katholt's Top Recommendations

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	A bimodal pattern of relatedness between the Salmonella Paratyphi A and Typhi genomes: Convergence or divergence by homologous recombination. [My Copy] Genome Res (7 November 2006) by Xavier Didelot, Mark Achtman, Julian Parkhill, Nicholas R R. Thomson, Daniel Falush posted by 6 people druvus AaronDarling aswin aiolozil pnicolas Xavier
	Complete genomic characterization of a pathogenic A.II strain of Francisella tularensis subspecies tularensis. [My Copy] PloS one, Vol. 2, No. 9. (26 September 2007), e947. by Stephen M. Beckstrom-Sternberg, Raymond K. Auerbach, Shubhada Godbole, et al.John V. Pearson, James S. Beckstrom-Sternberg, Zuoming Deng, Christine Munk, Kristy Kubota, Yan Zhou, David Bruce, Jyothi Noronha, Richard H. Scheuermann, Aihui Wang, Xianying Wei, Jianjun Wang, Jicheng Hao, David M. Wagner, Thomas S. Brettin, Nancy Brown, Paul Gilna, Paul S. Keim posted by 4 people ssiddara treangen Xavier druvus
	Genome sequencing in microfabricated high-density picolitre reactors [My Copy] Nature, Vol. 437, No. 7057. (31 July 2005), pp. 376-380. by Marcel Margulies, Michael Egholm, William E. Altman, et al.Said Attiya, Joel S. Bader, Lisa A. Bemben, Jan Berka, Michael S. Braverman, Yi-Ju Chen, Zhoutao Chen, Scott B. Dewell, Lei Du, Joseph M. Fierro, Xavier V. Gomes, Brian C. Godwin, Wen He, Scott Helgesen, Chun H. Ho, Gerard P. Irzyk, Szilveszter C. Jando, Maria L. I. Alenquer, Thomas P. Jarvie, Kshama B. Jirage, Jong-Bum Kim, James R. Knight, Janna R. Lanza, John H. Leamon, Steven M. Lefkowitz, Ming Lei, Jing Li, Kenton L. Lohman, Hong Lu, Vinod B. Makhijani, Keith E. McDade, Michael P. McKenna, Eugene W. Myers, Elizabeth Nickerson, John R. Nobile, Ramona Plant, Bernard P. Puc, Michael T. Ronan, George T. Roth, Gary J. Sarkis, Jan F. Simons, John W. Simpson, Maithreyan Srinivasan, Karrie R. Tartaro, Alexander Tomasz, Kari A. Vogt, Greg A. Volkmer, Shally H. Wang, Yong Wang, Michael P. Weiner, Pengguang Yu, Richard F. Begley, Jonathan M. Rothberg posted by 44 people n00c rshe seb1 pachorip katiehumphry jonilaserson michaelbarton sandfire natstreet daforerog idoerg mmartin azazello jbhiatt alessandrobrozzi leechuck bjorns dayjm jmeppley arve RMGraze JAShapiro balajis cdawson AaronDarling treangen usagi-kirin beatrizfernandez wenhan xingxu erbon Microbial-Ecology GIG gatech-compgenomics tpreeprem farhat carpi bpb mcox GustavoLacerda jlgreen Green Lab iSEEM kieran101
	A Bayesian approach to the estimation of ancestral genome arrangements. [My Copy] Molecular phylogenetics and evolution, Vol. 36, No. 2. (August 2005), pp. 214-223. by B. Larget, J. B. Kadane, D. L. Simon posted by 3 people AaronDarling druvus treangen
	FastBLAST: Homology Relationships for Millions of Proteins [My Copy] PLoS ONE, Vol. 3, No. 10. (31 October 2008), e3589. by Morgan N. Price, Paramvir S. Dehal, Adam P. Arkin posted by 5 people AaronDarling treangen natstreet druvus reyez
	A simple, fast, and accurate method of phylogenomic inference [My Copy] Genome Biology, Vol. 9, No. 10. (13 October 2008), R151. by Martin Wu, Jonathan Eisen posted by 15 people dakelley jeargle AaronDarling zwang cgaugain treangen microbiology_nijmegen Katje operon ellakat scryrps iSEEM djkt aramata druvus
	Modular networks and cumulative impact of lateral transfer in prokaryote genome evolution [My Copy] Proceedings of the National Academy of Sciences, Vol. 105, No. 29. (22 July 2008), pp. 10039-10044. by Tal Dagan, Yael Artzy-Randrup, William Martin posted by 4 people treangen AaronDarling tomhebbron druvus
	Dynamics of Genome Rearrangement in Bacterial Populations [My Copy] PLoS Genet, Vol. 4, No. 7. (18 July 2008), e1000128. by Aaron E. Darling, István Miklós, Mark A. Ragan posted by 9 people nyyu AaronDarling lewista treangen neils druvus Ema djkt jjray
	OWEN: aligning long collinear regions of genomes. [My Copy] Bioinformatics, Vol. 18, No. 12. (December 2002), pp. 1703-1704. by A. Y. Ogurtsov, M. A. Roytberg, S. A. Shabalina, A. S. Kondrashov posted by 4 people druvus treangen operon AaronDarling
	The bacterial species definition in the genomic era. [My Copy] Philos Trans R Soc Lond B Biol Sci, Vol. 361, No. 1475. (29 November 2006), pp. 1929-1940. by K. T. Konstantinidis, A. Ramette, J. M. Tiedje posted by 10 people druvus AaronDarling skembel treangen iSEEM jmeppley kinestetika Microbial-Ecology microbiology_nijmegen Thaverkamp
