Publications

Tuddenham, S., M. Shafiq, J.S. Mathad, M. Alexander, S. Naik, V. Kulkarni, P. Deshpande, M.S. Humphrys, J.B. Holm, N. Khan, S. Yadana, A. Cheedalla, R. Bhosale, K.G. Ghanem, T. Wang, S. Wang, B. Ma, J. Ravel, A. Gupta, and R. Shivakoti, Association of Pregnancy and HIV Status with Molecular-Bacterial Vaginosis in Indian Women. J Acquir Immune Defic Syndr, 2023.

Tebben, K., S. Yirampo, D. Coulibaly, A.K. Kone, M.B. Laurens, E.M. Stucke, A. Dembele, Y. Tolo, K. Traore, A. Niangaly, A.A. Berry, B. Kouriba, C.V. Plowe, O.K. Doumbo, K.E. Lyke, S. Takala-Harrison, M.A. Thera, M.A. Travassos, and D. Serre, Malian children infected with Plasmodium ovale and Plasmodium falciparum display very similar gene expression profiles. PLoS Negl Trop Dis, 2023. 17(1): p. e0010802.

Smith, A.B., M. Jung, S.J. Pressler, E. Mocci, and S.G. Dorsey, Differential Gene Expression Among Patients With Heart Failure Experiencing Pain. Nurs Res, 2023.

Shamsuzzaman, M., N. Rahman, B. Gregory, A. Bommakanti, J.M. Zengel, V.M. Bruno, and L. Lindahl, Inhibition of Ribosome Assembly and Ribosome Translation Has Distinctly Different Effects on Abundance and Paralogue Composition of Ribosomal Protein mRNAs in Saccharomyces cerevisiae. mSystems, 2023: p. e0109822.

Shallom, S.J., H. Tettelin, P. Chandrasekaran, I.K. Park, S. Agrawal, K. Arora, L. Sadzewicz, A.M. Milestone, M.L. Aitken, B.A. Brown-Elliott, R.J. Wallace, Jr., E.P. Sampaio, M. Niederweis, K.N. Olivier, S.M. Holland, and A.M. Zelazny, Evolution of Mycobacterium abscessus in the human lung: Cumulative mutations and genomic rearrangement of porin genes in patient isolates. Virulence, 2023: p. 2215602.

Rudenko, N., M. Golovchenko, A. Horak, L. Grubhoffer, E.F. Mongodin, C.M. Fraser, W. Qiu, B.J. Luft, R.G. Morgan, S.R. Casjens, and S.E. Schutzer, Genomic Confirmation of Borrelia garinii, United States. Emerg Infect Dis, 2023. 29(1): p. 64-69.

Murphy, T.F., C. Kirkham, A. D'Mello, S. Sethi, M.M. Pettigrew, and H. Tettelin, Adaptation of Nontypeable Haemophilus influenzae in Human Airways in COPD: Genome Rearrangements and Modulation of Expression of HMW1 and HMW2. mBio, 2023: p. e0014023.

Mullins, K.E., C. Seneviratne, A.C. Shetty, F. Jiang, R. Christenson, and S. Stass, Proof of Concept: detection of cell free RNA from EDTA plasma in patients with lung cancer and non-cancer patients. Clin Biochem, 2023.

Ma, B., S.J. Gavzy, V. Saxena, Y. Song, W. Piao, H.W. Lwin, R. Lakhan, J. Lyyathurai, L. Li, M. France, C. Paluskievicz, M.W. Shirkey, L. Hittle, A. Munawwar, E.F. Mongodin, and J.S. Bromberg, Strain-specific alterations in gut microbiome and host immune responses elicited by tolerogenic Bifidobacterium pseudolongum. Sci Rep, 2023. 13(1): p. 1023

Kensara, A., H. Saito, E.F. Mongodin, and R. Masri, Microbiological profile of peri-implantitis: Analyses of microbiome within dental implants. J Prosthodont, 2023.

Hazen, T.H., J.M. Michalski, S.M. Tennant, and D.A. Rasko, Genomic diversity of non-diarrheagenic fecal Escherichia coli from children in sub-Saharan Africa and south Asia and their relatedness to diarrheagenic E. coli. Nat Commun, 2023. 14(1): p. 1400.

Haddad, L.B., J.H. Tang, N.L. Davis, A.P. Kourtis, L. Chinula, A. Msika, G. Tegha, M.C. Hosseinipour, J.A.E. Nelson, M.M. Hobbs, P. Gajer, J. Ravel, and K. De Paris, Influence of Hormonal Contraceptive Use and HIV on Cervicovaginal Cytokines and Microbiota in Malawi. mSphere, 2023: p. e0058522.

Elsasser, T.H., B. Ma, J. Ravel, S. Kahl, P. Gajer, and A. Cross, Short-term feeding of defatted bovine colostrum mitigates inflammation in the gut via changes in metabolites and microbiota in a chicken animal model. Anim Microbiome, 2023. 5(1): p. 6.

Armstrong, E., A. Hemmerling, V. Joag, S. Huibner, M. Kulikova, E. Crawford, G.R. Castaneda, O. Anzala, O. Obila, K. Shahabi, J. Ravel, B. Coburn, C.R. Cohen, and R. Kaul, Treatment Success Following Standard Antibiotic Treatment for Bacterial Vaginosis Is Not Associated With Pretreatment Genital Immune or Microbial Parameters. Open Forum Infect Dis, 2023. 10(1): p. ofad007.

Tvedte, E.S., M. Gasser, X. Zhao, L.J. Tallon, L. Sadzewicz, R.E. Bromley, M. Chung, J. Mattick, B.C. Sparklin, and J.C. Dunning Hotopp, Accumulation of endosymbiont genomes in an insect autosome followed by endosymbiont replacement. Curr Biol, 2022.

Thurman, A.R., J. Ravel, P. Gajer, M.A. Marzinke, L.A. Ouattara, T. Jacot, M.M. Peet, M.R. Clark, and G.F. Doncel, Vaginal Microbiota and Mucosal Pharmacokinetics of Tenofovir in Healthy Women Using a 90-Day Tenofovir/Levonorgestrel Vaginal Ring. Front Cell Infect Microbiol, 2022. 12: p. 799501.

