wenhan's watchlist [at least 200 articles] Export

Recent papers matching wenhan's watchlist criteria

	Meningococcal disease. [My Copy] The New England journal of medicine, Vol. 344, No. 18. (3 May 2001), pp. 1378-1388. by N. E. Rosenstein, B. A. Perkins, D. S. Stephens, T. Popovic, J. M. Hughes posted to prok-seq-cg-pipeline by azazello on 2009-12-18 03:42:36 as
	DNA-templated carbon nanotube field-effect transistor. [My Copy] Science (New York, N.Y.), Vol. 302, No. 5649. (21 November 2003), pp. 1380-1382. by Kinneret Keren, Rotem S. Berman, Evgeny Buchstab, Uri Sivan, Erez Braun posted to dna-nanotechnology by bluto on 2009-12-17 12:29:34 as
	Molecular computation of solutions to combinatorial problems. [My Copy] Science (New York, N.Y.), Vol. 266, No. 5187. (11 November 1994), pp. 1021-1024. by L. M. Adleman posted to dna-computing by bluto on 2009-12-17 10:31:19 as along with 3 people nzm jorisslob dullhunk
	Comparative genomics identifies the genetic islands that distinguish Neisseria meningitidis, the agent of cerebrospinal meningitis, from other Neisseria species. [My Copy] Infection and immunity, Vol. 70, No. 12. (1 December 2002), pp. 7063-7072. by Agnès Perrin, Stéphane Bonacorsi, Etienne Carbonnelle, et al.Driss Talibi, Philippe Dessen, Xavier Nassif, Colin Tinsley posted to prok-seq-cg-pipeline by azazello on 2009-11-24 19:39:50 as along with 1 person treangen
	Comparative genomics of Neisseria meningitidis: core genome, islands of horizontal transfer and pathogen-specific genes. [My Copy] Microbiology (Reading, England), Vol. 152, No. Pt 12. (1 December 2006), pp. 3733-3749. by Julie Dunning C. Hotopp, Renata Grifantini, Nikhil Kumar, et al.Yih Ling L. Tzeng, Derrick Fouts, Elisabetta Frigimelica, Monia Draghi, Marzia Monica M. Giuliani, Rino Rappuoli, David S. Stephens, Guido Grandi, Hervé Tettelin posted to prok-seq-cg-pipeline by azazello on 2009-11-24 19:37:37 as along with 3 people and 1 group disrael treangen tpreeprem gatech-compgenomics
	The Influence of Mutation, Recombination, Population History, and Selection on Patterns of Genetic Diversity in Neisseria meningitidis [My Copy] Mol Biol Evol, Vol. 22, No. 3. (1 March 2005), pp. 562-569. by K. A. Jolley, D. J. Wilson, P. Kriz, G. Mcvean, M. C. J. Maiden posted to prok-seq-cg-pipeline by azazello on 2009-11-24 18:49:22 as along with 3 people katholt treangen vplagnol
	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 scaffolding mapped_assembly by azazello on 2009-11-16 15:49:53 as along with 21 people and 2 groups orzenil humburg jfr hzoltan cthachuk GustavoLacerda jasontsai n00c nuin dakelley skembel Thaverkamp reyez TRHvidsten djkt hpaces APRegier pengchy natstreet druvus darian iSEEM Bioinformatics
	The pangenome structure of Escherichia coli: comparative genomic analysis of E. coli commensal and pathogenic isolates. [My Copy] Journal of bacteriology, Vol. 190, No. 20. (October 2008), pp. 6881-6893. by David A. Rasko, M. J. Rosovitz, Garry S. Myers, et al.Emmanuel F. Mongodin, W. Florian Fricke, Pawel Gajer, Jonathan Crabtree, Mohammed Sebaihia, Nicholas R. Thomson, Roy Chaudhuri, Ian R. Henderson, Vanessa Sperandio, Jacques Ravel posted to core-pan by azazello on 2009-11-08 01:02:59 as along with 2 people nyyu druvus
	Predicting transmembrane protein topology with a hidden markov model: application to complete genomes1 [My Copy] Journal of Molecular Biology, Vol. 305, No. 3. (19 January 2001), pp. 567-580. by Anders Krogh, Björn Larsson, Gunnar von Heijne, Erik L. L. Sonnhammer posted to prok-seq-cg-pipeline by azazello on 2009-11-03 20:16:03 as along with 11 people tfuji niallhaslam katholt thaliana bjorns andreasauerwein j3xucite happy_manatee massivemayhem twenta sebk
