Student Publications

Export 400 results:
Castellana NE, Shen Z, He Y, et al. "An Automated Proteogenomic Method Utilizes Mass Spectrometry to Reveal Novel Genes in Zea mays." Mol. Cell Proteomics. 2013.
Hu M, Deng K, Qin Z, et al. "Bayesian inference of spatial organizations of chromosomes." PLoS Comput. Biol.. 2013;9(1):e1002893.
Nagarajan H, Embree M, Rotaru A-E, et al. "Characterization and modelling of interspecies electron transfer mechanisms and microbial community dynamics of a syntrophic association." Nat Commun. 2013;4:2809.
Nagarajan H, Sahin M, Nogales J, et al. "Characterizing acetogenic metabolism using a genome-scale metabolic reconstruction of Clostridium ljungdahlii." Microb. Cell Fact.. 2013;12(1):118.
Qiu Y, Nagarajan H, Embree M, et al. "Characterizing the interplay between multiple levels of organization within bacterial sigma factor regulatory networks." Nat Commun. 2013;4:1755.
Loriaux P M, Tesler G, Hoffmann A. "Characterizing the relationship between steady state and response using analytical expressions for the steady states of mass action models." PLoS Comput. Biol.. 2013;9(2):e1002901.
Ebrahim A, Lerman JA, Palsson BO, Hyduke DR. "COBRApy: COnstraints-Based Reconstruction and Analysis for Python." BMC Syst Biol. 2013;7:74.
Babrzadeh F, Varghese V, Pacold M, et al. "Collinearity of protease mutations in HIV-1 samples with high-level protease inhibitor class resistance." J. Antimicrob. Chemother.. 2013;68(2):414-8.
Behar M, Barken D, Werner SL, Hoffmann A. "The dynamics of signaling as a pharmacological target." Cell. 2013;155(2):448-61.
Chaillon A, Wagner GA, Hepler LN, et al. "Dynamics of Viral Evolution and Neutralizing Antibody Response after HIV-1 Superinfection." J. Virol.. 2013;87(23):12737-44.
Heinz S, Romanoski CE, Benner C, et al. "Effect of natural genetic variation on enhancer selection and function." Nature. 2013.
Schmitz RJ, He Y, Valdés-López O, et al. "Epigenome-wide inheritance of cytosine methylation variants in a recombinant inbred population." Genome Res.. 2013;23(10):1663-74.
Xie W, Schultz MD, Lister R, et al. "Epigenomic analysis of multilineage differentiation of human embryonic stem cells." Cell. 2013;153(5):1134-48.
Hua Z, Pool JE, Schmitz RJ, et al. "Epigenomic programming contributes to the genomic drift evolution of the F-Box protein superfamily in Arabidopsis." Proc. Natl. Acad. Sci. U.S.A.. 2013;110(42):16927-32.
Feldman KE, Loriaux PM, Saito M, et al. "Ex vivo innate immune cytokine signature of enhanced risk of relapsing brucellosis." PLoS Negl Trop Dis. 2013;7(9):e2424.
Shokhirev M N, Hoffmann A. "FlowMax: A Computational Tool for Maximum Likelihood Deconvolution of CFSE Time Courses." PLoS ONE. 2013;8(6):e67620.
Latif H, Lerman JA, Portnoy VA, et al. "The genome organization of Thermotoga maritima reflects its lifestyle." PLoS Genet.. 2013;9(4):e1003485.
O'Brien EJ, Lerman JA, Chang RL, Hyduke DR, Palsson BØ. "Genome-scale models of metabolism and gene expression extend and refine growth phenotype prediction." Mol. Syst. Biol.. 2013;9:693.
Shen L, Wu H, Diep D, et al. "Genome-wide analysis reveals TET- and TDG-dependent 5-methylcytosine oxidation dynamics." Cell. 2013;153(3):692-706.
Lewis NE, Liu X, Li Y, et al. "Genomic landscapes of Chinese hamster ovary cell lines as revealed by the Cricetulus griseus draft genome." Nat. Biotechnol.. 2013;31(8):759-65.
Lister R, Mukamel EA, Nery JR, et al. "Global epigenomic reconfiguration during mammalian brain development." Science. 2013;341(6146):1237905.
Jin F, Li Y, Dixon JR, et al. "A high-resolution map of the three-dimensional chromatin interactome in human cells." Nature. 2013;503(7475):290-4.
Hightower GK, May SJ, Pérez-Santiago J, et al. "HIV-1 clade B pol evolution following primary infection." PLoS ONE. 2013;8(6):e68188.
Wagner GA, Pacold ME, Kosakovsky Pond SL, et al. "Incidence and Prevalence of Intrasubtype HIV-1 Dual Infection in At-Risk Men in the United States." J. Infect. Dis.. 2013.
Ronen R, Udpa N, Halperin E, Bafna V. "Learning natural selection from the site frequency spectrum." Genetics. 2013;195(1):181-93.