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phyloXML: XML for evolutionary biology and comparative genomics
Mira V Han, Christian M Zmasek
BMC Bioinformatics. 2009; 10: 356. Published online 2009 October 27. doi: 10.1186/1471-2105-10-356
PMCID:
PMC2774328
Abstract Full Text PDF–338K Supplementary Material

Is Cited by the Following 31 Articles in this Archive:

Very Small Embryonic-Like Stem Cells Purified from Umbilical Cord Blood Lack Stem Cell Characteristics
Ralitza Danova-Alt, Andreas Heider, Dietmar Egger, Michael Cross, Rüdiger Alt
PLoS One. 2012; 7(4): e34899. Published online 2012 April 3. doi: 10.1371/journal.pone.0034899
PMCID:
PMC3318011
Abstract Full Text PDF–1.5M Supplementary Material
CRDB: Database of Chemosensory Receptor Gene Families in Vertebrate
Dong Dong, Ke Jin, Xiaoli Wu, Yang Zhong
PLoS One. 2012; 7(2): e31540. Published online 2012 February 29. doi: 10.1371/journal.pone.0031540
PMCID:
PMC3290609
Abstract Full Text PDF–1.0M
Barcoding and Border Biosecurity: Identifying Cyprinid Fishes in the Aquarium Trade
Rupert A. Collins, Karen F. Armstrong, Rudolf Meier, Youguang Yi, Samuel D. J. Brown, Robert H. Cruickshank, Suzanne Keeling, Colin Johnston
PLoS One. 2012; 7(1): e28381. Published online 2012 January 20. doi: 10.1371/journal.pone.0028381
PMCID:
PMC3262790
Abstract Full Text PDF–931K Supplementary Material
IMG: the integrated microbial genomes database and comparative analysis system
Victor M. Markowitz, I-Min A. Chen, Krishna Palaniappan, Ken Chu, Ernest Szeto, Yuri Grechkin, Anna Ratner, Biju Jacob, Jinghua Huang, Peter Williams, Marcel Huntemann, Iain Anderson, Konstantinos Mavromatis, Natalia N. Ivanova, Nikos C. Kyrpides
Nucleic Acids Res. 2012 January; 40(D1): D115–D122. Published online 2011 December 16. doi: 10.1093/nar/gkr1044
PMCID:
PMC3245086
Abstract Full Text PDF–13M
Niche adaptation by expansion and reprogramming of general transcription factors
Serdar Turkarslan, David J Reiss, Goodwin Gibbins, Wan Lin Su, Min Pan, J Christopher Bare, Christopher L Plaisier, Nitin S Baliga
Mol Syst Biol. 2011; 7: 554. Published online 2011 November 22. doi: 10.1038/msb.2011.87
PMCID:
PMC3261711
Abstract Full Text PDF–1.9M Supplementary Material
LegumeIP: an integrative database for comparative genomics and transcriptomics of model legumes
Jun Li, Xinbin Dai, Tingsong Liu, Patrick Xuechun Zhao
Nucleic Acids Res. 2012 January; 40(D1): D1221–D1229. Published online 2011 November 21. doi: 10.1093/nar/gkr939
PMCID:
PMC3245131
Abstract Full Text PDF–10M
DBETH: A Database of Bacterial Exotoxins for Human
Abhijit Chakraborty, Sudeshna Ghosh, Garisha Chowdhary, Ujjwal Maulik, Saikat Chakrabarti
Nucleic Acids Res. 2012 January; 40(D1): D615–D620. Published online 2011 November 17. doi: 10.1093/nar/gkr942
PMCID:
PMC3244994
Abstract Full Text PDF–3.0M
Cellulosomics, a Gene-Centric Approach to Investigating the Intraspecific Diversity and Adaptation of Ruminococcus flavefaciens within the Rumen
Jennifer M. Brulc, Carl J. Yeoman, Melissa K. Wilson, Margret E. Berg Miller, Patricio Jeraldo, Sadanari Jindou, Nigel Goldenfeld, Harry J. Flint, Raphael Lamed, Ilya Borovok, Maša Vodovnik, Karen E. Nelson, Edward A. Bayer, Bryan A. White
PLoS One. 2011; 6(10): e25329. Published online 2011 October 17. doi: 10.1371/journal.pone.0025329
PMCID:
PMC3197198
Abstract Full Text PDF–745K Supplementary Material
