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Journal Articles

Cummings MP, Huskamp J.C. 2005. Grid computing. EDUCAUSE ReviewEDUCAUSE Review. 40

Giancarlo R., Hannenhalli S. 2008. Guest Editors' Introduction to the Special Section on Algorithms in Bioinformatics (WABI'07). IEEE/ACM Transactions on Computational Biology and BioinformaticsIEEE/ACM Transactions on Computational Biology and Bioinformatics.

Haft DH, Selengut J., Mongodin EF, Nelson KE. 2005. A guild of 45 CRISPR-associated (Cas) protein families and multiple CRISPR/Cas subtypes exist in prokaryotic genomes. PLoS computational biologyPLOS Computational Biology. 1

Frezza C, Zheng L, Folger O, Rajagopalan KN, MacKenzie ED, Jerby L, Micaroni M, Chaneton B, Adam J, Hedley A et al.. 2011. Haem oxygenase is synthetically lethal with the tumour suppressor fumarate hydratase.. Nature. 477(7363):225-8.

DanČÍK V., Hannenhalli S, Muthukrishnan S.. 1997. Hardness of flip-cut problems from optical mapping. Journal of Computational BiologyJournal of Computational Biology. 4

Sharmin M, Bravo éctorCorrada, Hannenhalli S. 2016. Heterogeneity of transcription factor binding specificity models within and across cell lines. Genome Research. :gr.199166.115.

Sarda, ii S, Hannenhalli S. 2015. High throughput identification of cis-regulatory rewiring events in yeast.. Mol Biol Evol.

Trivedi CM, Zhu W, Wang Q, Jia C, Kee HJin, Li L, Hannenhalli S, Epstein JA. 2010. Hopx and Hdac2 Interact to Modulate Gata4 Acetylation and Embryonic Cardiac Myocyte Proliferation. Developmental CellDevelopmental Cell. 19

Hannenhalli S, Middleton R.P, Levy S., Perroud B., Holzwarth J.A, McDonald K., Hannah S.S,. 2006. Identification and cross-species comparison of canine osteoarthritic gene regulatory cis-elements. Osteoarthritis and cartilage/OARS, Osteoarthritis Research SocietyOsteoarthritis and cartilage/OARS, Osteoarthritis Research Society. 14

Hannenhalli S, Middleton R.P, Levy S., Perroud B., Holzwarth J.A, McDonald K., Hannah S.S,. 2006. Identification and cross-species comparison of canine osteoarthritic gene regulatory cis-elements. Osteoarthritis and cartilage/OARS, Osteoarthritis Research SocietyOsteoarthritis and cartilage/OARS, Osteoarthritis Research Society. 14

Hannenhalli S, Middleton R.P, Levy S., Perroud B., Holzwarth J.A, McDonald K., Hannah S.S,. 2006. Identification and cross-species comparison of canine osteoarthritic gene regulatory cis-elements. Osteoarthritis and cartilage/OARS, Osteoarthritis Research SocietyOsteoarthritis and cartilage/OARS, Osteoarthritis Research Society. 14

Goodheart J, Ellingson RA, Vital XG, Filho HC ão, McCarthy JB, Medrano SM, Bhave VJ, a-Méndez Kí, nez LM é, pez Gó et al.. 2016. Identification guide to the heterobranch sea slugs (Mollusca: Gastropoda) from Bocas del Toro, Panama. Marine Biodiversity Records. 96737453830254034557880541418411912544728739317415779780725696418782226404216145163412560451520488424050829677(12343–4)

Bringaud F, García-Pérez JLuis, Heras SR, Ghedin E, El-Sayed NM, Andersson B, Baltz T, Lopez MC. 2002. Identification of non-autonomous non-LTR retrotransposons in the genome of Trypanosoma cruzi.. Mol Biochem Parasitol. 124(1-2):73-8.

