Predicting gene function in a hierarchical context with an ensemble of classifiers (2008)
Guan, Yuanfang, Myers, Chad L, Hess, David C, Barutcuoglu, Zafer, Caudy, Amy A, Troyanskaya, Olga G
Abstract Background: The wide availability of genome-scale data for several organisms has stimulated interest in computational approaches to gene function prediction. Diverse machine learning methods...
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...
Nearest Neighbor Networks: clustering expression data based on gene neighborhoods (2007)
Huttenhower, Curtis, Flamholz, Avi I, Landis, Jessica N, Sahi, Sauhard, Myers, Chad L, Olszewski, Kellen L, ...
Abstract Background The availability of microarrays measuring thousands of genes simultaneously across hundreds of biological conditions represents an opportunity to understand both individual...
Miller, Daniel L, Myers, Chad L, Rickards, Brenden, Coller, Hilary A, Flint, S Jane
Abstract Background Human adenoviruses, such as serotype 5 (Ad5), encode several proteins that can perturb cellular mechanisms that regulate cell cycle progression and apoptosis, as well as those...
GOLEM: an interactive graph-based gene-ontology navigation and analysis tool (2006)
Sealfon, Rachel SG, Hibbs, Matthew A, Huttenhower, Curtis, Myers, Chad L, Troyanskaya, Olga G
Abstract Background The Gene Ontology has become an extremely useful tool for the analysis of genomic data and structuring of biological knowledge. Several excellent software tools for navigating the...
Finding function: evaluation methods for functional genomic data (2006)
Myers, Chad L, Barrett, Daniel R, Hibbs, Matthew A, Huttenhower, Curtis, Troyanskaya, Olga G
Abstract Background Accurate evaluation of the quality of genomic or proteomic data and computational methods is vital to our ability to use them for formulating novel biological hypotheses and...
Reguly, Teresa, Breitkreutz, Ashton, Boucher, Lorrie, Breitkreutz, Bobby-Joe, Hon, Gary C, Myers, Chad L, ...
Abstract Background The study of complex biological networks and prediction of gene function has been enabled by high-throughput (HTP) methods for detection of genetic and protein interactions....
Discovery of biological networks from diverse functional genomic data (2005)
Myers, Chad L, Robson, Drew, Wible, Adam, Hibbs, Matthew A, Chiriac, Camelia, Theesfeld, Chandra L, ...
Abstract We have developed a general probabilistic system for query-based discovery of pathway-specific networks through integration of diverse genome-wide data. This framework was validated by...
Visualization-based discovery and analysis of genomic aberrations in microarray data (2005)
Myers, Chad L, Chen, Xing, Troyanskaya, Olga G
Abstract Background Chromosomal copy number changes (aneuploidies) play a key role in cancer progression and molecular evolution. These copy number changes can be studied using microarray-based...
A Recursive QR Approach to Adaptive Equalization of Time-Varying MIMO Channels (2005)
Kung, S. Y., Zhang, Xinying, Myers, Chad L.
This paper presents a novel adaptive equalization algorithm for time-varying MIMO systems with ISI channel conditions. The algorithm avoids channel estimation before equalization and leads to a...
Discovery of biological networks from diverse functional genomic data
Myers, Chad L, Robson, Drew, Wible, Adam, Hibbs, Matthew A, Chiriac, Camelia, Theesfeld, Chandra L, ...
BioPIXIE is a probabilistic system for query-based discovery of pathway-specific networks through integration of diverse genome-wide data.
Finding function: evaluation methods for functional genomic data
Myers, Chad L, Barrett, Daniel R, Hibbs, Matthew A, Huttenhower, Curtis, Troyanskaya, Olga G
Comprehensive curation and analysis of global interaction networks in Saccharomyces cerevisiae
Reguly, Teresa, Breitkreutz, Ashton, Boucher, Lorrie, Breitkreutz, Bobby-Joe, Hon, Gary C, Myers, Chad L, ...
GOLEM: an interactive graph-based gene-ontology navigation and analysis tool
Sealfon, Rachel SG, Hibbs, Matthew A, Huttenhower, Curtis, Myers, Chad L, Troyanskaya, Olga G
Discovery of biological networks from diverse functional genomic data
Myers, Chad L, Robson, Drew, Wible, Adam, Hibbs, Matthew A, Chiriac, Camelia, Theesfeld, Chandra L, ...
BioPIXIE is a probabilistic system for query-based discovery of pathway-specific networks through integration of diverse genome-wide data.
Finding function: evaluation methods for functional genomic data
Myers, Chad L, Barrett, Daniel R, Hibbs, Matthew A, Huttenhower, Curtis, Troyanskaya, Olga G
Comprehensive curation and analysis of global interaction networks in Saccharomyces cerevisiae
Reguly, Teresa, Breitkreutz, Ashton, Boucher, Lorrie, Breitkreutz, Bobby-Joe, Hon, Gary C, Myers, Chad L, ...
GOLEM: an interactive graph-based gene-ontology navigation and analysis tool
Sealfon, Rachel SG, Hibbs, Matthew A, Huttenhower, Curtis, Myers, Chad L, Troyanskaya, Olga G
Global analysis of gene function in yeast by quantitative phenotypic profiling
Brown, James A, Sherlock, Gavin, Myers, Chad L, Burrows, Nicola M, Deng, Changchun, Wu, H Irene, ...
We present a method for the global analysis of the function of genes in budding yeast based on hierarchical clustering of the quantitative sensitivity profiles of the 4756 strains with individual...
Miller, Daniel L, Myers, Chad L, Rickards, Brenden, Coller, Hilary A, Flint, S Jane
The effects of the adenovirus Ad5 on basic host cell programs, such as cell-cycle regulation, were studied in a microarray analysis of human fibroblasts. About 2,000 genes were up- or down-regulated...
Nearest Neighbor Networks: clustering expression data based on gene neighborhoods
Huttenhower, Curtis, Flamholz, Avi I, Landis, Jessica N, Sahi, Sauhard, Myers, Chad L, Olszewski, Kellen L, ...
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, ...
Predicting gene function in a hierarchical context with an ensemble of classifiers
Guan, Yuanfang, Myers, Chad L, Hess, David C, Barutcuoglu, Zafer, Caudy, Amy A, Troyanskaya, Olga G
A Genomewide Functional Network for the Laboratory Mouse
Guan, Yuanfang, Myers, Chad L., Lu, Rong, Lemischka, Ihor R., Bult, Carol J., Troyanskaya, Olga G.
Establishing a functional network is invaluable to our understanding of gene function, pathways, and systems-level properties of an organism and can be a powerful resource in directing targeted...