Publications

67 Publications
Applied Filters: First Letter Of Last Name: P Reset

P

1.
Pane A, Jiang P, Zhao DY, Singh M, Schüpbach T. The Cutoff protein regulates piRNA cluster expression and piRNA production in the Drosophila germline. EMBO J. 2011;30(22):4601–15.
1.
Papatsenko D, Goltsev Y, Levine M. Organization of developmental enhancers in the Drosophila embryo. Nucleic Acids Res. 2009;37(17):5665–77.
1.
Papatsenko D, Levine MS. Dual regulation by the Hunchback gradient in the Drosophila embryo. Proc Natl Acad Sci U S A. 2008;105(8):2901–6.
1.
Papatsenko D, Kislyuk A, Levine M, Dubchak I. Conservation patterns in different functional sequence categories of divergent Drosophila species. Genomics. 2006;88(4):431–42.
1.
Papatsenko D, Levine M. Computational identification of regulatory DNAs underlying animal development. Nat Methods. 2005;2(7):529–34.
1.
Papazyan R, Sun Z, Kim YH, Titchenell PM, Hill DA, Lu W, Damle M, Wan M, Zhang Y, Briggs ER, Rabinowitz JD, Lazar MA. Physiological Suppression of Lipotoxic Liver Damage by Complementary Actions of HDAC3 and SCAP/SREBP. Cell Metab. 2016;24(6):863–874. PMCID: PMC5159233
1.
Park CY, Krishnan A, Zhu Q, Wong AK, Lee Y- suk, Troyanskaya OG. Tissue-aware data integration approach for the inference of pathway interactions in metazoan organisms. Bioinformatics. 2014;.
1.
Park CY, Hess DC, Huttenhower C, Troyanskaya OG. Simultaneous genome-wide inference of physical, genetic, regulatory, and functional pathway components. PLoS Comput Biol. 2010;6(11):e1001009.
1.
Park CY, Wong AK, Greene CS, Rowland J, Guan Y, Bongo LA, Burdine R, Troyanskaya OG. Functional knowledge transfer for high-accuracy prediction of under-studied biological processes. PLoS Comput Biol. 2013;9(3):e1002957.
1.
Park JO, Rubin SA, Xu Y-F, Amador-Noguez D, Fan J, Shlomi T, Rabinowitz JD. Metabolite concentrations, fluxes and free energies imply efficient enzyme usage. Nat Chem Biol. 2016;.
1.
Park JO, Tanner LB, Wei MH, Khana DB, Jacobson TB, Zhang Z, Rubin SA, Li SH-J, Higgins MB, Stevenson DM, Amador-Noguez D, Rabinowitz JD. Near-equilibrium glycolysis supports metabolic homeostasis and energy yield. Nat Chem Biol. 2019;15(10):1001–1008. PMID: 31548693
1.
1.
Parsch J, Novozhilov S, Saminadin-Peter SS, Wong KM, Andolfatto P. On the utility of short intron sequences as a reference for the detection of positive and negative selection in Drosophila. Mol Biol Evol. 2010;27(6):1226–34.
1.
Pavan WJ, Mac S, Cheng M, Tilghman SM. Quantitative trait loci that modify the severity of spotting in piebald mice. Genome Res. 1995;5(1):29–41.
1.
Pavan WJ, Tilghman SM. Piebald lethal (sl) acts early to disrupt the development of neural crest-derived melanocytes. Proc Natl Acad Sci U S A. 1994;91(15):7159–63.
1.
Pavlova NN, Hui S, Ghergurovich JM, Fan J, Intlekofer AM, White RM, Rabinowitz JD, Thompson CB, Zhang J. As Extracellular Glutamine Levels Decline, Asparagine Becomes an Essential Amino Acid. Cell Metab. 2018;27(2):428–438.e5. PMCID: PMC5803449
1.
Peifer M, Sweeton D, Casey M, Wieschaus E. wingless signal and Zeste-white 3 kinase trigger opposing changes in the intracellular distribution of Armadillo. Development. 1994;120(2):369–80.
1.
Peifer M, Rauskolb C, Williams M, Riggleman B, Wieschaus E. The segment polarity gene armadillo interacts with the wingless signaling pathway in both embryonic and adult pattern formation. Development. 1991;111(4):1029–43.
1.
Peifer M, Orsulic S, Sweeton D, Wieschaus E. A role for the Drosophila segment polarity gene armadillo in cell adhesion and cytoskeletal integrity during oogenesis. Development. 1993;118(4):1191–207.
1.
Pelham RJ, Rodgers L, Hall I, Lucito R, Nguyen KCQ, Navin N, Hicks J, Mu D, Powers S, Wigler M, Botstein D. Identification of alterations in DNA copy number in host stromal cells during tumor progression. Proc Natl Acad Sci U S A. 2006;103(52):19848–53.
1.
