TY - JOUR AU - Metzker, M. L. PY - 2010 DA - 2010// TI - Sequencing technologies - the next generation. JO - Nat Rev Genet VL - 11 UR - https://doi.org/10.1038/nrg2626 DO - 10.1038/nrg2626 ID - Metzker2010 ER - TY - JOUR AU - Pepke, S. AU - Wold, B. AU - Mortazavi, A. PY - 2009 DA - 2009// TI - Computation for ChIP-seq and RNA-seq studies. JO - Nat Methods VL - 6 UR - https://doi.org/10.1038/nmeth.1371 DO - 10.1038/nmeth.1371 ID - Pepke2009 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 - 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 - Birol, I. AU - Jackman, S. D. AU - Nielsen, C. B. AU - Qian, J. Q. AU - Varhol, R. AU - Stazyk, G. AU - Morin, R. D. AU - Zhao, Y. AU - Hirst, M. AU - Schein, J. E. AU - Horsman, D. E. AU - Connors, J. M. AU - Gascoyne, R. D. AU - Marra, M. A. AU - Jones, S. J. PY - 2009 DA - 2009// TI - De novotranscriptome assembly with ABySS. JO - Bioinformatics VL - 25 UR - https://doi.org/10.1093/bioinformatics/btp367 DO - 10.1093/bioinformatics/btp367 ID - Birol2009 ER - TY - JOUR AU - Guttman, M. AU - Garber, M. AU - Levin, J. Z. AU - Donaghey, J. AU - Robinson, J. AU - Adiconis, X. AU - Fan, L. AU - Koziol, M. J. AU - Gnirke, A. AU - Nusbaum, C. AU - Rinn, J. L. AU - Lander, E. S. AU - Regev, A. PY - 2010 DA - 2010// TI - Ab initioreconstruction of cell type-specific transcriptomes in mouse reveals the conserved multi-exonic structure of lincRNAs. JO - Nat Biotechnol VL - 28 UR - https://doi.org/10.1038/nbt.1633 DO - 10.1038/nbt.1633 ID - Guttman2010 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 - 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 - 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 - STD TI - Illumina Announces HiSeq(TM) 2000 Sequencing System. [http://investor.illumina.com/phoenix.zhtml?c=121127&p=irol-newsArticle&ID=1374339] UR - http://investor.illumina.com/phoenix.zhtml?c=121127&p=irol-newsArticle&ID=1374339 ID - ref10 ER - TY - STD TI - Illumina Presents Development Roadmap for Scaling its Genome Analyzer. [http://investor.illumina.com/phoenix.zhtml?c=121127&p=irol-newsArticle&ID=1252407] UR - http://investor.illumina.com/phoenix.zhtml?c=121127&p=irol-newsArticle&ID=1252407 ID - ref11 ER - TY - JOUR AU - Pushkarev, D. AU - Neff, N. F. AU - Quake, S. R. PY - 2009 DA - 2009// TI - Single-molecule sequencing of an individual human genome. JO - Nat Biotechnol VL - 27 UR - https://doi.org/10.1038/nbt.1561 DO - 10.1038/nbt.1561 ID - Pushkarev2009 ER - TY - JOUR AU - Stein, L. D. PY - 2010 DA - 2010// TI - The case for cloud computing in genome informatics. JO - Genome Biol VL - 11 UR - https://doi.org/10.1186/gb-2010-11-5-207 DO - 10.1186/gb-2010-11-5-207 ID - Stein2010 ER - TY - JOUR AU - Baker, M. PY - 2010 DA - 2010// TI - Next-generation sequencing: adjusting to data overload. JO - Nat Methods VL - 7 UR - https://doi.org/10.1038/nmeth0710-495 DO - 10.1038/nmeth0710-495 ID - Baker2010 ER - TY - JOUR AU - Langmead, B. AU - Schatz, M. C. AU - Lin, J. AU - Pop, M. AU - Salzberg, S. L. PY - 2009 DA - 2009// TI - Searching for SNPs with cloud computing. JO - Genome Biol VL - 10 UR - https://doi.org/10.1186/gb-2009-10-11-r134 DO - 10.1186/gb-2009-10-11-r134 ID - Langmead2009 ER - TY - JOUR AU - Schatz, M. AU - Langmead, B. AU - Salzberg, S. L. PY - 2010 DA - 2010// TI - Cloud computing and the DNA data race. JO - Nat Biotechnol VL - 28 UR - https://doi.org/10.1038/nbt0710-691 DO - 10.1038/nbt0710-691 ID - Schatz2010 ER - TY - JOUR AU - Schatz, M. C. PY - 2009 DA - 2009// TI - CloudBurst: highly sensitive read mapping with MapReduce. JO - Bioinformatics VL - 25 UR - https://doi.org/10.1093/bioinformatics/btp236 DO - 10.1093/bioinformatics/btp236 ID - Schatz2009 ER - TY - STD TI - Amazon Elastic Compute