dakelley's short-reads [36 articles] Export Sort

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	The GNUMAP algorithm: unbiased probabilistic mapping of oligonucleotides from next-generation sequencing [My Copy] Bioinformatics, Vol. 26, No. 1. (1 January 2010), pp. 38-45. by Nathan L. Clement, Quinn Snell, Mark J. Clement, et al.Peter C. Hollenhorst, Jahnvi Purwar, Barbara J. Graves, Bradley R. Cairns, W. Evan Johnson posted to short-reads sequence-alignment by dakelley on 2009-12-25 22:58:26 as along with 8 people djkt kshameer claire_jubin darian operon heliopais n00c druvus
	Effect of read-mapping biases on detecting allele-specific expression from RNA-sequencing data [My Copy] Bioinformatics In Bioinformatics, Vol. 25, No. 24. (15 December 2009), pp. 3207-3212. by Jacob F. Degner, John C. Marioni, Athma A. Pai, et al.Joseph K. Pickrell, Everlyne Nkadori, Yoav Gilad, Jonathan K. Pritchard posted to short-reads by dakelley on 2009-12-07 06:21:12 as along with 10 people and 2 groups jherrero68 djkt jperkins humburg natstreet chvlyl n00c papamicd torfinnnome heliopais Journal picks Orengo Group Journal Picks
	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 assembly by dakelley on 2009-11-24 22:47:44 as along with 7 people and 1 group GustavoLacerda jforment druvus bedo Jporci TRHvidsten davidmam Bioinformatics Core Service
	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 visualization short-reads by dakelley on 2009-11-11 06:26:20 as along with 28 people and 2 groups humburg hzoltan darian tonamswish inesdesantiago Thaverkamp idonaldson heliopais owhitney GustavoLacerda ngehlenborg sandfire fpattyn xianjun katholt stubrown orzenil operon guhjy kongl stajich n00c torfinnnome nuin kshameer neils druvus natstreet BergmanLab Mycology
	Cancer genome sequencing: a review [My Copy] Hum. Mol. Genet., Vol. 18, No. R2. (15 October 2009), pp. R163-168. by Elaine R. Mardis, Richard K. Wilson posted to short-reads review cancer by dakelley on 2009-11-02 17:13:02 as along with 3 people n00c desany jmanning2k
	Increasing the coverage of a metapopulation consensus genome by iterative read mapping and assembly [My Copy] Bioinformatics, Vol. 25, No. 21. (1 November 2009), pp. 2878-2881. by Bas E. Dutilh, Martijn A. Huynen, Marc Strous posted to short-reads sequence-alignment metagenomics assembly by dakelley on 2009-11-02 04:32:58 as along with 9 people and 1 group CorinYeats skennedy8 druvus kinestetika ThomasDOtto jasontsai skembel sharpton jmeppley iSEEM
	De novo transcriptome assembly with ABySS [My Copy] Bioinformatics In Bioinformatics, Vol. 25, No. 21. (1 November 2009), pp. 2872-2877. by Inanc Birol, Shaun D. Jackman, Cydney B. Nielsen, et al.Jenny Q. Qian, Richard Varhol, Greg Stazyk, Ryan D. Morin, Yongjun Zhao, Martin Hirst, Jacqueline E. Schein, Doug E. Horsman, Joseph M. Connors, Randy D. Gascoyne, Marco A. Marra, Steven J. M. Jones posted to short-reads rna-seq de-bruijn assembly by dakelley on 2009-11-02 04:28:46 as along with 12 people fstrozzi orzenil n00c dswan torfinnnome TRHvidsten rtogawa ramonvidal stubrown darshan GustavoLacerda druvus
	Pindel: a pattern growth approach to detect break points of large deletions and medium sized insertions from paired-end short reads. [My Copy] Bioinformatics (Oxford, England), Vol. 25, No. 21. (1 November 2009), pp. 2865-2871. by Kai Ye, Marcel H. Schulz, Quan Long, Rolf Apweiler, Zemin Ning posted to structural_variation short-reads by dakelley on 2009-11-01 22:41:59 as along with 6 people darian torfinnnome n00c natstreet druvus vplagnol