Bringaud F, García-Pérez JLuis, Heras SR, Ghedin E, El‐Sayed NM, Andersson B, Baltz T, Lopez MC. 2002. Identification of non-autonomous non-LTR retrotransposons in the genome of Trypanosoma cruzi. Molecular and Biochemical ParasitologyMolecular and Biochemical Parasitology. 124

Whitehouse CA, Baldwin C, Sampath R, Blyn LB, Melton R, Li F, Hall TA, Harpin V, Matthews H, Tediashvili M et al.. 2010. Identification of Pathogenic Vibrio Species by Multilocus PCR-Electrospray Ionization Mass Spectrometry and Its Application to Aquatic Environments of the Former Soviet Republic of Georgia. Applied and Environmental MicrobiologyAppl. Environ. Microbiol.Applied and Environmental MicrobiologyAppl. Environ. Microbiol.. 76

Whitehouse CA, Baldwin C, Sampath R, Blyn LB, Melton R, Li F, Hall TA, Harpin V, Matthews H, Tediashvili M et al.. 2010. Identification of Pathogenic Vibrio Species by Multilocus PCR-Electrospray Ionization Mass Spectrometry and Its Application to Aquatic Environments of the Former Soviet Republic of Georgia. Applied and Environmental MicrobiologyAppl. Environ. Microbiol.Applied and Environmental MicrobiologyAppl. Environ. Microbiol.. 76

Whitehouse CA, Baldwin C, Sampath R, Blyn LB, Melton R, Li F, Hall TA, Harpin V, Matthews H, Tediashvili M et al.. 2010. Identification of Pathogenic Vibrio Species by Multilocus PCR-Electrospray Ionization Mass Spectrometry and Its Application to Aquatic Environments of the Former Soviet Republic of Georgia. Applied and Environmental MicrobiologyAppl. Environ. Microbiol.Applied and Environmental MicrobiologyAppl. Environ. Microbiol.. 76

Levy S, Hannenhalli S. 2002. Identification of transcription factor binding sites in the human genome sequence. Mammalian GenomeMammalian Genome. 13

Haas BJ, Delcher AL, Mount SM, Wortman JR, Smith RK, Hannick LI, Maiti R, Ronning CM, Rusch DB, Town CD et al.. 2003. Improving the Arabidopsis genome annotation using maximal transcript alignment assemblies.. Nucleic Acids Res. 31(19):5654-66.

Haas BJ, Delcher AL, Mount SM, Wortman JR, Smith RK, Hannick LI, Maiti R, Ronning CM, Rusch DB, Town CD et al.. 2003. Improving the Arabidopsis genome annotation using maximal transcript alignment assemblies.. Nucleic Acids Res. 31(19):5654-66.

Hansen KDaniel, Timp W, Bravo HCorrada, Sabunciyan S, Langmead B, McDonald OG, Wen B, Wu H, Liu Y, Diep D et al.. 2011. Increased methylation variation in epigenetic domains across cancer types. Nature Genetics. 43(8):768-775.

Takala-Harrison S., Jacob C.G, Arze C., Cummings MP, Silva J.C, Dondorp A.M, Fukuda M.M, Hien T.T, Mayxay M., Noedl H. et al.. 2015. Independent Emergence of Artemisinin Resistance Mutations Among Plasmodium falciparum in Southeast Asia. Journal of Infectious Diseases. 211:670-679.

Takala-Harrison S., Jacob C.G, Arze C., Cummings MP, Silva J.C, Dondorp A.M, Fukuda M.M, Hien T.T, Mayxay M., Noedl H. et al.. 2015. Independent Emergence of Artemisinin Resistance Mutations Among Plasmodium falciparum in Southeast Asia. Journal of Infectious Diseases. 211:670-679.

Pop M, Paulson JN, Chakraborty S, Astrovskaya I, Lindsay BR, Li S, Bravo éctorCorrada, Harro C, Parkhill J, Walker AW et al.. 2016. Individual-specific changes in the human gut microbiota after challenge with enterotoxigenic Escherichia coli and subsequent ciprofloxacin treatment. BMC Genomics. 17183412111831230710512122489914142853341501081566039108377115651846133171373920352123327102188151723(1326124105778571763174155114260523Suppl 1611Suppl 26-7Suppl 197591Pt 11321131 Suppl241Database issue1612210375335)

Jia Z, Hannenhalli S. 2012. Inferring Evolution of Gene Duplicates Using Probabilistic Models and Nonparametric Belief Propagation. BMC GenomicsBMC Genomics.

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