Related references
Note: Only part of the references are listed.Statistical inferences for isoform expression in RNA-Seq
Hui Jiang et al.
BIOINFORMATICS (2009)
A clustering approach for identification of enriched domains from histone modification ChIP-Seq data
Chongzhi Zang et al.
BIOINFORMATICS (2009)
TopHat: discovering splice junctions with RNA-Seq
Cole Trapnell et al.
BIOINFORMATICS (2009)
Transcript length bias in RNA-seq data confounds systems biology
Alicia Oshlack et al.
BIOLOGY DIRECT (2009)
Next-generation DNA sequencing of paired-end tags (PET) for transcriptome and genome analyses
Melissa J. Fullwood et al.
GENOME RESEARCH (2009)
How to map billions of short reads onto genomes
Cole Trapnell et al.
NATURE BIOTECHNOLOGY (2009)
PeakSeq enables systematic scoring of ChIP-seq experiments relative to controls
Joel Rozowsky et al.
NATURE BIOTECHNOLOGY (2009)
Digital transcriptome profiling using selective hexamer priming for cDNA synthesis
Christopher D. Armour et al.
NATURE METHODS (2009)
A hierarchical Bayesian model for comparing transcriptomes at the individual transcript isoform level
Sika Zheng et al.
NUCLEIC ACIDS RESEARCH (2009)
RNA Pol II Accumulates at Promoters of Growth Genes During Developmental Arrest
L. Ryan Baugh et al.
SCIENCE (2009)
Genome-Wide Identification of Human RNA Editing Sites by Parallel DNA Capturing and Sequencing
Jin Billy Li et al.
SCIENCE (2009)
Ultrafast and memory-efficient alignment of short DNA sequences to the human genome
Ben Langmead et al.
GENOME BIOLOGY (2009)
Optimal spliced alignments of short sequence reads
Fabio De Bona et al.
BIOINFORMATICS (2008)
F-Seq: a feature density estimator for high-throughput sequence tags
Alan P. Boyle et al.
BIOINFORMATICS (2008)
An HMM approach to genome-wide identification of differential histone modification sites from ChIP-seq data
Han Xu et al.
BIOINFORMATICS (2008)
FindPeaks 3.1: a tool for identifying areas of enrichment from massively parallel short-read sequencing technology
Anthony P. Fejes et al.
BIOINFORMATICS (2008)
SOAP: short oligonucleotide alignment program
Ruiqiang Li et al.
BIOINFORMATICS (2008)
Empirical methods for controlling false positives and estimating confidence in ChIP-Seq peaks
David A. Nix et al.
BMC BIOINFORMATICS (2008)
Highly integrated single-base resolution maps of the epigenome in Arabidopsis
Ryan Lister et al.
CELL (2008)
RNA-seq: An assessment of technical reproducibility and comparison with gene expression arrays
John C. Marioni et al.
GENOME RESEARCH (2008)
Velvet: Algorithms for de novo short read assembly using de Bruijn graphs
Daniel R. Zerbino et al.
GENOME RESEARCH (2008)
Alternative isoform regulation in human tissue transcriptomes
Eric T. Wang et al.
NATURE (2008)
Dynamic repertoire of a eukaryotic transcriptome surveyed at single-nucleotide resolution
Brian T. Wilhelm et al.
NATURE (2008)
An integrated software system for analyzing ChIP-chip and ChIP-seq data
Hongkai Ji et al.
NATURE BIOTECHNOLOGY (2008)
Design and analysis of ChIP-seq experiments for DNA-binding proteins
Peter V. Kharchenko et al.
NATURE BIOTECHNOLOGY (2008)
Stem cell transcriptome profiling via massive-scale mRNA sequencing
Nicole Cloonan et al.
NATURE METHODS (2008)
Genome-wide analysis of transcription factor binding sites based on ChIP-Seq data
Anton Valouev et al.
NATURE METHODS (2008)
Mapping and quantifying mammalian transcriptomes by RNA-Seq
Ali Mortazavi et al.
NATURE METHODS (2008)
Genome-wide identification of in vivo protein-DNA binding sites from ChIP-Seq data
Raja Jothi et al.
NUCLEIC ACIDS RESEARCH (2008)
The transcriptional landscape of the yeast genome defined by RNA sequencing
Ugrappa Nagalakshmi et al.
SCIENCE (2008)
A global view of gene activity and alternative splicing by deep sequencing of the human transcriptome
Marc Sultan et al.
SCIENCE (2008)
ChromaSig: A Probabilistic Approach to Finding Common Chromatin Signatures in the Human Genome
Gary Hon et al.
PLOS COMPUTATIONAL BIOLOGY (2008)
Annotating genomes with massive-scale RNA sequencing
France Denoeud et al.
GENOME BIOLOGY (2008)
Model-based Analysis of ChIP-Seq (MACS)
Yong Zhang et al.
GENOME BIOLOGY (2008)
Genome-wide maps of chromatin state in pluripotent and lineage-committed cells
Tarjei S. Mikkelsen et al.
NATURE (2007)
Genome-wide profiles of STAT1 DNA association using chromatin immunoprecipitation and massively parallel sequencing
Gordon Robertson et al.
NATURE METHODS (2007)
Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project
Ewan Birney et al.
NATURE (2007)
Genome-wide mapping of in vivo protein-DNA interactions
David S. Johnson et al.
SCIENCE (2007)
High-resolution profiling of histone methylations in the human genome
Artern Barski et al.
CELL (2007)
Chromosome Conformation Capture Carbon Copy (5C): A massively parallel solution for mapping interactions between genomic elements
Josee Dostie et al.
GENOME RESEARCH (2006)
Comparative analysis of processed pseudogenes in the mouse and human genomes
ZL Zhang et al.
TRENDS IN GENETICS (2004)