The effects of death and post-mortem cold ischemia on human tissue transcriptomes

[1]  Nicola J. Rinaldi,et al.  Genetic effects on gene expression across human tissues , 2017, Nature.

[2]  Jeffrey T Leek,et al.  qSVA framework for RNA quality correction in differential expression analysis , 2017, Proceedings of the National Academy of Sciences of the United States of America.

[3]  M. Tress,et al.  Alternative Splicing May Not Be the Key to Proteome Complexity. , 2017, Trends in biochemical sciences.

[4]  D. Tautz,et al.  Tracing the dynamics of gene transcripts after organismal death , 2017, Open Biology.

[5]  B. Searle,et al.  Detecting Sources of Transcriptional Heterogeneity in Large-Scale RNA-Seq Data Sets , 2016, Genetics.

[6]  Francisco Salavert,et al.  High throughput estimation of functional cell activities reveals disease mechanisms and predicts relevant clinical outcomes , 2016, bioRxiv.

[7]  Ying Li,et al.  Measure transcript integrity using RNA-seq data , 2016, BMC Bioinformatics.

[8]  Ellen T. Gelfand,et al.  A Novel Approach to High-Quality Postmortem Tissue Procurement: The GTEx Project , 2015, Biopreservation and biobanking.

[9]  Xuegong Zhang,et al.  mRIN for direct assessment of genome-wide and gene-specific mRNA integrity from large-scale RNA-sequencing data , 2015, Nature Communications.

[10]  Dmitri D. Pervouchine,et al.  The human transcriptome across tissues and individuals , 2015, Science.

[11]  Jun S. Liu,et al.  The Genotype-Tissue Expression (GTEx) pilot analysis: Multitissue gene regulation in humans , 2015, Science.

[12]  Ash A. Alizadeh,et al.  Robust enumeration of cell subsets from tissue expression profiles , 2015, Nature Methods.

[13]  Qing-Yu He,et al.  DOSE: an R/Bioconductor package for disease ontology semantic and enrichment analysis , 2015, Bioinform..

[14]  Y. Gilad,et al.  RNA-seq: impact of RNA degradation on transcript quantification , 2014, BMC Biology.

[15]  Joakim Lundeberg,et al.  Sequencing Degraded RNA Addressed by 3' Tag Counting , 2014, PloS one.

[16]  J. Marchal,et al.  Studies on RNA integrity and gene expression in human myocardial tissue, pericardial fluid and blood, and its postmortem stability. , 2013, Forensic science international.

[17]  J. Harrow,et al.  Transcriptome analysis of human tissues and cell lines reveals one dominant transcript per gene , 2013, Genome Biology.

[18]  F. Carvalho,et al.  Correction: Profiling of RNA Degradation for Estimation of Post Mortem Interval , 2013, PloS one.

[19]  Ellen T. Gelfand,et al.  The Genotype-Tissue Expression (GTEx) project , 2013, Nature Genetics.

[20]  Manuela Gariboldi,et al.  Effects of Warm Ischemic Time on Gene Expression Profiling in Colorectal Cancer Tissues and Normal Mucosa , 2013, PloS one.

[21]  Roderic Guigó,et al.  Intron-centric estimation of alternative splicing from RNA-seq data , 2012, Bioinform..

[22]  M. Gilbert,et al.  Long-term RNA persistence in postmortem contexts , 2013, Investigative Genetics.

[23]  Bronwen L. Aken,et al.  GENCODE: The reference human genome annotation for The ENCODE Project , 2012, Genome research.

[24]  Guangchuang Yu,et al.  clusterProfiler: an R package for comparing biological themes among gene clusters. , 2012, Omics : a journal of integrative biology.

[25]  Chris Williams,et al.  RNA-SeQC: RNA-seq metrics for quality control and process optimization , 2012, Bioinform..

[26]  Marielle Vennemann,et al.  RNA integrity in post-mortem samples: influencing parameters and implications on RT-qPCR assays , 2011, International Journal of Legal Medicine.

[27]  Douglas G. Walker,et al.  Postmortem interval effect on RNA and gene expression in human brain tissue , 2011, Cell and Tissue Banking.

[28]  V. Pascali,et al.  Analysis of mRNA from human heart tissue and putative applications in forensic molecular pathology. , 2010, Forensic science international.

[29]  M. Vennemann,et al.  mRNA profiling in forensic genetics I: Possibilities and limitations. , 2010, Forensic science international.

[30]  Aaron R. Quinlan,et al.  BIOINFORMATICS APPLICATIONS NOTE , 2022 .

[31]  Mark D. Robinson,et al.  edgeR: a Bioconductor package for differential expression analysis of digital gene expression data , 2009, Bioinform..

[32]  M. Robinson,et al.  A scaling normalization method for differential expression analysis of RNA-seq data , 2010, Genome Biology.

[33]  Lior Pachter,et al.  Sequence Analysis , 2020, Definitions.

[34]  D. Tollervey,et al.  The Many Pathways of RNA Degradation , 2009, Cell.

[35]  Eric T. Wang,et al.  Alternative Isoform Regulation in Human Tissue Transcriptomes , 2008, Nature.

[36]  B. Williams,et al.  Mapping and quantifying mammalian transcriptomes by RNA-Seq , 2008, Nature Methods.

[37]  S. Lutz-Bonengel,et al.  Real-time PCR detection of five different "endogenous control gene" transcripts in forensic autopsy material. , 2007, Forensic science international. Genetics.

[38]  M. Bauer,et al.  RNA in forensic science. , 2007, Forensic science international. Genetics.

[39]  S. Lutz-Bonengel,et al.  Successful RNA extraction from various human postmortem tissues , 2007, International Journal of Legal Medicine.

[40]  Jay A. Siegel,et al.  Forensic Science: The Basics , 2006 .

[41]  Thomas Ragg,et al.  The RIN: an RNA integrity number for assigning integrity values to RNA measurements , 2006, BMC Molecular Biology.

[42]  Jennifer M. Taylor,et al.  A microarray study of post-mortem mRNA degradation in mouse brain tissue. , 2005, Brain research. Molecular brain research.

[43]  Albert Zlotnik,et al.  Effects of RNA degradation on gene expression analysis of human postmortem tissues , 2005, FASEB journal : official publication of the Federation of American Societies for Experimental Biology.

[44]  N. Cairns,et al.  Quantifying mRNA in postmortem human brain: influence of gender, age at death, postmortem interval, brain pH, agonal state and inter-lobe mRNA variance. , 2003, Brain research. Molecular brain research.

[45]  N. Cairns,et al.  An optimistic view for quantifying mRNA in post-mortem human brain. , 2003, Brain research. Molecular brain research.

[46]  M. Magnasco,et al.  Decay rates of human mRNAs: correlation with functional characteristics and sequence attributes. , 2003, Genome research.

[47]  J. Gregg,et al.  Allele-specific Holliday junction formation: a new mechanism of allelic discrimination for SNP scoring. , 2003, Genome research.

[48]  D. Morris,et al.  Postmortem stability of RNA isolated from bovine reproductive tissues. , 2002, Biochimica et biophysica acta.

[49]  Y. Benjamini,et al.  Controlling the false discovery rate: a practical and powerful approach to multiple testing , 1995 .

[50]  M. Stephens EDF Statistics for Goodness of Fit and Some Comparisons , 1974 .

[51]  F. Wilcoxon Individual Comparisons by Ranking Methods , 1945 .