TY - JOUR AU - Reinartz, J. AU - Bruyns, E. AU - Lin, J. Z. AU - Burcham, T. AU - Brenner, S. AU - Bowen, B. AU - Kramer, M. AU - Woychik, R. PY - 2002 DA - 2002// TI - Massively parallel signature sequencing (MPSS) as a tool for in-depth quantitative gene expression profiling in all organisms JO - Brief Funct Genomic Proteomic VL - 1 UR - https://doi.org/10.1093/bfgp/1.1.95 DO - 10.1093/bfgp/1.1.95 ID - Reinartz2002 ER - TY - JOUR AU - Saha, S. AU - Sparks, A. B. AU - Rago, C. AU - Akmaev, V. AU - Wang, C. J. AU - Vogelstein, B. AU - Kinzler, K. W. AU - Velculescu, V. E. PY - 2002 DA - 2002// TI - Using the transcriptome to annotate the genome JO - Nat Biotechnol VL - 20 UR - https://doi.org/10.1038/nbt0502-508 DO - 10.1038/nbt0502-508 ID - Saha2002 ER - TY - JOUR AU - Velculescu, V. E. AU - Zhang, L. AU - Vogelstein, B. AU - Kinzler, K. W. PY - 1995 DA - 1995// TI - Serial analysis of gene expression JO - Science VL - 270 UR - https://doi.org/10.1126/science.270.5235.484 DO - 10.1126/science.270.5235.484 ID - Velculescu1995 ER - TY - JOUR AU - Adams, M. D. AU - Kelley, J. M. AU - Gocayne, J. D. AU - Dubnick, M. AU - Polymeropoulos, M. H. AU - Xiao, H. AU - Merril, C. R. AU - Wu, A. AU - Olde, B. AU - Moreno, R. F. PY - 1991 DA - 1991// TI - Complementary DNA sequencing: expressed sequence tags and human genome project JO - Science VL - 252 UR - https://doi.org/10.1126/science.2047873 DO - 10.1126/science.2047873 ID - Adams1991 ER - TY - JOUR AU - Wang, Z. AU - Gerstein, M. AU - Snyder, M. PY - 2009 DA - 2009// TI - RNA-Seq: a revolutionary tool for transcriptomics JO - Nat Rev Genet VL - 10 UR - https://doi.org/10.1038/nrg2484 DO - 10.1038/nrg2484 ID - Wang2009 ER - TY - JOUR AU - Shendure, J. PY - 2008 DA - 2008// TI - The beginning of the end for microarrays? JO - Nat Methods VL - 5 UR - https://doi.org/10.1038/nmeth0708-585 DO - 10.1038/nmeth0708-585 ID - Shendure2008 ER - TY - JOUR AU - Marioni, J. C. AU - Mason, C. E. AU - Mane, S. M. AU - Stephens, M. AU - Gilad, Y. PY - 2008 DA - 2008// TI - RNA-seq: an assessment of technical reproducibility and comparison with gene expression arrays JO - Genome Res VL - 18 UR - https://doi.org/10.1101/gr.079558.108 DO - 10.1101/gr.079558.108 ID - Marioni2008 ER - TY - JOUR AU - t Hoen, P. A. C. AU - Ariyurek, Y. AU - Thygesen, H. H. AU - Vreugdenhil, E. AU - Vossen, R. H. A. M. AU - de Menezes, R. X. AU - Boer, J. M. AU - van Ommen, G. J. B. AU - den Dunnen, J. T. PY - 2008 DA - 2008// TI - Deep sequencing-based expression analysis shows major advances in robustness, resolution and inter-lab portability over five microarray platforms JO - Nucleic Acids Res VL - 36 UR - https://doi.org/10.1093/nar/gkn705 DO - 10.1093/nar/gkn705 ID - t Hoen2008 ER - TY - JOUR AU - Oshlack, A. AU - Wakefield, M. J. PY - 2009 DA - 2009// TI - Transcript length bias in RNA-seq data confounds systems biology JO - Biol Direct VL - 4 UR - https://doi.org/10.1186/1745-6150-4-14 DO - 10.1186/1745-6150-4-14 ID - Oshlack2009 ER - TY - JOUR AU - Mortazavi, A. AU - Williams, B. A. AU - McCue, K. AU - Schaeffer, L. AU - Wold, B. PY - 2008 DA - 2008// TI - Mapping and quantifying mammalian transcriptomes by RNA-Seq JO - Nat Methods VL - 5 UR - https://doi.org/10.1038/nmeth.1226 DO - 10.1038/nmeth.1226 ID - Mortazavi2008 ER - TY - JOUR AU - Trapnell, C. AU - Williams, B. A. AU - Pertea, G. AU - Mortazavi, A. AU - Kwan, G. AU - van Baren, M. J. AU - Salzberg, S. L. AU - Wold, B. J. AU - Pachter, L. PY - 2010 DA - 2010// TI - Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation JO - Nat Biotechnol VL - 28 UR - https://doi.org/10.1038/nbt.1621 