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
Arimoto, Kei-ichiro et al., Expansion of interferon inducible gene pool via USP18 inhibition promotes cancer cell pyroptosis. Nat Commun (2023). Link.
Bustin, Katelyn A. et al., Phenelzine-based probes reveal Secernin-3 is involved in thermal nociception. bioRxiv (2023). Link.
C, Bredthauer et al., Transmicron: accurate prediction of insertion probabilities improves detection of cancer driver genes from transposon mutagenesis screens. Nucleic Acids Res (2023). Link.
Chen, Weihao 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.
García‐Hernández, Violeta et al., β-Catenin activity induces an RNA biosynthesis program promoting therapy resistance in T-cell acute lymphoblastic leukemia. EMBO Mol Med (2023). Link.
Gong, Bo et al., Epigenetic and transcriptional activation of the secretory kinase FAM20C as an oncogene in glioma. J Genet Genom (2023). Link.
Hino, Shinjiro et al., Chromatin Immunoprecipitation Sequencing (ChIP-seq) for Detecting Histone Modifications and Modifiers. Methods Mol Biol (2023). Link.
Huo, Shengqi et al., ATF3/SPI1/SLC31A1 Signaling Promotes Cuproptosis Induced by Advanced Glycosylation End Products in Diabetic Myocardial Injury. Int J Mol Sci (2023). Link.
Iyer, Prajish et al., MGA deletion leads to Richter’s transformation via modulation of mitochondrial OXPHOS. bioRxiv (2023). Link.
Janacova, Lucia et al., Catechol-O-methyl transferase suppresses cell invasion and interplays with MET signaling in estrogen dependent breast cancer. Sci Rep (2023). Link.
Kaller, Markus et al., c-MYC-Induced AP4 Attenuates DREAM-Mediated Repression by p53. Cancers (2023). Link.
Kamimoto, Kenji et al., Dissecting cell identity via network inference and in silico gene perturbation. Nature (2023). Link.
Kumegawa, Kohei 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.
Kurosawa, Kiamu et al., ncBAF, a chromatin remodeler, enhances PXR-mediated transcriptional activation in the human and mouse liver. bioRxiv (2023). Link.
Lee, Jangho 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.
Li, Feng et al., VGLL4 and MENIN function as TEAD1 corepressors to block pancreatic β cell proliferation. Cell Rep (2023). Link.
Li, Jin et al., The Recurrent-Specific Regulation Network of Prognostic Stemness-Related Signatures in Low-Grade Glioma. Dis Markers (2023). Link.
Mannion, Aarren J. et al., The junctional mechanosensor AmotL2 regulates YAP promotor accessibility. bioRxiv (2023). Link.
Moreira, Pedro et al., Nuclear Factor-Y is a Pervasive Regulator of Neuronal Gene Expression. bioRxiv (2023). Link.
Morita, Tsuyoshi et al., Actin-related protein 5 suppresses the cooperative activation of cardiac gene transcription by myocardin and MEF2. FEBS Open Bio (2023). Link.
Nakamura, Jun et al., TFEB-mediated lysosomal exocytosis alleviates high fat diet-induced lipotoxicity in the kidney. JCI Insight (2023). Link.
Oey, Nicodemus E. 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.
Wen, Li et al., Tubular aryl hydratocarbon receptor upregulates EZH2 to promote cellular senescence in cisplatin-induced acute kidney injury. Cell Death Dis (2023). Link.
Yamakado, Nao 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.
Yang, Chong 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.
Zhang, Ning 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.
Acevedo, Adriana Franco et al., BCL6 regulates the endothelial pro-immunogenic phenotype relevant to organ transplant rejection. bioRxiv (2022). Link.
Acevedo, Adriana Franco et al., The DNA binding protein BCL6 regulates NFκB-controlled endothelial inflammatory gene expression. bioRxiv (2022). Link.
Ambrosini, Giovanna et al., The Breast Cancer Epigenomics Track Hub. bioRxiv (2022). Link.
Anderson, Craig J. et al., Strand-resolved mutagenicity of DNA damage and repair. bioRxiv (2022). Link.
Anerillas, Carlos et al., A BDNF-TrkB autocrine loop enhances senescent cell viability. Nat Commun (2022). Link.
Atindaana, Edmond 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.
Awamleh, Zain 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.
Baessler, Andrew et al., Tet2 coordinates with Foxo1 and Runx1 to balance T follicular helper cell and T helper 1 cell differentiation. Sci Adv (2022). Link.
Barlier, Céline et al., RNetDys: identification of disease-related impaired regulatory interactions due to SNPs. bioRxiv (2022). Link.
Bideyan, Lara et al., Hepatic GATA4 regulates cholesterol and triglyceride homeostasis in collaboration with LXRs. Genes Dev (2022). Link.
Bideyan, Lara et al., Integrative analysis reveals multiple modes of LXR transcriptional regulation in liver. Proc Natl Acad Sci U S A (2022). Link.
Booth, Lauren N. et al., Males induce premature demise of the opposite sex by multifaceted strategies. Nat Aging (2022). Link.
Bujnicki, Janusz et al., Editorial: the 20th annual Nucleic Acids Research Web Server Issue 2022. Nucleic Acids Res (2022). Link.
Butera, Alessio et al., p53-driven lipidome influences non-cell-autonomous lysophospholipids in pancreatic cancer. Biol Direct (2022). Link.
Cao, Meng 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.
Chai, Gaoshang 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.
Chandra, Omkar 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.
Chauvistré, Heike et al., Persister state-directed transitioning and vulnerability in melanoma. Nat Commun (2022). Link.
Chen, Fujia et al., Placental DNA methylation changes in gestational diabetes mellitus. Epigenetics (2022). Link.
Chen, Guangyi et al., Graph attention network for link prediction of gene regulations from single cell RNA-sequencing data. Bioinformatics (2022). Link.
Chen, Haobin et al., BET Inhibitors Target the SCLC-N subtype of Small Cell Lung Cancer by Blocking NEUROD1 Transactivation. Mol Cancer Res (2022). Link.
Chen, Jiayang et al., MYT1L is required for suppressing earlier neuronal development programs in the adult mouse brain. bioRxiv (2022). Link.
Chen, Ke Yun et al., Adipocyte-Specific Ablation of PU.1 Promotes Energy Expenditure and Ameliorates Metabolic Syndrome in Aging Mice. Front Aging (2022). Link.
Chen, Ming et al., Integrative analyses for the identification of idiopathic pulmonary fibrosis-associated genes and shared loci with other diseases. Thorax (2022). Link.
Chen, Tao et al., GSTM3 deficiency impedes DNA mismatch repair to promote gastric tumorigenesis via CAND1/NRF2-KEAP1 signaling. Cancer Lett (2022). Link.
Chirichella, Michele et al., RFX transcription factors control a miR-150/PDAP1 axis that restrains the proliferation of human T cells. PLoS Biol (2022). Link.
Corleone, G et al., Enhancer plasticity sustains oncogenic transformation and progression of B-Cell Acute Lymphoblastic leukemia. bioRxiv (2022). Link.
Del Giudice, Marco et al., FOXA1 regulates alternative splicing in prostate cancer. Cell Rep (2022). Link.
Dong, Ce et al., Curcumin Attenuates Hydrocephalus via Activation of E2F Transcription Factor 4. Cerebrovasc Dis (2022). Link.
Dufour, Catherine R. et al., The mTOR chromatin-bound interactome in prostate cancer. Cell Rep (2022). Link.
Eguchi, Ryohei et al., TRANSDIRE: data-driven direct reprogramming by a pioneer factor-guided trans-omics approach. Bioinformatics (2022). Link.
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.
Eustice, Moriah et al., Nutrient sensing pathways regulating adult reproductive diapause in C. elegans. PLoS One (2022). Link.
Fang, Xue-Quan et al., PGC1α Cooperates with FOXA1 to Regulate Epithelial Mesenchymal Transition through the TCF4-TWIST1. Int J Mol Sci (2022). Link.
Feng, Chenchen et al., Arborinine from Glycosmis parva leaf extract inhibits clear-cell renal cell carcinoma by inhibiting KDM1A/UBE2O signaling. Food Nutr Res (2022). Link.
Filipovic, David et al., Predictive Models of Genome-wide Aryl Hydrocarbon Receptor DNA Binding Reveal Tissue Specific Binding Determinants. bioRxiv (2022). Link.
Freimer, Jacob W. et al., Systematic discovery and perturbation of regulatory genes in human T cells reveals the architecture of immune networks. Nat Genet (2022). Link.
Fu, Liang-Yu et al., ChIP-Hub provides an integrative platform for exploring plant regulome. Nat Commun (2022). Link.
Gao, Yu et al., TRmir: A Comprehensive Resource for Human Transcriptional Regulatory Information of MiRNAs. Front Genet (2022). Link.
Gourisankar, Sai et al., Rewiring Cancer Drivers to Activate Apoptosis. bioRxiv (2022). Link.
Guan, Jinting et al., SRGS: sparse partial least squares-based recursive gene selection for gene regulatory network inference. BMC Genomics (2022). Link.
Gupta, Anuj et al., Dynamic Control Balancing Cell Proliferation and Inflammation is Crucial for an Effective Immune Response to Malaria. Front Mol Biosci (2022). Link.
Habano, Wataru et al., Aryl hydrocarbon receptor as a DNA methylation reader in the stress response pathway. CRC Crit Rev Toxicol (2022). Link.
Harada, Takeshi et al., Novel antimyeloma therapeutic option with inhibition of the HDAC1-IRF4 axis and PIM kinase. Blood Adv (2022). Link.
Hasegawa, Atsushi et al., Heterozygous variants in GATA2 contribute to DCML deficiency in mice by disrupting tandem protein binding. Commun Biol (2022). Link.
Hassan, Haider M. et al., Regulation of Chromatin Accessibility by the Farnesoid X Receptor Is Essential for Circadian and Bile Acid Homeostasis In Vivo. Cancers (2022). Link.
He, Shasha 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.
He, Xujun et al., PBRM1 presents a potential prognostic marker and therapeutic target in duodenal papillary carcinoma. Clin Transl Med (2022). Link.
Hersbach, Bob A et al., Probing cell identity hierarchies by fate titration and collision during direct reprogramming. Mol Syst Biol (2022). Link.
Hinton, Antentor et al., OPA1 Downregulation in Skeletal Muscle Induces MERC formation in an ATF4-Dependent Manner. bioRxiv (2022). Link.
