CoBRA: Containerized Bioinformatics Workflow for Reproducible ChIP/ATAC-seq Analysis

esATAC: an easy-to-use systematic pipeline for ATAC-seq data analysis

(2018) Zheng Wei et al.   BIOINFORMATICS

VIPER: Visualization Pipeline for RNA-seq, a Snakemake workflow for efficient and complete RNA-seq analysis

(2018) MacIntosh Cornwell et al.   BMC BIOINFORMATICS

Inflammation-associated microsatellite alterations: Mechanisms and significance in the prognosis of patients with colorectal cancer

(2018) Minoru Koi et al.   World Journal of Gastrointestinal Oncology

RNAs interact with BRD4 to promote enhanced chromatin engagement and transcription activation

(2018) Homa Rahnamoun et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Cistrome Data Browser: expanded datasets and new tools for gene regulatory analysis

(2018) Rongbin Zheng et al.   NUCLEIC ACIDS RESEARCH

Transforming Growth Factor β Superfamily Signaling in Development of Colorectal Cancer

(2017) Barbara Jung et al.   GASTROENTEROLOGY

Therapeutic targeting of polycomb and BET bromodomain proteins in diffuse intrinsic pontine gliomas

(2017) Andrea Piunti et al.   NATURE MEDICINE

Dynamic Gene Regulatory Networks of Human Myeloid Differentiation

(2017) Ricardo N. Ramirez et al.   Cell Systems

ChiLin: a comprehensive ChIP-seq and DNase-seq quality control and analysis pipeline

(2016) Qian Qin et al.   BMC BIOINFORMATICS

CCAT1 is an enhancer-templated RNA that predicts BET sensitivity in colorectal cancer

(2016) Mark L. McCleland et al.   JOURNAL OF CLINICAL INVESTIGATION

Prognostic Value ofBRAF and KRAS Mutations in MSI and MSS Stage III Colon Cancer

(2016) Julien Taieb et al.   JNCI-Journal of the National Cancer Institute

Effects on the transcriptome upon deletion of a distal element cannot be predicted by the size of the H3K27Ac peak in human cells

(2016) Yu Gyoung Tak et al.   NUCLEIC ACIDS RESEARCH

deepTools2: a next generation web server for deep-sequencing data analysis

(2016) Fidel Ramírez et al.   NUCLEIC ACIDS RESEARCH

Cistrome Data Browser: a data portal for ChIP-Seq and chromatin accessibility data in human and mouse

(2016) Shenglin Mei et al.   NUCLEIC ACIDS RESEARCH

Prognostic Value ofBRAF and KRAS Mutations in MSI and MSS Stage III Colon Cancer

(2016) Julien Taieb et al.   JNCI-Journal of the National Cancer Institute

Detecting differential peaks in ChIP-seq signals with ODIN

(2015) M. Allhoff et al.   BIOINFORMATICS

Role of DNA Methylation in Modulating Transcription Factor Occupancy

(2015) Matthew T. Maurano et al.   Cell Reports

CopywriteR: DNA copy number detection from off-target sequence data

(2015) Thomas Kuilman et al.   GENOME BIOLOGY

Identifying differential transcription factor binding in ChIP-seq

(2015) Dai-Ying Wu et al.   Frontiers in Genetics

DNA copy number analysis of fresh and formalin-fixed specimens by shallow whole-genome sequencing with identification and exclusion of problematic regions in the genome assembly

(2014) Ilari Scheinin et al.   GENOME RESEARCH

HMCan: a method for detecting chromatin modifications in cancer samples using ChIP-seq data

(2013) Haitham Ashoor et al.   BIOINFORMATICS

diffReps: Detecting Differential Chromatin Modification Sites from ChIP-seq Data with Biological Replicates

(2013) Li Shen et al.   PLoS One

Snakemake--a scalable bioinformatics workflow engine

(2012) J. Koster et al.   BIOINFORMATICS

Differential oestrogen receptor binding is associated with clinical outcome in breast cancer

(2012) Caryn S. Ross-Innes et al.   NATURE

MAnorm: a robust model for quantitative comparison of ChIP-Seq data sets

(2012) Zhen Shao et al.   GENOME BIOLOGY

Detecting differential binding of transcription factors with ChIP-seq

(2011) Kun Liang et al.   BIOINFORMATICS

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