	ALLPATHS 2: small genomes assembled accurately and with high continuity from short paired reads [My Copy] Genome Biology, Vol. 10, No. 10. (1 October 2009), R103. by Iain MacCallum, Dariusz Przybylski, Sante Gnerre, et al.Joshua Burton, Ilya Shlyakhter, Andreas Gnirke, Joel Malek, Kevin McKernan, Swati Ranade, Terrance Shea, Louise Williams, Sarah Young, Chad Nusbaum, David Jaffe posted to short-reads scaffolding de-bruijn assembly by dakelley on 2009-10-23 18:39:55 as along with 10 people and 1 group djkt n00c azazello jgill GustavoLacerda ramonvidal justinhjohnson stajich druvus neils Mycology
	BayesCall: A model-based base-calling algorithm for high-throughput short-read sequencing [My Copy] Genome Research, Vol. 19, No. 10. (6 October 2009), pp. 1884-1895. by Wei-Chun Kao, Kristian Stevens, Yun S. Song posted to short-reads base_calling by dakelley on 2009-10-15 21:03:49 as along with 15 people and 2 groups claire_jubin humburg heliopais lp2 megraw rdiaz torfinnnome djkt n00c farhat druvus polivares stajich fpattyn jbhiatt BergmanLab Mycology
	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 structural_variation short-reads assembly by dakelley on 2009-09-02 04:46:32 as along with 5 people seninp natstreet druvus jbhiatt abizar
	A Fast Hybrid Short Read Fragment Assembly Algorithm [My Copy] Bioinformatics In Bioinformatics, Vol. 25, No. 17. (17 June 2009), pp. btp374-2280. by Bertil Schmidt, Ranjan Sinha, Bryan Beresford-Smith, Simon J. Puglisi posted to short-reads assembly by dakelley on 2009-08-25 23:08:17 as along with 17 people and 2 groups darian torfinnnome hzoltan cthachuk orzenil GustavoLacerda APRegier katholt GeeSharpMinor dayjm djkt dswan pachorip natstreet druvus n00c jmeppley Bioinformatics Journal picks
	Swift: primary data analysis for the Illumina Solexa sequencing platform [My Copy] Bioinformatics, Vol. 25, No. 17. (1 September 2009), pp. 2194-2199. by Nava Whiteford, Tom Skelly, Christina Curtis, et al.Matt E. Ritchie, Andrea Lohr, Alexander W. Zaranek, Irina Abnizova, Clive Brown posted to short-reads by dakelley on 2009-08-25 22:51:45 as along with 23 people and 4 groups darian humburg n00c heliopais hzoltan sotacam lh49 djkt rtogawa cassj dswan torfinnnome rschulz natstreet druvus jasontsai jmeppley ghattem nuin polivares aprasad niallhaslam idoerg Bioinformatics BergmanLab SIMR bioinformatics Journal picks
	SHREC: a short-read error correction method [My Copy] Bioinformatics, Vol. 25, No. 17. (1 September 2009), pp. 2157-2163. by Jan Schroder, Heiko Schroder, Simon J. Puglisi, Ranjan Sinha, Bertil Schmidt posted to short-reads by dakelley on 2009-08-25 22:48:27 as along with 14 people and 1 group claire_jubin heliopais adthrasher skembel thegoose katholt sotacam djkt rtogawa torfinnnome natstreet druvus n00c jmeppley Journal picks
	Efficient frequency-based de novo short-read clustering for error trimming in next-generation sequencing. [My Copy] Genome research, Vol. 19, No. 7. (4 July 2009), pp. 1309-1315. by Wei Qu, Shin-Ichi Hashimoto, Shinichi Morishita posted to trimming short-reads by dakelley on 2009-07-14 22:48:50 as along with 9 people mpizbioinfo heliopais druvus n00c megraw nlapalu djkt operon natstreet
