatory modulators in a breast cancer model. Sci Rep (2021). Link.
661. Jiang, JC., et al. Widespread Exaptation of L1 Transposons for Transcription Factor Binding in Breast Cancer. Int J Mol Sci (2021). Link.
662. Jiang, X., et al. Heat shock induces the nuclear accumulation of YAP1 via SRC. Exp Cell Res (2021). Link.
663. Jin, X., et al. Smoking-associated upregulation of CBX3 suppresses ARHGAP24 expression to activate Rac1 signaling and promote tumor progression in lung adenocarcinoma. Oncogene (2021). Link.
664. Jung, S., et al. A computer-guided design tool to increase the efficiency of cellular conversions. Nat Commun (2021). Link.
665. Jungwirth, E., et al. Meta-analysis and Consolidation of Farnesoid X Receptor Chromatin Immunoprecipitation Sequencing Data Across Different Species and Conditions. Hepatol Commun (2021). Link.
666. K, K., et al. ATF4-mediated transcriptional regulation protects against β-cell loss during endoplasmic reticulum stress in a mouse model. Mol Metab (2021). Link.
667. K, N., et al. Profiling of Androgen-Dependent Enhancer RNAs Expression in Human Prostate Tumors: Search for Malignancy Transition Markers. Res Rep Urol (2021). Link.
668. K, S., et al. HMGB1 coordinates SASP-related chromatin folding and RNA homeostasis on the path to senescence. Mol Syst Biol (2021). Link.
669. Kaiser, M., et al. Regulation of otocyst patterning by Tbx2 and Tbx3 is required for inner ear morphogenesis in the mouse. Development (2021). Link.
670. Kalman, ZE., et al. A preliminary study on the cistrome of human postsynaptic density from an evolutionary and network-based perspective. bioRxiv (2021). Link.
671. Kanai, M., et al. Insights from complex trait fine-mapping across diverse populations. medRxiv (2021). Link.
672. Kanamori, Y., et al. Iron-rich Kupffer cells exhibit phenotypic changes during the development of liver fibrosis in NASH. iScience (2021). Link.
673. Katada, S., et al. Neural stem/precursor cells dynamically change their epigenetic landscape to differentially respond to BMP signaling for fate switching during brain development. Genes Dev (2021). Link.
674. Kidwell, A., et al. Translation rescue by targeting Ppp1r15a upstream open reading frame in vivo. bioRxiv (2021). Link.
675. Kikutake, C., et al. Pan-cancer analysis of non-coding recurrent mutations and their possible involvement in cancer pathogenesis. NAR Cancer (2021). Link.
676. Kim, J., et al. The RNA helicase DDX6 controls early mouse embryogenesis by repressing aberrant inhibition of BMP signaling through miRNA-mediated gene silencing. bioRxiv (2021). Link.
677. Kohrogi, K., et al. LSD1 de fi nes erythroleukemia metabolism by controlling the lineage-speci fi c transcription factors GATA1 and C / EBP a. Blood Adv (2021). Link.
678. Koike, Y., et al. Age-related demethylation of the TDP-43 autoregulatory region in the human motor cortex. Commun Biol (2021). Link.
679. Kosinsky, RL., et al. RNF20 and RNF40 regulate vitamin D receptor-dependent signaling in inflammatory bowel disease. Cell Death Differ (2021). Link.
680. Kwon, ATJ., et al. Development of p53 Knockout U87MG Cell Line for Unbiased Drug Delivery Testing System Using CRISPR-Cas9 and Transcriptomic Analysis. J Biotechnol (2021). Link.
681. L, W., et al. The Ubiquitin Sensor and Adaptor Protein p62 Mediates Signal Transduction of a Viral Oncogenic Pathway. mBio (2021). Link.
682. Labade, AS.., et al. Nup93 and CTCF modulate spatiotemporal dynamics and function of the HOXA gene locus during differentiation. J Cell Sci (2021). Link.
683. Lee, HC., et al. YAP1 overexpression contributes to the development of enzalutamide resistance by induction of cancer stemness and lipid metabolism in prostate cancer. Oncogene (2021). Link.
684. Lee, SA., et al. METTL8 mRNA Methyltransferase Enhances Cancer Cell Migration via Direct Binding to ARID1A. Int J Mol Sci (2021). Link.
685. Li, JN., et al. Expression of SnoRNA U50A Is Associated with Better Prognosis and Prolonged Mitosis in Breast Cancer. Cancers (2021). Link.
686. Liu, Y., et al. Tumors exploit FTO-mediated regulation of glycolytic metabolism to evade immune surveillance. Cell Metab (2021). Link.
687. Luginbühl, J., et al. Decoding Neuronal Diversification by Multiplexed Single-cell RNA-Seq. Stem Cell Rep (2021). Link.
688. M, F., et al. SUMO conjugation susceptibility of Akt/protein kinase B affects the expression of the pluripotency transcription factor Nanog in embryonic stem cells. PLoS One (2021). Link.
689. M, S., et al. PHLDA3 is an important downstream mediator of p53 in squamous cell carcinogenesis. J Invest Dermatol (2021). Link.
690. M, Y., et al. Chronological genome and single-cell transcriptome integration characterizes the evolutionary process of adult T cell leukemia-lymphoma. Nat Commun (2021). Link.
691. Ma, S., et al. Powerful gene-based testing by integrating long-range chromatin interactions and knockoff genotypes. medRxiv (2021). Link.
692. Ma, W., et al. BARTweb: a web server for transcriptional regulator association analysis. NAR Genom Bioinform (2021). Link.
693. Markouli, C.., et al. Sustained intrinsic WNT and BMP4 activation impairs hESC differentiation to definitive endoderm and drives the cells towards extra-embryonic mesoderm. Sci Rep (2021). Link.
694. Marques, IJ.., et al. Downregulation of WT1 transcription factor gene expression is required to promote myocardial fate. bioRxiv (2021). Link.
695. Matsuura, N., et al. NOTCH3 limits the epithelial–mesenchymal transition and predicts a favorable clinical outcome in esophageal cancer. Cancer Med (2021). Link.
696. Milanesi, E., et al. Whole Blood Expression Pattern of Inflammation and Redox Genes in Mild Alzheimer's Disease. J Inflamm Res (2021). Link.
697. Minnoye, L., et al. Chromatin accessibility profiling methods. Nat Rev Methods Primers (2021). Link.
698. Misawa, A., et al. Long Noncoding RNA HOXA11-AS and Transcription Factor HOXB13 Modulate the Expression of Bone Metastasis-Related Genes in Prostate Cancer. Genes (2021). Link.
699. Miyake, M., et al. Integrated stress response regulates GDF15 secretion from adipocytes, preferentially suppresses appetite for a high-fat diet and improves obesity. iScience (2021). Link.
700. Morishita, M., et al. Characterization of mouse embryonic fibroblasts derived from Rassf6 knockout mice shows the implication of Rassf6 in the regulation of NF-κB signaling. Genes Cells (2021). Link.
701. Morrow, AK., et al. Epitome: predicting epigenetic events in novel cell types with multi-cell deep ensemble learning. Nucleic Acids Res (2021). Link.
702. Mourao, L., et al. Hyperactive WNT/CTNNB1 signaling induces a competing cell proliferation and epidermal differentiation response in the mouse mammary epithelium. bioRxiv (2021). Link.
703. N, O., et al. mTOR inhibitors sensitize multiple myeloma cells to venetoclax via IKZF3-and Blimp-1-mediated BCL-2 up-regulation. Haematologica (2021). Link.
