Prediction of RNA Polymerase II recruitment, elongation and stalling from histone modification data

Regularization Paths for Generalized Linear Models via Coordinate Descent

(2015) Jerome Friedman et al.   Journal of Statistical Software

Mapping and analysis of chromatin state dynamics in nine human cell types

(2011) Jason Ernst et al.   NATURE

Systematic Clustering of Transcription Start Site Landscapes

(2011) Xiaobei Zhao et al.   PLoS One

Genomic and chromatin signals underlying transcription start-site selection

(2011) Eivind Valen et al.   TRENDS IN GENETICS

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

(2011) Chao Cheng et al.   GENOME BIOLOGY

Genome-wide promoter analysis of histone modifications in human monocyte-derived antigen presenting cells

(2010) Liina Tserel et al.   BMC GENOMICS

c-Myc Regulates Transcriptional Pause Release

(2010) Peter B. Rahl et al.   CELL

Discovery and characterization of chromatin states for systematic annotation of the human genome

(2010) Jason Ernst et al.   NATURE BIOTECHNOLOGY

Characterization of an antagonistic switch between histone H3 lysine 27 methylation and acetylation in the transcriptional regulation of Polycomb group target genes

(2010) Diego Pasini et al.   NUCLEIC ACIDS RESEARCH

Close association of RNA polymerase II and many transcription factors with Pol III genes

(2010) Debasish Raha et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Dynamic transcriptomes during neural differentiation of human embryonic stem cells revealed by short, long, and paired-end sequencing

(2010) J. Q. Wu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

Histone H3 lysine 4 (H3K4) methylation in development and differentiation

(2009) Joel C. Eissenberg et al.   DEVELOPMENTAL BIOLOGY

Distinct DNA methylation patterns characterize differentiated human embryonic stem cells and developing human fetal liver

(2009) A. L. Brunner et al.   GENOME RESEARCH

H3.3/H2A.Z double variant–containing nucleosomes mark 'nucleosome-free regions' of active promoters and other regulatory regions

(2009) Chunyuan Jin et al.   NATURE GENETICS

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

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

The UCSC Genome Browser database: update 2010

(2009) B. Rhead et al.   NUCLEIC ACIDS RESEARCH

ENCODE whole-genome data in the UCSC Genome Browser

(2009) K. R. Rosenbloom et al.   NUCLEIC ACIDS RESEARCH

F-Seq: a feature density estimator for high-throughput sequence tags

(2008) A. P. Boyle et al.   BIOINFORMATICS

Prediction of regulatory elements in mammalian genomes using chromatin signatures

(2008) Kyoung-Jae Won et al.   BMC BIOINFORMATICS

Dynamic Regulation of Nucleosome Positioning in the Human Genome

(2008) Dustin E. Schones et al.   CELL

Poised RNA Polymerase II Gives Pause for Thought

(2008) Thanasis Margaritis et al.   CELL

High-Resolution Mapping and Characterization of Open Chromatin across the Genome

(2008) Alan P. Boyle et al.   CELL

Genome-wide detection and analysis of hippocampus core promoters using DeepCAGE

(2008) E. Valen et al.   GENOME RESEARCH

What are artificial neural networks?

(2008) Anders Krogh   NATURE BIOTECHNOLOGY

Combinatorial patterns of histone acetylations and methylations in the human genome

(2008) Zhibin Wang et al.   NATURE GENETICS

The Transcriptional Landscape of the Yeast Genome Defined by RNA Sequencing

(2008) U. Nagalakshmi et al.   SCIENCE

Transcription Regulation Through Promoter-Proximal Pausing of RNA Polymerase II

(2008) L. J. Core et al.   SCIENCE

Nascent RNA Sequencing Reveals Widespread Pausing and Divergent Initiation at Human Promoters

(2008) Leighton J. Core et al.   SCIENCE

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY