idonaldson's ngs [26 articles] Export Sort

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	A practical comparison of methods for detecting transcription factor binding sites in ChIP-seq experiments [My Copy] BMC Genomics, Vol. 10, No. 1. (18 December 2009), 618. by Teemu Laajala, Sunil Raghav, Soile Tuomela, Riitta Lahesmaa, Tero Aittokallio, Laura Elo posted to tool peak_detection ngs comparison by idonaldson on 2009-12-21 09:34:38 as
	Impact of genome assembly status on ChIP-Seq and ChIP-PET data mapping. [My Copy] BMC research notes, Vol. 2, No. 1. (16 December 2009) by Nicolas Buisine, Laurent Sachs posted to ngs chip-seq by idonaldson on 2009-12-21 09:26:40 as
	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 tool short-read ngs mapping by idonaldson on 2009-12-15 14:32:13 as along with 23 people and 4 groups heliopais jfr cthachuk 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
	TopHat: discovering splice junctions with RNA-Seq [My Copy] Bioinformatics, Vol. 25, No. 9. (1 May 2009), pp. 1105-1111. by Cole Trapnell, Lior Pachter, Steven L. Salzberg posted to tool ngs chip-seq by idonaldson on 2009-12-15 14:31:32 as along with 27 people and 2 groups ongenetics juokcho cthachuk 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
	W-ChIPMotifs: a web application tool for de novo motif discovery from ChIP-based high-throughput data [My Copy] Bioinformatics In 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 4 people bsamal farhat nklee maximilianh
	BFAST: An Alignment Tool for Large Scale Genome Resequencing [My Copy] PloS one In 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 9 people darian MarkFiers gdb oannes n00c friendpine zwang druvus torfinnnome
	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 on 2009-11-03 12:07:51 as along with 28 people and 2 groups humburg 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 BergmanLab Mycology
	RNA-MATE: a recursive mapping strategy for high-throughput RNA-sequencing data [My Copy] Bioinformatics, Vol. 25, No. 19. (1 October 2009), pp. 2615-2616. by Nicole Cloonan, Qinying Xu, Geoffrey J. Faulkner, et al.Darrin F. Taylor, Dave T. P. Tang, Gabriel Kolle, Sean M. Grimmond posted to short-read rna-seq ngs mapping by idonaldson on 2009-10-28 10:21:04 as along with 14 people and 1 group hzoltan cthachuk ethanmj cassj GeeSharpMinor sbmontgomery shyamsg natstreet dswan druvus samgj n00c guhjy GustavoLacerda Journal picks
	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 short-read ngs mapping artefact by idonaldson on 2009-10-23 16:04:03 as along with 22 people and 1 group humburg darian orzenil hzoltan chvlyl operon kshameer djkt rtogawa seb1 nuin debasis jgill GeeSharpMinor sotacam torfinnnome walshtp heliopais jandot n00c rschulz druvus Journal picks
	Updates to the RMAP short-read mapping software [My Copy] Bioinformatics In Bioinformatics, Vol. 25, No. 21. (1 November 2009), pp. 2841-2842. by Andrew D. Smith, Wen-Yu Chung, Emily Hodges, et al.Jude Kendall, Greg Hannon, James Hicks, Zhenyu Xuan, Michael Q. Zhang posted to short-read ngs mapping by idonaldson on 2009-10-23 15:59:14 as along with 8 people and 1 group seb1 darian natstreet djkt rtogawa heliopais n00c druvus Journal picks
	A report on the 2009 SIG on short read sequencing and algorithms (Short-SIG) [My Copy] Bioinformatics, Vol. 25, No. 21. (1 November 2009), pp. 2863-2864. by Michael Brudno, Paul Medvedev, Jens Stoye, Francisco M. De La Vega posted to short-read ngs mapping by idonaldson on 2009-10-23 15:55:37 as along with 3 people seb1 n00c druvus
	Chromosome Conformation Capture Carbon Copy (5C): a massively parallel solution for mapping interactions between genomic elements. [My Copy] Genome research, Vol. 16, No. 10. (October 2006), pp. 1299-1309. by Josée Dostie, Todd A. Richmond, Ramy A. Arnaout, et al.Rebecca R. Selzer, William L. Lee, Tracey A. Honan, Eric D. Rubio, Anton Krumm, Justin Lamb, Chad Nusbaum, Roland D. Green, Job Dekker posted to ngs 5c by idonaldson on 2009-10-22 09:43:54 as along with 5 people TorstenWaldminghaus polivares WanderingAengus elzodw mdimon
	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 tool short-read ngs mapping by idonaldson on 2009-10-22 09:32:17 as along with 33 people and 2 groups joshdsullivan cthachuk hzoltan jfr walshtp 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
	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 short-read ngs mapping by idonaldson on 2009-10-22 09:25:47 as along with 48 people and 4 groups michaelbarton Jporci kevinemamy heliopais jforment jfr burak idoerg Geknitics cthachuk hzoltan chvlyl sameersoi hpaces gdv GeeSharpMinor 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 dswan reyez kshameer TRHvidsten djkt ppgardne Bioinformatics Core Service BergmanLab Bioinformatics Journal picks
	BayesPeak: Bayesian analysis of ChIP-seq data [My Copy] BMC Bioinformatics, Vol. 10, No. 1. (2009), 299. by Christiana Spyrou, Rory Stark, Andy Lynch, Simon Tavare posted to tool ngs chip-seq by idonaldson on 2009-09-28 10:30:42 as along with 11 people and 4 groups Vincent_Rouilly tonamswish dswan fenghezi inesdesantiago polivares mkiyer druvus stajich humburg rschulz Bioinformatics JLab BergmanLab Mycology
