Publications

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2009
Qasim AN, Metkus TS, Tadesse M, Lehrke M, Restine S, Wolfe ML, Hannenhalli S, Cappola T, Rader DJ, Reilly MP.  2009.  Resistin gene variation is associated with systemic inflammation but not plasma adipokine levels, metabolic syndrome or coronary atherosclerosis in nondiabetic Caucasians. Clinical EndocrinologyClinical Endocrinology. 70
Alam M, Chowdhury WB, Bhuiyan N.A, Islam A, Hasan NA, G. Nair B, Watanabe H., Siddique A.K, Huq A, R. Sack B et al..  2009.  Serogroup, Virulence, and Genetic Traits of Vibrio Parahaemolyticus in the Estuarine Ecosystem of Bangladesh. Applied and Environmental MicrobiologyAppl. Environ. Microbiol.Applied and Environmental MicrobiologyAppl. Environ. Microbiol.. 75
White JRobert, Nagarajan N, Pop M..  2009.  Statistical Methods for Detecting Differentially Abundant Features in Clinical Metagenomic Samples. PLoS Comput BiologyPLoS Comput BiolPLoS Comput BiologyPLoS Comput Biol. 5
Ward NL, Challacombe JF, Janssen PH, Henrissat B, Coutinho PM, Wu M, Xie G, Haft DH, Sait M, Badger J et al..  2009.  Three genomes from the phylum Acidobacteria provide insight into the lifestyles of these microorganisms in soils.. Appl Environ Microbiol. 75(7):2046-56.
Ward NL, Challacombe JF, Janssen PH, Henrissat B, Coutinho PM, Wu M, Xie G, Haft DH, Sait M, Badger J et al..  2009.  Three genomes from the phylum Acidobacteria provide insight into the lifestyles of these microorganisms in soils.. Appl Environ Microbiol. 75(7):2046-56.
Ward NL, Challacombe JF, Janssen PH, Henrissat B, Coutinho PM, Wu M, Xie G, Haft DH, Sait M, Badger J et al..  2009.  Three genomes from the phylum Acidobacteria provide insight into the lifestyles of these microorganisms in soils.. Appl Environ Microbiol. 75(7):2046-56.
Ward NL, Challacombe JF, Janssen PH, Henrissat B, Coutinho PM, Wu M, Xie G, Haft DH, Sait M, Badger J et al..  2009.  Three genomes from the phylum Acidobacteria provide insight into the lifestyles of these microorganisms in soils. Applied and environmental microbiologyApplied and environmental microbiology. 75
Ward NL, Challacombe JF, Janssen PH, Henrissat B, Coutinho PM, Wu M, Xie G, Haft DH, Sait M, Badger J et al..  2009.  Three genomes from the phylum Acidobacteria provide insight into the lifestyles of these microorganisms in soils. Applied and environmental microbiologyApplied and environmental microbiology. 75
Ward NL, Challacombe JF, Janssen PH, Henrissat B, Coutinho PM, Wu M, Xie G, Haft DH, Sait M, Badger J et al..  2009.  Three genomes from the phylum Acidobacteria provide insight into the lifestyles of these microorganisms in soils. Applied and environmental microbiologyApplied and environmental microbiology. 75
Regier J.C, Zwick A., Cummings MP, Kawahara A.Y, Cho S., Weller S., Roe A., Baixeras J., Brown J.W, Parr C. et al..  2009.  Toward reconstructing the evolution of advanced moths and butterflies (Lepidoptera: Ditrysia): an initial molecular study. BMC Evol BiolBMC Evol Biol. 9
2010
White JR, Navlakha S, Nagarajan N, Ghodsi M-R, Kingsford C, Pop M..  2010.  Alignment and clustering of phylogenetic markers - implications for microbial diversity studies. BMC BioinformaticsBMC Bioinformatics. 11
Joseph SJ, Fernández-Robledo JA, Gardner MJ, El-Sayed NM, Kuo C-H, Schott EJ, Wang H, Kissinger JC, Vasta GR.  2010.  The Alveolate Perkinsus marinus: biological insights from EST gene discovery.. BMC Genomics. 11:228.
Roe A., Weller S., Baixeras J., Brown J.W, Cummings MP, Davis D.R, Horak M., Kawahara A.Y, Mitter C., Parr C.S et al..  2010.  Evolutionary framework for Lepidoptera model systems. Genetics and Molecular Biology of LepidopteraGenetics and Molecular Biology of Lepidoptera.
Roe A., Weller S., Baixeras J., Brown J.W, Cummings MP, Davis D.R, Horak M., Kawahara A.Y, Mitter C., Parr C.S et al..  2010.  Evolutionary framework for Lepidoptera model systems. Genetics and Molecular Biology of LepidopteraGenetics and Molecular Biology of Lepidoptera.
Navlakha S, White J, Nagarajan N, Pop M., Kingsford C.  2010.  Finding Biologically Accurate Clusterings in Hierarchical Tree Decompositions Using the Variation of Information. Journal of Computational BiologyJournal of Computational Biology. 17
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
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
Wu H, Irizarry RA, Bravo HCorrada.  2010.  Intensity normalization improves color calling in SOLiD sequencing. Nat MethNat MethNat MethNat Meth. 7
2011
Wetzel J., Kingsford C, Pop M..  2011.  Assessing the benefits of using mate-pairs to resolve repeats in de novo short-read prokaryotic assemblies. BMC bioinformaticsBMC Bioinformatics. 12
Rasko D.A, Worsham P.L, Abshire T.G, Stanley S.T, Bannan J.D, Wilson M.R, Langham R.J, Decker R.S, Jiang L., Read T.D et al..  2011.  Bacillus anthracis comparative genome analysis in support of the Amerithrax investigation. Proceedings of the National Academy of SciencesProceedings of the National Academy of Sciences. 108
Rasko D.A, Worsham P.L, Abshire T.G, Stanley S.T, Bannan J.D, Wilson M.R, Langham R.J, Decker R.S, Jiang L., Read T.D et al..  2011.  Bacillus anthracis comparative genome analysis in support of the Amerithrax investigation. Proceedings of the National Academy of SciencesProceedings of the National Academy of Sciences. 108
Cho S, Zwick A, Regier JC, Mitter C, Cummings MP, Yao J, Du Z, Zhao H, Kawahara AY, Weller S et al..  2011.  Can Deliberately Incomplete Gene Sample Augmentation Improve a Phylogeny Estimate for the Advanced Moths and Butterflies (Hexapoda: Lepidoptera)? Systematic BiologySyst BiolSystematic BiologySyst Biol. 60
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
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.
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.

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