	InterPro and InterProScan: Tools for Protein Sequence Classification and Comparison. [My Copy] Methods Mol Biol, Vol. 396 (2007), pp. 59-70. by N. Mulder, R. Apweiler posted to prok-seq-cg-pipeline by azazello on 2009-11-03 20:01:39 as along with 2 people druvus DNAReplication
	The Universal Protein Resource (UniProt) 2009. [My Copy] Nucleic acids research, Vol. 37, No. Database issue. (1 January 2009), pp. D169-174. by Uniprot-Consortium posted to prok-seq-cg-pipeline by azazello on 2009-11-03 20:00:19 as along with 12 people saunders barmak7282 badi MarcoAlvarez tfuji nedwards niallhaslam bicko gjuggler lptolik coela sjcockell
	The Universal Protein Resource (UniProt) in 2010 [My Copy] Nucl. Acids Res. (20 October 2009), gkp846. by The UniProt Consortium posted to prok-seq-cg-pipeline by azazello on 2009-11-03 19:59:15 as along with 1 person sf11
	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 prok-seq-cg-pipeline by azazello on 2009-10-28 04:47:18 as along with 10 people and 1 group djkt n00c dakelley jgill GustavoLacerda ramonvidal justinhjohnson stajich druvus neils Mycology
	Minimus: a fast, lightweight genome assembler [My Copy] BMC Bioinformatics, Vol. 8, No. 1. (26 February 2007), 64. by Daniel Sommer, Arthur Delcher, Steven Salzberg, Mihai Pop posted to prok-seq-cg-pipeline by azazello on 2009-10-28 02:45:13 as along with 6 people michaelbarton n00c druvus Neeperando Thaverkamp eckart_bindewald
	CAMERA: A Community Resource for Metagenomics [My Copy] PLoS Biol, Vol. 5, No. 3. (13 March 2007), e75. by Rekha Seshadri, Saul A. Kravitz, Larry Smarr, Paul Gilna, Marvin Frazier posted to prok-seq-cg-pipeline by azazello on 2009-10-28 02:30:14 as along with 6 people and 1 group houniao007 idoerg eweaver jdelcampo beatrizfernandez AlexanderPico Microbial-Ecology
	The RAST Server: rapid annotations using subsystems technology. [My Copy] BMC genomics, Vol. 9, No. 1. (08 February 2008), 75. by Ramy K. Aziz, Daniela Bartels, Aaron A. Best, et al.Matthew DeJongh, Terrence Disz, Robert A. Edwards, Kevin Formsma, Svetlana Gerdes, Elizabeth M. Glass, Michael Kubal, Folker Meyer, Gary J. Olsen, Robert Olson, Andrei L. Osterman, Ross A. Overbeek, Leslie K. McNeil, Daniel Paarmann, Tobias Paczian, Bruce Parrello, Gordon D. Pusch, Claudia Reich, Rick Stevens, Olga Vassieva, Veronika Vonstein, Andreas Wilke, Olga Zagnitko posted to prok-seq-cg-pipeline by azazello on 2009-10-28 02:26:59 as along with 9 people and 2 groups hexaquo sgoetz stefanorb coela Thaverkamp barriot druvus JeremyZucker klager Waikato - Erebus MetabolicModeling
	The integrated microbial genomes (IMG) system in 2007: data content and analysis tool extensions [My Copy] Nucl. Acids Res. (12 October 2007), gkm846. by Victor M. Markowitz, Ernest Szeto, Krishna Palaniappan, et al.Yuri Grechkin, Ken Chu, I-Min A. Chen, Inna Dubchak, Iain Anderson, Athanasios Lykidis, Konstantinos Mavromatis, Natalia N. Ivanova, Nikos C. Kyrpides posted to prok-seq-cg-pipeline by azazello on 2009-10-28 02:22:28 as along with 3 people nlapalu druvus tbudnik
	Whole-genome random sequencing and assembly of Haemophilus influenzae Rd. [My Copy] Science (New York, N.Y.), Vol. 269, No. 5223. (28 July 1995), pp. 496-512. by R. D. Fleischmann, M. D. Adams, O. White, et al.R. A. Clayton, E. F. Kirkness, A. R. Kerlavage, C. J. Bult, J. F. Tomb, B. A. Dougherty, J. M. Merrick posted to prok-seq-cg-pipeline by azazello on 2009-10-27 20:36:02 as along with 7 people rshe katholt johanviklund Cortel dgront treangen hsekiguc
	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 prok-seq-cg-pipeline by azazello on 2009-10-26 18:33:39 as along with 45 people and 3 groups claire_jubin danbolser humburg ajsferreira vplagnol bedo jwhitney cthachuk hzoltan ajbattle jmanning2k n00c carlk pachorip APRegier jbhiatt jonilaserson operon jahwa jsatkosk sandfire thegoose2 katholt robsyme djkt hpaces AaronDarling mhz idoerg jmcq dswan dakelley jasontsai acn druvus natstreet nmohelli stajich farhat iris42 tharris Neeperando sharpton GustavoLacerda gdb Bioinformatics DeNovoAssembly-SIMR Mycology
