Base-resolution models of transcription-factor binding reveal soft motif syntax

Synthetic and genomic regulatory elements reveal aspects of cis-regulatory grammar in Mouse Embryonic Stem Cells

(2020) Dana M King et al.   eLife

Predicting Splicing from Primary Sequence with Deep Learning

(2019) Kishore Jaganathan et al.   CELL

FactorNet: a deep learning framework for predicting cell type specific transcription factor binding from nucleotide-resolution sequential data

(2019) Daniel Quang et al.   METHODS

The Kipoi repository accelerates community exchange and reuse of predictive models for genomics

(2019) Žiga Avsec et al.   NATURE BIOTECHNOLOGY

Functional evaluation of transposable elements as enhancers in mouse embryonic and trophoblast stem cells

(2019) Christopher D Todd et al.   eLife

A Deep Neural Network for Predicting and Engineering Alternative Polyadenylation

(2019) Nicholas Bogard et al.   CELL

Dynamic regulation of chromatin accessibility by pluripotency transcription factors across the cell cycle

(2019) Elias T Friman et al.   eLife

Dynamic changes in Sox2 spatio-temporal expression promote the second cell fate decision through Fgf4 / Fgfr2 signaling in preimplantation mouse embryos

(2018) Tapan Kumar Mistri et al.   BIOCHEMICAL JOURNAL

OUP accepted manuscript

(2018)   BIOINFORMATICS

Sequential regulatory activity prediction across chromosomes with convolutional neural networks

(2018) David R. Kelley et al.   GENOME RESEARCH

Capicua controls Toll/IL-1 signaling targets independently of RTK regulation

(2018) Aikaterini Papagianni et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Long-Range Enhancer Interactions Are Prevalent in Mouse Embryonic Stem Cells and Are Reorganized upon Pluripotent State Transition

(2018) Clara Lopes Novo et al.   Cell Reports

Characterizing protein–DNA binding event subtypes in ChIP-exo data

(2018) Naomi Yamada et al.   BIOINFORMATICS

The interaction landscape between transcription factors and the nucleosome

(2018) Fangjie Zhu et al.   NATURE

Esrrb extinction triggers dismantling of naïve pluripotency and marks commitment to differentiation

(2018) Nicola Festuccia et al.   EMBO JOURNAL

A dynamic interplay of enhancer elements regulates Klf4 expression in naïve pluripotency

(2017) Liangqi Xie et al.   GENES & DEVELOPMENT

Distinct Contributions of Tryptophan Residues within the Dimerization Domain to Nanog Function

(2017) Nicholas P. Mullin et al.   JOURNAL OF MOLECULAR BIOLOGY

Refined sgRNA efficacy prediction improves large- and small-scale CRISPR–Cas9 applications

(2017) Maurice Labuhn et al.   NUCLEIC ACIDS RESEARCH

Functional cis-regulatory modules encoded by mouse-specific endogenous retrovirus

(2017) Vasavi Sundaram et al.   Nature Communications

Identification of Human Lineage-Specific Transcriptional Coregulators Enabled by a Glossary of Binding Modules and Tunable Genomic Backgrounds

(2017) Luca Mariani et al.   Cell Systems

PeakXus: comprehensive transcription factor binding site discovery from ChIP-Nexus and ChIP-Exo experiments

(2016) Tuomo Hartonen et al.   BIOINFORMATICS

Interactions between pluripotency factors specifycis-regulation in embryonic stem cells

(2016) Chris Fiore et al.   GENOME RESEARCH

Drosophilapoised enhancers are generated during tissue patterning with the help of repression

(2016) Nina Koenecke et al.   GENOME RESEARCH

Basset: learning the regulatory code of the accessible genome with deep convolutional neural networks

(2016) David R. Kelley et al.   GENOME RESEARCH

Enhancers and super-enhancers have an equivalent regulatory role in embryonic stem cells through regulation of single or multiple genes

(2016) Sakthi D. Moorthy et al.   GENOME RESEARCH

Mapping nucleosome positions using DNase-seq

(2016) Jianling Zhong et al.   GENOME RESEARCH

Categorical spectral analysis of periodicity in nucleosomal DNA

(2016) Hu Jin et al.   NUCLEIC ACIDS RESEARCH

Quantitative perturbation-based analysis of gene expression predicts enhancer activity in early Drosophila embryo

