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Ayres DL, Darling A, Zwickl DJ, Beerli P, Holder MT, Lewis PO, Huelsenbeck JP, Ronquist F, Swofford DL, Cummings MP et al..  2012.  BEAGLE: An Application Programming Interface and High-Performance Computing Library for Statistical Phylogenetics. Systematic BiologySyst BiolSystematic BiologySyst Biol. 61
D. Avinash S, Aniba R., Chang Y.C, Hannenhalli S.  2012.  Epigenomic model of cardiac enhancers with application to Genome wideassociation studies. Pacific Symposium on BiocomputingPacific Symposium on Biocomputing.
Auslander N, Yizhak K, Weinstock A, Budhu A, Tang W, Wang XWei, Ambs S, Ruppin E.  2016.  A joint analysis of transcriptomic and metabolomic data uncovers enhanced enzyme-metabolite coupling in breast cancer.. Sci Rep. 6:29662.
Auslander N, Wagner A, Oberhardt M, Ruppin E.  2016.  Data-Driven Metabolic Pathway Compositions Enhance Cancer Survival Prediction. PLOS Computational Biology. 12(9):e1005125.
Attardo GM, Strickler-Dinglasan P, Perkin SAH, Caler E, Bonaldo MF, Soares MB, El-Sayeed N, Aksoy S.  2006.  Analysis of fat body transcriptome from the adult tsetse fly, Glossina morsitans morsitans.. Insect Mol Biol. 15(4):411-24.
Asakura H., Selengut J., Orme-Johnson W.H, Dretler S.P.  1998.  The effect of calprotectin on the nucleation and growth of struvite crystals as assayed by light microscopy in real-time. The Journal of urologyThe Journal of urology. 159
Aryee MJ, Jaffe AE, Corrada-Bravo H, Ladd-Acosta C, Feinberg AP, Hansen KD, Irizarry RA.  2014.  Minfi: a flexible and comprehensive Bioconductor package for the analysis of Infinium DNA methylation microarrays.. Bioinformatics. 30(10):1363-9.
Arkin EM, Belleville P, Mitchell JSB, Mount D, Romanik K, Salzberg S, Souvaine D.  1997.  Testing simple polygons. Computational GeometryComputational Geometry. 8
Almeida M, Pop M, Le Chatelier E, Prifti E, Pons N, Ghozlane A, S Ehrlich D.  2016.  Capturing the most wanted taxa through cross-sample correlations. The ISME Journal.
Almeida M, Hebert A, Abraham A-L, Rasmussen S, Monnet C, Pons N, Delbes C, Loux V, Batto J-M, Leonard P et al..  2014.  Construction of a dairy microbial genome catalog opens new perspectives for the metagenomic analysis of dairy fermented products. BMC GenomicsBMC Genomics. 15:1101.
Alemu E.Y, Carl J.W, H. Bravo C, Hannenhalli S..  2014.  Determinants of expression variability. Nucleic Acids Research. 42(6):3503-3514.
Alam M., Sultana M., Nair G.B, Siddique A.K, Hasan N.A, Sack R.B, Sack D.A, Ahmed K.U, Sadique A., Watanabe H. et al..  2007.  Viable but nonculturable Vibrio cholerae O1 in biofilms in the aquatic environment and their role in cholera transmission. Proceedings of the National Academy of SciencesProceedings of the National Academy of Sciences. 104
Alam M, Sultana M, G. Nair B, R. Sack B, Sack DA, Siddique A.K, Ali A, Huq A, Colwell RR.  2006.  Toxigenic Vibrio Cholerae in the Aquatic Environment of Mathbaria, Bangladesh. Applied and Environmental MicrobiologyAppl. Environ. Microbiol.Applied and Environmental MicrobiologyAppl. Environ. Microbiol.. 72
Alam M., Islam A., Bhuiyan N.A, Rahim N., Hossain A., Khan G.Y, Ahmed D., Watanabe H., Izumiya H., Faruque A.SG et al..  2011.  Clonal transmission, dual peak, and off-season cholera in Bangladesh. Infection Ecology & EpidemiologyInfection Ecology & Epidemiology. 1
Alam M, Chowdhury WB, Bhuiyan N.A, Islam A, Hasan NA, G. Nair B, Watanabe H., Siddique A.K, Huq A, R. Sack B et al..  2009.  Serogroup, Virulence, and Genetic Traits of Vibrio Parahaemolyticus in the Estuarine Ecosystem of Bangladesh. Applied and Environmental MicrobiologyAppl. Environ. Microbiol.Applied and Environmental MicrobiologyAppl. Environ. Microbiol.. 75
Alam M., Sadique A., Bhuiyan N.A, Nair G.B, Siddique A.K, Sack D.A, Ahsan S., Huq A., Sack R.B, Colwell RR et al..  2006.  Effect of transport at ambient temperature on detection and isolation of Vibrio cholerae from environmental samples. Applied and environmental microbiologyApplied and environmental microbiology. 72
Alam M, M. Islam T, Rashed SManzur, Johura F-T, Bhuiyan NA, Delgado G, Morales R, Mendez JLuis, Navarro A, Watanabe H et al..  2012.  Vibrio Cholerae Classical Biotype Strains Reveal Distinct Signatures in Mexico. Journal of Clinical MicrobiologyJ. Clin. Microbiol.Journal of Clinical MicrobiologyJ. Clin. Microbiol..
Alam M, Hasan NA, Sadique A, Bhuiyan N.A, Ahmed KU, Nusrin S, G. Nair B, Siddique A.K, R. Sack B, Sack DA et al..  2006.  Seasonal Cholera Caused by Vibrio Cholerae Serogroups O1 and O139 in the Coastal Aquatic Environment of Bangladesh. Applied and Environmental MicrobiologyAppl. Environ. Microbiol.Applied and Environmental MicrobiologyAppl. Environ. Microbiol.. 72
Akula N., Barb J., Jiang X., Wendland J.R, Choi K.H, Sen S.K, Hou L., Chen D.TW, Laje G., Johnson K. et al..  2014.  RNA-sequencing of the brain transcriptome implicates dysregulation of neuroplasticity, circadian rhythms and GTPase binding in bipolar disorder. Molecular psychiatry.
Akula N, Barb J, Jiang X, Wendland JR, Choi KH, Sen SK, Hou L, Chen DTW, Laje G, Johnson K et al..  2014.  RNA-sequencing of the brain transcriptome implicates dysregulation of neuroplasticity, circadian rhythms and GTPase binding in bipolar disorder.. Mol Psychiatry. 19(11):1179-85.
Aggarwal A, S. Kosaraju R, Pop M..  1998.  Drawing of Two-Dimensional Irregular Meshes. Graph DrawingGraph Drawing. 1547
Agarwala R., Batzoglou S., DanČÍK V., Decatur S.E, Hannenhalli S, Farach M., Muthukrishnan S., Skiena S..  1997.  Local rules for protein folding on a triangular lattice and generalized hydrophobicity in the HP model. Journal of Computational BiologyJournal of Computational Biology. 4
Adams MD, Celniker SE, Holt RA, Evans CA, Gocayne JD, Amanatides PG, Scherer SE, Li PW, Hoskins RA, Galle RF et al..  2000.  The genome sequence of Drosophila melanogaster.. Science. 287(5461):2185-95.
Acevedo MA, Corrada-Bravo CJ, Corrada-Bravo H, Villanueva-Rivera LJ, T. Aide M.  2009.  Automated classification of bird and amphibian calls using machine learning: A comparison of methods. Ecological Informatics. 4(4):206-214.

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