Neeperando's library 174 articles Export

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	An algorithm based on graph theory for the assembly of contigs in physical mapping of DNA. [My Copy] Computer applications in the biosciences : CABIOS, Vol. 10, No. 3. (June 1994), pp. 309-317. by P. Zhang, E. A. Schon, S. G. Fischer, et al.E. Cayanis, J. Weiss, S. Kistler, P. E. Bourne posted to graph interval scaffolding thesis by Neeperando on 2008-09-04 22:40:45 as along with 1 person AbnerCYH
	Four strikes against physical mapping of DNA. [My Copy] Journal of computational biology : a journal of computational molecular cell biology, Vol. 2, No. 1. (1995), pp. 139-152. by P. W. Goldberg, M. C. Golumbic, H. Kaplan, R. Shamir posted to dna mapping by Neeperando on 2008-09-04 22:40:06 as
	Genome-scale evolution: reconstructing gene orders in the ancestral species. [My Copy] Genome Res, Vol. 12, No. 1. (January 2002), pp. 26-36. by G. Bourque, P. A. Pevzner posted to genome reconstruction thesis by Neeperando on 2008-07-02 16:23:21 as along with 3 people druvus dbikard AaronDarling
	Construction of high-resolution comparative maps in mammals using BAC-end sequences. [My Copy] Methods in molecular biology (Clifton, N.J.), Vol. 422 (2008), pp. 79-90. by D. M. Larkin, H. A. Lewin posted to comparative map thesis by Neeperando on 2008-07-24 18:12:13 as
	Amniote phylogenomics: testing evolutionary hypotheses with BAC library scanning and targeted clone analysis of large-scale DNA sequences from reptiles. [My Copy] Methods in molecular biology (Clifton, N.J.), Vol. 422 (2008), pp. 91-117. by Andrew M. Shedlock, Daniel E. Janes, Scott V. Edwards posted to analysis comparative matepair by Neeperando on 2008-07-24 18:11:32 as along with 1 person dchughes
	End-sequence profiling: sequence-based analysis of aberrant genomes. [My Copy] Proc Natl Acad Sci U S A, Vol. 100, No. 13. (24 June 2003), pp. 7696-7701. by S. Volik, S. Zhao, K. Chin, et al.J. H. Brebner, D. R. Herndon, Q. Tao, D. Kowbel, G. Huang, A. Lapuk, W. L. Kuo, G. Magrane, P. De Jong, J. W. Gray, C. Collins posted to analysis end paired by Neeperando on 2008-06-09 18:15:11 as along with 1 person emb51
	A scaffold analysis tool using mate-pair information in genome sequencing. [My Copy] Journal of biomedicine & biotechnology, Vol. 2008 (2008) by Pan-Gyu G. Kim, Hwan-Gue G. Cho, Kiejung Park posted to assembly pair read thesis validation by Neeperando on 2008-05-19 16:30:45 as along with 2 people dakelley orzenil
	Assembly reconciliation [My Copy] Bioinformatics, Vol. 24, No. 1. (1 January 2008), pp. 42-45. by Aleksey V. Zimin, Douglas R. Smith, Granger Sutton, James A. Yorke posted to assembly reconciliation thesis by Neeperando on 2008-05-19 16:28:18 as along with 5 people dakelley jsatkosk orzenil druvus GustavoLacerda
	The fragment assembly string graph. [My Copy] Bioinformatics, Vol. 21 Suppl 2 (1 September 2005) by E. W. Myers posted to assembly fragment graph thesis by Neeperando on 2008-05-19 16:21:45 as along with 5 people idoerg dakelley mmartin azazello isimpson
	Automated whole-genome multiple alignment of rat, mouse, and human. [My Copy] Genome Res, Vol. 14, No. 4. (April 2004), pp. 685-692. by M. Brudno, A. Poliakov, A. Salamov, et al.G. M. Cooper, A. Sidow, E. M. Rubin, V. Solovyev, S. Batzoglou, I. Dubchak posted to alignment thesis by Neeperando on 2008-05-19 16:14:40 as along with 1 person balajis
	MAVID: Constrained Ancestral Alignment of Multiple Sequences [My Copy] Genome Research, Vol. 14, No. 4. (1 April 2004), pp. 693-699. by Nicolas Bray, Lior Pachter posted to alignment thesis by Neeperando on 2008-05-19 16:11:15 as along with 5 people nuin pradiptaray treangen operon jmeppley
