ngs references

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[Wang2008diploid] Jun Wang, Wei Wang, Ruiqiang Li, Yingrui Li, Geng Tian, Laurie Goodman, Wei Fan, Junqing Zhang, Jun Li, Juanbin Zhang, Yiran Guo, Binxiao Feng, Heng Li, Yao Lu, Xiaodong Fang, Huiqing Liang, Zhenglin Du, Dong Li, Yiqing Zhao, Yujie Hu, Zhenzhen Yang, Hancheng Zheng, Ines Hellmann, Michael Inouye, John Pool, Xin Yi, Jing Zhao, Jinjie Duan, Yan Zhou, Junjie Qin, Lijia Ma, Guoqing Li, Zhentao Yang, Guojie Zhang, Bin Yang, Chang Yu, Fang Liang, Wenjie Li, Shaochuan Li, Dawei Li, Peixiang Ni, Jue Ruan, Qibin Li, Hongmei Zhu, Dongyuan Liu, Zhike Lu, Ning Li, Guangwu Guo, J. Zhang, J. Ye, L. Fang, Q. Hao, Q. Chen, Y. Liang, Y. Su, A. San, C. Ping, S. Yang, F. Chen, L. Li, K. Zhou, H. Zheng, Y. Ren, L. Yang, Y. Gao, G. Yang, Z. Li, X. Feng, K. Kristiansen, G. K.-S. Wong, R. Nielsen, R. Durbin, L. Bolund, X. Zhang, S. Li, H. Yang, and J. Wang. The diploid genome sequence of an Asian individual. Nature, 456(7218):60-65, Nov 2008. [ bib | DOI | http | Abstract ]
[Morin2008Application] Ryan D Morin, Michael D O'Connor, Malachi Griffith, Florian Kuchenbauer, Allen Delaney, Anna-Liisa Prabhu, Yongjun Zhao, Helen McDonald, Thomas Zeng, Martin Hirst, Connie J Eaves, and Marco A Marra. Application of massively parallel sequencing to microrna profiling and discovery in human embryonic stem cells. Genome Res, 18(4):610-621, Apr 2008. [ bib | DOI | http | .pdf | Abstract ]
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[Chen2008Mapping] Wei Chen, Vera Kalscheuer, Andreas Tzschach, Corinna Menzel, Reinhard Ullmann, Marcel Holger Schulz, Fikret Erdogan, Na Li, Zofia Kijas, Ger Arkesteijn, Isidora Lopez Pajares, Margret Goetz-Sothmann, Uwe Heinrich, Imma Rost, Andreas Dufke, Ute Grasshoff, Birgitta Glaeser, Martin Vingron, and H. Hilger Ropers. Mapping translocation breakpoints by next-generation sequencing. Genome Res., 18(7):1143-1149, Jul 2008. [ bib | DOI | http | .pdf | Abstract ]
[Campbell2008Identification] Peter J Campbell, Philip J Stephens, Erin D Pleasance, Sarah O'Meara, Heng Li, Thomas Santarius, Lucy A Stebbings, Catherine Leroy, Sarah Edkins, Claire Hardy, Jon W Teague, Andrew Menzies, Ian Goodhead, Daniel J Turner, Christopher M Clee, Michael A Quail, Antony Cox, Clive Brown, Richard Durbin, Matthew E Hurles, Paul A W Edwards, Graham R Bignell, Michael R Stratton, and P. Andrew Futreal. Identification of somatically acquired rearrangements in cancer using genome-wide massively parallel paired-end sequencing. Nat. Genet., 40(6):722-729, Jun 2008. [ bib | DOI | http | .pdf | Abstract ]
[Bashir2008Evaluation] Ali Bashir, Stanislav Volik, Colin Collins, Vineet Bafna, and Benjamin J Raphael. Evaluation of paired-end sequencing strategies for detection of genome rearrangements in cancer. PLoS Comput. Biol., 4(4):e1000051, Apr 2008. [ bib | DOI | http | .pdf | Abstract ]
[Yoon2009Sensitive] Seungtai Yoon, Zhenyu Xuan, Vladimir Makarov, Kenny Ye, and Jonathan Sebat. Sensitive and accurate detection of copy number variants using read depth of coverage. Genome Res., 19(9):1586-1592, Sep 2009. [ bib | DOI | http | .pdf | Abstract ]
[Xie2009CNV-seq] Chao Xie and Martti T Tammi. Cnv-seq, a new method to detect copy number variation using high-throughput sequencing. BMC Bioinformatics, 10:80, 2009. [ bib | DOI | http | .pdf | Abstract ]
