"The PhyloFacts FAT-CAT Webserver: Ortholog Identification and Function Prediction using Fast Approximate Tree Classification," Nucleic Acids Research 2013; doi: 10.1093/nar/gkt399 PDF
"The interface of protein structure, protein biophysics, and molecular evolution," Protein Science 2012; doi: 10.1002/pro.2071
"Toward community standards in the quest for orthologs,"
Bioinformatics 2012; doi: 10.1093/bioinformatics/bts050
(Members of the Quest for Orthologs Consortium: Adrian Altenhoff, Rolf Apweiler, Michael Ashburner, Judith Blake, Brigitte Boeckmann, Alan Bridge, Elspeth Bruford, Mike Cherry, Matthieu Conte, Durand Dannie, Ruchira Datta, Christophe Dessimmoz, Jean-Baka Domelevo Entfellner, Ingo Ebersberger, Toni Gabaldon, Michael Galperin, Javier Herrero, Jacob Joseph, Tina Koestler, Evgenia Kriventseva, Odile Lecompte, Jack Leunissen, Suzanna Lewis, Benjamin Linard, Michael S. Livstone, Hui-Chun Lu, Maria Martin, Raja Mazumder, David Messina, Vincent Miele, Matthieu Muffato, Guy Perriere, Marco Punta, David Roos, Mathieu Rouard, Thomas Schmitt, Fabian Schreiber, Alan Silva, Kimmen Sjölander, Nives Skunca, Erik Sonnhammer, Eleanor Stanley, Radek Szklarczyk, Paul Thomas, Ikuo Uchiyama, Michiel Van Bel, Klaas Vandepoele, Albert J. Vilella, Andrew Yates and Evgeny Zdobnov).
"Distribution and Properties of the Genes Encoding the Biosynthesis of the Bacterial Cofactor, Pyrroloquinoline Quinone," Biochemistry 2012; doi: 10.1021/bi201763d
"Ortholog identification in the presence of domain architecture rearrangement," Briefings in Bioinformatics 2011; doi: 10.1093/bib/bbr036
"ModBase, a database of annotated comparative protein structure models, and associated resources," Nucleic Acids Research, 2010, 1–10 doi:10.1093/nar/gkq1091 PDF.
"Arabidopsis thaliana PGR7 Encodes a Conserved Chloroplast Protein That Is Necessary for Efficient Photosynthetic Electron Transport," PLoS One 5(7): e11688, doi:10.1371/journal.pone.0011688 PDF.
"SATCHMO-JS: a webserver for simultaneous protein multiple sequence alignment and phylogenetic tree construction," Nucleic Acids Research 2010, doi:10.1093/nar/gkq298 PDF. Selected as a Featured Article by NAR. From the NAR website: "Featured Articles represent the top 5% of NAR papers in terms of originality, significance and scientific excellence."
Getting started in Structural Phylogenomics. PLos Comput Biol 6(1): e1000621. doi:10.1371/journal.pcbi.1000621 PDF.(2010)
"Active Site Prediction using Evolutionary and Structural Information," Bioinformatics 2010; doi: 10.1093/bioinformatics/btq008 PDF.
"INTREPID: a web server for prediction of functionally important residues by evolutionary analysis," Nucleic Acids Research 2009; doi: 10.1093/nar/gkp339 PDF.
"ResBoost: characterizing and predicting catalytic residues in enzymes," BMC Bioinformatics 2009, 10:197doi:10.1186/1471-2105-10-197 PDF.
"Berkeley PHOG: PhyloFacts Orthology Group Prediction Web Server," Nucleic Acids Research 2009; doi: 10.1093/nar/gkp373 PDF Supplementary Materials.
"INTREPID - INformation-theoretic TREe traversal for Protein functional site IDentification," Bioinformatics 2008; doi: 10.1093/bioinformatics/btn474 PDF.