	Reordering contigs of draft genomes using the Mauve Aligner [My Copy] Bioinformatics, Vol. 25, No. 16. (15 August 2009), pp. 2071-2073. by Anna I. Rissman, Bob Mau, Bryan S. Biehl, Aaron E. Darling, Jeremy D. Glasner, Nicole T. Perna posted to prok-seq-cg-pipeline by azazello on 2009-10-26 18:14:30 as along with 2 people and 1 group natstreet druvus Journal picks
	Prediction of lipoprotein signal peptides in Gram-negative bacteria. [My Copy] Protein science : a publication of the Protein Society, Vol. 12, No. 8. (1 August 2003), pp. 1652-1662. by Agnieszka S. Juncker, Hanni Willenbrock, Gunnar Von Heijne, Søren Brunak, Henrik Nielsen, Anders Krogh posted to prok-seq-cg-pipeline by azazello on 2009-10-25 20:31:31 as along with 2 people redlemon29 xingxu
	Locating proteins in the cell using TargetP, SignalP and related tools [My Copy] Nature Protocols In Nat. Protocols, Vol. 2, No. 4. (19 April 2007), pp. 953-971. by Olof Emanuelsson, Soren Brunak, Gunnar von Heijne, Henrik Nielsen posted to prok-seq-cg-pipeline by azazello on 2009-10-25 20:28:43 as along with 6 people dandaman nlapalu raiyar guhjy ptrobajo mdstobbe
	Improved prediction of signal peptides: SignalP 3.0. [My Copy] Journal of molecular biology, Vol. 340, No. 4. (16 July 2004), pp. 783-795. by Jannick Dyrløv D. Bendtsen, Henrik Nielsen, Gunnar von Heijne, Søren Brunak posted to prok-seq-cg-pipeline by azazello on 2009-10-25 20:27:14 as along with 10 people BioNica tfuji rpetrenko katholt nedwards kreibich niallhaslam richter80 sebk raiyar
	tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. [My Copy] Nucleic acids research, Vol. 25, No. 5. (1 March 1997), pp. 955-964. by T. M. Lowe, S. R. Eddy posted to prok-seq-cg-pipeline by azazello on 2009-10-25 20:18:19 as along with 12 people and 1 group codonusage tfuji danatcaret gdb ziquje evaf arcticrasta dquest vwchan djkt dandaman timflutre beta
	A versatile computational pipeline for bacterial genome annotation improvement and comparative analysis, with Brucella as a use case. [My Copy] Nucleic acids research, Vol. 35, No. 12. (9 June 2007), pp. 3953-3962. by G. X. Yu, E. E. Snyder, S. M. Boyle, et al.O. R. Crasta, M. Czar, S. P. Mane, A. Purkayastha, B. Sobral, J. C. Setubal posted to prok-seq-cg-pipeline by azazello on 2009-10-25 19:38:40 as along with 2 people dansullivanblk druvus
	MOSAIC: an online database dedicated to the comparative genomics of bacterial strains at the intra-species level. [My Copy] BMC bioinformatics, Vol. 9 (27 November 2008), 498. by Hélène Chiapello, Annie Gendrault, Christophe Caron, Jérome Blum, Marie-Agnès A. Petit, Meriem El Karoui posted to prok-seq-cg-pipeline by azazello on 2009-10-25 19:35:10 as along with 3 people operon treangen druvus
	Annotation, comparison and databases for hundreds of bacterial genomes [My Copy] Research in Microbiology, Vol. 158, No. 10. (December 2007), pp. 724-736. by Claudine Médigue, Ivan Moszer posted to prok-seq-cg-pipeline by azazello on 2009-10-25 19:34:02 as along with 3 people ajsferreira katholt druvus
	DIYA: a bacterial annotation pipeline for any genomics lab [My Copy] Bioinformatics, Vol. 25, No. 7. (1 April 2009), pp. 962-963. by Andrew C. Stewart, Brian Osborne, Timothy D. Read posted to prok-seq-cg-pipeline by azazello on 2009-10-25 19:33:19 as along with 6 people toszko jamselem robfsouza druvus dswan jmeppley
	PHACCS, an online tool for estimating the structure and diversity of uncultured viral communities using metagenomic information. [My Copy] BMC Bioinformatics, Vol. 6, No. 1. (2 March 2005) by F. Angly, B. Rodriguez-Brito, D. Bangor, et al.P. McNairnie, M. Breitbart, P. Salamon, B. Felts, J. Nulton, J. Mahaffy, F. Rohwer posted to metagenomics by azazello on 2009-09-20 23:50:38 as along with 3 people knaseanka jmeppley bluto
