Publications

As an independent investigator

Newkirk SJ, Lee S, Grandi FC, Gaysinskaya V, Rosser JM, Vanden Berg N, Hogarth CA, Marchetto MCN, Muotri AR, Griswold MD, Ye P, Bortvin A, Gage FH, Boeke JD, An W. Intact piRNA pathway prevents L1 mobilization in male meiosis. Proc Natl Acad Sci U S A, 2017.

Blais EM, Rawls KD, Dougherty BV, Li ZI, Kolling GL, Ye P, Wallqvist A, Papin JA. Reconciled rat and human metabolic networks for comparative toxicogenomics and biomarker predictions. Nat Commun, 2017, 8:14250.

Chastain M, Zhou Q, Shiva O, Whitmore L, Jia P, Dai X, Huang C, Fadri-Moskwik M, Ye P, Chai W. Human CST Facilitates Genome-wide RAD51 Recruitment to GC-Rich Repetitive Sequences in Response to Replication Stress. Cell Reports, 2016, 16, 1300-1314.

Wallqvist A, Fang X, Tewari SG, Ye P, Reifman J. Metabolic host responses to malarial infection during the intraerythrocytic developmental cycle. BMC Systems Biology, 2016, 10:58.

Whitmore LS, Ye P. Dissecting Germ Cell Metabolism through Network Modeling. PLoS One, 2015, 10(9):e0137607.

Grandi FC, Rosser JM, Newkirk SJ, Yin J, Jiang X, Xing Z, Whitmore L, Bashir S, Ivics Z, Izsvák Z, Ye P, Yu YE, An W. Retrotransposition creates sloping shores: a graded influence of hypomethylated CpG islands on flanking CpG sites. Genome research, 2015, 25(8):1135-46.

Ray D, Pitts PB, Hogarth CA, Whitmore LS, Griswold MD, Ye P. Computer simulations of the mouse spermatogenic cycle. Biology Open, 2014, BIO20149068.

Liu C, Morishima M, Jiang X, Yu T, Meng K, Ray D, Pao A, Ye P, Parmacek MS, Yu YE. Engineered chromosome-based genetic mapping establishes a 3.7-Mb critical genomic region for Down syndrome-associated heart defects in mice. Human Genetics, 2014, 133(6): 743-53.

Zhang L, Meng K, Jiang X, Liu C, Pao A, Belichenko PV, Kleschevnikov AM, Josselyn S, Liang P, Ye P, Mobley WC, Yu YE. Human chromosome 21 orthologous region on mouse chromosome 17 is a major determinant for Down syndrome-related developmental cognitive deficits. Human Molecular Genetics, 2014, 23(3): 578-89.

Ray D, Su Y, Ye P. Dynamic modeling of yeast meiotic initiation. BMC Systems Biology, 2013, 7:37.

Ray D, Ye P. Characterization of the metabolic requirements in yeast meiosis. PLOS ONE, 2013, 8(5):e63707.

Li Y, Ray D, Ye P. Identification of germ cell-specific genes in mammalian meiotic prophase. BMC Bioinformatics, 2013, 14:72.

Ray D, Hogarth CA, Evans EB, An W, Griswold MD, Ye P. Experimental validation of Ankrd17 and Anapc10, two novel meiotic genes predicted by computational models in mice. Biology of Reproduction, 2012, 86(4):102.

Lockwood S, Krishnamoorthy B, Ye P. Neighborhood properties are important determinants of temperature sensitive mutations. PLOS ONE, 2011, 6(12): e28507.

Su Y, Li Y, Ye P. Mammalian meiosis is more conserved by sex than by species: conserved co-expression networks of meiotic prophase. Reproduction, 2011, 142(5): 675-687.

Lawson C, Gieske M, Murdoch B, Ye P, Li Y, Hassold T, Hunt PA. Gene expression in the fetal mouse ovary is altered by exposure to low doses of bisphenol A. Biology of Reproduction, 2011, 84(1): 79-86.

Li Y, Lam KS, Dasgupta N, Ye P. A yeast's eye view of mammalian reproduction: cross-species gene co-expression in meiotic prophase. BMC Systems Biology, 2010, 4:125.

Zheng P, Griswold MD, Hassold TJ, Hunt PA, Small CL, Ye P. Predicting meiotic pathways in human fetal oogenesis. Biology of Reproduction, 2010, 82(3), 543-551. (Commentary: Cohen PE, Holloway JK. Predicting gene networks in human oocyte meiosis. Biology of Reproduction, 2010, 82(3), 469-72.)

During postdoctoral training

Pan X, Yuan D, Ye P, Bader JS, Boeke JD. Response to Dr Stephen Cooper's 'On the use of metaphor to understand, explain, or rationalize redundant genes in yeast'. FEMS Yeast Research, 2008, 8(3), 349-350.

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, 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.

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.

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.

During PhD training

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 (Commentary: Grossman Z. Mathematical modeling of thymopoiesis in HIV infection: real data, virtual data, and data interpretation. Clinical Immunology, 2003, 107(3), 137-139).

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.

Ye P, Kirschner DE. Reevaluation of T cell receptor excision circles as a measure of human recent thymic emigrants. Journal of Immunology, 2002, 168(10), 4968-4979.