jfr's deep_sequencing [42 articles] Export

Recent papers added to jfr's library classified by the tag deep_sequencing. You can also see everyone's deep_sequencing.

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	High-resolution mapping of copy-number alterations with massively parallel sequencing. [My Copy] Nature methods, Vol. 6, No. 1. (30 January 2009), pp. 99-103. by Derek Y. Chiang, Gad Getz, David B. Jaffe, et al.Michael J. O'Kelly, Xiaojun Zhao, Scott L. Carter, Carsten Russ, Chad Nusbaum, Matthew Meyerson, Eric S. Lander posted to deep_sequencing copy-number by jfr on 2009-11-25 14:59:37 as along with 6 people Annab stubrown stsaft jbhiatt absterga xwbcn
	Limitations and possibilities of small RNA digital gene expression profiling [My Copy] Nat Meth, Vol. 6, No. 7. (01 July 2009), pp. 474-476. by Sam E. V. Linsen, Elzo de Wit, Georges Janssens, et al.Sheila Heater, Laura Chapman, Rachael K. Parkin, Brian Fritz, Stacia K. Wyman, Ewart de Bruijn, Emile E. Voest, Scott Kuersten, Muneesh Tewari, Edwin Cuppen posted to technology mirna deep_sequencing by jfr on 2009-11-25 11:15:03 as along with 8 people and 2 groups vingron pengchy guhjy lp2 timhubbard stajich gdb fpattyn RGASP Mycology
	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 software read_mapping deep_sequencing by jfr on 2009-11-19 11:28:31 as along with 36 people and 4 groups hzoltan cthachuk 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
	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 software read_mapping deep_sequencing by jfr on 2009-11-19 11:26:57 as along with 26 people and 2 groups cthachuk 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
	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 software read_mapping deep_sequencing by jfr on 2009-11-18 13:06:08 as along with 22 people and 4 groups heliopais 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
	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 software read_mapping deep_sequencing by jfr on 2009-11-15 15:51:50 as along with 13 people and 2 groups Julien_Fayolle mmartin n00c guhjy nuin idonaldson AlexBateman bmajoros humburg Thaverkamp druvus svenrahmann djkt Bioinformatics Journal picks
	A transcriptional sketch of a primary human breast cancer by 454 deep sequencing. [My Copy] BMC genomics, Vol. 10, No. 1. (2009), 163. by Alessandro Guffanti, Michele Iacono, Paride Pelucchi, et al.Namshin Kim, Giulia Soldà, Larry J. Croft, Ryan J. Taft, Ermanno Rizzi, Marjan Askarian-Amiri, Raoul J. Bonnal, Maurizio Callari, Flavio Mignone, Graziano Pesole, Giovanni Bertalot, Luigi Rossi R. Bernardi, Alberto Albertini, Christopher Lee, John S. Mattick, Ileana Zucchi, Gianluca De Bellis posted to deep_sequencing breast_cancer 454 by jfr on 2009-11-15 14:36:27 as along with 4 people guhjy jonilaserson fenghezi alessandro_guffanti
	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 software review read_mapping deep_sequencing by jfr on 2009-11-10 17:28:25 as along with 30 people and 5 groups agbiotec burak cthachuk hzoltan tonamswish heliopais giovenko 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
