Student Publications

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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.
Barrett CL, Herrgard MJ, Palsson B. "Decomposing complex reaction networks using random sampling, principal component analysis and basis rotation." BMC Syst Biol. 2009;3:30.
Barrera L, Benner C, Tao Y-C, Winzeler E, Zhou Y. "Leveraging two-way probe-level block design for identifying differential gene expression with high-density oligonucleotide arrays." BMC Bioinformatics. 2004;5:42.
Barrera LO, Li Z, Smith AD, et al. "Genome-wide mapping and analysis of active promoters in mouse embryonic stem cells and adult organs." Genome Res.. 2008;18(1):46-59.
Barrera LO, Ren B. "The transcriptional regulatory code of eukaryotic cells--insights from genome-wide analysis of chromatin organization and transcription factor binding." Curr. Opin. Cell Biol.. 2006;18(3):291-8.
Barken D, Wang C J, Kearns J, Cheong R, Hoffmann A, Levchenko A. "Comment on "Oscillations in NF-kappaB signaling control the dynamics of gene expression"." Science. 2005;308(5718):52; author reply 52.
Bansal V, Bashir A, Bafna V. "Evidence for large inversion polymorphisms in the human genome from HapMap data." Genome Res.. 2007;17(2):219-30.
Bandyopadhyay S, Kelley R, Krogan NJ, Ideker T. "Functional maps of protein complexes from quantitative genetic interaction data." PLoS Comput. Biol.. 2008;4(4):e1000065.
Bandyopadhyay S, Sharan R, Ideker T. "Systematic identification of functional orthologs based on protein network comparison." Genome Res.. 2006;16(3):428-35.
Bandyopadhyay S, Cookson MR. "Evolutionary and functional relationships within the DJ1 superfamily." BMC Evol. Biol.. 2004;4:6.
Bandyopadhyay S, Kelley R, Ideker T. "Discovering regulated networks during HIV-1 latency and reactivation." Pac Symp Biocomput. 2006:354-66.
Baker CW, Miller CR, Thaweethai T, et al. "Genetically Determined Variation in Lysis Time Variance in the Bacteriophage φX174." G3 (Bethesda). 2016;6(4):939-55.
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.
Arnold ES, Ling S-C, Huelga SC, et al. "ALS-linked TDP-43 mutations produce aberrant RNA splicing and adult-onset motor neuron disease without aggregation or loss of nuclear TDP-43." Proc. Natl. Acad. Sci. U.S.A.. 2013;110(8):E736-45.
Appleton E, Tao J, Haddock T, Densmore D. "Interactive assembly algorithms for molecular cloning." Nat. Methods. 2014;11(6):657-62.
Applebee KM, Herrgård MJ, Palsson BØ. "Impact of individual mutations on increased fitness in adaptively evolved strains of Escherichia coli." J. Bacteriol.. 2008;190(14):5087-94.
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.
Allison KA, Kaikkonen MU, Gaasterland T, Glass CK. "Vespucci: a system for building annotated databases of nascent transcripts." Nucleic Acids Res.. 2013.
Allen TE, Price ND, Joyce AR, Palsson BØ. "Long-range periodic patterns in microbial genomes indicate significant multi-scale chromosomal organization." PLoS Comput. Biol.. 2006;2(1):e2.
Allen TE, Herrgård MJ, Liu M, et al. "Genome-scale analysis of the uses of the Escherichia coli genome: model-driven analysis of heterogeneous data sets." J. Bacteriol.. 2003;185(21):6392-9.
Albuquerque CP, Smolka MB, Payne SH, Bafna V, Eng J, Zhou H. "A multidimensional chromatography technology for in-depth phosphoproteome analysis." Mol. Cell Proteomics. 2008;7(7):1389-96.
Aktulga H M, Kontoyiannis I, Lyznik AL, Szpankowski L, Grama AY, Szpankowski W. "Identifying statistical dependence in genomic sequences via mutual information estimates." EURASIP J Bioinform Syst Biol. 2007:14741.
Abdulla M-H, Ruelas DS, Wolff B, et al. "Drug discovery for schistosomiasis: hit and lead compounds identified in a library of known drugs by medium-throughput phenotypic screening." PLoS Negl Trop Dis. 2009;3(7):e478.