Tag ngs [at least 200 articles] Export

Recent papers classified by the tag ngs.

	High-resolution nucleosome mapping reveals transcription-dependent promoter packaging [My Copy] Genome Research (21 October 2009) by Assaf Weiner, Amanda Hughes, Moran Yassour, Oliver J. Rando, Nir Friedman posted to nucleosome ngs by natstreet on 2009-11-26 16:00:42 as along with 2 people and 1 group sebastien_vigneau idonaldson Epigenetics
	A consistency-based consensus algorithm for de novo and reference-guided sequence assembly of short reads [My Copy] Bioinformatics, Vol. 25, No. 9. (1 May 2009), pp. 1118-1124. by Tobias Rausch, Sergey Koren, Gennady Denisov, et al.David Weese, Anne-Katrin Emde, Andreas Doring, Knut Reinert posted to software ngs assembly by jfr on 2009-11-26 13:18:41 as along with 19 people and 2 groups azazello hzoltan cthachuk GustavoLacerda jasontsai n00c nuin dakelley skembel Thaverkamp reyez TRHvidsten djkt hpaces APRegier pengchy natstreet druvus darian iSEEM Bioinformatics
	The B73 Maize Genome: Complexity, Diversity, and Dynamics [My Copy] Science, Vol. 326, No. 5956. (20 November 2009), pp. 1112-1115. by Patrick S. Schnable, Doreen Ware, Robert S. Fulton, et al.Joshua C. Stein, Fusheng Wei, Shiran Pasternak, Chengzhi Liang, Jianwei Zhang, Lucinda Fulton, Tina A. Graves, Patrick Minx, Amy D. Reily, Laura Courtney, Scott S. Kruchowski, Chad Tomlinson, Cindy Strong, Kim Delehaunty, Catrina Fronick, Bill Courtney, Susan M. Rock, Eddie Belter, Feiyu Du, Kyung Kim, Rachel M. Abbott, Marc Cotton, Andy Levy, Pamela Marchetto, Kerri Ochoa, Stephanie M. Jackson, Barbara Gillam, Weizu Chen, Le Yan, Jamey Higginbotham, Marco Cardenas, Jason Waligorski, Elizabeth Applebaum, Lindsey Phelps, Jason Falcone, Krishna Kanchi, Thynn Thane, Adam Scimone, Nay Thane, Jessica Henke, Tom Wang, Jessica Ruppert, Neha Shah, Kelsi Rotter, Jennifer Hodges, Elizabeth Ingenthron, Matt Cordes, Sara Kohlberg, Jennifer Sgro, Brandon Delgado, Kelly Mead, Asif Chinwalla, Shawn Leonard, Kevin Crouse, Kristi Collura, Dave Kudrna, Jennifer Currie, Ruifeng He, Angelina Angelova, Shanmugam Rajasekar, Teri Mueller, Rene Lomeli, Gabriel Scara, Ara Ko, Krista Delaney, Marina Wissotski, Georgina Lopez, David Campos, Michele Braidotti, Elizabeth Ashley, Wolfgang Golser, HyeRan Kim, Seunghee Lee, Jinke Lin, Zeljko Dujmic, Woojin Kim, Jayson Talag, Andrea Zuccolo, Chuanzhu Fan, Aswathy Sebastian, Melissa Kramer, Lori Spiegel, Lidia Nascimento, Theresa Zutavern, Beth Miller, Claude Ambroise, Stephanie Muller, Will Spooner, Apurva Narechania, Liya Ren, Sharon Wei, Sunita Kumari, Ben Faga, Michael J. Levy, Linda McMahan, Peter Van Buren, Matthew W. Vaughn, Kai Ying, Cheng-Ting Yeh, Scott J. Emrich, Yi Jia, Ananth Kalyanaraman, An-Ping Hsia, W. Brad Barbazuk, Regina S. Baucom, Thomas P. Brutnell, Nicholas C. Carpita, Cristian Chaparro, Jer-Ming Chia, Jean-Marc Deragon, James C. Estill, Yan Fu, Jeffrey A. Jeddeloh, Yujun Han, Hyeran Lee, Pinghua Li, Damon R. Lisch, Sanzhen Liu, Zhijie Liu, Dawn H. Nagel, Maureen C. McCann, Phillip SanMiguel, Alan M. Myers, Dan Nettleton, John Nguyen, Bryan W. Penning, Lalit Ponnala, Kevin L. Schneider, David C. Schwartz, Anupma Sharma, Carol Soderlund, Nathan M. Springer, Qi Sun, Hao Wang, Michael Waterman, Richard Westerman, Thomas K. Wolfgruber, Lixing Yang, Yeisoo Yu, Lifang Zhang, Shiguo Zhou, Qihui Zhu, Jeffrey L. Bennetzen, R. Kelly Dawe, Jiming Jiang, Ning Jiang, Gernot G. Presting, Susan R. Wessler, Srinivas Aluru, Robert A. Martienssen, Sandra W. Clifton, W. Richard McCombie, Rod A. Wing, Richard K. Wilson posted to ngs genome-assembly genome by natstreet on 2009-11-24 05:53:05 as along with 5 people toszko barneb druvus maren operon
	Searching for SNPs with cloud computing [My Copy] Genome Biology, Vol. 10, No. 11. (2009), R134. by Ben Langmead, Michael Schatz, Jimmy Lin, Mihai Pop, Steven Salzberg posted to snp ngs alignment by natstreet on 2009-11-24 05:52:43 as along with 8 people oinizan owenlancaster druvus kshameer jamesmorris jandot neils n00c
	Next-generation DNA sequencing techniques. [My Copy] New biotechnology, Vol. 25, No. 4. (03 April 2009), pp. 195-203. by Wilhelm J. Ansorge posted to ngs by manduca on 2009-11-24 04:04:04 as along with 8 people inesdesantiago heliopais natstreet druvus guhjy n00c svenrahmann ImranRaoufMalik
