Publications

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Kirschner A.KT, Schauer S., Steinberger B., Wilhartitz I., Grim C.J, Huq A., Colwell RR, Herzig A., Sommer R..  2011.  Interaction of Vibrio cholerae non-O1/non-O139 with Copepods, Cladocerans and Competing Bacteria in the Large Alkaline Lake Neusiedler See, Austria. Microbial ecologyMicrobial ecology. 61
Bringaud F, Biteau N, Zuiderwijk E, Berriman M, El-Sayed NM, Ghedin E, Melville SE, Hall N, Baltz T.  2004.  The ingi and RIME non-LTR retrotransposons are not randomly distributed in the genome of Trypanosoma brucei.. Mol Biol Evol. 21(3):520-8.
Bringaud F., Biteau N., Zuiderwijk E., Berriman M., El‐Sayed NM, Ghedin E., Melville S.E, Hall N., Baltz T..  2004.  The ingi and RIME non-LTR retrotransposons are not randomly distributed in the genome of Trypanosoma brucei. Molecular biology and evolutionMolecular biology and evolution. 21
Otto S.P, Cummings MP, Wakeley J..  1996.  Inferring phylogenies from DNA sequence data: The effects of sampling. New Uses for New PhylogeniesNew Uses for New Phylogenies.
Jia Z, Hannenhalli S.  2012.  Inferring Evolution of Gene Duplicates Using Probabilistic Models and Nonparametric Belief Propagation. BMC GenomicsBMC Genomics.
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)
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.
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.
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.
Seaver SMD, Bradbury LMT, Frelin O, Zarecki R, Ruppin E, Hanson AD, Henry CS.  2015.  Improved evidence-based genome-scale metabolic models for maize leaf, embryo, and endosperm.. Front Plant Sci. 6:142.
Seaver SMD, Bradbury LMT, Frelin O, Zarecki R, Ruppin E, Hanson AD, Henry CS.  2015.  Improved evidence-based genome-scale metabolic models for maize leaf, embryo, and endosperm.. Front Plant Sci. 6:142.
Levy S, Hannenhalli S.  2002.  Identification of transcription factor binding sites in the human genome sequence. Mammalian GenomeMammalian Genome. 13
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
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
Wang K, Das A, Xiong Z-M, Cao K, Hannenhalli S.  2013.  Identification of gene clusters with phenotype-dependent expression with application to normal and premature ageing. Proceedings of the International Conference on Bioinformatics, Computational Biology and Biomedical Informatics. :377-383.
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)
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
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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

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