704. Nagai, Y., et al. Glucotoxicity-induced suppression of Cox6a2 expression provokes β-cell dysfunction via augmented ROS production. Biochem Biophys Res Commun (2021). Link.
705. Namba, S., et al. Transcript-targeted analysis reveals isoform alterations and double-hop fusions in breast cancer. Commun Biol (2021). Link.
706. Nurtdinov, R., et al. Alu-mediated weak CEBPA binding and slow B cell transdifferentiation in human. bioRxiv (2021). Link.
707. Ogino, T., et al. Post-transcriptional repression of circadian component CLOCK regulates cancer-stemness in murine breast cancer cells. Elife (2021). Link.
708. Oh, TI., et al. PGC1α Loss Promotes Lung Cancer Metastasis through Epithelial-Mesenchymal Transition. Cancers (2021). Link.
709. Omiya, H., et al. BMP signaling suppresses Gemc1 expression and ependymal differentiation of mouse telencephalic progenitors. Sci Rep (2021). Link.
710. P, ME., et al. DNA Methylome Alterations are Associated with Airway Macrophage Differentiation and Phenotype During Lung Fibrosis. Am J Respir Crit Care Med (2021). Link.
711. P, Wü., et al. Transcription factors: Bridge between cell signaling and gene regulation. Proteomics (2021). Link.
712. PM, T., et al. Human autoinflammatory disease reveals ELF4 as a transcriptional regulator of inflammation. Nat Immunol (2021). Link.
713. Papagiannopoulos, CI., et al. The histone methyltransferase inhibitor A-366 enhances hemoglobin expression in erythroleukemia cells upon co-exposure with chemical inducers in culture. J Biol Res (2021). Link.
714. Pecori, F., et al. A defined glycosylation regulatory network modulates total glycome dynamics during pluripotency state transition. Sci Rep (2021). Link.
715. Petrone, MíV., et al. The pluripotency transcription factor OCT4 represses heme oxygenase-1 gene expression. FEBS Lett (2021). Link.
716. Piette, BL.., et al. Comprehensive interactome profiling of the human Hsp70 network highlights functional differentiation of J domains. Mol Cell (2021). Link.
717. Q, L., et al. SIGNET: single-cell RNA-seq-based gene regulatory network prediction using multiple-layer perceptron bagging. Brief Bioinform (2021). Link.
718. Quinn, HM., et al. YAP and β-catenin cooperate to drive oncogenesis in basal breast cancer. Cancer Res (2021). Link.
719. RC, Z., et al. Conserved immunomodulatory transcriptional networks underlie antipsychotic-induced weight gain. Transl Psychiatry (2021). Link.
720. Reimegård, J., et al. A combined approach for single-cell mRNA and intracellular protein expression analysis. Commun Biol (2021). Link.
721. Ruiz, JéL., et al. The regulatory genome of the malaria vector Anopheles gambiae : integrating chromatin accessibility and gene expression . NAR Genom Bioinform (2021). Link.
722. S, H., et al. Targeting ATF4-dependent pro-survival autophagy to synergize glutaminolysis inhibition. Theranostics (2021). Link.
723. S, L., et al. Long noncoding RNA HOTAIR interacts with Y-Box Protein-1 (YBX1) to regulate cell proliferation. Life Sci Alliance (2021). Link.
724. S, M., et al. The alternative serotonin transporter promoter P2 impacts gene function in females with irritable bowel syndrome. J Cell Mol Med (2021). Link.
725. SY, W., et al. MYC suppresses STING-dependent innate immunity by transcriptionally upregulating DNMT1 in triple-negative breast cancer. J Immunother Cancer (2021). Link.
726. Sakuratani, T., et al. Downregulation of ARID1A in gastric cancer cells: a putative protective molecular mechanism against the Harakiri-mediated apoptosis pathway. Virchows Arch (2021). Link.
727. Sarkar, A., et al. Genome-wide DNA methylation and multi-omics study of human chondrocyte ontogeny and an epigenetic clock analysis of adult chondrocytes. bioRxiv (2021). Link.
728. Sekita, Y., et al. AKT signaling is associated with epigenetic reprogramming via the upregulation of TET and its cofactor, alpha-ketoglutarate during iPSC generation. Stem Cell Res Ther (2021). Link.
729. Sharma, A. Inferring molecular mechanisms of dexamethasone therapy in severe COVID-19 from existing transcriptomic data. Gene (2021). Link.
730. Shimizu, T., et al. Osteocytes as main responders to low-intensity pulsed ultrasound treatment during fracture healing. Sci Rep (2021). Link.
731. Shin, J., et al. Possible Involvement of Adipose Tissue in Patients With Older Age, Obesity, and Diabetes With Coronavirus SARS-CoV-2 Infection (COVID-19) via GRP78 (BIP/HSPA5): Significance of Hyperinsulinemia Management in COVID-19. Diabetes (2021). Link.
732. Shinohara, M., et al. Upregulated expression of a subset of genes in APP ; ob / ob mice: Evidence of an interaction between diabetes‐linked obesity and Alzheimer's disease. FASEB Bioadv (2021). Link.
733. Shirai, Y., et al. Elucidation of disease etiology by trans-layer omics analysis. Inflamm Regen (2021). Link.
734. Singh, I., et al. Heterogeneity in the Epigenetic Landscape of Murine Testis-Specific Histone Variants TH2A and TH2B Sharing the Same Bi-Directional Promoter. Front Cell Dev Biol (2021). Link.
735. Stirparo, GG.., et al. OCT4 induces embryonic pluripotency via STAT3 signaling and metabolic mechanisms. Proc Natl Acad Sci U S A (2021). Link.
736. Stuparević, I., et al. Regulation of the conserved 3′-5′ exoribonuclease EXOSC10/Rrp6 during cell division, development and cancer. Biol Rev (2021). Link.
737. Su, EY., et al. Reconstruction of dynamic regulatory networks reveals signaling-induced topology 3 changes associated with germ layer specification 4 5 6. bioRxiv (2021). Link.
738. Sun, Y., et al. Oleic Acid and Eicosapentaenoic Acid Reverse Palmitic Acid-induced Insulin Resistance in Human HepG2 Cells via the Reactive Oxygen Species / JUN Pathway. Genomics Proteomics Bioinformatics (2021). Link.
739. T, S., et al. Androgen-dependent and DNA binding-independent association of androgen receptor with chromatic regions coding androgen-induced non-coding RNAs. Biosci Biotechnol Biochem (2021). Link.
740. T, Y., et al. Saikosaponin-D Alleviates Renal Inflammation and Cell Apoptosis in a Mouse Model of Sepsis via TCF7/FOSL1/MMP9 Inhibition. Mol Cell Biol (2021). Link.
741. Takai, J., et al. Gata2 heterozygous mutant mice exhibit reduced inflammatory responses and impaired bacterial clearance. iScience (2021). Link.
742. Takeda, T., et al. A stem cell marker KLF5 regulates CCAT1 via three-dimensional genome structure in colorectal cancer cells. Br J Cancer (2021). Link.
743. Takeuchi, Y., et al. The membrane-linked adaptor FRS2β fashions a cytokine-rich inflammatory microenvironment that promotes breast cancer carcinogenesis. Proc Natl Acad Sci U S A (2021). Link.
744. Tan, D., et al. Quantitative control of noise in mammalian gene expression by dynamic histone regulation. Elife (2021). Link.
