Student Publications

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Rentas S, Holzapfel NT, Belew MS, et al. "Musashi-2 attenuates AHR signalling to expand human haematopoietic stem cells." Nature. 2016;532(7600):508-11.
Wu J, Okamura D, Li M, et al. "An alternative pluripotent state confers interspecies chimaeric competency." Nature. 2015;521(7552):316-21.
Singh G, Pratt G, Yeo GW, Moore MJ. "The Clothes Make the mRNA: Past and Present Trends in mRNP Fashion." Annu. Rev. Biochem.. 2015;84:325-54.
O'Brien EJ, Palsson BO. "Computing the functional proteome: recent progress and future prospects for genome-scale models." Curr. Opin. Biotechnol.. 2015;34:125-34.
Gross AM, Ideker T. "Molecular networks in context." Nat. Biotechnol.. 2015;33(7):720-1.
Hung T, Pratt GA, Sundararaman B, et al. "The Ro60 autoantigen binds endogenous retroelements and regulates inflammatory gene expression." Science. 2015;350(6259):455-9.
Lee SR, Pratt GA, Martinez FJ, Yeo GW, Lykke-Andersen J. "Target Discrimination in Nonsense-Mediated mRNA Decay Requires Upf1 ATPase Activity." Mol. Cell. 2015;59(3):413-25.
O'Brien EJ, Monk JM, Palsson BO. "Using Genome-scale Models to Predict Biological Capabilities." Cell. 2015;161(5):971-87.
Lin MS, Cherny JJ, Fournier CT, Roth SJ, Krizanc D, Weir MP. "Assessment of MS/MS search algorithms with parent-protein profiling." J. Proteome Res.. 2014;13(4):1823-32.
Anandasabapathy N, Feder R, Mollah S, et al. "Classical Flt3L-dependent dendritic cells control immunity to protein vaccine." J. Exp. Med.. 2014;211(9):1875-91.
Buganim Y, Markoulaki S, van Wietmarschen N, et al. "The developmental potential of iPSCs is greatly influenced by reprogramming factor selection." Cell Stem Cell. 2014;15(3):295-309.
Hauff SJ, Raju SC, Orosco RK, et al. "Matrix-metalloproteinases in head and neck carcinoma-cancer genome atlas analysis and fluorescence imaging in mice." Otolaryngol Head Neck Surg. 2014;151(4):612-8.
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.
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.
Xie W, Schultz MD, Lister R, et al. "Epigenomic analysis of multilineage differentiation of human embryonic stem cells." Cell. 2013;153(5):1134-48.
Lister R, Mukamel EA, Nery JR, et al. "Global epigenomic reconfiguration during mammalian brain development." Science. 2013;341(6146):1237905.
Margeridon-Thermet S, Svarovskaia ES, Babrzadeh F, et al. "Low-level persistence of drug resistance mutations in hepatitis B virus-infected subjects with a past history of Lamivudine treatment." Antimicrob. Agents Chemother.. 2013;57(1):343-9.
Nakatsuji T, Chiang H-I, Jiang SB, Nagarajan H, Zengler K, Gallo RL. "The microbiome extends to subepidermal compartments of normal skin." Nat Commun. 2013;4:1431.
Hofree M, Shen JP, Carter H, Gross A, Ideker T. "Network-based stratification of tumor mutations." Nat. Methods. 2013;10(11):1108-15.
Feupe S F, Frias PF, Mednick SC, McDevitt EA, Heintzman ND. "Nocturnal continuous glucose and sleep stage data in adults with type 1 diabetes in real-world conditions." J Diabetes Sci Technol. 2013;7(5):1337-45.
Lovci MT, Ghanem D, Marr H, et al. "Rbfox proteins regulate alternative mRNA splicing through evolutionarily conserved RNA bridges." Nat. Struct. Mol. Biol.. 2013;20(12):1434-42.
Wagner GA, Pacold ME, Vigil E, et al. "Using ultradeep pyrosequencing to study HIV-1 coreceptor usage in primary and dual infection." J. Infect. Dis.. 2013;208(2):271-4.
DeBoever C, Reid EG, Smith EN, et al. "Whole transcriptome sequencing enables discovery and analysis of viruses in archived primary central nervous system lymphomas." PLoS ONE. 2013;8(9):e73956.
Zhou D, Udpa N, Ronen R, et al. "Whole-genome sequencing uncovers the genetic basis of chronic mountain sickness in Andean highlanders." Am. J. Hum. Genet.. 2013;93(3):452-62.