	Alta-Cyclic: a self-optimizing base caller for next-generation sequencing [My Copy] Nat Meth, Vol. 5, No. 8. (06 July 2008), pp. 679-682. by Yaniv Erlich, Partha P. Mitra, Melissa delaBastide, W. Richard McCombie, Gregory J. Hannon posted to svm short-reads machine_learning base_calling by dakelley on 2009-06-19 05:30:16 as along with 6 people n00c guhjy druvus natstreet caseybrown gdb
	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 short-reads base_calling by dakelley on 2009-06-17 21:18:10 as along with 16 people and 1 group heliopais orzenil n00c jfr usagi-kirin magusina malcook natstreet druvus iris42 abizar caseybrown reyez pengchy waszak nuin SIMR bioinformatics
	MapView: visualization of short reads alignment on a desktop computer [My Copy] Bioinformatics, Vol. 25, No. 12. (15 June 2009), pp. 1554-1555. by Hua Bao, Hui Guo, Jinwei Wang, Renchao Zhou, Xuemei Lu, Suhua Shi posted to short-reads visualization by dakelley on 2009-06-09 16:13:43 as along with 9 people and 1 group seb1 guhjy jmeppley n00c idonaldson dswan operon natstreet druvus 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 assembly short-reads by dakelley on 2009-05-18 15:52:23 as along with 19 people and 1 group claire_jubin darian n00c carlk APRegier jandot jonilaserson natstreet jessopher orzenil AaronDarling sphsmith jasontsai nmohelli jbhiatt druvus hpaces GustavoLacerda stajich Mycology
	Short read fragment assembly of bacterial genomes [My Copy] Genome Research, Vol. 18, No. 2. (1 February 2008), pp. 324-330. by Mark J. Chaisson, Pavel A. Pevzner posted to assembly short-reads by dakelley on 2009-05-18 15:49:06 as along with 17 people n00c pachorip APRegier thegoose2 Neeperando hpaces idoerg druvus jasontsai acn orzenil azazello GustavoLacerda dandaman caseybrown iris42 tharris
	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 assembly short-reads by dakelley on 2009-05-12 03:48:57 as along with 18 people and 2 groups darian GustavoLacerda n00c APRegier jonilaserson idoerg orzenil ela503 natstreet druvus azazello acn jasontsai jmeppley cisevol malcook Neeperando djkt BergmanLab SIMR bioinformatics
	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 assembly short-reads by dakelley on 2009-05-07 16:45:01 as along with 21 people and 2 groups orzenil humburg jfr azazello hzoltan cthachuk GustavoLacerda jasontsai n00c nuin skembel Thaverkamp reyez TRHvidsten djkt hpaces APRegier pengchy natstreet druvus darian iSEEM Bioinformatics
	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 assembly hpc short-reads by dakelley on 2009-04-30 18:05:40 as along with 27 people and 2 groups darian jfr cthachuk hzoltan ramonvidal orzenil pachorip GustavoLacerda jonilaserson operon polivares reyez jasontsai n00c humburg jessopher idonaldson robsyme neils natstreet AaronDarling druvus rpatward dswan stajich jbhiatt erikarner BergmanLab Mycology
	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 short-reads rna-seq hpc assembly by dakelley on 2009-04-30 18:04:42 as along with 3 people n00c natstreet Scis0000002
	QSRA: a quality-value guided de novo short read assembler. [My Copy] BMC bioinformatics, Vol. 10, No. 1. (2009) by Douglas W. Bryant, Weng-Keen K. Wong, Todd C. Mockler posted to assembly short-reads by dakelley on 2009-03-17 05:12:24 as along with 11 people and 2 groups michaelbarton hzoltan GustavoLacerda GeeSharpMinor jfr n00c pengchy natstreet stajich idoerg druvus Bioinformatics Mycology