	mRNA-Seq whole-transcriptome analysis of a single cell [My Copy] Nature Methods, Vol. 6, No. 5. (06 April 2009), pp. 377-382. by Fuchou Tang, Catalin Barbacioru, Yangzhou Wang, et al.Ellen Nordman, Clarence Lee, Nanlan Xu, Xiaohui Wang, John Bodeau, Brian B. Tuch, Asim Siddiqui, Kaiqin Lao, M. Azim Surani posted to technology single_cell mrna-seq deep_sequencing by jfr on 2009-11-09 14:42:04 as along with 16 people hzoltan inesdesantiago heliopais manduca debasis Vincent_Rouilly mtagaya woodson8 gdb guhjy kintoki fenghezi absterga jbhiatt pengchy sleepingcell
	Genome-wide massively parallel sequencing of formaldehyde fixed-paraffin embedded (FFPE) tumor tissues for copy-number- and mutation-analysis. [My Copy] PloS one, Vol. 4, No. 5. (2009) by Michal R. Schweiger, Martin Kerick, Bernd Timmermann, et al.Marcus W. Albrecht, Tatjana Borodina, Dmitri Parkhomchuk, Kurt Zatloukal, Hans Lehrach posted to technology mutation ffpe deep_sequencing copy-number by jfr on 2009-11-08 23:11:35 as along with 1 person reyez
	Power of deep, all-exon resequencing for discovery of human trait genes. [My Copy] Proceedings of the National Academy of Sciences of the United States of America, Vol. 106, No. 10. (10 March 2009), pp. 3871-3876. by Gregory V. Kryukov, Alexander Shpunt, John A. Stamatoyannopoulos, Shamil R. Sunyaev posted to deep_sequencing by jfr on 2009-11-02 16:06:33 as along with 5 people daforerog jsatkosk guhjy lp2 bpcusack
	MOM: maximum oligonucleotide mapping [My Copy] Bioinformatics, Vol. 25, No. 7. (1 April 2009), pp. 969-970. by Hugh L. Eaves, Yuan Gao posted to alignment deep_sequencing software by jfr on 2009-07-22 16:26:50 as along with 9 people Julien_Fayolle heliopais seb1 n00c cassj rschulz mmartin guhjy druvus
	Ab initio construction of a eukaryotic transcriptome by massively parallel mRNA sequencing [My Copy] Proceedings of the National Academy of Sciences, Vol. 106, No. 9. (3 March 2009), pp. 3264-3269. by Moran Yassour, Tommy Kaplan, Hunter B. Fraser, et al.Joshua Z. Levin, Jenna Pfiffner, Xian Adiconis, Gary Schroth, Shujun Luo, Irina Khrebtukova, Andreas Gnirke, Chad Nusbaum, Dawn-Anne Thompson, Nir Friedman, Aviv Regev posted to deep_sequencing genomics by jfr on 2009-07-22 12:57:26 as along with 8 people and 1 group hzoltan fstrozzi GustavoLacerda stubrown stajich GeeSharpMinor jmcq provero Mycology
	QSRA: a quality-value guided de novo short read assembler. [My Copy] BMC bioinformatics, Vol. 10, No. 1. (2009) by D. W. Bryant, W. K. Wong, T. C. Mockler posted to deep_sequencing software by jfr on 2009-07-09 13:04:13 as along with 10 people and 2 groups hzoltan GustavoLacerda GeeSharpMinor n00c dakelley pengchy natstreet stajich idoerg druvus Bioinformatics Mycology
	What would you do if you could sequence everything? [My Copy] Nature Biotechnology, Vol. 26, No. 10. (01 October 2008), pp. 1125-1133. by Avak Kahvejian, John Quackenbush, John F. Thompson posted to comment deep_sequencing genomics integration by jfr on 2009-06-11 11:26:31 as along with 19 people n00c hzoltan seb1 inesdesantiago heliopais stubrown installe Annab Borelli jbhiatt Pascalichouchou bertelsen frohike natstreet druvus reyez alexknight psique GeeSharpMinor