	HMMoC a compiler for hidden Markov models [My Copy] Bioinformatics, Vol. 23, No. 18. (15 September 2007), pp. 2485-2487. by Gerton Lunter posted by 11 people aprasad druvus treangen alexeid guhjy operon AaronDarling rdiaz niallhaslam carlescorbi Alfie
	Measuring the accuracy of genome-size multiple alignments [My Copy] Genome Biology, Vol. 8 (26 June 2007), R124. by Amol Prakash, Martin Tompa posted by 8 people druvus treangen dpollard AaronDarling stajich lilou EisenLab Mycology
	Genetic flux over time in the Salmonella lineage [My Copy] Genome Biology, Vol. 8 (04 June 2007), R100. by Georgios S. Vernikos, Nicholas R. Thomson, Julian Parkhill posted by 3 people treangen druvus AaronDarling
	M-GCAT: interactively and efficiently constructing large-scale multiple genome comparison frameworks in closely related species [My Copy] BMC Bioinformatics, Vol. 7, No. 1. (05 October 2006), 433. by Todd Treangen, Xavier Messeguer posted by 4 people natstreet druvus AaronDarling treangen
	Bayesian coestimation of phylogeny and sequence alignment [My Copy] BMC Bioinformatics, Vol. 6, No. 1. (2005), 83. by Gerton Lunter, Istvan Miklos, Alexei Drummond, Jens Jensen, Jotun Hein posted by 11 people cmzmasek operon treangen alexeid druvus bpb pradiptaray AaronDarling timflutre adsmitty Patola
	Simultaneous statistical multiple alignment and phylogeny reconstruction. [My Copy] Syst Biol, Vol. 54, No. 4. (August 2005), pp. 548-561. by R. Fleissner, D. Metzler, A. von Haeseler posted by 4 people carlk druvus treangen AaronDarling
	Statistical methods and insights for protein and DNA sequences. [My Copy] Annu Rev Biophys Biophys Chem, Vol. 20 (1991), pp. 175-203. by S. Karlin, P. Bucher, V. Brendel, S. F. Altschul posted by 3 people druvus treangen AaronDarling
	Recombination and the population structures of bacterial pathogens. [My Copy] Annu Rev Microbiol, Vol. 55 (2001), pp. 561-590. by E. J. Feil, B. G. Spratt posted by 5 people druvus treangen jmeppley AaronDarling CharlesM
	Evidence for symmetric chromosomal inversions around the replication origin in bacteria. [My Copy] Genome Biol, Vol. 1, No. 6. (2000) by J. A. Eisen, J. F. Heidelberg, O. White, S. L. Salzberg posted by 4 people druvus AaronDarling braneyboo treangen
	Evolution at the nucleotide level: the problem of multiple whole-genome alignment [My Copy] Hum. Mol. Genet., Vol. 15, No. suppl_1. (15 April 2006), pp. R51-56. by Colin N. Dewey, Lior Pachter posted by 12 people druvus skembel treangen operon Ayest tny dchughes AaronDarling echinotrix G4ID Genetics-of-Gambling Neeperando
	ASAP, a systematic annotation package for community analysis of genomes. [My Copy] Nucleic Acids Res, Vol. 31, No. 1. (1 January 2003), pp. 147-151. by J. D. Glasner, P. Liss, G. Plunkett, et al.A. Darling, T. Prasad, M. Rusch, A. Byrnes, M. Gilson, B. Biehl, F. R. Blattner, N. T. Perna posted by 4 people natstreet druvus treangen AaronDarling
	GRIL: genome rearrangement and inversion locator [My Copy] Bioinformatics, Vol. 20, No. 1. (1 January 2004), pp. 122-124. by Aaron E. Darling, Bob Mau, Frederick R. Blattner, Nicole T. Perna posted by 5 people druvus operon aprasad AaronDarling treangen
	Versatile and open software for comparing large genomes. [My Copy] Genome Biol, Vol. 5, No. 2. (2004) by S. Kurtz, A. Phillippy, A. L. Delcher, et al.M. Smoot, M. Shumway, C. Antonescu, S. L. Salzberg posted by 10 people pachorip APRegier treangen natstreet druvus adelcher AaronDarling michC yoanjacquemin Neeperando
	Gene transfer in bacteria: speciation without species? [My Copy] Theor Popul Biol, Vol. 61, No. 4. (June 2002), pp. 449-460. by J. G. Lawrence posted by 5 people druvus treangen jmeppley AaronDarling manzanita
	PhyloGibbs: a Gibbs sampling motif finder that incorporates phylogeny. [My Copy] PLoS computational biology, Vol. 1, No. 7. (December 2005) by Rahul Siddharthan, Eric D. Siggia, Erik van Nimwegen posted by 21 people farhat wowalz aprasad cajunsushi treangen druvus ana postrational dquest AaronDarling nickluscombe noano adsmitty lusk lilou structural_bioinformatics Bioinformatics EBI-regulation idonaldson yevishere isimpson
	MRBAYES: Bayesian inference of phylogenetic trees [My Copy] Bioinformatics, Vol. 17, No. 8. (1 August 2001), pp. 754-755. by John P. Huelsenbeck, Fredrik Ronquist posted by 11 people ckenaley BioNica lmichan druvus treangen bpb rvosa spavey AaronDarling FAB-lab CharlesM
