- Global analysis of phase locking in gene expression during cell cycle: the potential in network modeling
Department of Physics, University of Alabama at Birmingham, Birmingham, Alabama 35294, USA
BMC Syst Biol 4:167. 2010
..Conversely, the synchrony information can be utilized to infer interaction. Increasing evidence suggests that frequency modulation is also common in transcription regulation...
- Accurate, precise modeling of cell proliferation kinetics from time-lapse imaging and automated image analysis of agar yeast culture arrays
Najaf A Shah
Department of Genetics, University of Alabama School of Medicine, Birmingham, Alabama 35294, USA
BMC Syst Biol 1:3. 2007
..To improve HTCP performance and advance capabilities for quantifying interactions, YeastXtract software was developed for automated analysis of cell array images...
- Buffering of deoxyribonucleotide pool homeostasis by threonine metabolism
John L Hartman
Department of Genetics, University of Alabama at Birmingham, Birmingham, AL 35294, USA
Proc Natl Acad Sci U S A 104:11700-5. 2007
..Validation of these hypotheses substantiates the added benefit of quantitative phenotyping for identifying subtleties in gene interaction networks that modulate cellular phenotypes...
- Stringent mating-type-regulated auxotrophy increases the accuracy of systematic genetic interaction screens with Saccharomyces cerevisiae mutant arrays
Department of Genetics, University of Alabama, Birmingham, Alabama 35294, USA
Genetics 181:289-300. 2009
..Modifications engineered to reduce haploid MRA escape reduced false negative results in SGA-type analysis, resulting in >95% sensitivity for detecting gene-gene interactions...
- Recursive expectation-maximization clustering: a method for identifying buffering mechanisms composed of phenomic modules
Department of Genetics, University of Alabama at Birmingham, Birmingham, Alabama 35294, USA
Chaos 20:026103. 2010
..It facilitates identification of phenomic modules, which contribute to buffering mechanisms that underlie cellular homeostasis and the regulation of phenotypic expression...
- Defining genetic interaction
Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, 250 Longwood Avenue, Boston, MA 02115, USA
Proc Natl Acad Sci U S A 105:3461-6. 2008
..Additionally, we show that the Additive and Log definitions, each commonly used in population genetics, lead to differing conclusions related to the selective advantages of sexual reproduction...
- Systematic quantification of gene interactions by phenotypic array analysis
John L Hartman
Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue North, Seattle, WA 98109, USA
Genome Biol 5:R49. 2004
..The work provides an example of, and a general experimental framework for, quantitative analysis of gene interaction networks that buffer cell growth...