Publications

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Book Chapters
Kim Y, Patro R, Ip CYiu, O'Leary DP, Anishkin A, Sukharev S, Varshney A.  2009.  Salient Frame Detection for Molecular Dynamics Simulations. Scientific VisualizationScientific Visualization.
Conference Proceedings
Patro R., Ip CYiu, Bista S., Cho S.S, Thirumalai D., Varshney A.  2011.  MDMap: A system for data-driven layout and exploration of molecular dynamics simulations. Biological Data Visualization (BioVis), 2011 IEEE Symposium on.
Borah M., Bajwa R.S, Hannenhalli S, Irwin M.J.  1994.  A SIMD solution to the sequence comparison problem on the MGAP. International Conference on Application Specific Array Processors, 1994. Proceedings.
Journal Article
Pop M, Walker AW, Paulson J, Lindsay B, Antonio M, M Hossain A, Oundo J, Tamboura B, Mai V, Astrovskaya I et al..  2014.  Diarrhea in young children from low-income countries leads to large-scale alterations in intestinal microbiota composition.. Genome Biol. 15(6):R76.
Korpal M, Ell BJ, Buffa FM, Ibrahim T, Blanco MA, Terrassa Tà-, Mercatali L, Khan Z, Goodarzi H, Hua Y et al..  2011.  Direct targeting of Sec23a by miR-200s influences cancer cell secretome and promotes metastatic colonization. Nature Medicine. 17(9):1101-1108.
Ish-Am O, Kristensen DM, Ruppin E.  2015.  Evolutionary Conservation of Bacterial Essential Metabolic Genes across All Bacterial Culture Media. PLOS ONE. 10(4):e0123785.
Balch T, Dellaert F, Feldman A, Guillory A, Isbell C, Khan Z, Stein A, Wilde H.  2006.  How A.I. and multi-robot systems research will accelerate our understanding of social animal behavior. Proceedings of the IEEE. 94(7):1445-1463.
Balch T., Dellaert F., Feldman A., Guillory A., Isbell C.L., Khan Z., Pratt S.C., Stein A.N., Wilde H..  2006.  How Multirobot Systems Research will Accelerate our Understanding of Social Animal Behavior. Proceedings of the IEEE. 94(7):1445-1463.
Timp W, Bravo HCorrada, McDonald OG, Goggins M, Umbricht C, Zeiger M, Feinberg AP, Irizarry RA.  2014.  Large hypomethylated blocks as a universal defining epigenetic alteration in human solid tumors.. Genome Med. 6(8):61.
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.
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HCorrada, Davis S, Gatto L, Girke T et al..  2015.  Orchestrating high-throughput genomic analysis with Bioconductor.. Nat Methods. 12(2):115-21.
Journal Articles
R. Sack B, A. Siddique K, Longini IM, Nizam A, Yunus M, M. Islam S, Morris, Ali A, Huq A, G. Nair B et al..  2003.  A 4-Year Study of the Epidemiology of Vibrio Cholerae in Four Rural Areas of Bangladesh. Journal of Infectious DiseasesJ Infect Dis.Journal of Infectious DiseasesJ Infect Dis.. 187
El‐Sayed NM, Bartholomeu D, Ivens A, Johnston DA, LoVerde PT.  2004.  Advances in schistosome genomics. Trends in ParasitologyTrends in Parasitology. 20
Ishimori N., Walsh K., Zheng X., Lu F., Hannenhalli S, Nusskern D., Mural R., Paigen B..  2004.  CHARACTERIZATION OF< i> Ath17, A QUANTITATIVE TRAIT LOCUS FOR ATHEROSCLEROSIS SUSCEPTIBILITY BETWEEN C57BL/6J AND 129S1/SvImJ; SINGLE-NUCLEOTIDE POLYMORPHISMS HAVE IMPORTANT IMPLICATIONS ON IDENTIFYING ATHEROSCLEROSIS MODIFIER GENES. Cardiovascular PathologyCardiovascular Pathology. 13
Ivanova EP, Matte GR, Matte MH, Coenye T, Huq A, Colwell RR.  2002.  Characterization of Pseudoalteromonas citrea and P. nigrifaciens Isolated from Different Ecological Habitats Based on REP-PCR Genomic Fingerprints. Systematic and Applied MicrobiologySystematic and Applied Microbiology. 25
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., 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
El‐Sayed NM, Myler PJ, Blandin G, Berriman M, Crabtree J, Aggarwal G, Caler E, Renauld H, Worthey EA, Hertz-Fowler C et al..  2005.  Comparative Genomics of Trypanosomatid Parasitic Protozoa. ScienceScience. 309
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.
Keeley MB, Wood MA, Isiegas C, Stein J, Hellman K, Hannenhalli S, Abel T.  2006.  Differential Transcriptional Response to Nonassociative and Associative Components of Classical Fear Conditioning in the Amygdala and Hippocampus. Learning & MemoryLearn. Mem.Learning & MemoryLearn. Mem.. 13
Korpal M, Ell BJ, Buffa FM, Ibrahim T, Blanco MA, Celià-Terrassa T, Mercatali L, Khan Z, Goodarzi H, Hua Y et al..  2011.  Direct targeting of Sec23a by miR-200s influences cancer cell secretome and promotes metastatic colonization.. Nat Med. 17(9):1101-8.
Rabinovich S, Adler L, Yizhak K, Sarver A, Silberman A, Agron S, Stettner N, Sun Q, Brandis A, Helbling D et al..  2015.  Diversion of aspartate in ASS1-deficient tumours fosters de novo pyrimidine synthesis. Nature. 527(7578):379-383.
Purdy AE, Balch D, Lizárraga‐Partida MLeonardo, Islam MSirajul, Martinez‐Urtaza J, Huq A, Colwell RR, Bartlett DH.  2010.  Diversity and distribution of cholix toxin, a novel ADP‐ribosylating factor from Vibrio cholerae. Environmental Microbiology ReportsEnvironmental Microbiology Reports. 2
Dehal P, Satou Y, Campbell RK, Chapman J, Degnan B, De Tomaso A, Davidson B, Di Gregorio A, Gelpke M, Goodstein DM et al..  2002.  The draft genome of Ciona intestinalis: insights into chordate and vertebrate origins.. Science. 298(5601):2157-67.
Dehal P, Satou Y, Campbell RK, Chapman J, Degnan B, De Tomaso A, Davidson B, Di Gregorio A, Gelpke M, Goodstein DM et al..  2002.  The draft genome of Ciona intestinalis: insights into chordate and vertebrate origins.. Science. 298(5601):2157-67.

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