745. Teschendorff, AE., et al. Statistical mechanics meets single-cell biology. Nat Rev Genet (2021). Link.
746. Tian, Y., et al. Novel role of prostate cancer risk variant rs7247241 on PPP1R14A isoform transition through allelic TF binding and CpG methylation. Hum Mol Genet (2021). Link.
747. Umarov, R., et al. DeepCellState: An autoencoder-based framework for predicting cell type specific transcriptional states induced by drug treatment. PLoS Comput Biol (2021). Link.
748. Unno, K., et al. Activated ALK Cooperates with N-Myc via Wnt/β-catenin Signaling to Induce Neuroendocrine Prostate Cancer. Cancer Res (2021). Link.
749. Wan, R., et al. Direct Reconstruction of Gene Regulatory Networks underlying Cellular state Transitions without Pseudo-time Inference. bioRxiv (2021). Link.
750. Wang, J., et al. HPV E7 affects the function of cervical cancer cells via the TAL1/lnc‑EBIC/KLHDC7B axis. Oncol Rep (2021). Link.
751. Wang, L., et al. ASXL1 promotes adrenocortical carcinoma and is associated with chemoresistance to EDP regimen. Aging (2021). Link.
752. Wei, KC., et al. An innovative targeted therapy for fluoroscopy-induced chronic radiation dermatitis. J Mol Med (2021). Link.
753. Wen, L., et al. Selective EZH2 inhibitor zld1039 alleviates inflammation in cisplatin-induced acute kidney injury partially by enhancing RKIP and suppressing NF-κB p65 pathway. Zhongguo Yao Li Xue Bao (2021). Link.
754. Wierzbicka, JM.., et al. The Effects of Vitamin D on the Expression of IL-33 and Its Receptor ST2 in Skin Cells; Potential Implication for Psoriasis. Int J Mol Sci (2021). Link.
755. Wu, B., et al. ORAI1 establishes resistance to SARS-CoV-2 infection by regulating tonic type I interferon signaling. bioRxiv (2021). Link.
756. X, C., et al. Poly-L-arginine promotes asthma angiogenesis through induction of FGFBP1 in airway epithelial cells via activation of the mTORC1-STAT3 pathway. Cell Death Dis (2021). Link.
757. X, L., et al. Defining Proximity Proteomics of Histone Modifications by Antibody-mediated Protein A-APEX2 Labeling. Genomics Proteomics Bioinformatics (2021). Link.
758. X, Z., et al. Combinatorial CRISPR/Cas9 Screening Reveals Epistatic Networks of Interacting Tumor Suppressor Genes and Therapeutic Targets in Human Breast Cancer. Cancer Res (2021). Link.
759. Xiang, T., et al. The novel ZEB1-upregulated protein PRTG induced by Helicobacter pylori infection promotes gastric carcinogenesis through the cGMP/PKG signaling pathway. Cell Death Dis (2021). Link.
760. Y, H., et al. Norrie disease protein is essential for cochlear hair cell maturation. Proc Natl Acad Sci U S A (2021). Link.
761. Y, O., et al. Multi-Omic Meta-Analysis of Transcriptomes and the Bibliome Uncovers Novel Hypoxia-Inducible Genes. Biomedicines (2021). Link.
762. Y, Z., et al. TcoFBase: a comprehensive database for decoding the regulatory transcription co-factors in human and mouse. Nucleic Acids Res (2021). Link.
763. YH, C., et al. The Induction of Alpha-1 Antitrypsin by Vitamin D in Human T Cells Is TGF-β Dependent: A Proposed Anti-inflammatory Role in Airway Disease. Front Nutr (2021). Link.
764. Yagi, M., et al. Mitochondrial translation deficiency impairs NAD ⁺ ‐mediated lysosomal acidification. EMBO J (2021). Link.
765. Yao, X., et al. TP53/miR-129/MDM2/4/TP53 feedback loop modulates cell proliferation and apoptosis in retinoblastoma. Cell Cycle (2021). Link.
766. Yazar, V., et al. Integrative genome-wide analysis of dopaminergic neuron-specific PARIS expression in Drosophila dissects recognition of multiple PPAR-γ associated gene regulation. Sci Rep (2021). Link.
767. Yi, L., et al. The FOXM1/RNF26/p57 axis regulates the cell cycle to promote the aggressiveness of bladder cancer. Cell Death Dis (2021). Link.
768. Yi, X., et al. Interrogating cell type-specific cooperation of transcriptional regulators in 3D chromatin. iScience (2021). Link.
769. Yoneda, M., et al. Nucleosome assembly protein 1 (NAP-1) is a regulator of histone H1 acetylation. J Biochem (2021). Link.
770. Yoshizaki, K., et al. Paternal age affects offspring via an epigenetic mechanism involving REST/NRSF. EMBO Rep (2021). Link.
771. Zampieri, C., et al. p53 mutations define the chromatin landscape to confer drug tolerance in pancreatic cancer. Mol Oncol (2021). Link.
772. Zhang, S., et al. RNA polymerase II is required for spatial chromatin reorganization following exit from mitosis. Sci Adv (2021). Link.
773. Zhao, X., et al. CircleBase: an integrated resource and analysis platform for human eccDNAs. Nucleic Acids Res (2021). Link.
774. Zhao, Y., et al. Identification of Unique Transcriptomic Signatures and Hub Genes Through RNA Sequencing and Integrated WGCNA and PPI Network Analysis in Nonerosive Reflux Disease. J Inflamm Res (2021). Link.
775. de Roover, A., et al. Hypoxia induces DOT1L in articular cartilage to protect against osteoarthritis. JCI Insight (2021). Link.
776. Łasut-Szyszka, B., et al. Transcriptome Analysis of Cells Exposed to Actinomycin D and Nutlin-3a Reveals New Candidate p53-Target Genes and Indicates That CHIR-98014 Is an Important Inhibitor of p53 Activity. Int J Mol Sci (2021). Link.
777. Ahmed, M., et al. Integrating binding and expression data to predict transcription factors combined function. BMC Genomics (2020). Link.
778. Azim, K., et al. Resolving the transcriptional transitions associated with oligodendrocyte generation from adult neural stem cells by 2 single cell sequencing Running Title: Oligodendroglial transcriptional networks 4 5 6. bioRxiv (2020). Link.
779. B, Z., et al. Mi-2β-targeted inhibition induces immunotherapy response in melanoma. Research Square (2020). Link.
780. Beknazarov, N., et al. Deep learning approach for predicting functional Z-DNA regions using omics data. Sci Rep (2020). Link.
781. Bono, H., et al. Meta-analysis of hypoxic transcriptomes from public databases. Biomedicines (2020). Link.
782. Booth, LN., et al. Males deploy multifaceted strategies and hijack longevity pathways to induce premature demise of the opposite sex. bioRxiv (2020). Link.
783. Bunina, D., et al. Genomic Rewiring of SOX2 Chromatin Interaction Network during Differentiation of ESCs to Postmitotic Neurons. Cell Syst (2020). Link.
784. Caruana, BT., et al. The NF-κB signalling pathway regulates GLUT6 expression in endometrial cancer. Cell Signal (2020). Link.
785. Cataldo, A., et al. MiR-302b as a Combinatorial Therapeutic Approach to Improve Cisplatin Chemotherapy Efficacy in Human Triple-Negative Breast Cancer. Cancers (2020). Link.