Tessandier, N., I.B. Uysal, B. Elie, C. Selinger, C. Bernat, V. Boue, S. Grasset, S. Groc, M. Rahmoun, B. Reyne, N. Bender, M. Bonneau, C. Graf, V. Tribout, V. Foulongne, J. Ravel, T. Waterboer, C. Hirtz, I.G. Bravo, J. Reynes, M. Segondy, C.L. Murall, N. Boulle, T. Kamiya, and S. Alizon, Does exposure to different types of menstrual protections affect the vaginal environment? Mol Ecol, 2022.

Tamarelle, J., M.D. Shardell, J. Ravel, and R.M. Brotman, Factors Associated With Incidence and Spontaneous Clearance of Molecular-Bacterial Vaginosis: Results From a Longitudinal Frequent-Sampling Observational Study. Sex Transm Dis, 2022. 49(9): p. 649-656.

Mocci, E., T. Goto, J. Chen, S. Ament, R.J. Traub, and S.G. Dorsey, Early and Late Transcriptional Changes in Blood, Neural, and Colon Tissues in Rat Models of Stress-Induced and Comorbid Pain Hypersensitivity Reveal Regulatory Roles in Neurological Disease. Front Pain Res (Lausanne), 2022. 3: p. 886042.

Ma, B., S. Sundararajan, G. Nadimpalli, M. France, E. McComb, L. Rutt, J.M. Lemme-Dumit, E. Janofsky, L.S. Roskes, P. Gajer, L. Fu, H. Yang, M. Humphrys, L.J. Tallon, L. Sadzewicz, M.F. Pasetti, J. Ravel, and R.M. Viscardi, Highly Specialized Carbohydrate Metabolism Capability in Bifidobacterium Strains Associated with Intestinal Barrier Maturation in Early Preterm Infants. mBio, 2022: p. e0129922.

Lemme-Dumit, J.M., Y. Song, H.W. Lwin, C. Hernandez-Chavez, S. Sundararajan, R.M. Viscardi, J. Ravel, M.F. Pasetti, and B. Ma, Altered Gut Microbiome and Fecal Immune Phenotype in Early Preterm Infants With Leaky Gut. Front Immunol, 2022. 13: p. 815046.

Heryanto, C., J.J. Hanly, A. Mazo-Vargas, A. Tendolkar, and A. Martin, Mapping and CRISPR homology-directed repair of a recessive white eye mutation in Plodia moths. iScience, 2022. 25(3): p. 103885.

Hanly, J.J., L. Livraghi, C. Heryanto, W.O. McMillan, C.D. Jiggins, L.E. Gilbert, and A. Martin, A large deletion at the cortex locus eliminates butterfly wing patterning. G3 (Bethesda), 2022.

Grant-Beurmann, S., J. Jumare, N. Ndembi, O. Matthew, A. Shutt, A. Omoigberale, O.A. Martin, C.M. Fraser, and M. Charurat, Dynamics of the infant gut microbiota in the first 18 months of life: the impact of maternal HIV infection and breastfeeding. Microbiome, 2022. 10(1): p. 61.

Goedert, J.J., Z. Wu, C.H. Yonehara, T.B. Frankland, R. Sinha, G.S. Jones, Y. Wan, J. Ravel, N. Zhao, and S.A. Honda, Reusing a prepaid health plan's fecal immunochemical tests for microbiome associations with colorectal adenoma. Sci Rep, 2022. 12(1): p. 14801.

Ficarrotta, V., J.J. Hanly, L.S. Loh, C.M. Francescutti, A. Ren, K. Tunstrom, C.W. Wheat, A.H. Porter, B.A. Counterman, and A. Martin, A genetic switch for male UV iridescence in an incipient species pair of sulphur butterflies. Proc Natl Acad Sci U S A, 2022. 119(3).

Delgado-Diaz, D.J., B. Jesaveluk, J.A. Hayward, D. Tyssen, A. Alisoltani, M. Potgieter, L. Bell, E. Ross, A. Iranzadeh, I. Allali, S. Dabee, S. Barnabas, H. Gamieldien, J.M. Blackburn, N. Mulder, S.B. Smith, V.L. Edwards, A.D. Burgener, L.G. Bekker, J. Ravel, J.S. Passmore, L. Masson, A.C. Hearps, and G. Tachedjian, Lactic acid from vaginal microbiota enhances cervicovaginal epithelial barrier integrity by promoting tight junction protein expression. Microbiome, 2022. 10(1): p. 141.

Byrska-Bishop, M., U.S. Evani, X. Zhao, A.O. Basile, H.J. Abel, A.A. Regier, A. Corvelo, W.E. Clarke, R. Musunuri, K. Nagulapalli, S. Fairley, A. Runnels, L. Winterkorn, E. Lowy, C. Human Genome Structural Variation, F. Paul, S. Germer, H. Brand, I.M. Hall, M.E. Talkowski, G. Narzisi, and M.C. Zody, High-coverage whole-genome sequencing of the expanded 1000 Genomes Project cohort including 602 trios. Cell, 2022. 185(18): p. 3426-3440 e19.

Brown, S.E., X. He, M.D. Shardell, J. Ravel, K.G. Ghanem, J.M. Zenilman, and R.M. Brotman, Douching cessation and molecular bacterial vaginosis: a reanalysis of archived specimens. Sex Transm Infect, 2022.

Adedrian, T., S. Hitchcock, L.M. O'Hara, J.M. Michalski, J.K. Johnson, D.P. Calfee, L.G. Miller, T.H. Hazen, A.D. Harris, and D.A. Rasko, Comparative Genomics Identifies Features Associated with Methicillin-Resistant Staphylococcus aureus (MRSA) Transmission in Hospital Settings. mSphere, 2022: p. e0011622.

Zhao, N., D.F. Khamash, H. Koh, A. Voskertchian, E. Egbert, E.F. Mongodin, J.R. White, L. Hittle, E. Colantuoni, and A.M. Milstone, Low Diversity in Nasal Microbiome Associated With Staphylococcus aureus Colonization and Bloodstream Infections in Hospitalized Neonates. Open Forum Infect Dis, 2021. 8(10): p. ofab475.

Younis, R.H., I. Ghita, M. Elnaggar, R. Chaisuparat, V.I. Theofilou, D. Dyalram, R.A. Ord, E. Davila, L.J. Tallon, J.C. Papadimitriou, T.J. Webb, S.M. Bentzen, and J.E. Lubek, Soluble Sema4D in Plasma of Head and Neck Squamous Cell Carcinoma Patients Is Associated With Underlying Non-Inflamed Tumor Profile. Front Immunol, 2021. 12: p. 596646.

