jwfoley's library 36 articles Export

	Identifiability of isoform deconvolution from junction arrays and RNA-Seq [My Copy] Bioinformatics, Vol. 25, No. 23. (1 December 2009), pp. 3056-3059. by David Hiller, Hui Jiang, Weihong Xu, Wing H. Wong posted to rna-seq data_analysis by jwfoley on 2009-11-17 18:47:53 as along with 5 people and 2 groups djkt hzoltan cajunsushi ghattem GeeSharpMinor Journal picks SIMR bioinformatics
	Statistical inferences for isoform expression in RNA-Seq [My Copy] Bioinformatics, Vol. 25, No. 8. (15 April 2009), pp. 1026-1032. by Hui Jiang, Wing H. Wong posted to rna-seq data_analysis by jwfoley on 2009-11-13 17:00:21 as along with 16 people and 2 groups hzoltan heliopais stubrown GustavoLacerda woodson8 ThomasDOtto stajich guhjy ghattem djkt shikin pengchy vplagnol rschulz jmcq GeeSharpMinor Mycology SIMR bioinformatics
	Transcript quantification with RNA-Seq data [My Copy] BMC Bioinformatics, Vol. 10, No. Suppl 13. (19 October 2009), P5. by Regina Bohnert, Jonas Behr, Gunnar Ratsch posted to rna-seq data_analysis by jwfoley on 2009-11-12 01:38:04 as along with 3 people hzoltan inesdesantiago heliopais
	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 rna-seq peak_calling mouse by jwfoley on 2009-11-10 07:27:17 as along with 24 people and 2 groups cthachuk hzoltan 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
	Many human large intergenic noncoding RNAs associate with chromatin-modifying complexes and affect gene expression [My Copy] Proceedings of the National Academy of Sciences, Vol. 106, No. 28. (14 July 2009), pp. 11667-11672. by Ahmad M. Khalil, Mitchell Guttman, Maite Huarte, et al.Manuel Garber, Arjun Raj, Dianali Rivea Morales, Kelly Thomas, Aviva Presser, Bradley E. Bernstein, Alexander van Oudenaarden, Aviv Regev, Eric S. Lander, John L. Rinn posted to ncrna by jwfoley on 2009-11-09 21:38:49 as along with 7 people and 1 group inesdesantiago xianjun daforerog clearbluespring wsjames scjparker fenghezi Oxford Virology
	Chromatin signature reveals over a thousand highly conserved large non-coding RNAs in mammals [My Copy] Nature, Vol. 458, No. 7235. (01 February 2009), pp. 223-227. by Mitchell Guttman, Ido Amit, Manuel Garber, et al.Courtney French, Michael F. Lin, David Feldser, Maite Huarte, Or Zuk, Bryce W. Carey, John P. Cassady, Moran N. Cabili, Rudolf Jaenisch, Tarjei S. Mikkelsen, Tyler Jacks, Nir Hacohen, Bradley E. Bernstein, Manolis Kellis, Aviv Regev, John L. Rinn, Eric S. Lander posted to ncrna mouse by jwfoley on 2009-11-09 21:37:52 as along with 29 people and 2 groups hzoltan rsaito greg mkiyer gdb YukaH galka8_diploma antonkratz bertelsen natstreet fenghezi TRHvidsten megraw tonamswish biomcgary inesdesantiago djkt samgj dchughes admash neils absterga cisevol jm12 WanderingAengus daforerog bpcusack ericsuh mhamada Chinnaiyan Lab JLab
	Induced ncRNAs allosterically modify RNA-binding proteins in cis to inhibit transcription [My Copy] Nature, Vol. 454, No. 7200. (28 May 2008), pp. 126-130. by Xiangting Wang, Shigeki Arai, Xiaoyuan Song, et al.Donna Reichart, Kun Du, Gabriel Pascual, Paul Tempst, Michael G. Rosenfeld, Christopher K. Glass, Riki Kurokawa posted to ncrna by jwfoley on 2009-11-09 21:28:04 as along with 3 people galka8_diploma maximilianh rdowell
	Widespread Shortening of 32UTRs by Alternative Cleavage and Polyadenylation Activates Oncogenes in Cancer Cells [My Copy] Vol. 138, No. 4. (21 August 2009), pp. 673-684. by Christine Mayr, David P. Bartel posted to cancer 3prime by jwfoley on 2009-11-09 05:32:23 as along with 3 people and 1 group djkt lwaldron PabloMarin Journal picks
