Publications by authors named "Kevin Karplus"

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Altering under-represented DNA sequences elevates bacterial transformation efficiency.
Shuai Hu, Stefani Giacopazzi, Ryan Modlin, Kevin Karplus, David L Bernick

mBio· December 2023

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Fallacy of the Unique Genome: Sequence Diversity within Single Strains.
Jenny L Draper, Lori M Hansen, David L Bernick, Samar Abedrabbo, Jason G Underwood, Kevin Karplus

mBio· February 2017

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Analysis of nanopore data using hidden Markov models.
Jacob Schreiber, Kevin Karplus

Bioinformatics· June 2015

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Error rates for nanopore discrimination among cytosine, methylcytosine, and hydroxymethylcytosine along individual DNA strands.
Jacob Schreiber, Zachary L Wescoe, Robin Abu-Shumays, John T Vivian, Baldandorj Baatar, Kevin Karplus

Proc Natl Acad Sci U S A· November 2013

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Complete genome sequence of Pyrobaculum oguniense.
David L Bernick, Kevin Karplus, Lauren M Lui, Joanna K C Coker, Julie N Murphy

Stand Genomic Sci· July 2012

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Automated forward and reverse ratcheting of DNA in a nanopore at 5-Å precision.
Gerald M Cherf, Kate R Lieberman, Hytham Rashid, Christopher E Lam, Kevin Karplus

Nat Biotechnol· February 2012

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Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega.
Fabian Sievers, Andreas Wilm, David Dineen, Toby J Gibson, Kevin Karplus

Mol Syst Biol· October 2011

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Identification of a chemoreceptor zinc-binding domain common to cytoplasmic bacterial chemoreceptors.
Jenny Draper, Kevin Karplus, Karen M Ottemann

J Bacteriol· September 2011

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Identification of prokaryotic small proteins using a comparative genomic approach.
Josue Samayoa, Fitnat H Yildiz, Kevin Karplus

Bioinformatics· July 2011

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Improving protein secondary structure prediction using a simple k-mer model.
Martin Madera, Ryan Calmus, Grant Thiltgen, Kevin Karplus, Julian Gough

Bioinformatics· March 2010

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Applying Undertaker to quality assessment.
John G Archie, Martin Paluszewski, Kevin Karplus

Proteins· January 2010

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Improving physical realism, stereochemistry, and side-chain accuracy in homology modeling: Four approaches that performed well in CASP8.
Elmar Krieger, Keehyoung Joo, Jinwoo Lee, Jooyoung Lee, Srivatsan Raman, Kevin Karplus

Proteins· January 2010

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SAM-T08, HMM-based protein structure prediction.
Kevin Karplus

Nucleic Acids Res· July 2009

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Pokefind: a novel topological filter for use with protein structure prediction.
Firas Khatib, Carol A Rohl, Kevin Karplus

Bioinformatics· June 2009

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Model quality assessment using distance constraints from alignments.
Martin Paluszewski, Kevin Karplus

Proteins· May 2009

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Applying undertaker cost functions to model quality assessment.
John Archie, Kevin Karplus

Proteins· May 2009

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PREDICT-2ND: a tool for generalized protein local structure prediction.
Sol Katzman, Christian Barrett, Grant Thiltgen, Rachel Karchin, Kevin Karplus

Bioinformatics· November 2008

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Contact prediction using mutual information and neural nets.
George Shackelford, Kevin Karplus

Proteins· January 2008

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SAM-T04: what is new in protein-structure prediction for CASP6.
Kevin Karplus, Sol Katzman, George Shackleford, Martina Koeva, Jenny Draper

Proteins· May 2006

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Identification and characterization of RbmA, a novel protein required for the development of rugose colony morphology and biofilm structure in Vibrio cholerae.
Jiunn C N Fong, Kevin Karplus, Gary K Schoolnik, Fitnat H Yildiz

J Bacteriol· February 2006

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Methods of translating NMR proton distances into their corresponding heavy atom distances for protein structure prediction with limited experimental data.
Oscar Hur, Kevin Karplus

Protein Eng Des Sel· December 2005

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Calibrating E-values for hidden Markov models using reverse-sequence null models.
Kevin Karplus, Rachel Karchin, George Shackelford, Richard Hughey

Bioinformatics· November 2005

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Evaluation of local structure alphabets based on residue burial.
Rachel Karchin, Melissa Cline, Kevin Karplus

Proteins· May 2004

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Combining local-structure, fold-recognition, and new fold methods for protein structure prediction.
Kevin Karplus, Rachel Karchin, Jenny Draper, Jonathan Casper, Yael Mandel-Gutfreund

Proteins· January 2004

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Hidden Markov models that use predicted local structure for fold recognition: alphabets of backbone geometry.
Rachel Karchin, Melissa Cline, Yael Mandel-Gutfreund, Kevin Karplus

Proteins· June 2003

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