Group: iSEEM - with tag phylogenetics [75 articles] Export

Recent papers posted by members of the iSEEM group with tag phylogenetics

	Comparative Analysis of Pyrosequencing and a Phylogenetic Microarray for Exploring Microbial Community Structures in the Human Distal Intestine [My Copy] PLoS ONE, Vol. 4, No. 8. (20 August 2009), e6669. by Marcus J. Claesson, Orla O'Sullivan, Qiong Wang, et al.Janne Nikkilä, Julian R. Marchesi, Hauke Smidt, Willem M. de Vos, R. Paul Ross, Paul W. O'Toole posted to pyrosequencing phylogenetics metagenomics bootstrap by skembel to the group iSEEM on 2009-11-15 18:23:10 as along with 2 people nnnagara neils
	Distributions of Tree Comparison Metrics--Some New Results [My Copy] Syst Biol, Vol. 42, No. 2. (1 June 1993), pp. 126-141. by Mike A. Steel, David Penny posted to phylogenetics methods by skembel to the group iSEEM on 2009-11-04 19:13:37 as
	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 to phylogenetics incongruence genomes by skembel to the group iSEEM on 2009-10-28 20:32:38 as along with 7 people biomcgary nlapalu druvus knaseanka aprasad AaronDarling srfairclough
	Intertwined Evolutionary Histories of Marine Synechococcus and Prochlorococcus marinus [My Copy] Genome Biol Evol, Vol. 2009, No. 0. (23 September 2009), pp. 325-339. by Olga Zhaxybayeva, W. Ford Doolittle, R. Thane Papke, J. Peter Gogarten posted to phylogenetics microbes ecology by djkt to the group iSEEM on 2009-10-01 00:13:13 as along with 1 person skembel
	Bayesian Phylogeography Finds Its Roots [My Copy] PLoS Comput Biol, Vol. 5, No. 9. (25 September 2009), e1000520. by Philippe Lemey, Andrew Rambaut, Alexei J. Drummond, Marc A. Suchard posted to virus phylogenetics model geography bayesian by djkt to the group iSEEM on 2009-09-25 19:55:42 as along with 2 people scmelton nuin
	Species Tree Inference by Minimizing Deep Coalescences [My Copy] PLoS Comput Biol, Vol. 5, No. 9. (11 September 2009), e1000501. by Cuong Than, Luay Nakhleh posted to phylogenetics by djkt to the group iSEEM on 2009-09-11 16:30:16 as along with 6 people and 1 group parnell qcjones gdb gjuggler ppgardne druvus Journal picks
	Evolutionary Triplet Models of Structured RNA [My Copy] PLoS Comput Biol, Vol. 5, No. 8. (28 August 2009), e1000483. by Robert K. Bradley, Ian Holmes posted to structure rna phylogenetics alignment by djkt to the group iSEEM on 2009-08-31 19:26:10 as along with 1 person and 1 group ppgardne Journal picks
	PhyloBayes 3: a Bayesian software package for phylogenetic reconstruction and molecular dating [My Copy] Bioinformatics, Vol. 25, No. 17. (1 September 2009), pp. 2286-2288. by Nicolas Lartillot, Thomas Lepage, Samuel Blanquart posted to phylogenetics molclock bayesian by djkt to the group iSEEM on 2009-08-20 18:55:41 as along with 6 people nesnidal leemond31 operon nuin grahamc phoenixzxl
	A Machine-Learning Approach Reveals That Alignment Properties Alone Can Accurately Predict Inference of Lateral Gene Transfer from Discordant Phylogenies [My Copy] Mol Biol Evol, Vol. 26, No. 9. (1 September 2009), pp. 1931-1939. by Mayo Roettger, William Martin, Tal Dagan posted to phylogenetics gene-transfer alignment by djkt to the group iSEEM on 2009-08-13 22:57:54 as along with 3 people and 1 group gwallau stajich operon Mycology
	Identifying Currents in the Gene Pool for Bacterial Populations Using an Integrative Approach [My Copy] PLoS Comput Biol, Vol. 5, No. 8. (7 August 2009), e1000455. by Jing Tang, William P. Hanage, Christophe Fraser, Jukka Corander posted to metagenomics phylogenetics popgen by djkt to the group iSEEM on 2009-08-07 17:16:25 as along with 3 people jjray operon skembel
	HaMStR: Profile hidden markov model based search for orthologs in ESTs [My Copy] BMC Evolutionary Biology, Vol. 9, No. 1. (08 July 2009), 157. by Ingo Ebersberger, Sascha Strauss, Arndt von Haeseler posted to alignment hmm phylogenetics by djkt to the group iSEEM on 2009-07-27 18:02:32 as
