Kimmen Sjölander

25 papers A 2B 1Misc 2Journal 20
YearRankTypeTitle / Venue / Authors
2013 J jnl
The PhyloFacts FAT-CAT web server: ortholog identification and function prediction using fast approximate tree classification.
Nucleic Acids Res.
Cyrus Afrasiabi, Bushra Samad, David Dineen, Christopher Meacham, Kimmen Sjölander
2011 J jnl
ModBase, a database of annotated comparative protein structure models, and associated resources.
Nucleic Acids Res.
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
2011 J jnl
Ortholog identification in the presence of domain architecture rearrangement.
Briefings Bioinform.
Kimmen Sjölander, Ruchira S. Datta, Yaoqing Shen, Grant M. Shoffner
2010 J jnl
Active site prediction using evolutionary and structural information.
Bioinform.
Sriram Sankararaman, Fei Sha, Jack F. Kirsch, Michael I. Jordan, Kimmen Sjölander
2010 J jnl
Getting Started in Structural Phylogenomics.
PLoS Comput. Biol.
Kimmen Sjölander
2010 J jnl
SATCHMO-JS: a webserver for simultaneous protein multiple sequence alignment and phylogenetic tree construction.
Nucleic Acids Res.
Raffi Hagopian, John R. Davidson, Ruchira S. Datta, Bushra Samad, Glen R. Jarvis, Kimmen Sjölander
2009 J jnl
Berkeley PHOG: PhyloFacts orthology group prediction web server.
Nucleic Acids Res.
Ruchira S. Datta, Christopher Meacham, Bushra Samad, Christoph Neyer, Kimmen Sjölander
2009 J jnl
Collaborative annotation of genes and proteins between UniProtKB/Swiss-Prot and dictyBase.
Database J. Biol. Databases Curation
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
2009 J jnl
INTREPID: a web server for prediction of functionally important residues by evolutionary analysis.
Nucleic Acids Res.
Sriram Sankararaman, Bryan Kolaczkowski, Kimmen Sjölander
2009 J jnl
ResBoost: characterizing and predicting catalytic residues in enzymes.
BMC Bioinform.
Ron Alterovitz, Aaron Arvey, Sriram Sankararaman, Carolina Dallett, Yoav Freund, Kimmen Sjölander
2008 J jnl
INTREPID - INformation-theoretic TREe traversal for Protein functional site IDentification.
Bioinform.
Sriram Sankararaman, Kimmen Sjölander
2008 J jnl
The Generation Challenge Programme comparative plant stress-responsive gene catalogue.
Nucleic Acids Res.
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
2007 J jnl
Automated Protein Subfamily Identification and Classification.
PLoS Comput. Biol.
Duncan P. Brown, Nandini Krishnamurthy, Kimmen Sjölander
2007 J jnl
Berkeley Phylogenomics Group web servers: resources for structural phylogenomic analysis.
Nucleic Acids Res.
Jake Gunn Glanville, Dan Kirshner, Nandini Krishnamurthy, Kimmen Sjölander
2006 J jnl
Functional Classification Using Phylogenomic Inference.
PLoS Comput. Biol.
Duncan P. Brown, Kimmen Sjölander
2005 Misc conf
Subfamily HMMS in Functional Genomics.
Pacific Symposium on Biocomputing
Duncan P. Brown, Nandini Krishnamurthy, Joseph M. Dale, Wayne Christopher, Kimmen Sjölander
2004 J jnl
A comparison of scoring functions for protein sequence profile alignment.
Bioinform.
Robert C. Edgar, Kimmen Sjölander
2004 J jnl
COACH: profile-profile alignment of protein families using hidden Markov models.
Bioinform.
Robert C. Edgar, Kimmen Sjölander
2004 J jnl
Phylogenomic inference of protein molecular function: advances and challenges.
Bioinform.
Kimmen Sjölander
2003 J jnl
SATCHMO: Sequence Alignment and Tree Construction Using Hidden Markov Models.
Bioinform.
Robert C. Edgar, Kimmen Sjölander
2003 Misc conf
Simultaneous Sequence Alignment and Tree Construction Using Hidden Markov Models.
Pacific Symposium on Biocomputing
Robert C. Edgar, Kimmen Sjölander
1998 A conf
Phylogenetic Inference in Protein Superfamilies: Analysis of SH2 Domains.
ISMB
Kimmen Sjölander
1996 J jnl
Dirichlet mixtures: a method for improved detection of weak but significant protein sequence homology.
Comput. Appl. Biosci.
Kimmen Sjölander, Kevin Karplus, Michael Brown, Richard Hughey, Anders Krogh, I. Saira Mian, David Haussler
1994 B conf
Recent Methods for RNA Modeling Using Stochastic Context-Free Grammars.
CPM
Yasubumi Sakakibara, Michael Brown, Richard Hughey, I. Saira Mian, Kimmen Sjölander, Rebecca C. Underwood, David Haussler
1993 A conf
Using Dirichlet Mixture Priors to Derive Hidden Markov Models for Protein Families.
ISMB
Michael Brown, Richard Hughey, Anders Krogh, I. Saira Mian, Kimmen Sjölander, David Haussler