Molecular Profiling of RNA Tumors Using High-Throughput RNA Sequencing: From Raw Data to Systems Level Analyses.
暂无分享,去创建一个
Gary Hardiman | Dongjun Chung | Willian A da Silveira | E Starr Hazard | G. Hardiman | Dongjun Chung | W. D. da Silveira | E. S. Hazard
[1] David Gomez-Cabrero,et al. Erratum to: A survey of best practices for RNA-seq data analysis , 2016, Genome Biology.
[2] Wolfgang Huber,et al. Love MI, Huber W, Anders S.. Moderated estimation of fold change and dispersion for RNA-Seq data with DESeq2. Genome Biol 15: 550 , 2014 .
[3] Peter M. Rice,et al. The Sanger FASTQ file format for sequences with quality scores, and the Solexa/Illumina FASTQ variants , 2009, Nucleic acids research.
[4] Rafael A. Irizarry,et al. Bioinformatics and Computational Biology Solutions using R and Bioconductor , 2005 .
[5] Cole Trapnell,et al. Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. , 2010, Nature biotechnology.
[6] Gordon K. Smyth,et al. limma: Linear Models for Microarray Data , 2005 .
[7] Charlotte Soneson,et al. A comparison of methods for differential expression analysis of RNA-seq data , 2013, BMC Bioinformatics.
[8] Pablo Tamayo,et al. Gene set enrichment analysis: A knowledge-based approach for interpreting genome-wide expression profiles , 2005, Proceedings of the National Academy of Sciences of the United States of America.
[9] Zhifu Sun,et al. A genetic cell context-dependent role for ZEB1 in lung cancer , 2016, Nature Communications.
[10] David R. Kelley,et al. Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks , 2012, Nature Protocols.
[11] W. Huber,et al. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2 , 2014, Genome Biology.
[12] Jennifer M. Bolin,et al. Single Read and Paired End mRNA-Seq Illumina Libraries from 10 Nanograms Total RNA , 2011, Journal of visualized experiments : JoVE.
[13] Brian T. Lee,et al. The UCSC Genome Browser database: 2015 update , 2014, Nucleic Acids Res..
[14] M. Daly,et al. PGC-1α-responsive genes involved in oxidative phosphorylation are coordinately downregulated in human diabetes , 2003, Nature Genetics.
[15] Carleton T. Garrett,et al. Molecular Biology Basics in the “Omics” Era: Genes to Proteins , 2015 .
[16] Somnath Datta,et al. Statistical analysis of next generation sequencing date , 2014 .
[17] Daniel J. Gaffney,et al. A survey of best practices for RNA-seq data analysis , 2016, Genome Biology.
[18] B. Wold,et al. Sequence census methods for functional genomics , 2008, Nature Methods.
[19] Jing Chen,et al. ToppGene Suite for gene list enrichment analysis and candidate gene prioritization , 2009, Nucleic Acids Res..
[20] David R. Kelley,et al. Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks , 2012, Nature Protocols.
[21] W. Alkema,et al. BioVenn – a web application for the comparison and visualization of biological lists using area-proportional Venn diagrams , 2008, BMC Genomics.
[22] Marcel Martin. Cutadapt removes adapter sequences from high-throughput sequencing reads , 2011 .
[23] R. Gentleman,et al. Independent filtering increases detection power for high-throughput experiments , 2010, Proceedings of the National Academy of Sciences.
[24] Michael I. Love,et al. Differential analysis of count data – the DESeq2 package , 2013 .
[25] M. Gerstein,et al. RNA-Seq: a revolutionary tool for transcriptomics , 2009, Nature Reviews Genetics.
[26] Charity W. Law,et al. voom: precision weights unlock linear model analysis tools for RNA-seq read counts , 2014, Genome Biology.
[27] U. Alon. An introduction to systems biology : design principles of biological circuits , 2019 .
[28] Matthew E. Ritchie,et al. limma powers differential expression analyses for RNA-sequencing and microarray studies , 2015, Nucleic acids research.
[29] Viktor Mayer-Schnberger,et al. Big Data: A Revolution That Will Transform How We Live, Work, and Think , 2013 .
[30] C. Sim,et al. Transcript Assembly and Quantification by RNA-Seq Reveals Significant Differences in Gene Expression and Genetic Variants in Mosquitoes of the Culex pipiens (Diptera: Culicidae) Complex , 2020, Journal of Medical Entomology.
[31] Lior Pachter,et al. Sequence Analysis , 2020, Definitions.
[32] E. Lundberg,et al. Towards a knowledge-based Human Protein Atlas , 2010, Nature Biotechnology.
[33] Paul Theodor Pyl,et al. HTSeq—a Python framework to work with high-throughput sequencing data , 2014, bioRxiv.
[34] Olha Buchel,et al. Big Data: A Revolution That Will Transform How We Live, Work, and Think , 2015 .
[35] Tsippi Iny Stein,et al. In-silico human genomics with GeneCards , 2011, Human Genomics.