	Genome-Wide Analysis of Transposon Insertion Polymorphisms Reveals Intraspecific Variation in Cultivated Rice [My Copy] Plant Physiol., Vol. 148, No. 1. (1 September 2008), pp. 25-40. by Xuehui Huang, Guojun Lu, Qiang Zhao, Xiaohui Liu, Bin Han posted to structural transposon variation by Neeperando on 2008-09-04 22:41:40 as along with 3 people and 1 group operon orzenil cisevol BergmanLab
	A KNOWLEDGE-BASED APPROACH TO PREDICT INTRAGENIC DELETIONS OR DUPLICATIONS [My Copy] Bioinformatics (21 July 2008), btn370. by Krishna R. Kalari, Thomas L. Casavant, Todd E. Scheetz posted to read short structural variation by Neeperando on 2008-07-24 23:24:34 as along with 3 people ealloza pengchy APRegier
	Update of the Anopheles gambiae PEST genome assembly [My Copy] Genome Biology, Vol. 8 (08 January 2007), R5. by Maria V. Sharakhova, Martin P. Hammond, Neil F. Lobo, et al.Jaroslaw Krzywinski, Maria F. Unger, Maureen E. Hillenmeyer, Robert V. Bruggner, Ewan Birney, Frank H. Collins posted to assembly gambiae thesis by Neeperando on 2008-06-27 20:21:07 as along with 1 group Notre Dame Bioinformatics
	Population Genomics: Whole-Genome Analysis of Polymorphism and Divergence in Drosophila simulans [My Copy] PLoS Biol, Vol. 5, No. 11. (6 November 2007), e310. by David J. Begun, Alisha K. Holloway, Kristian Stevens, et al.Ladeana W. Hillier, Yu-Ping Poh, Matthew W. Hahn, Phillip M. Nista, Corbin D. Jones, Andrew D. Kern, Colin N. Dewey, Lior Pachter, Eugene Myers, Charles H. Langley posted to drosophila genomics population by Neeperando on 2008-06-27 19:12:08 as along with 8 people and 4 groups jlin daveGerrard APRegier juanitogarcia cwbrown xingxu caseybrown druvus BergmanLab Computational-Genomics EisenLab Notre Dame Bioinformatics
	Sequence-specific reconstruction from fragmentary databases using seed sequences: implementation and validation on SAGE, proteome and generic sequencing data [My Copy] Bioinformatics (9 June 2008), btn283. by Tiago J. Sobreira, Arthur Gruber posted to assembly by Neeperando on 2008-06-11 16:03:34 as along with 1 person sconlan
	Measuring Global Credibility with Application to Local Sequence Alignment [My Copy] PLoS Comput Biol, Vol. 4, No. 5. (May 2008) by Bobbie, Lee A. Mccue, Charles E. Lawrence posted to alignment by Neeperando on 2008-05-28 15:39:51 as
	Extending assembly of short DNA sequences to handle error. [My Copy] Bioinformatics, Vol. 23, No. 21. (1 November 2007), pp. 2942-2944. by W. R. Jeck, J. A. Reinhardt, D. A. Baltrus, et al.M. T. Hickenbotham, V. Magrini, E. R. Mardis, J. L. Dangl, C. D. Jones posted to assembly read short thesis by Neeperando on 2008-05-28 15:35:21 as along with 6 people idoerg floatingpoint natstreet druvus guhjy azazello
	Improving Phrap-Based Assembly of the Rat Using "Reliable" Overlaps [My Copy] PLoS ONE, Vol. 3, No. 3. (2008) by Michael Roberts, Aleksey V. Zimin, Wayne Hayes, et al.Brian R. Hunt, Cevat Ustun, James R. White, Paul Havlak, James Yorke posted to assembly thesis by Neeperando on 2008-05-27 16:53:17 as
	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 human parallel sequencing thesis by Neeperando on 2008-05-27 16:48:35 as along with 23 people and 2 groups rshe n00c jonilaserson jessopher daforerog behindtherabbit frohike reyez pengchy adijr jo_davies jfr orzenil dullhunk djkt ramensky psique caseybrown melting dbensasson bpb Huub_odc guhjy parkinson's disease references microbiology_nijmegen
	Assembly of the working draft of the human genome with GigAssembler. [My Copy] Genome research, Vol. 11, No. 9. (September 2001), pp. 1541-1548. by W. J. Kent, D. Haussler posted to assembly scaffolding by Neeperando on 2008-05-19 16:29:05 as along with 1 person and 1 group daveGerrard BergmanLab
	Hierarchical Scaffolding With Bambus [My Copy] Genome Research, Vol. 14, No. 1. (January 2004), pp. 149-159. by Mihai Pop, Daniel S. Kosack, Steven L. Salzberg posted to amos scaffolding thesis by Neeperando on 2008-05-19 16:27:18 as along with 4 people and 1 group dakelley druvus azazello wenhan MBLAB