	Analyzing patterns of microbial evolution using the mauve genome alignment system. [My Copy] Methods in molecular biology (Clifton, N.J.), Vol. 396 (2007), pp. 135-152. by A. E. Darling, T. J. Treangen, X. Messeguer, N. T. Perna posted by 2 people Xavier druvus
	Chromosome Rearrangement and Diversification of Francisella tularensis Revealed by the Type B (OSU18) Genome Sequence [My Copy] J. Bacteriol., Vol. 188, No. 19. (1 October 2006), pp. 6977-6985. by Joseph F. Petrosino, Qin Xiang, Sandor E. Karpathy, et al.Huaiyang Jiang, Shailaja Yerrapragada, Yamei Liu, Jason Gioia, Lisa Hemphill, Arely Gonzalez, T. M. Raghavan, Akif Uzman, George E. Fox, Sarah Highlander, Mason Reichard, Rebecca J. Morton, Kenneth D. Clinkenbeard, George M. Weinstock posted by 2 people Xavier druvus
	Approximate Bayesian Computation in Population Genetics [My Copy] Genetics, Vol. 162, No. 4. (1 December 2002), pp. 2025-2035. by Mark A. Beaumont, Wenyang Zhang, David J. Balding posted by 4 people skembel druvus ryanraaum Xavier
	Displaying the relatedness among isolates of bacterial species - the eBURST approach [My Copy] FEMS Microbiology Letters, Vol. 241, No. 2. (2004), pp. 129-134. by Brian G. Spratt, William P. Hanage, Bao Li, David M. Aanensen, Edward J. Feil posted by 2 people druvus Xavier
	Tracking the in vivo evolution of multidrug resistance in Staphylococcus aureus by whole-genome sequencing [My Copy] Proceedings of the National Academy of Sciences, Vol. 104, No. 22. (29 May 2007), pp. 9451-9456. by Michael M. Mwangi, Shang W. Wu, Yanjiao Zhou, et al.Krzysztof Sieradzki, Herminia de Lencastre, Paul Richardson, David Bruce, Edward Rubin, Eugene Myers, Eric D. Siggia, Alexander Tomasz posted by 5 people druvus gwenknight lewista aprasad Xavier
	Comparison of Francisella tularensis genomes reveals evolutionary events associated with the emergence of human-pathogenic strains [My Copy] Genome Biology, Vol. 8 (05 June 2007), R102. by Laurence Rohmer, Christine Fong, Simone Abmayr, et al.Michael Wasnick, Theodore, Matthew Radey, Tina Guina, Kerstin Svensson, Hillary S. Hayden, Michael Jacobs, Larry A. Gallagher, Colin Manoil, Robert K. Ernst, Becky Drees, Danielle Buckley, Eric Haugen, Donald Bovee, Yang Zhou, Jean Chang, Ruth Levy, Regina Lim, Will Gillett, Don Guenthener, Allison Kang, Scott A. Shaffer, Greg Taylor, Jinzhi Chen, Byron Gallis, David A. D'Argenio, Mats Forsman, Maynard V. Olson, David R. Goodlett, Rajinder Kaul, Samuel I. Miller, Mitchell J. Brittnacher posted by 4 people druvus biomcgary Xavier Marcotte_Lab
	Inference of Population Structure Using Multilocus Genotype Data: Linked Loci and Correlated Allele Frequencies [My Copy] Genetics, Vol. 164, No. 4. (1 August 2003), pp. 1567-1587. by Daniel Falush, Matthew Stephens, Jonathan K. Pritchard posted by 9 people Latimeria carlk druvus cchurc1 sriram_s hms Xavier dmc pcarbo
	The complete genome sequence of Francisella tularensis, the causative agent of tularemia. [My Copy] Nat Genet, Vol. 37, No. 2. (February 2005), pp. 153-159. by P. Larsson, P. C. Oyston, P. Chain, et al.M. C. Chu, M. Duffield, H. H. Fuxelius, E. Garcia, G. Hälltorp, D. Johansson, K. E. Isherwood, P. D. Karp, E. Larsson, Y. Liu, S. Michell, J. Prior, R. Prior, S. Malfatti, A. Sjöstedt, K. Svensson, N. Thompson, L. Vergez, J. K. Wagg, B. W. Wren, L. E. Lindler, S. G. Andersson, M. Forsman, R. W. Titball posted by 4 people carpi greger_halltorp Xavier druvus
	How To Choose a Good Scientific Problem [My Copy] Molecular Cell, Vol. 35, No. 6. (24 September 2009), pp. 726-728. by Uri Alon posted by 132 people sdaehne artaban421 cefa gvdh penneyft welliegirl bertelsen thegoose Brain-like research group xawen chriswillmott nellapower ishiken andreff claudiushauptmann cermak bmoores karthikraman applebyb mordiano Gorzomagnificent Horduna ajaymalik mmwoodman dbikard toszko mthomure timflutre cyounkin marsl0am jmzhuo dmorti renatomilani ibre kevinemamy Sergey_gerbek huberse ddbb12 seneca mattbiehl mmborges GeeSharpMinor jjjpppfff zhangfh andreacapocci melo_mcr aaltenburger iannis jichok josephjose TorstenWaldminghaus kshameer rudalert kvalyi UWA Science Communication duel_jetty allaves milab@yzu rabit fercosber hax123 iskanbasal livingthingdan poojamaj gonzalez amynmoore ramalldf pvdg sfalsharif dill2009 singhsh rogermug aha jarekadam Jansen04 cgravlee lkakinami anuragsethi flips robfree kaliczp yyfwuhan luciensamary elsantosneto mgaldino daveGerrard sandfire tnhh lesandrop munzmarci pdpcosta Information Integration Architecture mxro wangngu myriasofo OliverHarriman AnthonySoprano robertlischke R_C_Cordeiro daforerog operon nandipati wenhaosparty jeffcrow leocmcheung fgibson snakehsu cisevol BergmanLab michaelbarton dna dullhunk danilov m_lew abellogin cxshang grahamc SantoshKalwar Xusheng leonardo roys benoitvalley zchen75 darshan druvus Asclepius Roswell Cancer Crosstalk Zephyrus songpku aalibes flieder pedromts