786. Cavalli, M., et al. A Multi-Omics Approach to Liver Diseases: Integration of Single Nuclei Transcriptomics with Proteomics and HiCap Bulk Data in Human Liver. OMICS (2020). Link.
787. Charmpi, K., et al. Convergent network effects along the axis of gene expression during prostate cancer progression. Genome Biol (2020). Link.
788. Chauvistré, H., et al. The Janus-faced role of KDM5B heterogeneity in melanoma: differentiation as a situational driver of both growth arrest and drug-resistance. bioRxiv (2020). Link.
789. Chen, CCL., et al. Histone H3.3G34-Mutant Interneuron Progenitors Co-opt PDGFRA for Gliomagenesis. Cell (2020). Link.
790. Chen, H., et al. PARK2 promotes mitochondrial pathway of apoptosis and antimicrotubule drugs chemosensitivity via degradation of phospho-BCL-2. Theranostics (2020). Link.
791. Chen, J., et al. LncSEA: a platform for long non-coding RNA related sets and enrichment analysis. Nucleic Acids Res (2020). Link.
792. Choi, JH., et al. Histone demethylase KDM4D cooperates with NFIB and MLL1 complex to regulate adipogenic differentiation of C3H10T1/2 mesenchymal stem cells. Sci Rep (2020). Link.
793. Choudhury, A., et al. Meningioma epigenetic grouping reveals biologic drivers and therapeutic vulnerabilities. medRxiv (2020). Link.
794. Czipa, E., et al. ChIPSummitDB: a ChIP-seq-based database of human transcription factor binding sites and the topological arrangements of the proteins bound to them. Database (2020). Link.
795. Devailly, G., et al. Comprehensive analysis of epigenetic signatures of human transcrip-tion control †. bioRxiv (2020). Link.
796. Dorotea, D., et al. Recent Insights Into SREBP as a Direct Mediator of Kidney Fibrosis via Lipid-Independent Pathways. Front Pharmacol (2020). Link.
797. Farahmand, S., et al. ModEx: A text mining system for extracting mode of regulation of transcription factor-gene regulatory interaction. J Biomed Inform (2020). Link.
798. Feng, C., et al. KnockTF: A comprehensive human gene expression profile database with knockdown/knockout of transcription factors. Nucleic Acids Res (2020). Link.
799. Fornes, O., et al. JASPAR 2020: Update of the open-Access database of transcription factor binding profiles. Nucleic Acids Res (2020). Link.
800. Gao, L., et al. Ozone therapy promotes the differentiation of basal keratinocytes via increasing Tp63-mediated transcription of KRT10 to improve psoriasis. J Cell Mol Med (2020). Link.
801. Gerisch, B., et al. HLH-30/TFEB Is a Master Regulator of Reproductive Quiescence. Dev Cell (2020). Link.
802. Grujic, O., et al. Identification and characterization of constrained non-exonic bases lacking predictive epigenomic and transcription factor binding annotations. Nat Commun (2020). Link.
803. Guan, S., et al. TGF-β1 induces CREB1-mediated miR-1290 upregulation to antagonize lung fibrosis via Napsin A. Int J Mol Med (2020). Link.
804. Hayashi, A., et al. A unifying paradigm for transcriptional heterogeneity and squamous features in pancreatic ductal adenocarcinoma. Nat Cancer (2020). Link.
805. Hayashi, A., et al. Evolutionary Dynamics of Non-Coding Regions in Pancreatic Ductal Adenocarcinoma. bioRxiv (2020). Link.
806. Hirano, K., et al. Indonesian ginger (Bangle) extract promotes neurogenesis of human neural stem cells through WNT pathway activation. Int J Mol Sci (2020). Link.
807. Horn, M., et al. Hexosamine Pathway Activation Improves Protein Homeostasis through the Integrated Stress Response. iScience (2020). Link.
808. Hsiao, WY., et al. The Lipid Handling Capacity of Subcutaneous Fat Is Programmed by mTORC2 during Development. Cell Rep (2020). Link.
809. Hänsel-Hertsch, R., et al. Landscape of G-quadruplex DNA structural regions in breast cancer. Nat Genet (2020). Link.
810. Kaminuma, E., et al. DDBJ data analysis challenge: A machine learning competition to predict arabidopsis chromatin feature annotations from DNA sequences. Genes Genet Syst (2020). Link.
811. Katahira, J., et al. Human THO maintains the stability of repetitive DNA. Genes Cells (2020). Link.
812. Kikuyama, T., et al. 25(OH)D3 stimulates the expression of vitamin D target genes in renal tubular cells when Cyp27b1 is abrogated. J Steroid Biochem Mol Biol (2020). Link.
813. Kim, YJ., et al. UBE2C Overexpression Aggravates Patient Outcome by Promoting Estrogen-Dependent/Independent Cell Proliferation in Early Hormone Receptor-Positive and HER2-Negative Breast Cancer. Front Oncol (2020). Link.
814. Knaupp, AS.., et al. TINC- A Method to Dissect Regulatory Complexes at Single-Locus Resolution- Reveals an Extensive Protein Complex at the Nanog Promoter. Stem Cell Rep (2020). Link.
815. Koga, T., et al. Expression of leukotriene B4 receptor 1 defines functionally distinct DCs that control allergic skin inflammation. Cell Mol Immunol (2020). Link.
816. Kohmoto, T., et al. Claudin-6 is a single prognostic marker and functions as a tumor-promoting gene in a subgroup of intestinal type gastric cancer. Gastric Cancer (2020). Link.
817. Kokaji, T., et al. Transomics analysis reveals allosteric and gene regulation axes for altered hepatic glucose-responsive metabolism in obesity. Sci Signal (2020). Link.
818. Kolmykov, S., et al. GTRD: an integrated view of transcription regulation. Nucleic Acids Res (2020). Link.
819. Kremsky, I., et al. Protection from DNA re-methylation by transcription factors in primordial germ cells and pre-implantation embryos can explain trans-generational epigenetic inheritance. Genome Biol (2020). Link.
820. Krześniak, Mł., et al. Synergistic activation of p53 by actinomycin D and nutlin-3a is associated with the upregulation of crucial regulators and effectors of innate immunity. Cell Signal (2020). Link.
821. Kubota, N., et al. An integrated analysis of public genomic data unveils a possible functional mechanism of psoriasis risk via a long-range ERRFI1 enhancer. BMC Med Genomics (2020). Link.
822. Kutscher, L., et al. Functional loss of a non-canonical BCOR-PRC1.1 complex accelerates SHH-driven medulloblastoma formation. Genes Dev (2020). Link.
823. Kwiecien, K., et al. The methylation status of the chemerin promoter region located from − 252 to + 258 bp regulates constitutive but not acute-phase cytokine-inducible chemerin expression levels. Sci Rep (2020). Link.
824. Kwon, ATJ., et al. Efficient Development of Platform Cell Lines Using CRISPR-Cas9 and Transcriptomics Analysis. bioRxiv (2020). Link.
825. L, H., et al. A Regulation Loop between YAP and NR4A1 Balances Cell Proliferation and Apoptosis. Cell Rep (2020). Link.
826. LM, K., et al. Cytosolic pH regulates proliferation and tumour growth by promoting expression of cyclin D1. Nat Metab (2020). Link.
827. Larsen, EG.., et al. TMEM184B controls pruriceptor specification and function. bioRxiv (2020). Link.
828. Lei, X., et al. Crystal Structures of Ternary Complexes of MEF2 and NKX2–5 Bound to DNA Reveal a Disease Related Protein–Protein Interaction Interface. J Mol Biol (2020). Link.
