Discovery of cell-type specific DNA motif grammar in cis-regulatory elements using random Forest

Role of estrogen receptor in breast cancer cell gene expression

(2016) YABING ZHENG et al.   Molecular Medicine Reports

DNA context represents transcription regulation of the gene in mouse embryonic stem cells

(2016) Misook Ha et al.   Scientific Reports

Regulation and function of the NFE2 transcription factor in hematopoietic and non-hematopoietic cells

(2015) Jadwiga J. Gasiorek et al.   CELLULAR AND MOLECULAR LIFE SCIENCES

Transcription factor binding dynamics during human ES cell differentiation

(2015) Alexander M. Tsankov et al.   NATURE

Predicting the sequence specificities of DNA- and RNA-binding proteins by deep learning

(2015) Babak Alipanahi et al.   NATURE BIOTECHNOLOGY

Alternative human liver transcripts of TCF7L2 bind to the gluconeogenesis regulator HNF4α at the protein level

(2014) Bernadette Neve et al.   DIABETOLOGIA

A Single Amino Acid in EBNA-2 Determines Superior B Lymphoblastoid Cell Line Growth Maintenance by Epstein-Barr Virus Type 1 EBNA-2

(2014) S. Tzellos et al.   JOURNAL OF VIROLOGY

Hepatocyte nuclear factor 4-alpha involvement in liver and intestinal inflammatory networks

(2014) Jean-Philippe Babeu   WORLD JOURNAL OF GASTROENTEROLOGY

MYC, MAX, and Small Cell Lung Cancer

(2014) C. M. Rudin et al.   Cancer Discovery

Control of cell cycle transcription during G1 and S phases

(2013) Cosetta Bertoli et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Systematic discovery and characterization of regulatory motifs in ENCODE TF binding experiments

(2013) P. Kheradpour et al.   NUCLEIC ACIDS RESEARCH

Jun dimerization protein 2 is a critical component of the Nrf2/MafK complex regulating the response to ROS homeostasis

(2013) S Tanigawa et al.   Cell Death & Disease

Probing transcription factor diffusion dynamics in the living mammalian embryo with photoactivatable fluorescence correlation spectroscopy

(2013) Gurpreet Kaur et al.   Nature Communications

MAX Inactivation in Small Cell Lung Cancer Disrupts MYC-SWI/SNF Programs and Is Synthetic Lethal with BRG1

(2013) O. A. Romero et al.   Cancer Discovery

Rule-Based Design of Synthetic Transcription Factors in Eukaryotes

(2013) Oliver Purcell et al.   ACS Synthetic Biology

Expression features of SOX9 associate with tumor progression and poor prognosis of hepatocellular carcinoma

(2012) Xiaodong Guo et al.   Diagnostic Pathology

Sequence and chromatin determinants of cell-type-specific transcription factor binding

(2012) A. Arvey et al.   GENOME RESEARCH

Sequence features and chromatin structure around the genomic regions bound by 119 human transcription factors

(2012) J. Wang et al.   GENOME RESEARCH

An integrated encyclopedia of DNA elements in the human genome

(2012)   NATURE

Transcription factors: from enhancer binding to developmental control

(2012) François Spitz et al.   NATURE REVIEWS GENETICS

Deciphering the transcriptional cis-regulatory code

(2012) J. Omar Yáñez-Cuna et al.   TRENDS IN GENETICS

High Resolution Genome Wide Binding Event Finding and Motif Discovery Reveals Transcription Factor Spatial Binding Constraints

(2012) Yuchun Guo et al.   PLoS Computational Biology

Cell type-specific binding patterns reveal that TCF7L2 can be tethered to the genome by association with GATA3

(2012) Seth Frietze et al.   GENOME BIOLOGY

Letter to the Editor: On the stability and ranking of predictors from random forest variable importance measures

(2011) K. K. Nicodemus   BRIEFINGS IN BIOINFORMATICS

Master Transcription Factors Determine Cell-Type-Specific Responses to TGF-β Signaling

(2011) Alan C. Mullen et al.   CELL

Lineage Regulators Direct BMP and Wnt Pathways to Cell-Specific Programs during Differentiation and Regeneration

(2011) Eirini Trompouki et al.   CELL

Chromatin occupancy of transcription factor 7-like 2 (TCF7L2) and its role in hepatic glucose metabolism

(2011) L. Norton et al.   DIABETOLOGIA

Wnt signaling meets internal dissent

(2011) E. A. Grove   GENES & DEVELOPMENT

Nuclear Factor Erythroid-derived 2 (Nfe2) Regulates JunD DNA-binding Activity via Acetylation

(2011) Muhammed Kashif et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Berberine modulates AP-1 activity to suppress HPV transcription and downstream signaling to induce growth arrest and apoptosis in cervical cancer cells

(2011) Sutapa Mahata et al.   Molecular Cancer

Moving pictures of the human microbiome

(2011) J Gregory Caporaso et al.   GENOME BIOLOGY

Pluripotency and Cellular Reprogramming: Facts, Hypotheses, Unresolved Issues

(2010) Jacob H. Hanna et al.   CELL

Disease-associated loci are significantly over-represented among genes bound by transcription factor 7-like 2 (TCF7L2) in vivo

(2010) J. Zhao et al.   DIABETOLOGIA

A screening methodology based on Random Forests to improve the detection of gene–gene interactions

(2010) Lizzy De Lobel et al.   EUROPEAN JOURNAL OF HUMAN GENETICS

Simple Combinations of Lineage-Determining Transcription Factors Prime cis-Regulatory Elements Required for Macrophage and B Cell Identities

(2010) Sven Heinz et al.   MOLECULAR CELL

Integrative analysis of genomic, functional and protein interaction data predicts long-range enhancer-target gene interactions

(2010) Christian Rödelsperger et al.   NUCLEIC ACIDS RESEARCH

The Lmo2 Oncogene Initiates Leukemia in Mice by Inducing Thymocyte Self-Renewal

(2010) M. P. McCormack et al.   SCIENCE

Developmental roles of 21 Drosophila transcription factors are determined by quantitative differences in binding to an overlapping set of thousands of genomic regions

(2009) Stewart MacArthur et al.   GENOME BIOLOGY

Clinical significance of Gata-1, Gata-2, EKLF, and c-MPL expression in acute myeloid leukemia

(2008) Rosa M. Ayala et al.   AMERICAN JOURNAL OF HEMATOLOGY

Epigenetic Profiles Distinguish Pleural Mesothelioma from Normal Pleura and Predict Lung Asbestos Burden and Clinical Outcome

(2008) B. C. Christensen et al.   CANCER RESEARCH

Integration of External Signaling Pathways with the Core Transcriptional Network in Embryonic Stem Cells

(2008) Xi Chen et al.   CELL

The Role of LEF/TCF Factors in Neoplastic Transformation

(2008) Mohamed El-Tanani et al.   CURRENT MOLECULAR MEDICINE

Synergistic Function of E2F7 and E2F8 Is Essential for Cell Survival and Embryonic Development

(2008) Jing Li et al.   DEVELOPMENTAL CELL

Interferon Regulatory Factor 4 Is Involved in Epstein-Barr Virus-Mediated Transformation of Human B Lymphocytes

(2008) D. Xu et al.   JOURNAL OF VIROLOGY

Minireview: The Wnt Signaling Pathway Effector TCF7L2 and Type 2 Diabetes Mellitus

(2008) Tianru Jin et al.   MOLECULAR ENDOCRINOLOGY