	Primer: Sequencing--the next generation. [My Copy] Nature methods, Vol. 5, No. 1. (January 2008) by Nicole Rusk, Veronique Kiermer posted to thesis ngs by manduca on 2009-11-24 03:57:56 as along with 2 people guhjy dchughes
	Probabilistic resolution of multi-mapping reads in massively parallel sequencing data using MuMRescueLite. [My Copy] Bioinformatics (Oxford, England), Vol. 25, No. 19. (1 October 2009), pp. 2613-2614. by Takehiro Hashimoto, Michiel J. de Hoon, Sean M. Grimmond, Carsten O. Daub, Yoshihide Hayashizaki, Geoffrey J. Faulkner posted to software ngs by orzenil on 2009-11-23 21:41:15 as along with 4 people and 1 group guhjy mkiyer natstreet druvus Chinnaiyan Lab
	TagDust--a program to eliminate artifacts from next generation sequencing data [My Copy] Bioinformatics, Vol. 25, No. 21. (1 November 2009), pp. 2839-2840. by Timo Lassmann, Yoshihide Hayashizaki, Carsten O. Daub posted to software ngs 454 by orzenil on 2009-11-23 21:38:29 as along with 20 people and 1 group hzoltan chvlyl operon kshameer djkt rtogawa seb1 idonaldson nuin debasis jgill GeeSharpMinor sotacam torfinnnome walshtp heliopais jandot n00c rschulz druvus Journal picks
	The genome of the cucumber, Cucumis sativus L. [My Copy] Nature Genetics, Vol. advance online publication (01 November 2009) by Sanwen Huang, Ruiqiang Li, Zhonghua Zhang, et al.Li Li, Xingfang Gu, Wei Fan, William J. Lucas, Xiaowu Wang, Bingyan Xie, Peixiang Ni, Yuanyuan Ren, Hongmei Zhu, Jun Li, Kui Lin, Weiwei Jin, Zhangjun Fei, Guangcun Li, Jack Staub, Andrzej Kilian, Edwin A. G. van der Vossen, Yang Wu, Jie Guo, Jun He, Zhiqi Jia, Yi Ren, Geng Tian, Yao Lu, Jue Ruan, Wubin Qian, Mingwei Wang, Quanfei Huang, Bo Li, Zhaoling Xuan, Jianjun Cao, Asan, Zhigang Wu, Juanbin Zhang, Qingle Cai, Yinqi Bai, Bowen Zhao, Yonghua Han, Ying Li, Xuefeng Li, Shenhao Wang, Qiuxiang Shi, Shiqiang Liu, Won K. Cho, Jae-Yean Kim, Yong Xu, Katarzyna Heller-Uszynska, Han Miao, Zhouchao Cheng, Shengping Zhang, Jian Wu, Yuhong Yang, Houxiang Kang, Man Li, Huiqing Liang, Xiaoli Ren, Zhongbin Shi, Ming Wen, Min Jian, Hailong Yang, Guojie Zhang, Zhentao Yang, Rui Chen, Shifang Liu, Jianwen Li, Lijia Ma, Hui Liu, Yan Zhou, Jing Zhao, Xiaodong Fang, Guoqing Li, Lin Fang, Yingrui Li, Dongyuan Liu, Hongkun Zheng, Yong Zhang, Nan Qin, Zhuo Li, Guohua Yang, Shuang Yang, Lars Bolund, Karsten Kristiansen, Hancheng Zheng, Shaochuan Li, Xiuqing Zhang, Huanming Yang, Jian Wang, Rifei Sun, Baoxi Zhang, Shuzhi Jiang, Jun Wang, Yongchen Du, Songgang Li posted to ngs genome by manduca on 2009-11-23 19:41:49 as along with 4 people and 1 group ppgardne kiekyon druvus natstreet Journal picks
	Mapping epigenetic mutations in fission yeast using whole-genome next-generation sequencing [My Copy] Genome Research, Vol. 19, No. 6. (7 June 2009), pp. 1077-1083. by Danielle V. Irvine, Derek B. Goto, Matthew W. Vaughn, et al.Yukinobu Nakaseko, W. Richard McCombie, Mitsuhiro Yanagida, Rob Martienssen posted to thesis ngs genome by manduca on 2009-11-23 19:39:13 as
	De novo genome sequence assembly of a filamentous fungus using Sanger, 454 and Illumina sequence data [My Copy] Genome Biology, Vol. 10, No. 9. (2009), R94. by Scott DiGuistini, Nancy Liao, Darren Platt, et al.Gordon Robertson, Michael Seidel, Simon Chan, T. Roderick Docking, Inanc Birol, Robert Holt, Martin Hirst, Elaine Mardis, Marco Marra, Richard Hamelin, Jorg Bohlmann, Colette Breuil, Steven Jones posted to ngs fungi assembly by orzenil on 2009-11-23 18:50:55 as along with 10 people and 2 groups GustavoLacerda sotacam gillianturgeon natstreet druvus jamselem sujaikumar kiekyon ppgardne stajich Journal picks Mycology
	Deep sequencing-based expression analysis shows major advances in robustness, resolution and inter-lab portability over five microarray platforms. [My Copy] Nucleic acids research, Vol. 36, No. 21. (1 December 2008), e141. by Peter A. 't Hoen, Yavuz Ariyurek, Helene H. Thygesen, et al.Erno Vreugdenhil, Rolf H. Vossen, Renée X. de Menezes, Judith M. Boer, Gert-Jan J. van Ommen, Johan T. den Dunnen posted to ngs microarray by manduca on 2009-11-23 05:14:03 as along with 25 people hzoltan GustavoLacerda stubrown GeeSharpMinor n00c guhjy hcoller daed poschm stsaft azazello jfr slevy03 felsani usagi-kirin shikin coela cthachuk ojabado caseybrown abizar natstreet druvus rschulz pengchy
