Author details

Full Name

Kimmen Sj??lander

Affiliation

University of California berkeley

ORCID

Career Start Year

1993

Papers

H Index

Expertise

CM4AI Collaborator

Andrej Sali (CM4AI)

PMID	Paper Title	Journal Title	Published Year
27043882	Standardized benchmarking in the quest for orthologs.	Nat Methods	2016
23685612	The PhyloFacts FAT-CAT web server: ortholog identification and function prediction using fast approximate tree classification.	Nucleic Acids Res	2013
24013487	The COMBREX project: design, methodology, and initial results.	PLoS Biol	2013
22324760	Distribution and properties of the genes encoding the biosynthesis of the bacterial cofactor, pyrroloquinoline quinone.	Biochemistry	2012
22528593	The interface of protein structure, protein biophysics, and molecular evolution.	Protein Sci	2012
21097780	ModBase, a database of annotated comparative protein structure models, and associated resources.	Nucleic Acids Res	2011
21712343	Ortholog identification in the presence of domain architecture rearrangement.	Brief Bioinform	2011
20080507	Active site prediction using evolutionary and structural information.	Bioinformatics	2010
20657737	Arabidopsis thaliana PGR7 encodes a conserved chloroplast protein that is necessary for efficient photosynthetic electron transport.	PLoS One	2010
20126522	Getting started in structural phylogenomics.	PLoS Comput Biol	2010
20430824	SATCHMO-JS: a webserver for simultaneous protein multiple sequence alignment and phylogenetic tree construction.	Nucleic Acids Res	2010
19558703	ResBoost: characterizing and predicting catalytic residues in enzymes.	BMC Bioinformatics	2009
20157489	Collaborative annotation of genes and proteins between UniProtKB/Swiss-Prot and dictyBase.	Database (Oxford)	2009
19435885	Berkeley PHOG: PhyloFacts orthology group prediction web server.	Nucleic Acids Res	2009
19443452	INTREPID: a web server for prediction of functionally important residues by evolutionary analysis.	Nucleic Acids Res	2009
17933772	The Generation Challenge Programme comparative plant stress-responsive gene catalogue.	Nucleic Acids Res	2008
18776193	INTREPID--INformation-theoretic TREe traversal for Protein functional site IDentification.	Bioinformatics	2008
17488835	Berkeley Phylogenomics Group web servers: resources for structural phylogenomic analysis.	Nucleic Acids Res	2007
17708678	Automated protein subfamily identification and classification.	PLoS Comput Biol	2007
17288570	FlowerPower: clustering proteins into domain architecture classes for phylogenomic inference of protein function.	BMC Evol Biol	2007
17284584	Arabidopsis downy mildew resistance gene RPP27 encodes a receptor-like protein similar to CLAVATA2 and tomato Cf-9.	Plant Physiol	2007
16901231	Taking the first steps towards a standard for reporting on phylogenies: Minimum Information About a Phylogenetic Analysis (MIAPA).	OMICS	2006
16846248	Functional classification using phylogenomic inference.	PLoS Comput Biol	2006
16973001	PhyloFacts: an online structural phylogenomic encyclopedia for protein functional and structural classification.	Genome Biol	2006
15759638	Subfamily hmms in functional genomics.	Pac Symp Biocomput	2005
18265355	Basic protein sequence analysis.	Curr Protoc Mol Biol	2005
18429280	Basic protein sequence analysis.	Curr Protoc Protein Sci	2005
18428751	Phylogenomic inference of protein molecular function.	Curr Protoc Bioinformatics	2005
15901827	Proteome analysis of the rice etioplast: metabolic and regulatory networks and novel protein functions.	Mol Cell Proteomics	2005
15955925	Phylogenomic analysis of the receptor-like proteins of rice and Arabidopsis.	Plant Physiol	2005
15598806	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.	Plant Cell	2005
15684089	Molecular characterization of proteolytic cleavage sites of the Pseudomonas syringae effector AvrRpt2.	Proc Natl Acad Sci U S A	2005
15668378	Predicted hexameric structure of the Agrobacterium VirB4 C terminus suggests VirB4 acts as a docking site during type IV secretion.	Proc Natl Acad Sci U S A	2005
15028209	The Arabidopsis thaliana chloroplast proteome reveals pathway abundance and novel protein functions.	Curr Biol	2004
15319480	From endonucleases to transcription factors: evolution of the AP2 DNA binding domain in plants.	Plant Cell	2004
14962936	A comparison of scoring functions for protein sequence profile alignment.	Bioinformatics	2004
14962937	COACH: profile-profile alignment of protein families using hidden Markov models.	Bioinformatics	2004
14734307	Phylogenomic inference of protein molecular function: advances and challenges.	Bioinformatics	2004
15155873	Arabidopsis downy mildew resistance gene RPP27 encodes a receptor-like protein similar to CLAVATA2 and tomato Cf-9.	Plant Physiol	2004
12603027	Simultaneous sequence alignment and tree construction using hidden Markov models.	Pac Symp Biocomput	2003
12874053	SATCHMO: sequence alignment and tree construction using hidden Markov models.	Bioinformatics	2003
11181995	The sequence of the human genome.	Science	2001
9783222	Phylogenetic inference in protein superfamilies: analysis of SH2 domains.	Proc Int Conf Intell Syst Mol Biol	1998
9485505	Predicting protein structure using hidden Markov models.	Proteins	1997
8902360	Dirichlet mixtures: a method for improved detection of weak but significant protein sequence homology.	Comput Appl Biosci	1996
7800507	Stochastic context-free grammars for tRNA modeling.	Nucleic Acids Res	1994
8107089	Hidden Markov models in computational biology. Applications to protein modeling.	J Mol Biol	1994
7584370	Using Dirichlet mixture priors to derive hidden Markov models for protein families.	Proc Int Conf Intell Syst Mol Biol	1993