ViPR: an open bioinformatics database and analysis resource for virology research
Brett E. Pickett, Eva L. Sadat, Yun Zhang, Jyothi M. Noronha, R. Burke Squires, Victoria Hunt, Mengya Liu, Sanjeev Kumar, Sam Zaremba, Zhiping Gu, Liwei Zhou, Christopher N. Larson, Jonathan Dietrich, Edward B. Klem, Richard H. Scheuermann
Nucleic Acids Res. 2012 January; 40(D1): D593–D598. Published online 2011 October 17. doi: 10.1093/nar/gkr859
PMCID:
PMC3245011
Abstract Full Text PDF–2.6M
Characterization of Partial and Near Full-Length Genomes of HIV-1 Strains Sampled from Recently Infected Individuals in São Paulo, Brazil
Sabri Saeed Sanabani, Évelyn Regina de Souza Pastena, Antonio Charlys da Costa, Vanessa Pouza Martinez, Walter Kleine-Neto, Ana Carolina Soares de Oliveira, Mariana Melillo Sauer, Katia Cristina Bassichetto, Solange Maria Santos Oliveira, Helena Tomoko Iwashita Tomiyama, Ester Cerdeira Sabino, Esper Georges Kallas
PLoS One. 2011; 6(10): e25869. Published online 2011 October 14. doi: 10.1371/journal.pone.0025869
PMCID:
PMC3193532
Abstract Full Text PDF–1013K
Novel Metabolic Attributes of the Genus Cyanothece, Comprising a Group of Unicellular Nitrogen-Fixing Cyanobacteria
Anindita Bandyopadhyay, Thanura Elvitigala, Eric Welsh, Jana Stöckel, Michelle Liberton, Hongtao Min, Louis A. Sherman, Himadri B. Pakrasi
mBio. 2011 Sep-Oct; 2(5): e00214-11. Published online 2011 October 4. doi: 10.1128/mBio.00214-11
PMCID:
PMC3187577
Abstract Full Text PDF–1.0M Supplementary Material
Mycobacterium tuberculosis Rv0899 defines a family of membrane proteins widespread in nitrogen-fixing bacteria
Francesca M. Marassi
Proteins. Author manuscript; available in PMC 2012 October 1.
Published in final edited form as: Proteins. 2011 October; 79(10): 2946–2955. Published online 2011 August 26. doi: 10.1002/prot.23151
PMCID:
PMC3172613
Free in PMC on 2012/10/01
TreeRipper web application: towards a fully automated optical tree recognition software
Joseph Hughes
BMC Bioinformatics. 2011; 12: 178. Published online 2011 May 20. doi: 10.1186/1471-2105-12-178
PMCID:
PMC3111373
Abstract Full Text PDF–640K Supplementary Material
Rebooting the human mitochondrial phylogeny: an automated and scalable methodology with expert knowledge
Roberto Blanco, Elvira Mayordomo, Julio Montoya, Eduardo Ruiz-Pesini
BMC Bioinformatics. 2011; 12: 174. Published online 2011 May 19. doi: 10.1186/1471-2105-12-174
PMCID:
PMC3123235
Abstract Full Text PDF–542K
Wolbachia Prophage DNA Adenine Methyltransferase Genes in Different Drosophila-Wolbachia Associations
Aggeliki Saridaki, Panagiotis Sapountzis, Harriet L. Harris, Philip D. Batista, Jennifer A. Biliske, Harris Pavlikaki, Stefan Oehler, Charalambos Savakis, Henk R. Braig, Kostas Bourtzis
PLoS One. 2011; 6(5): e19708. Published online 2011 May 6. doi: 10.1371/journal.pone.0019708
PMCID:
PMC3089641
Abstract Full Text PDF–544K
PhyleasProg: a user-oriented web server for wide evolutionary analyses
Joël Busset, Cédric Cabau, Camille Meslin, Géraldine Pascal
Nucleic Acids Res. 2011 July 1; 39(Web Server issue): W479–W485. Published online 2011 April 29. doi: 10.1093/nar/gkr243
PMCID:
PMC3125726
Abstract Full Text PDF–6.3M
CDAO-Store: Ontology-driven Data Integration for Phylogenetic Analysis
Brandon Chisham, Ben Wright, Trung Le, Tran Cao Son, Enrico Pontelli
BMC Bioinformatics. 2011; 12: 98. Published online 2011 April 15. doi: 10.1186/1471-2105-12-98
PMCID:
PMC3101187
Abstract Full Text PDF–1.7M
