Identification of protein complexes by comparative analysis of yeast and bacterial protein interaction data
Hybridization and Post-Hybridization Washing
Visualization and Integration of Protein-Protein Interactions
Global analysis of host-pathogen interactions that regulate early-stage HIV-1 replication.
...Published in Cell
Human Immunodeficiency Viruses (HIV-1 and HIV-2) rely upon host-encoded proteins to facilitate their replication. Here, we combined genome-wide siRNA analyses with interrogation of human interactome databases to assemble a host-pathogen biochemical network containing 213 confirmed host cellular factors and 11 HIV-1-encoded proteins. Protein complex...
Multilineage priming of enhancer repertoires precedes commitment to the B and myeloid cell lineages in hematopoietic pro...
...Published in Immunity
Recent studies have documented genome-wide binding patterns of transcriptional regulators and their associated epigenetic marks in hematopoietic cell lineages. In order to determine how epigenetic marks are established and maintained during developmental progression, we have generated long-term cultures of hematopoietic progenitors by enforcing the...
Integrating physical and genetic maps: from genomes to interaction networks.
Published in Nature Reviews Genetics
Physical and genetic mapping data have become as important to network biology as they once were to the Human Genome Project. Integrating physical and genetic networks currently faces several challenges: increasing the coverage of each type of network; establishing methods to assemble individual interaction measurements into contiguous pathway model...
Decoupling epigenetic and genetic effects through systematic analysis of gene position.
Published in Cell Reports
Classic "position-effect" experiments repositioned genes near telomeres to demonstrate that the epigenetic landscape can dramatically alter gene expression. Here, we show that systematic gene knockout collections provide an exceptional resource for interrogating position effects, not only near telomeres but at every genetic locus. Because a single ...
Combined TP53 mutation/3p loss correlates with decreased radiosensitivity and increased matrix-metalloproteinase activit...
...Published in Oral Oncology
Differential network biology.
Published in Molecular Systems Biology
Protein and genetic interaction maps can reveal the overall physical and functional landscape of a biological system. To date, these interaction maps have typically been generated under a single condition, even though biological systems undergo differential change that is dependent on environment, tissue type, disease state, development or speciati...
Functional maps of protein complexes from quantitative genetic interaction data.
Published in PLoS Computational Biology
Recently, a number of advanced screening technologies have allowed for the comprehensive quantification of aggravating and alleviating genetic interactions among gene pairs. In parallel, TAP-MS studies (tandem affinity purification followed by mass spectroscopy) have been successful at identifying physical protein interactions that can indicate pro...