	TreeTime: an extensible C++ software package for Bayesian phylogeny reconstruction with time-calibration. [My Copy] Bioinformatics (Oxford, England), Vol. 25, No. 18. (15 September 2009), pp. 2440-2441. by Lin Himmelmann, Dirk Metzler posted to estimation phylogenetics by djkt to the group iSEEM on 2009-07-18 00:34:20 as along with 2 people nuin nlapalu
	SOrt-ITEMS: Sequence orthology based approach for improved taxonomic estimation of metagenomic sequences [My Copy] Bioinformatics, Vol. 25, No. 14. (15 July 2009), pp. 1722-1730. by M. Monzoorul Haque, Tarini S. Ghosh, Dinakar Komanduri, Sharmila S. Mande posted to binning metagenomics otu phylogenetics by djkt to the group iSEEM on 2009-07-02 19:02:47 as along with 5 people dakelley sharpton sriesenfeld guhjy operon
	Rapid and Accurate Large-Scale Coestimation of Sequence Alignments and Phylogenetic Trees [My Copy] Science, Vol. 324, No. 5934. (19 June 2009), pp. 1561-1564. by Kevin Liu, Sindhu Raghavan, Serita Nelesen, C. Randal Linder, Tandy Warnow posted to alignment phylogenetics by djkt to the group iSEEM on 2009-06-19 21:41:58 as along with 26 people and 3 groups gjuggler parnell kinestetika robertrentzsch xianjun gdb jbhiatt stajich operon biomcgary kieran101 zwang michaelbarton vingron tatman303 hryk lizbiogen pkonings ppgardne dokky aprasad timflutre inquil TRHvidsten fenghezi phoenixzxl Orengo Group Journal Picks Mycology Journal picks
	Efficient computation of the phylogenetic likelihood function on multi-gene alignments and multi-core architectures [My Copy] Philosophical Transactions of the Royal Society B: Biological Sciences, Vol. 363, No. 1512. (27 December 2008), pp. 3977-3984. by Alexandros Stamatakis, Michael Ott posted to alignment phylogenetics by skembel to the group iSEEM on 2009-06-17 22:24:36 as along with 1 person operon
	FastTree: Computing Large Minimum Evolution Trees with Profiles instead of a Distance Matrix [My Copy] Mol Biol Evol, Vol. 26, No. 7. (1 July 2009), pp. 1641-1650. by Morgan N. Price, Paramvir S. Dehal, Adam P. Arkin posted to phylogenetics by djkt to the group iSEEM on 2009-06-09 19:06:37 as along with 8 people and 1 group druvus houniao007 pyilmaz rneches ppgardne jwm skembel nuin Journal picks
	The Red Queen and the Court Jester: Species Diversity and the Role of Biotic and Abiotic Factors Through Time [My Copy] Science, Vol. 323, No. 5915. (6 February 2009), pp. 728-732. by Michael J. Benton posted to diversity phylogenetics by jlgreen to the group iSEEM on 2009-05-14 18:58:16 as along with 4 people kinestetika ryevans anphony kshundyak
	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 computing phylogenetics by djkt to the group iSEEM on 2009-05-14 18:22:17 as along with 9 people mlangill druvus nuin AlexBateman bmajoros jmeppley svenrahmann rdiaz Neeperando
	Simultaneous Bayesian gene tree reconstruction and reconciliation analysis [My Copy] Proceedings of the National Academy of Sciences, Vol. 106, No. 14. (7 April 2009), pp. 5714-5719. by Ãrjan Ãkerborg, Bengt Sennblad, Lars Arvestad, Jens Lagergren posted to bayesian duplication phylogenetics by djkt to the group iSEEM on 2009-05-11 17:45:45 as along with 2 people pinney mhamada
	Phylogenetic Signals in DNA Composition: Limitations and Prospects [My Copy] Mol Biol Evol, Vol. 26, No. 5. (1 May 2009), pp. 1163-1169. by Jan Mrazek posted to phylogenetics by djkt to the group iSEEM on 2009-04-14 16:25:47 as along with 5 people dakelley jmeppley skembel druvus nuin
	Inferring phylogenies with incomplete data sets: a 5-gene, 567-taxon analysis of angiosperms [My Copy] BMC Evolutionary Biology, Vol. 9 (17 March 2009), 61. by Gordon, Douglas E. Soltis posted to phylogenetics by djkt to the group iSEEM on 2009-03-23 19:25:51 as
	Phylogenetic analysis of community assembly and structure over space and time [My Copy] Trends in Ecology & Evolution, Vol. 23, No. 11. (November 2008), pp. 619-630. by B. Emerson, R. Gillespie posted to phylogenetics by jlgreen to the group iSEEM on 2009-03-02 05:30:32 as along with 5 people and 2 groups anphony inquil skembel roosevelg cmm Savage Lab, UCLA Rosenblum-Harmon Lab Papers
