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Kevin Karplus - Publications

Affiliations: 
University of California, Santa Cruz, Santa Cruz, CA, United States 
Area:
Bioinformatics Biology, Biochemistry
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39 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2017 Draper JL, Hansen LM, Bernick DL, Abedrabbo S, Underwood JG, Kong N, Huang BC, Weis AM, Weimer BC, van Vliet AH, Pourmand N, Solnick JV, Karplus K, Ottemann KM. Fallacy of the Unique Genome: Sequence Diversity within Single Helicobacter pylori Strains. Mbio. 8. PMID 28223462 DOI: 10.1128/Mbio.02321-16  0.376
2015 Schreiber J, Karplus K. Analysis of nanopore data using hidden Markov models. Bioinformatics (Oxford, England). 31: 1897-903. PMID 25649617 DOI: 10.1093/Bioinformatics/Btv046  0.384
2012 Bernick DL, Karplus K, Lui LM, Coker JK, Murphy JN, Chan PP, Cozen AE, Lowe TM. Complete genome sequence of Pyrobaculum oguniense. Standards in Genomic Sciences. 6: 336-45. PMID 23407329 DOI: 10.4056/Sigs.2645906  0.321
2011 Sievers F, Wilm A, Dineen D, Gibson TJ, Karplus K, Li W, Lopez R, McWilliam H, Remmert M, Söding J, Thompson JD, Higgins DG. Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega. Molecular Systems Biology. 7: 539. PMID 21988835 DOI: 10.1038/Msb.2011.75  0.48
2011 Samayoa J, Yildiz FH, Karplus K. Identification of prokaryotic small proteins using a comparative genomic approach. Bioinformatics (Oxford, England). 27: 1765-71. PMID 21551138 DOI: 10.1093/bioinformatics/btr275  0.796
2011 Fonseca R, Winter P, Karplus K. Protein packing quality using Delaunay complexes Proceedings - 2011 8th International Symposium On Voronoi Diagrams in Science and Engineering, Isvd 2011. 117-122. DOI: 10.1109/ISVD.2011.23  0.322
2010 Madera M, Calmus R, Thiltgen G, Karplus K, Gough J. Improving protein secondary structure prediction using a simple k-mer model. Bioinformatics (Oxford, England). 26: 596-602. PMID 20130034 DOI: 10.1093/Bioinformatics/Btq020  0.797
2009 Krieger E, Joo K, Lee J, Lee J, Raman S, Thompson J, Tyka M, Baker D, Karplus K. Improving physical realism, stereochemistry, and side-chain accuracy in homology modeling: Four approaches that performed well in CASP8. Proteins. 77: 114-22. PMID 19768677 DOI: 10.1002/Prot.22570  0.514
2009 Archie JG, Paluszewski M, Karplus K. Applying Undertaker to quality assessment. Proteins. 77: 191-5. PMID 19639637 DOI: 10.1002/Prot.22508  0.339
2009 Karplus K. SAM-T08, HMM-based protein structure prediction. Nucleic Acids Research. 37: W492-7. PMID 19483096 DOI: 10.1093/Nar/Gkp403  0.549
2009 Khatib F, Rohl CA, Karplus K. Pokefind: a novel topological filter for use with protein structure prediction. Bioinformatics (Oxford, England). 25: i281-8. PMID 19478000 DOI: 10.1093/Bioinformatics/Btp198  0.743
2009 Archie J, Karplus K. Applying undertaker cost functions to model quality assessment. Proteins. 75: 550-5. PMID 19004017 DOI: 10.1002/Prot.22288  0.452
2009 Paluszewski M, Karplus K. Model quality assessment using distance constraints from alignments. Proteins. 75: 540-9. PMID 19003987 DOI: 10.1002/prot.22262  0.366
2008 Katzman S, Barrett C, Thiltgen G, Karchin R, Karplus K. PREDICT-2ND: a tool for generalized protein local structure prediction. Bioinformatics (Oxford, England). 24: 2453-9. PMID 18757875 DOI: 10.1093/Bioinformatics/Btn438  0.739
2007 Shackelford G, Karplus K. Contact prediction using mutual information and neural nets. Proteins. 69: 159-64. PMID 17932918 DOI: 10.1002/Prot.21791  0.729
2006 Fong JC, Karplus K, Schoolnik GK, Yildiz FH. Identification and characterization of RbmA, a novel protein required for the development of rugose colony morphology and biofilm structure in Vibrio cholerae. Journal of Bacteriology. 188: 1049-59. PMID 16428409 DOI: 10.1128/Jb.188.3.1049-1059.2006  0.39
2005 Karplus K, Katzman S, Shackleford G, Koeva M, Draper J, Barnes B, Soriano M, Hughey R. SAM-T04: what is new in protein-structure prediction for CASP6. Proteins. 61: 135-42. PMID 16187355 DOI: 10.1002/Prot.20730  0.543
2005 Karplus K, Karchin R, Shackelford G, Hughey R. Calibrating E-values for hidden Markov models using reverse-sequence null models. Bioinformatics (Oxford, England). 21: 4107-15. PMID 16123115 DOI: 10.1093/Bioinformatics/Bti629  0.739
2004 Karchin R, Cline M, Karplus K. Evaluation of local structure alphabets based on residue burial. Proteins. 55: 508-18. PMID 15103615 DOI: 10.1002/Prot.20008  0.776