	ALLPATHS: De novo assembly of whole-genome shotgun microreads [My Copy] Genome Research, Vol. 18, No. 5. (13 May 2008), pp. 810-820. by Jonathan Butler, Iain MacCallum, Michael Kleber, et al.Ilya A. Shlyakhter, Matthew K. Belmonte, Eric S. Lander, Chad Nusbaum, David B. Jaffe posted to assembly short-reads by dakelley on 2009-02-23 19:59:31 as along with 23 people and 1 group ajsferreira n00c carlk jmanning2k APRegier pachorip jonilaserson operon thegoose2 natstreet AaronDarling mhz druvus stajich azazello hpaces tharris jwhitney iris42 Neeperando sharpton GustavoLacerda GeeSharpMinor Mycology
	Velvet: algorithms for de novo short read assembly using de Bruijn graphs. [My Copy] Genome research In Genome Research, Vol. 18, No. 5. (18 May 2008), pp. 821-829. by Daniel R. Zerbino, Ewan Birney posted to assembly de-bruijn short-reads by dakelley on 2009-02-11 16:37:37 as along with 45 people and 3 groups claire_jubin danbolser humburg ajsferreira vplagnol bedo jwhitney cthachuk hzoltan azazello ajbattle jmanning2k n00c carlk pachorip APRegier jbhiatt jonilaserson operon jahwa jsatkosk sandfire thegoose2 katholt robsyme djkt hpaces AaronDarling mhz idoerg jmcq dswan jasontsai acn druvus natstreet nmohelli stajich farhat iris42 tharris Neeperando sharpton GustavoLacerda gdb Bioinformatics DeNovoAssembly-SIMR 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. A. Reinhardt, David A. A. Baltrus, Marc T. T. Nishimura, William R. R. Jeck, Corbin D. D. Jones, Jeffery R. R. Dangl posted to assembly short-reads by dakelley on 2009-02-08 18:34:41 as along with 15 people and 2 groups darian n00c michaelbarton pachorip ThomasDOtto robsyme orzenil AaronDarling druvus Huub_odc usagi-kirin abizar acn jbhiatt hpaces SIMR bioinformatics Bioinformatics
	Gene-Boosted Assembly of a Novel Bacterial Genome from Very Short Reads [My Copy] PLoS Comput Biol In PLoS Comput Biol, Vol. 4, No. 9. (26 September 2008), e1000186. by Steven L. Salzberg, Daniel D. Sommer, Daniela Puiu, Vincent T. Lee posted to assembly short-reads by dakelley on 2009-02-06 22:47:52 as along with 17 people and 5 groups skembel n00c operon michaelbarton azazello Thaverkamp sconlan GustavoLacerda treangen natstreet antonkratz druvus vaulot djkt Katje stajich semrich BergmanLab Papers recommended by the Roscoff Plankton Group iSEEM microbiology_nijmegen Mycology
	De novo bacterial genome sequencing: Millions of very short reads assembled on a desktop computer [My Copy] Genome Research, Vol. 18, No. 5. (10 May 2008), pp. 802-809. by David Hernandez, Patrice FranÃ§ois, Laurent Farinelli, Magne Ãsterã¥s, Jacques Schrenzel posted to assembly short-reads by dakelley on 2009-02-03 19:25:34 as along with 15 people and 4 groups n00c GeeSharpMinor pachorip operon druvus acn nmohelli GustavoLacerda jmeppley stajich azazello Katje iris42 balicea Neeperando DeNovoAssembly-SIMR microbiology_nijmegen Mycology gatech-compgenomics
	SHARCGS, a fast and highly accurate short-read assembly algorithm for de novo genomic sequencing. [My Copy] Genome research, Vol. 17, No. 11. (November 2007), pp. 1697-1706. by J. C. Dohm, C. Lottaz, T. Borodina, H. Himmelbauer posted to assembly short-reads by dakelley on 2009-01-27 23:08:24 as along with 16 people and 2 groups operon n00c robsyme acn druvus nmohelli natstreet timflutre stajich ghattem azazello GustavoLacerda niallhaslam flexer jwhitney iris42 DeNovoAssembly-SIMR Mycology