	Virtual terminator nucleotides for next-generation DNA sequencing [My Copy] Nature Methods, Vol. 6, No. 8. (20 July 2009), pp. 593-595. by Jayson Bowers, Judith Mitchell, Eric Beer, et al.Philip R. Buzby, Marie Causey, J. William Efcavitch, Mirna Jarosz, Edyta Krzymanska-Olejnik, Li Kung, Doron Lipson, Geoffrey M. Lowman, Subramanian Marappan, Peter McInerney, Adam Platt, Atanu Roy, Suhaib M. Siddiqi, Kathleen Steinmann, John F. Thompson posted to thesis ngs by manduca on 2009-11-23 05:08:43 as along with 2 people guhjy jbhiatt
	Evaluation of next generation sequencing platforms for population targeted sequencing studies [My Copy] Genome Biology, Vol. 10, No. 3. (2009), R32. by Olivier Harismendy, Pauline Ng, Robert Strausberg, et al.Xiaoyun Wang, Timothy Stockwell, Karen Beeson, Nicholas Schork, Sarah Murray, Eric Topol, Samuel Levy, Kelly Frazer posted to platform_comparison ngs by jfr on 2009-11-20 13:06:18 as along with 25 people and 2 groups heliopais hzoltan dbensasson GustavoLacerda adijr agbiotec jgill darian jandot n00c jonilaserson maren inesdesantiago mlog ppgardne kiekyon michaelbarton idoerg stajich skembel giovanni druvus lwaldron djkt natstreet Journal picks Mycology
	Mutational evolution in a lobular breast tumour profiled at single nucleotide resolution. [My Copy] Nature, Vol. 461, No. 7265. (8 October 2009), pp. 809-813. by Sohrab P. Shah, Ryan D. Morin, Jaswinder Khattra, et al.Leah Prentice, Trevor Pugh, Angela Burleigh, Allen Delaney, Karen Gelmon, Ryan Guliany, Janine Senz, Christian Steidl, Robert A. Holt, Steven Jones, Mark Sun, Gillian Leung, Richard Moore, Tesa Severson, Greg A. Taylor, Andrew E. Teschendorff, Kane Tse, Gulisa Turashvili, Richard Varhol, René L. Warren, Peter Watson, Yongjun Zhao, Carlos Caldas, David Huntsman, Martin Hirst, Marco A. Marra, Samuel Aparicio posted to ngs cancer breast by pst on 2009-11-18 21:34:20 as along with 13 people and 2 groups misonneh jwfoley stubrown chvlyl giovenko frohike brianb Zephyrus jsuchit mkiyer torfinnnome merpublic djkt Chinnaiyan Lab Journal picks
	Computation for ChIP-seq and RNA-seq studies. [My Copy] Nature methods, Vol. 6, No. 11 Suppl. (15 November 2009), pp. S22-S32. by Shirley Pepke, Barbara Wold, Ali Mortazavi posted to ngs by pst on 2009-11-18 21:16:48 as along with 23 people and 2 groups urgi Jporci epigenetics timflutre molnet-mna Vincent_Rouilly guhjy cajunsushi mpizbioinfo stubrown hzoltan robertrentzsch xingxu oannes74 tonamswish inesdesantiago Baschl polivares jwfoley druvus GeeSharpMinor chvlyl heliopais molnet-macs Orengo Group Journal Picks
	Computational methods for discovering structural variation with next-generation sequencing [My Copy] Nature Methods, Vol. 6, No. 11s. (15 October 2009), pp. S13-S20. by Paul Medvedev, Monica Stanciu, Michael Brudno posted to ngs by pst on 2009-11-18 21:12:48 as along with 17 people and 2 groups seb1 owenlancaster robertrentzsch oannes74 toszko kiekyon michaelbarton jasontsai sameersoi heliopais druvus GeeSharpMinor Peiyong n00c gdv desany qayub Orengo Group Journal Picks Journal picks
	Sense from sequence reads: methods for alignment and assembly [My Copy] Nature Methods, Vol. 6, No. 11s. (15 October 2009), pp. S6-S12. by Paul Flicek, Ewan Birney posted to ngs by pst on 2009-11-18 21:10:30 as along with 15 people and 1 group idoerg ajsferreira owenlancaster robertrentzsch oannes74 Thaverkamp jasontsai natstreet seb1 druvus chvlyl GeeSharpMinor n00c venancio desany Orengo Group Journal Picks
	Next-generation gap [My Copy] Nat Meth, Vol. 6, No. 11s. (15 November 2009), pp. S2-S5. by John D. McPherson posted to ngs by pst on 2009-11-18 21:05:30 as along with 8 people owenlancaster torfinnnome Vincent_Rouilly seb1 idoerg oannes74 heliopais GeeSharpMinor
	Exome sequencing identifies the cause of a mendelian disorder [My Copy] Nature Genetics, Vol. advance online publication (13 November 2009) by Sarah B. Ng, Kati J. Buckingham, Choli Lee, et al.Abigail W. Bigham, Holly K. Tabor, Karin M. Dent, Chad D. Huff, Paul T. Shannon, Ethylin W. Jabs, Deborah A. Nickerson, Jay Shendure, Michael J. Bamshad posted to ngs by pst on 2009-11-18 19:54:24 as along with 5 people cajunsushi seb1 daforerog Peiyong psique