2004 Dolinsky TJ, Burgers PMJ, Karplus K, Baker NA. SPrCY: Comparison of structural predictions in the Saccharomyces cerevisiae genome Bioinformatics. 20: 2312-2314. PMID 15059824 DOI: 10.1093/Bioinformatics/Bth223  0.53
2003 Karplus K, Karchin R, Draper J, Casper J, Mandel-Gutfreund Y, Diekhans M, Hughey R. Combining local-structure, fold-recognition, and new fold methods for protein structure prediction. Proteins. 53: 491-6. PMID 14579338 DOI: 10.1002/Prot.10540  0.673
2003 Karchin R, Cline M, Mandel-Gutfreund Y, Karplus K. Hidden Markov models that use predicted local structure for fold recognition: alphabets of backbone geometry. Proteins. 51: 504-14. PMID 12784210 DOI: 10.1002/Prot.10369  0.809
2002 Cline MS, Karplus K, Lathrop RH, Smith TF, Rogers RG, Haussler D. Information-theoretic dissection of pairwise contact potentials. Proteins. 49: 7-14. PMID 12211011 DOI: 10.1002/Prot.10198  0.647
2002 Cline M, Hughey R, Karplus K. Predicting reliable regions in protein sequence alignments. Bioinformatics (Oxford, England). 18: 306-14. PMID 11847078 DOI: 10.1093/Bioinformatics/18.2.306  0.778
2002 Karchin R, Karplus K, Haussler D. Classifying G-protein coupled receptors with support vector machines. Bioinformatics (Oxford, England). 18: 147-59. PMID 11836223 DOI: 10.1093/Bioinformatics/18.1.147  0.696
2001 Karplus K, Karchin R, Barrett C, Tu S, Cline M, Diekhans M, Grate L, Casper J, Hughey R. What is the value added by human intervention in protein structure prediction? Proteins. 86-91. PMID 11835485 DOI: 10.1002/Prot.10021  0.811
2001 Gough J, Karplus K, Hughey R, Chothia C. Assignment of homology to genome sequences using a library of hidden Markov models that represent all proteins of known structure Journal of Molecular Biology. 313: 903-919. PMID 11697912 DOI: 10.1006/Jmbi.2001.5080  0.561
2001 Karplus K, Hu B. Evaluation of protein multiple alignments by SAM-T99 using the BAliBASE multiple alignment test set Bioinformatics. 17: 713-720. PMID 11524372 DOI: 10.1093/Bioinformatics/17.8.713  0.438
2000 Zhu C, Karplus K, Grate L, Coffino P. A homolog of mammalian antizyme is present in fission yeast Schizosaccharomyces pombe but not detected in budding yeast Saccharomyces cerevisiae Bioinformatics. 16: 478-481. PMID 10871270 DOI: 10.1093/Bioinformatics/16.5.478  0.432
1999 Fischer D, Barret C, Bryson K, Elofsson A, Godzik A, Jones D, Karplus KJ, Kelley LA, MacCallum RM, Pawowski K, Rost B, Rychlewski L, Sternberg M. CAFASP-1: critical assessment of fully automated structure prediction methods. Proteins. 209-17. PMID 10526371 DOI: 10.1002/(Sici)1097-0134(1999)37:3+<209::Aid-Prot27>3.0.Co;2-Y  0.438
1999 Karplus K, Barrett C, Cline M, Diekhans M, Grate L, Hughey R. Predicting protein structure using only sequence information Proteins: Structure, Function and Genetics. 37: 121-125. PMID 10526360  0.571
1999 Karplus K, Barrett C, Cline M, Diekhans M, Grate L, Hughey R. Predicting protein structure using only sequence information Proteins. 37: 121-125. DOI: 10.1002/(Sici)1097-0134(1999)37:3+<121::Aid-Prot16>3.0.Co;2-Q  0.765
1998 Karplus K, Barrett C, Hughey R. Hidden Markov models for detecting remote protein homologies Bioinformatics. 14: 846-856. PMID 9927713 DOI: 10.1093/Bioinformatics/14.10.846  0.723
1998 Park J, Karplus K, Barrett C, Hughey R, Haussler D, Hubbard T, Chothia C. Sequence comparisons using multiple sequences detect three times as many remote homologues as pairwise methods Journal of Molecular Biology. 284: 1201-1210. PMID 9837738 DOI: 10.1006/Jmbi.1998.2221  0.705
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. 134-9. PMID 9485505 DOI: 10.1002/(SICI)1097-0134(1997)1+<134::AID-PROT18>3.0.CO;2-P  0.505
1997 Barrett C, Hughey R, Karplus K. Scoring hidden Markov models Computer Applications in the Biosciences. 13: 191-199. PMID 9146967 DOI: 10.1093/Bioinformatics/13.2.191  0.658
1997 Karplus K, Sjolander K, Barrett C, Cline M, Haussler D, Hughey R, Holm L. Predicting Protein Structure Using Hidden Markov Models Proteins. 29: 134-139. DOI: 10.1002/(Sici)1097-0134(1997)1+<134::Aid-Prot18>3.0.Co;2-P  0.787
1996 Sjölander K, Karplus K, Brown M, Hughey R, Krogh A, Mian IS, Haussler D. Dirichlet mixtures: a method for improved detection of weak but significant protein sequence homology. Computer Applications in the Biosciences : Cabios. 12: 327-45. PMID 8902360 DOI: 10.1093/Bioinformatics/12.4.327  0.446
1996 Bucher P, Karplus K, Moeri N, Hofmann K. A flexible motif search technique based on generalized profiles Computers and Chemistry. 20: 3-23. PMID 8867839 DOI: 10.1016/S0097-8485(96)80003-9  0.397
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