(2016) Rupinder Sayal et al.   eLife

Pioneer Transcription Factors Target Partial DNA Motifs on Nucleosomes to Initiate Reprogramming

(2015) Abdenour Soufi et al.   CELL

Selective influence of Sox2 on POU transcription factor binding in embryonic and neural stem cells

(2015) T. K. Mistri et al.   EMBO REPORTS

Zelda overcomes the high intrinsic nucleosome barrier at enhancers duringDrosophilazygotic genome activation

(2015) Yujia Sun et al.   GENOME RESEARCH

ChIP-exo signal associated with DNA-binding motifs provides insight into the genomic binding of the glucocorticoid receptor and cooperating transcription factors

(2015) Stephan R. Starick et al.   GENOME RESEARCH

Integrative analysis of 111 reference human epigenomes

(2015) Anshul Kundaje et al.   NATURE

DNA-dependent formation of transcription factor pairs alters their binding specificity

(2015) Arttu Jolma et al.   NATURE

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

(2015) Babak Alipanahi et al.   NATURE BIOTECHNOLOGY

ChIP-nexus enables improved detection of in vivo transcription factor binding footprints

(2015) Qiye He et al.   NATURE BIOTECHNOLOGY

Predicting effects of noncoding variants with deep learning–based sequence model

(2015) Jian Zhou et al.   NATURE METHODS

Structure-based discovery of NANOG variant with enhanced properties to promote self-renewal and reprogramming of pluripotent stem cells

(2015) Yohei Hayashi et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Suboptimization of developmental enhancers

(2015) E. K. Farley et al.   SCIENCE

Cooperative DNA Recognition Modulated by an Interplay between Protein-Protein Interactions and DNA-Mediated Allostery

(2015) Felipe Merino et al.   PLoS Computational Biology

CCTop: An Intuitive, Flexible and Reliable CRISPR/Cas9 Target Prediction Tool

(2015) Manuel Stemmer et al.   PLoS One

Explicit DNase sequence bias modeling enables high-resolution transcription factor footprint detection

(2014) Galip Gürkan Yardımcı et al.   NUCLEIC ACIDS RESEARCH

Constrained transcription factor spacing is prevalent and important for transcriptional control of mouse blood cells

(2014) Felicia SL Ng et al.   NUCLEIC ACIDS RESEARCH

Absence of a simple code: how transcription factors read the genome

(2014) Matthew Slattery et al.   TRENDS IN BIOCHEMICAL SCIENCES

Subtle Changes in Motif Positioning Cause Tissue-Specific Effects on Robustness of an Enhancer's Activity

(2014) Jelena Erceg et al.   PLoS Genetics

Identifying transcriptional cis -regulatory modules in animal genomes

(2014) Kushal Suryamohan et al.   Wiley Interdisciplinary Reviews-Developmental Biology

DNA-Binding Specificities of Human Transcription Factors

(2013) Arttu Jolma et al.   CELL

A direct physical interaction between Nanog and Sox2 regulates embryonic stem cell self-renewal

(2013) Alessia Gagliardi et al.   EMBO JOURNAL

DNase-seq predicts regions of rotational nucleosome stability across diverse human cell types

(2013) D. R. Winter et al.   GENOME RESEARCH

Comprehensive prediction in 78 human cell lines reveals rigidity and compactness of transcription factor dimers

(2013) A. Jankowski et al.   GENOME RESEARCH

Rotational positioning of nucleosomes facilitates selective binding of p53 to response elements associated with cell cycle arrest

(2013) F. Cui et al.   NUCLEIC ACIDS RESEARCH

Probing Allostery Through DNA

(2013) S. Kim et al.   SCIENCE

Computational Identification of Diverse Mechanisms Underlying Transcription Factor-DNA Occupancy

(2013) Qiong Cheng et al.   PLoS Genetics

A Transcription Factor Collective Defines Cardiac Cell Fate and Reflects Lineage History

(2012) Guillaume Junion et al.   CELL

Facilitators and Impediments of the Pluripotency Reprogramming Factors' Initial Engagement with the Genome

