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Introduction
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Lander et al.Initial sequencing and analysis of the human genomehttp://www.nature.com/nature/journal/v409/n6822/full/409860a0.html2001Nature9.12
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Technologies
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MetzkerSequencing technologies — the next generationhttp://www.nature.com/nrg/journal/v11/n1/full/nrg2626.html2010NRG9.19
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Rothberg et alAn integrated semiconductor device enabling non-optical genome sequencinghttp://www.nature.com/nature/journal/v475/n7356/full/nature10242.html2011Nature9.19
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Applications
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Kahvejian et al.Review of expected applicationshttp://www.nature.com/nbt/journal/v26/n10/full/nbt1494.html2008NBT9.26*
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Hawkins et al.Next-generation genomics: an integrative approachhttp://www.nature.com/nrg/journal/v11/n7/full/nrg2795.html2010NRG9.26*
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Cancer
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Mardis & Wilsoncancer genome sequencinghttp://hmg.oxfordjournals.org/content/18/R2/R163.long2009HMG10.3
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Ding et al.Analysis of next-generation genomic data in cancer: accomplishments and challengeshttp://hmg.oxfordjournals.org/content/19/R2/R188.full2010HMG10.3
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Chin et al.Making sense of cancer genomic datahttp://genesdev.cshlp.org/content/25/6/534.long2011G&D10.10.
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RNA-seq
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Pepke et al.computation for ChIP-seq + RNA-seqhttp://www.nature.com/nmeth/journal/v6/n11s/full/nmeth.1371.html2009NMeth10.10.
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Trapnell et al.TopHat: discovering splice junctions with RNA-Seqhttp://bioinformatics.oxfordjournals.org/content/25/9/1105.full2009Bioinf10.17
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Haas & ZodyAdvancing RNA-Seq analysishttp://www.nature.com/nbt/journal/v28/n5/full/nbt0510-421.html2010NBT10.17
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Trapnell et alTranscript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiationhttp://www.nature.com/nbt/journal/v28/n5/full/nbt.1621.html2010NBT10.24
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Guttman et al.Ab initio reconstruction of cell type–specific transcriptomes in mouse reveals the conserved multi-exonic structure of lincRNAshttp://www.nature.com/nbt/journal/v28/n5/full/nbt.1633.html2010NBT10.24
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ChIP-seq
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ParkChIP–seq: advantages and challenges of a maturing technologyhttp://www.nature.com/nrg/journal/v10/n10/full/nrg2641.html2009NRG10.31
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Qin et al.HPeak: an HMM-based algorithm for defining read-enriched regions in ChIP-Seq datahttp://www.biomedcentral.com/1471-2105/11/3692010BMC Bioinf10.31
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FAIRE-seq
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Song et al.Open chromatin defined by DNaseI and FAIRE identifies regulatory elements that shape cell-type identityhttp://genome.cshlp.org/content/early/2011/08/19/gr.121541.111.long2011GR11.14*
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Genomic sequencing
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Koboldt et alChallenges of sequencing human genomeshttp://bib.oxfordjournals.org/content/11/5/484.full2010BIB11.14*
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Li et alDe novo assembly of human genomes with massively parallel short read sequencinghttp://genome.cshlp.org/content/20/2/265.full2010GR11.21
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Asimit & ZegginiRare Variant Association Analysis Methods for Complex Traitshttp://www.annualreviews.org/doi/full/10.1146/annurev-genet-102209-1634212010ARG11.21
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Gerber et alComputational methods for transcriptome annotation and quantification using RNA-seqhttp://www.nature.com/nmeth/journal/v8/n6/full/nmeth.1613.html2011NMeth11.28
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Ajay et al. Accurate and comprehensive sequencing of personal genomeshttp://genome.cshlp.org/content/21/9/1498.full2011GR11.28
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Reserved for new papers12.5
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ELSI
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McGowan et al.Personal genomics and individual identities: motivations and moral imperatives of early usershttp://www.tandfonline.com/doi/full/10.1080/14636778.2010.5074852010Gen Med12.12
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Ransohoff & KhouryPersonal genomics: information can be harmfulhttp://onlinelibrary.wiley.com/doi/10.1111/j.1365-2362.2009.02232.x/full2010EJ Clin. Inv.12.12
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