Interactive Tree Of Life v2: online annotation and display of phylogenetic trees made easy
Ivica Letunic, Peer Bork
Nucleic Acids Res. 2011 July 1; 39(Web Server issue): W475–W478. Published online 2011 April 5. doi: 10.1093/nar/gkr201
PMCID:
PMC3125724
Abstract Full Text PDF–4.7M
Performance, Accuracy, and Web Server for Evolutionary Placement of Short Sequence Reads under Maximum Likelihood
Simon A. Berger, Denis Krompass, Alexandros Stamatakis
Syst Biol. 2011 May; 60(3): 291–302. Published online 2011 March 23. doi: 10.1093/sysbio/syr010
PMCID:
PMC3078422
Abstract Full Text PDF–263K Supplementary Material
iPhy: an integrated phylogenetic workbench for supermatrix analyses
Martin O Jones, Georgios D Koutsovoulos, Mark L Blaxter
BMC Bioinformatics. 2011; 12: 30. Published online 2011 January 24. doi: 10.1186/1471-2105-12-30
PMCID:
PMC3037854
Abstract Full Text PDF–2.1M Supplementary Material
Two new subfamilies of DNA mismatch repair proteins (MutS) specifically abundant in the marine environment
Hiroyuki Ogata, Jessica Ray, Kensuke Toyoda, Ruth-Anne Sandaa, Keizo Nagasaki, Gunnar Bratbak, Jean-Michel Claverie
ISME J. 2011 July; 5(7): 1143–1151. Published online 2011 January 20. doi: 10.1038/ismej.2010.210
PMCID:
PMC3146287
Free in PMC on 2012/07/01
Strong functional patterns in the evolution of eukaryotic genomes revealed by the reconstruction of ancestral protein domain repertoires
Christian M Zmasek, Adam Godzik
Genome Biol. 2011; 12(1): R4. Published online 2011 January 17. doi: 10.1186/gb-2011-12-1-r4
PMCID:
PMC3091302
Abstract Full Text PDF–604K Supplementary Material
GreenPhylDB v2.0: comparative and functional genomics in plants
Mathieu Rouard, Valentin Guignon, Christelle Aluome, Marie-Angélique Laporte, Gaëtan Droc, Christian Walde, Christian M. Zmasek, Christophe Périn, Matthieu G. Conte
Nucleic Acids Res. 2011 January; 39(Database issue): D1095–D1102. Published online 2010 September 22. doi: 10.1093/nar/gkq811
PMCID:
PMC3013755
Abstract Full Text PDF–4.8M
Multi-Platform Next-Generation Sequencing of the Domestic Turkey (Meleagris gallopavo): Genome Assembly and Analysis
Rami A. Dalloul, Julie A. Long, Aleksey V. Zimin, Luqman Aslam, Kathryn Beal, Le Ann Blomberg, Pascal Bouffard, David W. Burt, Oswald Crasta, Richard P. M. A. Crooijmans, Kristal Cooper, Roger A. Coulombe, Supriyo De, Mary E. Delany, Jerry B. Dodgson, Jennifer J. Dong, Clive Evans, Karin M. Frederickson, Paul Flicek, Liliana Florea, Otto Folkerts, Martien A. M. Groenen, Tim T. Harkins, Javier Herrero, Steve Hoffmann, Hendrik-Jan Megens, Andrew Jiang, Pieter de Jong, Pete Kaiser, Heebal Kim, Kyu-Won Kim, Sungwon Kim, David Langenberger, Mi-Kyung Lee, Taeheon Lee, Shrinivasrao Mane, Guillaume Marcais, Manja Marz, Audrey P. McElroy, Thero Modise, Mikhail Nefedov, Cédric Notredame, Ian R. Paton, William S. Payne, Geo Pertea, Dennis Prickett, Daniela Puiu, Dan Qioa, Emanuele Raineri, Magali Ruffier, Steven L. Salzberg, Michael C. Schatz, Chantel Scheuring, Carl J. Schmidt, Steven Schroeder, Stephen M. J. Searle, Edward J. Smith, Jacqueline Smith, Tad S. Sonstegard, Peter F. Stadler, Hakim Tafer, Zhijian (Jake) Tu, Curtis P. Van Tassell, Albert J. Vilella, Kelly P. Williams, James A. Yorke, Liqing Zhang, Hong-Bin Zhang, Xiaojun Zhang, Yang Zhang, Kent M. Reed
PLoS Biol. 2010 September; 8(9): e1000475. Published online 2010 September 7. doi: 10.1371/journal.pbio.1000475