	A Bayesian approach for evaluating the impact of historical events on rates of diversification [My Copy] Proceedings of the National Academy of Sciences (26 February 2009) by Brian R. Moore, Michael J. Donoghue posted to phylogenetics by jlgreen to the group iSEEM on 2009-03-01 23:02:10 as along with 1 person skembel
	Mega-phylogeny approach for comparative biology: an alternative to supertree and supermatrix approaches [My Copy] BMC Evolutionary Biology, Vol. 9, No. 1. (2009) by Stephen Smith, Jeremy Beaulieu, Michael Donoghue posted to phylogenetics by djkt to the group iSEEM on 2009-02-24 23:59:01 as along with 5 people and 1 group rs Schmidtc stajich skembel druvus Mycology
	Addressing the Shortcomings of Three Recent Bayesian Methods for Detecting Interspecific Recombination in DNA Sequence Alignments [My Copy] Statistical Applications in Genetics and Molecular Biology, Vol. 7, No. 1., article 34. by Dirk Husmeier, Alexander V. Mantzaris posted to bayesian phylogenetics recombination by djkt to the group iSEEM on 2009-02-18 02:51:53 as
	RAMI, a tool for identification and characterization of phylogenetic clusters in microbial communities [My Copy] Bioinformatics (17 February 2009), btp051. by Thomas Pommier, Bjorn Canback, Per Lundberg, Ake Hagstrom, Anders Tunlid posted to clustering metagenomics microbiome phylogenetics by djkt to the group iSEEM on 2009-02-17 18:03:50 as along with 4 people and 1 group elbrodie hpaces skembel sriesenfeld phylocom
	A hierarchical model for incomplete alignments in phylogenetic inference [My Copy] Bioinformatics, Vol. 25, No. 5. (1 March 2009), pp. 592-598. by Fuxia Cheng, Stefanie Hartmann, Mayetri Gupta, Joseph G. Ibrahim, Todd J. Vision posted to alignment metagenomics phylogenetics proteins by djkt to the group iSEEM on 2009-01-20 05:15:50 as along with 7 people nuin druvus skembel mhamada jmeppley sriesenfeld jameswasmuth
	Prokaryote phylogeny without sequence alignment: from avoidance signature to composition distance. [My Copy] Journal of bioinformatics and computational biology, Vol. 2, No. 1. (March 2004), pp. 1-19. by B. Hao, J. Qi posted to phylogenetics by skembel to the group iSEEM on 2009-01-20 00:02:07 as along with 1 person druvus
	Detecting coevolution without phylogenetic trees? Tree-ignorant metrics of coevolution perform as well as tree-aware metrics [My Copy] BMC Evolutionary Biology, Vol. 8, No. 1. (03 December 2008), 327. by J. Gregory Caporaso, Sandra Smit, Brett Easton, Lawrence Hunter, Gavin Huttley, Rob Knight posted to evolution phylogenetics proteins by djkt to the group iSEEM on 2009-01-13 23:21:53 as along with 4 people dfdong mgomes qluo sjcockell
	A likelihood look at the supermatrix–supertree controversy [My Copy] Gene, Vol. 441, No. 1-2. (15 July 2009), pp. 119-125. by Fengrong Ren, Hiroshi Tanaka, Ziheng Yang posted to phylogenetics supermatrix supertrees by skembel to the group iSEEM on 2009-01-07 20:19:46 as along with 2 people calderonv inquil
	Parallel adaptations to high temperatures in the Archaean eon. [My Copy] Nature, Vol. 456, No. 7224. (18 December 2008), pp. 942-945. by B. Boussau, S. Blanquart, A. Necsulea, N. Lartillot, M. Gouy posted to evolution phylogenetics by djkt to the group iSEEM on 2008-12-17 22:38:36 as along with 3 people chica idoerg cmzmasek
	Microbial diversity - insights from population genetics [My Copy] Environmental Microbiology, Vol. 0, No. 0. (0000), pp. ???-???. by Ted H. Mes posted to metagenomic phylogenetics population by jonathaneisen to the group iSEEM on 2008-12-16 18:47:35 as along with 7 people and 2 groups skembel adgrativol jmeppley kinestetika Katje Thaverkamp Olaf_Ilzins Microbial-Ecology microbiology_nijmegen
