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Mount SM, Rubin GM.  1985.  Complete nucleotide sequence of the Drosophila transposable element copia: homology between copia and retroviral proteins.. Mol Cell Biol. 5(7):1630-8.
Campbell MA, Haas BJ, Hamilton JP, Mount SM, C Buell R.  2006.  Comprehensive analysis of alternative splicing in rice and comparative analyses with Arabidopsis.. BMC Genomics. 7:327.
Essien K, Hannenhalli S, Stoeckert CJ.  2008.  Computational Analysis of Constraints on Noncoding Regions, Coding Regions and Gene Expression in Relation to Plasmodium Phenotypic Diversity. PLoS ONEPLoS ONEPLoS ONEPLoS ONE. 3
Choi J.H, Tang H., Kim S., Pop M..  2010.  Computational Approaches for Genome Assembly Validation. Biological Data MiningBiological Data Mining.
Leparc G.G, Mitra R.D, Vardhanabhuti S., Wang J., Hannenhalli S, Smit S., Widmann J., Knight R., Wu S., Zhang Y. et al..  2007.  COMPUTATIONAL BIOLOGY. Nucleic acids researchNucleic Acids Research. 35
Pop M.  2015.  Computational challenges in microbiome research. 2015 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)2015 IEEE International Conference on Bioinformatics and Biomedicine (BIBM).
Mendelowitz L, Pop M.  2014.  Computational methods for optical mapping. GigaScienceGigaScience. 3:33.
Goodall S., Reggia JA, Chen Y., Ruppin E., Whitney C..  1997.  A computational model of acute focal cortical lesions. StrokeStroke. 28
Kanodia J.S, Kim Y., Tomer R., Khan Z., Chung K., Storey J.D, Lu H., Keller P.J, Shvartsman S.Y.  2011.  A computational statistics approach for estimating the spatial range of morphogen gradients. Development. 138(22):4867-4874.
Kanodia JS, Kim Y, Tomer R, Khan Z, Chung K, Storey JD, Lu H, Keller PJ, Shvartsman SY.  2011.  A computational statistics approach for estimating the spatial range of morphogen gradients.. Development. 138(22):4867-74.
Ruppin E., Horn D., Levy N., Reggia JA.  1996.  Computational studies of synaptic alterations in Alzheimer’s disease. Neural modeling of brain and cognitive disordersNeural modeling of brain and cognitive disorders.
Yizhak K, Le Dévédec SE, Rogkoti VMaria, Baenke F, de Boer VC, Frezza C, Schulze A, van de Water B, Ruppin E.  2014.  A computational study of the Warburg effect identifies metabolic targets inhibiting cancer migration.. Mol Syst Biol. 10:744.
Pertea M, Mount SM, Salzberg SL.  2007.  A computational survey of candidate exonic splicing enhancer motifs in the model plant Arabidopsis thaliana.. BMC Bioinformatics. 8:159.
Reggia JA, Ruppin E., Berndt R.S.  1997.  Computer models: A new approach to the investigation of disease. MD ComputingMD Computing. 14
Bazinet AL, Cummings MP.  2011.  Computing the Tree of Life: Leveraging the Power of Desktop and Service Grids. Parallel and Distributed Processing Workshops and Phd Forum (IPDPSW), 2011 IEEE International Symposium on.
Park S, Hannenhalli S, Choi S.  2014.  Conservation in first introns is positively associated with the number of exons within genes and the presence of regulatory epigenetic signals. BMC Genomics. 15(1):526.
Evans P, Donahue G, Hannenhalli S.  2006.  Conservation Patterns in cis-Elements Reveal Compensatory Mutations. Comparative GenomicsComparative Genomics. 4205
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.
He X, Chatterjee R, John S, Bravo H, Sathyanarayana BK, Biddie SC, FitzGerald PC, Stamatoyannopoulos JA, Hager GL, Vinson C.  2013.  Contribution of nucleosome binding preferences and co-occurring DNA sequences to transcription factor binding. BMC Genomics. 14(1):428.
Senoh M, Ghosh‐Banerjee J, Ramamurthy T, Hamabata T, Kurakawa T, Takeda M, Colwell RR, G. Nair B, Takeda Y.  2010.  Conversion of viable but nonculturable Vibrio cholerae to the culturable state by co‐culture with eukaryotic cells. Microbiology and ImmunologyMicrobiology and Immunology. 54
Lapizco-Encinas G., Kingsford C, Reggia JA.  2009.  A cooperative combinatorial Particle Swarm Optimization algorithm for side-chain packing. IEEE Swarm Intelligence Symposium, 2009. SIS '09.
Voytas D.F, Cummings MP, Koniczny A., Ausubel F.M, Rodermel S.R.  1992.  copia-like retrotransposons are ubiquitous among plants. Proc Natl Acad Sci USAProc Natl Acad Sci USA. 89
Cummings MP.  1992.  Copia-like retrotransposons in plants: a brief introduction. The Plant Genetics NewsletterThe Plant Genetics Newsletter. 8
Singh LN, Hannenhalli S.  2010.  Correlated Changes Between Regulatory Cis Elements and Condition-Specific Expression in Paralogous Gene Families. Nucleic Acids ResearchNucl. Acids Res.Nucleic Acids ResearchNucl. Acids Res.. 38
Mukherjee R., Singh L.NS, Evans P., Hannenhalli S.  2013.  Correlated evolution of positions within mammalian cis elements . Plos One. 8:e55521.

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