	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 deep_sequencing review by jfr on 2009-06-11 11:20:39 as along with 47 people and 3 groups burak Jporci daforerog dchughes hzoltan cthachuk giovenko heliopais seb1 installe niallhaslam Vincent_Rouilly rschulz fishtank bluto Annab katholt jmcq michaelbarton n00c 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
	The development and impact of 454 sequencing [My Copy] Nat Biotech, Vol. 26, No. 10. (October 2008), pp. 1117-1124. by Jonathan M. Rothberg, John H. Leamon posted to deep_sequencing review by jfr on 2009-06-11 11:19:11 as along with 11 people katholt n00c yupu frohike natstreet druvus nuin alexknight reyez psique GeeSharpMinor
	A large genome center's improvements to the Illumina sequencing system [My Copy] Nature Methods, Vol. 5, No. 12. (25 November 2008), pp. 1005-1010. by Michael A. Quail, Iwanka Kozarewa, Frances Smith, et al.Aylwyn Scally, Philip J. Stephens, Richard Durbin, Harold Swerdlow, Daniel J. Turner posted to deep_sequencing protocol quality_control by jfr on 2009-03-23 15:59:27 as along with 13 people and 1 group seb1 Annab polivares katholt hagechouchin443 sandfire natstreet druvus vmsr azazello clearbluespring jbhiatt caseybrown JLab
	Deep surveying of alternative splicing complexity in the human transcriptome by high-throughput sequencing [My Copy] Nature Genetics, Vol. 40, No. 12. (02 November 2008), pp. 1413-1415. by Qun Pan, Ofer Shai, Leo J. Lee, Brendan J. Frey, Benjamin J. Blencowe posted to alternative_splicing deep_sequencing by jfr on 2009-03-12 10:48:29 as along with 21 people ongenetics hzoltan torfinnnome n00c ericrpaquet jonilaserson ThomasDOtto giovanni frohike fenghezi zxmon21 jmcq poschm wimufi xingxu inesdesantiago jbhiatt rschulz djkt dchughes GeeSharpMinor
	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 deep_sequencing low_level quality_control by jfr on 2009-02-23 11:34:50 as along with 38 people and 2 groups seninp 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 druvus dandaman xingxu rschulz jmcq inesdesantiago Neeperando nmohelli matthewsuderman bpb gdb farhat SIMR bioinformatics BergmanLab
	In-depth characterization of the microRNA transcriptome in a leukemia progression model [My Copy] Genome Research, Vol. 18, No. 11. (November 2008), pp. 1787-1797. by Florian Kuchenbauer, Ryan D. Morin, Bob Argiropoulos, et al.Oleh I. Petriv, Malachi Griffith, Michael Heuser, Eric Yung, Jessica Piper, Allen Delaney, Anna-Liisa Prabhu, Yongjun Zhao, Helen Mcdonald, Thomas Zeng, Martin Hirst, Carl L. Hansen, Marco A. Marra, R. Keith Humphries posted to deep_sequencing leukemia mirna progression by jfr on 2009-02-23 10:57:42 as along with 3 people and 1 group heliopais gdb samgj microRNA
	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 deep_sequencing low_level quality_control by jfr on 2009-02-20 16:36:20 as along with 16 people and 1 group heliopais orzenil n00c dakelley usagi-kirin magusina malcook natstreet druvus iris42 abizar caseybrown reyez pengchy waszak nuin SIMR bioinformatics
	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 comparison deep_sequencing inter-laboratory microarray_technology by jfr on 2009-02-20 12:41:03 as along with 26 people zufar manduca hzoltan GustavoLacerda stubrown GeeSharpMinor n00c guhjy hcoller daed poschm stsaft azazello slevy03 felsani usagi-kirin shikin coela cthachuk ojabado caseybrown abizar natstreet druvus rschulz pengchy