	Characterizing natural variation using next-generation sequencing technologies [My Copy] Trends in Genetics, Vol. 25, No. 10. (02 October 2009), pp. 463-471. by Yoav Gilad, Jonathan K. Pritchard, Kevin Thornton posted to rna-seq review by jwfoley on 2009-11-06 18:27:18 as along with 5 people and 1 group operon skembel djkt n00c natstreet iSEEM
	RNA-Seq: a revolutionary tool for transcriptomics. [My Copy] Nature reviews. Genetics, Vol. 10, No. 1. (01 January 2009), pp. 57-63. by Zhong Wang, Mark Gerstein, Michael Snyder posted to rna-seq review by jwfoley on 2009-11-06 16:52:19 as along with 41 people and 1 group hongkeun_park ngehlenborg hzoltan sandfire maren urgi RNA-protein cthachuk heliopais GustavoLacerda rdiaz TRHvidsten dswan roys woodson8 jonilaserson gdb n00c ThomasDOtto burak natstreet athma druvus tonamswish fishtank daed JohnBallam jmcq dandaman cassj xingxu idonaldson raiyar inesdesantiago vplagnol jbhiatt giovanni orzenil nuin guhjy GeeSharpMinor CUBES
	Loss of Mitogen-Activated Protein Kinase Kinase Kinase 4 (MAP3K4) Reveals a Requirement for MAPK Signalling in Mouse Sex Determination [My Copy] PLoS Biol, Vol. 7, No. 9. (15 September 2009), e1000196. by Debora Bogani, Pam Siggers, Rachel Brixey, et al.Nick Warr, Sarah Beddow, Jessica Edwards, Debbie Williams, Dagmar Wilhelm, Peter Koopman, Richard A. Flavell, Hongbo Chi, Harry Ostrer, Sara Wells, Michael Cheeseman, Andy Greenfield posted to sex mouse by jwfoley on 2009-11-05 20:57:28 as
	United States Patent Application 0090093378: Method for sequencing a polynucleotide template [My Copy] posted to rna-seq by jwfoley on 2009-11-04 02:53:23 as
	Identification of suitable normalizing genes for quantitative real-time RT-PCR analysis of gene expression in fetal mouse gonads. [My Copy] Sexual development : genetics, molecular biology, evolution, endocrinology, embryology, and pathology of sex determination and differentiation, Vol. 3, No. 4. (2009), pp. 194-204. by T. Svingen, C. M. Spiller, K. Kashimada, V. R. Harley, P. Koopman posted to sex rna-seq mouse data_analysis by jwfoley on 2009-11-04 02:35:14 as
	Sexual dimorphism in mammalian gene expression. [My Copy] Trends in genetics : TIG, Vol. 21, No. 5. (May 2005), pp. 298-305. by John L. Rinn, Michael Snyder posted to sex mouse by jwfoley on 2009-11-04 02:34:34 as
	Transcriptional Control of Ovarian Development in Somatic Cells [My Copy] posted to sex mouse by jwfoley on 2009-11-04 02:33:22 as
	Determination and Stability of Gonadal Sex -- Schlessinger et al., 10.2164/jandrol.109.008201 -- Journal of Andrology [My Copy] posted to sex review mouse by jwfoley on 2009-11-04 02:32:56 as
	Foxl2 functions in sex determination and histogenesis throughout mouse ovary development [My Copy] BMC Developmental Biology, Vol. 9, No. 1. (18 June 2009), 36. by Jose G. Ortiz, Emanuele Pelosi, Shakib Omari, et al.Timur Nedorezov, Yulan Piao, Jesse Karmazin, Manuela Uda, Antonio Cao, Steve Cole, Antonino Forabosco, David Schlessinger, Chris Ottolenghi posted to sex mouse by jwfoley on 2009-11-04 02:31:23 as
	Conserved regulatory modules in the Sox9 testis-specific enhancer predict roles for SOX, TCF/LEF, Forkhead, DMRT, and GATA proteins in vertebrate sex determination [My Copy] posted to sex by jwfoley on 2009-11-04 02:30:21 as
	Global survey of protein expression during gonadal sex determination in mice [My Copy] Mol Cell Proteomics (17 July 2009), M900108-MCP200. by Katherine A. Ewen, Mark A. Baker, Dagmar Wilhelm, R. John Aitken, Peter A. Koopman posted to sex mouse by jwfoley on 2009-11-04 02:29:52 as