Cloud (Amazon EC2). [http://aws.amazon.com/ec2/] UR - http://aws.amazon.com/ec2/ ID - ref18 ER - TY - STD TI - Amazon Elastic MapReduce. [http://aws.amazon.com/elasticmapreduce/] UR - http://aws.amazon.com/elasticmapreduce/ ID - ref19 ER - TY - STD TI - Google and IBM look to the next generation of programmers. [http://www.ibm.com/ibm/ideasfromibm/us/google/index.shtml] UR - http://www.ibm.com/ibm/ideasfromibm/us/google/index.shtml ID - ref20 ER - TY - STD TI - Magellan | Argonne's DOE Cloud Computing. [http://magellan.alcf.anl.gov/] UR - http://magellan.alcf.anl.gov/ ID - ref21 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 - JOUR AU - Frazer, K. A. AU - Ballinger, D. G. AU - Cox, D. R. AU - Hinds, D. A. AU - Stuve, L. L. AU - Gibbs, R. A. AU - Belmont, J. W. AU - Boudreau, A. AU - Hardenbol, P. AU - Leal, S. M. AU - Pasternak, S. AU - Wheeler, D. A. AU - Willis, T. D. AU - Yu, F. AU - Yang, H. AU - Zeng, C. AU - Gao, Y. AU - Hu, H. AU - Hu, W. AU - Li, C. AU - Lin, W. AU - Liu, S. AU - Pan, H. AU - Tang, X. AU - Wang, J. AU - Wang, W. AU - Yu, J. AU - Zhang, B. AU - Zhang, Q. PY - 2007 DA - 2007// TI - A second generation human haplotype map of over 3.1 million SNPs. JO - Nature VL - 449 UR - https://doi.org/10.1038/nature06258 DO - 10.1038/nature06258 ID - Frazer2007 ER - TY - JOUR AU - Langmead, B. AU - Trapnell, C. AU - Pop, M. AU - Salzberg, S. L. PY - 2009 DA - 2009// TI - Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. JO - Genome Biol VL - 10 UR - https://doi.org/10.1186/gb-2009-10-3-r25 DO - 10.1186/gb-2009-10-3-r25 ID - Langmead2009 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 - 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 - 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 - CHAP AU - Anders, S. AU - Huber, W. PY - 2010 DA - 2010// TI - Differential expression analysis for sequence count data. BT - Nat Precedings ID - Anders2010 ER - TY - JOUR AU - Baldi, P. AU - Long, A. D. PY - 2001 DA - 2001// TI - A Bayesian framework for the analysis of microarray expression data: regularized t -test and statistical inferences of gene changes. JO - Bioinformatics VL - 17 UR - https://doi.org/10.1093/bioinformatics/17.6.509 DO - 10.1093/bioinformatics/17.6.509 ID - Baldi2001 ER - TY - JOUR AU - Tusher, V. G. AU - Tibshirani, R. AU - Chu, G. PY - 2001 DA - 2001// TI - Significance analysis of microarrays applied to the ionizing radiation response. JO - Proc Natl Acad Sci USA VL - 98 UR - https://doi.org/10.1073/pnas.091062498 DO - 10.1073/pnas.091062498 ID - Tusher2001 ER - TY - STD TI - Amazon Simple Storage Service (Amazon S3). [http://aws.amazon.com/s3/] UR - http://aws.amazon.com/s3/ ID - ref31 ER - TY - STD TI - Data from Pickrell et al. study. [http://eqtl.uchicago.edu/RNA_Seq_data/unmapped_reads/] UR - http://eqtl.uchicago.edu/RNA_Seq_data/unmapped_reads/ ID - ref32 ER - TY - STD TI - Welcome to Apache Hadoop!. [http://hadoop.apache.org/] UR - http://hadoop.apache.org/ ID - ref33 ER - TY - STD TI - Dean J, Ghemawat S: MapReduce: simplified data processing on large clusters. [http://static.googleusercontent.com/external_content/untrusted_dlcp/labs.google.com/en//papers/mapreduce-osdi04.pdf] UR - http://static.googleusercontent.com/external_content/untrusted_dlcp/labs.google.com/en//papers/mapreduce-osdi04.pdf ID - ref34 ER - TY - JOUR AU - Storey, J. D. AU - Tibshirani, R. PY - 2003 DA - 2003// TI - Statistical significance for genomewide studies. JO - Proc Natl Acad Sci USA VL - 100 UR - https://doi.org/10.1073/pnas.1530509100 DO - 10.1073/pnas.1530509100 ID - Storey2003 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 - STD TI - Myrna. [http://bowtie-bio.sf.net/myrna] UR - http://bowtie-bio.sf.net/myrna ID - ref37 ER -