Hirata, Hirohito et al., A novel role of helix-loop-helix transcriptional factor Bhlhe40 in osteoclast activation. J Cell Physiol (2022). Link.
Hoffmann, Markus et al., TF-Prioritizer: a java pipeline to prioritize condition-specific transcription factors. bioRxiv (2022). Link.
Hsieh, Yu-Ting et al., Equilibrative Nucleoside Transporter 3 is an IFN-stimulated Gene that Facilitates Viral Genome Release. bioRxiv (2022). Link.
Hu, Xiuchuan et al., Aryl hydrocarbon receptor utilises cellular zinc signals to maintain the gut epithelial barrier. bioRxiv (2022). Link.
Hu, Yixiang et al., RUNX1 inhibits the antiviral immune response against influenza A virus through attenuating type I interferon signaling. Virol J (2022). Link.
Huang, Tinghua et al., Identification of upstream transcription factor binding sites in orthologous genes using mixed Student's t-test statistics. PLoS Comput Biol (2022). Link.
Ideno, Hirosato et al., Human PSCs determine the competency of cerebral organoid differentiation via FGF signaling and epigenetic mechanisms. iScience (2022). Link.
Ito, Naoto 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.
Itokazu, Maki 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.
Iwata, Michio et al., Regulome-based characterization of drug activity across the human diseasome. NPJ Syst Biol Appl (2022). Link.
J, Huang et al., ChIPBase v3.0: the encyclopedia of transcriptional regulations of non-coding RNAs and protein-coding genes. Nucleic Acids Res (2022). Link.
J, Wang et al., CohesinDB: a comprehensive database for decoding cohesin-related epigenomes, 3D genomes and transcriptomes in human cells. Nucleic Acids Res (2022). Link.
Jiang, Junyao et al., IReNA: Integrated regulatory network analysis of single-cell transcriptomes and chromatin accessibility profiles. iScience (2022). Link.
Jing, Fang et al., Prediction of the transcription factor binding sites with meta-learning. Methods (2022). Link.
Kaizuka, Takeshi et al., Developmental dynamics of the postsynaptic proteome to understand synaptic maturation and dysmaturation. bioRxiv (2022). Link.
Kanemoto, Yoshiaki 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.
Kim, Dong Kyu et al., Aβ-induced mitochondrial dysfunction in neural progenitors controls KDM5A to influence neuronal differentiation. Exp Mol Med (2022). Link.
Kim, Iljin et al., AURKB, in concert with REST, acts as an oxygen-sensitive epigenetic regulator of the hypoxic induction of MDM2. BMB Rep (2022). Link.
Kitami, Kazuhisa 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.
Kobelyatskaya, Anastasiya A. 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.
Kojima, Shin et al., Epigenome editing reveals core DNA methylation for imprinting control in the Dlk1-Dio3 imprinted domain. Nucleic Acids Res (2022). Link.
Kokaji, Toshiya et al., Construction of an inter-organ transomic network for whole-body metabolism. Curr Opin Endocr Metab Res (2022). Link.
Kokaji, Toshiya 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.
Kondo, Jumpei 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.
Kong, Siyuan et al., Nucleosome-Omics: A Perspective on the Epigenetic Code and 3D Genome Landscape. Genes (2022). Link.
Kozlova, Alena A. et al., Assessment of DDAH1 and DDAH2 Contributions to Psychiatric Disorders via In Silico Methods. Int J Mol Sci (2022). Link.
Kreiß, Marius et al., Human 5-lipoxygenase regulates transcription by association to euchromatin. Biochem Pharmacol (2022). Link.
Larsen, Erik G. et al., Transmembrane protein TMEM184B is necessary for interleukin-31-induced itch. Pain (2022). Link.
Lee, Shi Hao et al., Activation function 1 of progesterone receptor is required for progesterone antagonism of oestrogen action in the uterus. BMC Biol (2022). Link.
Letson, Christopher T. et al., Targeting BET Proteins downregulates miR-33a to promote synergy with PIM inhibitors in CMML. bioRxiv (2022). Link.
Li, Feng et al., TEAD1 regulates cell proliferation through a pocket-independent transcription repression mechanism. Nucleic Acids Res (2022). Link.
Li, Ruizhi 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.
Li, Wei 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.
Li, Yafei et al., ARID3A promotes the chemosensitivity of colon cancer by inhibiting AKR1C3. Cell Biol Int (2022). Link.
Li, Yaohua et al., Immunoglobulin superfamily 9 (IGSF9) is trans-activated by p53, inhibits breast cancer metastasis via FAK. Oncogene (2022). Link.
Liao, Yuandong 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.
Lisacek, Frederique et al., Worldwide Glycoscience Informatics Infrastructure: The GlySpace Alliance. JACS Au (2022). Link.
Liu, Tianyuan et al., Computational identification of preneoplastic cells displaying high stemness and risk of cancer progression. Cancer Res (2022). Link.
Liu, Wentao 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.
Liu, Zhen et al., JAK2/STAT3 inhibition attenuates intestinal ischemia-reperfusion injury via promoting autophagy: in vitro and in vivo study. Mol Biol Rep (2022). Link.
Lu, Yuanjun 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.
Lyu, Qingji 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.
M, Watzky et al., Hexokinase 2 is a transcriptional target and a positive modulator of AHR signalling. Nucleic Acids Res (2022). Link.
M, Zhang et al., MethBank 4.0: an updated database of DNA methylation across a variety of species. Nucleic Acids Res (2022). Link.
Ma, Xiaolong et al., Single-cell RNA sequencing reveals B cell-T cell interactions in vascular adventitia of hyperhomocysteinemia-accelerated atherosclerosis. Protein Cell (2022). Link.
MacKay, Harry 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.
Maity, Alok K. et al., Inference of age-associated transcription factor regulatory activity changes in single cells. Nat Aging (2022). Link.
Maixner, Nitzan et al., Visceral Adipose Tissue E2F1-miRNA206/210 Pathway Associates with Type 2 Diabetes in Humans with Extreme Obesity. Cells (2022). Link.
Mamivand, Ali 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.
Marques, Ines J. et al., Wt1 transcription factor impairs cardiomyocyte specification and drives a phenotypic switch from myocardium to epicardium. Development (2022). Link.
Martínez Corrales, Guillermo et al., Transcriptional memory of dFOXO activation in youth curtails later-life mortality through chromatin remodeling and Xbp1. Nat Aging (2022). Link.
Masamoto, Yosuke et al., EVI1 exerts distinct roles in AML via ERG and cyclin D1 promoting a chemoresistance and immune-suppressive environment. Blood Adv (2022). Link.
Matsumoto, Akifumi et al., C11orf21, a novel RUNX1 target gene, is down-regulated by RUNX1-ETO. BBA Adv (2022). Link.
Mbebi, Alain J. et al., Gene regulatory network inference using mixed-norms regularized multivariate model with covariance selection. bioRxiv (2022). Link.
McKowen, J Keller et al., The Drosophila BEAF Insulator Protein Interacts with the Polybromo Subunit of the PBAP Chromatin Remodeling Complex. Genes Genomes Genet (2022). Link.
Mei, Heng et al., Autophagy Facilitates Cancer-Intrinsic Evasion of CAR T Cell-Mediated Cytotoxicity in B-Cell Malignancies. Blood (2022). Link.
Meller, Anna et al., Mining Proteomics Datasets to Uncover Functional Pseudogenes. Methods Mol Biol (2022). Link.
Metcalf, Melissa G. et al., Cell non-autonomous control of autophagy and metabolism by glial cells. bioRxiv (2022). Link.
Miao, Jiamin et al., Sp1 Inhibits PGC-1α via HDAC2-Catalyzed Histone Deacetylation in Chronic Constriction Injury-Induced Neuropathic Pain. ACS Chem Neurosci (2022). Link.
Migdał, Maciej et al., xcore: an R package for inference of gene expression regulators. bioRxiv (2022). Link.
Mori, Jinichi 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.
Mori, Tatsufumi 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.
Morin, Alexander et al., Characterizing the targets of transcription regulators by aggregating ChIP-seq and perturbation expression data sets. bioRxiv (2022). Link.
Morita, Tsuyoshi et al., Actin-related protein 5 functions as a novel modulator of MyoD and MyoG in skeletal muscle and in rhabdomyosarcoma. Elife (2022). Link.
Mouri, Kousuke et al., Prioritization of autoimmune disease-associated genetic variants that perturb regulatory element activity in T cells. Nat Genet (2022). Link.
Muromoto, Ryuta et al., Regulation of NFKBIZ gene promoter activity by STAT3, C/EBPβ, and STAT1. Biochem Biophys Res Commun (2022). Link.
Nair, Praful R. et al., MLL1 regulates cytokine-driven cell migration and metastasis. bioRxiv (2022). Link.
Nakamura, Hideaki 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.
Neal, Alice et al., Finding and Verifying Enhancers for Endothelial-Expressed Genes. Methods Mol Biol (2022). Link.
Ng, Krystle Joy et al., Sox2 in the dermal papilla regulates hair follicle pigmentation. Cell Rep (2022). Link.
Nie, Meng et al., Targeting acetylcholine signaling modulates persistent drug tolerance in EGFR-mutant lung cancer and impedes tumor relapse. J Clin Invest (2022). Link.
Nishi, Kentaro et al., Novel estrogen-responsive genes (ERGs) for the evaluation of estrogenic activity. PLoS One (2022). Link.
Ochsner, Scott A. et al., Transcriptional regulatory networks of circulating immune cells in type 1 diabetes: A community knowledgebase. iScience (2022). Link.
Ohnishi, Tomokazu 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.
Ono, Koya et al., Congenital sideroblastic anemia model due to ALAS2 mutation is susceptible to ferroptosis. Sci Rep (2022). Link.
Panatta, Emanuele et al., Metabolic regulation by p53 prevents R-loop-associated genomic instability. Cell Rep (2022). Link.
Panatta, Emanuele et al., p53 regulates expression of nuclear envelope components in cancer cells. Biol Direct (2022). Link.
Peng, Liang et al., Bombesin receptor-activated protein exacerbates cisplatin-induced AKI by regulating the degradation of SIRT2. Nephrol Dial Transplant (2022). Link.
Pontis, Julien et al., Primate-specific transposable elements shape transcriptional networks during human development. Nat Commun (2022). Link.
Q, Zhou et al., ChromLoops: a comprehensive database for specific protein-mediated chromatin loops in diverse organisms. Nucleic Acids Res (2022). Link.
