Next generation software for functional trend analysis (2009)
Berriz, Gabriel F., Beaver, John E., Cenik, Can, Tasan, Murat, Roth, Frederick P.
Summary: FuncAssociate is a web application that discovers properties enriched in lists of genes or proteins that emerge from large-scale experimentation. Here we describe an updated application with...
Peña-Castillo, Lourdes, Tasan, Murat, Myers, Chad L, Lee, Hyunju, Joshi, Trupti, Zhang, Chao, ...
Abstract Background: Several years after sequencing the human genome and the mouse genome, much remains to be discovered about the functions of most human and mouse genes. Computational prediction of...
808 RESEARCH ARTICLE Global Mapping of the Yeast Genetic Interaction Network (2008)
Amy Hin, Yan Tong, Guillaume Lesage, Gary D. Bader, Huiming Ding, Hong Xu, ...
A genetic interaction network containing �1000 genes and �4000 interactions was mapped by crossing mutations in 132 different query genes into a set of �4700 viable gene yeast deletion mutants...
The Synergizer service for translating gene, protein and other biological identifiers (2008)
Berriz, Gabriel F., Roth, Frederick P.
Summary: The Synergizer is a database and web service that provides translations of biological database identifiers. It is accessible both programmatically and interactively. Availability: The...
Han, Jing-Dong J., Bertin, Nicolas, Hao, Tong, Goldberg, Debra S., Berriz, Gabriel F., Zhang, Lan V., ...
In apparently scale-free protein-protein interaction networks, or 'interactome' networks, most proteins interact with few partners, whereas a small but significant proportion of proteins, the 'hubs',...
Characterizing gene sets with FuncAssociate (2003)
Summary: FuncAssociate is a web-based tool to help researchers use Gene Ontology attributes to characterize large sets of genes derived from experiment. Distinguishing features of FuncAssociate...
Characterizing gene sets with FuncAssociate (2003)
Berriz, Gabriel F., King, Oliver D., Bryant, Barbara, Sander, Chris, Roth, Frederick P.
Summary: FuncAssociate is a web-based tool to help researchers use Gene Ontology attributes to characterize large sets of genes derived from experiment. Distinguishing features of FuncAssociate...
Cooperativity and Stability in a Langevin Model of Protein Folding (1996)
Berriz, Gabriel F., Gutin, Alexander M., Shakhnovich, Eugene I.
We present two simplified models of protein dynamics based on Langevin's equation of motion in a viscous medium. We explore the effect of the potential energy function's symmetry on the kinetics and...
A critical assessment of Mus musculus gene function prediction using integrated genomic evidence
Peña-Castillo, Lourdes, Tasan, Murat, Myers, Chad L, Lee, Hyunju, Joshi, Trupti, Zhang, Chao, ...
The Synergizer service for translating gene, protein and other biological identifiers
Berriz, Gabriel F., Roth, Frederick P.
Summary: The Synergizer is a database and web service that provides translations of biological database identifiers. It is accessible both programmatically and interactively.