Tag short_reads [30 articles] Export

Recent papers classified by the tag short_reads.

	Genome-wide profiles of STAT1 DNA association using chromatin immunoprecipitation and massively parallel sequencing [My Copy] Nature Methods, Vol. 4, No. 8. (11 June 2007), pp. 651-657. by Gordon Robertson, Martin Hirst, Matthew Bainbridge, et al.Misha Bilenky, Yongjun Zhao, Thomas Zeng, Ghia Euskirchen, Bridget Bernier, Richard Varhol, Allen Delaney, Nina Thiessen, Obi L. Griffith, Ann He, Marco Marra, Michael Snyder, Steven Jones posted to short_reads peak_detection by bedo on 2009-12-11 01:12:41 as along with 14 people and 1 group absterga samanthacooper stubrown ewilban1 fpattyn polivares caseybrown guhjy vega kengg ghattem slevy03 dquest raiyar Plantandetc
	Archiving next generation sequencing data. [My Copy] Nucleic acids research In Nucl. Acids Res. (3 December 2009), gkp1078. by Martin Shumway, Guy Cochrane, Hideaki Sugawara posted to sra short_reads next_generation_sequencing by Julien_Fayolle on 2009-12-09 14:19:17 as along with 4 people n00c Garamonfok heliopais davidmam
	De novo sequencing of plant genomes using second-generation technologies [My Copy] Brief Bioinform, Vol. 10, No. 6. (1 November 2009), pp. 609-618. by Michael Imelfort, David Edwards posted to short_reads sequencing review plant dna 454 by bedo on 2009-11-27 02:57:41 as along with 7 people and 1 group GustavoLacerda jforment druvus dakelley Jporci TRHvidsten davidmam Bioinformatics Core Service
	Sensitive, specific polymorphism discovery in bacteria using massively parallel sequencing. [My Copy] Nature methods, Vol. 6, No. 1. (14 January 2009), pp. 67-69. by Chad Nusbaum, Toshiro K. Ohsumi, James Gomez, et al.John Aquadro, Thomas C. Victor, Robert M. Warren, Deborah T. Hung, Bruce W. Birren, Eric S. Lander, David B. Jaffe posted to short_reads by seninp on 2009-11-23 12:49:54 as along with 5 people dakelley natstreet druvus jbhiatt abizar
	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 short_reads by seninp on 2009-11-23 12:48:46 as along with 40 people and 2 groups claire_jubin urgi heliopais hzoltan cthachuk 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
	Simultaneous alignment of short reads against multiple genomes [My Copy] Genome Biology, Vol. 10, No. 9. (17 September 2009), R98. by Korbinian Schneeberger, Jorg Hagmann, Stephan Ossowski, et al.Norman Warthmann, Sandra Gesing, Oliver Kohlbacher, Detlef Weigel posted to short_reads by seninp on 2009-11-23 12:46:43 as along with 12 people n00c darian maren megraw djkt fstrozzi jamselem justinhjohnson torfinnnome reyez natstreet druvus
	Sequencing of natural strains of Arabidopsis thaliana with short reads. [My Copy] Genome research, Vol. 18, No. 12. (29 December 2008), pp. 2024-2033. by Stephan Ossowski, Korbinian Schneeberger, Richard M. Clark, Christa Lanz, Norman Warthmann, Detlef Weigel posted to short_reads by seninp on 2009-11-23 12:45:32 as along with 11 people and 2 groups n00c APRegier sameersoi dandaman jasontsai stajich xwbcn natstreet druvus GustavoLacerda semrich Mycology Notre Dame Bioinformatics
	Whole-genome sequencing and variant discovery in C. elegans. [My Copy] Nature methods, Vol. 5, No. 2. (20 February 2008), pp. 183-188. by LaDeana W. Hillier, Gabor T. Marth, Aaron R. Quinlan, et al.David Dooling, Ginger Fewell, Derek Barnett, Paul Fox, Jarret I. Glasscock, Matthew Hickenbotham, Weichun Huang, Vincent J. Magrini, Ryan J. Richt, Sacha N. Sander, Donald A. Stewart, Michael Stromberg, Eric F. Tsung, Todd Wylie, Tim Schedl, Richard K. Wilson, Elaine R. Mardis posted to short_reads by seninp on 2009-11-23 12:43:51 as along with 14 people Annab n00c APRegier thegoose2 druvus semrich AaronDarling usagi-kirin matthewsuderman inesdesantiago orzenil mdimon farhat tharris