"The Generation Challenge Programme comparative plant stress-responsive gene catalogue," Nucleic Acids Research 2007; doi:10.1093/nar/gkm798 PDF.
"Automated Protein Subfamily Identification and Classification," PLoS Computational Biology 2007, 3(8): e160 doi:10.1371/journal.pcbi.0030160 PDF Supplementary Data. Selected by the Faculty of 1000 as a technological advance.
"Berkeley Phylogenomics Group web servers: resources for structural phylogenomic analysis" Nucleic Acids Research 2007; doi:10.1093/nar/gkm325 PDF.
"FlowerPower: clustering proteins into domain architecture classes for phylogenomic inference of protein function", BMC Evolutionary Biology 2007, 7 Suppl 1:S12 doi:10.1186/1471-2148-7-S1-S12 PDF.
"Functional prediction through phylogenetic inference and structural classification of proteins" Encyclopedia of Genetics, Genomics, Proteomics and Bioinformatics, John Wiley and Sons (Short Specialist Review) July 2006.
"Functional Classification using Phylogenomic Inference." PLoS Computational Biology, Vol 2, Issue 6, June 2006 PDF.
"Basic protein sequence analysis". Current Protocols in Protein Science, Unit 2.11, 2005. PDF
"Phylogenomic inference of protein molecular function," Current Protocols in Bioinformatics, Unit 6.9, 2005 PDF.
"Basic protein sequence analysis". Current Protocols in Molecular Biology, Unit 19.5, 2005 PDF.
"Phylogenomic analysis of the receptor-like proteins of rice and Arabidopsis", Plant Physiology, June 2005, Vol. 138, pp. 611-623 PDF.
"Molecular characterization of proteolytic cleavage sites of the Pseudomonas syringae effector AvrRpt2", Proceedings of the National Academy of Sciences, February 8, 2005, vol. 102, no. 6, 2087-2092 PDF.
"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 2005 Feb 1;102(5):1685-90 PDF.
"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. Jan;17(1):295-310. 2005 PubMed PDF.
"SATCHMO: Sequence Alignment and Tree Construction using Hidden Markov models," Bioinformatics. 2003 Jul 22;19(11):1404-11 PDF. Selected by the Faculty of 1000 as a "Must Read" for Technological Advance (rating 6.0).
"Simultaneous sequence alignment and tree construction using hidden Markov models." Proceedings of the Pacific Symposium on Biocomputing HI. 2003; 180-91., PubMed PDF.
"The sequence of the human genome," Science, 2001 Feb 16;291(5507):1304-51. (My contributions: the algorithms used for the Panther HMM library construction and functional classification of the human genome. (1) FlowerPower clustering and alignment of homologs; (2) Bayesian Evolutionary Tree Estimation and subfamily identification; (3) Subfamily HMM construction.) Cover
"Bayesian Evolutionary Tree Estimation", Proceedings of the Eleventh International Conference on Mathematical and Computer Modelling and Scientific Computing, Computational Biology Session: "Conference Computing in the Genome Era" 1997 PDF.
"Predicting protein structure using hidden Markov models," Proteins: Structure, Function and Genetics , Suppl 1:134-139. 1997. Invited paper for special issue covering the second Critical Assessment for Protein Structure Prediction (CASP) competition. PubMed PDF.
"Dirichlet Mixtures: A Method for Improved Detection of Weak but Significant Protein Sequence Homology," 1996 Aug;12(4):327-45. Computing Applications in the Biosciences (CABIOS) Postscript PDF.
"Using Dirichlet mixture priors to derive hidden Markov models for protein families," Proceedings of the First International Conference on Intelligent Systems for Molecular Biology 1993 1:47-55 PubMed PDF.
"Protein Modeling using Hidden Markov Models: Analysis of Globins", Proceedings of the Hawaii International Conference on System Sciences , 1993. Voted best in the category AI Technologies for Molecular Biology Analysis. IEEE PDF.