	Male-specific expression of <i>Sox9</i> during gonad development of crocodile and mouse is mediated by alternative splicing of its proline-glutamine-alanine rich domain [My Copy] FEBS Journal, Vol. 276, No. 15. (2009), pp. 4184-4196. by Raman Agrawal, Oliver Wessely, Amit Anand, Lalji Singh, Ramesh K. Aggarwal posted to sex mouse by jwfoley on 2009-11-04 02:28:10 as
	A large-scale analysis of mRNA polyadenylation of human and mouse genes [My Copy] Nucl. Acids Res., Vol. 33, No. 1. (12 January 2005), pp. 201-212. by Bin Tian, Jun Hu, Haibo Zhang, Carol S. Lutz posted to 3prime by jwfoley on 2009-11-04 02:26:39 as along with 4 people miguel Cortel bertelsen kcrawlik
	Genome-Wide Analysis in Vivo of Translation with Nucleotide Resolution Using Ribosome Profiling [My Copy] Science, Vol. 324, No. 5924. (10 April 2009), pp. 218-223. by Nicholas T. Ingolia, Sina Ghaemmaghami, John R. S. Newman, Jonathan S. Weissman posted to rna-seq by jwfoley on 2009-11-04 02:25:39 as along with 18 people and 3 groups hzoltan yyfwuhan gbloeb guhjy dpollard fenghezi gangcai idonaldson coela fpattyn jbhiatt kshundyak absterga myzhang bertelsen VGreiff provero kinestetika RockmanLab NYU Journal Review microbiology_nijmegen
	High-Resolution Analysis of the 5′-End Transcriptome Using a Next Generation DNA Sequencer [My Copy] PLoS ONE, Vol. 4, No. 1. (1 January 2009), e4108. by Shin-ichi Hashimoto, Wei Qu, Budrul Ahsan, et al.Katsumi Ogoshi, Atsushi Sasaki, Yoichiro Nakatani, Yongjun Lee, Masako Ogawa, Akio Ametani, Yutaka Suzuki, Sumio Sugano, Clarence C. Lee, Robert C. Nutter, Shinichi Morishita, Kouji Matsushima posted to rna-seq by jwfoley on 2009-11-04 02:24:51 as along with 8 people and 1 group tprpip guhjy poschm jfr jasontsai GustavoLacerda Cortel stajich Mycology
	Stem cell transcriptome profiling via massive-scale mRNA sequencing [My Copy] Nature Methods, Vol. 5, No. 7. (30 May 2008), pp. 613-619. by Nicole Cloonan, Alistair R. R. Forrest, Gabriel Kolle, et al.Brooke B. A. Gardiner, Geoffrey J. Faulkner, Mellissa K. Brown, Darrin F. Taylor, Anita L. Steptoe, Shivangi Wani, Graeme Bethel, Alan J. Robertson, Andrew C. Perkins, Stephen J. Bruce, Clarence C. Lee, Swati S. Ranade, Heather E. Peckham, Jonathan M. Manning, Kevin J. McKernan, Sean M. Grimmond posted to rna-seq by jwfoley on 2009-11-04 02:23:53 as along with 22 people manduca hzoltan heliopais jmanning2k stubrown cassj n00c burak natstreet poschm felsani jbhiatt vplagnol rschulz umit myourshaw megraw inesdesantiago GeeSharpMinor caseybrown guhjy gdb
	Somite as a Morphological Reference for Staging and Axial Levels of Developing Structures in Mouse Embryos [My Copy] posted to mouse by jwfoley on 2009-11-04 02:21:58 as
	Widespread Shortening of 3′UTRs by Alternative Cleavage and Polyadenylation Activates Oncogenes in Cancer Cells [My Copy] Cell, Vol. 138, No. 4. (21 August 2009), pp. 673-684. by Christine Mayr, David P. Bartel posted to 3prime by jwfoley on 2009-11-04 02:20:20 as along with 11 people and 1 group ongenetics frohike colinveal bertelsen manto hcoller gbloeb jbhiatt ashkelon13 megraw rschulz cube_and_beyond
	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 cancer by jwfoley on 2009-11-04 02:18:43 as along with 13 people and 2 groups misonneh pst stubrown chvlyl giovenko frohike brianb Zephyrus jsuchit mkiyer torfinnnome merpublic djkt Chinnaiyan Lab Journal picks
	Genome-wide analysis of transcription factor binding sites based on ChIP-Seq data [My Copy] Nature Methods, Vol. 5, No. 9. (17 August 2008), pp. 829-834. by Anton Valouev, David S. Johnson, Andreas Sundquist, et al.Catherine Medina, Elizabeth Anton, Serafim Batzoglou, Richard M. Myers, Arend Sidow posted to peak_calling by jwfoley on 2009-11-03 19:23:52 as along with 19 people and 1 group ewilban1 nklee bertelsen stajich smiddha clearbluespring WanderingAengus polivares ptrobajo mdperry idonaldson gdb megraw kengg alhufton guhjy kjglennie bryankr maximilianh Mycology
