Ye, Ping
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Research Interests
Bioinformatic, computational, and experimental analyses of cellular responses to pathogens and stimuli

Research in our lab focuses on mechanisms by which cells respond to external perturbations. We are interested in examining host immune responses, microbial virulence factors, and dynamic interplay between host cells and pathogens. We are also interested in defining the structure and dynamics of functional pathways when cells experience environmental stimuli, such as DNA damaging agents and temperature change. Our ultimate goal is to create an integrated digital image of how cells operate under external perturbations over multiple temporal and spatial scales. We aim to achieve this goal through high-throughput and low-throughput data acquisition and integration, followed by computational prediction and experimental validation. We apply a two-pronged computational approach, bioinformatics data mining and mechanistic mathematical modeling. Our main experimental systems include unicellular eukaryote yeast and mammalian cell culture.

Publications
Stuart LM, Boulais J, Charriere GM, Hennessy EJ, Brunet S, Jutras I, Goyette G, Rondeau C, Letarte S, Huang H, Ye P, Morales F, Kocks C, Bader JS, Desjardins M, Ezekowitz RA. A systems biology analysis of the Drosophila phagosome. Nature, 2007, 445, 95-101.

An W, Han JS, Wheelan SJ, Davis ES, Coombes CE, Ye P, Triplett C, Boeke JD. Active retrotransposition by a synthetic L1 element in Mice. PNAS, 2006, 103, 18662-18667.

Pan X, Ye P, Yuan DS, Wang X, Bader JS, Boeke JD. A DNA integrity network in the yeast Saccharomyces cerevisiae. Cell, 2006, 124, 1069-1081.

Ooi SL, Pan X, Peyser BD, Ye P, Meluh PB, Yuan DS, Irizarry RA, Bader JS, Spencer FA, Boeke JD. Global synthetic-lethality analysis and yeast functional profiling. Trends in Genetics, 2006, 22(1), 56-63.

Ye P, Peyser BD, Spencer FA, Bader JS. Commensurate distances and similar motifs in genetic congruence and protein interaction networks in yeast. BMC Bioinformatics, 2005, 6:270.

Ye P, Peyser BD, Pan X, Boeke JD, Spencer FA, Bader JS. Gene function prediction from congruent synthetic lethal interactions in yeast. Molecular Systems Biology (Nature Publishing Group), 2005, 1:2005.0026.

Qi Y, Ye P, Bader JS. Genetic interaction motif finding by expectation maximization – a novel statistical framework for inferring gene modules from synthetic lethality. BMC Bioinformatics, 2005, 6:288.

Ye P, Kazanjian P, Kunkel SL, Kirschner DE. Lack of good correlation of serum CC-chemokine levels with HIV-1 disease stage and response to treatment. Journal of Laboratory and Clinical Medicine, 2004 143(5), 310-319.

Ye P, Kirschner DE, Kourtis AP. The thymus during HIV disease: role in pathogenesis and in immune recovery. Current HIV Research, 2004, 2(2), 177-183.

Ye P, Kourtis AP, Kirschner DE. Reconstitution of thymic function in HIV-1 patients treated with highly active anti-retroviral therapy. Clinical Immunology, 2003, 106(2), 95-105.

Ye P, Kourtis AP, Kirschner DE. The effects of different HIV type I strains on human thymic function. AIDS Research and Human Retroviruses, 2002, 18(17), 1239-1251.

Ye P, Kirschner DE. Measuring emigration of human thymocytes by T cell receptor excision circles. Critical Reviews in Immunology, 2002, 22(5&6), 483-497.