DO - 10.1038/nbt.1621 ID - Trapnell2010 ER - TY - JOUR AU - Gao, L. AU - Fang, Z. AU - Zhang, K. AU - Zhi, D. AU - Cui, X. PY - 2010 DA - 2010// TI - Length bias correction for RNA-seq data in gene set analyses JO - Bioinformatics VL - 27 UR - https://doi.org/10.1093/bioinformatics/btr005 DO - 10.1093/bioinformatics/btr005 ID - Gao2010 ER - TY - JOUR AU - Li, B. AU - Ruotti, V. AU - Stewart, R. M. AU - Thomson, J. A. AU - Dewey, C. N. PY - 2010 DA - 2010// TI - RNA-Seq gene expression estimation with read mapping uncertainty JO - Bioinformatics VL - 26 UR - https://doi.org/10.1093/bioinformatics/btp692 DO - 10.1093/bioinformatics/btp692 ID - Li2010 ER - TY - JOUR AU - Hansen, K. D. AU - Brenner, S. E. AU - Dudoit, S. PY - 2010 DA - 2010// TI - Biases in Illumina transcriptome sequencing caused by random hexamer priming JO - Nucleic Acids Res VL - 38 UR - https://doi.org/10.1093/nar/gkq224 DO - 10.1093/nar/gkq224 ID - Hansen2010 ER - TY - JOUR AU - Li, J. AU - Jiang, H. AU - Wong, W. H. PY - 2010 DA - 2010// TI - Modeling non-uniformity in short-read rates in RNA-Seq data JO - Genome Biol VL - 11 UR - https://doi.org/10.1186/gb-2010-11-5-r50 DO - 10.1186/gb-2010-11-5-r50 ID - Li2010 ER - TY - JOUR PY - 2001 DA - 2001// TI - Initial sequencing and analysis of the human genome JO - Nature VL - 409 UR - https://doi.org/10.1038/35057062 DO - 10.1038/35057062 ID - ref16 ER - TY - JOUR AU - Kong, A. AU - Gudbjartsson, D. F. AU - Sainz, J. AU - Jonsdottir, G. M. AU - Gudjonsson, S. A. AU - Richardsson, B. AU - Sigurdardottir, S. AU - Barnard, J. AU - Hallbeck, B. AU - Masson, G. PY - 2002 DA - 2002// TI - A high-resolution recombination map of the human genome JO - Nat Genet VL - 31 ID - Kong2002 ER - TY - JOUR AU - Jabbari, K. AU - Bernardi, G. PY - 1998 DA - 1998// TI - CpG doublets, CpG islands and Alu repeats in long human DNA sequences from different isochore families JO - Gene VL - 224 UR - https://doi.org/10.1016/S0378-1119(98)00474-0 DO - 10.1016/S0378-1119(98)00474-0 ID - Jabbari1998 ER - TY - JOUR AU - Sémon, M. AU - Mouchiroud, D. AU - Duret, L. PY - 2005 DA - 2005// TI - Relationship between gene expression and GC-content in mammals: statistical significance and biological relevance JO - Hum Mol Genet VL - 14 UR - https://doi.org/10.1093/hmg/ddi038 DO - 10.1093/hmg/ddi038 ID - Sémon2005 ER - TY - JOUR AU - Dunning, M. J. AU - Barbosa-Morais, N. L. AU - Lynch, A. G. AU - Tavaré, S. AU - Ritchie, M. E. PY - 2008 DA - 2008// TI - Statistical issues in the analysis of Illumina data JO - BMC Bioinformatics VL - 9 UR - https://doi.org/10.1186/1471-2105-9-85 DO - 10.1186/1471-2105-9-85 ID - Dunning2008 ER - TY - JOUR AU - Dohm, J. C. AU - Lottaz, C. AU - Borodina, T. AU - Himmelbauer, H. PY - 2008 DA - 2008// TI - Substantial biases in ultra-short read data sets from high-throughput DNA sequencing JO - Nucleic Acids Res VL - 36 UR - https://doi.org/10.1093/nar/gkn425 DO - 10.1093/nar/gkn425 ID - Dohm2008 ER - TY - JOUR AU - Bullard, J. H. AU - Purdom, E. AU - Hansen, K. D. AU - Dudoit, S. PY - 2010 DA - 2010// TI - Evaluation of statistical methods for normalization and differential expression in mRNA-Seq experiments JO - BMC Bioinformatics VL - 11 UR - https://doi.org/10.1186/1471-2105-11-94 DO - 10.1186/1471-2105-11-94 ID - Bullard2010 ER - TY - JOUR AU - Canales, R. D. AU - Luo, Y. AU - Willey, J. C. AU - Austermiller, B. AU - Barbacioru, C. C. AU - Boysen, C. AU - Hunkapiller, K. AU - Jensen, R. V. AU - Knight, C. R. AU - Lee, K. Y. PY - 2006 DA - 2006// TI - Evaluation of DNA microarray results with quantitative gene expression