Complex impact of DNA methylation on transcriptional dysregulation across 22 human cancer types

Dependency of the Cancer-Specific Transcriptional Regulation Circuitry on the Promoter DNA Methylome

(2019) Yu Liu et al.   Cell Reports

Gain-of-Function Mutations: An Emerging Advantage for Cancer Biology

(2019) Yongsheng Li et al.   TRENDS IN BIOCHEMICAL SCIENCES

Unique DNA Methylation Profiles Are Associated with cis-Variation in Honey Bees

(2019) Boris Yagound et al.   Genome Biology and Evolution

The Human Transcription Factors

(2018) Samuel A. Lambert et al.   CELL

Robust prediction of gene regulation in colorectal cancer tissues from DNA methylation profiles

(2018) Hagen Klett et al.   Epigenetics

LncMAP: Pan-cancer atlas of long noncoding RNA-mediated transcriptional network perturbations

(2018) Yongsheng Li et al.   NUCLEIC ACIDS RESEARCH

Gene Regulatory Network Perturbation by Genetic and Epigenetic Variation

(2018) Yongsheng Li et al.   TRENDS IN BIOCHEMICAL SCIENCES

MERIT: Systematic analysis and characterization of Mutational Effect on RNA Interactome Topology

(2018) Yongsheng Li et al.   HEPATOLOGY

FACER: comprehensive molecular and functional characterization of epigenetic chromatin regulators

(2018) Jianping Lu et al.   NUCLEIC ACIDS RESEARCH

MethMotif: an integrative cell specific database of transcription factor binding motifs coupled with DNA methylation profiles

(2018) Quy Xiao Xuan Lin et al.   NUCLEIC ACIDS RESEARCH

Lnc2Cancer v2.0: updated database of experimentally supported long non-coding RNAs in human cancers

(2018) Yue Gao et al.   NUCLEIC ACIDS RESEARCH

MeDReaders: a database for transcription factors that bind to methylated DNA

(2017) Guohua Wang et al.   NUCLEIC ACIDS RESEARCH

Impact of cytosine methylation on DNA binding specificities of human transcription factors

(2017) Yimeng Yin et al.   SCIENCE

A pathology atlas of the human cancer transcriptome

(2017) Mathias Uhlen et al.   SCIENCE

A screening system to identify transcription factors that induce binding site-directed DNA demethylation

(2017) Takahiro Suzuki et al.   Epigenetics & Chromatin

Revealing the Determinants of Widespread Alternative Splicing Perturbation in Cancer

(2017) Yongsheng Li et al.   Cell Reports

THAP1: Role in Mouse Embryonic Stem Cell Survival and Differentiation

(2017) Francesca Aguilo et al.   Stem Cell Reports

Measuring quantitative effects of methylation on transcription factor–DNA binding affinity

(2017) Zheng Zuo et al.   Science Advances

Diversity of human and mouse homeobox gene expression in development and adult tissues

(2016) Thomas L. Dunwell et al.   BMC DEVELOPMENTAL BIOLOGY

ChIPBase v2.0: decoding transcriptional regulatory networks of non-coding RNAs and protein-coding genes from ChIP-seq data

(2016) Ke-Ren Zhou et al.   NUCLEIC ACIDS RESEARCH

Systematic dissection of dysregulated transcription factor–miRNA feed-forward loops across tumor types

(2015) Wei Jiang et al.   BRIEFINGS IN BIOINFORMATICS

Competition between DNA methylation and transcription factors determines binding of NRF1

(2015) Silvia Domcke et al.   NATURE

Tissue-based map of the human proteome

(2015) M. Uhlen et al.   SCIENCE

Differential regulation of MMPs by E2F1, Sp1 and NF-kappa B controls the small cell lung cancer invasive phenotype

(2014) Zunling Li et al.   BMC CANCER

Comparative epigenetic analyses reveal distinct patterns of oncogenic pathways activation in breast cancer subtypes

(2014) Yongsheng Li et al.   HUMAN MOLECULAR GENETICS

ImmPort: disseminating data to the public for the future of immunology

(2014) Sanchita Bhattacharya et al.   IMMUNOLOGIC RESEARCH

Gene regulatory networks in the immune system

(2014) Harinder Singh et al.   TRENDS IN IMMUNOLOGY

Transcriptional Regulation and Its Misregulation in Disease

(2013) Tong Ihn Lee et al.   CELL

Comprehensive analysis of the functional microRNA–mRNA regulatory network identifies miRNA signatures associated with glioma malignant progression

(2013) Yongsheng Li et al.   NUCLEIC ACIDS RESEARCH

Understanding Variation in Transcription Factor Binding by Modeling Transcription Factor Genome-Epigenome Interactions

(2013) Chieh-Chun Chen et al.   PLoS Computational Biology

DNA methylation presents distinct binding sites for human transcription factors

(2013) Shaohui Hu et al.   eLife

PU.1 target genes undergo Tet2-coupled demethylation and DNMT3b-mediated methylation in monocyte-to-osteoclast differentiation

(2013) Lorenzo de la Rica et al.   GENOME BIOLOGY

A miRNA-regulatory network explains how dysregulated miRNAs perturb oncogenic processes across diverse cancers

(2012) C. L. Plaisier et al.   GENOME RESEARCH

Architecture of the human regulatory network derived from ENCODE data

(2012) Mark B. Gerstein et al.   NATURE

Functional analysis of transcription factor binding sites in human promoters

(2012) Troy W Whitfield et al.   GENOME BIOLOGY

The Cyc8-Tup1 complex inhibits transcription primarily by masking the activation domain of the recruiting protein

(2011) K. H. Wong et al.   GENES & DEVELOPMENT

Integrative annotation of human large intergenic noncoding RNAs reveals global properties and specific subclasses

(2011) M. N. Cabili et al.   GENES & DEVELOPMENT

Regulation of Vascular Endothelial Growth Factor Receptors by Rb and E2F1: Role of Acetylation

(2010) Smitha Pillai et al.   CANCER RESEARCH

Accurate inference of transcription factor binding from DNA sequence and chromatin accessibility data

(2010) R. Pique-Regi et al.   GENOME RESEARCH

Genome-wide prediction of transcription factor binding sites using an integrated model

(2010) Kyoung-Jae Won et al.   GENOME BIOLOGY

DNA methylation of cancer genome

(2009) Hoi-Hung Cheung et al.   BIRTH DEFECTS RESEARCH PART C-EMBRYO TODAY-REVIEWS

Putative Tumor-Suppressive Function of Kruppel-Like Factor 4 in Primary Lung Carcinoma

(2009) W. Hu et al.   CLINICAL CANCER RESEARCH

ChIP-seq accurately predicts tissue-specific activity of enhancers

(2009) Axel Visel et al.   NATURE

Sensitive digital quantification of DNA methylation in clinical samples

(2009) Meng Li et al.   NATURE BIOTECHNOLOGY

Insights from genomic profiling of transcription factors

(2009) Peggy J. Farnham   NATURE REVIEWS GENETICS

ChIP–seq: advantages and challenges of a maturing technology

(2009) Peter J. Park   NATURE REVIEWS GENETICS

DNA Binding Site Sequence Directs Glucocorticoid Receptor Structure and Activity

(2009) S. H. Meijsing et al.   SCIENCE