	Model-based Analysis of ChIP-Seq (MACS) [My Copy] Genome Biology, Vol. 9, No. 9. (2008), R137. by Yong Zhang, Tao Liu, Clifford Meyer, et al.Jerome Eeckhoute, David Johnson, Bradley Bernstein, Chad Nussbaum, Richard Myers, Myles Brown, Wei Li, X. Shirley Liu posted to chip-seq deep_sequencing software by jfr on 2009-01-10 11:01:19 as along with 24 people and 2 groups hzoltan Vincent_Rouilly darian stubrown mkiyer humburg cassj floatingpoint WanderingAengus bryankr rschulz mcm polivares gdb ghattem yadadi djkt stajich mdperry fpattyn bcondon idonaldson caseybrown kengg SIMR bioinformatics Mycology
	F-Seq: a feature density estimator for high-throughput sequence tags [My Copy] Bioinformatics, Vol. 24, No. 21. (1 November 2008), pp. 2537-2538. by Alan P. Boyle, Justin Guinney, Gregory E. Crawford, Terrence S. Furey posted to chip-seq deep_sequencing software by jfr on 2008-12-09 16:04:20 as along with 18 people and 2 groups hzoltan n00c darian idonaldson michaelbarton inesdesantiago gdb ewilban1 tonamswish guhjy kmdaily cassj fhalbrit rschulz polivares cthachuk zhouyu aprasad JLab BergmanLab
	Analysis of large-scale sequencing of small RNAs. [My Copy] Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing (2008), pp. 126-136. by A. J. Olson, J. Brennecke, A. A. Aravin, G. J. Hannon, R. Sachidanandam posted to deep_sequencing non-coding by jfr on 2008-11-28 14:27:01 as along with 2 people tonamswish lp2
	Using quality scores and longer reads improves accuracy of Solexa read mapping [My Copy] BMC Bioinformatics, Vol. 9, No. 1. (28 February 2008), 128. by Andrew Smith, Zhenyu Xuan, Michael Zhang posted to deep_sequencing quality_control by jfr on 2008-11-18 15:50:15 as along with 18 people hzoltan seb1 heliopais bozdagd katholt inesdesantiago n00c maren floatingpoint lukaswindhager natstreet druvus pengchy farhat ghattem mdimon kmdaily caseybrown
	Rapid whole-genome mutational profiling using next-generation sequencing technologies. [My Copy] Genome research, Vol. 18, No. 10. (4 October 2008), pp. 1638-1642. by Douglas R. Smith, Aaron R. Quinlan, Heather E. Peckham, et al.Kathryn Makowsky, Wei Tao, Betty Woolf, Lei Shen, William F. Donahue, Nadeem Tusneem, Michael P. Stromberg, Donald A. Stewart, Lu Zhang, Swati S. Ranade, Jason B. Warner, Clarence C. Lee, Brittney E. Coleman, Zheng Zhang, Stephen F. McLaughlin, Joel A. Malek, Jon M. Sorenson, Alan P. Blanchard, Jarrod Chapman, David Hillman, Feng Chen, Daniel S. Rokhsar, Kevin J. McKernan, Thomas W. Jeffries, Gabor T. Marth, Paul M. Richardson posted to deep_sequencing mutation by jfr on 2008-11-17 14:28:18 as along with 7 people n00c robsyme druvus skoddet yupu jmcq GeeSharpMinor
	An integrated genomic analysis of human glioblastoma multiforme. [My Copy] Science (New York, N.Y.), Vol. 321, No. 5897. (26 September 2008), pp. 1807-1812. by D. Williams Parsons, Siân Jones, Xiaosong Zhang, et al.Jimmy Cheng-Ho C. Lin, Rebecca J. Leary, Philipp Angenendt, Parminder Mankoo, Hannah Carter, I-Mei M. Siu, Gary L. Gallia, Alessandro Olivi, Roger McLendon, B. Ahmed Rasheed, Stephen Keir, Tatiana Nikolskaya, Yuri Nikolsky, Dana A. Busam, Hanna Tekleab, Luis A. Diaz, James Hartigan, Doug