	W-ChIPMotifs: a web application tool for de novo motif discovery from ChIP-based high-throughput data [My Copy] Bioinformatics, Vol. 25, No. 23. (1 December 2009), pp. 3191-3193. by Victor X. Jin, Jeff Apostolos, Naga S. Nagisetty, Peggy J. Farnham posted to tool ngs motif-discovery by idonaldson on 2009-11-18 09:50:10 as along with 3 people farhat nklee maximilianh
	High-throughput sequence alignment using Graphics Processing Units [My Copy] BMC Bioinformatics, Vol. 8, No. 1. (2007), 474. by Michael Schatz, Cole Trapnell, Arthur Delcher, Amitabh Varshney posted to ngs gpu by cthachuk on 2009-11-17 22:16:45 as along with 20 people and 3 groups aheilbut druvus polivares naoya n00c natstreet rschulz operon orzenil Yanno guhjy sephy lusk laughcry nedwards mdimon cndewey heliopais urgi tpreeprem BergmanLab KCL & UCL Bioinformatics gatech-compgenomics
	Fast mapping of short sequences with mismatches, insertions and deletions using index structures. [My Copy] PLoS computational biology, Vol. 5, No. 9. (11 September 2009), e1000502. by Steve Hoffmann, Christian Otto, Stefan Kurtz, et al.Cynthia M. Sharma, Philipp Khaitovich, Jörg Vogel, Peter F. Stadler, Jörg Hackermüller posted to ngs csa by cthachuk on 2009-11-17 22:14:56 as along with 19 people and 4 groups hzoltan darian nuin fenghezi behindtherabbit jandot walshtp torfinnnome stubrown dswan polivares orzenil natstreet djkt jmcq n00c heliopais ppgardne druvus Bioinformatics BergmanLab iSEEM Journal picks
	PASS: a program to align short sequences [My Copy] Bioinformatics, Vol. 25, No. 7. (1 April 2009), pp. 967-968. by Davide Campagna, Alessandro Albiero, Alessandra Bilardi, et al.Elisa Caniato, Claudio Forcato, Svetlin Manavski, Nicola Vitulo, Giorgio Valle posted to ngs by cthachuk on 2009-11-17 22:13:54 as along with 19 people and 1 group hzoltan seb1 bozdagd adijr heliopais darian maren n00c nuin skembel cassj Neeperando helminth_lab rschulz guhjy natstreet druvus renatomilani WanderingAengus iSEEM
	SOAP: short oligonucleotide alignment program [My Copy] Bioinformatics, Vol. 24, No. 5. (1 March 2008), pp. 713-714. by Ruiqiang Li, Yingrui Li, Karsten Kristiansen, Jun Wang posted to ngs by cthachuk on 2009-11-17 22:13:28 as along with 26 people hzoltan antonkratz adijr jmanning2k pachorip jmcq jsatkosk jasontsai n00c hpaces skembel maren natstreet druvus orzenil pengchy umit guhjy ghattem GustavoLacerda niallhaslam mdimon caseybrown urgi bozdagd waszak
	ABySS: a parallel assembler for short read sequence data. [My Copy] Genome research, Vol. 19, No. 6. (1 June 2009), pp. 1117-1123. by Jared T. Simpson, Kim Wong, Shaun D. Jackman, Jacqueline E. Schein, Steven J. Jones, Inanç Birol posted to ngs assembler by cthachuk on 2009-11-17 22:13:12 as along with 26 people and 2 groups jfr hzoltan ramonvidal orzenil pachorip GustavoLacerda jonilaserson operon polivares reyez jasontsai n00c humburg dakelley jessopher idonaldson robsyme neils natstreet AaronDarling druvus rpatward dswan stajich jbhiatt erikarner BergmanLab Mycology
	Bioinformatics challenges of new sequencing technology [My Copy] Trends in Genetics, Vol. 24, No. 3. (11 February 2008), pp. 142-149. by M. Pop, S. Salzberg posted to review ngs by cthachuk on 2009-11-17 22:12:45 as along with 36 people Jporci hzoltan hpaces heliopais imaginatio operon daforerog n00c ptrobajo orzenil APRegier katholt michaelbarton kiekyon thegoose2 xingxu floatingpoint polivares yupu treangen jmcq delenickphd giovenko jmeppley dchughes djkt GustavoLacerda niallhaslam urgi Neeperando jfr tharris mariakmejia caseybrown yoonk druvus
	RNA-seq: an assessment of technical reproducibility and comparison with gene expression arrays. [My Copy] Genome research, Vol. 18, No. 9. (11 September 2008), pp. 1509-1517. by John C. Marioni, Christopher E. Mason, Shrikant M. Mane, Matthew Stephens, Yoav Gilad posted to rna-seq ngs by cthachuk on 2009-11-17 22:12:13 as along with 46 people and 2 groups hzoltan jwfoley heliopais debasis maren mtagaya mkiyer stubrown woodson8 jonilaserson burak Ayest ThomasDOtto huali n00c natstreet bandrewfox daed dandaman slevy03 pengchy felsani coela shikin fhalbrit inesdesantiago jmcq lp2 caseybrown jfr dakelley Ema balicea vega lusk semrich vmarshal fpattyn stajich giovanni ela503 Stew guhjy kengg shurjo GustavoLacerda SIMR bioinformatics Mycology