1 - 48 of 48

Matt E Oates

University of Bristol

Career Start Year 2013

Number of shared co-authors 15

Mario Stanke

Institut fur Mathematik und Informatik, Universitat Greifswald

Career Start Year 2003

Number of shared co-authors 16

Jonathan G Lees

University College London, Institute of Structural and Molecular Biology

Career Start Year 2003

Number of shared co-authors 8

L??szl?? Kaj??n

TUM (Technische Universitat Munchen)

Career Start Year 2003

Number of shared co-authors 2

Julian Gough

Medical Research Council Laboratory of Molecular Biology

Career Start Year 2001

Number of shared co-authors 23

Lenore J Cowen

Tufts University, 177 College Avenue

Career Start Year 2001

Number of shared co-authors 0

Dariusz Przybylski

Howard Hughes Medical Institute, Brandeis University

Career Start Year 2001

Number of shared co-authors 4

Weizhong Li

J. Craig Venter Institute

Career Start Year 2000

Number of shared co-authors 9

Evgenia V Kriventseva

University of Geneva Medical School

Career Start Year 1999

Number of shared co-authors 11

Ian Sillitoe

University College London

Career Start Year 1999

Number of shared co-authors 23

Kevin Bryson

University of Glasgow

Career Start Year 1999

Number of shared co-authors 9

Robert D Finn

European Bioinformatics Institute

Career Start Year 1999

Number of shared co-authors 21

Dong Xu

University of Missouri

Career Start Year 1998

Number of shared co-authors 2

Florencio Pazos

National Centre for Biotechnology (CNB-CSIC)

Career Start Year 1997

Number of shared co-authors 2

Kentaro Tomii

National Institute of Advanced Industrial Science and Technology (AIST)