Reagor, Caleb C. et al., Depicting pseudotime-lagged causality across single-cell trajectories for accurate gene-regulatory inference. bioRxiv (2022). Link.
Ren, Jiannan et al., Downregulation of CBX7 induced by EZH2 upregulates FGFR3 expression to reduce sensitivity to cisplatin in bladder cancer. Br J Cancer (2022). Link.
Rhizobium, Growth-promoting Endophyte, TFSyntax: a database of transcription factors binding syntax in mammalian genomes. Nucleic Acids Res (2022). Link.
Richard, Daniel et al., Intronic regulation of SARS-CoV-2 receptor (ACE2) expression mediated by immune signaling and oxidative stress pathways. iScience (2022). Link.
Richard, Daniel et al., Lineage-Specific Differences and Regulatory Networks Governing Human Chondrocyte Development. bioRxiv (2022). Link.
Rykaczewska, Urszula 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.
Saadey, Abbey A. et al., Rebalancing TGFβ1/BMP signals in exhausted T cells unlocks responsiveness to immune checkpoint blockade therapy. Nat Immunol (2022). Link.
Sakai, Hiroshi et al., Uhrf1 governs the proliferation and differentiation of muscle satellite cells. iScience (2022). Link.
Samelson, Avi J. et al., BRD2 inhibition blocks SARS-CoV-2 infection by reducing transcription of the host cell receptor ACE2. Nat Cell Biol (2022). Link.
Sasaki, Norihiko et al., Gp130-Mediated STAT3 Activation Contributes to the Aggressiveness of Pancreatic Cancer through H19 Long Non-Coding RNA Expression. Cancers (2022). Link.
Sasaki, Norihiko 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.
Sato, Fumiaki et al., COL8A1 facilitates the growth of triple-negative breast cancer via FAK/Src activation. Breast Cancer Res Treat (2022). Link.
Sawada, Takahiro 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.
Schihada, Hannes 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.
Schuhwerk, Harald et al., The EMT transcription factor ZEB1 governs a fitness-promoting but vulnerable DNA replication stress response. Cell Rep (2022). Link.
Serrano-Zayas, Candilianne et al., Regulation of cellular LDL uptake by PROX1 and CHD7. bioRxiv (2022). Link.
Shen, Shang-Hang 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.
Shin, Jihoon 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.
Silvennoinen, Katri 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.
Singh, Anupama et al., Conserved neuropeptidergic regulation of intestinal integrity in invertebrate models of aging. bioRxiv (2022). Link.
Siswanto, Ferbian Milas 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.
Smirnov, Dmitrii et al., SIRT6 is a key regulator of mitochondrial function in the brain. bioRxiv (2022). Link.
Sokolowska, Katarzyna Ewa et al., Identified in blood diet-related methylation changes stratify liver biopsies of NAFLD patients according to fibrosis grade. Clin Epigenetics (2022). Link.
Sokolowski, Dustin J. et al., Differential Expression Enrichment Tool (DEET): An interactive atlas of human differential gene expression. bioRxiv (2022). Link.
Sugawara, Sho et al., RNaseH2A downregulation drives inflammatory gene expression via genomic DNA fragmentation in senescent and cancer cells. Commun Biol (2022). Link.
Sun, Jichun et al., The lncRNA CASC2 Modulates Hepatocellular Carcinoma Cell Sensitivity and Resistance to TRAIL Through Apoptotic and Non-Apoptotic Signaling. Front Oncol (2022). Link.
Tahara, Saeko et al., MOCCS profile analysis clarifies the cell type dependency of transcription factor-binding sequences and cis-regulatory SNPs in humans. bioRxiv (2022). Link.
Takayama, Shun et al., GATA6 regulates expression of annexin A10 (ANXA10) associated with epithelial-mesenchymal transition of oral squamous cell carcinoma. Arch Oral Biol (2022). Link.
Takeuchi, Chikara et al., Mod(mdg4) variants repress telomeric retrotransposon HeT-A by blocking subtelomeric enhancers. bioRxiv (2022). Link.
Talamanca, Lorenzo et al., Sex-dimorphic and age-dependent organization of 24 hour gene expression rhythms in human. bioRxiv (2022). Link.
Tanigawa, Yosuke et al., WhichTF is functionally important in your open chromatin data?. PLoS Comput Biol (2022). Link.
Terakawa, Akira et al., Trans-omics analysis of insulin action reveals a cell growth subnetwork which co-regulates anabolic processes. iScience (2022). Link.
Toyoda, Kosuke et al., Reprogramming of lactate metabolism is linked to the oncogenesis of the virus-induced leukemia. bioRxiv (2022). Link.
Tsujino, Takuya et al., CRISPR screens reveal genetic determinants of PARP inhibitor sensitivity and resistance in prostate cancer. bioRxiv (2022). Link.
Vorontsova, Julia E. 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.
Wang, Yijie et al., NetREX-CF integrates incomplete transcription factor data with gene expression to reconstruct gene regulatory networks. Commun Biol (2022). Link.
Wang, Zixuan et al., Towards a better understanding of TF-DNA binding prediction from genomic features. Comput Biol Med (2022). Link.
Woogeng, Ivo Ngundu et al., Inducing human retinal pigment epithelium-like cells from somatic tissue. Stem Cell Rep (2022). Link.
Wu, Beibei et al., ORAI1 Limits SARS-CoV-2 Infection by Regulating Tonic Type I IFN Signaling. J Immunol (2022). Link.
Wu, Shizhong 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.
Y, Hino et al., Mitochondrial stress induces AREG expression and epigenomic remodeling through c-JUN and YAP-mediated enhancer activation. Nucleic Acids Res (2022). Link.
Yamada, Minami et al., KLF5-regulated extracellular matrix remodeling secures biliary epithelial tissue integrity against cholestatic liver injury. bioRxiv (2022). Link.
Yamamoto-Imoto, Hitomi et al., Age-associated decline of MondoA drives cellular senescence through impaired autophagy and mitochondrial homeostasis. Cell Rep (2022). Link.
Yamashita, Yu et al., Osteoblast lineage cells-derived Sema3A regulates bone homeostasis independently of androgens. Endocrinology (2022). Link.
Yamazaki, Masaya et al., ROR1 plays a critical role in pancreatic tumor-initiating cells with a partial EMT signature. bioRxiv (2022). Link.
Yan, Bingyu 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.
Yang, Kaixin et al., Prognostic and Immunotherapeutic Roles of KRAS in Pan-Cancer. Cells (2022). Link.
Yang, Lihua et al., Sevoflurane Offers Neuroprotection in a Cerebral Ischemia/Reperfusion Injury Rat Model Through the E2F1/EZH2/TIMP2 Regulatory Axis. Mol Neurobiol (2022). Link.
Yashar, William M. et al., GoPeaks: histone modification peak calling for CUT&Tag. Genome Biol (2022). Link.
Yheskel, Matanel et al., Proximity labeling reveals a new in vivo network of interactors for the histone demethylase KDM5. bioRxiv (2022). Link.
Yonezawa, Yoshiro 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.
Zelenka, Tomas et al., The 3D enhancer network of the developing T cell genome is shaped by SATB1. Nat Commun (2022). Link.
Zhang, Huan et al., CBX3 Regulated By YBX1 Promotes Smoking-induced Pancreatic Cancer Progression via Inhibiting SMURF2 Expression. Int J Biol Sci (2022). Link.
Zhang, Liang et al., STAT3 is a biologically relevant therapeutic target in H3K27M-mutant diffuse midline glioma. Neuro Oncol (2022). Link.
Zhang, Ting et al., ADAR1 masks the cancer immunotherapeutic promise of ZBP1-driven necroptosis. Nature (2022). Link.
Zhang, Yongqing et al., Fusion prior gene network for high reliable single-cell gene regulatory network inference. Comput Biol Med (2022). Link.
Zhao, Jianmei et al., CanMethdb: a database for genome-wide DNA methylation annotation in cancers. Bioinformatics (2022). Link.
Zhao, Mengyuan et al., A hybrid deep learning framework for gene regulatory network inference from single-cell transcriptomic data. Brief Bioinform (2022). Link.
Zheng, Xianchong 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.
Zhong, Xiaoling et al., CBX3 is associated with metastasis and glutathione/ glycosphingolipid metabolism in colon adenocarcinoma. J Gerontol A Biol Sci Med Sci (2022). Link).
Zhu, Tianyu et al., A pan-tissue DNA methylation atlas enables in silico decomposition of human tissue methylomes at cell-type resolution. Nat Methods (2022). Link.
Zou, Zhaonan et al., Epigenetic landscape of drug responses revealed through large-scale ChIP-seq data analyses. BMC Bioinformatics (2022). Link.
A, Mamivand 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.
A, Meiler 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.
A, Nagalingam 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.
A, Wanet 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.
AP, Wu et al., Bayesian information sharing enhances detection of regulatory associations in rare cell types. Bioinformatics (2021). Link.
Agudelo, Leandro Z. et al., Metabolic resilience is encoded in genome plasticity. bioRxiv (2021). Link.
Aizawa, Shiho et al., Early reactivation of clustered genes on the inactive X chromosome during somatic cell reprogramming. Stem Cell Rep (2021). Link.
Alfeghaly, Charbel et al., Implication of repeat insertion domains in the trans -activity of the long non-coding RNA ANRIL . Nucleic Acids Res (2021). Link.
Astudillo, Pablo, Analysis in silico of the functional interaction between WNT5A and YAP/TEAD signaling in cancer. PeerJ (2021). Link.
B. Tóth, Beáta et al., Regulatory modules of human thermogenic adipocytes: functional genomics of large cohort and Meta-analysis derived marker-genes. BMC Genomics (2021). Link.
Bang, Jeyoung et al., Identification of Signaling Pathways for Early Embryonic Lethality and Developmental Retardation in Sephs1 -/- Mice. Int J Mol Sci (2021). Link.
Biani, M.C. et al., Small extracellular vesicles from iPSC-MSC lose their regenerative potential upon UV-C irradiation. bioRxiv (2021). Link.
Bono, Hidemasa, Meta-analysis of oxidative transcriptomes in insects. Antioxidants (2021). Link.
C, Feng 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.
CA, Anene et al., ACSNI: An unsupervised machine-learning tool for prediction of tissue-specific pathway components using gene expression profiles. Patterns (2021). Link.
