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Items: 42

1.

Fallacy of the Unique Genome: Sequence Diversity within Single Helicobacter pylori Strains.

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.

MBio. 2017 Feb 21;8(1). pii: e02321-16. doi: 10.1128/mBio.02321-16.

2.

Analysis of nanopore data using hidden Markov models.

Schreiber J, Karplus K.

Bioinformatics. 2015 Jun 15;31(12):1897-903. doi: 10.1093/bioinformatics/btv046. Epub 2015 Feb 3.

3.

Error rates for nanopore discrimination among cytosine, methylcytosine, and hydroxymethylcytosine along individual DNA strands.

Schreiber J, Wescoe ZL, Abu-Shumays R, Vivian JT, Baatar B, Karplus K, Akeson M.

Proc Natl Acad Sci U S A. 2013 Nov 19;110(47):18910-5. doi: 10.1073/pnas.1310615110. Epub 2013 Oct 28.

4.

Complete genome sequence of Pyrobaculum oguniense.

Bernick DL, Karplus K, Lui LM, Coker JK, Murphy JN, Chan PP, Cozen AE, Lowe TM.

Stand Genomic Sci. 2012 Jul 30;6(3):336-45. doi: 10.4056/sigs.2645906. Epub 2012 Jul 20.

5.

Automated forward and reverse ratcheting of DNA in a nanopore at 5-Å precision.

Cherf GM, Lieberman KR, Rashid H, Lam CE, Karplus K, Akeson M.

Nat Biotechnol. 2012 Feb 14;30(4):344-8. doi: 10.1038/nbt.2147.

6.

Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega.

Sievers F, Wilm A, Dineen D, Gibson TJ, Karplus K, Li W, Lopez R, McWilliam H, Remmert M, Söding J, Thompson JD, Higgins DG.

Mol Syst Biol. 2011 Oct 11;7:539. doi: 10.1038/msb.2011.75.

7.

Identification of a chemoreceptor zinc-binding domain common to cytoplasmic bacterial chemoreceptors.

Draper J, Karplus K, Ottemann KM.

J Bacteriol. 2011 Sep;193(17):4338-45. doi: 10.1128/JB.05140-11. Epub 2011 Jul 1.

8.

Identification of prokaryotic small proteins using a comparative genomic approach.

Samayoa J, Yildiz FH, Karplus K.

Bioinformatics. 2011 Jul 1;27(13):1765-71. doi: 10.1093/bioinformatics/btr275. Epub 2011 May 5.

9.

Improving protein secondary structure prediction using a simple k-mer model.

Madera M, Calmus R, Thiltgen G, Karplus K, Gough J.

Bioinformatics. 2010 Mar 1;26(5):596-602. doi: 10.1093/bioinformatics/btq020. Epub 2010 Feb 3.

10.

Improving physical realism, stereochemistry, and side-chain accuracy in homology modeling: Four approaches that performed well in CASP8.

Krieger E, Joo K, Lee J, Lee J, Raman S, Thompson J, Tyka M, Baker D, Karplus K.

Proteins. 2009;77 Suppl 9:114-22. doi: 10.1002/prot.22570.

11.

Applying Undertaker to quality assessment.

Archie JG, Paluszewski M, Karplus K.

Proteins. 2009;77 Suppl 9:191-5. doi: 10.1002/prot.22508.

12.

SAM-T08, HMM-based protein structure prediction.

Karplus K.

Nucleic Acids Res. 2009 Jul;37(Web Server issue):W492-7. doi: 10.1093/nar/gkp403. Epub 2009 May 29.

13.

Pokefind: a novel topological filter for use with protein structure prediction.

Khatib F, Rohl CA, Karplus K.

Bioinformatics. 2009 Jun 15;25(12):i281-8. doi: 10.1093/bioinformatics/btp198.

14.

Applying undertaker cost functions to model quality assessment.

Archie J, Karplus K.

Proteins. 2009 May 15;75(3):550-5. doi: 10.1002/prot.22288.

15.

Model quality assessment using distance constraints from alignments.

Paluszewski M, Karplus K.

Proteins. 2009 May 15;75(3):540-9. doi: 10.1002/prot.22262.

16.

PREDICT-2ND: a tool for generalized protein local structure prediction.

Katzman S, Barrett C, Thiltgen G, Karchin R, Karplus K.

Bioinformatics. 2008 Nov 1;24(21):2453-9. doi: 10.1093/bioinformatics/btn438. Epub 2008 Aug 30.

17.

Contact prediction using mutual information and neural nets.

Shackelford G, Karplus K.

Proteins. 2007;69 Suppl 8:159-64.

