Academic lineage
Standardized benchmarking in the quest for orthologs
- Adrian M Altenhoff, Brigitte Boeckmann, Salvador Capella-Gutierrez, …, Paul D Thomas, Erik Sonnhammer, Christophe Dessimoz
- Nat Methods, 10.1038/nmeth.3830
The COMBREX project: design, methodology, and initial results
- Brian P Anton, Yi-Chien Chang, Peter Brown, …, Richard J Roberts, Martin Steffen, Simon Kasif
- PLoS Biol, 10.1371/journal.pbio.1001638
The PhyloFacts FAT-CAT web server: ortholog identification and function prediction using fast approximate tree classification
- Cyrus Afrasiabi, Bushra Samad, David Dineen, Christopher Meacham, Kimmen Sjölander
- Nucleic Acids Res, 10.1093/nar/gkt399
The interface of protein structure, protein biophysics, and molecular evolution
- David A Liberles, Sarah A Teichmann, Ivet Bahar, …, Joseph W Thornton, Daniel M Weinreich, Simon Whelan
- Protein Sci, 10.1002/pro.2071
Distribution and properties of the genes encoding the biosynthesis of the bacterial cofactor, pyrroloquinoline quinone
- Yao-Qing Shen, Florence Bonnot, Erin M Imsand, Jordan M RoseFigura, Kimmen Sjölander, Judith P Klinman
- Biochemistry, 10.1021/bi201763d
Ortholog identification in the presence of domain architecture rearrangement
- Kimmen Sjölander, Ruchira S Datta, Yaoqing Shen, Grant M Shoffner
- Brief Bioinform, 10.1093/bib/bbr036
ModBase, a database of annotated comparative protein structure models, and associated resources
- Ursula Pieper, Benjamin M Webb, David T Barkan, …, Thomas E Ferrin, Stephen K Burley, Andrej Sali
- Nucleic Acids Res, 10.1093/nar/gkq1091
Arabidopsis thaliana PGR7 encodes a conserved chloroplast protein that is necessary for efficient photosynthetic electron transport
- Hou-Sung Jung, Yuki Okegawa, Patrick M Shih, …, Kimmen Sjölander, Toshiharu Shikanai, Krishna K Niyogi
- PLoS One, 10.1371/journal.pone.0011688
SATCHMO-JS: a webserver for simultaneous protein multiple sequence alignment and phylogenetic tree construction
- Raffi Hagopian, John R Davidson, Ruchira S Datta, Bushra Samad, Glen R Jarvis, Kimmen Sjölander
- Nucleic Acids Res, 10.1093/nar/gkq298
Collaborative annotation of genes and proteins between UniProtKB/Swiss-Prot and dictyBase
- P Gaudet, L Lane, P Fey, …, L Bougueleret, R L Chisholm, A Bairoch
- Database (Oxford), 10.1093/database/bap016
Getting started in structural phylogenomics
- Kimmen Sjölander
- PLoS Comput Biol, 10.1371/journal.pcbi.1000621
Active site prediction using evolutionary and structural information
- Sriram Sankararaman, Fei Sha, Jack F Kirsch, Michael I Jordan, Kimmen Sjölander
- Bioinformatics, 10.1093/bioinformatics/btq008
ResBoost: characterizing and predicting catalytic residues in enzymes
- Ron Alterovitz, Aaron Arvey, Sriram Sankararaman, Carolina Dallett, Yoav Freund, Kimmen Sjölander
- BMC Bioinformatics, 10.1186/1471-2105-10-197
INTREPID: a web server for prediction of functionally important residues by evolutionary analysis
- Sriram Sankararaman, Bryan Kolaczkowski, Kimmen Sjölander
- Nucleic Acids Res, 10.1093/nar/gkp339
Berkeley PHOG: PhyloFacts orthology group prediction web server
- Ruchira S Datta, Christopher Meacham, Bushra Samad, Christoph Neyer, Kimmen Sjölander
- Nucleic Acids Res, 10.1093/nar/gkp373
The Generation Challenge Programme comparative plant stress-responsive gene catalogue
- Samart Wanchana, Supat Thongjuea, Victor Jun Ulat, …, Kimmen Sjolander, Theo van Hintum, Richard M Bruskiewich
- Nucleic Acids Res, 10.1093/nar/gkm798