Scientific Publications (in reverse chronological order)

Afrasiabi, C., Samad, B., Dineen, D., Meacham, C. Sjölander, K., "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

Liberles, D., Teichmann, S., Bahar, I., Bastolla, U., Bloom, J., Bornberg-Bauer, E., Colwell, L., de Koning, J., Dokholyan, N., Echave, J., Elofsson, A., Gerloff, D., Goldstein, R., Grahnen, J., Holder, M., Lakner, C., Lartillot, N., Lovell, S., Naylor, G., Perica, T., Pollock, D., Pupko, T., Regan, L., Roger, A., Rubinstein, N., Shakhnovich, E., Sjölander, K., Sunyaev, S., Teufel, A., Thorne, J., Thornton, J., Weinreich, D., Whelan, S., "The interface of protein structure, protein biophysics, and molecular evolution," Protein Science 2012; doi: 10.1002/pro.2071

Dessimoz, C., Gabaldon, T., Roos, D., Sonnhammer, E., Herrero, J., and the Quest for Orthologs Consortium, "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).

Shen, Y., Bonnot, F., Imsand, E., Rosefigure, J., Sjölander, K., Kilnman, J., "Distribution and Properties of the Genes Encoding the Biosynthesis of the Bacterial Cofactor, Pyrroloquinoline Quinone," Biochemistry 2012; doi: 10.1021/bi201763d

Sjölander, K., Datta, R., Shen, Y., Shoffner, G., "Ortholog identification in the presence of domain architecture rearrangement," Briefings in Bioinformatics 2011; doi: 10.1093/bib/bbr036

Pieper, U., Webb, B., Barkan, D., Schneidman-Duhovny, D., Schlessinger, A., Braberg, H., Yang, Z., Meng, E., Pettersen, E., Huang, C., Datta, R., Sampathkumar, P., Madhusudhan, M.S., Sjölander, K., Ferrin, T., Burley, S., and Sali, A., "ModBase, a database of annotated comparative protein structure models, and associated resources," Nucleic Acids Research, 2010, 1–10 doi:10.1093/nar/gkq1091 PDF.

Jung H-S, Okegawa Y, Shih PM, Kellogg E, Abdel-Ghany SE, Pilon M, Sjölander K, Shikanai T, and Niyogi KK, "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.

Hagopian, R., Davidson, J., Datta, R., Samad, B., Jarvis, G., and Sjölander, K. "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."

Sjölander K (2010) Getting started in Structural Phylogenomics. PLos Comput Biol 6(1): e1000621. doi:10.1371/journal.pcbi.1000621 PDF.

Sriram Sankararaman, Fei Sha, Jack F. Kirsch, Michael I. Jordan, and Kimmen Sjölander, "Active Site Prediction using Evolutionary and Structural Information," Bioinformatics 2010; doi: 10.1093/bioinformatics/btq008 PDF.

P. Gaudet, L. Lane, P. Fey, A. Bridge, S. Poux, A. Auchincloss, K. Axelsen, S. Braconi Quintaje, E. Boutet, P. Brown, E. Coudert, R.S. Datta, W.C.de Lima, T. de Oliveira Lima, S. Duvaud, N. Farriol-Mathis, S. Ferro Rojas, M. Feuermann, A. Gateau, U. Hinz, C. Hulo, J. James, S. Jimenez, F. Jungo, G. Keller, P. Lemercier, D. Lieberherr, M. Moinat, A. Nikolskaya, I. Pedruzzi, C. Rivoire, B. Roechert, M. Schneider, E. Stanley, M. Tognolli, K. Sjölander, L. Bougueleret, R.L. Chisholm, and A. Bairoch, "Collaborative annotation of genes and proteins between UniProtKB/Swiss-Prot and dictyBase," Database 2009:bap016, DOI 10.1093/database/bap016 PDF.

Sriram Sankararaman, Bryan Kolaczkowski and Kimmen Sjölander "INTREPID: a web server for prediction of functionally important residues by evolutionary analysis," Nucleic Acids Research 2009; doi: 10.1093/nar/gkp339 PDF.