PMID:
17932918
19.
20.

SAM-T04: what is new in protein-structure prediction for CASP6.

Karplus K, Katzman S, Shackleford G, Koeva M, Draper J, Barnes B, Soriano M, Hughey R.

Proteins. 2005;61 Suppl 7:135-42.

PMID:
16187355
21.

Calibrating E-values for hidden Markov models using reverse-sequence null models.

Karplus K, Karchin R, Shackelford G, Hughey R.

Bioinformatics. 2005 Nov 15;21(22):4107-15. Epub 2005 Aug 25.

PMID:
16123115
22.

Evaluation of local structure alphabets based on residue burial.

Karchin R, Cline M, Karplus K.

Proteins. 2004 May 15;55(3):508-18.

PMID:
15103615
23.

SPrCY: comparison of structural predictions in the Saccharomyces cerevisiae genome.

Dolinsky TJ, Burgers PM, Karplus K, Baker NA.

Bioinformatics. 2004 Sep 22;20(14):2312-4. Epub 2004 Apr 1.

PMID:
15059824
24.

Combining local-structure, fold-recognition, and new fold methods for protein structure prediction.

Karplus K, Karchin R, Draper J, Casper J, Mandel-Gutfreund Y, Diekhans M, Hughey R.

Proteins. 2003;53 Suppl 6:491-6.

PMID:
14579338
25.

Hidden Markov models that use predicted local structure for fold recognition: alphabets of backbone geometry.

Karchin R, Cline M, Mandel-Gutfreund Y, Karplus K.

Proteins. 2003 Jun 1;51(4):504-14.

PMID:
12784210
26.

Information-theoretic dissection of pairwise contact potentials.

Cline MS, Karplus K, Lathrop RH, Smith TF, Rogers RG Jr, Haussler D.

Proteins. 2002 Oct 1;49(1):7-14.

PMID:
12211011
27.

Predicting reliable regions in protein sequence alignments.

Cline M, Hughey R, Karplus K.

Bioinformatics. 2002 Feb;18(2):306-14.

PMID:
11847078
28.

Classifying G-protein coupled receptors with support vector machines.

Karchin R, Karplus K, Haussler D.

Bioinformatics. 2002 Jan;18(1):147-59.

PMID:
11836223
29.

What is the value added by human intervention in protein structure prediction?

Karplus K, Karchin R, Barrett C, Tu S, Cline M, Diekhans M, Grate L, Casper J, Hughey R.

Proteins. 2001;Suppl 5:86-91.

PMID:
11835485
30.
31.
32.

Nucleotide excision repair "a legacy of creativity".

Cleaver JE, Karplus K, Kashani-Sabet M, Limoli CL.

Mutat Res. 2001 Feb 25;485(1):23-36. Review.

PMID:
11341991
33.
34.

CAFASP-1: critical assessment of fully automated structure prediction methods.

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.

Proteins. 1999;Suppl 3:209-17.

PMID:
10526371
35.

Predicting protein structure using only sequence information.

Karplus K, Barrett C, Cline M, Diekhans M, Grate L, Hughey R.

Proteins. 1999;Suppl 3:121-5.

PMID:
10526360
36.

Hidden Markov models for detecting remote protein homologies.

Karplus K, Barrett C, Hughey R.

Bioinformatics. 1998;14(10):846-56.

PMID:
9927713
37.

Sequence comparisons using multiple sequences detect three times as many remote homologues as pairwise methods.

Park J, Karplus K, Barrett C, Hughey R, Haussler D, Hubbard T, Chothia C.

J Mol Biol. 1998 Dec 11;284(4):1201-10.

PMID:
9837738
38.

Scoring hidden Markov models.

Barrett C, Hughey R, Karplus K.

Comput Appl Biosci. 1997 Apr;13(2):191-9.

PMID:
9146967
39.

Predicting protein structure using hidden Markov models.

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

Proteins. 1997;Suppl 1:134-9.

PMID:
9485505
40.

Dirichlet mixtures: a method for improved detection of weak but significant protein sequence homology.

Sjölander K, Karplus K, Brown M, Hughey R, Krogh A, Mian IS, Haussler D.

Comput Appl Biosci. 1996 Aug;12(4):327-45.

PMID:
8902360
41.

A flexible motif search technique based on generalized profiles.

Bucher P, Karplus K, Moeri N, Hofmann K.

Comput Chem. 1996 Mar;20(1):3-23.

PMID:
8867839
42.

Evaluating regularizers for estimating distributions of amino acids.

Karplus K.

Proc Int Conf Intell Syst Mol Biol. 1995;3:188-96.

PMID:
7584436

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