Erik Sonnhammer, Toni Gabaldón, Alan Wilter Sousa da Silva, Maria Martin,Marc Robinson-Rechavi, Brigitte Boeckmann, Paul Thomas, Christophe Dessimoz, and the Quest for Orthologs consortium. "Big Data and Other Challenges in the Quest for Orthologs," Bioinformatics (2014) doi: 10.1093/bioinformatics/btu492 (PDF)

Brian P. Anton, Yi-Chien Chang, Peter Brown, Han-Pil Choi, Lina L. Faller, Jyotsna Guleria, Zhenjun Hu, Niels Klitgord, Ami Levy-Moonshine, Almaz Maksad, Varun Mazumdar, Mark McGettrick, Lais Osmani, Revonda Pokrzywa, John Rachlin, Rajeswari Swaminathan, Benjamin Allen, Genevieve Housman, Caitlin Monahan, Krista Rochussen, Kevin Tao, Ashok S. Bhagwat, Steven E. Brenner, Linda Columbus, Valérie de Crécy-Lagard, Donald Ferguson, Alexey Fomenkov, Giovanni Gadda, Richard D. Morgan, Andrei L. Osterman, Dmitry A. Rodionov, Irina A. Rodionova, Kenneth E. Rudd, Dieter Söll, James Spain, Shuang-yong Xu, Alex Bateman, Robert M. Blumenthal, J. Martin Bollinger, Woo-Suk Chang, Manuel Ferrer, Iddo Friedberg, Michael Y. Galperin, Julien Gobeill, Daniel Haft, John Hunt, Peter Karp, William Klimke, Carsten Krebs, Dana Macelis, Ramana Madupu, Maria J. Martin, Jeffrey H. Miller, Claire O'Donovan, Bernhard Palsson, Patrick Ruch, Aaron Setterdahl, Granger Sutton, John Tate, Alexander Yakunin, Dmitri Tchigvintsev, Germán Plata, Jie Hu, Russell Greiner, David Horn, Kimmen Sjölander, Steven L. Salzberg, Dennis Vitkup, Stanley Letovsky, Daniel Segrè, Charles DeLisi, Richard J. Roberts, Martin Steffen, Simon Kasif. "The COMBREX Project: Design, Methodology, and Initial Results," PLoS Biol 11(8): e1001638. doi:10.1371/journal.pbio.1001638 (PDF)

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 (PDF)

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). (PDF)

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 (PDF)

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 (PDF)

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. 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." (PDF)

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," Database2009: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 Bioinformatics2009, 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)

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. Selected by the Faculty of 1000 as a technological advance. (PDF)

Jake Gunn Glanville, Dan Kirshner, Nandini Krishnamurthy and Kimmen Sjölander, "Berkeley Phylogenomics Group web servers: resources for structural phylogenomic analysis" Nucleic Acids Research2007; 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 Biology2007, 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. (PDF)

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.

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

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

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. Selected by the Faculty of 1000 as a "Must Read". (PDF)

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. Selected by the Faculty of 1000 as a "Must Read" for Technological Advance (rating 6.0). (PDF)

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 (PDF)

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 BiologySession: "Conference Computing in the Genome Era" 1997.

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). (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):1501-31PubMed. (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)