829. Leporcq, Cé., et al. TFmotifView: a webserver for the visualization of transcription factor motifs in genomic regions. Nucleic Acids Res (2020). Link.
830. Li, X., et al. ERRα activates SHMT2 transcription to enhance the resistance of breast cancer to lapatinib via modulating the mitochondrial metabolic adaption. Biosci Rep (2020). Link.
831. Li, Y., et al. TRlnc: a comprehensive database for human transcriptional regulatory information of lncRNAs. Brief Bioinform (2020). Link.
832. Li, YH., et al. FGF9 is a downstream target of SRY and sufficient to determine male sex fate in ex vivo XX gonad culture. Biol Reprod (2020). Link.
833. Li, Z., et al. Runx2 (Runt-Related Transcription Factor 2)-Mediated Microcalcification Is a Novel Pathological Characteristic and Potential Mediator of Abdominal Aortic Aneurysm. Arterioscler Thromb Vasc Biol (2020). Link.
834. Lin, QXX., et al. TFregulomeR reveals transcription factors' context-specific features and functions. Nucleic Acids Res (2020). Link.
835. Lorenzo, JP., et al. APOBEC2 binds Chromatin and Represses Transcription during Myoblast Differentiation. bioRxiv (2020). Link.
836. Lou, S., et al. TopicNet: a framework for measuring transcriptional regulatory network change. Bioinformatics (2020). Link.
837. Lyu, J., et al. Synthetic lethality of RB1 and aurora A is driven by stathmin-mediated disruption of microtubule dynamics. Nat Commun (2020). Link.
838. Maharjan, M., et al. Overlapping but Distinct Sequences Play Roles in the Insulator and Promoter Activities of the Drosophila BEAF-Dependent scs' Insulator. Genetics (2020). Link.
839. Mao, N., et al. Oncogenic ERG represses PI3K signaling through downregulation of IRS2. Cancer Res (2020). Link.
840. McErlean, P., et al. Profiling of H3K27Ac Reveals the Influence of Asthma on the Epigenome of the Airway Epithelium. Front Genet (2020). Link.
841. Meng, Y., et al. Transcriptomic landscape profiling of metformin-treated healthy mice: Implication for potential hypertension risk when prophylactically used. J Cell Mol Med (2020). Link.
842. Mercatelli, D., et al. Gene regulatory network inference resources: A practical overview. Biochim Biophys Acta Gene Regul Mech (2020). Link.
843. Merrett, JE., et al. Identification of DNA response elements regulating expression of CCAAT/enhancer-binding protein (C/EBP) β and δ and MAP kinase-interacting kinases during early adipogenesis. Adipocyte (2020). Link.
844. Miyamoto, Y., et al. Genetic loss of importin α4 causes abnormal sperm morphology and impacts on male fertility in mouse. FASEB J (2020). Link.
845. Nam, A.R., et al. Alternative methylation of intron motifs is associated with cancer-related gene expression in both canine mammary tumor and human breast cancer. Clin Epigenetics (2020). Link.
846. Namekawa, T., et al. ALDH1A1 in patient-derived bladder cancer spheroids activates retinoic acid signaling leading to TUBB3 overexpression and tumor progression. Int J Cancer (2020). Link.
847. Namekawa, T., et al. HIF1α inhibitor 2-methoxyestradiol decreases NRN1 expression and represses in vivo and in vitro growth of patient-derived testicular germ cell tumor spheroids. Cancer Lett (2020). Link.
848. Ochiai, K., et al. Chromatin Protein PC4 Orchestrates B Cell Differentiation by Collaborating with IKAROS and IRF4. Cell Rep (2020). Link.
849. Ochsner, SA.., et al. Consensus transcriptional regulatory networks of coronavirus-infected human cells. Sci Data (2020). Link.
850. Ohishi, H., et al. Characterization of genetic-origin-dependent monoallelic expression in mouse embryonic stem cells. Genes Cells (2020). Link.
851. Okada, R., et al. RNaseH2A Downregulation Drives Chromosomal DNA Fragmentation and Accumulation of RNA-DNA Hybrids in Senescent Cells. SSRN (2020). Link.
852. Okazaki, Y., et al. Increased glucose metabolism in Arid5b-/- skeletal muscle is associated with the down-regulation of TBC1 domain family member 1 (TBC1D1). Biol Res (2020). Link.
853. P, Sé., et al. Chromatin interactions in differentiating keratinocytes reveal novel atopic dermatitis- and psoriasis-associated genes. J Allergy Clin Immunol (2020). Link.
854. Pecori, F., et al. Mucin-type O-glycosylation controls pluripotency in mouse embryonic stem cells via Wnt receptor endocytosis. J Cell Sci (2020). Link.
855. Pradhananga, S., et al. Promoter anchored interaction landscape of THP-1 macrophages captures early immune response processes. Cell Immunol (2020). Link.
856. Pratapa, A., et al. Benchmarking algorithms for gene regulatory network inference from single-cell transcriptomic data. Nat Methods (2020). Link.
857. Q, P., et al. VARAdb: a comprehensive variation annotation database for human. Nucleic Acids Res (2020). Link.
858. Ray, JP., et al. Prioritizing disease and trait causal variants at the TNFAIP3 locus using functional and genomic features. Nat Commun (2020). Link.
859. Rikitake, M., et al. Analysis of GPI-anchored proteins involved in germline stem cell proliferation in the Caenorhabditis elegans germline stem cell niche. J Biochem (2020). Link.
860. Roels, J., et al. Aging of preleukemic thymocytes drives CpG island hypermethylation in T-cell acute lymphoblastic leukemia. Blood Cancer Discov (2020). Link.
861. Roels, J., et al. Distinct and temporary-restricted epigenetic mechanisms regulate human αβ and γδ T cell development. Nat Immunol (2020). Link.
862. Ronzio, M., et al. Integrating Peak Colocalization and Motif Enrichment Analysis for the Discovery of Genome-Wide Regulatory Modules and Transcription Factor Recruitment Rules. Front Genet (2020). Link.
863. SN, R., et al. STAT3 in the dorsal raphe gates behavioural reactivity and regulates gene networks associated with psychopathology. Mol Psychiatry (2020). Link.
864. Sakuratani, T., et al. Downregulation of ARID1A in gastric cancer cells: a putative protective molecular mechanism against the Harakiri-mediated apoptosis pathway. Virchows Arch (2020). Link.
865. Sharipov, RN., et al. Assessment of transcriptional importance of cell line-specific features based on GTRD and FANTOM5 data. PLoS One (2020). Link.
866. Shikov, AE., et al. Phenome-wide functional dissection of pleiotropic effects highlights key molecular pathways for human complex traits. Sci Rep (2020). Link.
867. Sugasawa, T., et al. Influence of intermittent cold stimulations on CREB and its targeting genes in muscle: Investigations into molecular mechanisms of local cryotherapy. Int J Mol Sci (2020). Link.
868. Sukumaran, A., et al. Insight on Transcriptional Regulation of the Energy Sensing AMPK and Biosynthetic mTOR Pathway Genes. Front Cell Dev Biol (2020). Link.
869. Swoboda, A., et al. STAT3 promotes melanoma metastasis by CEBP-induced repression of the MITF pathway. Oncogene (2020). Link.
870. Tamura, I., et al. Transcription factor C/EBPβ induces genome-wide H3K27ac and upregulates gene expression during decidualization of human endometrial stromal cells. Molec Cell Endocr (2020). Link.