R. Smith, Robert L. Strausberg, Suely Kazue Nagahashi K. Marie, Sueli Mieko Oba M. Shinjo, Hai Yan, Gregory J. Riggins, Darell D. Bigner, Rachel Karchin, Nick Papadopoulos, Giovanni Parmigiani, Bert Vogelstein, Victor E. Velculescu, Kenneth W. Kinzler posted to brain_cancer deep_sequencing by jfr on 2008-11-07 09:39:29 as along with 15 people and 2 groups VGreiff stubrown Zephyrus zufar dolchan frohike caseybrown wimufi srp33 renatomilani brianb shikin aheilbut songpku giovenko GeneGo Roswell Cancer Crosstalk
	Core Signaling Pathways in Human Pancreatic Cancers Revealed by Global Genomic Analyses [My Copy] Science (4 September 2008), 1164368. by Sian Jones, Xiaosong Zhang, D. Williams Parsons, et al.Jimmy C. Lin, Rebecca J. Leary, Philipp Angenendt, Parminder Mankoo, Hannah Carter, Hirohiko Kamiyama, Antonio Jimeno, Seung-Mo Hong, Baojin Fu, Ming-Tseh Lin, Eric S. Calhoun, Mihoko Kamiyama, Kimberly Walter, Tatiana Nikolskaya, Yuri Nikolsky, James Hartigan, Douglas R. Smith, Manuel Hidalgo, Steven D. Leach, Alison P. Klein, Elizabeth M. Jaffee, Michael Goggins, Anirban Maitra, Christine Iacobuzio-Donahue, James R. Eshleman, Scott E. Kern, Ralph H. Hruban, Rachel Karchin, Nickolas Papadopoulos, Giovanni Parmigiani, Bert Vogelstein, Victor E. Velculescu, Kenneth W. Kinzler posted to deep_sequencing pancreatic_cancer by jfr on 2008-11-07 09:36:28 as along with 18 people and 3 groups zufar jbhiatt dolchan wimufi jo_davies srp33 whh98 roys cmzmasek thomaskelder fongkoh AlexanderPico SaraNasser renatomilani brianb shikin songpku giovenko ConklinLab GeneGo Roswell Cancer Crosstalk
	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 deep_sequencing quality_control by jfr on 2008-11-05 14:19:17 as along with 19 people and 1 group heliopais hzoltan jonilaserson n00c druvus orzenil burak woodson8 sameersoi humburg poschm polivares Huub_odc usagi-kirin inesdesantiago natstreet dakelley caseybrown GustavoLacerda microbiology_nijmegen
	A global view of gene activity and alternative splicing by deep sequencing of the human transcriptome. [My Copy] Science (New York, N.Y.), Vol. 321, No. 5891. (15 August 2008), pp. 956-960. by M. Sultan, M. H. Schulz, H. Richard, et al.A. Magen, A. Klingenhoff, M. Scherf, M. Seifert, T. Borodina, A. Soldatov, D. Parkhomchuk, D. Schmidt, S. O'Keeffe, S. Haas, M. Vingron, H. Lehrach, M. L. Yaspo posted to alternative_splicing deep_sequencing by jfr on 2008-10-15 14:51:01 as along with 28 people and 2 groups hzoltan zufar eszczurek n00c dna inesdesantiago ilyashl TRHvidsten poschm bertelsen ivanek guhjy wutongbin raistrick gracio xingxu psique oelemento Ema reyez caseybrown kjglennie dh0000 GeeSharpMinor balicea djkt ArtemPankin zwang BenosLab Khavkin's lab
	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 comparison deep_sequencing microarray_technology by jfr on 2008-10-14 17:54:03 as along with 48 people and 3 groups AndersI zufar cthachuk 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 dakelley Ema balicea vega lusk semrich vmarshal fpattyn stajich giovanni ela503 Stew guhjy kengg shurjo GustavoLacerda CPI UU SIMR bioinformatics Mycology