	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 short_reads sequencing by gdv on 2009-10-30 18:04:33 as along with 17 people and 2 groups seb1 pst owenlancaster robertrentzsch oannes74 toszko kiekyon michaelbarton jasontsai sameersoi heliopais druvus GeeSharpMinor Peiyong n00c desany qayub Orengo Group Journal Picks Journal picks
	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 suffix_arrays short_reads ngs by orzenil on 2009-09-13 03:38:36 as along with 20 people and 4 groups humburg cthachuk hzoltan darian nuin fenghezi behindtherabbit jandot walshtp torfinnnome stubrown dswan polivares natstreet djkt jmcq n00c heliopais ppgardne druvus Bioinformatics BergmanLab iSEEM Journal picks
	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 short_reads ngs genome_assembly by orzenil on 2009-08-20 16:55:31 as along with 27 people and 2 groups darian jfr cthachuk hzoltan ramonvidal 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 : TIG, Vol. 24, No. 3. (11 March 2008), pp. 142-149. by Mihai Pop, Steven L. Salzberg posted to short_reads genome_assembly by orzenil on 2009-08-20 12:54:40 as along with 36 people michaelbarton Jporci cthachuk hzoltan hpaces heliopais imaginatio operon daforerog n00c ptrobajo APRegier katholt kiekyon thegoose2 xingxu floatingpoint polivares yupu treangen jmcq delenickphd giovenko jmeppley dchughes djkt GustavoLacerda niallhaslam urgi Neeperando jfr tharris mariakmejia caseybrown yoonk druvus
	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 short_reads scientific_visualization by orzenil on 2009-08-16 18:32:44 as along with 28 people and 2 groups humburg hzoltan darian dakelley tonamswish inesdesantiago Thaverkamp idonaldson heliopais owhitney GustavoLacerda ngehlenborg sandfire fpattyn xianjun katholt stubrown operon guhjy kongl stajich n00c torfinnnome nuin kshameer neils druvus natstreet BergmanLab Mycology
	Substantial biases in ultra-short read data sets from high-throughput DNA sequencing [My Copy] Nucl. Acids Res., Vol. 36, No. 16. (1 September 2008), e105. by Juliane C. Dohm, Claudio Lottaz, Tatiana Borodina, Heinz Himmelbauer posted to short_reads ngs dna_sequencing by orzenil on 2009-08-12 00:13:12 as along with 21 people and 1 group claire_jubin darian heliopais hzoltan jonilaserson n00c druvus burak woodson8 sameersoi humburg poschm polivares Huub_odc usagi-kirin inesdesantiago jfr natstreet dakelley caseybrown GustavoLacerda microbiology_nijmegen
	Overlapping pools for high-throughput targeted resequencing [My Copy] Genome Research, Vol. 19, No. 7. (15 July 2009), pp. 1254-1261. by Snehit Prabhu, Itsik Pe'er posted to pooling resequencing short_reads by orzenil on 2009-07-14 13:42:06 as along with 14 people and 1 group humburg hzoltan jandot guhjy pkonings jcbarret natstreet druvus n00c dandaman xingxu sameersoi djkt jdbowes Journal picks
	Probabilistic base calling of Solexa sequencing data [My Copy] BMC Bioinformatics, Vol. 9, No. 1. (2008), 431. by Jacques Rougemont, Arnaud Amzallag, Christian Iseli, Laurent Farinelli, Ioannis Xenarios, Felix Naef posted to base_calling illumina short_reads by orzenil on 2009-07-13 14:53:06 as along with 16 people and 1 group heliopais n00c dakelley jfr usagi-kirin magusina malcook natstreet druvus iris42 abizar caseybrown reyez pengchy waszak nuin SIMR bioinformatics
	Slider--maximum use of probability information for alignment of short sequence reads and SNP detection [My Copy] Bioinformatics, Vol. 25, No. 1. (1 January 2009), pp. 6-13. by Nawar Malhis, Yaron S. N. Butterfield, Martin Ester, Steven J. M. Jones posted to snps snp_discovery short_reads illumina by orzenil on 2009-07-13 14:08:39 as along with 10 people claire_jubin Julien_Fayolle darian seb1 torfinnnome jsatkosk n00c mdimon druvus jmeppley