[Wang2009RNA] Z. Wang, M. Gerstein, and M. Snyder. RNA-Seq: a revolutionary tool for transcriptomics. Nat. Rev. Genet., 10(1):57-63, Jan 2009. [ bib | DOI | http | .pdf | Abstract ]
[Tuteja2009Extracting] Geetu Tuteja, Peter White, Jonathan Schug, and Klaus H Kaestner. Extracting transcription factor targets from chip-seq data. Nucleic Acids Res, 37(17):e113, Sep 2009. [ bib | DOI | http | .pdf | Abstract ]
[Spyrou2009BayesPeak] Christiana Spyrou, Rory Stark, Andy G Lynch, and Simon Tavaré. Bayespeak: Bayesian analysis of chip-seq data. BMC Bioinformatics, 10:299, 2009. [ bib | DOI | http | .pdf | Abstract ]
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[Praz2009CleanEx:] Viviane Praz and Philipp Bucher. Cleanex: new data extraction and merging tools based on mesh term annotation. Nucleic Acids Res, 37(Database issue):D880-D884, Jan 2009. [ bib | DOI | http | Abstract ]
[McKernan2009Sequence] Kevin Judd McKernan, Heather E Peckham, Gina L Costa, Stephen F McLaughlin, Yutao Fu, Eric F Tsung, Christopher R Clouser, Cisyla Duncan, Jeffrey K Ichikawa, Clarence C Lee, Zheng Zhang, Swati S Ranade, Eileen T Dimalanta, Fiona C Hyland, Tanya D Sokolsky, Lei Zhang, Andrew Sheridan, Haoning Fu, Cynthia L Hendrickson, Bin Li, Lev Kotler, Jeremy R Stuart, Joel A Malek, Jonathan M Manning, Alena A Antipova, Damon S Perez, Michael P Moore, Kathleen C Hayashibara, Michael R Lyons, Robert E Beaudoin, Brittany E Coleman, Michael W Laptewicz, Adam E Sannicandro, Michael D Rhodes, Rajesh K Gottimukkala, Shan Yang, Vineet Bafna, Ali Bashir, Andrew MacBride, Can Alkan, Jeffrey M Kidd, Evan E Eichler, Martin G Reese, Francisco M De La Vega, and Alan P Blanchard. Sequence and structural variation in a human genome uncovered by short-read, massively parallel ligation sequencing using two-base encoding. Genome Res., 19(9):1527-1541, Sep 2009. [ bib | DOI | http | .pdf | Abstract ]
[Lieberman-Aiden2009Comprehensive] Erez Lieberman-Aiden, Nynke L van Berkum, Louise Williams, Maxim Imakaev, Tobias Ragoczy, Agnes Telling, Ido Amit, Bryan R Lajoie, Peter J Sabo, Michael O Dorschner, Richard Sandstrom, Bradley Bernstein, M. A. Bender, Mark Groudine, Andreas Gnirke, John Stamatoyannopoulos, Leonid A Mirny, Eric S Lander, and Job Dekker. Comprehensive mapping of long-range interactions reveals folding principles of the human genome. Science, 326(5950):289-293, Oct 2009. [ bib | DOI | http | .pdf | Abstract ]
[Li2009SNP] R. Li, Y. Li, X. Fang, H. Yang, J. Wang, K. Kristiansen, and J. Wang. SNP detection for massively parallel whole-genome resequencing. Genome Res., 19(6):1124-1132, Jun 2009. [ bib | DOI | http | .pdf | Abstract ]
[Langmead2009Ultrafast] B. Langmead, C. Trapnell, M. Pop, and S. L. Salzberg. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol, 10(3):R25, 2009. [ bib | DOI | http | .pdf | Abstract ]
[Korbel2009PEMer] J. Korbel, A. Abyzov, X. Mu, N. Carriero, P. Cayting, Z. Zhang, Z. Snyder, and M. Gerstein. PEMer: a computational framework with simulation-based error models for inferring genomic structural variants from massive paired-end sequencing data. Genome Biol., 10(2):R23, Feb 2009. [ bib | DOI | http | .pdf | Abstract ]
[Jiang2009Statistical] H. Jiang and W. H. Wong. Statistical inferences for isoform expression in RNA-Seq. Bioinformatics, 25(8):1026-1032, Apr 2009. [ bib | DOI | http | .pdf | Abstract ]