Centenera, Margaret M. et al., ELOVL5 is a critical and targetable fatty acid elongase in prostate cancer. Cancer Res (2021). Link.
Cerase, Andrea et al., Chd8 regulates X chromosome inactivation in mouse through fine-tuning control of Xist expression. Commun Biol (2021). Link.
Chen, Haobin et al., BET Bromodomain Inhibitors Target the NEUROD1-subtype SCLC by Blocking NEUROD1 Transactivation. bioRxiv (2021). Link.
Chen, Ming et al., Integrative Analyses Reveal Novel Disease-associated Loci and Genes for Idiopathic Pulmonary Fibrosis. medRxiv (2021). Link.
Choi, Sangyong 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.
Cofer, Evan M. et al., Modeling transcriptional regulation of model species with deep learning. Genome Res (2021). Link.
De Smedt, Jonathan et al., PU.1 drives specification of pluripotent stem cell-derived endothelial cells to LSEC-like cells. Cell Death Dis (2021). Link.
Dhaka, Bhavya et al., Differential chromatin accessibility landscape of gain-of-function mutant p53 tumours. BMC Cancer (2021). Link.
Droin, Colas et al., Space-time logic of liver gene expression at sub-lobular scale. Nat Metab (2021). Link.
Durand, Sébastien et al., RSL24D1 sustains steady-state ribosome biogenesis and pluripotency translational programs in embryonic stem cells. bioRxiv (2021). Link.
E, Mammarella et al., NUAK2 and RCan2 participate in the p53 mutant pro-tumorigenic network. Biol Direct (2021). Link.
Feng, Haizhou et al., Identification of core miRNAs and regulatory pathways in breast cancer by integrated bioinformatics analysis. Mol Omics (2021). Link.
Feng, Lei 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.
Feng, Peiyuan et al., A machine learning-based framework for modeling transcription elongation. Proc Natl Acad Sci U S A (2021). Link.
Fernandez Lahore, Gonzalo et al., Polymorphic estrogen receptor binding site causes Cd2-dependent sex bias in the susceptibility to autoimmune diseases. Nat Commun (2021). Link.
Franco, Elisa De et al., Primate-specific ZNF808 is essential for pancreatic development in humans. medRxiv (2021). Link.
Fujino, Kan et al., A human endogenous bornavirus-like nucleoprotein encodes a mitochondrial protein associated with cell viability. J Virol (2021). Link.
Fujino, Shiki et al., HNF1A regulates colorectal cancer progression and drug resistance as a downstream of POU5F1. Sci Rep (2021). Link.
G, Devailly et al., Comprehensive analysis of epigenetic signatures of human transcription control. Mol Omics (2021). Link.
Gallo, Alberto et al., NF-Y subunits overexpression in gastric adenocarcinomas (STAD). Sci Rep (2021). Link.
Gharavi, Erfaneh et al., Embeddings of genomic region sets capture rich biological associations in lower dimensions. Bioinformatics (2021). Link.
H, Doi 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.
H, Mizuno et al., Evi1 upregulates Fbp1 and supports progression of acute myeloid leukemia through pentose phosphate pathway activation. Cancer Sci (2021). Link.
H, Ohguchi et al., Lysine Demethylase 5A is Required for MYC Driven Transcription in Multiple Myeloma. Blood Cancer Discov (2021). Link.
Hamano, Momoko et al., Prediction of single-cell mechanisms for disease progression in hypertrophic remodelling by a trans-omics approach. Sci Rep (2021). Link.
Hammal, Fayrouz 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.
Hanaki, Shunsuke et al., PP1 regulatory subunit NIPP1 regulates transcription of E2F1 target genes following DNA damage. Cancer Sci (2021). Link.
Harada, Yukihiro et al., ETS‐dependent enhancers for endothelial‐specific expression of serum/glucocorticoid‐regulated kinase 1 during mouse embryo development. Genes Cells (2021). Link.
He, Lingli 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.
Hernández-Nava, Elizabeth et al., Transcriptional and Epigenetic Bioinformatic Analysis of Claudin-9 Regulation in Gastric Cancer. J Oncol (2021). Link.
Hiebert, Paul, The Nrf2 transcription factor: A multifaceted regulator of the extracellular matrix. Matrix Biol Plus (2021). Link.
Hisamatsu, Yoji et al., Matrix Metalloproteinases in Human Decidualized Endometrial Stromal Cells. Curr Issues Mol Biol (2021). Link.
Hisano, Osamu et al., Short single-stranded DNAs with putative non-canonical structures comprise a new class of plasma cell-free DNA. BMC Biol (2021). Link.
Hosoi, Hiroki et al., Super-enhancers for RUNX3 are required for cell proliferation in EBV-infected B cell lines. Gene (2021). Link.
Hosoya, Tadashi et al., Chondroprotective effects of CDK4/6 inhibition via enhanced ubiquitin-dependent degradation of JUN in synovial fibroblasts. Baillieres Clin Rheumatol (2021). Link.
Hossain, Sk Md Mosaddek et al., Discovering key transcriptomic regulators in pancreatic ductal adenocarcinoma using Dirichlet process Gaussian mixture model. Sci Rep (2021). Link.
Huang, Chia Chi Flora et al., Functional mapping of androgen receptor enhancer activity. Genome Biol (2021). Link.
Hudecova, Irena et al., Characteristics, origin, and potential for cancer diagnostics of ultrashort plasma cell-free DNA. Genome Res (2021). Link.
Inazumi, Hideaki et al., NRSF-GNAO1 Pathway Contributes to the Regulation of Cardiac Ca 2+ Homeostasis. Circ Res (2021). Link.
J, Dahlqvist et al., Systematic identification of genomic elements that regulate FCGR2A expression and harbor variants linked with autoimmune disease. Hum Mol Genet (2021). Link.
J, Studd et al., Cancer drivers and clonal dynamics in acute lymphoblastic leukaemia subtypes. Research Square (2021). Link.
J, Wutschka et al., JUNB suppresses distant metastasis by influencing the initial metastatic stage. Clin Exp Metastasis (2021). Link.
Jang, Minjeong et al., Matrix stiffness epigenetically regulates the oncogenic activation of the Yes-associated protein in gastric cancer. Nat Biomed Eng (2021). Link.
Jarvis, Lorna B. et al., Therapeutically expanded human regulatory T-cells are super-suppressive due to HIF1A induced expression of CD73. Commun Biol (2021). Link.
Jia, Yunlu et al., Super enhancer-mediated upregulation of HJURP promotes growth and survival of t(4;14)-positive multiple myeloma. Cancer Res (2021). Link.
Jiang, Jiayue-Clara 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.
Jiang, Jiayue-Clara et al., Widespread Exaptation of L1 Transposons for Transcription Factor Binding in Breast Cancer. Int J Mol Sci (2021). Link.
Jiang, Xinliang et al., Heat shock induces the nuclear accumulation of YAP1 via SRC. Exp Cell Res (2021). Link.
Jin, Xin et al., Smoking-associated upregulation of CBX3 suppresses ARHGAP24 expression to activate Rac1 signaling and promote tumor progression in lung adenocarcinoma. Oncogene (2021). Link.
Jung, Sascha et al., A computer-guided design tool to increase the efficiency of cellular conversions. Nat Commun (2021). Link.
Jungwirth, Emilian et al., Meta-analysis and Consolidation of Farnesoid X Receptor Chromatin Immunoprecipitation Sequencing Data Across Different Species and Conditions. Hepatol Commun (2021). Link.
K, Kitakaze et al., ATF4-mediated transcriptional regulation protects against β-cell loss during endoplasmic reticulum stress in a mouse model. Mol Metab (2021). Link.
K, Nishimura et al., Profiling of Androgen-Dependent Enhancer RNAs Expression in Human Prostate Tumors: Search for Malignancy Transition Markers. Res Rep Urol (2021). Link.
K, Sofiadis et al., HMGB1 coordinates SASP-related chromatin folding and RNA homeostasis on the path to senescence. Mol Syst Biol (2021). Link.
Kaiser, Marina et al., Regulation of otocyst patterning by Tbx2 and Tbx3 is required for inner ear morphogenesis in the mouse. Development (2021). Link.
Kalman, Zsofia E et al., A preliminary study on the cistrome of human postsynaptic density from an evolutionary and network-based perspective. bioRxiv (2021). Link.
Kanai, Masahiro et al., Insights from complex trait fine-mapping across diverse populations. medRxiv (2021). Link.
Kanamori, Yohei et al., Iron-rich Kupffer cells exhibit phenotypic changes during the development of liver fibrosis in NASH. iScience (2021). Link.
Katada, Sayako 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.
Kidwell, Ashley et al., Translation rescue by targeting Ppp1r15a upstream open reading frame in vivo. bioRxiv (2021). Link.
Kikutake, Chie et al., Pan-cancer analysis of non-coding recurrent mutations and their possible involvement in cancer pathogenesis. NAR Cancer (2021). Link.
Kim, Jessica 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.
Kohrogi, Kensaku 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.
Koike, Yuka et al., Age-related demethylation of the TDP-43 autoregulatory region in the human motor cortex. Commun Biol (2021). Link.
Kosinsky, Robyn Laura et al., RNF20 and RNF40 regulate vitamin D receptor-dependent signaling in inflammatory bowel disease. Cell Death Differ (2021). Link.
Kwon, Andrew Tae-Jun 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.
L, Wang et al., The Ubiquitin Sensor and Adaptor Protein p62 Mediates Signal Transduction of a Viral Oncogenic Pathway. mBio (2021). Link.
Labade, Ajay S. et al., Nup93 and CTCF modulate spatiotemporal dynamics and function of the HOXA gene locus during differentiation. J Cell Sci (2021). Link.
Lee, Hsiu-Chi 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.
Lee, Shin-Ae et al., METTL8 mRNA Methyltransferase Enhances Cancer Cell Migration via Direct Binding to ARID1A. Int J Mol Sci (2021). Link.
Li, Jie-Ning et al., Expression of SnoRNA U50A Is Associated with Better Prognosis and Prolonged Mitosis in Breast Cancer. Cancers (2021). Link.
Liu, Yi et al., Tumors exploit FTO-mediated regulation of glycolytic metabolism to evade immune surveillance. Cell Metab (2021). Link.
Luginbühl, Joachim et al., Decoding Neuronal Diversification by Multiplexed Single-cell RNA-Seq. Stem Cell Rep (2021). Link.
M, Francia 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.
