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PhyloFacts: an online structural phylogenomic encyclopedia for protein functional and structural classification
Nandini Krishnamurthy, Duncan P Brown, Dan Kirshner, Kimmen Sjölander
Genome Biol. 2006; 7(9): R83. Published online 2006 September 14. doi: 10.1186/gb-2006-7-9-r83
PMCID:
PMC1794543
Abstract Full Text PDF–2.4M Supplementary Material

Is Cited by the Following 20 Articles in this Archive:

The FGGY Carbohydrate Kinase Family: Insights into the Evolution of Functional Specificities
Ying Zhang, Olga Zagnitko, Irina Rodionova, Andrei Osterman, Adam Godzik
PLoS Comput Biol. 2011 December; 7(12): e1002318. Published online 2011 December 22. doi: 10.1371/journal.pcbi.1002318
PMCID:
PMC3245297
Abstract Full Text PDF–3.0M Supplementary Material
Ortho2ExpressMatrix—a web server that interprets cross-species gene expression data by gene family information
Thomas Meinel, Michal R Schweiger, Andreas H Ludewig, Ramu Chenna, Sylvia Krobitsch, Ralf Herwig
BMC Genomics. 2011; 12: 483. Published online 2011 October 4. doi: 10.1186/1471-2164-12-483
PMCID:
PMC3202273
Abstract Full Text PDF–880K Supplementary Material
Ortholog identification in the presence of domain architecture rearrangement
Kimmen Sjölander, Ruchira S. Datta, Yaoqing Shen, Grant M. Shoffner
Brief Bioinform. 2011 September; 12(5): 413–422. Published online 2011 June 28. doi: 10.1093/bib/bbr036
PMCID:
PMC3178056
Abstract Full Text PDF–343K
In vivo phosphorylation patterns of key stressosome proteins define a second feedback loop that limits activation of Bacillus subtilis σB
Christine Eymann, Stephan Schulz, Katrin Gronau, Dörte Becher, Michael Hecker, Chester W. Price
Mol Microbiol. Author manuscript; available in PMC 2012 May 1.
Published in final edited form as: Mol Microbiol. 2011 May; 80(3): 798–810. Published online 2011 March 16. doi: 10.1111/j.1365-2958.2011.07609.x
PMCID:
PMC3206960
Abstract Full Text PDF–2.1M
BiologicalNetworks - tools enabling the integration of multi-scale data for the host-pathogen studies
Sergey Kozhenkov, Mayya Sedova, Yulia Dubinina, Amarnath Gupta, Animesh Ray, Julia Ponomarenko, Michael Baitaluk
BMC Syst Biol. 2011; 5: 7. Published online 2011 January 14. doi: 10.1186/1752-0509-5-7
PMCID:
PMC3027118
Abstract Full Text PDF–10M Supplementary Material
Objective sequence-based subfamily classifications of mouse homeodomains reflect their in vitro DNA-binding preferences
Miguel A. Santos, Andrei L. Turinsky, Serene Ong, Jennifer Tsai, Michael F. Berger, Gwenael Badis, Shaheynoor Talukder, Andrew R. Gehrke, Martha L. Bulyk, Timothy R. Hughes, Shoshana J. Wodak
Nucleic Acids Res. 2010 December; 38(22): 7927–7942. Published online 2010 August 12. doi: 10.1093/nar/gkq714
PMCID:
PMC3001082
Abstract Full Text PDF–6.8M Supplementary Material
Arabidopsis thaliana PGR7 Encodes a Conserved Chloroplast Protein That Is Necessary for Efficient Photosynthetic Electron Transport
Hou-Sung Jung, Yuki Okegawa, Patrick M. Shih, Elizabeth Kellogg, Salah E. Abdel-Ghany, Marinus Pilon, Kimmen Sjölander, Toshiharu Shikanai, Krishna K. Niyogi
PLoS One. 2010; 5(7): e11688. Published online 2010 July 21. doi: 10.1371/journal.pone.0011688
PMCID:
PMC2908147
Abstract Full Text PDF–1.5M Supplementary Material
Getting Started in Structural Phylogenomics
Kimmen Sjölander
PLoS Comput Biol. 2010 January; 6(1): e1000621. Published online 2010 January 29. doi: 10.1371/journal.pcbi.1000621
PMCID:
PMC2813252
Full Text PDF–110K
GeMMA: functional subfamily classification within superfamilies of predicted protein structural domains
David A. Lee, Robert Rentzsch, Christine Orengo
Nucleic Acids Res. 2010 January; 38(3): 720–737. Published online 2010 January. doi: 10.1093/nar/gkp1049
PMCID:
PMC2817468
Abstract Full Text PDF–931K
RNRdb, a curated database of the universal enzyme family ribonucleotide reductase, reveals a high level of misannotation in sequences deposited to Genbank
Daniel Lundin, Eduard Torrents, Anthony M Poole, Britt-Marie Sjöberg
BMC Genomics. 2009; 10: 589. Published online 2009 December 8. doi: 10.1186/1471-2164-10-589
PMCID:
PMC2795772
Abstract Full Text PDF–266K
Collaborative annotation of genes and proteins between UniProtKB/Swiss-Prot and dictyBase
P. Gaudet, L. Lane, P. Fey, A. Bridge, S. Poux, A. Auchincloss, K. Axelsen, S. Braconi Quintaje, E. Boutet, P. Brown, E. Coudert, R.S. Datta, W.C. de Lima, T. de Oliveira Lima, S. Duvaud, N. Farriol-Mathis, S. Ferro Rojas, M. Feuermann, A. Gateau, U. Hinz, C. Hulo, J. James, S. Jimenez, F. Jungo, G. Keller, P. Lemercier, D. Lieberherr, M. Moinat, A. Nikolskaya, I. Pedruzzi, C. Rivoire, B. Roechert, M. Schneider, E. Stanley, M. Tognolli, K. Sjölander, L. Bougueleret, R.L. Chisholm, A. Bairoch
Database (Oxford) 2009; 2009: bap016. Published online 2009 October 15. doi: 10.1093/database/bap016
PMCID:
PMC2790310
Abstract Full Text PDF–703K
PhyloPattern: regular expressions to identify complex patterns in phylogenetic trees
Philippe Gouret, Julie D Thompson, Pierre Pontarotti
BMC Bioinformatics. 2009; 10: 298. Published online 2009 September 19. doi: 10.1186/1471-2105-10-298
PMCID:
PMC2759962
Abstract Full Text PDF–957K Supplementary Material
A Comparative Genomics, Network-Based Approach to Understanding Virulence in Vibrio cholerae
Jianying Gu, Yufeng Wang, Timothy Lilburn
J Bacteriol. 2009 October; 191(20): 6262–6272. Published online 2009 August 7. doi: 10.1128/JB.00475-09
PMCID:
PMC2753031
Abstract Full Text PDF–2.0M Supplementary Material
Berkeley PHOG: PhyloFacts orthology group prediction web server
Ruchira S. Datta, Christopher Meacham, Bushra Samad, Christoph Neyer, Kimmen Sjölander
Nucleic Acids Res. 2009 July 1; 37(Web Server issue): W84–W89. Published online 2009 July 1. doi: 10.1093/nar/gkp373
PMCID:
PMC2703887
Abstract Full Text PDF–3.7M Supplementary Material
INTREPID: a web server for prediction of functionally important residues by evolutionary analysis
Sriram Sankararaman, Bryan Kolaczkowski, Kimmen Sjölander
Nucleic Acids Res. 2009 July 1; 37(Web Server issue): W390–W395. Published online 2009 July 1. doi: 10.1093/nar/gkp339
PMCID:
PMC2703888
Abstract Full Text PDF–6.0M
Exploring the structure and function paradigm
Oliver Redfern, Benoit Dessailly, Christine Orengo
Curr Opin Struct Biol. Author manuscript; available in PMC 2009 June 1.
Published in final edited form as: Curr Opin Struct Biol. 2008 June; 18(3): 394–402. doi: 10.1016/j.sbi.2008.05.007
PMCID:
PMC2561214
Full Text PDF–557K
TreeFam: 2008 Update
Jue Ruan, Heng Li, Zhongzhong Chen, Avril Coghlan, Lachlan James M. Coin, Yiran Guo, Jean-Karim Hériché, Yafeng Hu, Karsten Kristiansen, Ruiqiang Li, Tao Liu, Alan Moses, Junjie Qin, Søren Vang, Albert J. Vilella, Abel Ureta-Vidal, Lars Bolund, Jun Wang, Richard Durbin
Nucleic Acids Res. 2008 January; 36(Database issue): D735–D740. Published online 2008 January. doi: 10.1093/nar/gkm1005
PMCID:
PMC2238856
Abstract Full Text PDF–260K
Insight into the haem d1 biosynthesis pathway in heliobacteria through bioinformatics analysis
Jin Xiong, Carl E. Bauer, Anjly Pancholy
Microbiology. Author manuscript; available in PMC 2009 November 9.
Published in final edited form as: Microbiology. 2007 October; 153(Pt 10): 3548–3562. doi: 10.1099/mic.0.2007/007930-0
PMCID:
PMC2774728
Abstract Full Text PDF–3.5M
Automated Protein Subfamily Identification and Classification
Duncan P Brown, Nandini Krishnamurthy, Kimmen Sjölander
PLoS Comput Biol. 2007 August; 3(8): e160. Published online 2007 August 17. doi: 10.1371/journal.pcbi.0030160
PMCID:
PMC1950344
Abstract Full Text PDF–513K Supplementary Material
Berkeley Phylogenomics Group web servers: resources for structural phylogenomic analysis
Jake Gunn Glanville, Dan Kirshner, Nandini Krishnamurthy, Kimmen Sjölander
Nucleic Acids Res. 2007 July; 35(Web Server issue): W27–W32. Published online 2007 July. doi: 10.1093/nar/gkm325
PMCID:
PMC1933202
Abstract Full Text PDF–645K
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