	The supermatrix approach to systematics [My Copy] Trends in Ecology & Evolution, Vol. 22, No. 1. (January 2007), pp. 34-41. by A. Dequeiroz, J. Gatesy posted to phylogenetics supermatrix by skembel to the group iSEEM on 2008-12-16 05:36:43 as along with 4 people and 2 groups calderonv inquil druvus dchughes G4ID Genetics-of-Gambling
	Statistical Assignment of DNA Sequences Using Bayesian Phylogenetics [My Copy] Syst Biol, Vol. 57, No. 5. (1 October 2008), pp. 750-757. by Kasper Munch, Wouter Boomsma, John P. Huelsenbeck, Eske Willerslev, Rasmus Nielsen posted to metagenomics phylogenetics by djkt to the group iSEEM on 2008-12-16 05:25:16 as along with 3 people polivares druvus sim82
	Assessment of phylogenomic and orthology approaches for phylogenetic inference [My Copy] Bioinformatics, Vol. 23, No. 7. (1 April 2007), pp. 815-824. by B. E. Dutilh, V. van Noort, R. T. J. M. van der Heijden, T. Boekhout, B. Snel, M. A. Huynen posted to phylogenetics by skembel to the group iSEEM on 2008-12-16 04:48:46 as along with 3 people calderonv maximilianh svdate
	Using ESTs for phylogenomics: can one accurately infer a phylogenetic tree from a gappy alignment? [My Copy] BMC Evolutionary Biology, Vol. 8 (26 March 2008), 95. by Stefanie Hartmann, Todd J. Vision posted to missingdata phylogenetics phylogenomics by skembel to the group iSEEM on 2008-12-16 04:48:02 as along with 7 people and 1 group sriesenfeld treangen natstreet druvus stajich Patola aprasad Mycology
	Missing data and the design of phylogenetic analyses [My Copy] Journal of Biomedical Informatics In Phylogenetic Inferencing: Beyond Biology, Vol. 39, No. 1. (February 2006), pp. 34-42. by John J. Wiens posted to phylogenetics by skembel to the group iSEEM on 2008-12-16 04:47:40 as along with 2 people calderonv aprasad
	Signature Genes as a Phylogenomic Tool. [My Copy] Molecular biology and evolution (19 May 2008) by Bas E E. Dutilh, Berend Snel, Thijs J G J. Ettema, Martijn A A. Huynen posted to phylogenetics phylogenomics phylotyping by skembel to the group iSEEM on 2008-11-30 22:56:05 as along with 2 people and 2 groups sriesenfeld mjetten anammox microbiology_nijmegen
	Intraspecific gene genealogies: trees grafting into networks [My Copy] Trends in Ecology & Evolution, Vol. 16, No. 1. (1 January 2001), pp. 37-45. by D. Posada posted to phylogenetics by jlgreen to the group iSEEM on 2008-11-24 21:35:52 as along with 1 person and 1 group anphony Green Lab
	A Comparison of Phylogenetic Network Methods Using Computer Simulation [My Copy] PLoS ONE, Vol. 3, No. 4. (April 2008), e1913. by Steven M. Woolley, David Posada, Keith A. Crandall posted to phylogenetics by jlgreen to the group iSEEM on 2008-11-24 21:30:09 as along with 2 people and 1 group fridab skembel Green Lab
	Exploring Microbial Diversity and Taxonomy Using SSU rRNA Hypervariable Tag Sequencing [My Copy] PLoS Genet, Vol. 4, No. 11. (21 November 2008), e1000255. by Susan M. Huse, Les Dethlefsen, Julie A. Huber, David M. Welch, David A. Relman, Mitchell L. Sogin posted to 16s metagenomics otu phylogenetics sequencing by djkt to the group iSEEM on 2008-11-22 01:24:16 as along with 4 people and 1 group Huub_odc azazello sconlan skembel microbiology_nijmegen
	Predicting Functional Gene Links from Phylogenetic-Statistical Analyses of Whole Genomes [My Copy] PLoS Comput Biol, Vol. 1, No. 1. (24 June 2005), e3. by Daniel Barker, Mark Pagel posted to comparativemethods methods phylogenetics by skembel to the group iSEEM on 2008-11-14 22:35:57 as along with 10 people jperkins biomcgary Robinder rw294 balajis maryee arunyan bartleby pradiptaray rvosa
	Coined quantum walks lift the cospectrality of graphs and trees [My Copy] Pattern Recognition (06 November 2008) by D. Emms, S. Severini, R. Wilson, E. Hancock posted to phylogenetics by djkt to the group iSEEM on 2008-11-14 22:03:45 as
	Pattern Classification of Phylogeny Signals [My Copy] Statistical Applications in Genetics and Molecular Biology, Vol. 7, No. 1., article 30. by Xiaofei, Hong, Chris posted to clustering phylogenetics proteins by djkt to the group iSEEM on 2008-11-12 00:15:26 as