	SHRiMP: Accurate Mapping of Short Color-space Reads [My Copy] PLoS Comput Biol, Vol. 5, No. 5. (22 May 2009), e1000386. by Stephen M. Rumble, Phil Lacroute, Adrian V. Dalca, Marc Fiume, Arend Sidow, Michael Brudno posted to ngs by cthachuk on 2009-11-17 22:11:55 as along with 22 people and 4 groups heliopais jfr hzoltan bozdagd ilanc burak guhjy djkt trfield n00c natstreet adijr druvus Stew farhat humburg kshameer operon stajich GeeSharpMinor AlexBateman barry Bioinformatics - CRUK Mycology Journal picks Bioinformatics
	Velvet: Algorithms for de novo short read assembly using de Bruijn graphs [My Copy] Genome Research, Vol. 18, No. 5. (18 May 2008), pp. 821-829. by Daniel R. Zerbino, Ewan Birney posted to ngs denovo assembly by cthachuk on 2009-11-17 22:11:36 as along with 42 people and 3 groups ajsferreira vplagnol bedo jwhitney hzoltan azazello ajbattle jmanning2k n00c carlk pachorip APRegier jbhiatt jonilaserson operon jahwa jsatkosk sandfire thegoose2 katholt robsyme djkt hpaces AaronDarling mhz idoerg jmcq dswan dakelley jasontsai acn druvus natstreet nmohelli stajich farhat iris42 tharris Neeperando sharpton GustavoLacerda gdb Bioinformatics DeNovoAssembly-SIMR Mycology
	The Sequence Alignment/Map format and SAMtools [My Copy] Bioinformatics, Vol. 25, No. 16. (15 August 2009), pp. 2078-2079. by Heng Li, Bob Handsaker, Alec Wysoker, et al.Tim Fennell, Jue Ruan, Nils Homer, Gabor Marth, Goncalo Abecasis, Richard Durbin, 1000 Genome Project Data Processing Subgroup posted to tool software ngs file-format by cthachuk on 2009-11-17 22:11:15 as along with 27 people and 2 groups hzoltan seb1 heliopais urgi idonaldson GustavoLacerda stubrown cassj kshameer ciax polivares carlosjavierna jandot katholt jmcq guhjy orzenil jasontsai operon farhat AlexBateman chrisamiller nuin n00c natstreet sandfire druvus BergmanLab Journal picks
	TopHat: discovering splice junctions with RNA-Seq. [My Copy] Bioinformatics (Oxford, England), Vol. 25, No. 9. (1 May 2009), pp. 1105-1111. by Cole Trapnell, Lior Pachter, Steven L. Salzberg posted to rna-seq ngs by cthachuk on 2009-11-17 22:10:50 as along with 25 people and 2 groups juokcho hzoltan jwfoley heliopais dakelley druvus GustavoLacerda stubrown polivares torfinnnome jmcq mtagaya jonilaserson gdb guhjy ThomasDOtto n00c ghattem xingxu djkt vplagnol bertelsen natstreet idoerg vmsr BergmanLab SIMR bioinformatics
	CloudBurst: highly sensitive read mapping with MapReduce [My Copy] Bioinformatics, Vol. 25, No. 11. (1 June 2009), pp. 1363-1369. by Michael C. Schatz posted to ngs by cthachuk on 2009-11-17 22:10:33 as along with 33 people and 2 groups joshdsullivan hzoltan jfr walshtp idonaldson orzenil heliopais dakelley bozdagd agbiotec jandot guhjy n00c cymacs semrich nuin operon AlexBateman fgibson rschulz dswan mitko djkt humburg jmeppley coela vagoskar svenrahmann natstreet brianb Neeperando druvus neils KCL & UCL Bioinformatics Bioinformatics
	How to map billions of short reads onto genomes [My Copy] Nature Biotechnology, Vol. 27, No. 5. (01 May 2009), pp. 455-457. by Cole Trapnell, Steven L. Salzberg posted to review ngs by cthachuk on 2009-11-17 22:10:10 as along with 28 people and 5 groups hzoltan tonamswish heliopais giovenko jfr torfinnnome daforerog jonilaserson mkiyer Annab darian polivares ghattem kiekyon n00c GeeSharpMinor guhjy nuin reyez orzenil Thaverkamp natstreet druvus fenghezi Stew inesdesantiago idonaldson neils Bioinformatics Chinnaiyan Lab BergmanLab SIMR bioinformatics Bioinformatics - CRUK
	Mapping and quantifying mammalian transcriptomes by RNA-Seq. [My Copy] Nature methods, Vol. 5, No. 7. (30 July 2008), pp. 621-628. by Ali Mortazavi, Brian A. Williams, Kenneth McCue, Lorian Schaeffer, Barbara Wold posted to rna-seq ngs by cthachuk on 2009-11-17 22:09:46 as along with 42 people and 2 groups manduca hzoltan jwfoley heliopais juokcho aktas debasis bertelsen idonaldson darian stubrown dswan ewilban1 mtagaya woodson8 burak jonilaserson inesdesantiago ThomasDOtto n00c GustavoG ghattem vplagnol druvus cfvillalta vmsr poschm dandaman shikin jmcq rschulz lp2 tmcphillips jfr myourshaw megraw GeeSharpMinor caseybrown xingxu guhjy shurjo gdb Bioinformatics SIMR bioinformatics