Tvedte, E.S., J. Michalski, S. Cheng, R.S. Patkus, L.J. Tallon, L. Sadzewicz, V.M. Bruno, J.C. Silva, D.A. Rasko, and J.C. Dunning Hotopp, Evaluation of a high-throughput, cost-effective Illumina library preparation kit. Sci Rep, 2021. 11(1): p. 15925.

Tvedte, E.S., M. Gasser, B.C. Sparklin, J. Michalski, C.E. Hjelmen, J.S. Johnston, X. Zhao, R. Bromley, L.J. Tallon, L. Sadzewicz, D.A. Rasko, and J.C.D. Hotopp, Comparison of long read sequencing technologies in interrogating bacteria and fly genomes.G3 (Bethesda), 2021.

Tuddenham, S., C.A. Stennett, R.A. Cone, J. Ravel, A.N. Macintyre, K.G. Ghanem, X. He, and R.M. Brotman, Vaginal cytokine profile and microbiota before and after lubricant use compared with condomless vaginal sex: a preliminary observational study. BMC Infect Dis, 2021. 21(1): p. 973.

Thapa, E., J. Aluvathingal, S. Nadendla, A. Mehta, H. Tettelin, and N.J. Weyand, Complete Genome Sequence of Neisseria musculi Using Illumina and PacBio Sequencing. Microbiol Resour Announc, 2021. 10(23): p. e0045221.

Stucke, E.M., A. Dara, A. Dwivedi, T.K. Hodges, S. Ott, D. Coulibaly, A.K. Kone, K. Traore, B. Guindo, B.M. Tangara, A. Niangaly, M. Daou, I. Diarra, Y. Tolo, M. Sissoko, L.J. Tallon, L. Sadzewicz, A.E. Zhou, M.B. Laurens, A. Ouattara, B. Kouriba, O.K. Doumbo, S. Takala-Harrison, D. Serre, C.V. Plowe, M.A. Thera, M.A. Travassos, and J.C. Silva, Successful Profiling of Plasmodium falciparum var Gene Expression in Clinical Samples via a Custom Capture Array. mSystems, 2021: p. e0022621.

Sikorski, M.J., T.H. Hazen, G. Vyas, J.M. Michalski, and D.A. Rasko, Draft Genome Sequences of Two Enteroinvasive Escherichia coli Strains Representative of Major Enteroinvasive E. coli Clades.Microbiol Resour Announc, 2021. 10(23): p. e0031921.

Shardell, M., P.E. Gravitt, A.E. Burke, J. Ravel, and R.M. Brotman, Association of Vaginal Microbiota with Signs and Symptoms of the Genitourinary Syndrome of Menopause across Reproductive Stages. J Gerontol A Biol Sci Med Sci, 2021.

Shah, Z., M.T. Naung, K.A. Moser, M. Adams, A.G. Buchwald, A. Dwivedi, A. Ouattara, K.B. Seydel, D.P. Mathanga, A.E. Barry, D. Serre, M.K. Laufer, J.C. Silva, and S. Takala-Harrison, Whole-genome analysis of Malawian Plasmodium falciparum isolates identifies possible targets of allele-specific immunity to clinical malaria. PLoS Genet, 2021. 17(5): p. e1009576.

Roghmann, M.C., A.D. Lydecker, M. Shardell, R.T. DeBoy, J.K. Johnson, L. Zhao, L.L. Hittle, and E.F. Mongodin, Effect of mupirocin for Staphylococcus aureus decolonization on the microbiome of the nose and throat in community and nursing home dwelling adults. PLoS One, 2021. 16(6): p. e0252004.

Piacentino, D., S. Grant-Beurmann, C. Vizioli, X. Li, C.F. Moore, V. Ruiz-Rodado, M.R. Lee, P.V. Joseph, C.M. Fraser, E.M. Weerts, and L. Leggio, Gut microbiome and metabolome in a non-human primate model of chronic excessive alcohol drinking. Transl Psychiatry, 2021. 11(1): p. 609.

Novak, J., J. Ravel, B. Ma, C.S.T. Ferreira, A.D.R. Tristao, M.G. Silva, and C. Marconi, Characteristics associated with Lactobacillus iners-dominated vaginal microbiota. Sex Transm Infect, 2021.

Mtshali, A., J.E. San, F. Osman, N. Garrett, C. Balle, J. Giandhari, H. Onywera, K. Mngomezulu, G. Mzobe, T. de Oliveira, A. Rompalo, A. Mindel, S.S. Abdool Karim, J. Ravel, J.S. Passmore, Q. Abdool Karim, H.B. Jaspan, L.J.P. Liebenberg, and S. Ngcapu, Temporal Changes in Vaginal Microbiota and Genital Tract Cytokines Among South African Women Treated for Bacterial Vaginosis. Front Immunol, 2021. 12: p. 730986.

Milon, B., E.D. Shulman, K.S. So, C.R. Cederroth, E.L. Lipford, M. Sperber, J.B. Sellon, H. Sarlus, G. Pregernig, B. Shuster, Y. Song, S. Mitra, J. Orvis, Z. Margulies, Y. Ogawa, C. Shults, D.A. Depireux, A.T. Palermo, B. Canlon, J. Burns, R. Elkon, and R. Hertzano, A cell-type-specific atlas of the inner ear transcriptional response to acoustic trauma. Cell Rep, 2021. 36(13): p. 109758.

Mattick, J., S. Libro, R. Bromley, W. Chaicumpa, M. Chung, D. Cook, M.B. Khan, N. Kumar, Y.L. Lau, S. Misra-Bhattacharya, R. Rao, L. Sadzewicz, A. Saeung, M. Shahab, B.C. Sparklin, A. Steven, J.D. Turner, L.J. Tallon, M.J. Taylor, A.R. Moorhead, M. Michalski, J.M. Foster, and J.C. Dunning Hotopp, X-treme loss of sequence diversity linked to neo-X chromosomes in filarial nematodes. PLoS Negl Trop Dis, 2021. 15(10): p. e0009838.

Martin, O.A., S. Grant-Beurmann, E.R. Orellana, A. Hajnal, and C.M. Fraser, Changes in the Gut Microbiota Following Bariatric Surgery Are Associated with Increased Alcohol Intake in a Female Rat Model. Alcohol Alcohol, 2021.