PMCID:
PMC2935454
Abstract Full Text PDF–881K Supplementary Material
BioXSD: the common data-exchange format for everyday bioinformatics web services
Matúš Kalaš, Pæl Puntervoll, Alexandre Joseph, Edita Bartaševičiūtė, Armin Töpfer, Prabakar Venkataraman, Steve Pettifer, Jan Christian Bryne, Jon Ison, Christophe Blanchet, Kristoffer Rapacki, Inge Jonassen
Bioinformatics. 2010 September 15; 26(18): i540–i546. Published online 2010 September 4. doi: 10.1093/bioinformatics/btq391
PMCID:
PMC2935419
Abstract Full Text PDF–590K
Comparative Genomics of Gardnerella vaginalis Strains Reveals Substantial Differences in Metabolic and Virulence Potential
Carl J. Yeoman, Suleyman Yildirim, Susan M. Thomas, A. Scott Durkin, Manolito Torralba, Granger Sutton, Christian J. Buhay, Yan Ding, Shannon P. Dugan-Rocha, Donna M. Muzny, Xiang Qin, Richard A. Gibbs, Steven R. Leigh, Rebecca Stumpf, Bryan A. White, Sarah K. Highlander, Karen E. Nelson, Brenda A. Wilson
PLoS One. 2010; 5(8): e12411. Published online 2010 August 26. doi: 10.1371/journal.pone.0012411
PMCID:
PMC2928729
Abstract Full Text PDF–1.1M Supplementary Material
BioRuby: bioinformatics software for the Ruby programming language
Naohisa Goto, Pjotr Prins, Mitsuteru Nakao, Raoul Bonnal, Jan Aerts, Toshiaki Katayama
Bioinformatics. 2010 October 15; 26(20): 2617–2619. Published online 2010 August 25. doi: 10.1093/bioinformatics/btq475
PMCID:
PMC2951089
Abstract Full Text PDF–312K
The DBCLS BioHackathon: standardization and interoperability for bioinformatics web services and workflows. The DBCLS BioHackathon Consortium*
Toshiaki Katayama, Kazuharu Arakawa, Mitsuteru Nakao, Keiichiro Ono, Kiyoko F Aoki-Kinoshita, Yasunori Yamamoto, Atsuko Yamaguchi, Shuichi Kawashima, Hong-Woo Chun, Jan Aerts, Bruno Aranda, Lord Hendrix Barboza, Raoul JP Bonnal, Richard Bruskiewich, Jan C Bryne, José M Fernández, Akira Funahashi, Paul MK Gordon, Naohisa Goto, Andreas Groscurth, Alex Gutteridge, Richard Holland, Yoshinobu Kano, Edward A Kawas, Arnaud Kerhornou, Eri Kibukawa, Akira R Kinjo, Michael Kuhn, Hilmar Lapp, Heikki Lehvaslaiho, Hiroyuki Nakamura, Yasukazu Nakamura, Tatsuya Nishizawa, Chikashi Nobata, Tamotsu Noguchi, Thomas M Oinn, Shinobu Okamoto, Stuart Owen, Evangelos Pafilis, Matthew Pocock, Pjotr Prins, René Ranzinger, Florian Reisinger, Lukasz Salwinski, Mark Schreiber, Martin Senger, Yasumasa Shigemoto, Daron M Standley, Hideaki Sugawara, Toshiyuki Tashiro, Oswaldo Trelles, Rutger A Vos, Mark D Wilkinson, William York, Christian M Zmasek, Kiyoshi Asai, Toshihisa Takagi
J Biomed Semantics. 2010; 1: 8. Published online 2010 August 21. doi: 10.1186/2041-1480-1-8
PMCID:
PMC2939597
Abstract Full Text PDF–487K
jsPhyloSVG: A Javascript Library for Visualizing Interactive and Vector-Based Phylogenetic Trees on the Web
Samuel A. Smits, Cleber C. Ouverney
PLoS One. 2010; 5(8): e12267. Published online 2010 August 18. doi: 10.1371/journal.pone.0012267
PMCID:
PMC2923619
Abstract Full Text PDF–1.0M Supplementary Material
HyperCAT: an extension of the SuperCAT database for global multi-scheme and multi-datatype phylogenetic analysis of the Bacillus cereus group population
Nicolas J. Tourasse, Ole Andreas Økstad, Anne-Brit Kolstø
Database (Oxford) 2010; 2010: baq017. Published online 2010 July 30. doi: 10.1093/database/baq017
PMCID:
PMC2997605
Abstract Full Text PDF–1.0M
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