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Distribution and Properties of the Genes Encoding the Biosynthesis of the Bacterial Cofactor, Pyrroloquinoline Quinone

Biochemistry (Easton), 2012-03, Vol.51 (11), p.2265-2275

2012

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From endonucleases to transcription factors: evolution of the AP2 DNA binding domain in plants

The Plant cell, 2004-09, Vol.16 (9), p.2265-2277

2004

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Phylogenomic inference of protein molecular function: advances and challenges

Bioinformatics, 2004-01, Vol.20 (2), p.170-179

Sjolander, K

2004

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

Bioinformatics, 2008-11, Vol.24 (21), p.2445-2452

2008

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Automated protein subfamily identification and classification

PLoS computational biology, 2007-08, Vol.3 (8), p.e160-e160

2007

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Active site prediction using evolutionary and structural information

Bioinformatics, 2010-03, Vol.26 (5), p.617-624

2010

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Functional classification using phylogenomic inference

PLoS computational biology, 2006-06, Vol.2 (6), p.e77-e77

2006

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Getting started in structural phylogenomics

PLoS computational biology, 2010-01, Vol.6 (1), p.e1000621-e1000621

2010

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Berkeley PHOG: PhyloFacts orthology group prediction web server

Nucleic acids research, 2009-07, Vol.37 (Web Server issue), p.W84-W89

2009

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The Arabidopsis thaliana Chloroplast Proteome Reveals Pathway Abundance and Novel Protein Functions

Current biology, 2004-03, Vol.14 (5), p.354-362

2004

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A comparison of scoring functions for protein sequence profile alignment

Bioinformatics, 2004-05, Vol.20 (8), p.1301-1308

2004

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Gearing up to handle the mosaic nature of life in the quest for orthologs

Bioinformatics, 2018-01, Vol.34 (2), p.323-329

2018

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

Nucleic acids research, 2009-07, Vol.37 (Web Server issue), p.W390-W395

2009

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Functional analysis of Avr9/Cf-9 rapidly elicited genes identifies a protein kinase, ACIK1, that is essential for full Cf-9-dependent disease resistance in tomato

The Plant cell, 2005-01, Vol.17 (1), p.295-310

2005

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The COMBREX project: design, methodology, and initial results

PLoS biology, 2013-08, Vol.11 (8), p.e1001638-e1001638

2013

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SATCHMO: sequence alignment and tree construction using hidden Markov models

Bioinformatics, 2003-07, Vol.19 (11), p.1404-1411

2003

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COACH: profile–profile alignment of protein families using hidden Markov models

Bioinformatics, 2004-05, Vol.20 (8), p.1309-1318

2004

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ResBoost: characterizing and predicting catalytic residues in enzymes

BMC bioinformatics, 2009-06, Vol.10 (1), p.197-197, Article 197

2009

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Predicted hexameric structure of the Agrobacterium VirB4 C terminus suggests VirB4 acts as a docking site during type IV secretion

Proceedings of the National Academy of Sciences - PNAS, 2005-02, Vol.102 (5), p.1685-1690

2005

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Phylogenomic Analysis of the Receptor-like Proteins of Rice and Arabidopsis

Plant physiology (Bethesda), 2005-06, Vol.138 (2), p.611-623

2005

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Standardized benchmarking in the quest for orthologs

Nature methods, 2016-05, Vol.13 (5), p.425-430

2016

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Arabidopsis downy mildew resistance gene RPP27 encodes a receptor-like protein similar to CLAVATA2 and tomato Cf-9

Plant physiology (Bethesda), 2004-06, Vol.135 (2), p.1100-1112

2004

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Stochastic context-free grammers for tRNA modeling

Nucleic acids research, 1994-11, Vol.22 (23), p.5112-5120

1994

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Getting Started in Structural Phylogenomics: e1000621

PLoS computational biology, 2010-01, Vol.6 (1)

Sjölander, Kimmen

2010

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Distribution and Properties of the Genes Encoding the Biosynthesis of the Bacterial Cofactor, Pyrroloquinoline Quinone

From endonucleases to transcription factors: evolution of the AP2 DNA binding domain in plants

Phylogenomic inference of protein molecular function: advances and challenges

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

Automated protein subfamily identification and classification

Active site prediction using evolutionary and structural information

Functional classification using phylogenomic inference

Getting started in structural phylogenomics

Berkeley PHOG: PhyloFacts orthology group prediction web server

The Arabidopsis thaliana Chloroplast Proteome Reveals Pathway Abundance and Novel Protein Functions

A comparison of scoring functions for protein sequence profile alignment

Gearing up to handle the mosaic nature of life in the quest for orthologs

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

Functional analysis of Avr9/Cf-9 rapidly elicited genes identifies a protein kinase, ACIK1, that is essential for full Cf-9-dependent disease resistance in tomato

The COMBREX project: design, methodology, and initial results

SATCHMO: sequence alignment and tree construction using hidden Markov models

COACH: profile–profile alignment of protein families using hidden Markov models

ResBoost: characterizing and predicting catalytic residues in enzymes

Predicted hexameric structure of the Agrobacterium VirB4 C terminus suggests VirB4 acts as a docking site during type IV secretion

Phylogenomic Analysis of the Receptor-like Proteins of Rice and Arabidopsis

The interface of protein structure, protein biophysics, and molecular evolution

Standardized benchmarking in the quest for orthologs

Arabidopsis downy mildew resistance gene RPP27 encodes a receptor-like protein similar to CLAVATA2 and tomato Cf-9

Stochastic context-free grammers for tRNA modeling

Getting Started in Structural Phylogenomics: e1000621

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