Rachel Karchin, Melissa Cline, Kevin Karplus
ABSTRACT Residue burial, which describes a protein residue’s exposure to solvent and neighboring atoms, is key to protein structure prediction, modeling, and analysis. We assessed 21 alphabets...
Rachel Karchin, Melissa Cline, Yael M, Kevin Karplus
ABSTRACT An important problem in computational biology is predicting the structure of the large number of putative proteins discovered by genome sequencing projects. Fold-recognition methods attempt...
Olivier Garcia, Cosmin Saveanu, Melissa Cline, Micheline Fromont-racine, Alain Jacquier, Benno Schwikowski, ...
Summary: We have implemented a graph layout algorithm that exposes Gene Ontology (GO) class structure on the network nodes. It can be used in conjunction with BiNGO plug-in to Cytoscape, which finds...
Predicting protein structure using hidden Markov models (2008)
Kevin Karplus Y, David Haussler, Kimmen Sjolander, Richard Hughey, Christian Barrett, Liisa Holm, ...
We discuss how methods based on hidden Markov models performed in the fold-recognition section of the CASP2 experiment. Hidden Markov models were built for a representative set of just over one...
STRUCTURE-BASED COMPARISON OF FOUR EUKARYOTIC GENOMES (2008)
Melissa Cline, Guoying Liu, Ann E. Loraine, Ronald Shigeta, Jill Cheng, Gangwu Mei, ...
The field of comparative genomics allows us to elucidate the molecular mechanisms necessary for the machinery of an organism by contrasting its genome against those of other organisms. In this paper,...
STRUCTURE-BASED COMPARISON OF FOUR EUKARYOTIC GENOMES (2007)
Melissa Cline, Guoying Liu, Ann E. Loraine, Ronald Shigeta, Jill Cheng, Gangwu Mei, ...
The field of comparative genomics allows us to elucidate the molecular mechanisms necessary for the machinery of an organism by contrasting its genome against those of other organisms. In this paper,...
Kevin Karplus, Christian Barrett, Christian Barrett, David Haussler, ...
den Markov model (HMM) for searching databases or aligning sequences. { Search results and alignments for searching PDB (or Swissprot or NR) with the HMM. SAM-T98 master web page...
Garcia, Olivier, Saveanu, Cosmin, Cline, Melissa, Fromont-Racine, Micheline, Jacquier, Alain, Schwikowski, Benno, ...
Summary: We have implemented a graph layout algorithm that exposes Gene Ontology (GO) class structure on the network nodes. It can be used in conjunction with BiNGO plug-in to Cytoscape, which finds...
Gene Ontology-based layout and coloring (2006)
Olivier Garcia, Cosmin Saveanu, Melissa Cline, Micheline Fromont-racine, Alain Jacquier, Benno Schwikowski, ...
doi:10.1093/bioinformatics/btl605 GOlorize: a Cytoscape plug-in for network visualization with
DOI: 10.1093/bioinformatics/btg1044 (2003)
Hui Wang, Earl Hubbell, Jing-shan Hu, Gangwu Mei, Melissa Cline, Gang Lu, ...
Vol. 19 Suppl. 1 2003, pages i315–i322
Rachel Karchin, Yael Mandel-gutfreund, Melissa Cline, Kevin Karplus
An important problem in computational biology is predicting the structure of the large number of pu-tative proteins discovered by genome sequencing projects. Fold-recognition methods attempt to solve...
NetAffx: Affymetrix probesets and annotations (2003)
Guoying Liu, Ann E. Loraine, Ron Shigeta, Melissa Cline, Jill Cheng, Venu Valmeekam, ...
NetAffx
GPCR-GRAPA-LIB--a refined library of hidden Markov Models for annotating GPCRs (2003)
Shigeta, Ron, Cline, Melissa, Liu, Guoying, Siani-Rose, Michael A.
Summary: GPCR-GRAPA-LIB is a library of HMMs describing G protein coupled receptor families. These families are initially defined by class of receptor ligand, with divergent families divided into...
NetAffx: Affymetrix probesets and annotations (2003)
Liu, Guoying, Loraine, Ann E., Shigeta, Ron, Cline, Melissa, Cheng, Jill, Valmeekam, Venu, ...
NetAffx (http://www.affymetrix.com) details and annotates probesets on Affymetrix GeneChip microarrays. These annotations include (i) static information specific to the probeset composition; (ii)...
Gene structure-based splice variant deconvolution using a microarry platform (2003)
Wang, Hui, Hubbell, Earl, Hu, Jing-shan, Mei, Gangwu, Cline, Melissa, Lu, Gang, ...
Motivation: Alternative splicing allows a single gene to generate multiple mRNAs, which can be translated into functionally and structurally diverse proteins. One gene can have multiple variants...
Predicting reliable regions in protein sequence alignments (2002)
Cline, Melissa, Hughey, Richard, Karplus, Kevin
Motivation: Protein sequence alignments have a myriad of applications in bioinformatics, including secondary and tertiary structure prediction, homology modeling, and phylogeny. Unfortunately, all...
Predicting Protein Structure using only Sequence Information (1999)
Kevin Karplus, Christian Barrett, Melissa Cline, Mark Diekhans, Leslie Grate, Richard Hughey
A prediction server using the SAM-T98 method dis-This paper presents results of blind predictions subcussed here is available on the World-Wide Web mitted to the CASP3 protein structure prediction...
Predicting Protein Structure using only Sequence Information (1999)
Kevin Karplus, Christian Barrett, Melissa Cline, Mark Diekhans, Leslie Grate, Richard Hughey
This paper presents results of blind predictions submitted to the CASP3 protein structure prediction experiment. We made predictions using the SAM-T98 method, an iterative hidden Markov model based...
Predicting protein structure using hidden Markov models (1997)
Kevin Karplus, Kimmen Sjölander, Christian Barrett, Melissa Cline, David Haussler, Richard Hughey, ...
We discuss how methods based on hidden Markov models performed in the fold-recognition section of the CASP2 experiment. Hidden Markov models were built for a representative set of just over one...
Predicting protein structure using hidden Markov models (1997)
Kevin Karplus Computer, Kevin Karplus, Kimmen Sjolander, Christian Barrett, Melissa Cline, David Haussler, ...
We discuss how methods based on hidden Markov models performed in the fold-recognition section of the CASP2 experiment. Hidden Markov models were built for a representative set of just over one...
Predicting protein structure using hidden Markov models (1997)
Kevin Karplus, Kimmen Sjölander, Christian Barrett, Melissa Cline, David Haussler, Richard Hughey, ...
We discuss how methods based on hidden Markov models performed in the fold-recognition section of the CASP2 experiment. Hidden Markov models were built for a representative set of just over one...
NetAffx: Affymetrix probesets and annotations
Liu, Guoying, Loraine, Ann E., Shigeta, Ron, Cline, Melissa, Cheng, Jill, Valmeekam, Venu, ...
NetAffx (http://www.affymetrix.com) details and annotates probesets on Affymetrix GeneChip microarrays. These annotations include (i) static information specific to the probeset composition; (ii)...
NetAffx: Affymetrix probesets and annotations
Liu, Guoying, Loraine, Ann E., Shigeta, Ron, Cline, Melissa, Cheng, Jill, Valmeekam, Venu, ...
NetAffx (http://www.affymetrix.com) details and annotates probesets on Affymetrix GeneChip microarrays. These annotations include (i) static information specific to the probeset composition; (ii)...