	Genomic analysis of uncultured marine viral communities. [My Copy] Proceedings of the National Academy of Sciences of the United States of America, Vol. 99, No. 22. (29 October 2002), pp. 14250-14255. by Mya Breitbart, Peter Salamon, Bjarne Andresen, et al.Joseph M. Mahaffy, Anca M. Segall, David Mead, Farooq Azam, Forest Rohwer posted to metagenomics by azazello on 2009-09-20 23:49:42 as along with 5 people idoerg knaseanka jmeppley bluto qlli
	Phymm and PhymmBL: metagenomic phylogenetic classification with interpolated Markov models [My Copy] Nature Methods, Vol. 6, No. 9. (02 August 2009), pp. 673-676. by Arthur Brady, Steven L. Salzberg posted to metagenomics binning by azazello on 2009-09-12 00:27:28 as along with 8 people and 4 groups idoerg robertrentzsch dakelley skembel Thaverkamp sharpton jbhiatt stajich Orengo Group Journal Picks iSEEM Journal picks Mycology
	Efficient q-Gram Filters for Finding All e-Matches over a Given Length [My Copy] Research in Computational Molecular Biology (2005), pp. 189-203. by Kim R. Rasmussen, Jens Stoye, Eugene W. Myers posted to mapped_assembly alignment by azazello on 2009-09-01 03:09:04 as
	Extreme genomic variation in a natural population [My Copy] Proceedings of the National Academy of Sciences, Vol. 104, No. 13. (27 March 2007), pp. 5698-5703. by Kerrin S. Small, Michael Brudno, Matthew M. Hill, Arend Sidow posted to polymorphism by azazello on 2009-09-01 03:03:47 as along with 5 people and 1 group qwermish operon balicea adijr nhp Bioinformatics
	PatternHunter II: highly sensitive and fast homology search. [My Copy] Genome informatics. International Conference on Genome Informatics, Vol. 14 (2003), pp. 164-175. by Ming Li, Bin Ma, Derek Kisman, John Tromp posted to ngst mapped_assembly alignment 2gst by azazello on 2009-09-01 02:58:30 as along with 3 people maria_hauser nuke2005 treangen
	Estimating the Number of Classes via Sample Coverage [My Copy] Journal of the American Statistical Association, Vol. 87, No. 417. (1992), pp. 210-217. by Anne Chao, Shen M. Lee posted to core-pan by azazello on 2009-08-14 23:36:47 as
	Estimating the size of the bacterial pan-genome. [My Copy] Trends in genetics : TIG, Vol. 25, No. 3. (23 March 2009), pp. 107-110. by Pascal Lapierre, J. Peter Gogarten posted to core-pan by azazello on 2009-08-14 23:36:07 as along with 4 people and 1 group treangen skembel djkt nyyu iSEEM
	Frameshift detection in prokaryotic genomic sequences. [My Copy] International journal of bioinformatics research and applications, Vol. 5, No. 4. (2009), pp. 458-477. by Andrey Kislyuk, Alexandre Lomsadze, Alla L. Lapidus, Mark Borodovsky posted to prok-seq-cg-pipeline frameshift my by azazello on 2009-08-09 13:48:23 as along with 1 person druvus
	Meningococcus genome informatics platform: a system for analyzing multilocus sequence typing data. [My Copy] Nucleic acids research, Vol. 37, No. Web Server issue. (1 July 2009), pp. W606-611. by Lee S. Katz, Chris R. Bolen, Brian H. Harcourt, et al.Susanna Schmink, Xin Wang, Andrey Kislyuk, Robert T. Taylor, Leonard W. Mayer, I. King Jordan posted to prok-seq-cg-pipeline my neisseria-hgt by azazello on 2009-08-09 13:47:57 as along with 1 person lskatz
	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 next_generation_sequencing by bluto on 2009-08-06 11:16:44 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 Annab katholt jmcq michaelbarton n00c jfr dna nzm farhat idoerg mhz mmartin 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