	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 deep_sequencing genomics by jfr on 2008-09-18 15:52:35 as along with 42 people and 2 groups manduca cthachuk 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 myourshaw megraw GeeSharpMinor caseybrown xingxu guhjy shurjo gdb Bioinformatics SIMR bioinformatics
	The complete genome of an individual by massively parallel DNA sequencing. [My Copy] Nature, Vol. 452, No. 7189. (17 April 2008), pp. 872-876. by David A. Wheeler, Maithreyan Srinivasan, Michael Egholm, et al.Yufeng Shen, Lei Chen, Amy McGuire, Wen He, Yi-Ju J. Chen, Vinod Makhijani, G. Thomas Roth, Xavier Gomes, Karrie Tartaro, Faheem Niazi, Cynthia L. Turcotte, Gerard P. Irzyk, James R. Lupski, Craig Chinault, Xing-zhi Z. Song, Yue Liu, Ye Yuan, Lynne Nazareth, Xiang Qin, Donna M. Muzny, Marcel Margulies, George M. Weinstock, Richard A. Gibbs, Jonathan M. Rothberg posted to deep_sequencing by jfr on 2008-09-05 13:40:11 as along with 23 people and 2 groups rshe n00c jonilaserson jessopher daforerog behindtherabbit frohike reyez pengchy adijr jo_davies orzenil dullhunk djkt ramensky psique caseybrown melting dbensasson bpb Neeperando Huub_odc guhjy parkinson's disease references microbiology_nijmegen
	Identification of somatically acquired rearrangements in cancer using genome-wide massively parallel paired-end sequencing. [My Copy] Nature genetics, Vol. 40, No. 6. (27 June 2008), pp. 722-729. by Peter J. Campbell, Philip J. Stephens, Erin D. Pleasance, et al.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. Edwards, Graham R. Bignell, Michael R. Stratton, P. Andrew Futreal posted to deep_sequencing lung_cancer by jfr on 2008-09-03 16:36:05 as along with 12 people chvlyl dakelley APRegier myzhang jessopher frohike smiddha xingxu daed matthewsuderman caseybrown chrisamiller
	The new paradigm of flow cell sequencing [My Copy] Genome Research, Vol. 18, No. 6. (1 June 2008), pp. 839-846. by Robert A. Holt, Steven J. M. Jones posted to deep_sequencing review sequencing by jfr on 2008-08-04 15:50:41 as along with 18 people and 1 group n00c mtagaya thegoose2 idoerg treangen druvus kintoki tmmurali stajich reyez lp2 GustavoLacerda tharris balicea caseybrown dchughes hpaces serdarbozdag Mycology
	Discovering microRNAs from deep sequencing data using miRDeep [My Copy] Nat Biotech, Vol. 26, No. 4. (April 2008), pp. 407-415. by Marc R. Friedlander, Wei Chen, Catherine Adamidi, et al.Jonas Maaskola, Ralf Einspanier, Signe Knespel, Nikolaus Rajewsky posted to deep_sequencing mirna by jfr on 2008-06-27 09:11:18 as along with 13 people and 3 groups hzoltan thegoose2 natstreet fishtank ealloza GustavoLacerda iris42 tharris tmmurali giovanni stajich heliopais gdb C. elegans / WormBase Mycology microRNA
	Application of massively parallel sequencing to microRNA profiling and discovery in human embryonic stem cells. [My Copy] Genome research, Vol. 18, No. 4. (19 April 2008), pp. 610-621. by Ryan D. Morin, Michael D. O'Connor, Malachi Griffith, et al.Florian Kuchenbauer, Allen Delaney, Anna-Liisa L. Prabhu, Yongjun Zhao, Helen McDonald, Thomas Zeng, Martin Hirst, Connie J. Eaves, Marco A. Marra posted to deep_sequencing mirna stem_cell by jfr on 2008-05-16 10:35:12 as along with 11 people and 2 groups hzoltan giovenko ealloza fishtank inesdesantiago GustavoLacerda heliopais stajich maralena caseybrown gdb microRNA 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 bioinformatics deep_sequencing review by jfr on 2008-04-30 17:58:27 as along with 36 people Jporci cthachuk 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 tharris mariakmejia caseybrown yoonk druvus