	Managing and Analyzing Next-Generation Sequence Data [My Copy] PLoS Comput Biol, Vol. 5, No. 6. (26 June 2009), e1000369. by Brent G. Richter, David P. Sexton posted to ngs by cthachuk on 2009-11-17 22:09:26 as along with 42 people and 3 groups idoerg Geknitics hzoltan chvlyl sameersoi hpaces gdv GeeSharpMinor idonaldson darian daveGerrard tharris Yanno inesdesantiago jcaddy agbiotec humburg Zephyrus daforerog stubrown GustavoLacerda torfinnnome natstreet polivares orzenil kongl guhjy druvus n00c leemond31 nuin operon jasontsai jmeppley rdiaz michaelbarton dswan reyez kshameer TRHvidsten djkt ppgardne BergmanLab Bioinformatics Journal picks
	Genome-wide analysis reveals rapid and dynamic changes in miRNA and siRNA sequence and expression during ovule and fiber development in allotetraploid cotton (Gossypium hirsutum L) [My Copy] Genome Biology, Vol. 10, No. 11. (4 November 2009), R122. by Mingxiong Pang, Andrew Woodward, Vikram Agarwal, et al.Xueying Guan, Misook Ha, Vanitharani Ramachandran, Xuemei Chen, Barbara Triplett, David Stelly, Z. Jeffrey Chen posted to small_interfering_rnas sirna sequencing ngs illumina by davidmam on 2009-11-13 10:15:20 as along with 2 people natstreet samgj
	Parallel short sequence assembly of transcriptomes [My Copy] BMC Bioinformatics, Vol. 10, No. Suppl 1. (2009), S14. by Benjamin Jackson, Patrick Schnable, Srinivas Aluru posted to ngs de-novo assembly by natstreet on 2009-11-12 11:57:50 as along with 2 people Scis0000002 dakelley
	BFAST: An Alignment Tool for Large Scale Genome Resequencing [My Copy] PLoS ONE, Vol. 4, No. 11. (11 November 2009), e7767. by Nils Homer, Barry Merriman, Stanley F. Nelson posted to short-read ngs mapping by idonaldson on 2009-11-11 08:32:57 as along with 5 people n00c friendpine zwang druvus torfinnnome
	Human Genome Sequencing Using Unchained Base Reads on Self-Assembling DNA Nanoarrays [My Copy] Science (5 November 2009), 1181498. by Radoje Drmanac, Andrew B. Sparks, Matthew J. Callow, et al.Aaron L. Halpern, Norman L. Burns, Bahram G. Kermani, Paolo Carnevali, Igor Nazarenko, Geoffrey B. Nilsen, George Yeung, Fredrik Dahl, Andres Fernandez, Bryan Staker, Krishna P. Pant, Jonathan Baccash, Adam P. Borcherding, Anushka Brownley, Ryan Cedeno, Linsu Chen, Dan Chernikoff, Alex Cheung, Razvan Chirita, Benjamin Curson, Jessica C. Ebert, Coleen R. Hacker, Robert Hartlage, Brian Hauser, Steve Huang, Yuan Jiang, Vitali Karpinchyk, Mark Koenig, Calvin Kong, Tom Landers, Catherine Le, Jia Liu, Celeste E. McBride, Matt Morenzoni, Robert E. Morey, Karl Mutch, Helena Perazich, Kimberly Perry, Brock A. Peters, Joe Peterson, Charit L. Pethiyagoda, Kaliprasad Pothuraju, Claudia Richter, Abraham M. Rosenbaum, Shaunak Roy, Jay Shafto, Uladzislau Sharanhovich, Karen W. Shannon, Conrad G. Sheppy, Michel Sun, Joseph V. Thakuria, Anne Tran, Dylan Vu, Alexander W. Zaranek, Xiaodi Wu, Snezana Drmanac, Arnold R. Oliphant, William C. Banyai, Bruce Martin, Dennis G. Ballinger, George M. Church, Clifford A. Reid posted to ngs by natstreet on 2009-11-11 06:45:18 as along with 13 people and 1 group dakelley JonD qayub sandfire daforerog Peiyong chvlyl JamesBarger heliopais rwst orzenil zufar frohike Journal picks
	Accurate whole human genome sequencing using reversible terminator chemistry. [My Copy] Nature, Vol. 456, No. 7218. (6 November 2008), pp. 53-59. by David R. Bentley, Shankar Balasubramanian, Harold P. Swerdlow, et al.Geoffrey P. Smith, John Milton, Clive G. Brown, Kevin P. Hall, Dirk J. Evers, Colin L. Barnes, Helen R. Bignell, Jonathan M. Boutell, Jason Bryant, Richard J. Carter, R. Keira Cheetham, Anthony J. Cox, Darren J. Ellis, Michael R. Flatbush, Niall A. Gormley, Sean J. Humphray, Leslie J. Irving, Mirian S. Karbelashvili, Scott M. Kirk, Heng Li, Xiaohai Liu, Klaus S. Maisinger, Lisa J. Murray, Bojan Obradovic, Tobias Ost, Michael L. Parkinson, Mark R. Pratt, Isabelle M. Rasolonjatovo, Mark T. Reed, Roberto Rigatti, Chiara Rodighiero, Mark T. Ross, Andrea Sabot, Subramanian V. Sankar, Aylwyn Scally, Gary P. Schroth, Mark E. Smith, Vincent P. Smith, Anastassia Spiridou, Peta E. Torrance, Svilen S. Tzonev, Eric H. Vermaas, Klaudia Walter, Xiaolin Wu, Lu Zhang, Mohammed D. Alam, Carole Anastasi, Ify C. Aniebo, David M. Bailey, Iain R. Bancarz, Saibal Banerjee, Selena G. Barbour, Primo A. Baybayan, Vincent A. Benoit, Kevin F. Benson, Claire Bevis, Phillip J. Black, Asha Boodhun, Joe S. Brennan, John A. Bridgham, Rob C. Brown, Andrew A. Brown, Dale H. Buermann, Abass A. Bundu, James C. Burrows, Nigel P. Carter, Nestor