platforms JO - Nat Biotechnol VL - 24 UR - https://doi.org/10.1038/nbt1236 DO - 10.1038/nbt1236 ID - Canales2006 ER - TY - JOUR AU - Robinson, M. D. AU - Oshlack, A. PY - 2010 DA - 2010// TI - A scaling normalization method for differential expression analysis of RNA-seq data JO - Genome Biol VL - 11 UR - https://doi.org/10.1186/gb-2010-11-3-r25 DO - 10.1186/gb-2010-11-3-r25 ID - Robinson2010 ER - TY - JOUR AU - Lee, A. AU - Hansen, K. D. AU - Bullard, J. AU - Dudoit, S. AU - Sherlock, G. PY - 2008 DA - 2008// TI - Novel low abundance and transient RNAs in yeast revealed by tiling microarrays and ultra high-throughput sequencing are not conserved across closely related yeast species JO - PLoS Genet VL - 4 UR - https://doi.org/10.1371/journal.pgen.1000299 DO - 10.1371/journal.pgen.1000299 ID - Lee2008 ER - TY - JOUR AU - Nagalakshmi, U. AU - Wang, Z. AU - Waern, K. AU - Shou, C. AU - Raha, D. AU - Gerstein, M. AU - Snyder, M. PY - 2008 DA - 2008// TI - The transcriptional landscape of the yeast genome defined by RNA sequencing JO - Science VL - 320 UR - https://doi.org/10.1126/science.1158441 DO - 10.1126/science.1158441 ID - Nagalakshmi2008 ER - TY - JOUR AU - Mamanova, L. AU - Andrews, R. M. AU - James, K. D. AU - Sheridan, E. M. AU - Ellis, P. D. AU - Langford, C. F. AU - Ost, T. W. B. AU - Collins, J. E. AU - Turner, D. J. PY - 2010 DA - 2010// TI - FRT-seq: amplification-free, strand-specific transcriptome sequencing JO - Nat Methods VL - 7 UR - https://doi.org/10.1038/nmeth.1417 DO - 10.1038/nmeth.1417 ID - Mamanova2010 ER - TY - JOUR AU - Trapnell, C. AU - Pachter, L. AU - Salzberg, S. L. PY - 2009 DA - 2009// TI - TopHat: discovering splice junctions with RNA-Seq JO - Bioinformatics VL - 25 UR - https://doi.org/10.1093/bioinformatics/btp120 DO - 10.1093/bioinformatics/btp120 ID - Trapnell2009 ER - TY - JOUR AU - Jiang, H. AU - Wong, W. H. PY - 2009 DA - 2009// TI - Statistical inferences for isoform expression in RNA-Seq JO - Bioinformatics VL - 25 UR - https://doi.org/10.1093/bioinformatics/btp113 DO - 10.1093/bioinformatics/btp113 ID - Jiang2009 ER - TY - JOUR AU - Gabriel, K. R. PY - 1971 DA - 1971// TI - Biplot Graphic Display of Matrices with Application to Principal Component Analysis JO - Biometrika VL - 58 UR - https://doi.org/10.1093/biomet/58.3.453 DO - 10.1093/biomet/58.3.453 ID - Gabriel1971 ER - TY - JOUR AU - Roberts, A. AU - Trapnell, C. AU - Donaghey, J. AU - Rinn, J. L. AU - Pachter, L. PY - 2010 DA - 2010// TI - Improving RNA-Seq expression estimates by correcting for fragment bias JO - Genome Biol VL - 12 UR - https://doi.org/10.1186/gb-2011-12-3-r22 DO - 10.1186/gb-2011-12-3-r22 ID - Roberts2010 ER - TY - JOUR AU - Pickrell, J. K. AU - Marioni, J. C. AU - Pai, A. A. AU - Degner, J. F. AU - Engelhardt, B. E. AU - Nkadori, E. AU - Veyrieras, J. B. AU - Stephens, M. AU - Gilad, Y. AU - Pritchard, J. K. PY - 2010 DA - 2010// TI - Understanding mechanisms underlying human gene expression variation with RNA sequencing JO - Nature VL - 464 UR - https://doi.org/10.1038/nature08872 DO - 10.1038/nature08872 ID - Pickrell2010 ER - TY - CHAP AU - Lassmann, T. AU - Hayashizaki, Y. AU - Daub, C. O. PY - 2010 DA - 2010// TI - SAMStat: monitoring biases in next generation sequencing data BT - Bioinformatics ID - Lassmann2010 ER - TY - JOUR AU - Frith, M. C. AU - Valen, E. AU - Krogh, A. AU - Hayashizaki, Y. AU - Carninci, P. AU - Sandelin, A. PY - 2008 DA - 2008// TI - A code for transcription initiation in mammalian genomes JO - Genome Res VL - 18 UR - https://doi.org/10.1101/gr.6831208 DO - 10.1101/gr.6831208 ID - Frith2008 ER -