Career Start Year 1996

Number of shared co-authors 2

John-Marc Chandonia

Lawrence Berkeley National Laboratory

Career Start Year 1995

Number of shared co-authors 9

Lukasz Jaroszewski

University of California Riverside School of Medicine

Career Start Year 1995

Number of shared co-authors 13

Aron Marchler-Bauer

National Center for Biotechnology Information, National Institutes of Health

Career Start Year 1994

Number of shared co-authors 18

Terry Gaasterland

Scripps Institution of Oceanography, University of California San Diego

Career Start Year 1994

Number of shared co-authors 6

Inna Dubchak

Lawrence Berkeley National Laboratory

Career Start Year 1993

Number of shared co-authors 22

Martijn A Huynen

Radboud University Medical Centre Nijmegen

Career Start Year 1992

Number of shared co-authors 7

Burkhard Rost

Technical University of Munich (TUM)

Career Start Year 1992

Number of shared co-authors 24

Robert B Russell

Heidelberg University

Career Start Year 1991

Number of shared co-authors 4

Jaap Heringa

VU University Amsterdam

Career Start Year 1991

Number of shared co-authors 2

Asaf Salamov

US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory

Career Start Year 1991

Number of shared co-authors 15

Roland L Dunbrack

Fox Chase Cancer Center

Career Start Year 1989

Number of shared co-authors 5

Ramanathan Sowdhamini

Indian Institute of Science

Career Start Year 1989

Number of shared co-authors 7

Christine Orengo

University College London, Institute of Structural and Molecular Biology

Career Start Year 1989

Number of shared co-authors 28

Adam Godzik

University of California Riverside

Career Start Year 1987

Number of shared co-authors 20

William R Pearson

University of Virginia

Career Start Year 1974

Number of shared co-authors 0

row(s) 1 - 30 of 30

Ruchira S Datta

Center for Evolution and Cancer, University of California San Francisco San Francisco

Co-authored papers 5

David Haussler

Genomics Institute, University of California Santa Cruz

Co-authored papers 5

Maria J Martin

European Bioinformatics Institute (EMBL-EBI)

Co-authored papers 2

Granger G Sutton

J. Craig Venter Institute

Co-authored papers 2

Steven L Salzberg

Center for Computational Biology, Johns Hopkins University

Co-authored papers 2

Paul D Thomas

University of Southern California

Co-authored papers 2

Yong Liang

Michigan State University

Co-authored papers 1

Bixiong Chris Shue

Co-authored papers 1

Sylvain Poux

carnegie mellon university

Co-authored papers 1

Hannes Braberg

University of California San Francisco

Co-authored papers 1

Andrej Sali (CM4AI)

University of California San Francisco

Co-authored papers 1

Dac-Trung Nguyen

Co-authored papers 1

Serenella Ferro

Co-authored papers 1

Tim Howland

Co-authored papers 1

David A Liberles

Temple University

Co-authored papers 1

Erich Bornberg-Bauer

Institute for Evolution and Biodiversity, University of Munster

Co-authored papers 1

Carlos C Evangelista

Co-authored papers 1

Dana Busam

J. Craig Venter Institute

Co-authored papers 1

Richard Bruskiewich

Delphinai Corporation

Co-authored papers 1

Guillaume Keller

carnegie mellon university

Co-authored papers 1

Lisa Doup

Co-authored papers 1

Petra Fey

Center for Genetic Medicine, Northwestern University.

Co-authored papers 1

Mallur S Madhusudhan

Indian Institute of Science Education and Research Pune

Co-authored papers 1

Mark Yandell

University of Utah

Co-authored papers 1

Zhongwu Lai

Oncology R&D

Co-authored papers 1

Seung Y Rhee

Carnegie Institution for Science

Co-authored papers 1

Stephen K Burley

The State University of New Jersey

Co-authored papers 1

Dmitry A Rodionov

Sanford Burnham Prebys Medical Discovery Institute

Co-authored papers 1

Christophe Dessimoz

University of Lausanne

Co-authored papers 1

Chinnappa D Kodira

GE Global Research Center

Co-authored papers 1

1 - 30

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