Student Publications

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Gupta N, Benhamida J, Bhargava V, et al. "Comparative proteogenomics: combining mass spectrometry and comparative genomics to analyze multiple genomes." Genome Res.. 2008;18(7):1133-42.
Gupta N, Tanner S, Jaitly N, et al. "Whole proteome analysis of post-translational modifications: applications of mass-spectrometry for proteogenomic annotation." Genome Res.. 2007;17(9):1362-77.
Gupta N, Pevzner PA. "False discovery rates of protein identifications: a strike against the two-peptide rule." J. Proteome Res.. 2009;8(9):4173-81.
Grubisic I, Shokhirev MN, Orzechowski M, Miyashita O, Tama F. "Biased coarse-grained molecular dynamics simulation approach for flexible fitting of X-ray structure into cryo electron microscopy maps." J. Struct. Biol.. 2010;169(1):95-105.
Gross AM, Ideker T. "Molecular networks in context." Nat. Biotechnol.. 2015;33(7):720-1.
Gross AM, Kreisberg JF, Ideker T. "Analysis of Matched Tumor and Normal Profiles Reveals Common Transcriptional and Epigenetic Signals Shared across Cancer Types." PLoS ONE. 2015;10(11):e0142618.
Gross AM, Jaeger PA, Kreisberg JF, et al. "Methylome-wide Analysis of Chronic HIV Infection Reveals Five-Year Increase in Biological Age and Epigenetic Targeting of HLA." Mol. Cell. 2016;62(2):157-68.
Gross AM, Orosco RK, Shen JP, et al. "Multi-tiered genomic analysis of head and neck cancer ties TP53 mutation to 3p loss." Nat. Genet.. 2014;46(9):939-43.
Gross AM, Cohen EEW. "Towards a personalized treatment of head and neck cancer." Am Soc Clin Oncol Educ Book. 2015;35:28-32.
Gianella S, Delport W, Pacold ME, et al. "Detection of minority resistance during early HIV-1 infection: natural variation and spurious detection rather than transmission and evolution of multiple viral variants." J. Virol.. 2011;85(16):8359-67.
Gianchandani EP, Papin JA, Price ND, Joyce AR, Palsson BO. "Matrix formalism to describe functional states of transcriptional regulatory systems." PLoS Comput. Biol.. 2006;2(8):e101.
Gianchandani EP, Brautigan DL, Papin JA. "Systems analyses characterize integrated functions of biochemical networks." Trends Biochem. Sci.. 2006;31(5):284-91.
Gendron JM, Pruneda-Paz JL, Doherty CJ, Gross AM, S Kang E, Kay SA. "Arabidopsis circadian clock protein, TOC1, is a DNA-binding transcription factor." Proc. Natl. Acad. Sci. U.S.A.. 2012;109(8):3167-72.
Gay SC, Shah MB, Talakad JC, et al. "Crystal structure of a cytochrome P450 2B6 genetic variant in complex with the inhibitor 4-(4-chlorophenyl)imidazole at 2.0-A resolution." Mol. Pharmacol.. 2010;77(4):529-38.
Garcia-Bassets I, Kwon Y-S, Telese F, et al. "Histone methylation-dependent mechanisms impose ligand dependency for gene activation by nuclear receptors." Cell. 2007;128(3):505-18.