871. Tanaka, H., et al. The NSD2/WHSC1/MMSET methyltransferase prevents cellular senescence-associated epigenomic remodeling. Aging Cell (2020). Link.
872. Teschendorff, AE., et al. Improved detection of tumor suppressor events in single-cell RNA-Seq data. NPJ Genom Med (2020). Link.
873. Teschendorff, AE.., et al. EPISCORE: Cell type deconvolution of bulk tissue DNA methylomes from single-cell RNA-Seq data. Genome Biol (2020). Link.
874. Thonsri, U., et al. High glucose-ROS conditions enhance the progression in cholangiocarcinoma via upregulation of MAN2A2 and CHD8. Cancer Sci (2020). Link.
875. Toro, Aé., et al. Novel Interplay between p53 and HO-1 in Embryonic Stem Cells. Cells (2020). Link.
876. Totani, H., et al. Autocrine HGF/c-Met signaling pathway confers aggressiveness in lymph node adult T-cell leukemia/lymphoma. Oncogene (2020). Link.
877. Ueda, MT., et al. Comprehensive genomic analysis reveals dynamic evolution of endogenous retroviruses that code for retroviral-like protein domains. Mob DNA (2020). Link.
878. Wang, A., et al. Single-cell multiomic profiling of human lungs reveals cell-type-specific and age-dynamic control of SARS-CoV2 host genes. Elife (2020). Link.
879. Wang, R., et al. Transient IGF-1R inhibition combined with osimertinib eradicates AXL-low expressing EGFR mutated lung cancer. Nat Commun (2020). Link.
880. Wu, X., et al. Regulation of cellular sterol homeostasis by the oxygen responsive noncoding RNA lincNORS. Nat Commun (2020). Link.
881. X, L., et al. The role of MYB proto-oncogene like 2 in tamoxifen resistance in breast cancer. J Mol Histol (2020). Link.
882. Y, L., et al. Single-Cell Transcriptome Analysis Reveals Dynamic Cell Populations and Differential Gene Expression Patterns in Control and Aneurysmal Human Aortic Tissue. Circulation (2020). Link.
883. Y, S., et al. UTX maintains functional integrity of murine hematopoietic system by globally regulating aging-associated genes. Blood (2020). Link.
884. Y, Y., et al. SAA1 is upregulated in gastric cancer-associated fibroblasts possibly by its enhancer activation. Carcinogenesis (2020). Link.
885. Yumimoto, K., et al. Recent insight into the role of FBXW7 as a tumor suppressor. Semin Cancer Biol (2020). Link.
886. Zhao, W., et al. Epigenetic Regulation of m6A Modifications in Human Cancer. Mol Ther Nucleic Acids (2020). Link.
887. Zhou, S., et al. Noncoding mutations target cis-regulatory elements of the FOXA1 plexus in prostate cancer. Nat Commun (2020). Link.
888. Zhou, Y., et al. epiCOLOC: Integrating Large-Scale and Context-Dependent Epigenomics Features for Comprehensive Colocalization Analysis. Front Genet (2020). Link.
889. Abugessaisa, I., et al. refTSS: A Reference Data Set for Human and Mouse Transcription Start Sites. J Mol Biol (2019). Link.
890. Ahn, H., et al. Propanet: Time-varying condition-specific transcriptional network construction by network propagation. Front Plant Sci (2019). Link.
891. Ando, M., et al. Chromatin dysregulation and DNA methylation at transcription start sites associated with transcriptional repression in cancers. Nat Commun (2019). Link.
892. Aono, S., et al. β-catenin/TCF4 complex-mediated induction of the NRF3 (NFE2L3) gene in cancer cells. Int J Mol Sci (2019). Link.
893. Arata, Y., et al. Defective induction of the proteasome associated with T-cell receptor signaling underlies T-cell senescence. Genes Cells (2019). Link.
894. Bakhmet, EI., et al. hnRNP-K Targets Open Chromatin in Mouse Embryonic Stem Cells in Concert with Multiple Regulators. Stem Cells (2019). Link.
895. Banerjee, S., et al. Identifying transcriptional regulatory modules among different chromatin states in mouse neural stem cells. Front Genet (2019). Link.
896. Bocci, M., et al. Activin receptor-like kinase 1 is associated with immune cell infiltration and regulates CLEC14A transcription in cancer. Angiogenesis (2019). Link.
897. Bravo González-Blas, C., et al. cisTopic: cis-regulatory topic modeling on single-cell ATAC-seq data. Nat Methods (2019). Link.
898. Chang, HC., et al. Investigating the role of super-enhancer RNAs underlying embryonic stem cell differentiation. BMC Genomics (2019). Link.
899. Chereji, RăV., et al. Quantitative MNase-seq accurately maps nucleosome occupancy levels. Genome Biol (2019). Link.
900. Chow, KT.., et al. IRF5 regulates unique subset of genes in dendritic cells during West Nile virus infection. J Leukoc Biol (2019). Link.
901. Delicado, D., et al. Multilocus phylogeny, species delimitation and biogeography of Iberian valvatiform springsnails (Caenogastropoda: Hydrobiidae), with the description of a new genus. Zool J Linn Soc (2019). Link.
902. Duforestel, M., et al. Glyphosate primes mammary cells for tumorigenesis by reprogramming the epigenome in a TET3-dependent manner. Front Genet (2019). Link.
903. Farahmand, S., et al. Causal Inference Engine: A platform for directional gene set enrichment analysis and inference of active transcriptional regulators. Nucleic Acids Res (2019). Link.
904. Ferris, E., et al. Parallel Accelerated Evolution in Distant Hibernators Reveals Candidate Cis Elements and Genetic Circuits Regulating Mammalian Obesity. Cell Rep (2019). Link.
905. Fleming, AM.., et al. Location dependence of the transcriptional response of a potential G-quadruplex in gene promoters under oxidative stress. Nucleic Acids Res (2019). Link.
906. Fontela, MG., et al. The conserved non-coding sequence 2 (CNS2) enhances CD69 transcription through cooperation between the transcription factors oct1 and RUNX1. Genes (2019). Link.
907. Horie, K., et al. Down-regulation of GATA1-dependent erythrocyte-related genes in the spleens of mice exposed to a space travel. Sci Rep (2019). Link.
908. Hotta, M., et al. Farnesoid X receptor induces cell death and sensitizes to TRAIL-induced inhibition of growth in colorectal cancer cells through the up-regulation of death receptor 5. Biochem Biophys Res Commun (2019). Link.
909. Hurtz, C., et al. Rationale for targeting BCL6 in MLL-rearranged acute lymphoblastic leukemia. Genes Dev (2019). Link.
910. Ishijima, Y., et al. The Gata2 repression during 3T3-L1 preadipocyte differentiation is dependent on a rapid decrease in histone acetylation in response to glucocorticoid receptor activation. Molec Cell Endocr (2019). Link.
911. Kang, H., et al. HSF1 regulates mevalonate and cholesterol biosynthesis pathways. Cancers (2019). Link.
912. Kehl, T., et al. The role of TCF3 as potential master regulator in blastemal Wilms tumors. Int J Cancer (2019). Link.
913. Kikuchi, M., et al. Enhancer variants associated with Alzheimer's disease affect gene expression via chromatin looping. BMC Med Genomics (2019). Link.
914. Klein, JC., et al. Functional testing of thousands of osteoarthritis-associated variants for regulatory activity. Nat Commun (2019). Link.