	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 tool ngs by idonaldson on 2009-09-28 10:04:43 as along with 29 people and 2 groups MarkFiers n00c darian cthachuk hzoltan seb1 heliopais urgi GustavoLacerda stubrown cassj kshameer ciax polivares carlosjavierna jandot katholt jmcq guhjy orzenil jasontsai operon farhat AlexBateman chrisamiller nuin natstreet sandfire druvus BergmanLab Journal picks
	The transcriptional program controlled by the stem cell leukemia gene Scl/Tal1 during early embryonic hematopoietic development. [My Copy] Blood, Vol. 113, No. 22. (28 May 2009), pp. 5456-5465. by Nicola K. Wilson, Diego Miranda-Saavedra, Sarah Kinston, et al.Nicolas Bonadies, Samuel D. Foster, Fernando Calero-Nieto, Mark A. Dawson, Ian J. Donaldson, Stephanie Dumon, Jonathan Frampton, Rekin's Janky, Xiao-Hong H. Sun, Sarah A. Teichmann, Andrew J. Bannister, Berthold Göttgens posted to ngs me gottgens chip-seq by idonaldson on 2009-09-10 14:43:46 as
	ID1 promotes expansion and survival of primary erythroid cells and is a target of JAK2V617F-STAT5 signaling. [My Copy] Blood, Vol. 114, No. 9. (27 August 2009), pp. 1820-1830. by Andrew D. Wood, Edwin Chen, Ian J. Donaldson, et al.Shilpa Hattangadi, Karly A. Burke, Mark A. Dawson, Diego Miranda-Saavedra, Harvey F. Lodish, Anthony R. Green, Berthold Göttgens posted to ngs me gottgens chip-seq by idonaldson on 2009-09-10 14:42:52 as
	ChIP\|[ndash]\|seq: advantages and challenges of a maturing technology [My Copy] Nature Reviews Genetics, Vol. 10, No. 10. (08 September 2009), pp. 669-680. by Peter J. Park posted to review ngs chip-seq by idonaldson on 2009-09-10 11:45:38 as along with 25 people and 6 groups guhjy akakak hzoltan dchughes RyuOgawa heliopais giovenko inesdesantiago pradiptaray dakelley clearbluespring akundaje rdiaz kimorley leliavski humburg reyez qayub fenghezi tonamswish robertrentzsch polivares rschulz cvaldes danmaclean Journal picks Orengo Group Journal Picks JLab BergmanLab CTCF Chromatin
	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 short-read ngs mapping by idonaldson on 2009-07-23 12:00:25 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 michaelbarton polivares darian orzenil cassj inesdesantiago TRHvidsten djkt operon ghattem n00c danmaclean ppgardne nuin rschulz natstreet druvus humburg BergmanLab SIMR bioinformatics Bioinformatics Journal picks
	SOAP2: an improved ultrafast tool for short read alignment [My Copy] Bioinformatics, Vol. 25, No. 15. (1 August 2009), pp. 1966-1967. by Ruiqiang Li, Chang Yu, Yingrui Li, et al.Tak-Wah Lam, Siu-Ming Yiu, Karsten Kristiansen, Jun Wang posted to short-read ngs mapping by idonaldson on 2009-07-20 13:09:06 as along with 28 people and 6 groups darian nuin hzoltan agbiotec torfinnnome natstreet cthachuk jforment GustavoLacerda adijr bozdagd stubrown polivares guhjy ollieredfernwork operon cassj adamjamesreid Stew jamselem dswan TRHvidsten humburg djkt farhat n00c jmeppley druvus Bioinformatics Core Service BergmanLab Orengo Group Journal Picks Bioinformatics - CRUK Bioinformatics Journal picks
	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 visualisation tool ngs mapping by idonaldson on 2009-05-29 10:00:06 as along with 9 people and 1 group seb1 guhjy jmeppley dakelley n00c dswan operon natstreet druvus Bioinformatics
	ProbeMatch: rapid alignment of oligonucleotides to genome allowing both gaps and mismatches [My Copy] Bioinformatics, Vol. 25, No. 11. (1 June 2009), pp. 1424-1425. by You Jung Kim, Nikhil Teletia, Victor Ruotti, et al.Christopher A. Maher, Arul M. Chinnaiyan, Ron Stewart, James A. Thomson, Jignesh M. Patel posted to tool short-read ngs mapping by idonaldson on 2009-05-22 10:36:30 as along with 14 people and 2 groups bsamal Julien_Fayolle jfr mmartin n00c guhjy nuin AlexBateman bmajoros humburg Thaverkamp druvus svenrahmann djkt Bioinformatics Journal picks
	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 short-read ngs mapping by idonaldson on 2009-05-12 09:23:28 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 orzenil Thaverkamp natstreet druvus fenghezi Stew inesdesantiago neils Bioinformatics Chinnaiyan Lab BergmanLab SIMR bioinformatics Bioinformatics - CRUK
	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 short-read ngs mapping by idonaldson on 2009-05-01 14:53:10 as along with 39 people and 4 groups oannes mijam nuin jfr hzoltan cthachuk darshan fstrozzi adijr debasis bozdagd polivares torfinnnome n00c talponer jmcq rschulz ghattem operon humburg 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
	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-read ngs assembler by idonaldson on 2009-04-27 09:57:13 as along with 27 people and 2 groups darian jfr cthachuk hzoltan ramonvidal orzenil pachorip GustavoLacerda jonilaserson operon polivares reyez jasontsai n00c humburg dakelley jessopher robsyme neils natstreet AaronDarling druvus rpatward dswan stajich jbhiatt erikarner BergmanLab Mycology

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evolutionary_constraint	1
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indirect	1
g4	1
sumoylation	1
transcription	1
ucsc	1
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