Ron Alterovitz, Aaron Arvey, Sriram Sankararaman, Carolina Dallett, Yoav Freund, and Kimmen Sjölander, "ResBoost: characterizing and predicting catalytic residues in enzymes," BMC Bioinformatics 2009, 10:197doi:10.1186/1471-2105-10-197 PDF.

Ruchira S. Datta, Christopher Meacham, Bushra Samad, Christoph Neyer and Kimmen Sjölander "Berkeley PHOG: PhyloFacts Orthology Group Prediction Web Server," Nucleic Acids Research 2009; doi: 10.1093/nar/gkp373 PDF Supplementary Materials.

Sriram Sankararaman and Kimmen Sjölander, "INTREPID - INformation-theoretic TREe traversal for Protein functional site IDentification," Bioinformatics 2008; doi: 10.1093/bioinformatics/btn474 PDF.

Samart Wanchana, Supat Thongjuea, Victor Jun Ulat, Mylah Anacleto, Ramil Mauleon, Matthieu Conte, Mathieu Rouard, Manuel Ruiz, Nandini Krishnamurthy, Kimmen Sjölander, Theo van Hintum and Richard M. Bruskiewich "The Generation Challenge Programme comparative plant stress-responsive gene catalogue," Nucleic Acids Research 2007; doi:10.1093/nar/gkm798 PDF.

Brown DP, Krishnamurthy N, Sjölander K, "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.

Jake Gunn Glanville, Dan Kirshner, Nandini Krishnamurthy and Kimmen Sjölander, "Berkeley Phylogenomics Group web servers: resources for structural phylogenomic analysis" Nucleic Acids Research 2007; doi:10.1093/nar/gkm325 PDF.

Nandini Krishnamurthy, Duncan Brown and Kimmen Sjölander, "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.

Nandini Krishnamurthy, Duncan Brown, Dan Kirshner and Kimmen Sjölander, "PhyloFacts: An online structural phylogenomic encyclopedia for protein functional and structural classification," Genome Biology 2006, 7:R83 PDF.

Leebens-Mack J, Vision T, Brenner E, Bowers JE, Cannon S, Clement MJ, Cunningham CW, Depamphilis C, Desalle R, Doyle JJ, Eisen JA, Gu X, Harshman J, Jansen RK, Kellogg EA, Koonin EV, Mishler BD, Philippe H, Pires JC, Qiu YL, Rhee SY, Sjolander K, Soltis DE, Soltis PS, Stevenson DW, Wall K, Warnow T, Zmasek C. "Taking the First Steps towards a Standard for Reporting on Phylogenies: Minimum Information about a Phylogenetic Analysis (MIAPA)." OMICS 2006 PubMed PDF.

Kimmen Sjölander and Chelsea Specht, "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.

Duncan Brown and Kimmen Sjölander, "Functional Classification using Phylogenomic Inference." PLoS Computational Biology, Vol 2, Issue 6, June 2006 PDF.

Nandini Krishnamurthy and Kimmen Sjölander, "Basic protein sequence analysis". Current Protocols in Protein Science, Unit 2.11, 2005. PDF

Nandini Krishnamurthy and Kimmen Sjölander, "Phylogenomic inference of protein molecular function," Current Protocols in Bioinformatics, Unit 6.9, 2005 PDF.

Nandini Krishnamurthy and Kimmen Sjölander, "Basic protein sequence analysis". Current Protocols in Molecular Biology, Unit 19.5, 2005 PDF.

von Zychlinski A, Kleffmann T, Krishnamurthy N, Sjölander K, Baginsky S, Gruissem W., "Proteome analysis of the rice etioplast: metabolic and regulatory networks and novel protein functions", Mol Cell Proteomics. 2005 May 20 PDF.

Lillian Fritz-Laylin, Nandini Krishamurthy, Mahmut Tor, Kimmen Sjölander and Jonathan Jones. "Phylogenomic analysis of the receptor-like proteins of rice and Arabidopsis", Plant Physiology, June 2005, Vol. 138, pp. 611-623 PDF.