M, Saito et al., PHLDA3 is an important downstream mediator of p53 in squamous cell carcinogenesis. J Invest Dermatol (2021). Link.
M, Yamagishi et al., Chronological genome and single-cell transcriptome integration characterizes the evolutionary process of adult T cell leukemia-lymphoma. Nat Commun (2021). Link.
Ma, Shiyang et al., Powerful gene-based testing by integrating long-range chromatin interactions and knockoff genotypes. medRxiv (2021). Link.
Ma, Wenjing et al., BARTweb: a web server for transcriptional regulator association analysis. NAR Genom Bioinform (2021). Link.
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.
Marques, Ines J. et al., Downregulation of WT1 transcription factor gene expression is required to promote myocardial fate. bioRxiv (2021). Link.
Matsuura, Norihiro et al., NOTCH3 limits the epithelial–mesenchymal transition and predicts a favorable clinical outcome in esophageal cancer. Cancer Med (2021). Link.
Milanesi, Elena et al., Whole Blood Expression Pattern of Inflammation and Redox Genes in Mild Alzheimer's Disease. J Inflamm Res (2021). Link.
Misawa, Aya 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.
Miyake, Masato et al., Integrated stress response regulates GDF15 secretion from adipocytes, preferentially suppresses appetite for a high-fat diet and improves obesity. iScience (2021). Link.
Miyazawa, Kazuo et al., Trans-ancestry genome-wide analysis of atrial fibrillation provides new insights into disease biology and enables polygenic prediction of cardioembolic risk. medRxiv (2021). Link.
Morishita, Mayu 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.
Morrow, Alyssa Kramer et al., Epitome: predicting epigenetic events in novel cell types with multi-cell deep ensemble learning. Nucleic Acids Res (2021). Link.
Mourao, Larissa et al., Hyperactive WNT/CTNNB1 signaling induces a competing cell proliferation and epidermal differentiation response in the mouse mammary epithelium. bioRxiv (2021). Link.
N, Osada et al., mTOR inhibitors sensitize multiple myeloma cells to venetoclax via IKZF3-and Blimp-1-mediated BCL-2 up-regulation. Haematologica (2021). Link.
Nagai, Yasuki et al., Glucotoxicity-induced suppression of Cox6a2 expression provokes β-cell dysfunction via augmented ROS production. Biochem Biophys Res Commun (2021). Link.
Namba, Shinichi et al., Transcript-targeted analysis reveals isoform alterations and double-hop fusions in breast cancer. Commun Biol (2021). Link.
Nurtdinov, Ramil et al., Alu-mediated weak CEBPA binding and slow B cell transdifferentiation in human. bioRxiv (2021). Link.
Ogino, Takashi et al., Post-transcriptional repression of circadian component CLOCK regulates cancer-stemness in murine breast cancer cells. Elife (2021). Link.
Oh, Taek In et al., PGC1α Loss Promotes Lung Cancer Metastasis through Epithelial-Mesenchymal Transition. Cancers (2021). Link.
Omiya, Hanae et al., BMP signaling suppresses Gemc1 expression and ependymal differentiation of mouse telencephalic progenitors. Sci Rep (2021). Link.
P, McErlean et al., DNA Methylome Alterations are Associated with Airway Macrophage Differentiation and Phenotype During Lung Fibrosis. Am J Respir Crit Care Med (2021). Link.
P, Weidemüller et al., Transcription factors: Bridge between cell signaling and gene regulation. Proteomics (2021). Link.
PM, Tyler et al., Human autoinflammatory disease reveals ELF4 as a transcriptional regulator of inflammation. Nat Immunol (2021). Link.
Papagiannopoulos, Christos I 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.
Pecori, Federico et al., A defined glycosylation regulatory network modulates total glycome dynamics during pluripotency state transition. Sci Rep (2021). Link.
Petrone, María Victoria et al., The pluripotency transcription factor OCT4 represses heme oxygenase-1 gene expression. FEBS Lett (2021). Link.
Piette, Benjamin L. et al., Comprehensive interactome profiling of the human Hsp70 network highlights functional differentiation of J domains. Mol Cell (2021). Link.
Q, Luo et al., SIGNET: single-cell RNA-seq-based gene regulatory network prediction using multiple-layer perceptron bagging. Brief Bioinform (2021). Link.
Quinn, Hazel M et al., YAP and β-catenin cooperate to drive oncogenesis in basal breast cancer. Cancer Res (2021). Link.
Reimegård, Johan et al., A combined approach for single-cell mRNA and intracellular protein expression analysis. Commun Biol (2021). Link.
Ruiz, José L et al., The regulatory genome of the malaria vector Anopheles gambiae : integrating chromatin accessibility and gene expression . NAR Genom Bioinform (2021). Link.
S, Han et al., Targeting ATF4-dependent pro-survival autophagy to synergize glutaminolysis inhibition. Theranostics (2021). Link.
S, Li et al., Long noncoding RNA HOTAIR interacts with Y-Box Protein-1 (YBX1) to regulate cell proliferation. Life Sci Alliance (2021). Link.
S, Mohr et al., The alternative serotonin transporter promoter P2 impacts gene function in females with irritable bowel syndrome. J Cell Mol Med (2021). Link.
SY, Wu et al., MYC suppresses STING-dependent innate immunity by transcriptionally upregulating DNMT1 in triple-negative breast cancer. J Immunother Cancer (2021). Link.
Sarkar, Arijita 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.
Sekita, Yoichi 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.
Sharma, Abhay, Inferring molecular mechanisms of dexamethasone therapy in severe COVID-19 from existing transcriptomic data. Gene (2021). Link.
Shimizu, Tatsuya et al., Osteocytes as main responders to low-intensity pulsed ultrasound treatment during fracture healing. Sci Rep (2021). Link.
Shin, Jihoon 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.
Shinohara, Mitsuru 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.
Shirai, Yuya et al., Elucidation of disease etiology by trans-layer omics analysis. Inflamm Regen (2021). Link.
Singh, Isha 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.
Stirparo, Giuliano G. et al., OCT4 induces embryonic pluripotency via STAT3 signaling and metabolic mechanisms. Proc Natl Acad Sci U S A (2021). Link.
Stuparević, Igor et al., Regulation of the conserved 3′-5′ exoribonuclease EXOSC10/Rrp6 during cell division, development and cancer. Biol Rev (2021). Link.
Su, Emily Y et al., Reconstruction of dynamic regulatory networks reveals signaling-induced topology 3 changes associated with germ layer specification 4 5 6. bioRxiv (2021). Link.
Sun, Yaping 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.
T, Sawada 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.
T, Yao 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.
Takai, Jun et al., Gata2 heterozygous mutant mice exhibit reduced inflammatory responses and impaired bacterial clearance. iScience (2021). Link.
Takeda, Takashi et al., A stem cell marker KLF5 regulates CCAT1 via three-dimensional genome structure in colorectal cancer cells. Br J Cancer (2021). Link.
Takeuchi, Yasuto 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.
Tan, Deng et al., Quantitative control of noise in mammalian gene expression by dynamic histone regulation. Elife (2021). Link.
Teschendorff, Andrew E et al., Statistical mechanics meets single-cell biology. Nat Rev Genet (2021). Link.
Tian, Yijun 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.
Umarov, Ramzan et al., DeepCellState: An autoencoder-based framework for predicting cell type specific transcriptional states induced by drug treatment. PLoS Comput Biol (2021). Link.
Unno, Kenji et al., Activated ALK Cooperates with N-Myc via Wnt/β-catenin Signaling to Induce Neuroendocrine Prostate Cancer. Cancer Res (2021). Link.
Wan, Ruosi et al., Direct Reconstruction of Gene Regulatory Networks underlying Cellular state Transitions without Pseudo-time Inference. bioRxiv (2021). Link.
Wang, Jun et al., HPV E7 affects the function of cervical cancer cells via the TAL1/lnc‑EBIC/KLHDC7B axis. Oncol Rep (2021). Link.
Wang, Liang et al., ASXL1 promotes adrenocortical carcinoma and is associated with chemoresistance to EDP regimen. Aging (2021). Link.
Wei, Kai-Che et al., An innovative targeted therapy for fluoroscopy-induced chronic radiation dermatitis. J Mol Med (2021). Link.
Wen, Li 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.
Wierzbicka, Justyna M. 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.
Wu, Beibei et al., ORAI1 establishes resistance to SARS-CoV-2 infection by regulating tonic type I interferon signaling. bioRxiv (2021). Link.
X, Chen 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.
X, Li et al., Defining Proximity Proteomics of Histone Modifications by Antibody-mediated Protein A-APEX2 Labeling. Genomics Proteomics Bioinformatics (2021). Link.
X, Zhao 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.
Xiang, Tian 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.
Y, Hayashi et al., Norrie disease protein is essential for cochlear hair cell maturation. Proc Natl Acad Sci U S A (2021). Link.
Y, Ono et al., Multi-Omic Meta-Analysis of Transcriptomes and the Bibliome Uncovers Novel Hypoxia-Inducible Genes. Biomedicines (2021). Link.
Y, Zhang et al., TcoFBase: a comprehensive database for decoding the regulatory transcription co-factors in human and mouse. Nucleic Acids Res (2021). Link.
YH, Chen 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.
Yagi, Mikako et al., Mitochondrial translation deficiency impairs NAD + ‐mediated lysosomal acidification. EMBO J (2021). Link.
Yao, Xiaolei et al., TP53/miR-129/MDM2/4/TP53 feedback loop modulates cell proliferation and apoptosis in retinoblastoma. Cell Cycle (2021). Link.
Yazar, Volkan 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.
Yi, Lu et al., The FOXM1/RNF26/p57 axis regulates the cell cycle to promote the aggressiveness of bladder cancer. Cell Death Dis (2021). Link.
Yi, Xianfu et al., Interrogating cell type-specific cooperation of transcriptional regulators in 3D chromatin. iScience (2021). Link.
Yoneda, Mitsuhiro et al., Nucleosome assembly protein 1 (NAP-1) is a regulator of histone H1 acetylation. J Biochem (2021). Link.
Yoshizaki, Kaichi et al., Paternal age affects offspring via an epigenetic mechanism involving REST/NRSF. EMBO Rep (2021). Link.
Zampieri, Carlotta et al., p53 mutations define the chromatin landscape to confer drug tolerance in pancreatic cancer. Mol Oncol (2021). Link.
Zhang, Shu et al., RNA polymerase II is required for spatial chromatin reorganization following exit from mitosis. Sci Adv (2021). Link.
