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ORCIDKimmen Sjölander
Person information
- affiliation: University of California, Berkeley, USA
- award (2003): Presidential Early Career Award for Scientists and Engineers
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2010 – 2019
- 2013
[j20]Cyrus Afrasiabi, Bushra Samad
, David Dineen, Christopher Meacham, Kimmen Sjölander:
The PhyloFacts FAT-CAT web server: ortholog identification and function prediction using fast approximate tree classification. Nucleic Acids Res. 41(Webserver-Issue): 242-248 (2013)- 2011
- [j19]Kimmen Sjölander, Ruchira S. Datta, Yaoqing Shen, Grant M. Shoffner:
Ortholog identification in the presence of domain architecture rearrangement. Briefings Bioinform. 12(5): 413-422 (2011) - [j18]Ursula Pieper, Benjamin M. Webb, David T. Barkan, Dina Schneidman-Duhovny, Avner Schlessinger, Hannes Braberg, Zheng Yang, Elaine C. Meng, Eric F. Pettersen, Conrad C. Huang, Ruchira S. Datta, Parthasarathy Sampathkumar, Mallur S. Madhusudhan, Kimmen Sjölander, Thomas E. Ferrin, Stephen K. Burley, Andrej Sali:
ModBase, a database of annotated comparative protein structure models, and associated resources. Nucleic Acids Res. 39(Database-Issue): 465-474 (2011) - 2010
- [j17]Sriram Sankararaman, Fei Sha, Jack F. Kirsch, Michael I. Jordan, Kimmen Sjölander:
Active site prediction using evolutionary and structural information. Bioinform. 26(5): 617-624 (2010) - [j16]Raffi Hagopian, John R. Davidson, Ruchira S. Datta, Bushra Samad, Glen R. Jarvis, Kimmen Sjölander:
SATCHMO-JS: a webserver for simultaneous protein multiple sequence alignment and phylogenetic tree construction. Nucleic Acids Res. 38(Web-Server-Issue): 29-34 (2010) - [j15]Kimmen Sjölander:
Getting Started in Structural Phylogenomics. PLoS Comput. Biol. 6(1) (2010)
2000 – 2009
- 2009
- [j14]Pascale Gaudet, Lydie Lane, Petra Fey, Alan J. Bridge, Sylvain Poux, Andrea H. Auchincloss, Kristian B. Axelsen, Silvia Braconi-Quintaje, Emmanuel Boutet, P. Brown, Elisabeth Coudert, Ruchira S. Datta, W. C. de Lima, Tulio de Oliveira, Severine Duvaud, N. Farriol-Mathis, Serenella Ferro-Rojas, Marc Feuermann, Alain Gateau, Ursula Hinz, Chantal Hulo, Janet James, Silvia Jimenez, Florence Jungo, Guillaume Keller, Phillippe Lemercier, Damien Lieberherr, Madelaine Moinat, Anastasia N. Nikolskaya, Ivo Pedruzzi, Catherine Rivoire, Bernd Roechert, Michel Schneider, E. Stanley, Michael Tognolli, Kimmen Sjölander, Lydie Bougueleret, Rex L. Chisholm, Amos Bairoch:
Collaborative annotation of genes and proteins between UniProtKB/Swiss-Prot and dictyBase. Database J. Biol. Databases Curation 2009 (2009) - [j13]Ron Alterovitz, Aaron Arvey, Sriram Sankararaman, Carolina Dallett, Yoav Freund, Kimmen Sjölander:
ResBoost: characterizing and predicting catalytic residues in enzymes. BMC Bioinform. 10 (2009) - [j12]Ruchira S. Datta, Christopher Meacham, Bushra Samad, Christoph Neyer, Kimmen Sjölander:
Berkeley PHOG: PhyloFacts orthology group prediction web server. Nucleic Acids Res. 37(Web-Server-Issue): 84-89 (2009) - [j11]Sriram Sankararaman, Bryan Kolaczkowski, Kimmen Sjölander:
INTREPID: a web server for prediction of functionally important residues by evolutionary analysis. Nucleic Acids Res. 37(Web-Server-Issue): 390-395 (2009) - 2008
- [j10]Sriram Sankararaman, Kimmen Sjölander:
INTREPID - INformation-theoretic TREe traversal for Protein functional site IDentification. Bioinform. 24(21): 2445-2452 (2008) - [j9]Samart Wanchana, Supat Thongjuea, Victor Jun M. Ulat, Mylah Anacleto, Ramil Mauleon, Matthieu G. Conte, Mathieu Rouard, Manuel Ruiz, Nandini Krishnamurthy, Kimmen Sjölander, Theo J. L. van Hintum, Richard M. Bruskiewich:
The Generation Challenge Programme comparative plant stress-responsive gene catalogue. Nucleic Acids Res. 36(Database-Issue): 943-946 (2008) - 2007
- [j8]Jake Gunn Glanville, Dan Kirshner, Nandini Krishnamurthy, Kimmen Sjölander:
Berkeley Phylogenomics Group web servers: resources for structural phylogenomic analysis. Nucleic Acids Res. 35(Web-Server-Issue): 27-32 (2007) - [j7]Duncan P. Brown, Nandini Krishnamurthy, Kimmen Sjölander:
Automated Protein Subfamily Identification and Classification. PLoS Comput. Biol. 3(8) (2007) - 2006
- [j6]Duncan P. Brown, Kimmen Sjölander:
Functional Classification Using Phylogenomic Inference. PLoS Comput. Biol. 2(6) (2006) - 2005
- [c5]Duncan P. Brown, Nandini Krishnamurthy, Joseph M. Dale, Wayne Christopher, Kimmen Sjölander:
Subfamily HMMS in Functional Genomics. Pacific Symposium on Biocomputing 2005 - 2004
- [j5]Kimmen Sjölander:
Phylogenomic inference of protein molecular function: advances and challenges. Bioinform. 20(2): 170-179 (2004) - [j4]Robert C. Edgar, Kimmen Sjölander:
A comparison of scoring functions for protein sequence profile alignment. Bioinform. 20(8): 1301-1308 (2004) - [j3]Robert C. Edgar, Kimmen Sjölander:
COACH: profile-profile alignment of protein families using hidden Markov models. Bioinform. 20(8): 1309-1318 (2004) - 2003
- [j2]Robert C. Edgar, Kimmen Sjölander:
SATCHMO: Sequence Alignment and Tree Construction Using Hidden Markov Models. Bioinform. 19(11): 1404-1411 (2003) - [c4]Robert C. Edgar, Kimmen Sjölander:
Simultaneous Sequence Alignment and Tree Construction Using Hidden Markov Models. Pacific Symposium on Biocomputing 2003: 180-191
1990 – 1999
- 1998
- [c3]Kimmen Sjölander:
Phylogenetic Inference in Protein Superfamilies: Analysis of SH2 Domains. ISMB 1998: 165-174 - 1996
- [j1]Kimmen Sjölander, Kevin Karplus, Michael Brown, Richard Hughey, Anders Krogh, I. Saira Mian, David Haussler:
Dirichlet mixtures: a method for improved detection of weak but significant protein sequence homology. Comput. Appl. Biosci. 12(4): 327-345 (1996) - 1994
- [c2]Yasubumi Sakakibara, Michael Brown, Richard Hughey, I. Saira Mian, Kimmen Sjölander, Rebecca C. Underwood, David Haussler:
Recent Methods for RNA Modeling Using Stochastic Context-Free Grammars. CPM 1994: 289-306 - 1993
- [c1]Michael Brown, Richard Hughey, Anders Krogh, I. Saira Mian, Kimmen Sjölander, David Haussler:
Using Dirichlet Mixture Priors to Derive Hidden Markov Models for Protein Families. ISMB 1993: 47-55
Coauthor Index
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