Peña-Castillo L, Tasan M, Myers CL, Lee H, Joshi T, Zhang C, Guan Y, Leone M, Pagnani A, Kim WK, Krumpelman C, Tian W, Obozinski G, Qi Y, Mostafavi S, Lin GN, Berriz GF, Gibbons FD, Lanckriet G, Qiu J, Grant C, Barutcuoglu Z, Hill DP, Warde-Farley D, Grouios C, Ray D, Blake JA, Deng M, Jordan MI, Noble WS, Morris Q, Klein-Seetharaman J, Bar-Joseph Z, Chen T, Sun F, Troyanskaya OG, Marcotte EM, Xu D, Hughes TR, Roth FP. A critical assessment of Mus musculus gene function prediction using integrated genomic evidence. Genome Biol. 2008;9 Suppl 1:S2.
1.
Perez A, Pritykin Y, Vidigal J, Chhangawala S, Zamparo L, Leslie C, Ventura A. GuideScan software for improved single and paired CRISPR guide RNA design. Nature biotechnology. 2017;35(4):347–349. PMCID: PMC5607865
1.
Perry MW, Boettiger AN, Bothma JP, Levine M. Shadow enhancers foster robustness of Drosophila gastrulation. Curr Biol. 2010;20(17):1562–7.
1.
Perry MW, Bothma JP, Luu RD, Levine M. Precision of hunchback expression in the Drosophila embryo. Curr Biol. 2012;22(23):2247–52.
1.
Perry MW, Boettiger AN, Levine M. Multiple enhancers ensure precision of gap gene-expression patterns in the Drosophila embryo. Proc Natl Acad Sci U S A. 2011;108(33):13570–5.
1.
Persikov A V, Wetzel JL, Rowland EF, Oakes BL, Xu DJ, Singh M, Noyes MB. A systematic survey of the Cys2His2 zinc finger DNA-binding landscape. Nucleic Acids Res. 2015;43(3):1965–84.
1.
Persikov A V, Osada R, Singh M. Predicting DNA recognition by Cys2His2 zinc finger proteins. Bioinformatics. 2009;25(1):22–9.
1.
Persikov A V, Singh M. An expanded binding model for Cys2His2 zinc finger protein-DNA interfaces. Phys Biol. 2011;8(3):035010.
1.
Persikov A V, Rowland EF, Oakes BL, Singh M, Noyes MB. Deep sequencing of large library selections allows computational discovery of diverse sets of zinc fingers that bind common targets. Nucleic Acids Res. 2014;42(3):1497–508.
1.
Persikov A V, Singh M. De novo prediction of DNA-binding specificities for Cys2His2 zinc finger proteins. Nucleic Acids Res. 2014;42(1):97–108.
1.
Peterson CN, Levchenko I, Rabinowitz JD, Baker TA, Silhavy TJ. RpoS proteolysis is controlled directly by ATP levels in Escherichia coli. Genes Dev. 2012;26(6):548–53.
1.
Petkova M, Tkačik G, Bialek W, Wieschaus E, Gregor T. Optimal Decoding of Cellular Identities in a Genetic Network. Cell. 2019;176(4):844–855.e15. PMCID: PMC6526179
1.
Petkova MD, Little SC, Liu F, Gregor T. Maternal origins of developmental reproducibility. Curr Biol. 2014;24(11):1283–8.
1.
Petti AA, Crutchfield CA, Rabinowitz JD, Botstein D. Survival of starving yeast is correlated with oxidative stress response and nonrespiratory mitochondrial function. Proc Natl Acad Sci U S A. 2011;108(45):E1089–98.
1.
Petti AA, McIsaac S, Ho-Shing O, Bussemaker HJ, Botstein D. Combinatorial control of diverse metabolic and physiological functions by transcriptional regulators of the yeast sulfur assimilation pathway. Mol Biol Cell. 2012;23(15):3008–24.
1.
Pfeifer K, Leighton PA, Tilghman SM. The structural H19 gene is required for transgene imprinting. Proc Natl Acad Sci U S A. 1996;93(24):13876–83.
1.
Pfeifer K, Tilghman SM. Allele-specific gene expression in mammals: the curious case of the imprinted RNAs. Genes Dev. 1994;8(16):1867–74.
1.
Piazza M, Feng X-J, Rabinowitz JD, Rabitz H. Diverse metabolic model parameters generate similar methionine cycle dynamics. J Theor Biol. 2008;251(4):628–39.
1.
1.
Pilizota T, Shaevitz JW. Fast, multiphase volume adaptation to hyperosmotic shock by Escherichia coli. PLoS One. 2012;7(4):e35205.
1.
Poillet-Perez L, Xie X, Zhan L, Yang Y, Sharp DW, Hu ZS, Su X, Maganti A, Jiang C, Lu W, Zheng H, Bosenberg MW, Mehnert JM, Guo JY, Lattime E, Rabinowitz JD, White E. Autophagy maintains tumour growth through circulating arginine. Nature. 2018;563(7732):569–573. PMCID: PMC6287937
1.
Pollack JR, Sørlie T, Perou CM, Rees CA, Jeffrey SS, Lonning PE, Tibshirani R, Botstein D, Børresen-Dale A-L, Brown PO. Microarray analysis reveals a major direct role of DNA copy number alteration in the transcriptional program of human breast tumors. Proc Natl Acad Sci U S A. 2002;99(20):12963–8.
1.
Pollack JR, van de Rijn M, Botstein D. Challenges in developing a molecular characterization of cancer. Semin Oncol. 2002;29(3):280–5.