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 (ISMB, 1993)

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 (CPM, 1994)

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)

Phylogenetic Inference in Protein Superfamilies: Analysis of SH2 Domains. - Kimmen Sjölander (ISMB, 1998)

Simultaneous Sequence Alignment and Tree Construction Using Hidden Markov Models. - Robert C. Edgar; Kimmen Sjölander (Pacific Symposium on Biocomputing, 2003)

SATCHMO: Sequence Alignment and Tree Construction Using Hidden Markov Models. - Robert C. Edgar; Kimmen Sjölander (Bioinform., 2003)

A comparison of scoring functions for protein sequence profile alignment. - Robert C. Edgar; Kimmen Sjölander (Bioinform., 2004)

COACH: profile-profile alignment of protein families using hidden Markov models. - Robert C. Edgar; Kimmen Sjölander (Bioinform., 2004)

Phylogenomic inference of protein molecular function: advances and challenges. - Kimmen Sjölander (Bioinform., 2004)

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

Functional Classification Using Phylogenomic Inference. - Duncan P. Brown; Kimmen Sjölander (PLoS Comput. Biol., 2006)

Berkeley Phylogenomics Group web servers: resources for structural phylogenomic analysis. - Jake Gunn Glanville; Dan Kirshner 001; Nandini Krishnamurthy; Kimmen Sjölander (Nucleic Acids Res., 2007)

Automated Protein Subfamily Identification and Classification. - Duncan P. Brown; Nandini Krishnamurthy; Kimmen Sjölander (PLoS Comput. Biol., 2007)

INTREPID - INformation-theoretic TREe traversal for Protein functional site IDentification. - Sriram Sankararaman; Kimmen Sjölander (Bioinform., 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)

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; et al. (Database J. Biol. Databases Curation, 2009)

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

Berkeley PHOG: PhyloFacts orthology group prediction web server. - Ruchira S. Datta; Christopher Meacham; Bushra Samad; Christoph Neyer; Kimmen Sjölander (Nucleic Acids Res., 2009)

INTREPID: a web server for prediction of functionally important residues by evolutionary analysis. - Sriram Sankararaman; Bryan Kolaczkowski; Kimmen Sjölander (Nucleic Acids Res., 2009)

Active site prediction using evolutionary and structural information. - Sriram Sankararaman; Fei Sha; Jack F. Kirsch; Michael I. Jordan; Kimmen Sjölander (Bioinform., 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)

Getting Started in Structural Phylogenomics. - Kimmen Sjölander (PLoS Comput. Biol., 2010)

Ortholog identification in the presence of domain architecture rearrangement. - Kimmen Sjölander; Ruchira S. Datta; Yaoqing Shen; Grant M. Shoffner (Briefings Bioinform., 2011)

ModBase, a database of annotated comparative protein structure models, and associated resources. - Ursula Pieper 001; 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; et al. (Nucleic Acids Res., 2011)

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)