(2012) Abdenour Soufi et al.   CELL

ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia

(2012) S. G. Landt 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

Enhancer decommissioning by LSD1 during embryonic stem cell differentiation

(2012) Warren A. Whyte et al.   NATURE

An integrated encyclopedia of DNA elements in the human genome

(2012)   NATURE

Architecture of the human regulatory network derived from ENCODE data

(2012) Mark B. Gerstein et al.   NATURE

Inferring gene regulatory logic from high-throughput measurements of thousands of systematically designed promoters

(2012) Eilon Sharon et al.   NATURE BIOTECHNOLOGY

Transcription factors: from enhancer binding to developmental control

(2012) François Spitz et al.   NATURE REVIEWS GENETICS

Inferring direct DNA binding from ChIP-seq

(2012) Timothy L. Bailey et al.   NUCLEIC ACIDS RESEARCH

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

(2012) Yuchun Guo et al.   PLoS Computational Biology

Role of Architecture in the Function and Specificity of Two Notch-Regulated Transcriptional Enhancer Modules

(2012) Feng Liu et al.   PLoS Genetics

Measuring reproducibility of high-throughput experiments

(2011) Qunhua Li et al.   Annals of Applied Statistics

Comprehensive Genome-wide Protein-DNA Interactions Detected at Single-Nucleotide Resolution

(2011) Ho Sung Rhee et al.   CELL

Discriminative prediction of mammalian enhancers from DNA sequence

(2011) D. Lee et al.   GENOME RESEARCH

A Statistical Framework for the Analysis of ChIP-Seq Data

(2011) Pei Fen Kuan et al.   JOURNAL OF THE AMERICAN STATISTICAL ASSOCIATION

Discovering homotypic binding events at high spatial resolution

(2010) Yuchun Guo et al.   BIOINFORMATICS

BigWig and BigBed: enabling browsing of large distributed datasets

(2010) W. J. Kent et al.   BIOINFORMATICS

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

PeakAnalyzer: Genome-wide annotation of chromatin binding and modification loci

(2010) Mali Salmon-Divon et al.   BMC BIOINFORMATICS

Structural Rules and Complex Regulatory Circuitry Constrain Expression of a Notch- and EGFR-Regulated Eye Enhancer

(2010) Christina I. Swanson et al.   DEVELOPMENTAL CELL

Rewirable gene regulatory networks in the preimplantation embryonic development of three mammalian species

(2010) D. Xie et al.   GENOME RESEARCH

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

Transposable elements have rewired the core regulatory network of human embryonic stem cells

(2010) Galih Kunarso et al.   NATURE GENETICS

Human RNA polymerase III transcriptomes and relationships to Pol II promoter chromatin and enhancer-binding factors

(2010) Andrew J Oler et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Evolutionary Mirages: Selection on Binding Site Composition Creates the Illusion of Conserved Grammars in Drosophila Enhancers

(2010) Richard W. Lusk et al.   PLoS Genetics

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

Distinguishing direct versus indirect transcription factor-DNA interactions

(2009) R. Gordan et al.   GENOME RESEARCH

PeakSeq enables systematic scoring of ChIP-seq experiments relative to controls

(2009) Joel Rozowsky et al.   NATURE BIOTECHNOLOGY

Organization of developmental enhancers in the Drosophila embryo

(2009) Dmitri Papatsenko et al.   NUCLEIC ACIDS RESEARCH

MEME SUITE: tools for motif discovery and searching

(2009) T. L. Bailey et al.   NUCLEIC ACIDS RESEARCH

A Biophysical Model for Analysis of Transcription Factor Interaction and Binding Site Arrangement from Genome-Wide Binding Data

(2009) Xin He et al.   PLoS One

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

(2008) Xi Chen et al.   CELL

Design flexibility in cis-regulatory control of gene expression: Synthetic and comparative evidence

(2008) Louisa M. Liberman et al.   DEVELOPMENTAL BIOLOGY

Evolution of the mammalian transcription factor binding repertoire via transposable elements

(2008) G. Bourque et al.   GENOME RESEARCH

Design and analysis of ChIP-seq experiments for DNA-binding proteins

(2008) Peter V Kharchenko et al.   NATURE BIOTECHNOLOGY

Requirement of Nanog dimerization for stem cell self-renewal and pluripotency

(2008) J. Wang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA