Kimmen Sjolander

Summary

Affiliation: University of California
Country: USA

Publications

  1. pmc Berkeley Phylogenomics Group web servers: resources for structural phylogenomic analysis
    Jake Gunn Glanville
    Berkeley Phylogenomics Group, University of California, Berkeley, USA
    Nucleic Acids Res 35:W27-32. 2007
  2. pmc ResBoost: characterizing and predicting catalytic residues in enzymes
    Ron Alterovitz
    Department of Computer Science, University of North Carolina at Chapel Hill, USA
    BMC Bioinformatics 10:197. 2009
  3. pmc Ortholog identification in the presence of domain architecture rearrangement
    Kimmen Sjolander
    308C Stanley Hall 1762, Department of Bioengineering, University of California, Berkeley, CA 94720, USA
    Brief Bioinform 12:413-22. 2011
  4. pmc SATCHMO-JS: a webserver for simultaneous protein multiple sequence alignment and phylogenetic tree construction
    Raffi Hagopian
    Department of Bioengineering, University of California, Berkeley, CA 94720, USA
    Nucleic Acids Res 38:W29-34. 2010
  5. pmc INTREPID: a web server for prediction of functionally important residues by evolutionary analysis
    Sriram Sankararaman
    Department of Computer Science, University of California, Berkeley, USA
    Nucleic Acids Res 37:W390-5. 2009
  6. pmc Active site prediction using evolutionary and structural information
    Sriram Sankararaman
    Computer Science Division, University of California, Berkeley, USA
    Bioinformatics 26:617-24. 2010
  7. pmc PhyloFacts: an online structural phylogenomic encyclopedia for protein functional and structural classification
    Nandini Krishnamurthy
    Department of Bioengineering, 473 Evans Hall 1762, University of California, Berkeley, CA 94720, USA
    Genome Biol 7:R83. 2006
  8. pmc FlowerPower: clustering proteins into domain architecture classes for phylogenomic inference of protein function
    Nandini Krishnamurthy
    Department of Bioengineering, 473 Evans Hall 1762, University of California, Berkeley, CA 94720 1762, USA
    BMC Evol Biol 7:S12. 2007
  9. doi request reprint Phylogenomic inference of protein molecular function
    Nandini Krishnamurthy
    University of California, Berkeley, California, USA
    Curr Protoc Bioinformatics . 2005
  10. pmc The PhyloFacts FAT-CAT web server: ortholog identification and function prediction using fast approximate tree classification
    Cyrus Afrasiabi
    QB3 Institute, University of California, Berkeley, Berkeley, CA 94720 1762, USA
    Nucleic Acids Res 41:W242-8. 2013

Research Grants

Collaborators

Detail Information

Publications21

  1. pmc Berkeley Phylogenomics Group web servers: resources for structural phylogenomic analysis
    Jake Gunn Glanville
    Berkeley Phylogenomics Group, University of California, Berkeley, USA
    Nucleic Acids Res 35:W27-32. 2007
    ..The Berkeley Phylogenomics Group resources are available at http://phylogenomics.berkeley.edu...
  2. pmc ResBoost: characterizing and predicting catalytic residues in enzymes
    Ron Alterovitz
    Department of Computer Science, University of North Carolina at Chapel Hill, USA
    BMC Bioinformatics 10:197. 2009
    ..Since experimentally determining catalytic sites is expensive, better computational methods for identifying catalytic residues are needed...
  3. pmc Ortholog identification in the presence of domain architecture rearrangement
    Kimmen Sjolander
    308C Stanley Hall 1762, Department of Bioengineering, University of California, Berkeley, CA 94720, USA
    Brief Bioinform 12:413-22. 2011
    ....
  4. pmc SATCHMO-JS: a webserver for simultaneous protein multiple sequence alignment and phylogenetic tree construction
    Raffi Hagopian
    Department of Bioengineering, University of California, Berkeley, CA 94720, USA
    Nucleic Acids Res 38:W29-34. 2010
    ..The SATCHMO-JS webserver is available at http://phylogenomics.berkeley.edu/satchmo-js. The datasets used in these experiments are available for download at http://phylogenomics.berkeley.edu/satchmo-js/supplementary/...
  5. pmc INTREPID: a web server for prediction of functionally important residues by evolutionary analysis
    Sriram Sankararaman
    Department of Computer Science, University of California, Berkeley, USA
    Nucleic Acids Res 37:W390-5. 2009
    ..The INTREPID web server is available at http://phylogenomics.berkeley.edu/intrepid...
  6. pmc Active site prediction using evolutionary and structural information
    Sriram Sankararaman
    Computer Science Division, University of California, Berkeley, USA
    Bioinformatics 26:617-24. 2010
    ....
  7. pmc PhyloFacts: an online structural phylogenomic encyclopedia for protein functional and structural classification
    Nandini Krishnamurthy
    Department of Bioengineering, 473 Evans Hall 1762, University of California, Berkeley, CA 94720, USA
    Genome Biol 7:R83. 2006
    ..Users can submit sequences for classification to families and functional subfamilies. PhyloFacts is available as a worldwide web resource from http://phylogenomics.berkeley.edu/phylofacts...
  8. pmc FlowerPower: clustering proteins into domain architecture classes for phylogenomic inference of protein function
    Nandini Krishnamurthy
    Department of Bioengineering, 473 Evans Hall 1762, University of California, Berkeley, CA 94720 1762, USA
    BMC Evol Biol 7:S12. 2007
    ..By contrast, most common homolog detection methods are optimized for retrieving local homologs, and do not address this requirement...
  9. doi request reprint Phylogenomic inference of protein molecular function
    Nandini Krishnamurthy
    University of California, Berkeley, California, USA
    Curr Protoc Bioinformatics . 2005
    ..Finally, the phylogenetic tree is overlaid with experimental data culled for the members of the family, and changes in biochemical function can be traced along the evolutionary tree...
  10. pmc The PhyloFacts FAT-CAT web server: ortholog identification and function prediction using fast approximate tree classification
    Cyrus Afrasiabi
    QB3 Institute, University of California, Berkeley, Berkeley, CA 94720 1762, USA
    Nucleic Acids Res 41:W242-8. 2013
    ..The FAT-CAT web server is available at http://phylogenomics.berkeley.edu/phylofacts/fatcat/. ..
  11. pmc Berkeley PHOG: PhyloFacts orthology group prediction web server
    Ruchira S Datta
    QB3 Institute, University of California, Berkeley, CA, USA
    Nucleic Acids Res 37:W84-9. 2009
    ..Predicted orthologs are linked to GO annotations, pathway information and biological literature. The PHOG web server is available at http://phylofacts.berkeley.edu/orthologs/...
  12. pmc INTREPID--INformation-theoretic TREe traversal for Protein functional site IDentification
    Sriram Sankararaman
    Department of Electrical Engineering and Computer Science and Department of Bioengineering, University of California, Berkeley, USA
    Bioinformatics 24:2445-52. 2008
    ..We evaluated INTREPID on two tasks: predicting catalytic residues and predicting specificity determinants...
  13. pmc Functional classification using phylogenomic inference
    Duncan Brown
    University of California Berkeley, Berkeley, California, USA
    PLoS Comput Biol 2:e77. 2006
  14. pmc Automated protein subfamily identification and classification
    Duncan P Brown
    Department of Bioengineering, University of California, Berkeley, California, United States of America
    PLoS Comput Biol 3:e160. 2007
    ..The Berkeley Phylogenomics Group PhyloFacts resource contains pre-calculated subfamily predictions and subfamily HMMs for more than 40,000 protein families and domains at http://phylogenomics.berkeley.edu/phylofacts/...
  15. ncbi request reprint Phylogenomic inference of protein molecular function: advances and challenges
    Kimmen Sjolander
    Berkeley Phylogenomics Group, Department of Bioengineering, University of California, 473 Evans Hall 1762, Berkeley, CA 94720 1762, USA
    Bioinformatics 20:170-9. 2004
    ..The explicit integration of structure prediction and analysis in this framework, which we call structural phylogenomics, provides additional insights into protein superfamily evolution...
  16. pmc Arabidopsis thaliana PGR7 encodes a conserved chloroplast protein that is necessary for efficient photosynthetic electron transport
    Hou Sung Jung
    Department of Plant and Microbial Biology, University of California, Berkeley, California, United States of America
    PLoS ONE 5:e11688. 2010
    ..Thus, we identified PGR7 as a novel, conserved nuclear gene that is necessary for efficient photosynthetic electron transport in chloroplasts of Arabidopsis...
  17. pmc Molecular characterization of proteolytic cleavage sites of the Pseudomonas syringae effector AvrRpt2
    Stephen T Chisholm
    Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA
    Proc Natl Acad Sci U S A 102:2087-92. 2005
    ..These results identify amino acids important for AvrRpt2 substrate recognition and cleavage as well as demonstrate AvrRpt2 protease activity eliminates multiple Arabidopsis proteins in a transient expression system...
  18. pmc Distribution and properties of the genes encoding the biosynthesis of the bacterial cofactor, pyrroloquinoline quinone
    Yao Qing Shen
    Department of Chemistry, University of California, Berkeley, California 94720, United States
    Biochemistry 51:2265-75. 2012
    ..These studies propose previously unidentified roles for several of the gene products, as well as identifying possible new targets for antibiotic design and application...
  19. pmc Predicted hexameric structure of the Agrobacterium VirB4 C terminus suggests VirB4 acts as a docking site during type IV secretion
    Rebecca Middleton
    Department of Plant and Microbial Biology, Koshland Hall, Evans Hall, University of California, Berkeley, CA 94720, USA
    Proc Natl Acad Sci U S A 102:1685-90. 2005
    ....
  20. pmc From endonucleases to transcription factors: evolution of the AP2 DNA binding domain in plants
    Enrico Magnani
    Department of Plant and Microbial Biology, University of California, Berkeley, California 94720, USA
    Plant Cell 16:2265-77. 2004
    ..We hypothesize that a horizontal transfer of an HNH-AP2 endonuclease from bacteria or viruses into plants may have led to the origin of the AP2/ERF family of transcription factors via transposition and homing processes...

Research Grants1

  1. High-throughput phylogenomic analysis of animal proteins
    Kimmen Sjolander; Fiscal Year: 2007
    ..sectors to submit sequences for classification against these hidden Markov models, and a graphic user interface will display the correlation of changes in protein sequence with changes in structure and function [unreadable] [unreadable]..