Zhao, Xiaolu et al., CircleBase: an integrated resource and analysis platform for human eccDNAs. Nucleic Acids Res (2021). Link.
Zhao, Ye 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.
de Roover, Astrid et al., Hypoxia induces DOT1L in articular cartilage to protect against osteoarthritis. JCI Insight (2021). Link.
Łasut-Szyszka, Barbara 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.
AS, Knaupp 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.
Ahmed, Mahmoud et al., Integrating binding and expression data to predict transcription factors combined function. BMC Genomics (2020). Link.
Azim, Kasum 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.
B, Zhu et al., Mi-2β-targeted inhibition induces immunotherapy response in melanoma. Research Square (2020). Link.
Beknazarov, Nazar et al., Deep learning approach for predicting functional Z-DNA regions using omics data. Sci Rep (2020). Link.
Bono, Hidemasa et al., Meta-analysis of hypoxic transcriptomes from public databases. Biomedicines (2020). Link.
Booth, Lauren N et al., Males deploy multifaceted strategies and hijack longevity pathways to induce premature demise of the opposite sex. bioRxiv (2020). Link.
Bunina, Daria et al., Genomic Rewiring of SOX2 Chromatin Interaction Network during Differentiation of ESCs to Postmitotic Neurons. Cell Syst (2020). Link.
Caruana, Beth T et al., The NF-κB signalling pathway regulates GLUT6 expression in endometrial cancer. Cell Signal (2020). Link.
Cataldo, Alessandra et al., MiR-302b as a Combinatorial Therapeutic Approach to Improve Cisplatin Chemotherapy Efficacy in Human Triple-Negative Breast Cancer. Cancers (2020). Link.
Cavalli, Marco 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.
Charmpi, Konstantina et al., Convergent network effects along the axis of gene expression during prostate cancer progression. Genome Biol (2020). Link.
Chauvistré, Heike 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.
Chen, Carol C L et al., Histone H3.3G34-Mutant Interneuron Progenitors Co-opt PDGFRA for Gliomagenesis. Cell (2020). Link.
Chen, Hengxing et al., PARK2 promotes mitochondrial pathway of apoptosis and antimicrotubule drugs chemosensitivity via degradation of phospho-BCL-2. Theranostics (2020). Link.
Chen, Jiaxin et al., LncSEA: a platform for long non-coding RNA related sets and enrichment analysis. Nucleic Acids Res (2020). Link.
Choi, Jang Hyun 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.
Choudhury, Abrar et al., Meningioma epigenetic grouping reveals biologic drivers and therapeutic vulnerabilities. medRxiv (2020). Link.
Czipa, Erik 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.
Devailly, Guillaume et al., Comprehensive analysis of epigenetic signatures of human transcrip-tion control †. bioRxiv (2020). Link.
Dorotea, Debra et al., Recent Insights Into SREBP as a Direct Mediator of Kidney Fibrosis via Lipid-Independent Pathways. Front Pharmacol (2020). Link.
Farahmand, Saman et al., ModEx: A text mining system for extracting mode of regulation of transcription factor-gene regulatory interaction. J Biomed Inform (2020). Link.
Feng, Chenchen et al., KnockTF: A comprehensive human gene expression profile database with knockdown/knockout of transcription factors. Nucleic Acids Res (2020). Link.
Fornes, Oriol et al., JASPAR 2020: Update of the open-Access database of transcription factor binding profiles. Nucleic Acids Res (2020). Link.
Gao, Lihua 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.
Gerisch, Birgit et al., HLH-30/TFEB Is a Master Regulator of Reproductive Quiescence. Dev Cell (2020). Link.
Grujic, Olivera et al., Identification and characterization of constrained non-exonic bases lacking predictive epigenomic and transcription factor binding annotations. Nat Commun (2020). Link.
Guan, Shuhong et al., TGF-β1 induces CREB1-mediated miR-1290 upregulation to antagonize lung fibrosis via Napsin A. Int J Mol Med (2020). Link.
Hayashi, Akimasa et al., A unifying paradigm for transcriptional heterogeneity and squamous features in pancreatic ductal adenocarcinoma. Nat Cancer (2020). Link.
Hayashi, Akimasa et al., Evolutionary Dynamics of Non-Coding Regions in Pancreatic Ductal Adenocarcinoma. bioRxiv (2020). Link.
Hirano, Kazumi et al., Indonesian ginger (Bangle) extract promotes neurogenesis of human neural stem cells through WNT pathway activation. Int J Mol Sci (2020). Link.
Horn, Moritz et al., Hexosamine Pathway Activation Improves Protein Homeostasis through the Integrated Stress Response. iScience (2020). Link.
Hsiao, Wen-Yu et al., The Lipid Handling Capacity of Subcutaneous Fat Is Programmed by mTORC2 during Development. Cell Rep (2020). Link.
Hänsel-Hertsch, Robert et al., Landscape of G-quadruplex DNA structural regions in breast cancer. Nat Genet (2020). Link.
Kaminuma, Eli et al., DDBJ data analysis challenge: A machine learning competition to predict arabidopsis chromatin feature annotations from DNA sequences. Genes Genet Syst (2020). Link.
Katahira, Jun et al., Human THO maintains the stability of repetitive DNA. Genes Cells (2020). Link.
Kikuyama, Takahiro 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.
Kim, Yu Jin 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.
Koga, Tomoaki et al., Expression of leukotriene B4 receptor 1 defines functionally distinct DCs that control allergic skin inflammation. Cell Mol Immunol (2020). Link.
Kohmoto, Tomohiro 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.
Kokaji, Toshiya et al., Transomics analysis reveals allosteric and gene regulation axes for altered hepatic glucose-responsive metabolism in obesity. Sci Signal (2020). Link.
Kolmykov, Semyon et al., GTRD: an integrated view of transcription regulation. Nucleic Acids Res (2020). Link.
Kremsky, Isaac 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.
Krześniak, Małgorzata 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.
Kubota, Naoto 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.
Kutscher, Lena et al., Functional loss of a non-canonical BCOR-PRC1.1 complex accelerates SHH-driven medulloblastoma formation. Genes Dev (2020). Link.
Kwiecien, Kamila 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.
Kwon, Andrew Tae-Jun et al., Efficient Development of Platform Cell Lines Using CRISPR-Cas9 and Transcriptomics Analysis. bioRxiv (2020). Link.
L, He et al., A Regulation Loop between YAP and NR4A1 Balances Cell Proliferation and Apoptosis. Cell Rep (2020). Link.
LM, Koch et al., Cytosolic pH regulates proliferation and tumour growth by promoting expression of cyclin D1. Nat Metab (2020). Link.
Larsen, Erik G. et al., TMEM184B controls pruriceptor specification and function. bioRxiv (2020). Link.
Lei, Xiao 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.
Leporcq, Clémentine et al., TFmotifView: a webserver for the visualization of transcription factor motifs in genomic regions. Nucleic Acids Res (2020). Link.
Li, Xin 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.
Li, Yanyu et al., TRlnc: a comprehensive database for human transcriptional regulatory information of lncRNAs. Brief Bioinform (2020). Link.
Li, Yi-Han 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.
Li, Zhiqing 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.
Lin, Quy Xiao Xuan et al., TFregulomeR reveals transcription factors' context-specific features and functions. Nucleic Acids Res (2020). Link.
Lorenzo, Jose Paulo et al., APOBEC2 binds Chromatin and Represses Transcription during Myoblast Differentiation. bioRxiv (2020). Link.
Lou, Shaoke et al., TopicNet: a framework for measuring transcriptional regulatory network change. Bioinformatics (2020). Link.
Lyu, Junfang et al., Synthetic lethality of RB1 and aurora A is driven by stathmin-mediated disruption of microtubule dynamics. Nat Commun (2020). Link.
Maharjan, Mukesh et al., Overlapping but Distinct Sequences Play Roles in the Insulator and Promoter Activities of the Drosophila BEAF-Dependent scs' Insulator. Genetics (2020). Link.
Mao, Ninghui et al., Oncogenic ERG represses PI3K signaling through downregulation of IRS2. Cancer Res (2020). Link.
McErlean, Peter et al., Profiling of H3K27Ac Reveals the Influence of Asthma on the Epigenome of the Airway Epithelium. Front Genet (2020). Link.
Meng, Yuhong et al., Transcriptomic landscape profiling of metformin-treated healthy mice: Implication for potential hypertension risk when prophylactically used. J Cell Mol Med (2020). Link.
Mercatelli, Daniele et al., Gene regulatory network inference resources: A practical overview. Biochim Biophys Acta Gene Regul Mech (2020). Link.
Merrett, James E 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.
Miyamoto, Yoichi et al., Genetic loss of importin α4 causes abnormal sperm morphology and impacts on male fertility in mouse. FASEB J (2020). Link.
Nam, A. Reum 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.
Namekawa, Takeshi 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.
Namekawa, Takeshi 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.
Ochiai, Kyoko et al., Chromatin Protein PC4 Orchestrates B Cell Differentiation by Collaborating with IKAROS and IRF4. Cell Rep (2020). Link.
Ochsner, Scott A et al., A transcriptional regulatory atlas of coronavirus infection of human cells. bioRxiv (2020). Link.
Ochsner, Scott A. et al., Consensus transcriptional regulatory networks of coronavirus-infected human cells. Sci Data (2020). Link.
Ohishi, Hiroaki et al., Characterization of genetic-origin-dependent monoallelic expression in mouse embryonic stem cells. Genes Cells (2020). Link.
Okada, Ryo et al., RNaseH2A Downregulation Drives Chromosomal DNA Fragmentation and Accumulation of RNA-DNA Hybrids in Senescent Cells. SSRN (2020). Link.
Okazaki, Yuri 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.
P, Sahlén et al., Chromatin interactions in differentiating keratinocytes reveal novel atopic dermatitis- and psoriasis-associated genes. J Allergy Clin Immunol (2020). Link.
Pecori, Federico et al., Mucin-type O-glycosylation controls pluripotency in mouse embryonic stem cells via Wnt receptor endocytosis. J Cell Sci (2020). Link.
Pradhananga, Sailendra et al., Promoter anchored interaction landscape of THP-1 macrophages captures early immune response processes. Cell Immunol (2020). Link.
Pratapa, Aditya et al., Benchmarking algorithms for gene regulatory network inference from single-cell transcriptomic data. Nat Methods (2020). Link.