	A Tool for Analyzing Mate Pairs in Assemblies (TAMPA) [My Copy] Journal of Computational Biology, Vol. 12, No. 5. (2005), pp. 497-513. by Ian M. Dew, Brian Walenz, Granger Sutton posted to assembly matepair pair read thesis validation by Neeperando on 2008-05-14 17:10:57 as
	Harnessing parallelism in multicore clusters with the all-pairs and wavefront abstractions [My Copy] In HPDC '09: Proceedings of the 18th ACM international symposium on High performance distributed computing (2009), pp. 1-10. by Li Yi, Christopher Moretti, Scott Emrich, Kenneth Judd, Douglas Thain posted to workqueue thesis parallel distributed by Neeperando on 2009-10-23 22:43:32 as along with 1 person and 1 group bbjwerner Software-Architecture
	Patterns of somatic mutation in human cancer genomes [My Copy] Nature, Vol. 446, No. 7132. (08 March 2007), pp. 153-158. by Christopher Greenman, Philip Stephens, Raffaella Smith, et al.Gillian L. Dalgliesh, Christopher Hunter, Graham Bignell, Helen Davies, Jon Teague, Adam Butler, Claire Stevens, Sarah Edkins, Sarah O/'Meara, Imre Vastrik, Esther E. Schmidt, Tim Avis, Syd Barthorpe, Gurpreet Bhamra, Gemma Buck, Bhudipa Choudhury, Jody Clements, Jennifer Cole, Ed Dicks, Simon Forbes, Kris Gray, Kelly Halliday, Rachel Harrison, Katy Hills, Jon Hinton, Andy Jenkinson, David Jones, Andy Menzies, Tatiana Mironenko, Janet Perry, Keiran Raine, Dave Richardson, Rebecca Shepherd, Alexandra Small, Calli Tofts, Jennifer Varian, Tony Webb, Sofie West, Sara Widaa, Andy Yates, Daniel P. Cahill, David N. Louis, Peter Goldstraw, Andrew G. Nicholson, Francis Brasseur, Leendert Looijenga, Barbara L. Weber, Yoke-Eng Chiew, Anna deFazio, Mel F. Greaves, Anthony R. Green, Peter Campbell, Ewan Birney, Douglas F. Easton, Georgia Chenevix-Trench, Min-Han Tan, Sok K. Khoo, Bin T. Teh, Siu T. Yuen, Suet Y. Leung, Richard Wooster, P. Andrew Futreal, Michael R. Stratton posted to thesis by Neeperando on 2009-10-14 02:22:24 as along with 15 people xingxu ssgong dbensasson koller kentsis jfr massivemayhem efge Garamonfok daed Petersarkies ramensky frohike cerami srp33
	Mosaik - The Marth Lab [My Copy] posted to assembly comparative thesis by Neeperando on 2009-08-04 16:36:39 as
	Condor and the Grid [My Copy] by Douglas Thain, Todd Tannenbaum, Miron Livny posted to condor distributed grid thesis by Neeperando on 2009-07-30 20:02:53 as
	Chirp: a practical global filesystem for cluster and Grid computing [My Copy] Journal of Grid Computing, Vol. 7, No. 1. (1 March 2009), pp. 51-72. by Douglas Thain, Christopher Moretti, Jeffrey Hemmes posted to chirp distributed filesystem grid thesis by Neeperando on 2009-07-30 19:42:26 as along with 3 people and 1 group thiagomanel aespinosa schamm TELEPAT-ES
	Basic local alignment search tool. [My Copy] Journal of molecular biology, Vol. 215, No. 3. (5 October 1990), pp. 403-410. by S. F. Altschul, W. Gish, W. Miller, E. W. Myers, D. J. Lipman posted to alignment thesis by Neeperando on 2009-06-02 18:35:02 as along with 73 people and 6 groups rshe mtaschuk sjcockell niallhaslam djohnson thegoose humburg timhubbard pachorip n00c maria_hauser rpetrenko parnell yylin esyoun APRegier idoerg robert85 thegoose2 daforerog mcbla coela alessandroparini bertelsen Blackbeard florisbuijzen laurabailey treangen pwais mmartin tharris dmp camster davidng evaf dragonrez jwm jmeppley Ayest RMGraze ea yas balajis alexg indigoviolet moborg arcticrasta dullhunk dgront caporaso michC myui BioNica CitoJam rabio timflutre lusk cjeans incovoma beatrizfernandez wenhan jtomasch GustavoLacerda sgoetz siebertm ichbins81 jofiel Thaverkamp shung marti ashaytan benwei granujilla C. elegans / WormBase dbk-lab EisenLab T_lab biomedical-nlp Microbial-Ecology
