Computation for ChIP-seq and RNA-seq studies

Keywords

RNA-Seq, Computer science, Software, Computational biology, DNA sequencing

References

• Detection of single nucleotide variations in expressed exons of the human genome using RNA-SeqIouri Chepelev, Gang Wei, Qingsong Tang — 2009
• The Transcriptional Landscape of the Yeast Genome Defined by RNA SequencingUgrappa Nagalakshmi, Zhong Wang, Karl Waern — 2008
• How to map billions of short reads onto genomesCole Trapnell, Steven L. Salzberg — 2009
• PeakSeq: Systematic Scoring of ChIP-Seq Experiments Relative to ControlsJoel Rozowsky, Ghia Euskirchen, Raymond K. Auerbach — 2009
• Sequence census methods for functional genomicsB Wold, R Myers — 2008
• ChromaSig: A Probabilistic Approach to Finding Common Chromatin Signatures in the Human GenomeGary C. Hon, Bing Ren, Wei Wang — 2008
• Chromosome Conformation Capture Carbon Copy (5C): a massively parallel solution for mapping interactions between genomic elements.Josée Dostie, Todd Richmond, Ramy Arnaout — 2006
• High-resolution profiling of histone methylations in the human genome.Artem Barski, Suresh Cuddapah, Kairong Cui — 2007
• Genome-wide maps of chromatin state in pluripotent and lineage-committed cellsTarjei S. Mikkelsen, Manching Ku, David B. Jaffe — 2007
• Digital transcriptome profiling using selective hexamer priming for cDNA synthesisChristopher D. Armour, John C. Castle, Ronghua Chen — 2009
• Dynamic repertoire of a eukaryotic transcriptome surveyed at single-nucleotide resolutionBrian T. Wilhelm, Samuel Marguerat, Stephen Watt — 2008
• RNA Pol II Accumulates at Promoters of Growth Genes During Developmental ArrestL. Ryan Baugh, John DeModena, Paul W. Sternberg — 2009
• Genome-wide profiles of STAT1 DNA association using chromatin immunoprecipitation and massively parallel sequencingGordon Robertson, Martin Hirst, Matthew N. Bainbridge — 2007
• Highly integrated single-base resolution maps of the epigenome in Arabidopsis.Ryan Lister, Ronan C. O’Malley, Julian Tonti‐Filippini — 2008
• Genome-Wide Identification of Human RNA Editing Sites by Parallel DNA Capturing and SequencingJin Billy Li, Erez Y. Levanon, Jung-Ki Yoon — 2009
• Empirical methods for controlling false positives and estimating confidence in ChIP-Seq peaksDavid A. Nix, Samir Courdy, Kenneth M. Boucher — 2008
• A Global View of Gene Activity and Alternative Splicing by Deep Sequencing of the Human TranscriptomeMarc Sultan, Marcel H. Schulz, Hugues Richard — 2008
• Genome-Wide Analysis of Transcription Factor Binding Sites Based on ChIP-Seq DataAnton Valouev, David S. Johnson, Andreas Sundquist — 2008
• Statistical inferences for isoform expression in RNA-SeqHui Jiang, Wing Hung Wong — 2009
• Annotating genomes with massive-scale RNA sequencingFrance Denœud, Jean‐Marc Aury, Corinne Da Silva — 2008

Cited by

• Analyse bioinformatique du transcriptome des champignons mycorhiziens Tuber melanosporum et Glomus intraradicesÉmilie Tisserant — 2011
• Phenotypic Plasticity and Epigenetics In The Honeybee OvaryM. Leask — 2014
• Overview of DNA Sequencing StrategiesClaude Paul — 2011
• Shrinkage estimation of dispersion in Negative Binomial models for RNA-seq experiments with small sample sizeDanni Yu, Wolfgang Huber, Olga Vitek — 2013
• Discovering and mapping chromatin states using a tree hidden Markov modelБелый Николай Семенович — 2013
• Inference of RNA Polymerase II Transcription Dynamics from Chromatin Immunoprecipitation Time Course DataNeil J. Günther — 2013
• Computational approaches for isoform detection and estimation: good and bad newsKayla Nesbitt — 2014
• Is this the right normalization? A diagnostic tool for ChIP-seq normalizationStefan Szczelkun — 2015
• Integrated and comparative miRNA analysis of starvation-induced autophagy in mouse embryonic fibroblasts.Keith D. Alpine — 2015
• The Role of Genome Accessibility in Transcription Factor Binding in BacteriaMattie S. Edwards — 2016
• Embedding the Future of Regenerative Medicine into the Open Epigenomic Landscape of Pluripotent Human Embryonic Stem CellsXuejun H. Parsons — 2013
• Global identification of androgen response elements.Charles Massie, Ian G. Mills — 2011
• Interpreting and visualizing ChIP-seq data with the seqMINER software.Tao Ye, Sarina Ravens, Arnaud Krebs — 2014
• The brown midrib 2 (bm2) gene of maize encodes methylenetetrahydrofolate reductaseHo Man Tang — 2011
• DNA Sequence Variants in Human Autoimmune DiseasesChuan Wang — 2012
• DNA sequence motif: a jack of all trades for ChIP-Seq data.Ivan V. Kulakovskiy, Vsevolod J. Makeev — 2013
• Decoding the Structural Layer of Transcriptional Regulation : Computational Analyses of Chromatin and Chromosomal AberrationsRobin Andersson — 2010
• A Peak-Finder Meta Server for ChIP-Seq AnalysisHusen M. Umer — 2011
• The application and challenges of RNA-sequencing to the study of circadian rhythmsNicholas F. Lahens — 2014
• Finding Optimal Sets of Enriched Regions in ChIP-Seq DataAndreas Gogol‐Döring, Wei Chen — 2010

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