	Comparative genome and phenotypic analysis of Clostridium difficile 027 strains provides insight into the evolution of a hypervirulent bacterium. [My Copy] Genome biology, Vol. 10, No. 9. (25 September 2009), R102. by Richard A. Stabler, Miao He, Lisa Dawson, et al.Melissa Martin, Esmeralda Valiente, Craig Corton, Trevor D. Lawley, Mohammed Sebaihia, Michael A. Quail, Graham Rose, Dale N. Gerding, Maryse Gibert, Michel R. Popoff, Julian Parkhill, Gordon Dougan, Brendan W. Wren posted by 5 people gwenknight jlmoir sandfire jecouk druvus
	Detecting SNPs and estimating allele frequencies in clonal bacterial populations by sequencing pooled DNA. [My Copy] Bioinformatics (Oxford, England), Vol. 25, No. 16. (15 August 2009), pp. 2074-2075. by Kathryn E. Holt, Yik Y. Teo, Heng Li, et al.Satheesh Nair, Gordon Dougan, John Wain, Julian Parkhill posted by 10 people jsatkosk jandot Mycology stajich iSEEM djkt guhjy farhat sandfire druvus
	ABACAS: algorithm-based automatic contiguation of assembled sequences. [My Copy] Bioinformatics (Oxford, England), Vol. 25, No. 15. (1 August 2009), pp. 1968-1969. by Samuel Assefa, Thomas M. Keane, Thomas D. Otto, Chris Newbold, Matthew Berriman posted by 9 people sconlan GustavoLacerda adamjamesreid jmeppley sandfire druvus pengchy Journal picks AlexBateman
	Genome assembly reborn: recent computational challenges [My Copy] Brief Bioinform, Vol. 10, No. 4. (1 July 2009), pp. 354-366. by Mihai Pop posted by 32 people jfr hzoltan cthachuk GustavoLacerda n00c agbiotec shabhonam pachorip APRegier jmcq stevebs jonilaserson michaelbarton inesdesantiago GeeSharpMinor bertelsen aprasad ananta_samudra sandfire jmeppley mlangill fgibson Journal picks ppgardne TRHvidsten pengchy robsyme nuin kiekyon natstreet druvus idoerg
	SNP detection for massively parallel whole-genome resequencing [My Copy] Genome Research, Vol. 19, No. 6. (6 June 2009), pp. 1124-1132. by Ruiqiang Li, Yingrui Li, Xiaodong Fang, et al.Huanming Yang, Jian Wang, Karsten Kristiansen, Jun Wang posted by 20 people Julien_Fayolle torfinnnome hzoltan seb1 maren adijr greg jandot guhjy jonilaserson n00c druvus reyez sandfire jasontsai djkt sameersoi natstreet jbhiatt GeeSharpMinor
	De novo assembly of the Pseudomonas syringae pv. syringae B728a genome using Illumina/Solexa short sequence reads. [My Copy] FEMS microbiology letters (9 December 2008) by Rhys A A. Farrer, Eric Kemen, Jonathan D G D. Jones, David J J. Studholme posted by 12 people shabhonam pachorip sandfire natstreet microbiology_nijmegen Huub_odc usagi-kirin abizar GustavoLacerda SIMR bioinformatics malcook druvus
	Assessing the gene space in draft genomes. [My Copy] Nucleic acids research, Vol. 37, No. 1. (28 January 2009), pp. 289-297. by G. Parra, K. Bradnam, Z. Ning, T. Keane, I. Korf posted by 5 people guhjy sandfire orzenil druvus neils
	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 by 43 people CUBES hongkeun_park ngehlenborg hzoltan sandfire maren jwfoley 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
	Error-correcting barcoded primers for pyrosequencing hundreds of samples in multiplex [My Copy] Nature Methods, Vol. 5, No. 3. (10 February 2008), pp. 235-237. by Micah Hamady, Jeffrey J. Walker, J. Kirk Harris, Nicholas J. Gold, Rob Knight posted by 12 people natstreet druvus stubrown sandfire iSEEM jlgreen jbhiatt skembel pdexheimer guhjy slevy03 sconlan
	Evolution of pathogens in a man-made world [My Copy] Molecular Ecology, Vol. 17, No. 1. (January 2008), pp. 475-484. by Camille Lebarbenchon, Sam P. Brown, Robert Poulin, Michel Gauthier-Clerc, Frederic Thomas posted by 3 people sandfire druvus ryanraaum