Q, Pan et al., VARAdb: a comprehensive variation annotation database for human. Nucleic Acids Res (2020). Link.
Ray, John P et al., Prioritizing disease and trait causal variants at the TNFAIP3 locus using functional and genomic features. Nat Commun (2020). Link.
Rikitake, Marika 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.
Roels, Juliette et al., Aging of preleukemic thymocytes drives CpG island hypermethylation in T-cell acute lymphoblastic leukemia. Blood Cancer Discov (2020). Link.
Roels, Juliette et al., Distinct and temporary-restricted epigenetic mechanisms regulate human αβ and γδ T cell development. Nat Immunol (2020). Link.
Ronzio, Mirko 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.
SN, Reisinger et al., STAT3 in the dorsal raphe gates behavioural reactivity and regulates gene networks associated with psychopathology. Mol Psychiatry (2020). Link.
Sakuratani, Takuji et al., Downregulation of ARID1A in gastric cancer cells: a putative protective molecular mechanism against the Harakiri-mediated apoptosis pathway. Virchows Arch (2020). Link.
Sharipov, Ruslan N et al., Assessment of transcriptional importance of cell line-specific features based on GTRD and FANTOM5 data. PLoS One (2020). Link.
Shikov, Anton E et al., Phenome-wide functional dissection of pleiotropic effects highlights key molecular pathways for human complex traits. Sci Rep (2020). Link.
Sugasawa, Takehito 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.
Sukumaran, Abitha et al., Insight on Transcriptional Regulation of the Energy Sensing AMPK and Biosynthetic mTOR Pathway Genes. Front Cell Dev Biol (2020). Link.
Swoboda, Alexander et al., STAT3 promotes melanoma metastasis by CEBP-induced repression of the MITF pathway. Oncogene (2020). Link.
Tamura, Isao 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.
Tanaka, Hiroshi et al., The NSD2/WHSC1/MMSET methyltransferase prevents cellular senescence-associated epigenomic remodeling. Aging Cell (2020). Link.
Teschendorff, Andrew E et al., Improved detection of tumor suppressor events in single-cell RNA-Seq data. NPJ Genom Med (2020). Link.
Teschendorff, Andrew E. et al., EPISCORE: Cell type deconvolution of bulk tissue DNA methylomes from single-cell RNA-Seq data. Genome Biol (2020). Link.
Thonsri, Unchalee et al., High glucose-ROS conditions enhance the progression in cholangiocarcinoma via upregulation of MAN2A2 and CHD8. Cancer Sci (2020). Link.
Toro, Ayelén et al., Novel Interplay between p53 and HO-1 in Embryonic Stem Cells. Cells (2020). Link.
Totani, Haruhito et al., Autocrine HGF/c-Met signaling pathway confers aggressiveness in lymph node adult T-cell leukemia/lymphoma. Oncogene (2020). Link.
Ueda, Mahoko Takahashi et al., Comprehensive genomic analysis reveals dynamic evolution of endogenous retroviruses that code for retroviral-like protein domains. Mob DNA (2020). Link.
Wang, Allen 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.
Wang, Rong et al., Transient IGF-1R inhibition combined with osimertinib eradicates AXL-low expressing EGFR mutated lung cancer. Nat Commun (2020). Link.
Wu, Xue et al., Regulation of cellular sterol homeostasis by the oxygen responsive noncoding RNA lincNORS. Nat Commun (2020). Link.
X, Li et al., The role of MYB proto-oncogene like 2 in tamoxifen resistance in breast cancer. J Mol Histol (2020). Link.
Y, Li 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.
Y, Sera et al., UTX maintains functional integrity of murine hematopoietic system by globally regulating aging-associated genes. Blood (2020). Link.
Y, Yasukawa et al., SAA1 is upregulated in gastric cancer-associated fibroblasts possibly by its enhancer activation. Carcinogenesis (2020). Link.
Yumimoto, Kanae et al., Recent insight into the role of FBXW7 as a tumor suppressor. Semin Cancer Biol (2020). Link.
Zhao, Wei et al., Epigenetic Regulation of m6A Modifications in Human Cancer. Mol Ther Nucleic Acids (2020). Link.
Zhou, Stanley et al., Noncoding mutations target cis-regulatory elements of the FOXA1 plexus in prostate cancer. Nat Commun (2020). Link.
Zhou, Yao et al., epiCOLOC: Integrating Large-Scale and Context-Dependent Epigenomics Features for Comprehensive Colocalization Analysis. Front Genet (2020). Link.
Abugessaisa, Imad et al., refTSS: A Reference Data Set for Human and Mouse Transcription Start Sites. J Mol Biol (2019). Link.
Ahn, Hongryul et al., Propanet: Time-varying condition-specific transcriptional network construction by network propagation. Front Plant Sci (2019). Link.
Ando, Mizuo et al., Chromatin dysregulation and DNA methylation at transcription start sites associated with transcriptional repression in cancers. Nat Commun (2019). Link.
Aono, Shiori et al., β-catenin/TCF4 complex-mediated induction of the NRF3 (NFE2L3) gene in cancer cells. Int J Mol Sci (2019). Link.
Arata, Yoshiyuki et al., Defective induction of the proteasome associated with T-cell receptor signaling underlies T-cell senescence. Genes Cells (2019). Link.
Bakhmet, Evgeny I et al., hnRNP-K Targets Open Chromatin in Mouse Embryonic Stem Cells in Concert with Multiple Regulators. Stem Cells (2019). Link.
Banerjee, Sharmi et al., Identifying transcriptional regulatory modules among different chromatin states in mouse neural stem cells. Front Genet (2019). Link.
Bocci, Matteo et al., Activin receptor-like kinase 1 is associated with immune cell infiltration and regulates CLEC14A transcription in cancer. Angiogenesis (2019). Link.
Bravo González-Blas, Carmen et al., cisTopic: cis-regulatory topic modeling on single-cell ATAC-seq data. Nat Methods (2019). Link.
Chang, Hao Chun et al., Investigating the role of super-enhancer RNAs underlying embryonic stem cell differentiation. BMC Genomics (2019). Link.
Chereji, Răzvan V et al., Quantitative MNase-seq accurately maps nucleosome occupancy levels. Genome Biol (2019). Link.
Chow, Kwan T. et al., IRF5 regulates unique subset of genes in dendritic cells during West Nile virus infection. J Leukoc Biol (2019). Link.
Delicado, Diana 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.
Duforestel, Manon et al., Glyphosate primes mammary cells for tumorigenesis by reprogramming the epigenome in a TET3-dependent manner. Front Genet (2019). Link.
Farahmand, Saman et al., Causal Inference Engine: A platform for directional gene set enrichment analysis and inference of active transcriptional regulators. Nucleic Acids Res (2019). Link.
Ferris, Elliott et al., Parallel Accelerated Evolution in Distant Hibernators Reveals Candidate Cis Elements and Genetic Circuits Regulating Mammalian Obesity. Cell Rep (2019). Link.
Fleming, Aaron M. et al., Location dependence of the transcriptional response of a potential G-quadruplex in gene promoters under oxidative stress. Nucleic Acids Res (2019). Link.
Fontela, Miguel G et al., The conserved non-coding sequence 2 (CNS2) enhances CD69 transcription through cooperation between the transcription factors oct1 and RUNX1. Genes (2019). Link.
Horie, Kenta et al., Down-regulation of GATA1-dependent erythrocyte-related genes in the spleens of mice exposed to a space travel. Sci Rep (2019). Link.
Hotta, Masahiro 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.
Hurtz, Christian et al., Rationale for targeting BCL6 in MLL-rearranged acute lymphoblastic leukemia. Genes Dev (2019). Link.
Ishijima, Yasushi 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.
Kang, Hyeji et al., HSF1 regulates mevalonate and cholesterol biosynthesis pathways. Cancers (2019). Link.
Kehl, Tim et al., The role of TCF3 as potential master regulator in blastemal Wilms tumors. Int J Cancer (2019). Link.
Kikuchi, Masataka et al., Enhancer variants associated with Alzheimer's disease affect gene expression via chromatin looping. BMC Med Genomics (2019). Link.
Klein, Jason C et al., Functional testing of thousands of osteoarthritis-associated variants for regulatory activity. Nat Commun (2019). Link.
Kojima, Machiko et al., The histone methyltransferase WHSC1 is regulated by EZH2 and is important for ovarian clear cell carcinoma cell proliferation. BMC Cancer (2019). Link.
Kolmykov, Semyon K et al., Population size estimation for quality control of ChIP-Seq datasets. PLoS One (2019). Link.
Kondo, Takefumi et al., Two-step regulation of trachealess ensures tight coupling of cell fate with morphogenesis in the drosophila trachea. Elife (2019). Link.
Krug, Brian et al., Pervasive H3K27 Acetylation Leads to ERV Expression and a Therapeutic Vulnerability in H3K27M Gliomas. Cancer Cell (2019). Link.
Kulyté, Agné et al., MicroRNA-27a/b-3p and PPARG regulate SCAMP3 through a feed-forward loop during adipogenesis. Sci Rep (2019). Link.
Kunii, Yasuto 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.
Kuno, Akihiro et al., Conserved DNA-binding motif loci reflect functional transcription factor binding sites. Research Square (2019). Link.
Lin, Siyuan et al., Transcriptome and DNA methylome signatures associated with retinal Müller glia development, injury response, and aging. Invest Ophthalmol Vis Sci (2019). Link.
Lizio, Marina et al., Update of the FANTOM web resource: Expansion to provide additional transcriptome atlases. Nucleic Acids Res (2019). Link.
Maedera, Shotaro et al., GLUT6 is a lysosomal transporter that is regulated by inflammatory stimuli and modulates glycolysis in macrophages. FEBS Lett (2019). Link.
Matsuda, Taito et al., Pioneer Factor NeuroD1 Rearranges Transcriptional and Epigenetic Profiles to Execute Microglia-Neuron Conversion. Neuron (2019). Link.
Menzel, Michael et al., Enhort: A platform for deep analysis of genomic positions. PeerJ Comput Sci (2019). Link.
Murayama, Yuki et al., Glucocorticoid receptor suppresses gene expression of Rev-erbα (Nr1d1) through interaction with the CLOCK complex. FEBS Lett (2019). Link.
Neiman, Gabriel et al., Integrin alpha-5 subunit is critical for the early stages of human pluripotent stem cell cardiac differentiation. Sci Rep (2019). Link.