	miRanalyzer: a microRNA detection and analysis tool for next-generation sequencing experiments [My Copy] Nucl. Acids Res., Vol. 37, No. suppl_2. (1 July 2009), pp. W68-76. by Michael Hackenberg, Martin Sturm, David Langenberger, Juan M. Falcon-Perez, Ana M. Aransay posted to mirna mirna_expression ngs short_reads by orzenil on 2009-07-12 02:09:09 as along with 14 people and 3 groups jforment Peiyong hzoltan druvus heliopais fishtank tonamswish dswan natstreet guhjy fenghezi pengchy ealloza daforerog Bioinformatics Core Service microRNA Bioinformatics
	VarScan: variant detection in massively parallel sequencing of individual and pooled samples [My Copy] Bioinformatics, Vol. 25, No. 17. (1 September 2009), pp. 2283-2285. by Daniel C. Koboldt, Ken Chen, Todd Wylie, et al.David E. Larson, Michael D. McLellan, Elaine R. Mardis, George M. Weinstock, Richard K. Wilson, Li Ding posted to ngs resequencing short_reads snp by orzenil on 2009-07-12 02:08:03 as along with 16 people and 3 groups humburg hzoltan Peiyong darian seb1 heliopais mkiyer dakelley djkt PabloMarin guhjy n00c natstreet druvus stajich malcook Journal picks Mycology SIMR bioinformatics
	SNP-o-matic [My Copy] Bioinformatics, Vol. 25, No. 18. (15 September 2009), pp. 2434-2435. by Heinrich M. Manske, Dominic P. Kwiatkowski posted to genotyping ngs short_reads snp by orzenil on 2009-07-12 02:06:07 as along with 11 people and 1 group hzoltan darian GeeSharpMinor daforerog ThomasDOtto natstreet misonneh druvus guhjy Zephyrus n00c Journal picks
	The Sequence Alignment/Map format and SAMtools. [My Copy] Bioinformatics (Oxford, England), 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 ngs short_reads by orzenil on 2009-07-12 02:02:34 as along with 29 people and 2 groups MarkFiers n00c darian cthachuk hzoltan seb1 heliopais urgi idonaldson GustavoLacerda stubrown cassj kshameer ciax polivares carlosjavierna jandot katholt jmcq guhjy jasontsai operon farhat AlexBateman chrisamiller nuin natstreet sandfire druvus BergmanLab Journal picks
	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 short_reads by orzenil on 2009-07-12 02:01:54 as along with 35 people and 4 groups urgi agbiotec lianping hzoltan cthachuk maren bozdagd adijr heliopais jmanning2k GustavoLacerda stubrown jessopher guhjy katholt mkiyer jmcq idonaldson michaelbarton polivares darian cassj inesdesantiago TRHvidsten djkt operon ghattem n00c danmaclean ppgardne nuin rschulz natstreet druvus humburg BergmanLab SIMR bioinformatics Bioinformatics Journal picks
	Managing and analyzing next-generation sequence data. [My Copy] PLoS computational biology In PLoS Comput Biol, Vol. 5, No. 6. (26 June 2009), e1000369. by Brent G. Richter, David P. Sexton posted to ngs sequencing short_reads by orzenil on 2009-07-12 02:00:38 as along with 48 people and 4 groups michaelbarton Jporci kevinemamy heliopais jforment jfr burak idoerg Geknitics cthachuk hzoltan chvlyl sameersoi hpaces gdv GeeSharpMinor idonaldson darian daveGerrard tharris Yanno inesdesantiago jcaddy agbiotec humburg Zephyrus daforerog stubrown GustavoLacerda torfinnnome natstreet polivares kongl guhjy druvus n00c leemond31 nuin operon jasontsai jmeppley rdiaz dswan reyez kshameer TRHvidsten djkt ppgardne Bioinformatics Core Service BergmanLab Bioinformatics Journal picks
	Short-Read Sequencing Technologies for Transcriptional Analyses [My Copy] Annual Review of Plant Biology, Vol. 60, No. 1. (9 January 2009), pp. 305-333. by Stacey A. Simon, Jixian Zhai, Raja S. Nandety, et al.Kevin P. McCormick, Jia Zeng, Diego Mejia, Blake C. Meyers posted to plant_biology plant_genetics short_reads transcriptome by orzenil on 2009-06-13 01:02:18 as along with 7 people n00c darian giovenko heliopais manduca GeeSharpMinor abizar