	SNP-PHAGE - High throughput SNP discovery pipeline [My Copy] BMC Bioinformatics, Vol. 7, No. 1. (23 October 2006), 468. by Lakshmi Matukumalli, John Grefenstette, David Hyten, Ik Y. Choi, Perry Cregan, Curtis Van Tassell posted by 7 people sandfire n00c csrocha daforerog natstreet druvus guhjy
	Monte Carlo sampling methods using Markov chains and their applications [My Copy] Biometrika, Vol. 57, No. 1. (1 April 1970), pp. 97-109. by W. K. Hastings posted by 17 people gtaralds flbarroso AbnerCYH sdvillal Taguan carmenrg oannes muraken Maderlock alexeid AaronDarling tobin iris_2001 Xavier petermilner przem naegele
	How genomics has affected the concept of microbiology [My Copy] Current Opinion in Microbiology, Vol. 8, No. 5. (October 2005), pp. 564-571. by N. Ward, C. Fraser posted by 3 people druvus Thaverkamp AaronDarling
	Enteropathogen Resource Integration Center (ERIC): bioinformatics support for research on biodefense-relevant enterobacteria [My Copy] Nucl. Acids Res., Vol. 36, No. suppl_1. (11 January 2008), pp. D519-523. by Jeremy D. Glasner, Guy Plunkett, Bradley D. Anderson, et al.David J. Baumler, Bryan S. Biehl, Valerie Burland, Eric L. Cabot, Aaron E. Darling, Bob Mau, Eric C. Neeno-Eckwall, David Pot, Yu Qiu, Anna I. Rissman, Sara Worzella, Sam Zaremba, Joel Fedorko, Tom Hampton, Paul Liss, Michael Rusch, Matthew Shaker, Lorie Shaull, Panna Shetty, Silpa Thotakura, Jon Whitmore, Frederick R. Blattner, John M. Greene, Nicole T. Perna posted by 2 people druvus AaronDarling
	A Novel Heuristic for Local Multiple Alignment of Interspersed DNA Repeats [My Copy] IEEE/ACM Transactions on Computational Biology and Bioinformatics, Vol. 6, No. 2. (2009), pp. 180-189. by Todd J. Treangen, Aaron E. Darling, Guillaume Achaz, Mark A. Ragan, Xavier Messeguer, Eduardo P. C. Rocha posted by 2 people druvus AaronDarling
	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 by 29 people jfr cthachuk hzoltan ramonvidal orzenil pachorip GustavoLacerda jonilaserson operon BergmanLab polivares reyez jasontsai n00c humburg dakelley jessopher idonaldson robsyme neils natstreet AaronDarling druvus rpatward dswan Mycology stajich jbhiatt erikarner
	Are Protein Domains Modules of Lateral Genetic Transfer? [My Copy] PLoS ONE, Vol. 4, No. 2. (20 February 2009), e4524. by Cheong X. Chan, Aaron E. Darling, Robert G. Beiko, Mark A. Ragan posted by 4 people chancx druvus AaronDarling zwang
	Seevolution: visualizing chromosome evolution [My Copy] Bioinformatics, Vol. 25, No. 7. (1 April 2009), pp. 960-961. by Andres Esteban-Marcos, Aaron E. Darling, Mark A. Ragan posted by 4 people jandot AaronDarling nuin druvus
	Phylogenetic and functional assessment of orthologs inference projects and methods. [My Copy] PLoS computational biology, Vol. 5, No. 1. (16 January 2009), e1000262. by Adrian M. Altenhoff, Christophe Dessimoz posted by 12 people Ensembl Compara citations avilella AaronDarling skembel isimpson hpaces natstreet alpae kshameer djkt bpcusack druvus
	De novo fragment assembly with short mate-paired reads: Does the read length matter? [My Copy] Genome Research, Vol. 19, No. 2. (3 February 2009), pp. 336-346. by Mark J. Chaisson, Dumitru Brinza, Pavel A. Pevzner posted by 19 people n00c carlk APRegier jandot jonilaserson natstreet dakelley jessopher orzenil AaronDarling sphsmith jasontsai nmohelli jbhiatt druvus hpaces GustavoLacerda Mycology stajich
	Algorithm of OMA for large-scale orthology inference [My Copy] BMC Bioinformatics, Vol. 9 (04 December 2008), 518. by Alexander, Christophe Dessimoz posted by 6 people AaronDarling alpae cgaugain grahamc barriot druvus
	De novo assembly using low-coverage short read sequence data from the rice pathogen Pseudomonas syringae pv. oryzae. [My Copy] Genome research, Vol. 19, No. 2. (17 February 2009), pp. 294-305. by Josephine A. Reinhardt, David A. Baltrus, Marc T. Nishimura, William R. Jeck, Corbin D. Jones, Jeffery L. Dangl posted by 16 people michaelbarton pachorip ThomasDOtto robsyme orzenil AaronDarling druvus dakelley Huub_odc usagi-kirin abizar SIMR bioinformatics acn jbhiatt Bioinformatics hpaces
	The net of life: Reconstructing the microbial phylogenetic network [My Copy] Genome Research, Vol. 15, No. 7. (July 2005), pp. 954-959. by Victor Kunin, Leon Goldovsky, Nikos Darzentas, Christos A. Ouzounis posted by 4 people AaronDarling druvus LabDros operon
	ESTIMATING SPECIES TREES USING MULTIPLE-ALLELE DNA SEQUENCE DATA [My Copy] Evolution, Vol. 62, No. 8. (August 2008), pp. 2080-2091. by Liang Liu, Dennis K. Pearl, Robb T. Brumfield, Scott V. Edwards posted by 3 people lizbiogen AaronDarling druvus