Stephen T. Chisholm, Douglas Dahlbeck, Nandini Krishnamurthy, Brad Day, Kimmen Sjölander, and Brian J. Staskawicz, "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.

Rebecca Middleton, Kimmen Sjölander, Nandini Krishnamurthy, Jonathan Foley, and Patricia Zambryski, "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.

Brown D, Krishnamurthy N, Dale J, Christopher W, and Sjölander K, "Subfamily HMMs in Functional Genomics" , Proceedings of the Pacific Symposium on Biocomputing , 2005. PubMed PSB proceedings PDF.

Rowland O, Ludwig AA, Merrick CJ, Baillieul F, Tracy FE, Durrant WE, Fritz-Laylin L, Nekrasov V, Sjölander K, Yoshioka H, Jones JD. "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.

Magnani, E., Sjölander, K. , and Hake S., "From endonucleases to transcription factors: evolution of the AP2 DNA-binding domain in plants", Plant Cell, 2004 Sep;16(9):2265-77 PubMed PDF. Selected by the Faculty of 1000 as a "Must Read".

Kleffmann, T., Russenberger, D., von Zychlinski, A., Christopher, W., Sjölander, K., Gruissem, W., and Baginsky, S. "The Arabidopsis thaliana chloroplast proteome reveals pathway abundance and novel protein functions," Current Biology 2004 Mar 9;14(5):354-62 PubMed PDF.

Mahmut Tör, M., Brown D., Cooper, A., Woods-Tör, A., Sjölander, K., Jones, J.D.G. and Holub, E. "Arabidopsis Downy Mildew Resistance Gene RPP27 Encodes a Receptor-Like Protein Similar to CLAVATA2 and Tomato Cf-9," Plant Physiology, 2004 Jun;135(2):1100-12 PubMed PDF.

Edgar, R. and Sjölander, K., "A comparison of scoring functions for protein sequence profile alignment," Bioinformatics 2004 May 22;20(8):1301-8 PubMed PDF.

Edgar, R., and Sjölander, K., "COACH: profile-profile alignment of protein families using hidden Markov models," Bioinformatics 2004 May 22;20(8):1309-18 PubMed PDF.

Sjölander, K., "Phylogenomic inference of protein molecular function: advances and challenges," Bioinformatics 2004 (20)2:170-179. PDF.

Edgar, R., and Sjölander, K., "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).

Edgar, R., and Sjölander, K., "Simultaneous sequence alignment and tree construction using hidden Markov models." Proceedings of the Pacific Symposium on Biocomputing HI. 2003; 180-91., PubMed PDF.

Venter, C. et al, "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

Sjölander, K , "Phylogenetic inference in protein superfamilies: Analysis of SH2 domains," Proceedings of the Conference Intelligent Systems for Molecular Biology 1998 6:165-74 PubMed PDF.

Sjölander, K, "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.

Karplus, K, Sjölander K, Barrett C, Cline M, Haussler D, Hughey R, Holm L, Sander C., "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.

Sjölander, K., Karplus, K., Brown, M.P., Hughey, R., Krogh, A., Mian, I.S., Haussler D., "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.

Sakakibara, Y, Brown, M., Hughey, R., Mian, S., Sjölander, K., Underwood, R., Haussler, D. "Stochastic Context-Free Grammars for tRNA Modeling," Nucleic Acids Research 1994 Nov 25;22(23):5112-20 PDF.

Krogh, A., Brown, M., Mian, S., Sjölander, K. and Haussler, D., "Hidden Markov Models in Computational Biology: Applications to Protein Modeling," Journal of Molecular Biology 1994 Feb 4;235(5):1501-31 PubMed PDF.

Brown, M.P., Hughey, R., Krogh, A., Mian, I.S., Sjölander, K., Haussler, D., "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.

Haussler, D., Krogh, A., Mian, I.S., Sjölander, K., "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.