915. Kojima, M., et al. The histone methyltransferase WHSC1 is regulated by EZH2 and is important for ovarian clear cell carcinoma cell proliferation. BMC Cancer (2019). Link.
916. Kolmykov, SK., et al. Population size estimation for quality control of ChIP-Seq datasets. PLoS One (2019). Link.
917. Kondo, T., et al. Two-step regulation of trachealess ensures tight coupling of cell fate with morphogenesis in the drosophila trachea. Elife (2019). Link.
918. Krug, B., et al. Pervasive H3K27 Acetylation Leads to ERV Expression and a Therapeutic Vulnerability in H3K27M Gliomas. Cancer Cell (2019). Link.
919. Kulyté, Aé., et al. MicroRNA-27a/b-3p and PPARG regulate SCAMP3 through a feed-forward loop during adipogenesis. Sci Rep (2019). Link.
920. Kunii, Y., et al. Differential protein expression of DARPP-32 versus Calcineurin in the prefrontal cortex and nucleus accumbens in schizophrenia and bipolar disorder. Sci Rep (2019). Link.
921. Kuno, A., et al. Conserved DNA-binding motif loci reflect functional transcription factor binding sites. Research Square (2019). Link.
922. Lin, S., et al. Transcriptome and DNA methylome signatures associated with retinal Müller glia development, injury response, and aging. Invest Ophthalmol Vis Sci (2019). Link.
923. Lizio, M., et al. Update of the FANTOM web resource: Expansion to provide additional transcriptome atlases. Nucleic Acids Res (2019). Link.
924. Maedera, S., et al. GLUT6 is a lysosomal transporter that is regulated by inflammatory stimuli and modulates glycolysis in macrophages. FEBS Lett (2019). Link.
925. Matsuda, T., et al. Pioneer Factor NeuroD1 Rearranges Transcriptional and Epigenetic Profiles to Execute Microglia-Neuron Conversion. Neuron (2019). Link.
926. Menzel, M., et al. Enhort: A platform for deep analysis of genomic positions. PeerJ Comput Sci (2019). Link.
927. Murayama, Y., et al. Glucocorticoid receptor suppresses gene expression of Rev-erbα (Nr1d1) through interaction with the CLOCK complex. FEBS Lett (2019). Link.
928. Neiman, G., et al. Integrin alpha-5 subunit is critical for the early stages of human pluripotent stem cell cardiac differentiation. Sci Rep (2019). Link.
929. Ochsner, SA., et al. The Signaling Pathways Project, an integrated ‘omics knowledgebase for mammalian cellular signaling pathways. Sci Data (2019). Link.
930. Oulès, Béé., et al. Mutant Lef1 controls Gata6 in sebaceous gland development and cancer. EMBO J (2019). Link.
931. Peggion, C., et al. The Prion Protein Regulates Synaptic Transmission by Controlling the Expression of Proteins Key to Synaptic Vesicle Recycling and Exocytosis. Mol Neurobiol (2019). Link.
932. Qian, FC., et al. SEanalysis: A web tool for super-enhancer associated regulatory analysis. Nucleic Acids Res (2019). Link.
933. Ranjit, M., et al. Aberrant Active cis-Regulatory Elements Associated with Downregulation of RET Finger Protein Overcome Chemoresistance in Glioblastoma. Cell Rep (2019). Link.
934. Rauschmeier, Ré., et al. Bhlhe40 and Bhlhe41 transcription factors regulate alveolar macrophage self‐renewal and identity. EMBO J (2019). Link.
935. Robinson, CM., et al. AHypoxia-inducible HIF1-GAL3ST1-sulfatide axis enhances ccRCC immune evasion via increased tumor cell-platelet binding. Mol Cancer Res (2019). Link.
936. Saito, M., et al. A Polymorphic Variant in p19Arf Confers Resistance to Chemically Induced Skin Tumors by Activating the p53 Pathway. J Invest Dermatol (2019). Link.
937. Salameti, V., et al. NOTCH1 signaling in oral squamous cell carcinoma via a TEL2/ SERPINE1 axis. Oncotarget (2019). Link.
938. Simak, M., et al. Boolean function network analysis of time course liver transcriptome data to reveal novel circadian transcriptional regulators in mammals. J Chin Med Assoc (2019). Link.
939. Singh, R., et al. Enhancement of the gut barrier integrity by a microbial metabolite through the Nrf2 pathway. Nat Commun (2019). Link.
940. Solari, C., et al. The pluripotency transcription factor Nanog represses glutathione reductase gene expression in mouse embryonic stem cells. BMC Res Notes (2019). Link.
941. Studd, JB., et al. Genetic predisposition to B-cell acute lymphoblastic leukemia at 14q11.2 is mediated by a CEBPE promoter polymorphism. Leukemia (2019). Link.
942. Suda, K., et al. Reduction of Rpd3 suppresses defects in locomotive ability and neuronal morphology induced by the knockdown of Drosophila SLC25A46 via an epigenetic pathway. Exp Cell Res (2019). Link.
943. Tano, A., et al. The juvenility-associated long noncoding RNA Gm14230 maintains cellular juvenescence. J Cell Sci (2019). Link.
944. Tong, Z., et al. TransmiR v2.0: An updated transcription factor-microRNA regulation database. Nucleic Acids Res (2019). Link.
945. Ulirsch, JC., et al. Interrogation of human hematopoiesis at single-cell and single-variant resolution. Nat Genet (2019). Link.
946. Velychko, S., et al. Excluding Oct4 from Yamanaka Cocktail Unleashes the Developmental Potential of iPSCs. Cell Stem Cell (2019). Link.
947. Vijayakrishnan, J., et al. Identification of four novel associations for B-cell acute lymphoblastic leukaemia risk. Nat Commun (2019). Link.
948. Vogel, FCE., et al. Targeting the H3K4 Demethylase KDM5B Reprograms the Metabolome and Phenotype of Melanoma Cells. J Invest Dermatol (2019). Link.
949. Wu, CJ., et al. MiR-23~27~24–mediated control of humoral immunity reveals a TOX-driven regulatory circuit in follicular helper T cell differentiation. Sci Adv (2019). Link.
950. Wu, Z., et al. Cis-control of Six1 expression in neural crest cells during craniofacial development. Dev Dyn (2019). Link.
951. Yamada, T., et al. Contributions of regulated transcription and mRNA decay to the dynamics of gene expression. WIREs RNA (2019). Link.
952. Yashiro, T., et al. PU.1 plays a pivotal role in dendritic cell migration from the periphery to secondary lymphoid organs via regulating CCR7 expression. FASEB J (2019). Link.
953. Yevshin, I., et al. GTRD: A database on gene transcription regulation - 2019 update. Nucleic Acids Res (2019). Link.
954. Yoshizaki, K., et al. Paternal Age Affects Offspring'S Behavior Possibly Via Epigenetic Mechanism Recruiting a Transcriptional Repressor Rest. Eur Neuropsychopharmacol (2019). Link.
955. Zhang, L., et al. DeepHINT: Understanding HIV-1 integration via deep learning with attention. Bioinformatics (2019). Link.
956. Zheng, R., et al. Cistrome Data Browser: Expanded datasets and new tools for gene regulatory analysis. Nucleic Acids Res (2019). Link.
957. Åkerborg, Ö., et al. High-Resolution Regulatory Maps Connect Vascular Risk Variants to Disease-Related Pathways. Circulation (2019). Link.