	The infinite sites model of genome evolution [My Copy] Proceedings of the National Academy of Sciences, Vol. 105, No. 38. (23 September 2008), pp. 14254-14261. by Jian Ma, Aakrosh Ratan, Brian J. Raney, Bernard B. Suh, Webb Miller, David Haussler posted by 10 people sharpton Thaverkamp AaronDarling ilyashl druvus operon inesdesantiago Mycology stajich stringertheory
	Descendants of Whole Genome Duplication within Gene Order Phylogeny. [My Copy] Journal of computational biology : a journal of computational molecular cell biology (12 September 2008) by Chunfang Zheng, Qian Zhu, David Sankoff posted by 3 people AaronDarling druvus nuin
	BEST: Bayesian estimation of species trees under the coalescent model [My Copy] Bioinformatics, Vol. 24, No. 21. (1 November 2008), pp. 2542-2543. by Liang Liu posted by 7 people lizbiogen robfsouza AaronDarling gjuggler druvus alexeid nuin
	An Automated Phylogenetic Tree-Based Small Subunit rRNA Taxonomy and Alignment Pipeline (STAP) [My Copy] PLoS ONE, Vol. 3, No. 7. (2 July 2008), e2566. by Dongying Wu, Amber Hartman, Naomi Ward, Jonathan A. Eisen posted by 12 people microbiology_nijmegen Katje AaronDarling skembel sriesenfeld druvus Papers recommended by the Roscoff Plankton Group Microbial-Ecology vaulot skato_toyaku djkt iSEEM
	ALLPATHS: De novo assembly of whole-genome shotgun microreads [My Copy] Genome Research, Vol. 18, No. 5. (13 May 2008), pp. 810-820. by Jonathan Butler, Iain MacCallum, Michael Kleber, et al.Ilya A. Shlyakhter, Matthew K. Belmonte, Eric S. Lander, Chad Nusbaum, David B. Jaffe posted by 25 people ajsferreira n00c carlk jmanning2k APRegier pachorip jonilaserson operon thegoose2 natstreet AaronDarling mhz dakelley druvus stajich azazello hpaces Mycology tharris jwhitney iris42 Neeperando sharpton GustavoLacerda GeeSharpMinor
	Whole-genome sequencing and variant discovery in C. elegans. [My Copy] Nature methods, Vol. 5, No. 2. (20 February 2008), pp. 183-188. by LaDeana W. Hillier, Gabor T. Marth, Aaron R. Quinlan, et al.David Dooling, Ginger Fewell, Derek Barnett, Paul Fox, Jarret I. Glasscock, Matthew Hickenbotham, Weichun Huang, Vincent J. Magrini, Ryan J. Richt, Sacha N. Sander, Donald A. Stewart, Michael Stromberg, Eric F. Tsung, Todd Wylie, Tim Schedl, Richard K. Wilson, Elaine R. Mardis posted by 15 people seninp Annab n00c APRegier thegoose2 druvus semrich AaronDarling usagi-kirin matthewsuderman inesdesantiago orzenil mdimon farhat tharris
	Phylogenomics: improving functional predictions for uncharacterized genes by evolutionary analysis. [My Copy] Genome research, Vol. 8, No. 3. (1 March 1998), pp. 163-167. by J. A. Eisen posted by 5 people pansapiens AaronDarling druvus gjuggler sgoetz
	How to find small non-coding RNAs in bacteria. [My Copy] Biol Chem, Vol. 386, No. 12. (December 2005), pp. 1219-1238. by J. Vogel, C. M. Sharma posted by 2 people druvus AaronDarling
	Environmental Shotgun Sequencing: Its Potential and Challenges for Studying the Hidden World of Microbes [My Copy] PLoS Biol, Vol. 5, No. 3. (13 March 2007), e82. by Jonathan A. Eisen posted by 20 people druvus skembel hwright Thaverkamp AaronDarling anphony precale adgrativol silberbauer jmeppley jdelcampo azazello beatrizfernandez xingxu Microbial-Ecology jlgreen Green Lab olympos djkt iSEEM
	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 by 4 people druvus dbikard AaronDarling Neeperando
	Genome analysis of multiple pathogenic isolates of Streptococcus agalactiae: Implications for the microbial “pan-genome” [My Copy] Proceedings of the National Academy of Sciences of the United States of America, Vol. 102, No. 39. (27 September 2005), pp. 13950-13955. by Hervé Tettelin, Vega Masignani, Michael J. Cieslewicz, et al.Claudio Donati, Duccio Medini, Naomi L. Ward, Samuel V. Angiuoli, Jonathan Crabtree, Amanda L. Jones, A. Scott Durkin, Robert T. DeBoy, Tanja M. Davidsen, Marirosa Mora, Maria Scarselli, Margarit, Jeremy D. Peterson, Christopher R. Hauser, Jaideep P. Sundaram, William C. Nelson, Ramana Madupu, Lauren M. Brinkac, Robert J. Dodson, Mary J. Rosovitz, Steven A. Sullivan, Sean C. Daugherty, Daniel H. Haft, Jeremy Selengut, Michelle L. Gwinn, Liwei Zhou, Nikhat Zafar, Hoda Khouri, Diana Radune, George Dimitrov, Kisha Watkins, Kevin J. B. O'Connor, Shannon Smith, Teresa R. Utterback, Owen White, Craig E. Rubens, Guido Grandi, Lawrence C. Madoff, Dennis L. Kasper, John L. Telford, Michael R. Wessels, Rino Rappuoli, Claire M. Fraser posted by 6 people iSEEM sharpton nyyu azazello druvus AaronDarling