[Horner2009Bioinformatics] D. S. Horner, G. Pavesi, T. Castrignanò, P. D. De Meo, S. Liuni, M. Sammeth, E. Picardi, and G. Pesole. Bioinformatics approaches for genomics and post genomics applications of next-generation sequencing. Brief Bioinform, Oct 2009. [ bib | DOI | http | .pdf | Abstract ]
[Hormozdiari2009Combinatorial] Fereydoun Hormozdiari, Can Alkan, Evan E Eichler, and S. Cenk Sahinalp. Combinatorial algorithms for structural variation detection in high-throughput sequenced genomes. Genome Res., 19(7):1270-1278, Jul 2009. [ bib | DOI | http | .pdf | Abstract ]
[Harismendy2009Evaluation] O. Harismendy, P. C. Ng, R. L. Strausberg, X. Wang, T. B. Stockwell, K. Y. Beeson, N. J. Schork, S. S. Murray, E. J. Topol, S. Levy, and K. A. Frazer. Evaluation of next generation sequencing platforms for population targeted sequencing studies. Genome Biol., 10(3):R32, 2009. [ bib | DOI | http | .pdf | Abstract ]
[Girirajan2009Sequencing] Santhosh Girirajan, Lin Chen, Tina Graves, Tomas Marques-Bonet, Mario Ventura, Catrina Fronick, Lucinda Fulton, Mariano Rocchi, Robert S Fulton, Richard K Wilson, Elaine R Mardis, and Evan E Eichler. Sequencing human-gibbon breakpoints of synteny reveals mosaic new insertions at rearrangement sites. Genome Res., 19(2):178-190, Feb 2009. [ bib | DOI | http | .pdf | Abstract ]
[Chiang2009High-resolution] Derek Y Chiang, Gad Getz, David B Jaffe, Michael J T O'Kelly, Xiaojun Zhao, Scott L Carter, Carsten Russ, Chad Nusbaum, Matthew Meyerson, and Eric S Lander. High-resolution mapping of copy-number alterations with massively parallel sequencing. Nat. Methods, 6(1):99-103, Jan 2009. [ bib | DOI | http | .pdf | Abstract ]
[Bohnert2009Transcript] R. Bohnert, J. Behr, and G. Rätsch. Transcript quantification with RNA-Seq data. BMC Bioinformatics, 10 (Suppl 13):P5, 2009. [ bib | DOI | http | .pdf ]
[Alkan2009Personalized] Can Alkan, Jeffrey M Kidd, Tomas Marques-Bonet, Gozde Aksay, Francesca Antonacci, Fereydoun Hormozdiari, Jacob O Kitzman, Carl Baker, Maika Malig, Onur Mutlu, S. Cenk Sahinalp, Richard A Gibbs, and Evan E Eichler. Personalized copy number and segmental duplication maps using next-generation sequencing. Nat. Genet., 41(10):1061-1067, Oct 2009. [ bib | DOI | http | .pdf | Abstract ]
[Trapnell2009TopHat] C. Trapnell, L. Pachter, and S. L. Salzberg. TopHat: discovering splice junctions with RNA-Seq. Bioinformatics, 25(9):1105-1111, May 2009. [ bib | DOI | http | .pdf | Abstract ]
[Metzker2010Sequencing] M. L. Metzker. Sequencing technologies - the next generation. Nat. Rev. Genet., 11(1):31-46, Jan 2010. [ bib | DOI | http | Abstract ]
[Berkum2010HiC] N. L. van Berkum, E. Lieberman-Aiden, L. Williams, M. Imakaev, A. Gnirke, L. A. Mirny, J. Dekker, and E. S. Lander. Hi-C: a method to study the three-dimensional architecture of genomes. J. Vis. Exp., 39:e1869, 2010. [ bib | DOI | http | Abstract ]
[Trapnell2010Transcript] C. Trapnell, B. A. Williams, G. Pertea, A. Mortazavi, G. Kwan, M. J. van Baren, S. L. Salzberg, B. J. Wold, and L. Pachter. Transcript assembly and quantification by rna-seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat Biotechnol, 28(5):511-515, May 2010. [ bib | DOI | http | .pdf | Abstract ]
[Yaffe2011Probabilistic] E. Yaffe and A. Tanay. Probabilistic modeling of Hi-C contact maps eliminates systematic biases to characterize global chromosomal architecture. Nat. Genet., 43(11):1059-1065, 2011. [ bib | DOI | http | .pdf | Abstract ]
