Student Publications

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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.
Ross MK, Wei W, Ohno-Machado L. ""Big data" and the electronic health record." Yearb Med Inform. 2014;9(1):97-104.
Prlić A, Yates A, Bliven SE, et al. "BioJava: an open-source framework for bioinformatics in 2012." Bioinformatics. 2012;28(20):2693-5.
Hsiao A, Subramaniam S. "Bivariate microarray analysis: statistical interpretation of two-channel functional genomics data." Syst Synth Biol. 2008;2(3-4):95-104.
Bechtel JM, Rajesh P, Ilikchyan I, et al. "Calculation of splicing potential from the Alternative Splicing Mutation Database." BMC Res Notes. 2008;1:4.
Thiele I, Price ND, Vo TD, Palsson BØ. "Candidate metabolic network states in human mitochondria. Impact of diabetes, ischemia, and diet." J. Biol. Chem.. 2005;280(12):11683-95.
Price ND, Thiele I, Palsson BØ. "Candidate states of Helicobacter pylori's genome-scale metabolic network upon application of "loop law" thermodynamic constraints." Biophys. J.. 2006;90(11):3919-28.
Taheri-Araghi S, Bradde S, Sauls JT, et al. "Cell-Size Control and Homeostasis in Bacteria." Curr. Biol.. 2014.
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.
Chen J, Swamidass JS, Dou Y, Bruand J, Baldi P. "ChemDB: a public database of small molecules and related chemoinformatics resources." Bioinformatics. 2005;21(22):4133-9.
Shen JPaul, Srivas R, Gross A, et al. "Chemogenetic profiling identifies RAD17 as synthetically lethal with checkpoint kinase inhibition." Oncotarget. 2015;6(34):35755-69.
Devaraj NK, Miller GP, Ebina W, et al. "Chemoselective covalent coupling of oligonucleotide probes to self-assembled monolayers." J. Am. Chem. Soc.. 2005;127(24):8600-1.
Zheng M, Barrera LO, Ren B, Wu Y. "ChIP-chip: data, model, and analysis." Biometrics. 2007;63(3):787-96.
Kim T H, Barrera LO, Ren B. "ChIP-chip for genome-wide analysis of protein binding in mammalian cells." Curr Protoc Mol Biol. 2007;Chapter 21:Unit 21.13.
Hon G, Ren B, Wang W. "ChromaSig: a probabilistic approach to finding common chromatin signatures in the human genome." PLoS Comput. Biol.. 2008;4(10):e1000201.
Bliven S, Prlić A. "Circular permutation in proteins." PLoS Comput. Biol.. 2012;8(3):e1002445.
Hirose S, Payne SH, Loomis WF. "cis-Acting site controlling bidirectional transcription at the growth-differentiation transition in Dictyostelium discoideum." Eukaryotic Cell. 2006;5(7):1104-10.
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.
Pacold ME, Pond S KL, Wagner GA, et al. "Clinical, virologic, and immunologic correlates of HIV-1 intraclade B dual infection among men who have sex with men." AIDS. 2012;26(2):157-65.
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.
Frank AM, Bandeira N, Shen Z, et al. "Clustering millions of tandem mass spectra." J. Proteome Res.. 2008;7(1):113-22.
Ebrahim A, Lerman JA, Palsson BO, Hyduke DR. "COBRApy: COnstraints-Based Reconstruction and Analysis for Python." BMC Syst Biol. 2013;7:74.