	Genome-wide detection and analysis of homologous recombination among sequenced strains of Escherichia coli [My Copy] Genome Biology, Vol. 7, No. 5. (31 May 2006), R44. by Bob Mau, Jeremy Glasner, Aaron Darling, Nicole Perna posted by 4 people druvus jmeppley AaronDarling vplagnol
	Global multiple-sequence alignment with repeats. [My Copy] Proteins (11 April 2006) by Michael Sammeth, Jaap Heringa posted by 3 people druvus feenstra AaronDarling
	ASAP: a resource for annotating, curating, comparing, and disseminating genomic data [My Copy] Nucl. Acids Res., Vol. 34, No. suppl_1. (1 January 2006), pp. D41-45. by Jeremy D. Glasner, Michael Rusch, Paul Liss, et al.Guy Plunkett, Eric L. Cabot, Aaron Darling, Bradley D. Anderson, Paul Infield-Harm, Michael C. Gilson, Nicole T. Perna posted by 2 people druvus AaronDarling
	Estimating mutation parameters, population history and genealogy simultaneously from temporally spaced sequence data. [My Copy] Genetics, Vol. 161, No. 3. (July 2002), pp. 1307-1320. by A. J. Drummond, G. K. Nicholls, A. G. Rodrigo, W. Solomon posted by 5 people druvus alexeid kaspermunch AaronDarling Bioinformatics
	The population genetics of ecological specialization in evolving Escherichia coli populations. [My Copy] Nature, Vol. 407, No. 6805. (12 October 2000), pp. 736-739. by V. S. Cooper, R. E. Lenski posted by 2 people druvus AaronDarling
	Maximum likelihood estimation of a migration matrix and effective population sizes in n subpopulations by using a coalescent approach [My Copy] PNAS, Vol. 98, No. 8. (10 April 2001), pp. 4563-4568. by Peter Beerli, Joseph Felsenstein posted by 6 people senseable-urb druvus balicea spavey AaronDarling FAB-lab
	Mauve: Multiple Alignment of Conserved Genomic Sequence With Rearrangements [My Copy] Genome Research, Vol. 14, No. 7. (July 2004), pp. 1394-1403. by Aaron C. E. Darling, Bob Mau, Frederick R. Blattner, Nicole T. Perna posted by 16 people rneches foxpowa APRegier Khavkin's lab ArtemPankin hpaces Neeperando bcondon semrich operon catmat AaronDarling azazello gatech-compgenomics mariakmejia druvus
	Genome-scale approaches to resolving incongruence in molecular phylogenies [My Copy] Nature, Vol. 425, No. 6960. (23 October 2003), pp. 798-804. by Antonis Rokas, Barry L. Williams, Nicole King, Sean B. Carroll posted by 9 people iSEEM skembel biomcgary nlapalu druvus knaseanka aprasad AaronDarling srfairclough
	OrthoMCL: identification of ortholog groups for eukaryotic genomes. [My Copy] Genome research, Vol. 13, No. 9. (September 2003), pp. 2178-2189. by Li Li, Christian J. Stoeckert, David S. Roos posted by 18 people GustavoLacerda biomcgary sjcockell thegoose2 nlapalu dullhunk natstreet druvus C. elegans / WormBase tharris mdimmic operon indigoviolet AaronDarling bluto EisenLab maximilianh ninch
	Genome evolution and adaptation in a long-term experiment with Escherichia coli. [My Copy] Nature, Vol. 461, No. 7268. (29 October 2009), pp. 1243-1247. by Jeffrey E. Barrick, Dong Su S. Yu, Sung Ho H. Yoon, et al.Haeyoung Jeong, Tae Kwang K. Oh, Dominique Schneider, Richard E. Lenski, Jihyun F. Kim posted by 36 people pmalkus ronbun_2009au dokky samubernard ilyashl biomcgary kintoki zwang jasontsai Pedro Martinez EvoDevo lab Barcelona aaltenburger sawasthi nurban josepe tjandra venancio maren qayub Garamonfok yyfwuhan Asclepius dbikard nzm jjray iSEEM djkt treangen Journal picks lp2 operon diamantis BergmanLab michaelbarton druvus DrRichardBadge richardfranzese
	Rapidly evolving genes in pathogens: Methods for detecting positive selection and examples among fungi, bacteria, viruses and protists [My Copy] Infection, Genetics and Evolution, Vol. 9, No. 4. (July 2009), pp. 656-670. by Gabriela Aguileta, Guislaine Refrégier, Roxana Yockteng, Elisabeth Fournier, Tatiana Giraud posted by 4 people GustavoLacerda druvus treangen robsyme
	The meaning of alignment: lessons from structural diversity [My Copy] BMC Bioinformatics, Vol. 9, No. 1. (2008) by Walter Pirovano, Anton K. Feenstra, Jaap Heringa posted by 14 people pimmy swtimmer dimka mhamada reyez treangen markusd j3xucite nuin kshameer druvus chad_davis taguchi pansapiens