	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 prok-seq-cg-pipeline 2gst mapped_assembly scaffolding by azazello on 2009-07-10 12:51:24 as along with 17 people and 5 groups skembel n00c operon michaelbarton Thaverkamp dakelley sconlan GustavoLacerda treangen natstreet antonkratz druvus vaulot djkt Katje stajich semrich BergmanLab Papers recommended by the Roscoff Plankton Group iSEEM microbiology_nijmegen Mycology
	A novel ecological role of the Firmicutes identified in thermophilic microbial fuel cells [My Copy] ISME J, Vol. 2, No. 11. (4 September 2008), pp. 1146-1156. by Kelly C. Wrighton, Peter Agbo, Falk Warnecke, et al.Karrie A. Weber, Eoin L. Brodie, Todd Z. Desantis, Philip Hugenholtz, Gary L. Andersen, John D. Coates posted to biofuel microbial_fuel_cells by bluto on 2009-05-24 01:29:20 as along with 1 person Thaverkamp
	Microbiology: Metagenomics [My Copy] Nature, Vol. 455, No. 7212. (2008), pp. 481-483. by Philip Hugenholtz, Gene W. Tyson posted to metagenomics by bluto on 2009-05-24 01:26:43 as along with 4 people EKotlarska Pascalichouchou aramata neils
	Getting to the core of the gut microbiome [My Copy] Nat Biotech, Vol. 27, No. 4. (April 2009), pp. 344-346. by Matthias H. Tschop, Philip Hugenholtz, Christopher L. Karp posted to gut-microbiome metagenomics by bluto on 2009-05-24 01:21:30 as along with 2 people pansapiens neils
	Evolutionary genomics of archaeal viruses: unique viral genomes in the third domain of life. [My Copy] Virus research, Vol. 117, No. 1. (April 2006), pp. 52-67. by D. Prangishvili, R. A. Garrett, E. V. Koonin posted to archaea viruses by bluto on 2009-04-01 16:04:02 as
	Evolution of complexity in the viral world: The dawn of a new vision. [My Copy] Virus Res (21 February 2006) by Eugene V V. Koonin, Valerian V V. Dolja posted to viruses by bluto on 2009-04-01 16:02:10 as along with 1 person eckart_bindewald
	Multiple whole-genome alignments without a reference organism [My Copy] Genome Research, Vol. 19, No. 4. (28 April 2009), pp. 682-689. by Inna Dubchak, Alexander Poliakov, Andrey Kislyuk, Michael Brudno posted to prok-seq-cg-pipeline my by azazello on 2009-03-10 00:22:04 as along with 13 people fernan fstrozzi GustavoLacerda michaelbarton mlangill dakelley xwbcn Neeperando zwang nyyu djkt semrich mhamada
	Comparative bacterial proteomics: analysis of the core genome concept. [My Copy] PloS one, Vol. 3, No. 2. (6 February 2008), e1542. by Stephen J. Callister, Lee Ann A. McCue, Joshua E. Turse, et al.Matthew E. Monroe, Kenneth J. Auberry, Richard D. Smith, Joshua N. Adkins, Mary S. Lipton posted to prok-seq-cg-pipeline core-pan by azazello on 2009-03-03 16:55:46 as along with 4 people and 2 groups vikramjind treangen druvus jlgreen Green Lab iSEEM
	Evolution of the core and pan-genome of Streptococcus: positive selection, recombination, and genome composition [My Copy] Genome Biology, Vol. 8, No. 5. (02 May 2007), R71. by Tristan Lefebure, Michael Stanhope posted to prok-seq-cg-pipeline by azazello on 2009-03-01 17:41:19 as along with 3 people druvus operon rabu
	Multiple genome alignment for identifying the core structure among moderately related microbial genomes [My Copy] BMC Genomics, Vol. 9 (31 October 2008), 515. by Ikuo Uchiyama posted to prok-seq-cg-pipeline by azazello on 2009-03-01 17:40:59 as along with 2 people druvus treangen
	Essential genes of a minimal bacterium [My Copy] Proceedings of the National Academy of Sciences of the United States of America, Vol. 103, No. 2. (10 January 2006), pp. 425-430. by John I. Glass, Nacyra Assad-Garcia, Nina Alperovich, et al.Shibu Yooseph, Matthew R. Lewis, Mahir Maruf, Clyde A. Hutchison, Hamilton O. Smith, J. Craig Venter posted to mgs-nst by azazello on 2009-02-20 16:05:10 as along with 11 people and 2 groups Scis0000002 jwm balicea JKelly555 hillevi famoreira nurban westoll kevinchannon stringertheory mcox Radiation_Damage Stressosome