958. Anan, K., et al. LSD1 mediates metabolic reprogramming by glucocorticoids during myogenic differentiation. Nucleic Acids Res (2018). Link.
959. Baldi, S., et al. Genome-wide Rules of Nucleosome Phasing in Drosophila. Mol Cell (2018). Link.
960. Chatterjee, S., et al. Pre-operative progesterone benefits operable breast cancer patients by modulating surgical stress. Breast Cancer Res Treat (2018). Link.
961. Chen, Y., et al. PHLDA1, another PHLDA family protein that inhibits Akt. Cancer Sci (2018). Link.
962. Chishima, T., et al. Identification of transposable elements contributing to tissue-specific expression of long non-coding RNAs. Genes (2018). Link.
963. Chèneby, J., et al. ReMap 2018: An updated atlas of regulatory regions from an integrative analysis of DNA-binding ChIP-seq experiments. Nucleic Acids Res (2018). Link.
964. Cui, C., et al. Identification and Analysis of Human Sex-biased MicroRNAs. Genomics Proteomics Bioinformatics (2018). Link.
965. Dréos, Ré., et al. MGA repository: A curated data resource for ChIP-seq and other genome annotated data. Nucleic Acids Res (2018). Link.
966. Egashira, Y., et al. Development of lentiviral vectors for efficient glutamatergic-selective gene expression in cultured hippocampal neurons. Sci Rep (2018). Link.
967. Ferris, E., et al. Accelerated Evolution in Distinctive Species Reveals Candidate Elements for Clinically Relevant Traits, Including Mutation and Cancer Resistance. Cell Rep (2018). Link.
968. Fiziev, P., et al. ChromTime: Modeling spatio-temporal dynamics of chromatin marks. Genome Biol (2018). Link.
969. Groff, AF.., et al. Enhancers in the Peril lincRNA locus regulate distant but not local genes. Genome Biol (2018). Link.
970. Imrichova, H., et al. ChIP-seq meta-analysis yields high quality training sets for enhancer classification. bioRxiv (2018). Link.
971. Kawaji, H. dirHub: a trackHub configurator with directory structure projection. bioRxiv (2018). Link.
972. Kawata, K., et al. Trans-omic Analysis Reveals Selective Responses to Induced and Basal Insulin across Signaling, Transcriptional, and Metabolic Networks. iScience (2018). Link.
973. Kehl, T., et al. REGGAE: A novel approach for the identification of key transcriptional regulators. Bioinformatics (2018). Link.
974. Lasar, D., et al. Peroxisome Proliferator Activated Receptor Gamma Controls Mature Brown Adipocyte Inducibility through Glycerol Kinase. Cell Rep (2018). Link.
975. Mao, F., et al. EpiDenovo: A platform for linking regulatory de novo mutations to developmental epigenetics and diseases. Nucleic Acids Res (2018). Link.
976. Misawa, A., et al. lncRNA HOTAIR Inhibits Mineralization in Osteoblastic Osteosarcoma Cells by Epigenetically Repressing ALPL. Calcif Tissue Int (2018). Link.
977. Miura, I., et al. DNA methylation of ANKK1 and response to aripiprazole in patients with acute schizophrenia: A preliminary study. J Psychiatr Res (2018). Link.
978. Mochizuki, K., et al. SETDB1 is essential for mouse primordial germ cell fate determination by ensuring bmp signaling. Development (2018). Link.
979. Mourad, Rë., et al. Predicting double-strand DNA breaks using epigenome marks or DNA at kilobase resolution. Genome Biol (2018). Link.
980. Nishizawa, Y., et al. Oncogene c-Myc promotes epitranscriptome m6A reader YTHDF1 expression in colorectal cancer. Oncotarget (2018). Link.
981. Onodera, Y., et al. Inflammation-associated MIR-155 activates differentiation of muscular satellite cells. PLoS One (2018). Link.
982. Polouliakh, N., et al. Sequence homology in eukaryotes (SHOE): Interactive visual tool for promoter analysis 06 Biological Sciences 0604 Genetics. BMC Genomics (2018). Link.
983. Raffield, LM., et al. Common α-globin variants modify hematologic and other clinical phenotypes in sickle cell trait and disease. PLoS Genet (2018). Link.
984. Romero-Cordoba, SL., et al. Loss of function of miR-342-3p results in MCT1 over-expression and contributes to oncogenic metabolic reprogramming in triple negative breast cancer. Sci Rep (2018). Link.
985. Wang, H., et al. Myc and ChREBP transcription factors cooperatively regulate normal and neoplastic hepatocyte proliferation in mice. J Biol Chem (2018). Link.
986. Chen, Y., et al. Systems-epigenomics inference of transcription factor activity implicates aryl-hydrocarbon-receptor inactivation as a key event in lung cancer development. Genome Biol (2017). Link.
987. Govaere, O., et al. The PDGFRα-laminin B1-keratin 19 cascade drives tumor progression at the invasive front of human hepatocellular carcinoma. Oncogene (2017). Link.
988. Guoa, MH., et al. Comprehensive population-based genome sequencing provides insight into hematopoietic regulatory mechanisms. Proc Natl Acad Sci U S A (2017). Link.
989. Ishigaki, K., et al. Polygenic burdens on cell-specific pathways underlie the risk of rheumatoid arthritis. Nat Genet (2017). Link.
990. Kalender Atak, Z., et al. Identification of cis-regulatory mutations generating de novo edges in personalized cancer gene regulatory networks. Genome Med (2017). Link.
991. Kehl, T., et al. RegulatorTrail: A web service for the identification of key transcriptional regulators. Nucleic Acids Res (2017). Link.
992. Matsuda, K., et al. ChIP-seq analysis of genomic binding regions of five major transcription factors highlights a central role for ZIC2 in the mouse epiblast stem cell gene regulatory network. Development (2017). Link.
993. Naderi, A. C1orf64 is a novel androgen receptor target gene and coregulator that interacts with 14-3-3 protein in breast cancer. Oncotarget (2017). Link.
994. Onodera, Y., et al. miR-155 induces ROS generation through downregulation of antioxidation-related genes in mesenchymal stem cells. Aging Cell (2017). Link.
995. Sanosaka, T., et al. DNA Methylome Analysis Identifies Transcription Factor-Based Epigenomic Signatures of Multilineage Competence in Neural Stem/Progenitor Cells. Cell Rep (2017). Link.
996. Tanegashima, K., et al. Epigenetic regulation of the glucose transporter gene Slc2a1 by β-hydroxybutyrate underlies preferential glucose supply to the brain of fasted mice. Genes Cells (2017). Link.
997. Turrell, FK., et al. Lung tumors with distinct p53 mutations respond similarly to p53 targeted therapy but exhibit genotype-specific statin sensitivity. Genes Dev (2017). Link.
998. Umeyama, T., et al. DMS-Seq for In Vivo Genome-wide Mapping of Protein-DNA Interactions and Nucleosome Centers. Cell Rep (2017). Link.
999. Yevshin, I., et al. GTRD: A database of transcription factor binding sites identified by ChIP-seq experiments. Nucleic Acids Res (2017). Link.
1000. Yoshihara, M., et al. Hotspots of De Novo Point Mutations in Induced Pluripotent Stem Cells. Cell Rep (2017). Link.
1001. Sugeno, N., et al. α-Synuclein enhances histone H3 lysine-9 dimethylation and H3K9me2-dependent transcriptional responses. Sci Rep (2016). Link.