	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 assembly de-bruijn short-reads by dakelley on 2009-01-23 20:44:14 as along with 6 people darian n00c idoerg orzenil bioinfo nedwards
	Whole-Genome Sequencing and Assembly with High-Throughput, Short-Read Technologies [My Copy] PLoS ONE In PLoS ONE, Vol. 2, No. 5. (2007), e484. by Andreas Sundquist, Mostafa Ronaghi, Haixu Tang, Pavel Pevzner, Serafim Batzoglou posted to assembly short-reads by dakelley on 2009-01-22 20:01:27 as along with 12 people and 1 group n00c APRegier jessopher natstreet druvus idoerg GustavoLacerda orzenil guhjy azazello nedwards iris42 gatech-compgenomics
	Annotating genomes with massive-scale RNA sequencing. [My Copy] Genome biology, Vol. 9, No. 12. (2008), R175. by France Denoeud, Jean-Marc M. Aury, Corinne Da Silva, et al.Benjamin Noel, Odile Rogier, Massimo Delledonne, Michele Morgante, Giorgio Valle, Patrick Wincker, Claude Scarpelli, Olivier Jaillon, François Artiguenave posted to gene-finding rna-seq short-reads by dakelley on 2009-01-19 21:40:00 as along with 20 people and 1 group hzoltan cthachuk GustavoLacerda jamselem n00c jonilaserson ghattem nlapalu jmcq dandaman abizar inesdesantiago mhamada pengchy balicea fhalbrit GeeSharpMinor natstreet druvus neils SIMR bioinformatics
	Next-generation DNA sequencing [My Copy] Nature Biotechnology In Nat Biotech, Vol. 26, No. 10. (09 October 2008), pp. 1135-1145. by Jay Shendure, Hanlee Ji posted to review short-reads by dakelley on 2008-10-20 17:53:41 as along with 49 people and 3 groups tux2000 JamesBarger darian burak Jporci daforerog dchughes hzoltan cthachuk giovenko heliopais seb1 installe niallhaslam Vincent_Rouilly rschulz fishtank bluto Annab katholt jmcq michaelbarton n00c jfr dna nzm farhat idoerg mhz mmartin jbhiatt yupu behindtherabbit guhjy Pascalichouchou frohike ptrobajo zwang Zephyrus psique natstreet druvus nuin alexknight reyez dbk wsjames pengchy GeeSharpMinor Bioinformatics Roswell Cancer Crosstalk Oxford Virology
	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 by dakelley on 2008-09-12 03:42:28 as along with 21 people and 1 group claire_jubin darian heliopais hzoltan jonilaserson n00c druvus orzenil burak woodson8 sameersoi humburg poschm polivares Huub_odc usagi-kirin inesdesantiago jfr natstreet caseybrown GustavoLacerda microbiology_nijmegen

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assembly	65
short-reads	36
genetic-interactions	32
networks	27
metagenomics	26
review	24
duplications	24
clustering	20
structural_variation	18
haplotype	17
sequence-alignment	14
hmm	11
theory	10
modularity	10
gene-finding	10
genome_signatures	9
de-bruijn	9
gene-regulation	9
genome	7
network-evolution	7
epigenetics	7
classification	7
post-assembly	6
genomics	6
transcription	5
rna-seq	5
biology	5
crf	4
machine_learning	4
svm	4
cancer	4
statistics	4
comparative_assembly	4
scaffolding	4
base_calling	3
cow	3
visualization	3
hpc	3
molecular-evolution	3
dimension_reduction	3
rna	2
scaffold	2
intro	2
class	2
chip-seq	2
ncrna	1
gene-annotation	1
genetic_algorithm	1
education	1
mobile_genetic_elements	1
genome-evolution	1
parallel	1
trimming	1
strings	1
virology	1
mcmc	1
prokaryote	1
mirna	1

dakelley's short-reads [36 articles] Export Sort

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