Ochsner, Scott A et al., The Signaling Pathways Project, an integrated ‘omics knowledgebase for mammalian cellular signaling pathways. Sci Data (2019). Link.
Oulès, Bénédicte et al., Mutant Lef1 controls Gata6 in sebaceous gland development and cancer. EMBO J (2019). Link.
Peggion, Caterina 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.
Qian, Feng Cui et al., SEanalysis: A web tool for super-enhancer associated regulatory analysis. Nucleic Acids Res (2019). Link.
Ranjit, Melissa et al., Aberrant Active cis-Regulatory Elements Associated with Downregulation of RET Finger Protein Overcome Chemoresistance in Glioblastoma. Cell Rep (2019). Link.
Rauschmeier, René et al., Bhlhe40 and Bhlhe41 transcription factors regulate alveolar macrophage self‐renewal and identity. EMBO J (2019). Link.
Robinson, Claire M et al., AHypoxia-inducible HIF1-GAL3ST1-sulfatide axis enhances ccRCC immune evasion via increased tumor cell-platelet binding. Mol Cancer Res (2019). Link.
Saito, Megumi et al., A Polymorphic Variant in p19Arf Confers Resistance to Chemically Induced Skin Tumors by Activating the p53 Pathway. J Invest Dermatol (2019). Link.
Salameti, Vasiliki et al., NOTCH1 signaling in oral squamous cell carcinoma via a TEL2/ SERPINE1 axis. Oncotarget (2019). Link.
Simak, Maria 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.
Singh, Rajbir et al., Enhancement of the gut barrier integrity by a microbial metabolite through the Nrf2 pathway. Nat Commun (2019). Link.
Solari, Claudia et al., The pluripotency transcription factor Nanog represses glutathione reductase gene expression in mouse embryonic stem cells. BMC Res Notes (2019). Link.
Studd, James B et al., Genetic predisposition to B-cell acute lymphoblastic leukemia at 14q11.2 is mediated by a CEBPE promoter polymorphism. Leukemia (2019). Link.
Suda, Kojiro 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.
Tano, Ayami et al., The juvenility-associated long noncoding RNA Gm14230 maintains cellular juvenescence. J Cell Sci (2019). Link.
Tong, Zhan et al., TransmiR v2.0: An updated transcription factor-microRNA regulation database. Nucleic Acids Res (2019). Link.
Ulirsch, Jacob C et al., Interrogation of human hematopoiesis at single-cell and single-variant resolution. Nat Genet (2019). Link.
Velychko, Sergiy et al., Excluding Oct4 from Yamanaka Cocktail Unleashes the Developmental Potential of iPSCs. Cell Stem Cell (2019). Link.
Vijayakrishnan, Jayaram et al., Identification of four novel associations for B-cell acute lymphoblastic leukaemia risk. Nat Commun (2019). Link.
Vogel, Felix C E et al., Targeting the H3K4 Demethylase KDM5B Reprograms the Metabolome and Phenotype of Melanoma Cells. J Invest Dermatol (2019). Link.
Wu, Cheng Jang 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.
Wu, Zhaoming et al., Cis-control of Six1 expression in neural crest cells during craniofacial development. Dev Dyn (2019). Link.
Yamada, Toshimichi et al., Contributions of regulated transcription and mRNA decay to the dynamics of gene expression. WIREs RNA (2019). Link.
Yashiro, Takuya 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.
Yevshin, Ivan et al., GTRD: A database on gene transcription regulation - 2019 update. Nucleic Acids Res (2019). Link.
Yoshizaki, Kaichi et al., Paternal Age Affects Offspring'S Behavior Possibly Via Epigenetic Mechanism Recruiting a Transcriptional Repressor Rest. Eur Neuropsychopharmacol (2019). Link.
Zhang, Lei et al., DeepHINT: Understanding HIV-1 integration via deep learning with attention. Bioinformatics (2019). Link.
Zheng, Rongbin et al., Cistrome Data Browser: Expanded datasets and new tools for gene regulatory analysis. Nucleic Acids Res (2019). Link.
Åkerborg, Örjan et al., High-Resolution Regulatory Maps Connect Vascular Risk Variants to Disease-Related Pathways. Circulation (2019). Link.
Anan, Kotaro et al., LSD1 mediates metabolic reprogramming by glucocorticoids during myogenic differentiation. Nucleic Acids Res (2018). Link.
Baldi, Sandro et al., Genome-wide Rules of Nucleosome Phasing in Drosophila. Mol Cell (2018). Link.
Chatterjee, Shatakshee et al., Pre-operative progesterone benefits operable breast cancer patients by modulating surgical stress. Breast Cancer Res Treat (2018). Link.
Chen, Yu et al., PHLDA1, another PHLDA family protein that inhibits Akt. Cancer Sci (2018). Link.
Chishima, Takafumi et al., Identification of transposable elements contributing to tissue-specific expression of long non-coding RNAs. Genes (2018). Link.
Chèneby, Jeanne 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.
Cui, Chunmei et al., Identification and Analysis of Human Sex-biased MicroRNAs. Genomics Proteomics Bioinformatics (2018). Link.
Dréos, René et al., MGA repository: A curated data resource for ChIP-seq and other genome annotated data. Nucleic Acids Res (2018). Link.
Egashira, Yoshihiro et al., Development of lentiviral vectors for efficient glutamatergic-selective gene expression in cultured hippocampal neurons. Sci Rep (2018). Link.
Ferris, Elliott et al., Accelerated Evolution in Distinctive Species Reveals Candidate Elements for Clinically Relevant Traits, Including Mutation and Cancer Resistance. Cell Rep (2018). Link.
Fiziev, Petko et al., ChromTime: Modeling spatio-temporal dynamics of chromatin marks. Genome Biol (2018). Link.
Groff, Abigail F. et al., Enhancers in the Peril lincRNA locus regulate distant but not local genes. Genome Biol (2018). Link.
Imrichova, Hana et al., ChIP-seq meta-analysis yields high quality training sets for enhancer classification. bioRxiv (2018). Link.
Kawaji, Hideya, dirHub: a trackHub configurator with directory structure projection. bioRxiv (2018). Link.
Kawata, Kentaro et al., Trans-omic Analysis Reveals Selective Responses to Induced and Basal Insulin across Signaling, Transcriptional, and Metabolic Networks. iScience (2018). Link.
Kehl, Tim et al., REGGAE: A novel approach for the identification of key transcriptional regulators. Bioinformatics (2018). Link.
Lasar, David et al., Peroxisome Proliferator Activated Receptor Gamma Controls Mature Brown Adipocyte Inducibility through Glycerol Kinase. Cell Rep (2018). Link.
Mao, Fengbiao et al., EpiDenovo: A platform for linking regulatory de novo mutations to developmental epigenetics and diseases. Nucleic Acids Res (2018). Link.
Misawa, Aya et al., lncRNA HOTAIR Inhibits Mineralization in Osteoblastic Osteosarcoma Cells by Epigenetically Repressing ALPL. Calcif Tissue Int (2018). Link.
Miura, Itaru et al., DNA methylation of ANKK1 and response to aripiprazole in patients with acute schizophrenia: A preliminary study. J Psychiatr Res (2018). Link.
Mochizuki, Kentaro et al., SETDB1 is essential for mouse primordial germ cell fate determination by ensuring bmp signaling. Development (2018). Link.
Mourad, Raphaël et al., Predicting double-strand DNA breaks using epigenome marks or DNA at kilobase resolution. Genome Biol (2018). Link.
Nishizawa, Yujiro et al., Oncogene c-Myc promotes epitranscriptome m6A reader YTHDF1 expression in colorectal cancer. Oncotarget (2018). Link.
Onodera, Yuta et al., Inflammation-associated MIR-155 activates differentiation of muscular satellite cells. PLoS One (2018). Link.
Polouliakh, Natalia et al., Sequence homology in eukaryotes (SHOE): Interactive visual tool for promoter analysis 06 Biological Sciences 0604 Genetics. BMC Genomics (2018). Link.
Raffield, Laura M et al., Common α-globin variants modify hematologic and other clinical phenotypes in sickle cell trait and disease. PLoS Genet (2018). Link.
Romero-Cordoba, Sandra L 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.
Wang, Huabo et al., Myc and ChREBP transcription factors cooperatively regulate normal and neoplastic hepatocyte proliferation in mice. J Biol Chem (2018). Link.
Chen, Yuting 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.
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.
Guoa, Michael H et al., Comprehensive population-based genome sequencing provides insight into hematopoietic regulatory mechanisms. Proc Natl Acad Sci U S A (2017). Link.
Ishigaki, Kazuyoshi et al., Polygenic burdens on cell-specific pathways underlie the risk of rheumatoid arthritis. Nat Genet (2017). Link.
Kalender Atak, Zeynep et al., Identification of cis-regulatory mutations generating de novo edges in personalized cancer gene regulatory networks. Genome Med (2017). Link.
Kehl, Tim et al., RegulatorTrail: A web service for the identification of key transcriptional regulators. Nucleic Acids Res (2017). Link.
Matsuda, Kazunari 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.
Naderi, Ali, C1orf64 is a novel androgen receptor target gene and coregulator that interacts with 14-3-3 protein in breast cancer. Oncotarget (2017). Link.
Onodera, Yuta et al., miR-155 induces ROS generation through downregulation of antioxidation-related genes in mesenchymal stem cells. Aging Cell (2017). Link.
Sanosaka, Tsukasa et al., DNA Methylome Analysis Identifies Transcription Factor-Based Epigenomic Signatures of Multilineage Competence in Neural Stem/Progenitor Cells. Cell Rep (2017). Link.
Tanegashima, Kosuke 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.
Turrell, Frances K et al., Lung tumors with distinct p53 mutations respond similarly to p53 targeted therapy but exhibit genotype-specific statin sensitivity. Genes Dev (2017). Link.
Umeyama, Taichi et al., DMS-Seq for In Vivo Genome-wide Mapping of Protein-DNA Interactions and Nucleosome Centers. Cell Rep (2017). Link.
Yevshin, Ivan et al., GTRD: A database of transcription factor binding sites identified by ChIP-seq experiments. Nucleic Acids Res (2017). Link.
Yoshihara, Masahito et al., Hotspots of De Novo Point Mutations in Induced Pluripotent Stem Cells. Cell Rep (2017). Link.
Sugeno, Naoto et al., α-Synuclein enhances histone H3 lysine-9 dimethylation and H3K9me2-dependent transcriptional responses. Sci Rep (2016). Link.