Kimmen Sjölander

According to our database, Kimmen Sjölander authored at least 25 papers between 1993 and 2013.

Collaborative distances:

• Dijkstra number of four.
• Erdős number of three.

2013

The PhyloFacts FAT-CAT web server: ortholog identification and function prediction using fast approximate tree classification.

Cyrus Afrasiabi, Bushra Samad, David Dineen, Christopher Meacham, Kimmen Sjölander

Nucleic Acids Res., 2013

2011

ModBase, a database of annotated comparative protein structure models, and associated resources.

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

Nucleic Acids Res., 2011

Ortholog identification in the presence of domain architecture rearrangement.

Kimmen Sjölander, Ruchira S. Datta, Yaoqing Shen, Grant M. Shoffner

Briefings Bioinform., 2011

2010

Getting Started in Structural Phylogenomics.

Kimmen Sjölander

PLoS Comput. Biol., 2010

SATCHMO-JS: a webserver for simultaneous protein multiple sequence alignment and phylogenetic tree construction.

Raffi Hagopian, John R. Davidson, Ruchira S. Datta, Bushra Samad, Glen R. Jarvis, Kimmen Sjölander

Nucleic Acids Res., 2010

Active site prediction using evolutionary and structural information.

Sriram Sankararaman, Fei Sha, Jack F. Kirsch, Michael I. Jordan, Kimmen Sjölander

Bioinform., 2010

2009

INTREPID: a web server for prediction of functionally important residues by evolutionary analysis.

Sriram Sankararaman, Bryan Kolaczkowski, Kimmen Sjölander

Nucleic Acids Res., 2009

Berkeley PHOG: PhyloFacts orthology group prediction web server.

Ruchira S. Datta, Christopher Meacham, Bushra Samad, Christoph Neyer, Kimmen Sjölander

Nucleic Acids Res., 2009

ResBoost: characterizing and predicting catalytic residues in enzymes.

Ron Alterovitz, Aaron Arvey, Sriram Sankararaman, Carolina Dallett, Yoav Freund, Kimmen Sjölander

BMC Bioinform., 2009

Collaborative annotation of genes and proteins between UniProtKB/Swiss-Prot and dictyBase.

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

Database J. Biol. Databases Curation, 2009

2008

The Generation Challenge Programme comparative plant stress-responsive gene catalogue.

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

Nucleic Acids Res., 2008

INTREPID - INformation-theoretic TREe traversal for Protein functional site IDentification.

Sriram Sankararaman, Kimmen Sjölander

Bioinform., 2008

2007

Automated Protein Subfamily Identification and Classification.

Duncan P. Brown, Nandini Krishnamurthy, Kimmen Sjölander

PLoS Comput. Biol., 2007

Berkeley Phylogenomics Group web servers: resources for structural phylogenomic analysis.

Jake Gunn Glanville, Dan Kirshner, Nandini Krishnamurthy, Kimmen Sjölander

Nucleic Acids Res., 2007

2006

Functional Classification Using Phylogenomic Inference.

Duncan P. Brown, Kimmen Sjölander

PLoS Comput. Biol., 2006

2005

Subfamily HMMS in Functional Genomics.

Duncan P. Brown, Nandini Krishnamurthy, Joseph M. Dale, Wayne Christopher, Kimmen Sjölander

Proceedings of the Biocomputing 2005, 2005

2004

Phylogenomic inference of protein molecular function: advances and challenges.

Kimmen Sjölander

Bioinform., 2004

COACH: profile-profile alignment of protein families using hidden Markov models.

Robert C. Edgar, Kimmen Sjölander

Bioinform., 2004

A comparison of scoring functions for protein sequence profile alignment.

Robert C. Edgar, Kimmen Sjölander

Bioinform., 2004

2003

SATCHMO: Sequence Alignment and Tree Construction Using Hidden Markov Models.

Robert C. Edgar, Kimmen Sjölander

Bioinform., 2003

Simultaneous Sequence Alignment and Tree Construction Using Hidden Markov Models.

Robert C. Edgar, Kimmen Sjölander

Proceedings of the 8th Pacific Symposium on Biocomputing, 2003

1998

Phylogenetic Inference in Protein Superfamilies: Analysis of SH2 Domains.

Kimmen Sjölander

Proceedings of the 6th International Conference on Intelligent Systems for Molecular Biology (ISMB-98), Montréal, Québec, Canada, June 28, 1998

1996

Dirichlet mixtures: a method for improved detection of weak but significant protein sequence homology.

Kimmen Sjölander, Kevin Karplus, Michael Brown, Richard Hughey, Anders Krogh, I. Saira Mian, David Haussler

Comput. Appl. Biosci., 1996

1994

Recent Methods for RNA Modeling Using Stochastic Context-Free Grammars.

Yasubumi Sakakibara, Michael Brown, Richard Hughey, I. Saira Mian, Kimmen Sjölander, Rebecca C. Underwood, David Haussler

Proceedings of the Combinatorial Pattern Matching, 5th Annual Symposium, 1994

1993

Using Dirichlet Mixture Priors to Derive Hidden Markov Models for Protein Families.

Michael Brown, Richard Hughey, Anders Krogh, I. Saira Mian, Kimmen Sjölander, David Haussler

Proceedings of the 1st International Conference on Intelligent Systems for Molecular Biology, 1993