Computation for ChIP-seq and RNA-seq studies
暂无分享,去创建一个
[1] Martin Vingron,et al. Variance stabilization applied to microarray data calibration and to the quantification of differential expression , 2002, ISMB.
[2] M. Gerstein,et al. Comparative analysis of processed pseudogenes in the mouse and human genomes. , 2004, Trends in genetics : TIG.
[3] C. Nusbaum,et al. Chromosome Conformation Capture Carbon Copy (5C): a massively parallel solution for mapping interactions between genomic elements. , 2006, Genome research.
[4] T. Mikkelsen,et al. Genome-wide maps of chromatin state in pluripotent and lineage-committed cells , 2007, Nature.
[5] William Stafford Noble,et al. Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project , 2007, Nature.
[6] Allen D. Delaney,et al. Genome-wide profiles of STAT1 DNA association using chromatin immunoprecipitation and massively parallel sequencing , 2007, Nature Methods.
[7] Dustin E. Schones,et al. High-Resolution Profiling of Histone Methylations in the Human Genome , 2007, Cell.
[8] A. Mortazavi,et al. Genome-Wide Mapping of in Vivo Protein-DNA Interactions , 2007, Science.
[9] E. Birney,et al. Velvet: algorithms for de novo short read assembly using de Bruijn graphs. , 2008, Genome research.
[10] Terrence S. Furey,et al. F-Seq: a feature density estimator for high-throughput sequence tags , 2008, Bioinform..
[11] Gunnar Rätsch,et al. Optimal spliced alignments of short sequence reads , 2008, BMC Bioinformatics.
[12] Steven J. M. Jones,et al. FindPeaks 3.1: a tool for identifying areas of enrichment from massively parallel short-read sequencing technology , 2008, Bioinform..
[13] M. Stephens,et al. RNA-seq: an assessment of technical reproducibility and comparison with gene expression arrays. , 2008, Genome research.
[14] S. Ranade,et al. Stem cell transcriptome profiling via massive-scale mRNA sequencing , 2008, Nature Methods.
[15] Feng Lin,et al. An HMM approach to genome-wide identification of differential histone modification sites from ChIP-seq data , 2008, Bioinform..
[16] Eric T. Wang,et al. Alternative Isoform Regulation in Human Tissue Transcriptomes , 2008, Nature.
[17] R. Lister,et al. Highly Integrated Single-Base Resolution Maps of the Epigenome in Arabidopsis , 2008, Cell.
[18] F. Denoeud,et al. Annotating genomes with massive-scale RNA sequencing , 2008, Genome Biology.
[19] Clifford A. Meyer,et al. Model-based Analysis of ChIP-Seq (MACS) , 2008, Genome Biology.
[20] M. Gerstein,et al. The Transcriptional Landscape of the Yeast Genome Defined by RNA Sequencing , 2008, Science.
[21] Bing Ren,et al. ChromaSig: A Probabilistic Approach to Finding Common Chromatin Signatures in the Human Genome , 2008, PLoS Comput. Biol..
[22] B. Wold,et al. Sequence census methods for functional genomics , 2008, Nature Methods.
[23] Raja Jothi,et al. Genome-wide identification of in vivo protein–DNA binding sites from ChIP-Seq data , 2008, Nucleic acids research.
[24] Ruiqiang Li,et al. SOAP: short oligonucleotide alignment program , 2008, Bioinform..
[25] I. Goodhead,et al. Dynamic repertoire of a eukaryotic transcriptome surveyed at single-nucleotide resolution , 2008, Nature.
[26] S. Batzoglou,et al. Genome-Wide Analysis of Transcription Factor Binding Sites Based on ChIP-Seq Data , 2008, Nature Methods.
[27] Marcel H. Schulz,et al. A Global View of Gene Activity and Alternative Splicing by Deep Sequencing of the Human Transcriptome , 2008, Science.
[28] David A. Nix,et al. Empirical methods for controlling false positives and estimating confidence in ChIP-Seq peaks , 2008, BMC Bioinformatics.
[29] P. Park,et al. Design and analysis of ChIP-seq experiments for DNA-binding proteins , 2008, Nature Biotechnology.
[30] Cole Trapnell,et al. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome , 2009, Genome Biology.
[31] B. Williams,et al. Mapping and quantifying mammalian transcriptomes by RNA-Seq , 2008, Nature Methods.
[32] Ronghua Chen,et al. Digital transcriptome profiling using selective hexamer priming for cDNA synthesis , 2009, Nature Methods.
[33] Wing Hung Wong,et al. Statistical inferences for isoform expression in RNA-Seq , 2009, Bioinform..
[34] Chen Zeng,et al. A clustering approach for identification of enriched domains from histone modification ChIP-Seq data , 2009, Bioinform..
[35] G. Tuteja,et al. Extracting transcription factor targets from ChIP-Seq data , 2009, Nucleic acids research.
[36] Sean M. Grimmond,et al. RNA-MATE: a recursive mapping strategy for high-throughput RNA-sequencing data , 2009, Bioinform..
[37] Lior Pachter,et al. Sequence Analysis , 2020, Definitions.
[38] G. Church,et al. Genome-Wide Identification of Human RNA Editing Sites by Parallel DNA Capturing and Sequencing , 2009, Science.
[39] Inanç Birol,et al. De novo transcriptome assembly with ABySS , 2009, Bioinform..
[40] Raymond K. Auerbach,et al. PeakSeq enables systematic scoring of ChIP-seq experiments relative to controls , 2009, Nature Biotechnology.
[41] Cole Trapnell,et al. How to map billions of short reads onto genomes , 2009, Nature Biotechnology.
[42] Paul W. Sternberg,et al. RNA Pol II Accumulates at Promoters of Growth Genes During Developmental Arrest , 2009, Science.
[43] E. Liu,et al. Next-generation DNA sequencing of paired-end tags (PET) for transcriptome and genome analyses. , 2009, Genome research.
[44] K. Zhao,et al. Detection of single nucleotide variations in expressed exons of the human genome using RNA-Seq , 2009, Nucleic acids research.
[45] Liang Chen,et al. A hierarchical Bayesian model for comparing transcriptomes at the individual transcript isoform level , 2009, Nucleic acids research.
[46] A. Oshlack,et al. Transcript length bias in RNA-seq data confounds systems biology , 2009, Biology Direct.