Malayil, L., S. Chattopadhyay, E.F. Mongodin, and A.R. Sapkota, Coupled DNA-labeling and sequencing approach enables the detection of viable-but-non-culturable Vibrio spp. in irrigation water sources in the Chesapeake Bay watershed. Environ Microbiome, 2021. 16(1): p. 13.

Malaiya, S., M. Cortes-Gutierrez, B.R. Herb, S.R. Coffey, S.R.W. Legg, J.P. Cantle, C. Colantuoni, J.B. Carroll, and S.A. Ament, Single-Nucleus RNA-Seq Reveals Dysregulation of Striatal Cell Identity Due to Huntington's Disease Mutations. J Neurosci, 2021.

Lu, T.Y., C. Human Genome Structural Variation, and M.J.P. Chaisson, Profiling variable-number tandem repeat variation across populations using repeat-pangenome graphs. Nat Commun, 2021. 12(1): p. 4250.

Lewis, A., T.P. McKeon, A.J. De Roos, J. Ravel, M.A. Elovitz, and H.H. Burris, Associations of public water system trihalomethane exposure during pregnancy with spontaneous preterm birth and the cervicovaginal microbial-immune state. Environ Res, 2021: p. 111288.

Jasarevic, E., E.M. Hill, P.J. Kane, L. Rutt, T. Gyles, L. Folts, K.D. Rock, C.D. Howard, K.E. Morrison, J. Ravel, and T.L. Bale, The composition of human vaginal microbiota transferred at birth affects offspring health in a mouse model. Nat Commun, 2021. 12(1): p. 6289.

Im, H., K.L. Kruckow, A. D'Mello, F. Ganaie, E. Martinez, J.N. Luck, K.H. Cichos, A.N. Riegler, X. Song, E. Ghanem, J.S. Saad, M.H. Nahm, H. Tettelin, and C.J. Orihuela, Anatomical site-specific carbohydrate availability impacts Streptococcus pneumoniae virulence and fitness during colonization and disease. Infect Immun, 2021: p. IAI0045121.

Hsiao, C.J., J.N. Paulson, S. Singh, E.F. Mongodin, K.C. Carroll, C.M. Fraser, P. Rock, and N. Faraday, Nasal Microbiota and Infectious Complications After Elective Surgical Procedures. JAMA Netw Open, 2021. 4(4): p. e218386.

Hayward, R.J., M.S. Humphrys, W.M. Huston, and G.S.A. Myers, Dual RNA-seq analysis of in vitro infection multiplicity and RNA depletion methods in Chlamydia-infected epithelial cells. Sci Rep, 2021. 11(1): p. 10399.

Garofano, K., C.S. Park, C. Alarcon, J. Avitia, A. Barbour, D. Diemert, C.M. Fraser, P.N. Friedman, A. Horvath, K. Rashid, M. Shaazuddin, A. Sidahmed, T.J. O'Brien, M.A. Perera, and N.H. Lee, Differences in the platelet mRNA landscape portend racial disparities in platelet function and suggest novel therapeutic targets. Clin Pharmacol Ther, 2021.

Garcia-Bayona, L., M.J. Coyne, and L.E. Comstock, Mobile Type VI secretion system loci of the gut Bacteroidales display extensive intra-ecosystem transfer, multi-species spread and geographical clustering. PLoS Genet, 2021. 17(4): p. e1009541.

Ferreira, C.S.T., C. Marconi, C. Parada, J. Ravel, and M.G. da Silva, Sialidase Activity in the Cervicovaginal Fluid Is Associated With Changes in Bacterial Components of Lactobacillus-Deprived Microbiota. Front Cell Infect Microbiol, 2021. 11: p. 813520.

Feder, K.A., A. Patel, V.R. Vepachedu, C. Dominguez, E.N. Keller, L. Klein, C. Kim, T. Blood, J. Hyun, T.W. Williams, K.A. Feldman, H.H. Mostafa, C.P. Morris, J. Ravel, M. Duwell, D. Blythe, and R. Myers, Association of E484K spike protein mutation with SARS-CoV-2 infection in vaccinated persons---Maryland, January - May 2021. Clin Infect Dis, 2021.

Ebert, P., P.A. Audano, Q. Zhu, B. Rodriguez-Martin, D. Porubsky, M.J. Bonder, A. Sulovari, J. Ebler, W. Zhou, R. Serra Mari, F. Yilmaz, X. Zhao, P. Hsieh, J. Lee, S. Kumar, J. Lin, T. Rausch, Y. Chen, J. Ren, M. Santamarina, W. Hops, H. Ashraf, N.T. Chuang, X. Yang, K.M. Munson, A.P. Lewis, S. Fairley, L.J. Tallon, W.E. Clarke, A.O. Basile, M. Byrska-Bishop, A. Corvelo, U.S. Evani, T.Y. Lu, M.J.P. Chaisson, J. Chen, C. Li, H. Brand, A.M. Wenger, M. Ghareghani, W.T. Harvey, B. Raeder, P. Hasenfeld, A.A. Regier, H.J. Abel, I.M. Hall, P. Flicek, O. Stegle, M.B. Gerstein, J.M.C. Tubio, Z. Mu, Y.I. Li, X. Shi, A.R. Hastie, K. Ye, Z. Chong, A.D. Sanders, M.C. Zody, M.E. Talkowski, R.E. Mills, S.E. Devine, C. Lee, J.O. Korbel, T. Marschall, and E.E. Eichler, Haplotype-resolved diverse human genomes and integrated analysis of structural variation. Science, 2021.

Danko, D., D. Bezdan, E.E. Afshin, S. Ahsanuddin, C. Bhattacharya, D.J. Butler, K.R. Chng, D. Donnellan, J. Hecht, K. Jackson, K. Kuchin, M. Karasikov, A. Lyons, L. Mak, D. Meleshko, H. Mustafa, B. Mutai, R.Y. Neches, A. Ng, O. Nikolayeva, T. Nikolayeva, E. Png, K.A. Ryon, J.L. Sanchez, H. Shaaban, M.A. Sierra, D. Thomas, B. Young, O.O. Abudayyeh, J. Alicea, M. Bhattacharyya, R. Blekhman, E. Castro-Nallar, A.M. Canas, A.D. Chatziefthimiou, R.W. Crawford, F. De Filippis, Y. Deng, C. Desnues, E. Dias-Neto, M. Dybwad, E. Elhaik, D. Ercolini, A. Frolova, D. Gankin, J.S. Gootenberg, A.B. Graf, D.C. Green, I. Hajirasouliha, J.J.A. Hastings, M. Hernandez, G. Iraola, S. Jang, A. Kahles, F.J. Kelly, K. Knights, N.C. Kyrpides, P.P. Labaj, P.K.H. Lee, M.H.Y. Leung, P.O. Ljungdahl, G. Mason-Buck, K. McGrath, C. Meydan, E.F. Mongodin, M.O. Moraes, N. Nagarajan, M. Nieto-Caballero, H. Noushmehr, M. Oliveira, S. Ossowski, O.O. Osuolale, O. Ozcan, D. Paez-Espino, N. Rascovan, H. Richard, G. Ratsch, L.M. Schriml, T. Semmler, O.U. Sezerman, L. Shi, T. Shi, R. Siam, L.H. Song, H. Suzuki, D.S. Court, S.W. Tighe, X. Tong, K.I. Udekwu, J.A. Ugalde, B. Valentine, D.I. Vassilev, E.M. Vayndorf, T.P. Velavan, J. Wu, M.M. Zambrano, J. Zhu, S. Zhu, C.E. Mason, and S.U.B.C. International Meta, A global metagenomic map of urban microbiomes and antimicrobial resistance. Cell, 2021.

Dammann, A.N., A.B. Chamby, A.J. Catomeris, K.M. Davidson, H. Tettelin, J.P. van Pijkeren, K.P. Gopalakrishna, M.F. Keith, J.L. Elder, A.J. Ratner, and T.A. Hooven, Genome-Wide fitness analysis of group B Streptococcus in human amniotic fluid reveals a transcription factor that controls multiple virulence traits. PLoS Pathog, 2021. 17(3): p. e1009116.

Chung, M., R.S. Adkins, J.S.A. Mattick, K.R. Bradwell, A.C. Shetty, L. Sadzewicz, L.J. Tallon, C.M. Fraser, D.A. Rasko, A. Mahurkar, and J.C. Dunning Hotopp, FADU: a Quantification Tool for Prokaryotic Transcriptomic Analyses. mSystems, 2021. 6(1).

Chattopadhyay, S., L. Malayil, E.F. Mongodin, and A.R. Sapkota, Nicotine concentration and mentholation affect bacterial community diversity in SPECTRUM research cigarettes. Appl Microbiol Biotechnol, 2021.

Chattopadhyay, S., J.D. Arnold, L. Malayil, L. Hittle, E.F. Mongodin, K.S. Marathe, V. Gomez-Lobo, and A.R. Sapkota, Potential role of the skin and gut microbiota in premenarchal vulvar lichen sclerosus: A pilot case-control study. PLoS One, 2021. 16(1): p. e0245243.

Cannon, M.V., H.N. Bogale, D. Bhalerao, K. Keita, D. Camara, Y. Barry, M. Keita, D. Coulibaly, A.K. Kone, O.K. Doumbo, M.A. Thera, C.V. Plowe, M.A. Travassos, S.R. Irish, J. Yeroshefsky, J. Dorothy, B. Prendergast, B. St Laurent, M.L. Fritz, and D. Serre, High-throughput detection of eukaryotic parasites and arboviruses in mosquitoes. Biol Open, 2021. 10(7).

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Nickerson, K.P., S. Senger, Y. Zhang, R. Lima, S. Patel, L. Ingano, W.A. Flavahan, D.K.V. Kumar, C.M. Fraser, C.S. Faherty, M.B. Sztein, M. Fiorentino, and A. Fasano, Salmonella Typhi Colonization Provokes Extensive Transcriptional Changes Aimed at Evading Host Mucosal Immune Defense During Early Infection of Human Intestinal Tissue. EBioMedicine, 2018.

Murphy, T.F., A.L. Brauer, M.M. Pettigrew, E.R. LaFontaine, and H. Tettelin, Persistence of Moraxella catarrhalis in Chronic Obstructive Pulmonary Disease and Regulation of the Hag/MID Adhesin. J Infect Dis, 2018.

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Shannon, B., T.J. Yi, S. Perusini, P. Gajer, B. Ma, M.S. Humphrys, J. Thomas-Pavanel, L. Chieza, P. Janakiram, M. Saunders, W. Tharao, S. Huibner, K. Shahabi, J. Ravel, A. Rebbapragada, and R. Kaul, Association of HPV infection and clearance with cervicovaginal immunology and the vaginal microbiota. Mucosal Immunol, 2017.

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Hooven, T.A., A.J. Catomeris, M. Bonakdar, L.J. Tallon, I. Santana-Cruz, S. Ott, S.C. Daugherty, H. Tettelin, and A.J. Ratner, The Streptococcus agalactiae stringent response enhances virulence and persistence in human blood. Infect Immun, 2017.

Hazen, T.H., J. Michalski, S. Nagaraj, I.N. Okeke, and D.A. Rasko, Characterization of a large antibiotic resistance plasmid found in enteropathogenic Escherichia coli strain B171 and its relatedness to plasmids of diverse E. coli and Shigella. Antimicrob Agents Chemother, 2017.

Hazen, T.H., J. Michalski, Q. Luo, A.C. Shetty, S.C. Daugherty, J.M. Fleckenstein, and D.A. Rasko, Comparative genomics and transcriptomics of Escherichia coli isolates carrying virulence factors of both enteropathogenic and enterotoxigenic E. coli. Sci Rep, 2017. 7(1): p. 3513.

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Dunning Hotopp, J.C., B.E. Slatko, and J.M. Foster, Targeted Enrichment and Sequencing of Recent Endosymbiont-Host Lateral Gene Transfers. Sci Rep, 2017. 7(1): p. 857.

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Wallace, L., S.C. Daugherty, S. Nagaraj, J.K. Johnson, A.D. Harris, and D.A. Rasko, Use of Comparative Genomics To Characterize the Diversity of Acinetobacter baumannii Surveillance Isolates in a Health Care Institution. Antimicrob Agents Chemother, 2016. 60(10): p. 5933-41.

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Leonard, S.R., M.K. Mammel, D.A. Rasko, and D.W. Lacher, Hybrid Shiga Toxin-Producing and Enterotoxigenic Escherichia sp. Cryptic Lineage 1 Strain 7v Harbors a Hybrid Plasmid. Appl Environ Microbiol, 2016. 82(14): p. 4309-19.

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Hazen, T.H., S.R. Leonard, K.A. Lampel, D.W. Lacher, A.T. Maurelli, and D.A. Rasko, Investigating the Relatedness of Enteroinvasive Escherichia coli to Other E. coli and Shigella Isolates by Using Comparative Genomics. Infect Immun, 2016. 84(8): p. 2362-71.

Del Canto, F., M. O'Ryan, M. Pardo, A. Torres, D. Gutierrez, L. Cadiz, R. Valdes, A. Mansilla, R. Martinez, D. Hernandez, B. Caro, M.M. Levine, D.A. Rasko, C.M. Hill, M. Pop, O.C. Stine, and R. Vidal, Chaperone-Usher Pili Loci of Colonization Factor-Negative Human Enterotoxigenic Escherichia coli. Front Cell Infect Microbiol, 2016. 6: p. 200.

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Bruno, V.M., A.C. Shetty, J. Yano, P.L. Fidel, Jr., M.C. Noverr, and B.M. Peters, Transcriptomic Analysis of Vulvovaginal Candidiasis Identifies a Role for the NLRP3 Inflammasome. MBio, 2015. 6(2).

Brady, R.A., V.M. Bruno, and D.L. Burns, RNA-Seq Analysis of the Host Response to Staphylococcus aureus Skin and Soft Tissue Infection in a Mouse Model. PLoS One, 2015. 10(4): p. e0124877.

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Sanjar, F., T.H. Hazen, S.M. Shah, S.S. Koenig, S. Agrawal, S. Daugherty, L. Sadzewicz, L.J. Tallon, M.K. Mammel, P. Feng, R. Soderlund, P.I. Tarr, C. Debroy, E.G. Dudley, T.A. Cebula, J. Ravel, C.M. Fraser, D.A. Rasko, and M. Eppinger, Genome Sequence of Escherichia coli O157:H7 Strain 2886-75, Associated with the First Reported Case of Human Infection in the United States. Genome announcements, 2014. 2(1).

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Liggett, S.B., Y.A. Bochkov, T. Pappas, R.F. Lemanske, Jr., J.E. Gern, N. Sengamalay, X. Zhao, Q. Su, C.M. Fraser, and A.C. Palmenberg, Genome sequences of rhinovirus C isolates from wisconsin pediatric respiratory studies. Genome Announc, 2014. 2(2).

Klasson, L., N. Kumar, R. Bromley, K. Sieber, M. Flowers, S.H. Ott, L.J. Tallon, S.G. Andersson, and J.C. Dunning Hotopp, Extensive duplication of the Wolbachia DNA in chromosome four of Drosophila ananassae. BMC Genomics, 2014. 15(1): p. 1097.

Jacobs, A.C., M.G. Thompson, C.C. Black, J.L. Kessler, L.P. Clark, C.N. McQueary, H.Y. Gancz, B.W. Corey, J.K. Moon, Y. Si, M.T. Owen, J.D. Hallock, Y.I. Kwak, A. Summers, C.Z. Li, D.A. Rasko, W.F. Penwell, C.L. Honnold, M.C. Wise, P.E. Waterman, E.P. Lesho, R.L. Stewart, L.A. Actis, T.J. Palys, D.W. Craft, and D.V. Zurawski, AB5075, a Highly Virulent Isolate of Acinetobacter baumannii, as a Model Strain for the Evaluation of Pathogenesis and Antimicrobial Treatments. MBio, 2014. 5(3).

Ioannidis, P., Y. Lu, N. Kumar, T. Creasy, S. Daugherty, M.C. Chibucos, J. Orvis, A. Shetty, S. Ott, M. Flowers, N. Sengamalay, L.J. Tallon, L. Pick, and J.C. Hotopp, Rapid transcriptome sequencing of an invasive pest, the brown marmorated stink bug Halyomorpha halys. BMC Genomics, 2014. 15(1): p. 738.

Hosgood, H.D., 3rd, A.R. Sapkota, N. Rothman, T. Rohan, W. Hu, J. Xu, R. Vermeulen, X. He, J.R. White, G. Wu, F. Wei, E.F. Mongodin, and Q. Lan, The potential role of lung microbiota in lung cancer attributed to household coal burning exposures. Environ Mol Mutagen, 2014.

Hazen, T.H., L. Zhao, J.W. Sahl, G. Robinson, A.D. Harris, D.A. Rasko, and J.K. Johnson, Characterization of Klebsiella sp. 10982, a colonizer of humans that contains novel antibiotic resistance alleles and exhibits genetic similarities to plant and clinical Klebsiella isolates. Antimicrobial agents and chemotherapy, 2014.

Hazen, T.H., L. Zhao, M.A. Boutin, A. Stancil, G. Robinson, A.D. Harris, D.A. Rasko, and J.K. Johnson, Comparative genomics of an IncA/C multidrug resistance plasmid from Escherichia coli and Klebsiella species isolated from ICU patients: the utility of whole genome sequencing in healthcare settings. Antimicrob Agents Chemother, 2014.

Hazen, T.H., M.S. Humphrys, J.B. Ochieng, M. Parsons, C.A. Bopp, C.E. O'Reilly, E. Mintz, and D.A. Rasko, Draft Genome Sequences of Nine Enteropathogenic Escherichia coli Strains from Kenya. Genome Announc, 2014. 2(3).

Fadrosh, D.W., B. Ma, P. Gajer, N. Sengamalay, S. Ott, R.M. Brotman, and J. Ravel, An improved dual-indexing approach for multiplexed 16S rRNA gene sequencing on the Illumina MiSeq platform. Microbiome, 2014. 2(1): p. 6.

Etienne, K.A., M.C. Chibucos, Q. Su, J. Orvis, S. Daugherty, S. Ott, N.A. Sengamalay, C.M. Fraser, S.R. Lockhart, and V.M. Bruno, Draft Genome Sequence of Mortierella alpina Isolate CDC-B6842. Genome announcements, 2014. 2(1).

Eppinger, M., T. Pearson, S.S. Koenig, O. Pearson, N. Hicks, S. Agrawal, F. Sanjar, K. Galens, S. Daugherty, J. Crabtree, R.S. Hendriksen, L.B. Price, B.P. Upadhyay, G. Shakya, C.M. Fraser, J. Ravel, and P.S. Keim, Genomic epidemiology of the haitian cholera outbreak: a single introduction followed by rapid, extensive, and continued spread characterized the onset of the epidemic. MBio, 2014. 5(6).

Dugan, V.G., S.J. Emrich, G.I. Giraldo-Calderon, O.S. Harb, R.M. Newman, B.E. Pickett, L.M. Schriml, T.B. Stockwell, C.J. Stoeckert, Jr., D.E. Sullivan, I. Singh, D.V. Ward, A. Yao, J. Zheng, T. Barrett, B. Birren, L. Brinkac, V.M. Bruno, E. Caler, S. Chapman, F.H. Collins, C.A. Cuomo, V. Di Francesco, S. Durkin, M. Eppinger, M. Feldgarden, C. Fraser, W.F. Fricke, M. Giovanni, M.R. Henn, E. Hine, J.D. Hotopp, I. Karsch-Mizrachi, J.C. Kissinger, E.M. Lee, P. Mathur, E.F. Mongodin, C.I. Murphy, G. Myers, D.E. Neafsey, K.E. Nelson, W.C. Nierman, J. Puzak, D. Rasko, D.S. Roos, L. Sadzewicz, J.C. Silva, B. Sobral, R.B. Squires, R.L. Stevens, L. Tallon, H. Tettelin, D. Wentworth, O. White, R. Will, J. Wortman, Y. Zhang, and R.H. Scheuermann, Standardized metadata for human pathogen/vector genomic sequences. PLoS One, 2014. 9(6): p. e99979.

Donati, M., H. Huot-Creasy, M. Humphrys, M. Di Paolo, A. Di Francesco, and G.S. Myers, Genome Sequence of Chlamydia suis MD56, Isolated from the Conjunctiva of a Weaned Piglet. Genome Announc, 2014. 2(3).

Delaneau, O., J. Marchini, C. Genomes Project, and C. Genomes Project, Integrating sequence and array data to create an improved 1000 Genomes Project haplotype reference panel. Nat Commun, 2014. 5: p. 3934.

Colonna, V., Q. Ayub, Y. Chen, L. Pagani, P. Luisi, M. Pybus, E. Garrison, Y. Xue, C. Tyler-Smith, C. Genomes Project, G.R. Abecasis, A. Auton, L.D. Brooks, M.A. DePristo, R.M. Durbin, R.E. Handsaker, H.M. Kang, G.T. Marth, and G.A. McVean, Human genomic regions with exceptionally high levels of population differentiation identified from 911 whole-genome sequences. Genome Biol, 2014. 15(6): p. R88.

Zubair, S., E.P. de Villiers, M. Younan, G. Andersson, H. Tettelin, D.R. Riley, J. Jores, E. Bongcam-Rudloff, and R.P. Bishop, Genome Sequences of Two Pathogenic Streptococcus agalactiae Isolates from the One-Humped Camel Camelus dromedarius. Genome announcements, 2013. 1(4).

Zapata, J.C., M. Goicochea, Y. Nadai, L.M. Eyzaguirre, J.K. Carr, L.J. Tallon, L. Sadzewicz, G. Myers, C.M. Fraser, Q. Su, M. Djavani, I.S. Lukashevich, and M.S. Salvato, Genetic variation in vitro and in vivo of an attenuated Lassa vaccine candidate. Journal of virology, 2013.

Yu, G., D. Fadrosh, B. Ma, J. Ravel, and J.J. Goedert, Anal microbiota profiles in HIV-positive and HIV-negative MSM. AIDS, 2013.

Veluchamy, A., X. Lin, F. Maumus, M. Rivarola, J. Bhavsar, T. Creasy, K. O'Brien, N.A. Sengamalay, L.J. Tallon, A.D. Smith, E. Rayko, I. Ahmed, S.L. Crom, G.K. Farrant, J.Y. Sgro, S.A. Olson, S.S. Bondurant, A. Allen, P.D. Rabinowicz, M.R. Sussman, C. Bowler, and L. Tirichine, Insights into the role of DNA methylation in diatoms by genome-wide profiling in Phaeodactylum tricornutum. Nature communications, 2013. 4: p. 2091.

Subashchandrabose, S., T.H. Hazen, D.A. Rasko, and H.L. Mobley, Draft genome sequences of five recent human uropathogenic Escherichia coli isolates.Pathogens and disease, 2013.

Sambuughin, N., X. Liu, S. Bijarnia, T. Wallace, I.C. Verma, S. Hamilton, S. Muldoon, L.J. Tallon, and S. Wang, Exome sequencing reveals SCO2 mutations in a family presented with fatal infantile hyperthermia. J Hum Genet, 2013.

Robinson, C.K., J. Wierzchos, C. Black, A. Crits-Christoph, B. Ma, J. Ravel, C. Ascaso, O. Artieda, S. Valea, M. Roldan, B. Gomez-Silva, and J. Diruggiero, Microbial diversity and the presence of algae in halite endolithic communities are correlated to atmospheric moisture in the hyper-arid zone of the Atacama Desert. Environmental microbiology, 2013.

Ravel J, B.R., Gajer P, Ma B, Nandy M, Fadrosh D, Sakamoto J, Koenig S, Fu L, Zhou X, Hickey RJ, Schwebke JR, Forney LJ, Daily temporal dynamics of vaginal microbiota before, during and after episodes of bacterial vaginosis. Microbiome, 2013. 1(1).

Poelchau, M.F., J.A. Reynolds, C.G. Elsik, D.L. Denlinger, and P.A. Armbruster, Deep sequencing reveals complex mechanisms of diapause preparation in the invasive mosquito, Aedes albopictus. Proceedings. Biological sciences / The Royal Society, 2013. 280(1759): p. 20130143.

Poelchau M.F., R.J.A., Elsik C.G., Denlinger D.L., Armbruster P, Deep sequencing reveals complex mechanisms of diapuase preparation in the invasive mosquito, Aedes albopictus. Proceedings of the Royal Society of London, 2013. 280(20130143).

Planet, P.J., R. Rampersaud, S.R. Hymes, S. Whittier, P.A. Della-Latta, A. Narechania, S.C. Daugherty, I. Santana-Cruz, R. Desalle, J. Ravel, and A.J. Ratner, Genome Sequence of the Human Abscess Isolate Streptococcus intermedius BA1. Genome announcements, 2013. 1(1).

Mongodin, E.F., S.R. Casjens, J.F. Bruno, Y. Xu, E.F. Drabek, D.R. Riley, B.L. Cantarel, P.E. Pagan, Y.A. Hernandez, L.C. Vargas, J.J. Dunn, S.E. Schutzer, C.M. Fraser, W.G. Qiu, and B.J. Luft, Inter- and intra-specific pan-genomes of Borrelia burgdorferi sensu lato: genome stability and adaptive radiation. BMC Genomics, 2013. 14(1): p. 693.

Magoc, T., S. Pabinger, S. Canzar, X. Liu, Q. Su, D. Puiu, L.J. Tallon, and S.L. Salzberg, GAGE-B: An Evaluation of Genome Assemblers for Bacterial Organisms. Bioinformatics, 2013.

Liu, X., Q. Hu, S. Liu, L.J. Tallo, L. Sadzewicz, C.A. Schettine, M. Nikiforov, E.N. Klyushnenkova, and Y. Ionov, Serum Antibody Repertoire Profiling Using In Silico Antigen Screen. PLoS ONE, 2013. 8(6): p. e67181.

Kimaro Mlacha, S.Z., S. Romero-Steiner, J.C. Dunning Hotopp, N. Kumar, N. Ishmael, D.R. Riley, U. Farooq, T.H. Creasy, L.J. Tallon, X. Liu, C.S. Goldsmith, J. Sampson, G.M. Carlone, S.K. Hollingshead, J.A. Scott, and H. Tettelin, Phenotypic, genomic, and transcriptional characterization of Streptococcus pneumoniae interacting with human pharyngeal cells. BMC Genomics, 2013. 14(1): p. 383.

Khurana, E., Y. Fu, V. Colonna, X.J. Mu, H.M. Kang, T. Lappalainen, A. Sboner, L. Lochovsky, J. Chen, A. Harmanci, J. Das, A. Abyzov, S. Balasubramanian, K. Beal, D. Chakravarty, D. Challis, Y. Chen, D. Clarke, L. Clarke, F. Cunningham, U.S. Evani, P. Flicek, R. Fragoza, E. Garrison, R. Gibbs, Z.H. Gumus, J. Herrero, N. Kitabayashi, Y. Kong, K. Lage, V. Liluashvili, S.M. Lipkin, D.G. MacArthur, G. Marth, D. Muzny, T.H. Pers, G.R. Ritchie, J.A. Rosenfeld, C. Sisu, X. Wei, M. Wilson, Y. Xue, F. Yu, E.T. Dermitzakis, H. Yu, M.A. Rubin, C. Tyler-Smith, M. Gerstein, G.R. Abecasis, A. Auton, L.D. Brooks, M.A. DePristo, R.M. Durbin, R.E. Handsaker, and G.A. McVean, Integrative annotation of variants from 1092 humans: application to cancer genomics. Science, 2013. 342(6154): p. 1235587.

Ioannidis, P., K.L. Johnston, D.R. Riley, N. Kumar, J.R. White, K.T. Olarte, S. Ott, L.J. Tallon, J.M. Foster, M.J. Taylor, and J.C. Dunning Hotopp, Extensively duplicated and transcriptionally active recent lateral gene transfer from a bacterial Wolbachia endosymbiont to its host filarial nematode Brugia malayi. BMC Genomics, 2013. 14(1): p. 639.

Humphrys, M.S., T. Creasy, Y. Sun, A.C. Shetty, M.C. Chibucos, E.F. Drabek, C.M. Fraser, U. Farooq, N. Sengamalay, S. Ott, H. Shou, P.M. Bavoil, A. Mahurkar, and G.S. Myers, Simultaneous transcriptional profiling of bacteria and their host cells. PLoS ONE, 2013. 8(12): p. e80597.

Hazen, T.H., J.W. Sahl, C.M. Fraser, M.S. Donnenberg, F. Scheutz, and D.A. Rasko, Draft Genome Sequences of Three O157 Enteropathogenic Escherichia coli Isolates. Genome announcements, 2013. 1(4).

Harro, J.M., S. Daugherty, V.M. Bruno, M.A. Jabra-Rizk, D.A. Rasko, and M.E. Shirtliff, Draft Genome Sequence of the Methicillin-Resistant Staphylococcus aureus Isolate MRSA-M2. Genome announcements, 2013. 1(1).

Gray, T.A., J.A. Krywy, J. Harold, M.J. Palumbo, and K.M. Derbyshire, Distributive conjugal transfer in mycobacteria generates progeny with meiotic-like genome-wide mosaicism, allowing mapping of a mating identity locus. PLoS Biol, 2013. 11(7): p. e1001602.

Fricke, W.F., C. Maddox, Y. Song, and J.S. Bromberg, Human Microbiota Characterization in the Course of Renal Transplantation. American journal of transplantation : official journal of the American Society of Transplantation and the American Society of Transplant Surgeons, 2013.

Fischer, A., I. Santana-Cruz, M. Giglio, S. Nadendla, E. Drabek, E.M. Vilei, J. Frey, and J. Jores, Genome Sequence of Mycoplasma feriruminatoris sp. nov., a Fast-Growing Mycoplasma Species. Genome announcements, 2013. 1(1).

Eppinger, M., S. Daugherty, S. Agrawal, K. Galens, N. Sengamalay, L. Sadzewicz, L. Tallon, T.A. Cebula, M.K. Mammel, P. Feng, R. Soderlund, P.I. Tarr, C. Debroy, E.G. Dudley, C.M. Fraser, and J. Ravel, Whole-Genome Draft Sequences of 26 Enterohemorrhagic Escherichia coli O157:H7 Strains. Genome announcements, 2013. 1(2): p. e0013412.

Eloe-Fadrosh, E.A. and D.A. Rasko, The human microbiome: from symbiosis to pathogenesis. Annu Rev Med, 2013. 64: p. 145-63.

Eloe-Fadrosh, E.A., M.A. McArthur, A.M. Seekatz, E.F. Drabek, D.A. Rasko, M.B. Sztein, and C.M. Fraser, Impact of oral typhoid vaccination on the human gut microbiota and correlations with s. Typhi-specific immunological responses. PLoS ONE, 2013. 8(4): p. e62026.

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