Student Publications

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Butler DM, Pacold ME, Jordan PS, Richman DD, Smith DM. "The efficiency of single genome amplification and sequencing is improved by quantitation and use of a bioinformatics tool." J. Virol. Methods. 2009;162(1-2):280-3.
Bushman FD, Malani N, Fernandes J, et al. "Host cell factors in HIV replication: meta-analysis of genome-wide studies." PLoS Pathog.. 2009;5(5):e1000437.
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.
Brunk E, Mih N, Monk J, et al. "Systems biology of the structural proteome." BMC Syst Biol. 2016;10:26.
Brinza D, Schultz M, Tesler G, Bafna V. "RAPID detection of gene-gene interactions in genome-wide association studies." Bioinformatics. 2010;26(22):2856-62.
Briedis KM, Starr A, Bourne PE. "Analysis of the human kinome using methods including fold recognition reveals two novel kinases." PLoS ONE. 2008;3(2):e1597.
Brandler WM, Antaki D, Gujral M, et al. "Frequency and Complexity of De Novo Structural Mutation in Autism." Am. J. Hum. Genet.. 2016;98(4):667-79.
Bliven S, Prlić A. "Circular permutation in proteins." PLoS Comput. Biol.. 2012;8(3):e1002445.
Bhargava V, Head SR, Ordoukhanian P, Mercola M, Subramaniam S. "Technical Variations in Low-Input RNA-seq Methodologies." Sci Rep. 2014;4:3678.
Bhargava V, Ko P, Willems E, Mercola M, Subramaniam S. "Quantitative transcriptomics using designed primer-based amplification." Sci Rep. 2013;3:1740.
Beyer A, Bandyopadhyay S, Ideker T. "Integrating physical and genetic maps: from genomes to interaction networks." Nat. Rev. Genet.. 2007;8(9):699-710.
Berry RE, Shokhireva T K, Filippov I, Shokhirev MN, Zhang H, Walker AF. "Effect of the N-terminus on heme cavity structure, ligand equilibrium, rate constants, and reduction potentials of nitrophorin 2 from Rhodnius prolixus." Biochemistry. 2007;46(23):6830-43.
Berry RE, Shokhirev MN, Ho AYW, et al. "Effect of mutation of carboxyl side-chain amino acids near the heme on the midpoint potentials and ligand binding constants of nitrophorin 2 and its NO, histamine, and imidazole complexes." J. Am. Chem. Soc.. 2009;131(6):2313-27.
Bernard A, Lubbers LS, Tanis KQ, et al. "Transcriptional architecture of the primate neocortex." Neuron. 2012;73(6):1083-99.
Behar M, Barken D, Werner SL, Hoffmann A. "The dynamics of signaling as a pharmacological target." Cell. 2013;155(2):448-61.
Becker SA, Feist AM, Mo ML, Hannum G, Palsson BØ, Herrgard MJ. "Quantitative prediction of cellular metabolism with constraint-based models: the COBRA Toolbox." Nat Protoc. 2007;2(3):727-38.
Bechtel JM, Rajesh P, Ilikchyan I, et al. "Calculation of splicing potential from the Alternative Splicing Mutation Database." BMC Res Notes. 2008;1:4.
Bechtel JM, Rajesh P, Ilikchyan I, et al. "The Alternative Splicing Mutation Database: a hub for investigations of alternative splicing using mutational evidence." BMC Res Notes. 2008;1:3.
Bechtel JM, Wittenschlaeger T, Dwyer T, et al. "Genomic mid-range inhomogeneity correlates with an abundance of RNA secondary structures." BMC Genomics. 2008;9:284.
Bean GJ, Ideker T. "Differential analysis of high-throughput quantitative genetic interaction data." Genome Biol.. 2012;13(12):R123.
Bean GJ, Jaeger PA, Bahr S, Ideker T. "Development of ultra-high-density screening tools for microbial "omics"." PLoS ONE. 2014;9(1):e85177.
Baycin-Hizal D, Tabb DL, Chaerkady R, et al. "Proteomic analysis of Chinese hamster ovary cells." J. Proteome Res.. 2012;11(11):5265-76.
Bashir A, Volik S, Collins C, Bafna V, Raphael BJ. "Evaluation of paired-end sequencing strategies for detection of genome rearrangements in cancer." PLoS Comput. Biol.. 2008;4(4):e1000051.
Bashir A, Ye C, Price AL, Bafna V. "Orthologous repeats and mammalian phylogenetic inference." Genome Res.. 2005;15(7):998-1006.
Bashir A, Liu Y-T, Raphael BJ, Carson D, Bafna V. "Optimization of primer design for the detection of variable genomic lesions in cancer." Bioinformatics. 2007;23(21):2807-15.