	Probabilistic Phylogenetic Inference with Insertions and Deletions [My Copy] PLoS Comput Biol, Vol. 4, No. 9. (2008), e1000172. by Elena Rivas, Sean R. Eddy posted to evolution indel phylogenetics by djkt to the group iSEEM on 2008-11-06 18:14:53 as along with 11 people BioNica mhamada treangen pradiptaray zwang nuin timflutre druvus aprasad gjuggler emptyhb
	Phylogenetic distances are encoded in networks of interacting pathways [My Copy] Bioinformatics (26 September 2008), btn503. by Aurelien Mazurie, Danail Bonchev, Benno Schwikowski, Gregory A. Buck posted to evolution phylogenetics sysbio by djkt to the group iSEEM on 2008-11-05 16:07:48 as along with 4 people behindtherabbit markchen nuin renatomilani
	Factors affecting the concordance between orthologous gene trees and species tree in bacteria [My Copy] BMC Evolutionary Biology, Vol. 8 (30 October 2008), 300. by Santiago Castillo-Ramirez, Victor Gonzalez posted to phylogenetics proteins by djkt to the group iSEEM on 2008-11-03 19:43:57 as along with 1 person nklee
	Fusion and Fission of Genes Define a Metric between Fungal Genomes [My Copy] PLoS Comput Biol, Vol. 4, No. 10. (24 October 2008), e1000200. by Pascal Durrens, Macha Nikolski, David Sherman posted to duplication phylogenetics proteins yeast by djkt to the group iSEEM on 2008-10-24 19:25:52 as along with 5 people and 1 group jameswasmuth skembel cthachuk taguchi stajich Mycology
	Database-driven multi locus sequence typing (MLST) of bacterial pathogens. [My Copy] Bioinformatics (Oxford, England), Vol. 17, No. 11. (November 2001), pp. 1077-1083. by M. S. Chan, M. C. Maiden, B. G. Spratt posted to database mlst otu phylogenetics by djkt to the group iSEEM on 2008-10-23 22:02:44 as
	Phylogenetic clustering and overdispersion in bacterial communities. [My Copy] Ecology, Vol. 87, No. 7 Suppl. (July 2006) by M. C. Horner-Devine, B. J. Bohannan posted to community microbes phylogenetics by djkt to the group iSEEM on 2008-10-23 00:31:17 as

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evolution	579
selection	227
mutation	199
methods	139
genomics	114
tree	102
bioinformatics	96
phylogenomics	79
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alignment	55
software	55
bayesian	51
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review	44
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master	28
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doctorate	27
drosophila	26
likelihood	24
model	23
prokaryote	23
arthropod	22
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bayes	20
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maximum-likelihood	20
fungi	18
indel	18
primate	18
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ortholog	17
proteins	17
clustering	16
gene	16
genetics	16
molecular_clock	16
rare_genomic_characters	16
comparative_genomics	15
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duplication	15
protein	15
systematics	15
bioinformatics_software	14
parsimony	14
ploscb08	14
recombination	14
comparative	13
simulation	13
hiv	12
horizontal_transfer	12
molecular_evolution	12
platyrrhini	12
polyploidy	12
retroelement	12
bat	11
ecology	11
gene_tree	11
horizontal-gene-transfer	11
mcmc	11
microbes	11
sequence	11
statistics	11
virus	11
speciation	10
annotation	9
coalescence	9
molecular_markers	9
nsfprop	9
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root_eutheria	9
supertree	9
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molecular	8
mrbayes	8
msa	8
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theria	8
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analysis	7
codon_bias	7
congruence_landscapes	7
evolutionary_genomics	7
functional	7
metazoa	7
repeats	7
rna	7
taxonomy	7

Group: iSEEM - with tag phylogenetics [75 articles] Export

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