Kimmen Sjölander

发表

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

K. Sjölander, W. Gruissem, S. Baginsky, 2004, Current Biology.

Proteome Analysis of the Rice Etioplast

K. Sjölander, W. Gruissem, Nandini Krishnamurthy, 2005, Molecular & Cellular Proteomics.

The COMBREX Project: Design, Methodology, and Initial Results

Michael Y. Galperin, S. Salzberg, R. Greiner, 2013, PLoS biology.

Standardized benchmarking in the quest for orthologs

Adrian M. Altenhoff, Leszek P. Pryszcz, Alan Wilter Sousa da Silva, 2016, Nature Methods.

Phylogenomic Analysis of the Receptor-Like Proteins of Rice and Arabidopsis1[w]

Nandini Krishnamurthy, Mahmut Tör, Jonathan D. G. Jones, 2005, Plant Physiology.

Phylogenomic inference of protein molecular function: advances and challenges

Kimmen Sjölander, K. Sjölander, Kimmen Sjölander, 2004, Bioinform..

Hidden Markov models in computational biology. Applications to protein modeling.

D. Haussler, A. Krogh, M. Brown, 1993, Journal of molecular biology.

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

Lucy J. Colwell, Johan A. Grahnen, Nimrod D. Rubinstein, 2012, Protein science : a publication of the Protein Society.

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 Tomatow⃞

Jonathan D. G. Jones, K. Sjölander, H. Yoshioka, 2005, The Plant Cell Online.

Distribution and properties of the genes encoding the biosynthesis of the bacterial cofactor, pyrroloquinoline quinone.

K. Sjölander, J. Klinman, Yaoqing Shen, 2012, Biochemistry.

Predicting protein structure using hidden Markov models

C Sander, L Holm, K Karplus, 1997, Proteins.

Stochastic context-free grammars for tRNA modeling.

R. C. Underwood, Rebecca C. Underwood, D. Haussler, 1994, Nucleic acids research.

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

David Haussler, Anders Krogh, Michael Brown, 1993, ISMB.

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

Kimmen Sjölander, Robert C. Edgar, R. Edgar, 2003 .

From Endonucleases to Transcription Factors: Evolution of the AP2 DNA Binding Domain in Plantsw⃞

Sarah Hake, Enrico Magnani, K. Sjölander, 2004, The Plant Cell Online.

Taking the first steps towards a standard for reporting on phylogenies: Minimum Information About a Phylogenetic Analysis (MIAPA).

K. Sjölander, E. Koonin, R. DeSalle, 2006, Omics : a journal of integrative biology.

Genome Analysis Phylogenomic Analysis of the Receptor-Like Proteins of Rice and Arabidopsis 1 [ w ]

Jonathan D. G. Jones, K. Sjölander, Nandini Krishnamurthy, 2005 .

Arabidopsis Downy Mildew Resistance Gene RPP27 Encodes a Receptor-Like Protein Similar to CLAVATA2 and Tomato Cf-91

Jonathan D. G. Jones, K. Sjölander, Duncan P. Brown, 2004, Plant Physiology.

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

Jonathan D. G. Jones, K. Sjölander, Duncan P. Brown, 2004, Plant physiology.

Phylogenomic inference of protein molecular function: advances and challenges

Kimmen Sjölander, 2004, Bioinform..

A comparison of scoring functions for protein sequence profile alignment

Kimmen Sjölander, Robert C. Edgar, R. Edgar, 2004, Bioinform..

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

K. Sjölander, J. Foley, Nandini Krishnamurthy, 2005, Proceedings of the National Academy of Sciences of the United States of America.

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

David Haussler, Anders Krogh, Michael Brown, 1996, Comput. Appl. Biosci..

“dcGO”: a Domain-Centric Gene Ontology Predictor for Functional Genomics Julian Gough Flexible Graphlet Kernels for Functional Residue Prediction in Protein Structures Jose Lugo-Martinez FAT-CAT (Fast Approximate Tree ClassificATion): A Scalable Method for (Meta)Genome Functional and Taxonomic Class

K. Sjölander, Bushra Samad, J. Dobbie, 2012 .

Functional Classification Using Phylogenomic Inference

Duncan P. Brown, Kimmen Sjölander, K. Sjölander, 2006, PLoS Comput. Biol..

Phylogenetic Inference in Protein Superfamilies: Analysis of SH2 Domains

Kimmen Sjölander, K. Sjölander, Kimmen Sjölander, 1998, ISMB.

Standardized benchmarking in the quest for orthologs

Leszek P. Pryszcz, Alan Wilter Sousa da Silva, P. Bork, 2016, Nature Methods.

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

K. Karplus, Michael Brown, Kimmen Sjölander, 1996, Comput. Appl. Biosci..

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

John R. Davidson, Kimmen Sjölander, Ruchira S. Datta, 2010, Nucleic Acids Res..

SATCHMO: Sequence Alignment and Tree Construction Using Hidden Markov Models

Robert C. Edgar, Kimmen Sjölander, 2003, Bioinform..

Simultaneous Sequence Alignment and Tree Construction Using Hidden Markov Models

Kimmen Sjölander, Robert C. Edgar, Kimmen Sjölander, 2002, Pacific Symposium on Biocomputing.

Berkeley Phylogenomics Group web servers: resources for structural phylogenomic analysis

Kimmen Sjölander, Jake Gunn Glanville, Dan Kirshner, 2007, Nucleic Acids Res..

Automated Protein Subfamily Identification and Classification

Duncan P. Brown, Kimmen Sjölander, Nandini Krishnamurthy, 2007, PLoS Comput. Biol..