BAMscale: quantification of next-generation sequencing peaks and generation of scaled coverage tracks

The mitochondrial type IB topoisomerase drives mitochondrial translation and carcinogenesis

(2019) S. A. Baechler et al.   Nature Communications

Genome-wide stability of the DNA replication program in single mammalian cells

(2019) Saori Takahashi et al.   NATURE GENETICS

POU2F3 is a master regulator of a tuft cell-like variant of small cell lung cancer

(2018) Yu-Han Huang et al.   GENES & DEVELOPMENT

SLFN11 Blocks Stressed Replication Forks Independently of ATR

(2018) Junko Murai et al.   MOLECULAR CELL

Enhancer mapping uncovers phenotypic heterogeneity and evolution in patients with luminal breast cancer

(2018) Darren K. Patten et al.   NATURE MEDICINE

GIGGLE: a search engine for large-scale integrated genome analysis

(2018) Ryan M Layer et al.   NATURE METHODS

Genome-wide analysis of replication timing by next-generation sequencing with E/L Repli-seq

(2018) Claire Marchal et al.   Nature Protocols

The replication initiation determinant protein (RepID) modulates replication by recruiting CUL4 to chromatin

(2018) Sang-Min Jang et al.   Nature Communications

Dual Roles of Poly(dA:dT) Tracts in Replication Initiation and Fork Collapse

(2018) Anthony Tubbs et al.   CELL

Developmental and cancer-associated plasticity of DNA replication preferentially targets GC-poor, lowly expressed and late-replicating regions

(2018) Xia Wu et al.   NUCLEIC ACIDS RESEARCH

Enhancer Activity Requires CBP/P300 Bromodomain-Dependent Histone H3K27 Acetylation

(2018) Ryan Raisner et al.   Cell Reports

TPMCalculator: one-step software to quantify mRNA abundance of genomic features

(2018) Roberto Vera Alvarez et al.   BIOINFORMATICS

The UCSC Genome Browser database: 2019 update

(2018) Maximilian Haeussler et al.   NUCLEIC ACIDS RESEARCH

Bivariate Genomic Footprinting Detects Changes in Transcription Factor Activity

(2017) Songjoon Baek et al.   Cell Reports

DNA Breaks and End Resection Measured Genome-wide by End Sequencing

(2016) Andres Canela et al.   MOLECULAR CELL

Loss of the histone methyltransferase EZH2 induces resistance to multiple drugs in acute myeloid leukemia

(2016) Stefanie Göllner et al.   NATURE MEDICINE

Simulation-based comprehensive benchmarking of RNA-seq aligners

(2016) Giacomo Baruzzo et al.   NATURE METHODS

Combining ATAC-seq with nuclei sorting for discovery of cis-regulatory regions in plant genomes

(2016) Zefu Lu et al.   NUCLEIC ACIDS RESEARCH

Distinct epigenetic features of differentiation-regulated replication origins

(2016) Owen K. Smith et al.   Epigenetics & Chromatin

Replication landscape of the human genome

(2016) Nataliya Petryk et al.   Nature Communications

ASCL1 and NEUROD1 Reveal Heterogeneity in Pulmonary Neuroendocrine Tumors and Regulate Distinct Genetic Programs

(2016) Mark D. Borromeo et al.   Cell Reports

ColoWeb: a resource for analysis of colocalization of genomic features

(2015) RyangGuk Kim et al.   BMC GENOMICS

HISAT: a fast spliced aligner with low memory requirements

(2015) Daehwan Kim et al.   NATURE METHODS

A 26-hour system of highly sensitive whole genome sequencing for emergency management of genetic diseases

(2015) Neil A. Miller et al.   Genome Medicine

Discovery of Transcription Factors and Regulatory Regions Driving In Vivo Tumor Development by ATAC-seq and FAIRE-seq Open Chromatin Profiling

(2015) Kristofer Davie et al.   PLoS Genetics

Genetic Variation in Human DNA Replication Timing

(2014) Amnon Koren et al.   CELL

deepTools: a flexible platform for exploring deep-sequencing data

(2014) Fidel Ramírez et al.   NUCLEIC ACIDS RESEARCH

Allele-Specific Genome-wide Profiling in Human Primary Erythroblasts Reveal Replication Program Organization

(2014) Rituparna Mukhopadhyay et al.   PLoS Genetics

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

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

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

ChromHMM: automating chromatin-state discovery and characterization

(2012) Jason Ernst et al.   NATURE METHODS

Integrative annotation of chromatin elements from ENCODE data

(2012) Michael M. Hoffman et al.   NUCLEIC ACIDS RESEARCH

Measurement of mRNA abundance using RNA-seq data: RPKM measure is inconsistent among samples

(2012) Günter P. Wagner et al.   THEORY IN BIOSCIENCES

MLL-Rearranged Leukemia Is Dependent on Aberrant H3K79 Methylation by DOT1L

(2011) Kathrin M. Bernt et al.   CANCER CELL

Genome-wide depletion of replication initiation events in highly transcribed regions

(2011) M. M. Martin et al.   GENOME RESEARCH

Integrative genomics viewer

(2011) James T Robinson et al.   NATURE BIOTECHNOLOGY

Cistrome: an integrative platform for transcriptional regulation studies

(2011) Tao Liu et al.   GENOME BIOLOGY

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

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

(2010) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

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

Sequencing newly replicated DNA reveals widespread plasticity in human replication timing

(2009) R. S. Hansen et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Highly Integrated Single-Base Resolution Maps of the Epigenome in Arabidopsis

(2008) Ryan Lister et al.   CELL

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

(2008) Alan P. Boyle et al.   CELL

Mapping and quantifying mammalian transcriptomes by RNA-Seq

(2008) Ali Mortazavi et al.   NATURE METHODS

The Transcriptional Landscape of the Yeast Genome Defined by RNA Sequencing

(2008) U. Nagalakshmi et al.   SCIENCE

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY