Predictive modelling of gene expression from transcriptional regulatory elements

Models in biology: ‘accurate descriptions of our pathetic thinking’

(2014) Jeremy Gunawardena   BMC BIOLOGY

Supervised, semi-supervised and unsupervised inference of gene regulatory networks

(2013) S. R. Maetschke et al.   BRIEFINGS IN BIOINFORMATICS

Exploring the three-dimensional organization of genomes: interpreting chromatin interaction data

(2013) Job Dekker et al.   NATURE REVIEWS GENETICS

Ensembl 2014

(2013) Paul Flicek et al.   NUCLEIC ACIDS RESEARCH

Bayesian Inference of Spatial Organizations of Chromosomes

(2013) Ming Hu et al.   PLoS Computational Biology

Genome-wide in silico prediction of gene expression

(2012) Robert C. McLeay et al.   BIOINFORMATICS

Physical tethering and volume exclusion determine higher-order genome organization in budding yeast

(2012) H. Tjong et al.   GENOME RESEARCH

Raise standards for preclinical cancer research

(2012) C. Glenn Begley et al.   NATURE

A map of the cis-regulatory sequences in the mouse genome

(2012) Yin Shen et al.   NATURE

An integrated encyclopedia of DNA elements in the human genome

(2012)   NATURE

The accessible chromatin landscape of the human genome

(2012) Robert E. Thurman et al.   NATURE

Architecture of the human regulatory network derived from ENCODE data

(2012) Mark B. Gerstein et al.   NATURE

Wisdom of crowds for robust gene network inference

(2012) Daniel Marbach et al.   NATURE METHODS

Understanding the language of Lys36 methylation at histone H3

(2012) Eric J. Wagner et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Thermodynamic State Ensemble Models of cis-Regulation

(2012) Marc S. Sherman et al.   PLoS Computational Biology

Epigenetic priors for identifying active transcription factor binding sites

(2011) Gabriel Cuellar-Partida et al.   BIOINFORMATICS

FIMO: scanning for occurrences of a given motif

(2011) Charles E. Grant et al.   BIOINFORMATICS

Gene network inference and visualization tools for biologists: application to new human transcriptome datasets

(2011) Daniel Hurley et al.   NUCLEIC ACIDS RESEARCH

Modeling the relative relationship of transcription factor binding and histone modifications to gene expression levels in mouse embryonic stem cells

(2011) Chao Cheng et al.   NUCLEIC ACIDS RESEARCH

A statistical framework for modeling gene expression using chromatin features and application to modENCODE datasets

(2011) Chao Cheng et al.   GENOME BIOLOGY

A unique H3K4me2 profile marks tissue-specific gene regulation

(2010) A. Pekowska et al.   GENOME RESEARCH

Epigenetic control of embryonic stem cell fate

(2010) Nicolaj Strøyer Christophersen et al.   JOURNAL OF EXPERIMENTAL MEDICINE

Epigenetic modifications and human disease

(2010) Anna Portela et al.   NATURE BIOTECHNOLOGY

Epigenetic modifications in pluripotent and differentiated cells

(2010) Alexander Meissner   NATURE BIOTECHNOLOGY

Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation

(2010) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

Histone modification levels are predictive for gene expression

(2010) R. Karlic et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Thermodynamics-Based Models of Transcriptional Regulation by Enhancers: The Roles of Synergistic Activation, Cooperative Binding and Short-Range Repression

(2010) Xin He et al.   PLoS Computational Biology

Chromatin poises miRNA- and protein-coding genes for expression

(2009) A. Barski et al.   GENOME RESEARCH

The estimation of R 2 and adjusted R 2 in incomplete data sets using multiple imputation

(2009) Ofer Harel   JOURNAL OF APPLIED STATISTICS

Global Analysis of H3K4 Methylation Defines MLL Family Member Targets and Points to a Role for MLL1-Mediated H3K4 Methylation in the Regulation of Transcriptional Initiation by RNA Polymerase II

(2009) P. Wang et al.   MOLECULAR AND CELLULAR BIOLOGY

Universal protein-binding microarrays for the comprehensive characterization of the DNA-binding specificities of transcription factors

(2009) Michael F Berger et al.   Nature Protocols

Insights from genomic profiling of transcription factors

(2009) Peggy J. Farnham   NATURE REVIEWS GENETICS

A census of human transcription factors: function, expression and evolution

(2009) Juan M. Vaquerizas et al.   NATURE REVIEWS GENETICS

JASPAR 2010: the greatly expanded open-access database of transcription factor binding profiles

(2009) Elodie Portales-Casamar et al.   NUCLEIC ACIDS RESEARCH

ChIP-Seq of transcription factors predicts absolute and differential gene expression in embryonic stem cells

(2009) Z. Ouyang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

H3K79 Methylation Profiles Define Murine and Human MLL-AF4 Leukemias

(2008) Andrei V. Krivtsov et al.   CANCER CELL

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

(2008) Xi Chen et al.   CELL

Genome-scale DNA methylation maps of pluripotent and differentiated cells

(2008) Alexander Meissner et al.   NATURE

Stem cell transcriptome profiling via massive-scale mRNA sequencing

(2008) Nicole Cloonan et al.   NATURE METHODS

Mapping and quantifying mammalian transcriptomes by RNA-Seq

(2008) Ali Mortazavi et al.   NATURE METHODS

High-throughput chromatin information enables accurate tissue-specific prediction of transcription factor binding sites

(2008) Tom Whitington et al.   NUCLEIC ACIDS RESEARCH