Student Publications

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. PubMed PMC DOI

Bechtel JM, Rajesh P, Ilikchyan I, Deng Y, Mishra PK, Wang Q, Wu X, Afonin KA, Grose WE, Wang Y, Khuder S, Fedorov A. "The Alternative Splicing Mutation Database: a hub for investigations of alternative splicing using mutational evidence." BMC Res Notes. 2008;1:3. PubMed PMC DOI

Bechtel JM, Rajesh P, Ilikchyan I, Deng Y, Mishra PK, Wang Q, Wu X, Afonin KA, Grose WE, Wang Y, Khuder S, Fedorov A. "Calculation of splicing potential from the Alternative Splicing Mutation Database." BMC Res Notes. 2008;1:4. PubMed PMC DOI

Bechtel JM, Wittenschlaeger T, Dwyer T, Song J, Arunachalam S, Ramakrishnan SK, Shepard S, Fedorov A. "Genomic mid-range inhomogeneity correlates with an abundance of RNA secondary structures." BMC Genomics. 2008;9:284. PubMed PMC DOI

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. PubMed PMC DOI

Cachay ER, Frost SD, Poon AF, Looney D, Rostami SM, Pacold ME, Richman DD, Little SJ, Smith DM. "Herpes simplex virus type 2 acquisition during recent HIV infection does not influence plasma HIV levels." J Acquir Immune Defic Syndr. 2008;47(5):592-6. PubMed PMC DOI

Castellana NE, Payne SH, Shen Z, Stanke M, Bafna V, Briggs SP. "Discovery and revision of Arabidopsis genes by proteogenomics." Proc Natl Acad Sci U S A. 2008;105(52):21034-8. PubMed PMC DOI

Chaisson MJ, Pevzner PA. "Short read fragment assembly of bacterial genomes." Genome Res. 2008;18(2):324-30. PubMed PMC DOI

Chang MW, Belew RK, Carroll KS, Olson AJ, Goodsell DS. "Empirical entropic contributions in computational docking: evaluation in APS reductase complexes." J Comput Chem. 2008;29(11):1753-61. PubMed PMC DOI

Chen CY-C, Chen G-W, Chen WY-C. "Molecular Simulation of HER2/neu Degradation by HSP90 Inhibitors." J Chin Chem Soc. 2008;55(2):297-302. DOI

Chen Y, Rao F, Rodriguez-Flores JL, Mahapatra NR, Mahata M, Wen G, Salem RM, Shih PA, Das M, Schork NJ, Ziegler MG, Hamilton BA, Mahata SK, O'Connor DT. "Common genetic variants in the chromogranin A promoter alter autonomic activity and blood pressure." Kidney Int. 2008;74(1):115-25. PubMed PMC DOI

Chen Y, Rao F, Rodriguez-Flores JL, Mahata M, Fung MM, Stridsberg M, Vaingankar SM, Wen G, Salem RM, Das M, Cockburn MG, Schork NJ, Ziegler MG, Hamilton BA, Mahata SK, Taupenot L, O'Connor DT. "Naturally occurring human genetic variation in the 3'-untranslated region of the secretory protein chromogranin A is associated with autonomic blood pressure regulation and hypertension in a sex-dependent fashion." J Am Coll Cardiol. 2008;52(18):1468-81. PubMed PMC DOI

Cheng CS, Johnson TL, Hoffmann A. "Epigenetic control: slow and global, nimble and local." Genes Dev. 2008;22(9):1110-4. PubMed PMC DOI

Covert MW, Xiao N, Chen TJ, Karr JR. "Integrating metabolic, transcriptional regulatory and signal transduction models in Escherichia coli." Bioinformatics. 2008;24(18):2044-50. PubMed DOI

Dost B, Shlomi T, Gupta N, Ruppin E, Bafna V, Sharan R. "QNet: a tool for querying protein interaction networks." J Comput Biol. 2008;15(7):913-25. PubMed DOI

Frank AM, Bandeira N, Shen Z, Tanner S, Briggs SP, Smith RD, Pevzner PA. "Clustering millions of tandem mass spectra." J Proteome Res. 2008;7(1):113-22. PubMed PMC DOI

Gupta N, Benhamida J, Bhargava V, Goodman D, Kain E, Kerman I, Nguyen N, Ollikainen N, Rodriguez J, Wang J, Lipton MS, Romine M, Bafna V, Smith RD, Pevzner PA. "Comparative proteogenomics: combining mass spectrometry and comparative genomics to analyze multiple genomes." Genome Res. 2008;18(7):1133-42. PubMed PMC DOI

Herrgård MJ, Swainston N, Dobson P, Dunn WB, Arga KY, Arvas M, Blüthgen N, Borger S, Costenoble R, Heinemann M, Hucka M, Le Novère N, Li P, Liebermeister W, Mo ML, Oliveira AP, Petranovic D, Pettifer S, Simeonidis E, Smallbone K, Spasić I, Weichart D, Brent R, Broomhead DS, Westerhoff HV, Kirdar B, Penttilä M, Klipp E, Palsson BØ, Sauer U, Oliver SG, Mendes P, Nielsen J, Kell DB. "A consensus yeast metabolic network reconstruction obtained from a community approach to systems biology." Nat Biotechnol. 2008;26(10):1155-60. PubMed PMC DOI

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. PubMed PMC DOI

Hsiao A, Subramaniam S. "Bivariate microarray analysis: statistical interpretation of two-channel functional genomics data." Syst Synth Biol. 2008;2(3-4):95-104. PubMed PMC DOI

Joyce AR, Palsson BØ. "Predicting gene essentiality using genome-scale in silico models." Methods Mol Biol. 2008;416:433-57. PubMed DOI

Kang HM, Zaitlen NA, Wade CM, Kirby A, Heckerman D, Daly MJ, Eskin E. "Efficient control of population structure in model organism association mapping." Genetics. 2008;178(3):1709-23. PubMed PMC DOI

Kelley R, Feizi H, Ideker T. "Correcting for gene-specific dye bias in DNA microarrays using the method of maximum likelihood." Bioinformatics. 2008;24(1):71-7. PubMed PMC DOI

Kim S, Gupta N, Pevzner PA. "Spectral probabilities and generating functions of tandem mass spectra: a strike against decoy databases." J Proteome Res. 2008;7(8):3354-63. PubMed PMC DOI

König R, Zhou Y, Elleder D, Diamond TL, Bonamy GM, Irelan JT, Chiang CY, Tu BP, De Jesus PD, Lilley CE, Seidel S, Opaluch AM, Caldwell JS, Weitzman MD, Kuhen KL, Bandyopadhyay S, Ideker T, Orth AP, Miraglia LJ, Bushman FD, Young JA, Chanda SK. "Global analysis of host-pathogen interactions that regulate early-stage HIV-1 replication." Cell. 2008;135(1):49-60. PubMed PMC DOI