Castillo, Maria Chiara E Catenazzi, Simon Chang, R. Neil Cooley, Natasha R. Crake, Olubunmi O. Dada, Konstantinos D. Diakoumakos, Belen Dominguez-Fernandez, David J. Earnshaw, Ugonna C. Egbujor, David W. Elmore, Sergey S. Etchin, Mark R. Ewan, Milan Fedurco, Louise J. Fraser, Karin V. Fuentes Fajardo, W. Scott Furey, David George, Kimberley J. Gietzen, Colin P. Goddard, George S. Golda, Philip A. Granieri, David E. Green, David L. Gustafson, Nancy F. Hansen, Kevin Harnish, Christian D. Haudenschild, Narinder I. Heyer, Matthew M. Hims, Johnny T. Ho, Adrian M. Horgan, Katya Hoschler, Steve Hurwitz, Denis V. Ivanov, Maria Q. Johnson, Terena James, T. A. Huw Jones, Gyoung-Dong D. Kang, Tzvetana H. Kerelska, Alan D. Kersey, Irina Khrebtukova, Alex P. Kindwall, Zoya Kingsbury, Paula I. Kokko-Gonzales, Anil Kumar, Marc A. Laurent, Cynthia T. Lawley, Sarah E. Lee, Xavier Lee, Arnold K. Liao, Jennifer A. Loch, Mitch Lok, Shujun Luo, Radhika M. Mammen, John W. Martin, Patrick G. McCauley, Paul McNitt, Parul Mehta, Keith W. Moon, Joe W. Mullens, Taksina Newington, Zemin Ning, Bee Ling Ng, Sonia M. Novo, Michael J. O'Neill, Mark A. Osborne, Andrew Osnowski, Omead Ostadan, Lambros L. Paraschos, Lea Pickering, Andrew C. Pike, Alger C. Pike, D. Chris Pinkard, Daniel P. Pliskin, Joe Podhasky, Victor J. Quijano, Come Raczy, Vicki H. Rae, Stephen R. Rawlings, Ana Chiva Rodriguez, Phyllida M. Roe, John Rogers, Maria C. Rogert Bacigalupo, Nikolai Romanov, Anthony Romieu, Rithy K. Roth, Natalie J. Rourke, Silke T. Ruediger, Eli Rusman, Raquel M. Sanches-Kuiper, Martin R. Schenker, Josefina M. Seoane, Richard J. Shaw, Mitch K. Shiver, Steven W. Short, Ning L. Sizto, Johannes P. Sluis, Melanie A. Smith, Jean Ernest Sohna Sohna, Eric J. Spence, Kim Stevens, Neil Sutton, Lukasz Szajkowski, Carolyn L. Tregidgo, Gerardo Turcatti, Stephanie Vandevondele, Yuli Verhovsky, Selene M. Virk, Suzanne Wakelin, Gregory C. Walcott, Jingwen Wang, Graham J. Worsley, Juying Yan, Ling Yau, Mike Zuerlein, Jane Rogers, James C. Mullikin, Matthew E. Hurles, Nick J. McCooke, John S. West, Frank L. Oaks, Peter L. Lundberg, David Klenerman, Richard Durbin, Anthony J. Smith posted to ngs by pst on 2009-11-09 23:58:37 as along with 29 people and 1 group hzoltan rshe gbenson giovenko n00c clearbluespring xingxu dna austin jessopher daforerog vmsr jfr azazello nuin usagi-kirin Archaeogenetics malcook psique tsherig jbhiatt pengchy reyez jmcq inesdesantiago ojabado caseybrown pkonings djkt SIMR bioinformatics
	Next-generation DNA sequencing. [My Copy] Nature biotechnology, Vol. 26, No. 10. (09 October 2008), pp. 1135-1145. by Jay Shendure, Hanlee Ji posted to review ngs alignment by cthachuk on 2009-11-09 19:14:02 as along with 46 people and 3 groups Jporci daforerog dchughes hzoltan giovenko heliopais seb1 installe niallhaslam Vincent_Rouilly rschulz fishtank bluto Annab katholt jmcq michaelbarton n00c jfr dna nzm farhat idoerg mhz mmartin antonkratz jbhiatt yupu behindtherabbit guhjy Pascalichouchou frohike dakelley ptrobajo zwang Zephyrus psique natstreet druvus nuin alexknight reyez dbk wsjames pengchy GeeSharpMinor Bioinformatics Roswell Cancer Crosstalk Oxford Virology
	Ultrafast and memory-efficient alignment of short DNA sequences to the human genome [My Copy] Genome Biology, Vol. 10, No. 3. (2009), R25. by Ben Langmead, Cole Trapnell, Mihai Pop, Steven Salzberg posted to ngs alignment by cthachuk on 2009-11-09 19:13:06 as along with 36 people and 4 groups jfr hzoltan darshan fstrozzi adijr debasis bozdagd polivares torfinnnome n00c talponer jmcq rschulz ghattem operon humburg idonaldson mmartin skembel dquest heliopais djkt GeeSharpMinor bertelsen darian semrich dakelley idoerg vmsr hpaces admash pdexheimer mhamada fpattyn natstreet druvus BergmanLab SIMR bioinformatics iSEEM Notre Dame Bioinformatics
	Mapping short DNA sequencing reads and calling variants using mapping quality scores. [My Copy] Genome research, Vol. 18, No. 11. (19 November 2008), pp. 1851-1858. by Heng Li, Jue Ruan, Richard Durbin posted to snv snp ngs alignment by cthachuk on 2009-11-09 19:12:52 as along with 38 people and 2 groups seninp heliopais hzoltan darshan adijr darian bozdagd jmanning2k stubrown APRegier ghattem jbhiatt mmartin michaelbarton polivares jonilaserson humburg n00c jessopher maren GeeSharpMinor vmsr vplagnol natstreet poschm jfr druvus dandaman xingxu rschulz jmcq inesdesantiago Neeperando nmohelli matthewsuderman bpb gdb farhat SIMR bioinformatics BergmanLab
