Kimmen Sjölander

Kimmen Sjölander, Ruchira S. Datta, Yaoqing Shen, Grant M. Shoffner: Ortholog identification in the presence of domain architecture rearrangement. Briefings in Bioinformatics 12(5): 413-422 (2011)

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 Research 39(Database-Issue): 465-474 (2011)

Sriram Sankararaman, Fei Sha, Jack F. Kirsch, Michael I. Jordan, Kimmen Sjölander: Active site prediction using evolutionary and structural information. Bioinformatics 26(5): 617-624 (2010)

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 Research 38(Web-Server-Issue): 29-34 (2010)

Kimmen Sjölander: Getting Started in Structural Phylogenomics. PLoS Computational Biology 6(1) (2010)

Ron Alterovitz, Aaron Arvey, Sriram Sankararaman, Carolina Dallett, Yoav Freund, Kimmen Sjölander: ResBoost: characterizing and predicting catalytic residues in enzymes. BMC Bioinformatics 10 (2009)

Ruchira S. Datta, Christopher Meacham, Bushra Samad, Christoph Neyer, Kimmen Sjölander: Berkeley PHOG: PhyloFacts orthology group prediction web server. Nucleic Acids Research 37(Web-Server-Issue): 84-89 (2009)

Sriram Sankararaman, Bryan Kolaczkowski, Kimmen Sjölander: INTREPID: a web server for prediction of functionally important residues by evolutionary analysis. Nucleic Acids Research 37(Web-Server-Issue): 390-395 (2009)

Sriram Sankararaman, Kimmen Sjölander: INTREPID - INformation-theoretic TREe traversal for Protein functional site IDentification. Bioinformatics 24(21): 2445-2452 (2008)

Samart Wanchana, Supat Thongjuea, Victor Jun M. Ulat, Mylah Anacleto, Ramil Mauleon, Matthieu G. Conte, Mathieu Rouard, Manuel Ruiz, Nandini Krishnamurthy, Kimmen Sjölander, Theo van Hintum, Richard M. Bruskiewich: The Generation Challenge Programme comparative plant stress-responsive gene catalogue. Nucleic Acids Research 36(Database-Issue): 943-946 (2008)

Jake Gunn Glanville, Dan Kirshner, Nandini Krishnamurthy, Kimmen Sjölander: Berkeley Phylogenomics Group web servers: resources for structural phylogenomic analysis. Nucleic Acids Research 35(Web-Server-Issue): 27-32 (2007)

Duncan P. Brown, Nandini Krishnamurthy, Kimmen Sjölander: Automated Protein Subfamily Identification and Classification. PLoS Computational Biology 3(8) (2007)

Duncan P. Brown, Kimmen Sjölander: Functional Classification Using Phylogenomic Inference. PLoS Computational Biology 2(6) (2006)

Duncan P. Brown, Nandini Krishnamurthy, Joseph M. Dale, Wayne Christopher, Kimmen Sjölander: Subfamily HMMS in Functional Genomics. Pacific Symposium on Biocomputing 2005

Kimmen Sjölander: Phylogenomic inference of protein molecular function: advances and challenges. Bioinformatics 20(2): 170-179 (2004)

Robert C. Edgar, Kimmen Sjölander: A comparison of scoring functions for protein sequence profile alignment. Bioinformatics 20(8): 1301-1308 (2004)

Robert C. Edgar, Kimmen Sjölander: COACH: profile-profile alignment of protein families using hidden Markov models. Bioinformatics 20(8): 1309-1318 (2004)

Robert C. Edgar, Kimmen Sjölander: SATCHMO: Sequence Alignment and Tree Construction Using Hidden Markov Models. Bioinformatics 19(11): 1404-1411 (2003)

Robert C. Edgar, Kimmen Sjölander: Simultaneous Sequence Alignment and Tree Construction Using Hidden Markov Models. Pacific Symposium on Biocomputing 2003: 180-191

Kimmen Sjölander: Phylogenetic Inference in Protein Superfamilies: Analysis of SH2 Domains. ISMB 1998: 165-174

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. Computer Applications in the Biosciences 12(4): 327-345 (1996)

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

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