A5081325657- Fungal and yeast genetics research
- Cellular Mechanics and Interactions
- Cell Adhesion Molecules Research
- Bioinformatics and Genomic Networks
- Neutrophil, Myeloperoxidase and Oxidative Mechanisms
- Mitochondrial Function and Pathology
- RNA Research and Splicing
- Microtubule and mitosis dynamics
- Receptor Mechanisms and Signaling
- Genomics and Chromatin Dynamics
- Photoreceptor and optogenetics research
- CRISPR and Genetic Engineering
- Immune Response and Inflammation
- Prion Diseases and Protein Misfolding
- RNA and protein synthesis mechanisms
- Probiotics and Fermented Foods
- DNA Repair Mechanisms
- ATP Synthase and ATPases Research
- Ubiquitin and proteasome pathways
- Gene Regulatory Network Analysis
- Cellular transport and secretion
- Microbial Metabolic Engineering and Bioproduction
- Retinal Development and Disorders
- Advanced Fluorescence Microscopy Techniques
- Bacteriophages and microbial interactions
University of California, Davis
2016-2024
Stanford University
2009-2019
Center for Systems Biology
2016
QB3
2006-2009
Howard Hughes Medical Institute
2005-2009
University of California, San Francisco
2003-2009
University of Manchester
2009
University of California, San Diego
2008
National Cancer Institute
2008
Center for Cancer Research
2008
Communication between organelles is an important feature of all eukaryotic cells. To uncover components involved in mitochondria/endoplasmic reticulum (ER) junctions, we screened for mutants that could be complemented by a synthetic protein designed to artificially tether the two organelles. We identified Mmm1/Mdm10/Mdm12/Mdm34 complex as molecular ER and mitochondria. The tethering was composed proteins resident both With use genome-wide mapping genetic interactions, showed were...
Defining protein complexes is critical to virtually all aspects of cell biology. Two recent affinity purification/mass spectrometry studies in Saccharomyces cerevisiae have vastly increased the available interaction data. The practical utility such high throughput sets, however, substantially decreased by presence false positives. Here we created a novel probabilistic metric that takes advantage density these data, including both and absence individual associations, provide measure relative...
Protein folding in the endoplasmic reticulum is a complex process whose malfunction implicated disease and aging. By using cell's endogenous sensor (the unfolded protein response), we identified several hundred yeast genes with roles systematically characterized their functional interdependencies by measuring response levels double mutants. This strategy revealed multiple conserved factors critical for folding, including an intimate dependence on later secretory pathway, previously...
Abundant nonfibrillar oligomeric intermediates are a common feature of amyloid formation, and these oligomers, rather than the final fibers, have been suggested to be toxic species in some diseases. Whether such oligomers critical for fiber assembly or form an alternate, potentially separable pathway, however, remains unclear. Here we study polymerization amyloidogenic yeast prion protein Sup35. Rapid occurs absence observable intermediates, both targeted kinetic direct single-molecule...
To broadly explore mitochondrial structure and function as well the communication of mitochondria with other cellular pathways, we constructed a quantitative, high-density genetic interaction map (the MITO-MAP) in Saccharomyces cerevisiae. The MITO-MAP provides comprehensive view including insights into activity uncharacterized proteins functional connection between ER. also reveals large inner membrane–associated complex, which term MitOS for organizing structure, comprised Fcj1/Mitofilin,...
An epistasis map (E-MAP) was constructed in the fission yeast, Schizosaccharomyces pombe, by systematically measuring phenotypes associated with pairs of mutations. This high-density, quantitative genetic interaction focused on various aspects chromosome function, including transcription regulation and DNA repair/replication. The E-MAP uncovered a previously unidentified component RNA interference (RNAi) machinery (rsh1) linked RNAi pathway to several other biological processes. Comparison...
Abstract Recently, approaches have been developed for high-throughput identification of synthetic sick/lethal gene pairs. However, these are only a specific example the broader phenomenon epistasis, wherein presence one mutation modulates phenotype another. We present analysis techniques generating high-confidence quantitative epistasis scores from measurements made using genetic array and epistatic miniarray profile (E-MAP) technology, as well several tools higher-level resulting data that...
Article27 March 2007Open Access Backup without redundancy: genetic interactions reveal the cost of duplicate gene loss Jan Ihmels Corresponding Author Department Cellular and Molecular Pharmacology, University California, San Francisco, CA, USA The California Institute for Quantitative Biomedical Research, Howard Hughes Medical Institute, Search more papers by this author Sean R Collins Maya Schuldiner Nevan J Krogan Jonathan S Weissman Information 1,2,3, Collins1,2,3, Schuldiner1,2,3,...
Human neutrophils are central players in innate immunity, a major component of inflammatory responses, and leading model for cell motility chemotaxis. However, primary short-lived, limiting their experimental usefulness the laboratory. Thus, human myeloid lines have been characterized ability to undergo neutrophil-like differentiation vitro. The HL-60 line its PLB-985 sub-line commonly used neutrophil behavior, but how closely gene expression differentiated cells resembles that has remained unclear.