	Computational analysis of small RNA cloning data. [My Copy] Methods (San Diego, Calif.) In MicroRNAs: Part B, Vol. 44, No. 1. (January 2008), pp. 13-21. by Philipp Berninger, Dimos Gaidatzis, Erik van Nimwegen, Mihaela Zavolan posted to deep_sequencing methodology by jfr on 2008-04-14 10:22:27 as along with 3 people orzenil guhjy delenca
	Gene expression profiling by massively parallel sequencing. [My Copy] Genome research, Vol. 18, No. 1. (21 January 2008), pp. 172-177. by Tatiana Teixeira T. Torres, Muralidhar Metta, Birgit Ottenwälder, Christian Schlötterer posted to deep_sequencing genomics by jfr on 2008-02-29 16:48:19 as along with 19 people oannes hzoltan manduca n00c druvus daed floatingpoint inesdesantiago orzenil guhjy dchughes stsaft echinotrix giovanni caseybrown ghattem idonaldson ohara gracio

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breast_cancer	477
mirna	348
review	345
software	275
classification	272
colon_cancer	234
gene_expression	176
methodology	169
copy-number	161
network	148
integration	138
microarray_technology	133
bioinformatics	122
clustering	121
feature_selection	106
meta-analysis	97
affy	86
database	82
therapy	80
mirna_target	77
gene_set_analysis	69
array-cgh	69
crc_bib	69
regulation	67
low_level	66
rt-pcr	64
systems_biology	63
genomics	60
pathway_analysis	60
subtypes	58
snp-arrays	57
annotation	57
comment	53
quality_control	49
metastasis	47
normalization	46
mutations	43
deep_sequencing	42
ffpe	41
prognosis	41
microarray_analysis	40
estrogen	40
proteomics	39
cancer	38
bioconductor	37
statistics	37
protein_interaction	35
alternative_splicing	35
progression	35
markers	35
fdr	34
snp	33
methylation	32
r	31
standards	29
mutation	28
tamoxifen	28
class_discovery	28
exon_arrays	25
jfrbib	24
two-color	24
ovarian_cancer	23
mir17-92	23
microarray_protocol	23
pathway	22
experiment_design	22
comparison	21
brca	21
co-expression	21
tfbs	20
survival_analysis	20
model	20
kras	20
p53	19
treatment	19
functional_analysis	19
platform_comparison	18
technology	17
multiple_testing	17
biomarker	16
stem_cell	16
jfrbib04-09	16
module_detection	16
evaluation	16
illumina	16
chip-chip	16
text-mining	15
antisense	15
reproducible_research	15
nmf	15
sequencing	14
bio_signature	14
erbb	14
basal_subtype	14
lung_cancer	13
staging	13
rna_quality	13
stageii	13
egfr	13
tma	13
cell_line	12
cnv	12
marker	12
gene_ontology	12
maqc	12
genotyping	12
loh	11
drug_discovery	11
gene_lists	11
pten	11
missing_values	11
proliferation	11
protocol	11
semantic_web	11
immunohistochemistry	10
disease_genes	10
visualization	10
genome_browser	10
tissue_specificity	10
control_genes	10
tgfb	10
mirna_regulation	10
msi	9
inter-laboratory	9
probe_design	9
segmentation	9
e2f1	8
can_genes	8
chemotherapy	8
sample_size	8
consensus_clustering	8
chip-seq	8
boutique_arrays	8
personalized_medicine	8
myc	8
time-course	8
editorial	8
plos_start	7
18q_loh	7
tiling_array	7
validation	7
mir21	7
lymphoma	7
plos_rules	7
hpc	6
serum	6
er	6
read_mapping	6