	Whole genome assembly from 454 sequencing output via modified DNA graph concept [My Copy] Computational Biology and Chemistry, Vol. 33, No. 3. (04 June 2009), pp. 224-230. by Jacek Blazewicz, Marcin Bryja, Marek Figlerowicz, et al.Piotr Gawron, Marta Kasprzak, Edward Kirton, Darren Platt, Jakub Przybytek, Aleksandra Swiercz, Lukasz Szajkowski posted to assemblers dna_graph short_reads by orzenil on 2009-06-11 21:48:20 as along with 6 people and 1 group darian n00c GustavoLacerda stajich natstreet druvus Mycology
	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 bioinformatics short_reads by orzenil on 2009-05-17 02:30:17 as along with 32 people and 5 groups michaelbarton frohike agbiotec burak cthachuk hzoltan tonamswish heliopais giovenko jfr torfinnnome daforerog jonilaserson mkiyer Annab darian polivares ghattem kiekyon n00c GeeSharpMinor guhjy nuin reyez Thaverkamp natstreet druvus fenghezi Stew inesdesantiago idonaldson neils Bioinformatics Chinnaiyan Lab BergmanLab SIMR bioinformatics Bioinformatics - CRUK
	Aggressive assembly of pyrosequencing reads with mates [My Copy] Bioinformatics In Bioinformatics, Vol. 24, No. 24. (15 December 2008), pp. 2818-2824. by Jason R. Miller, Arthur L. Delcher, Sergey Koren, et al.Eli Venter, Brian P. Walenz, Anushka Brownley, Justin Johnson, Kelvin Li, Clark Mobarry, Granger Sutton posted to genome_assembly short_reads by orzenil on 2009-04-13 22:39:25 as along with 18 people and 2 groups darian GustavoLacerda n00c APRegier jonilaserson dakelley idoerg ela503 natstreet druvus azazello acn jasontsai jmeppley cisevol malcook Neeperando djkt BergmanLab SIMR bioinformatics
	De novo fragment assembly with short mate-paired reads: Does the read length matter? [My Copy] Genome research, Vol. 19, No. 2. (3 February 2009), pp. 336-346. by Mark J. Chaisson, Dumitru Brinza, Pavel A. Pevzner posted to genome_assembly short_reads by orzenil on 2009-04-13 22:38:36 as along with 19 people and 1 group claire_jubin darian n00c carlk APRegier jandot jonilaserson natstreet dakelley jessopher AaronDarling sphsmith jasontsai nmohelli jbhiatt druvus hpaces GustavoLacerda stajich Mycology
	De novo assembly using low-coverage short read sequence data from the rice pathogen Pseudomonas syringae pv. oryzae. [My Copy] Genome research In Genome Research, Vol. 19, No. 2. (17 February 2009), pp. 294-305. by Josephine A. Reinhardt, David A. Baltrus, Marc T. Nishimura, William R. Jeck, Corbin D. Jones, Jeffery L. Dangl posted to denovo_assembly short_reads by orzenil on 2009-04-12 03:53:01 as along with 15 people and 2 groups darian n00c michaelbarton pachorip ThomasDOtto robsyme AaronDarling druvus dakelley Huub_odc usagi-kirin abizar acn jbhiatt hpaces SIMR bioinformatics Bioinformatics
	Fragment assembly with short reads. [My Copy] Bioinformatics (Oxford, England) In Bioinformatics, Vol. 20, No. 13. (1 September 2004), pp. 2067-2074. by Mark Chaisson, Pavel Pevzner, Haixu Tang posted to genome_assembly short_reads by orzenil on 2008-11-19 16:00:00 as along with 6 people darian n00c idoerg dakelley bioinfo nedwards

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ngs	9
genome_assembly	7
sequencing	5
illumina	2
resequencing	2
snp	2
454	1
assemblers	1
base_calling	1
bioinformatics	1
denovo_assembly	1
dna	1
dna_graph	1
dna_sequencing	1
genotyping	1
mirna	1
mirna_expression	1
next_generation_sequencing	1
peak_detection	1
plant	1
plant_biology	1
plant_genetics	1
pooling	1
review	1
scientific_visualization	1
snp_discovery	1
snps	1
sra	1
suffix_arrays	1
transcriptome	1

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