	Fast and accurate short read alignment with Burrows-Wheeler transform. [My Copy] Bioinformatics (Oxford, England), Vol. 25, No. 14. (15 July 2009), pp. 1754-1760. by Heng Li, Richard Durbin posted to ngs alignment by cthachuk on 2009-11-09 19:12:15 as along with 33 people and 4 groups lianping hzoltan maren bozdagd adijr heliopais jmanning2k GustavoLacerda stubrown jessopher guhjy katholt mkiyer jmcq idonaldson michaelbarton polivares darian orzenil cassj inesdesantiago TRHvidsten djkt operon ghattem n00c danmaclean ppgardne nuin rschulz natstreet druvus humburg BergmanLab SIMR bioinformatics Bioinformatics Journal picks
	inGAP: an integrated next-generation genome analysis pipeline [My Copy] Bioinformatics (30 October 2009), btp615. by Ji Qi, Fangqing Zhao, Anne Buboltz, Stephan C. Schuster posted to ngs by jasontsai on 2009-11-04 14:38:22 as along with 4 people natstreet n00c heliopais druvus
	BARCRAWL and BARTAB: Software tools for the design and implementation of barcoded primers for highly multiplexed DNA sequencing [My Copy] BMC Bioinformatics, Vol. 10, No. 1. (29 October 2009), 362. by Daniel Frank posted to ngs barcode by natstreet on 2009-11-04 07:30:35 as along with 4 people and 1 group druvus MarkFiers ppgardne heliopais Journal picks
	LookSeq: A browser-based viewer for deep sequencing data [My Copy] Genome Research, Vol. 19, No. 11. (29 November 2009), pp. 2125-2132. by Heinrich M. Manske, Dominic P. Kwiatkowski posted to visualisation ngs genome_browser by idonaldson to the group BergmanLab on 2009-11-03 12:07:52 as along with 27 people and 1 group hzoltan darian dakelley tonamswish inesdesantiago Thaverkamp heliopais owhitney GustavoLacerda ngehlenborg sandfire fpattyn xianjun katholt stubrown orzenil operon guhjy kongl stajich n00c torfinnnome nuin kshameer neils druvus natstreet Mycology
	RePS: a sequence assembler that masks exact repeats identified from the shotgun data. [My Copy] Genome research, Vol. 12, No. 5. (1 May 2002), pp. 824-831. by Jun Wang, Gane Ka-Shu K. Wong, Peixiang Ni, et al.Yujun Han, Xiangang Huang, Jianguo Zhang, Chen Ye, Yong Zhang, Jianfei Hu, Kunlin Zhang, Xin Xu, Lijuan Cong, Hong Lu, Xide Ren, Xiaoyu Ren, Jun He, Lin Tao, Douglas A. Passey, Jian Wang, Huanming Yang, Jun Yu, Songgang Li posted to ngs combined-assembly assembly by natstreet on 2009-11-02 16:41:55 as along with 3 people seb1 n00c orzenil
	Next is now: new technologies for sequencing of genomes, transcriptomes, and beyond [My Copy] Current Opinion in Plant Biology, Vol. 12, No. 2. (20 April 2009), pp. 107-118. by Ryan Lister, Brian D. Gregory, Joseph R. Ecker posted to transcriptome_analysis ngs methods genomics by mlog on 2009-10-29 15:50:52 as along with 4 people debasis Vincent_Rouilly guhjy smiddha

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assembly	29
alignment	27
review	25
mapping	22
transcriptome	19
gene_expression	16
sequencing	15
rna-seq	14
short-read	14
454	13
snp	12
bioinformatics	11
software	11
rnaseq	10
genomics	9
short_reads	9
alternative_splicing	8
microrna	7
tool	7
paired-end	6
sel	6
technology	6
dna	5
error_model	5
genome	5
methylation	5
mirna	5
next_generation_sequencing	5
short-read-mapping	5
chip-seq	4
de-novo	4
map	4
metagenomics	4
methods	4
next_generation	4
resequencing	4
snps	4
bakalarka	3
barcode	3
chip_seq	3
de_novo_sequencing	3
genome-assembly	3
human	3
illumina	3
indel	3
nextgen	3
r	3
sequence_alignment	3
solexa	3
statistics	3
thesis	3
transcriptomics	3
visualisation	3
alternative-splicing	2
applications	2
assembler	2
assessment	2
association-mapping	2
bwa	2
cancer	2
chipseq	2
cnv	2
combinatorics	2
expression	2
genome-browser	2
genome_browser	2
gottgens	2
me	2
pooled	2
profiling	2
quality	2
selection	2
snp-calling	2
stem_cell	2
structural_variants	2
testing	2
variants	2
2006	1
abeta	1
anti_mglur5	1
deepcage	1
file-format	1
genome_assembly	1
grid	1
gwa	1
immunohistochemistry	1
ionomycin	1
multiple_sclerosis	1
next	1
next_gen_sequencing	1
nifedipine	1
probability_model	1
promoteromes	1
sar	1
scalability	1
sirna	1
splice-variant	1
suffix_arrays	1
universal_cnpq	1
variation	1

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