	Malaria Fact Sheet [My Copy] (January 2009) posted to malaria thesis by Neeperando on 2009-06-01 16:55:27 as
	Proposal for the Eight Genomes Cluster for Genus Anopheles [My Copy] (July 2004) by Nora J. Besansky posted to gambiae thesis by Neeperando on 2009-06-01 16:44:13 as
	Speciation Within Anopheles gambiae-- the Glass Is Half Full [My Copy] Science, Vol. 298, No. 5591. (4 October 2002), pp. 115-117. by Della A. Torre, C. Costantini, N. J. Besansky, et al.A. Caccone, V. Petrarca, J. R. Powell, M. Coluzzi posted to gambiae thesis by Neeperando on 2009-06-01 16:06:26 as
	PipMaker---A Web Server for Aligning Two Genomic DNA Sequences [My Copy] Genome Res., Vol. 10, No. 4. (1 April 2000), pp. 577-586. by Scott Schwartz, Zheng Zhang, Kelly A. Frazer, et al.Arian Smit, Cathy Riemer, John Bouck, Richard Gibbs, Ross Hardison, Webb Miller posted to alignment thesis by Neeperando on 2009-05-19 00:03:34 as along with 4 people aprasad michC adijr wenhan
	AVID: A Global Alignment Program [My Copy] Genome Research, Vol. 13, No. 1. (1 January 2003), pp. 97-102. by Nick Bray, Inna Dubchak, Lior Pachter posted to alignment thesis by Neeperando on 2009-05-18 23:41:47 as along with 5 people and 1 group n00c mhiromi indigoviolet adijr yoanjacquemin EisenLab
	Structural variation in the human genome [My Copy] Nature Reviews Genetics, Vol. 7, No. 2. (01 February 2006), pp. 85-97. by Lars Feuk, Andrew R. Carson, Stephen W. Scherer posted to structural thesis variation by Neeperando on 2009-05-14 20:26:58 as along with 25 people and 11 groups ajbattle bertelsen baizhang APRegier xingxu daforerog psique Zephyrus dlobo jandot cgreal balajis bala balicea dchughes tabu darcyduke adepace AaronDarling rdiaz massivemayhem cat_worth jmrivort ccr Lip GEB CGREL structural_bioinformatics Bioinformatics EisenLab SFX-Verde-team-MITLibraries G4ID G-quadruplex Supramolecular DictyosteliumGroup Genetics-of-Gambling
	PEMer: a computational framework with simulation-based error models for inferring genomic structural variants from massive paired-end sequencing data [My Copy] Genome Biology, Vol. 10, No. 2. (23 February 2009), R23. by Jan O. Korbel, Alexej Abyzov, Xinmeng J. Mu, et al.Nicholas Carriero, Philip Cayting, Zhengdong Zhang, Michael Snyder, Mark B. Gerstein posted to end paired structural thesis variation by Neeperando on 2009-05-14 20:25:01 as along with 11 people orzenil adthrasher jessopher jrvalcourt dakelley APRegier smiddha natstreet djkt poschm druvus
	Figaro: a novel statistical method for vector sequence removal [My Copy] Bioinformatics, Vol. 24, No. 4. (15 February 2008), pp. 462-467. by James R. White, Michael Roberts, James A. Yorke, Mihai Pop posted to assembly thesis by Neeperando on 2009-05-13 22:03:48 as along with 7 people and 1 group APRegier thegoose2 operon druvus guhjy GustavoLacerda tharris LabDros
	Minimus: a fast, lightweight genome assembler. [My Copy] BMC bioinformatics, Vol. 8 (26 February 2007), 64. by Daniel D. Sommer, Arthur L. Delcher, Steven L. Salzberg, Mihai Pop posted to amos assembly thesis by Neeperando on 2009-05-13 21:40:47 as along with 3 people azazello Thaverkamp eckart_bindewald
	AMOS - A Modular Open-Source Assembler [My Copy] posted to thesis by Neeperando on 2009-05-13 21:35:53 as along with 1 person n00c
	Assembling genomes on large-scale parallel computers [My Copy] Journal of Parallel and Distributed Computing, Vol. In Press, Corrected Proof by A. Kalyanaraman, S. J. Emrich, P. S. Schnable, S. Aluru posted to assembly parallel thesis by Neeperando on 2009-05-12 17:12:34 as along with 1 person GustavoLacerda
	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 read short thesis by Neeperando on 2009-05-11 21:39:01 as along with 17 people n00c pachorip APRegier thegoose2 dakelley hpaces idoerg druvus jasontsai acn orzenil azazello GustavoLacerda dandaman caseybrown iris42 tharris
