Exploring the human genome with functional maps (2009)
Huttenhower, Curtis, Haley, Erin M., Hibbs, Matthew A., Dumeaux, Vanessa, Barrett, Daniel R., Coller, Hilary A., ...
Human genomic data of many types are readily available, but the complexity and scale of human molecular biology make it difficult to integrate this body of data, understand it from a systems level,...
Hilary A. Coller, Joshua J. Forman, Aster Legesse-Miller
The recent revelation that there are small, noncoding RNAs that regulate the expression of many other genes has led to an exciting, emerging body of literature defining the biological role for these...
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...
Nearest Neighbor Networks: clustering expression data based on (2007)
Bmc Bioinformatics, Curtis Huttenhower, Avi I Flamholz, Jessica N L, Sauhard Sahi, Chad L Myers, ...
Software
Dynamics of the Cellular Metabolome during Human Cytomegalovirus Infection (2006)
Joshua Munger, Sunil U. Bajad, Hilary A. Coller, Thomas Shenk, Joshua D. Rabinowitz
Viral replication requires energy and macromolecular precursors derived from the metabolic network of the host cell. Despite this reliance, the effect of viral infection on host cell metabolic...
A New Description of Cellular Quiescence (2006)
Hilary A. Coller, Liyun Sang, James M. Roberts
Transcriptional profiling of fibroblasts induced to exit the cell cycle by distinct signals reveals distinctions and commonalities in the pathways to cellular quiescence.
A New Description of Cellular Quiescence (2006)
Hilary A. Coller, Liyun Sang, James M. Roberts
Cellular quiescence, defined as reversible growth/proliferation arrest, is thought to represent a homogenous state induced by diverse anti-mitogenic signals. We used transcriptional profiling to...
Khrapko, Konstantin, Bodyak, Natalya, Thilly, William G., Van Orsouw, Nathalie J., Zhang, Xiaomin, Coller, Hilary A., ...
Coller, Hilary A., Grandori, Carla, Tamayo, Pablo, Colbert, Trent, Lander, Eric S., Eisenman, Robert N., ...
MYC affects normal and neoplastic cell proliferation by altering gene expression, but the precise pathways remain unclear. We used oligonucleotide microarray analysis of 6,416 genes and expressed...
Mitochondrial mutational spectra in human cells and tissues
Khrapko, Konstantin, Coller, Hilary A., André, Paulo C., Li, Xiao-Cheng, Hanekamp, John S., Thilly, William G.
We have found that human organs such as colon, lung, and muscle, as well as their derived tumors, share nearly all mitochondrial hotspot point mutations. Seventeen hotspots, primarily G → A and A...
Chemosensitivity prediction by transcriptional profiling
Staunton, Jane E., Slonim, Donna K., Coller, Hilary A., Tamayo, Pablo, Angelo, Michael J., Park, Johnny, ...
In an effort to develop a genomics-based approach to the prediction of drug response, we have developed an algorithm for classification of cell line chemosensitivity based on gene expression profiles...
A New Description of Cellular Quiescence
Coller, Hilary A, Sang, Liyun, Roberts, James M
Cellular quiescence, defined as reversible growth/proliferation arrest, is thought to represent a homogenous state induced by diverse anti-mitogenic signals. We used transcriptional profiling to...
Coller, Hilary A., Grandori, Carla, Tamayo, Pablo, Colbert, Trent, Lander, Eric S., Eisenman, Robert N., ...
MYC affects normal and neoplastic cell proliferation by altering gene expression, but the precise pathways remain unclear. We used oligonucleotide microarray analysis of 6,416 genes and expressed...
Mitochondrial mutational spectra in human cells and tissues
Khrapko, Konstantin, Coller, Hilary A., André, Paulo C., Li, Xiao-Cheng, Hanekamp, John S., Thilly, William G.
We have found that human organs such as colon, lung, and muscle, as well as their derived tumors, share nearly all mitochondrial hotspot point mutations. Seventeen hotspots, primarily G → A and A...
Chemosensitivity prediction by transcriptional profiling
Staunton, Jane E., Slonim, Donna K., Coller, Hilary A., Tamayo, Pablo, Angelo, Michael J., Park, Johnny, ...
In an effort to develop a genomics-based approach to the prediction of drug response, we have developed an algorithm for classification of cell line chemosensitivity based on gene expression profiles...
A New Description of Cellular Quiescence
Coller, Hilary A, Sang, Liyun, Roberts, James M
Cellular quiescence, defined as reversible growth/proliferation arrest, is thought to represent a homogenous state induced by diverse anti-mitogenic signals. We used transcriptional profiling to...
Dynamics of the Cellular Metabolome during Human Cytomegalovirus Infection
Munger, Joshua, Bajad, Sunil U, Coller, Hilary A, Shenk, Thomas, Rabinowitz, Joshua D
Viral replication requires energy and macromolecular precursors derived from the metabolic network of the host cell. Despite this reliance, the effect of viral infection on host cell metabolic...
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, ...
Coller, Hilary A, Forman, Joshua J, Legesse-Miller, Aster
The recent revelation that there are small, noncoding RNAs that regulate the expression of many other genes has led to an exciting, emerging body of literature defining the biological role for these...
Forman, Joshua J., Legesse-Miller, Aster, Coller, Hilary A.
Recognition sites for microRNAs (miRNAs) have been reported to be located in the 3′ untranslated regions of transcripts. In a computational screen for highly conserved motifs within coding regions,...
Goodpaster, Tracy, Legesse-Miller, Aster, Hameed, Meera R., Aisner, Seena C., Randolph-Habecker, Julie, Coller, Hilary A.
Fibroblasts are critical for tissue homeostasis, and their inappropriate proliferation and activation can result in common and debilitating conditions including fibrosis and cancer. We currently have...