[Roberts2011Improving] A. Roberts, C. Trapnell, J. Donaghey, J. L. Rinn, and L. Pachter. Improving RNA-Seq expression estimates by correcting for fragment bias. Genome Biol, 12(3):R22, 2011. [ bib | DOI | http | .pdf | Abstract ]
[Roberts2011Identification] A. Roberts, H. Pimentel, C. Trapnell, and L. Pachter. Identification of novel transcripts in annotated genomes using RNA-Seq. Bioinformatics, 27(17):2325-2329, Sep 2011. [ bib | DOI | http | .pdf | Abstract ]
[Nielsen2011Genotype] R. Nielsen, J. S. Paul, A. Albrechtsen, and Y. S. Song. Genotype and SNP calling from next-generation sequencing data. Nat. Rev. Genet., 12(6):443-451, Jun 2011. [ bib | DOI | http | .pdf | Abstract ]
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[Boeva2011Control-free] V. Boeva, A. Zinovyev, K. Bleakley, J.-P. Vert, I. Janoueix-Lerosey, O. Delattre, and E. Barillot. Control-free calling of copy number alterations in deep-sequencing data using GC-content normalization. Bioinformatics, 27(2):268-269, Jan 2011. [ bib | DOI | http | .pdf | Abstract ]
[Li2011Sparse] J. J. Li, C.-R. Jiang, J. B. Brown, H. Huang, and P. J. Bickel. Sparse linear modeling of next-generation mRNA sequencing (RNA-Seq) data for isoform discovery and abundance estimation. Proc. Natl. Acad. Sci. USA, 108(50):19867-19872, December 2011. [ bib | DOI | http | .pdf | Abstract ]
[Zhang2012Spatial] Y. Zhang, R. A. McCord, Y.-J. Ho, B. R. Lajoie, D. G. Hildebrand, A. C. Simon, M. S. Becker, F. W. Alt, and J. Dekker. Spatial organization of the mouse genome and its role in recurrent chromosomal translocations. Cell, 148(5):908 - 921, 2012. [ bib | DOI | http | .pdf | Abstract ]
[Trapnell2012Differential] C. Trapnell, A. Roberts, L. Goff, G. Pertea, D. Kim, D. R. Kelley, H. Pimentel, S. L. Salzberg, J. L. Rinn, and L. Pachter. Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks. Nat Protoc, 7(3):562-578, Mar 2012. [ bib | DOI | http | .pdf | Abstract ]
[Dixon2012Topological] J. R. Dixon, S. Selvaraj, F. Yue, A. Kim, Y. Li, Y. Shen, M. Hu, J. S. Liu, and B. Ren. Topological domains in mammalian genomes identified by analysis of chromatin interactions. Nature, 485(5):376-80, 2012. [ bib | DOI | http | .pdf ]
[Trapnell2013Differential] C. Trapnell, D. G. Hendrickson, M. Sauvageau, L. Goff, J. L. Rinn, and L. Pachter. Differential analysis of gene regulation at transcript resolution with RNA-seq. Nat Biotechnol, 31(1):46-53, Jan 2013. [ bib | DOI | http | .pdf | Abstract ]
[Mezlini2013iReckon] A. M. Mezlini, E. J. M. Smith, M. Fiume, O. Buske, G. L. Savich, S. Shah, S. Aparicio, D. Y. Chiang, A. Goldenberg, and M. Brudno. iReckon: Simultaneous isoform discovery and abundance estimation from RNA-seq data. Genome Res, 23(3):519-529, Mar 2013. [ bib | DOI | http | .pdf | Abstract ]
[Homouz20133D] D. Homouz and A. S. Kudlicki. The 3D organization of the yeast genome correlates with co-expression and reflects functional relations between genes. PLoS ONE, 8(1):e54699, 01 2013. [ bib | DOI | http | .pdf | Abstract ]
[Ben-Elazar2013Spatial] S. Ben-Elazar, Z. Yakhini, and I. Yanai. Spatial localization of co-regulated genes exceeds genomic gene clustering in the saccharomyces cerevisiae genome. Nucleic Acids Res, 41(4):2191-2201, Feb 2013. [ bib | DOI | http | .pdf | Abstract ]

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