promoters	6
stem	6
motif	6
correlation	6
gene_interaction	6
non-coding	6
leukemia	6
community	6
ontology	6
nci60	6
graphs	6
plos_primer	5
radiation	5
cross-platform	5
grid_computing	5
gene_pairs	5
her2	5
trial	5
gwas	5
prostate_cancer	5
functional_genomics	5
survival	5
machine_learning	5
cin	5
prioritization	5
mir34	4
public_data	4
pooling	4
data_curation	4
resource	4
mirna_cluster	4
biobank	4
image_analysis	4
open-source	4
pr	4
web_services	4
lims	4
mir192	4
grading	4
functional_classification	4
go	4
micro_environment	3
primer	3
bim	3
confounders	3
tutorial	3
mass_spec	3
interaction	3
small_molecule	3
outlier	3
apc	3
low-level	3
wnt	3
svm	3
stroma	3
sop	3
epigenetics	3
chromatin	3
er-positive	3
copa	3
mage	3
sage	3
ngs	3
in-situ	3
roc	3
letter	3
pik3ca	3
evolution	3
hapmap	3
loops	3
cross-study	3
agilent	3
stability	3
glioblastoma	3
triple_negative	3
ontologies	3
biomarkers	3
pca	3
web_server	3
estradiol	2
guidelines	2
lymphocytes	2
ephb	2
ranked_lists	2
luminal_subtype	2
batch-effect	2
filtering	2
cloud_computing	2
serm	2
permutations	2
8q24	2
recommendation	2
protein_networks	2
sweave	2
mir20a	2
20q	2
diagnostic	2
akt	2
thyroid	2
chemo	2
qtl	2
compression	2
oncomine	2
caching	2
bcatenin	2
flow_cytometry	2
projection	2
tbfs	2
upd	2
mir215	2
translational	2
alignment	2
dna_damage	2
semi-supervised	2
cell_cycle	2
stageiii	2
dfs	2
smad	2
snp_arrays	2
target	2
web_resource	2
differential_expression	2
mutual_information	2
protein_microarray	2
meeting_report	2
priors	2
rin	2
cetuximab	2
gene_fusion	2
local_recurrence	2
cdk8	2
bayesian	1
invasion	1
assembly	1
oncogene	1
mirna222	1
mir16-1	1
model-based	1
mir199	1
mir135	1
single_cell	1
smad7	1
xml	1
randomization	1
mir449	1
target_discovery	1
est_analysis	1
funding	1
mir126	1
pre-post	1
circulating_tumor_cells	1
braf	1
neural_networks	1
au-rich	1
wiki	1
apoptosis	1
aroma	1
module	1
biclustering	1
beads	1
bmp	1
pancreatic_cancer	1
dcc	1
brain_cancer	1
cross-species	1
association_studies	1
rna-interference	1
taxane	1
er-negative	1
distance	1
melanoma	1
ccnd1	1
nomogram	1
gene_clusters	1
formats	1
454	1
dasl	1
gene_function_prediction	1
python	1
cervical_cancer	1
shrna	1
reproducibility	1
perturbation	1
stem_cells	1
mir31	1
dye_bias	1
p21	1
meta_analysis	1
plasma	1
in_situ_hybridization	1
formalization	1
metastatis	1
passenger_genes	1
met	1
mirna_discovery	1
cancer_hallmarks	1
tissue_origin	1
mir145	1
modules	1
aurora_kinase	1
selection_bias	1
erg	1
3utr	1
power_analysis	1
markup	1
pilot_study	1
ret	1
gene_networks	1
driver_genes	1
metagene	1
cables1	1
mixture_models	1
prb	1
data_mining	1
fgfr2	1
fantom	1
signaling	1
ecm	1
translocation	1
il8	1
mir217	1
concordance	1
simulation	1
mir101	1
graph_approach	1
peripheral_blood	1
news	1
mir203	1
mir15a	1
mcm7	1
genome_assembly	1
resampling	1
transfection	1
tcga	1
mir-106b-25	1
rnai	1
ndrg4	1
ependymoma	1
oncogene_addiction	1
hypoxia	1
mirna221	1
microrna	1
ucs	1
mir155	1
gastric_cancer	1
mir143	1
bambi	1
latex	1
genoty	1
fish	1
disease	1
ensemble	1
dimension_reduction	1
asco	1
genetics	1
mrna-seq	1
rb	1
myb	1
mir216a	1
aging	1
latent	1
translation	1
pattern_discovery	1
pbc	1
early-stage	1
eno1	1
study_design	1
clusterin	1
sampling	1

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