	Complex fate of paralogs [My Copy] BMC Evolutionary Biology, Vol. 8, No. 1. (2008) by Radek Szklarczyk, Martijn Huynen, Berend Snel posted by 5 people swp09 druvus treangen kshameer phoenixzxl
	On the origin and evolution of new genes--a genomic and experimental perspective. [My Copy] Journal of genetics and genomics = Yi chuan xue bao, Vol. 35, No. 11. (November 2008), pp. 639-648. by Q. Zhou, W. Wang posted by 4 people wangbo treangen druvus operon
	Comparison of methods for estimating the nucleotide substitution matrix [My Copy] BMC Bioinformatics, Vol. 9, No. 1. (2008) by Maribeth Oscamou, Daniel Mcdonald, Von B. Yap, Gavin Huttley, Manuel Lladser, Rob Knight posted by 5 people sconlan nklee nuin treangen 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 by 4 people azazello operon treangen druvus
	Building communities one bacterium at a time [My Copy] Proceedings of the National Academy of Sciences, Vol. 105, No. 47. (25 November 2008), pp. 18075-18076. by Douglas B. Weibel posted by 2 people druvus treangen
	Phylogenetic reconstruction from transpositions. [My Copy] BMC genomics, Vol. 9 Suppl 2 (2008) by F. Yue, M. Zhang, J. Tang posted by 2 people druvus treangen
	Automatic extraction of reliable regions from multiple sequence alignments [My Copy] BMC Bioinformatics, Vol. 8, No. Suppl 5. (2007) by Timo Lassmann, Erik Sonnhammer posted by 2 people druvus treangen
	Inferring species phylogenies from multiple genes: concatenated sequence tree versus consensus gene tree. [My Copy] Journal of experimental zoology. Part B. Molecular and developmental evolution, Vol. 304, No. 1. (15 January 2005), pp. 64-74. by S. R. Gadagkar, M. S. Rosenberg, S. Kumar posted by 2 people druvus treangen
	Ancestral sequence alignment under optimal conditions. [My Copy] BMC bioinformatics, Vol. 6 (2005) by A. K. Hudek, D. G. Brown posted by 2 people druvus treangen
	Detecting Repeat Families in Incompletely Sequenced Genomes [My Copy] Algorithms in Bioinformatics (2008), pp. 342-353. by Amgarten, Jens Stoye posted by 3 people natstreet druvus treangen
	Metagenome Annotation Using a Distributed Grid of Undergraduate Students [My Copy] PLoS Biol, Vol. 6, No. 11. (25 November 2008), e296. by Pascal Hingamp, Céline Brochier, Emmanuel Talla, Daniel Gautheret, Denis Thieffry, Carl Herrmann posted by 21 people daforerog operon azazello Bioinformatics - CRUK Stew JustinCrocker nuin jmeppley xingxu guhjy nitiniitk Centre de Recherches Interdisciplinaires dbikard dchughes druvus neils iSEEM djkt ptrobajo dullhunk treangen
	Computational reconstruction of ancestral DNA sequences. [My Copy] Methods in molecular biology (Clifton, N.J.), Vol. 422 (2008), pp. 171-184. by M. Blanchette, A. B. Diallo, E. D. Green, W. Miller, D. Haussler posted by 2 people druvus treangen
	Comparative analysis of CRISPR loci in lactic acid bacteria genomes. [My Copy] International journal of food microbiology (15 July 2008) by Philippe Horvath, Anne-Claire C. Coûté-Monvoisin, Dennis A A. Romero, Patrick Boyaval, Christophe Fremaux, Rodolphe Barrangou posted by 2 people druvus treangen
	Comparison of Correspondence Analysis Methods for Synonymous Codon Usage in Bacteria [My Copy] DNA Res (21 October 2008), dsn028. by Haruo Suzuki, Celeste J. Brown, Larry J. Forney, Eva M. Top posted by 3 people rshe druvus treangen
	Comparative analysis of Acinetobacters: three genomes for three lifestyles. [My Copy] PLoS ONE, Vol. 3, No. 3. (2008) by D. Vallenet, P. Nordmann, V. Barbe, et al.L. Poirel, S. Mangenot, E. Bataille, C. Dossat, S. Gas, A. Kreimeyer, P. Lenoble, S. Oztas, J. Poulain, B. Segurens, C. Robert, C. Abergel, J. M. Claverie, D. Raoult, C. Médigue, J. Weissenbach, S. Cruveiller posted by 2 people druvus treangen
	Ecology and genomics of Bacillus subtilis. [My Copy] Trends in microbiology, Vol. 16, No. 6. (June 2008), pp. 269-275. by A. M. Earl, R. Losick, R. Kolter posted by 2 people druvus treangen
	Robust E-values for gapped local alignments. [My Copy] Journal of computational biology : a journal of computational molecular cell biology, Vol. 13, No. 4. (May 2006), pp. 882-896. by D. Metzler posted by 2 people druvus treangen
	An improved string composition method for sequence comparison [My Copy] BMC Bioinformatics, Vol. 9, No. Suppl 6. (2008), S15. by Guoqing Lu, Shunpu Zhang, Xiang Fang posted by 2 people druvus treangen