	Separation of nearly identical repeats in shotgun assemblies using defined nucleotide positions, DNPs [My Copy] Bioinformatics, Vol. 18, No. 3. (1 March 2002), pp. 379-388. by Martti T. Tammi, Erik Arner, Tom Britton, Bjorn Andersson posted to assembly thesis validation by Neeperando on 2009-05-08 20:28:00 as along with 1 person dakelley
	An Eulerian path approach to DNA fragment assembly. [My Copy] Proceedings of the National Academy of Sciences of the United States of America, Vol. 98, No. 17. (14 August 2001), pp. 9748-9753. by P. A. Pevzner, H. Tang, M. S. Waterman posted to assembly thesis by Neeperando on 2009-05-07 21:49:57 as along with 14 people and 2 groups aheilbut jengeldk n00c robsyme idoerg dakelley brl A_Olympia briann jmeppley AaronDarling nedwards azazello jwhitney Philosophy_of_Information Blog_and_Wiki_Research
	Pash: Efficient Genome-Scale Sequence Anchoring by Positional Hashing [My Copy] Genome Res., Vol. 14, No. 4. (1 April 2004), pp. 672-678. by Ken J. Kalafus, Andrew R. Jackson, Aleksandar Milosavljevic posted to assembly comparative thesis by Neeperando on 2009-05-06 20:11:38 as along with 1 person yoanjacquemin
	Algorithms on strings, trees, and sequences : computer science and computational biology [My Copy] (15 January 2007) by Dan Gusfield posted to assembly string thesis tree by Neeperando on 2009-05-05 22:07:31 as along with 20 people and 2 groups abergeron n00c stharward enricos Scis0000002 mircea renewang timflutre ujh creswick tijl grzegorz luispedro emranmohdtamil hoangmit thonnardo pool007 nedwards ep161302 reyez Centre de Recherches Interdisciplinaires Pattern-Analysis
	Many-core algorithms for statistical phylogenetics [My Copy] Bioinformatics, Vol. 25, No. 11. (1 June 2009), pp. 1370-1376. by Marc A. Suchard, Andrew Rambaut posted to parallel phylogenetic tree by Neeperando on 2009-04-16 17:43:54 as along with 9 people and 1 group mlangill druvus nuin AlexBateman bmajoros djkt jmeppley svenrahmann rdiaz iSEEM
	Advances to Bayesian network inference for generating causal networks from observational biological data [My Copy] Bioinformatics, Vol. 20, No. 18. (12 December 2004), pp. 3594-3603. by Jing Yu, V. Anne Smith, Paul P. Wang, Alexander J. Hartemink, Erich D. Jarvis posted to inference network by Neeperando on 2009-04-15 21:59:42 as along with 5 people arsyed Borelli ggallone heliopais roys
	Triggers and tricks of Plasmodium sexual development [My Copy] Current Opinion in Microbiology, Vol. 10, No. 6. (December 2007), pp. 547-553. by T. Kooij, K. Matuschewski posted to network plasmodium by Neeperando on 2009-04-15 20:10:17 as
	Reverse engineering of regulatory networks in human B cells. [My Copy] Nat Genet (20 March 2005) by Katia Basso, Adam A A. Margolin, Gustavo Stolovitzky, Ulf Klein, Riccardo Dalla-Favera, Andrea Califano posted to inference network by Neeperando on 2009-04-15 18:53:19 as along with 12 people akraemer verdicchio ggallone snuppepuppan kentsis dragonrez jfr wnpx raiyar naegele heliopais lylu
	Cluster analysis and display of genome-wide expression patterns [My Copy] Proceedings of the National Academy of Sciences of the United States of America, Vol. 95, No. 25. (8 December 1998), pp. 14863-14868. by Michael B. Eisen, Paul T. Spellman, Patrick O. Brown, David Botstein posted to inference network by Neeperando on 2009-04-15 17:52:21 as along with 34 people and 3 groups antonkratz potatongy drungows colmryan jplatig rsaito baldigroup daforerog karinlag ronglais operon Borelli pengchy macowell ggrot miguel textoris okarsligil pcahan1 lfriedl balajis nuke2005 lyongu maryee wnpx nirfriedman dquest karfunkel dps kintoki jo_davies tvdbulck bozdagd roys kdl Bioinformatics BUiGEM

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Neeperando's library 174 articles Export

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