	Elucidation of the transcription network governing mammalian sex determination by exploiting strain-specific susceptibility to sex reversal [My Copy] Genes & Development, Vol. 23, No. 21. (1 November 2009), pp. 2521-2536. by Steven C. Munger, David L. Aylor, Haider A. Syed, Paul M. Magwene, David W. Threadgill, Blanche Capel posted to sex mouse by jwfoley on 2009-11-03 19:22:49 as
	Transcript length bias in RNA-seq data confounds systems biology. [My Copy] Biology direct, Vol. 4, No. 1. (16 April 2009), 14. by Alicia Oshlack, Matthew J. Wakefield posted to rna-seq peak_calling data_analysis by jwfoley on 2009-11-03 19:08:34 as along with 14 people and 1 group hzoltan manduca juokcho debasis stubrown dswan jmcq guhjy woodson8 n00c ghattem xingxu cajunsushi bandrewfox SIMR bioinformatics
	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 data_analysis by jwfoley on 2009-11-03 19:07:58 as along with 42 people and 2 groups manduca cthachuk hzoltan 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
	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 by jwfoley on 2009-11-03 19:07:04 as along with 46 people and 2 groups cthachuk hzoltan 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
	Determination of tag density required for digital transcriptome analysis: Application to an androgen-sensitive prostate cancer model [My Copy] Proceedings of the National Academy of Sciences, Vol. 105, No. 51. (23 December 2008), pp. 20179-20184. by Hairi Li, Michael T. Lovci, Young-Soo Kwon, Michael G. Rosenfeld, Xiang-Dong Fu, Gene W. Yeo posted to rna-seq data_analysis by jwfoley on 2009-11-03 19:06:08 as along with 3 people guhjy xingxu abizar
	Direct RNA sequencing. [My Copy] Nature, Vol. 461, No. 7265. (8 October 2009), pp. 814-818. by Fatih Ozsolak, Adam R. Platt, Dan R. Jones, et al.Jeffrey G. Reifenberger, Lauryn E. Sass, Peter McInerney, John F. Thompson, Jayson Bowers, Mirna Jarosz, Patrice M. Milos posted to rna-seq by jwfoley on 2009-11-03 18:58:53 as along with 20 people and 2 groups pmalkus hzoltan manduca gotgenes GeeSharpMinor mlc39 colinveal reyez TRHvidsten djkt ppgardne dchughes heliopais vingron nzm n00c lp2 toni_marco dswan kinestetika Journal picks Bioinformatics - CRUK
	Targeted next-generation sequencing of a cancer transcriptome enhances detection of sequence variants and novel fusion transcripts. [My Copy] Genome biology, Vol. 10, No. 10. (16 October 2009), R115. by Joshua Z. Levin, Michael F. Berger, Xian Adiconis, et al.Peter Rogov, Alexandre Melnikov, Timothy Fennell, Chad Nusbaum, Levi A. Garraway, Andreas Gnirke posted to rna-seq cancer by jwfoley on 2009-11-03 18:52:52 as along with 2 people and 1 group pst torfinnnome 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 rna-seq review peak_calling data_analysis by jwfoley on 2009-11-03 18:46:24 as along with 23 people and 2 groups urgi Jporci pst epigenetics timflutre molnet-mna Vincent_Rouilly guhjy cajunsushi mpizbioinfo stubrown hzoltan robertrentzsch xingxu oannes74 tonamswish inesdesantiago Baschl polivares druvus GeeSharpMinor chvlyl heliopais molnet-macs Orengo Group Journal Picks

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rna-seq	18
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review	4
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jwfoley's library 36 articles Export

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