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Protein Design by Sampling an Undirected Graphical Model of Residue Constraints
Found in: IEEE/ACM Transactions on Computational Biology and Bioinformatics
By John Thomas, Naren Ramakrishnan, Chris Bailey-Kellogg
Issue Date:July 2009
pp. 506-516
This paper develops an approach for designing protein variants by sampling sequences that satisfy residue constraints encoded in an undirected probabilistic graphical model. Due to evolutionary pressures on proteins to maintain structure and function, the ...
 
Graphical Models of Residue Coupling in Protein Families
Found in: IEEE/ACM Transactions on Computational Biology and Bioinformatics
By John Thomas, Naren Ramakrishnan, Chris Bailey-Kellogg
Issue Date:April 2008
pp. 183-197
Many statistical measures and algorithmic techniqueshave been proposed for studying residue coupling inprotein families. Generally speaking, two residue positions areconsidered coupled if, in the sequence record, some of theiramino acid type combinations a...
 
Sampling Strategies for Mining in Data-Scarce Domains
Found in: Computing in Science and Engineering
By Naren Ramakrishnan, Chris Bailey-Kellogg
Issue Date:July 2002
pp. 31-43
<p>Data mining has traditionally focused on the task of drawing inferences from large data sets. However, many scientific and engineering domains, such as fluid dynamics and aircraft design, are characterized by scarce data, due to the expense and co...
 
Improved Multiple Sequence Alignments Using Coupled Pattern Mining
Found in: IEEE/ACM Transactions on Computational Biology and Bioinformatics
By K.S.M.Tozammel Hossain,Debprakash Patnaik,Srivatsan Laxman,Prateek Jain,Chris Bailey-Kellogg,Naren Ramakrishnan
Issue Date:September 2013
pp. 1098-1112
We present alignment refinement by mining coupled residues (ARMiCoRe), a novel approach to a classical bioinformatics problem, viz., multiple sequence alignment (MSA) of gene and protein sequences. Aligning multiple biological sequences is a key step in el...
 
Service Learning in Software Engineering and Maintenance
Found in: Software Maintenance, IEEE International Conference on
By Panagiotis K. Linos, Chris Bailey-Kellogg
Issue Date:September 2003
pp. 336
No summary available.
   
Improved Multiple Sequence Alignments Using Coupled Pattern Mining
Found in: IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
By Chris Bailey-Kellogg, Debprakash Patnaik, K. S. M. Tozammel Hossain, Naren Ramakrishnan, Prateek Jain, Srivatsan Laxman
Issue Date:September 2013
pp. 1098-1112
We present alignment refinement by mining coupled residues (ARMiCoRe), a novel approach to a classical bioinformatics problem, viz., multiple sequence alignment (MSA) of gene and protein sequences. Aligning multiple biological sequences is a key step in el...
     
Using physicochemical properties of amino acids to induce graphical models of residue couplings
Found in: Proceedings of the Tenth International Workshop on Data Mining in Bioinformatics (BIOKDD '11)
By Alan M. Friedman, Chris Bailey-Kellogg, K. S. M. Tozammel Hossain, Michael J. Bradley, Naren Ramakrishnan, Nathan Baker
Issue Date:August 2011
pp. 1-10
Residue coupling in protein families is an important indicator for structural and functional conservation. Two residues are coupled if changes of amino acid at one residue location are correlated with changes in the other. Many algorithmic techniques have ...
     
Protein Design by Sampling an Undirected Graphical Model of Residue Constraints
Found in: IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
By Chris Bailey-Kellogg, John Thomas, John Thomas, John Thomas, Naren Ramakrishnan, Naren Ramakrishnan, Naren Ramakrishnan
Issue Date:July 2009
pp. 506-516
This paper develops an approach for designing protein variants by sampling sequences that satisfy residue constraints encoded in an undirected probabilistic graphical model. Due to evolutionary pressures on proteins to maintain structure and function, the ...
     
Graphical models of residue coupling in protein families
Found in: Proceedings of the 5th international workshop on Bioinformatics (BIOKDD '05)
By Chris Bailey-Kellogg, John Thomas, Naren Ramakrishnan
Issue Date:August 2005
pp. 12-20
Identifying residue coupling relationships within a protein family can provide important insights into the family's evolutionary record, and has significant applications in analyzing and optimizing sequence-structure-function relationships. We present the ...
     
The NOESY jigsaw: automated protein secondary structure and main-chain assignment from sparse, unassigned NMR data
Found in: Proceedings of the fourth annual international conference on Computational molecular biology (RECOMB '00)
By Alik Widge, Bruce Randall Donald, Chris Bailey-Kellogg, John H. Bushweller, John J. Kelley, Marcelo J. Berardi
Issue Date:April 2000
pp. 33-44
High-throughput, data-directed computational protocols for Structural Genomics (or Proteomics) are required in order to evaluate the protein products of genes for structure and function at rates comparable to current gene-sequencing technology. This paper ...
     
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