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Kurkulos M, Weinberg JM, Roy D, Mount SM. 1994. P element-mediated in vivo deletion analysis of white-apricot: deletions between direct repeats are strongly favored.. Genetics. 136(3):1001-11.

Islam M.S, Tasmin R, Khan SI s l a m, Bakht HBM, Mahmood ZH a y a t, Rahman M.Z i a u r, Bhuiyan NA m i n, Nishibuchi M, Nair G.B a l a k, e y Sack R.B r a d l et al.. 2004. Pandemic strains of O3:K6 Vibrio parahaemolyticus in the aquatic environment of Bangladesh. Canadian Journal of MicrobiologyCanadian Journal of Microbiology. 50

Hua K.A, Hannenhalli S. 1991. Parallel transitive closure computations using topological sort. Proceedings of the First International Conference on Parallel and Distributed Information Systems, 1991.

Nagarajan N, Pop M.. 2009. Parametric Complexity of Sequence Assembly: Theory and Applications to Next Generation Sequencing. Journal of Computational BiologyJournal of Computational Biology. 16

Mount SM, Green MM, Rubin GM. 1988. Partial revertants of the transposable element-associated suppressible allele white-apricot in Drosophila melanogaster: structures and responsiveness to genetic modifiers.. Genetics. 118(2):221-34.

Shi W, Wahba G, Irizarry RA, Bravo HCorrada, Wright SJ. 2012. The partitioned LASSO-patternsearch algorithm with application to gene expression data. BMC bioinformaticsBMC Bioinformatics. 13

Ruppin E., Reggia JA, Horn D.. 1996. Pathogenesis of schizophrenic delusions and hallucinations: a neural model. Schizophrenia bulletinSchizophrenia Bulletin. 22

Ruppin E., Ofer E., Reggia JA, Revett K.. 1999. Pathogenic mechanisms in ischemic damage: a computational study. Computers in biology and medicineComputers in biology and medicine. 29

Faruque SM, Kamruzzaman M., Meraj IM, Chowdhury N, G. Nair B, R. Sack B, Colwell RR, Sack DA. 2003. Pathogenic Potential of Environmental Vibrio Cholerae Strains Carrying Genetic Variants of the Toxin-Coregulated Pilus Pathogenicity Island. Infection and ImmunityInfect. Immun.Infection and ImmunityInfect. Immun.. 71

Pruzzo C., Huq A., Colwell RR, Donelli G.. 2005. Pathogenic Vibrio species in the marine and estuarine environment. Oceans and health: pathogens in the marine environmentOceans and health: pathogens in the marine environment.

Karathia H, Kingsford C, Girvan M, Hannenhalli S. 2016. A pathway-centric view of spatial proximity in the 3D nucleome across cell lines. Scientific Reports. 6:39279.

Cummings MP. 1992. Patterns and processes of sequence evolution: plant organelle genomes and copia-like retrotransposons.

Ruppin E., Reggia JA. 1995. Patterns of functional damage in neural network models of associative memory. Neural computationNeural computation. 7

Hadley D., Murphy T., Valladares O., Hannenhalli S, Ungar L., Kim J., Bucan M.,. 2006. Patterns of sequence conservation in presynaptic neural genes. Genome BiolGenome Biol. 7

Ruppin E., Revett K., Ofer E., Goodall S., Reggia JA. 1999. Penumbral tissue damage following acute stroke: a computational investigation. Progress in brain researchProgress in brain research. 121

Pruzzo C, Tarsi R, Lleò MDel Mar, Signoretto C, Zampini M, Pane L, Colwell RR, Canepari P. 2003. Persistence of adhesive properties in Vibrio cholerae after long‐term exposure to sea water. Environmental MicrobiologyEnvironmental Microbiology. 5

Nguyen N-phuong, Warnow T, Pop M, White B. 2016. A perspective on 16S rRNA operational taxonomic unit clustering using sequence similarity. npj Biofilms and Microbiomes. 2:16004.

Yizhak K, Gaude E, Le Dévédec S, Waldman YY, Stein GY, van de Water B, Frezza C, Ruppin E. 2014. Phenotype-based cell-specific metabolic modeling reveals metabolic liabilities of cancer.. Elife. 3

Wang K, Das A, Xiong Z-M, Cao K, Hannenhalli S. 2015. Phenotype-Dependent Coexpression Gene Clusters: Application to Normal and Premature Ageing. IEEE/ACM Transactions on Computational Biology and Bioinformatics. 12(1):30-39.

Cummings MP. 2004. PHYLIP (Phylogeny Inference Package).

García-Varela M., Cummings MP, G. de León P-P, Gardner S.L, Laclette J.P. 2002. Phylogenetic analysis based on 18S ribosomal RNA gene sequences supports the existence of class Polyacanthocephala (Acanthocephala). Mol Phylogenet EvolMol Phylogenet Evol. 23

Cummings MP, Nugent J.M, Olmstead R.G, Palmer J.D. 2003. Phylogenetic analysis reveals five independent transfers of the chloroplast gene ıt rbcL to the mitochondrial genome in angiosperms. Curr GenetCurr Genet. 43

Eng K.H, Bravo HCorrada, Keles S.. 2009. A phylogenetic mixture model for the evolution of gene expression. Molecular biology and evolutionMolecular biology and evolution. 26

García-Varela M., G. de León P-P, de la Torre P., Cummings MP, Sarma S.S, Laclette J.P. 2000. Phylogenetic relationships of Acanthocephala based on analysis of 18S ribosomal RNA gene sequences. J Mol EvolJ Mol Evol. 50

Förster H., Cummings MP, Coffey M.D. 2000. Phylogenetic relationships of ıt Phytophthora species based on ribosomal ITS I DNA sequence analysis with emphasis on Waterhouse groups V and VI. Mycol ResMycol Res. 104

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