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Journal Articles

Lindsay B., Oundo J., Hossain M.A, Antonio M., Tamboura B., Walker A.W, Paulson J.N, Parkhill J., Omore R., Faruque A.S et al.. 2015. Microbiota that affect risk for shigellosis in children in low-income countries. Emerg Infect DisEmerg Infect Dis. 21:242-50.

Lindsay B., Oundo J., Hossain M.A, Antonio M., Tamboura B., Walker A.W, Paulson J.N, Parkhill J., Omore R., Faruque A.S et al.. 2015. Microbiota that affect risk for shigellosis in children in low-income countries. Emerg Infect DisEmerg Infect Dis. 21:242-50.

Lindsay B., Oundo J., Hossain M.A, Antonio M., Tamboura B., Walker A.W, Paulson J.N, Parkhill J., Omore R., Faruque A.S et al.. 2015. Microbiota that affect risk for shigellosis in children in low-income countries. Emerg Infect DisEmerg Infect Dis. 21:242-50.

Lindsay B., Oundo J., Hossain M.A, Antonio M., Tamboura B., Walker A.W, Paulson J.N, Parkhill J., Omore R., Faruque A.S et al.. 2015. Microbiota that affect risk for shigellosis in children in low-income countries. Emerg Infect DisEmerg Infect Dis. 21:242-50.

Waisberg M, Lobo F, Cerqueira G, Passos L, Carvalho O, Franco G, El‐Sayed NM. 2007. Microarray analysis of gene expression induced by sexual contact in Schistosoma mansoni. BMC GenomicsBMC Genomics. 8

Liu B, Pop M.. 2011. MetaPath: identifying differentially abundant metabolic pathways in metagenomic datasets. BMC ProceedingsBMC Proceedings. 5

Treangen T, Koren S., Sommer D.D, Liu B., Astrovskaya I, Ondov B., Darling A.E, Phillippy A.M, Pop M.. 2013. MetAMOS: a modular and open source metagenomic assembly and analysis pipeline. Genome BiolGenome Biol. 14

Treangen T, Koren S., Sommer D.D, Liu B., Astrovskaya I, Ondov B., Darling A.E, Phillippy A.M, Pop M.. 2013. MetAMOS: a modular and open source metagenomic assembly and analysis pipeline. Genome BiolGenome Biol. 14

Ghurye JS, Cepeda-Espinoza V, Pop M. 2016. Metagenomic Assembly: Overview, Challenges and Applications. Yale J Biol Med. 89(3)

Gill SR, Pop M., DeBoy RT, Eckburg PB, Turnbaugh PJ, Samuel BS, Gordon JI, Relman DA, Fraser-Liggett CM, Nelson KE. 2006. Metagenomic Analysis of the Human Distal Gut Microbiome. ScienceScienceScienceScience. 312

Bringaud F, Müller M, Cerqueira GCoutinho, Smith M, Rochette A, el-Sayed NMA, Papadopoulou B, Ghedin E. 2007. Members of a large retroposon family are determinants of post-transcriptional gene expression in Leishmania.. PLoS Pathog. 3(9):1291-307.

Wan L.B, Pan H., Hannenhalli S, Cheng Y., Ma J., Fedoriw A., Lobanenkov V., Latham K.E, Schultz R.M, Bartolomei M.S. 2008. Maternal depletion of CTCF reveals multiple functions during oocyte and preimplantation embryo development. DevelopmentDevelopment. 135

Ondov BD, Treangen T, Melsted áll, Mallonee AB, Bergman NH, Koren S, Phillippy AM. 2016. Mash: fast genome and metagenome distance estimation using MinHash. Genome Biology. (1Suppl 19)

Mendelowitz LM, Schwartz DC, Pop M. 2016. Maligner: a fast ordered restriction map aligner.. Bioinformatics. 32(7):1016-22.

Mendelowitz LM, Schwartz DC, Pop M. 2015. Maligner: a fast ordered restriction map aligner. Bioinformatics. :btv711.

Vezzulli L, Brettar I, Pezzati E, Reid PC, Colwell RR, Höfle MG, Pruzzo C. 2011. Long-term effects of ocean warming on the prokaryotic community: evidence from the vibrios. The ISME JournalThe ISME journal. 6

Vezzulli L, Brettar I, Pezzati E, Reid PC, Colwell RR, Höfle MG, Pruzzo C. 2011. Long-term effects of ocean warming on the prokaryotic community: evidence from the vibrios. The ISME JournalThe ISME journal. 6

Morris A, Paulson JN, Talukder H, Tipton L, Kling H, Cui L, Fitch A, Pop M, Norris KA, Ghedin E. 2016. Longitudinal analysis of the lung microbiota of cynomolgous macaques during long-term SHIV infection. Microbiome. 4320384718719152130282021211818418719223326578105723(158836212108125732558101131110121arXiv:1006.3316)

Morris A, Paulson JN, Talukder H, Tipton L, Kling H, Cui L, Fitch A, Pop M, Norris KA, Ghedin E. 2016. Longitudinal analysis of the lung microbiota of cynomolgous macaques during long-term SHIV infection. Microbiome. 4320384718719152130282021211818418719223326578105723(158836212108125732558101131110121arXiv:1006.3316)

Regier JC, Mitter C, Zwick A, Bazinet AL, Cummings MP, Kawahara AY, Sohn J-C, Zwickl DJ, Cho S, Davis DR et al.. 2013. A large-scale, higher-level, molecular phylogenetic study of the insect order Lepidoptera (moths and butterflies). PLoS OnePLoS One. 8

Phillippy A, Treangen T. 2012. Irreconcilable differences: divorcing geographic mutation and recombination rates within a global MRSA clone. Genome Biology. 13

Hunter S, Jones P, Mitchell A, Apweiler R, Attwood TK, Bateman A, Bernard T, Binns D, Bork P, Burge S et al.. 2012. InterPro in 2011: new developments in the family and domain prediction database.. Nucleic Acids Res. 40(Database issue):D306-12.

Hunter S, Jones P, Mitchell A, Apweiler R, Attwood TK, Bateman A, Bernard T, Binns D, Bork P, Burge S et al.. 2012. InterPro in 2011: new developments in the family and domain prediction database. Nucleic acids researchNucleic Acids Research. 40

Hunter S, Jones P, Mitchell A, Apweiler R, Attwood TK, Bateman A, Bernard T, Binns D, Bork P, Burge S et al.. 2012. InterPro in 2011: new developments in the family and domain prediction database.. Nucleic Acids Res. 40(Database issue):D306-12.

Hunter S, Jones P, Mitchell A, Apweiler R, Attwood TK, Bateman A, Bernard T, Binns D, Bork P, Burge S et al.. 2012. InterPro in 2011: new developments in the family and domain prediction database. Nucleic acids researchNucleic Acids Research. 40

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