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Emmanuel F. Mongodin, PhD

Academic Title:

Assistant Professor

Primary Appointment:

Microbiology and Immunology

Additional Title:

Assistant Professor, Institute for Genome Sciences

Location:

BioPark II, Room # 622

Phone (Primary):

(410) 706-6717

Fax:

(410) 706-6756

Education and Training

  • 1995 - Bachelors Degree in Cellular Biology and Physiology, option Cellular and Molecular Genetic
    • Université d'Angers, France.
    • Fellowship from the Ministère de l'Education Nationale (Department of Education).
  • 1996 - Masters Degree in Physiology and Pathology of the Respiratory and Circulatory Systems
    • Université Paris VII – Denis Diderot, France.
    • Fellowship from the Ministère de l'Education Nationale (Department of Education).
    • Thesis advisor: Pr D. Feuvray, CNRS URA 1121 – Université de Paris-Sud (France).
    • Thesis title: Na+-HCO3- and Na+/H+ co-transporters in adult rat ventricular cardiomyocytes: characterization and modulation.
  • 09/1996 – 08/1997. Military Scientist (DRET/DGA)
    • Contract with the University of Reims-Champagne-Ardenne (France), INSERM U514.
    • Supervisor: Dr S. de Bentzmann.
    • Research project: Role of bacterial adherence in the colonization of the respiratory mucosa; development of in vitro (cell culture) and ex vivo (human tissues) models of infection.
  • 2000 - Ph.D. in Biological and Medical engineering
    • INSERM U514, Université de Reims-Champagne-Ardenne, France.
    • Ph.D. fellowship from the Ministère de la Défense (DRET/DGA).
    • Thesis advisor: Dr. Sophie de Bentzmann.
    • Thesis title: Study of cellular and molecular mechanisms involved in Staphylococcus aureus adherence to human airway epithelium.
  • 01/2001 - 11/2002 - Post-Doctoral Fellow
    • Virginia Commonwealth University (VCU ; Richmond, Virginia), Division of Infectious Diseases.
    • Advisor: Dr. Gordon L. Archer.
    • Research interests: Mechanisms of antibiotic resistance (oxacillin and vancomycin) in Staphylococcus aureus and Staphylococcus epidermidis.
  • 02/2001 – 11/2002 - Visiting scientist
    • The Institute for Genomic Research (TIGR - Rockville, Maryland).
    • Collaboration with Dr. Steven R. Gill, development of S. aureus and S. epidermidis microarrays.
  • 11/2002 - 12/2004 - Staff Scientist I
    • J. Craig Venter institute, formerly known as The Institute for Genomic Research (TIGR), Microbial Genomics Department.
    • Supervisor: Dr. Karen Nelson.
  • 01/2005 - 11/2007 - Staff Scientist II
    • J. Craig Venter institute, formerly known as The Institute for Genomic Research (TIGR), Microbial Genomics Department.
    • Supervisor: Dr. K. Nelson.
  • 11/2007 – 07/2012 -  Assistant Professor - Non Tenure Track
    • Department of Microbiology and Immunology and Institute for Genome Sciences, University of Maryland School of Medicine.
  •  07/2012 – Present - Assistant Professor - Tenure Track
    • Department of Microbiology and Immunology and Institute for Genome Sciences University of Maryland School of Medicine.

Biosketch

    Originally trained as a physiologist, I am also a microbiologist with specific training and expertise in top quality research dedicated to the improvement of human health. My research focuses on the application of microbial genomics, comparative genomics and metagenomic approaches to the study of host-bacteria interactions and the microbial populations colonizing the human body.

    After I received my Ph.D from the University of Reims-Champagne Ardenne in France in 2000, where I studied the interactions between Staphyloccus aureus and the human respiratory epithelium, I completed a postdoctoral training in the laboratory of Dr. Gordon Archer (VCU, Richmond, VA) carrying out research focused on the study of antibiotic resistance in Staphylococcus aureus and epidermidis, using both comparative genomics and transcriptomics (expression profiling using microarrays) approaches. I then joined The Institute for Genome Research (TIGR; Rockville, MD) as a Staff Scientist in 2002 and later the J. Craig Venter Institute, where I actively participated in numerous genome-sequencing projects (such as Campylobacter sp., Listeria monocytogenes, Staphylococcus aureus and Staphylococcus epidermidis) and developed a strong expertise in genomics, comparative genomics as well as metagenomics.

    More recently, I joined as an Assistant Professor the Department of Microbiology and Immunology at the University of Maryland School of Medicine (SOM) and the Institute for Genome Sciences (IGS), where I developed a strong expertise in microbiome analyses, both at the microbiome level (microbial species composition and abundance), but also at the functional level (gene expression). More specifically, I have been actively involved in various metagenomic projects funded under the NIH Human Microbiome Project, where I developed various protocols, from samples collection and DNA / RNA extraction, to the analysis of the sequencing datasets. Among these, I completed with Dr. Fraser a project aimed at characterizing the microbiome associated with the healthy oral cavity in collaboration with Dr. David Relman (Stanford University), as well as two projects focused on the microbial communities inhabiting the human gut and the impact they might have on diseases such as diabetes and Crohn’s disease. Additionally, I am currently completing studies with Dr. Roghman (U. of MD School of Medicine) aimed at investigating the effect of “decolonization” regimens using mupirocin or chlorhexidine on the bacterial communities of the nose, throat and two skin sites. The information gained from this project will be crucial to advance our understanding of decolonization on the bacterial communities inhabiting the human body.

    I am also a co-principal investigator on an R01 project within a P50 Center, “Rapid Response Characterization of New and Manipulated Tobacco Products” (P50CA180523). The goals of this study is to characterize the bacterial communities associated with tobacco products, their role of in tobacco specific nitrosamine (TSNA) production, and the impact of these tobacco bacterial communities on the composition and functions of the oral microbiome of tobacco users. Finally, I am co-PI on a research project aimed at investigating the mechanisms by which the human microbiota directly regulates the innate immunity, systemic inflammation and adaptive immunity to renal allograft, thereby determining the occurrence and progression of interstitial fibrosis/tubular atrophy and graft survival.

Research/Clinical Keywords

Bacterial Genomics and Comparative Genomics ; Host-Pathogens Interactions ; Metagenomics ; Microbiome ; Staphylococcus aureus ; Lyme Disease ; Borrelia

Highlighted Publications

Bromberg JS, Fricke WF, Brinkman CC, Simon T, Mongodin EF. Microbiota—implications for immunity and transplantation. Nat Rev Nephrol. 2015. Jun;11(6):342-53. doi: 10.1038/nrneph.2015.70. Epub 2015 May 12. Review. PMID: 25963591. 

Goldberg BE, Mongodin EF, Jones CE, Chung M, Fraser CM, Tate A, Zeichner SL. The Oral Bacterial Communities of Children with Well-Controlled HIV Infection and without HIV Infection. PLoS One. 2015 Jul 6;10(7):e0131615. PMID: 26146997; PMCID: PMC4492946.

Jackson HT*, Mongodin EF*, Davenport KP, Fraser CM, Sandler AD, Zeichner SL. Culture-independent evaluation of the appendix and rectum microbiomes in children with and without appendicitis. PLoS One. 2014 Apr 23;9(4):e95414. PMID: 24759879.

Mongodin EF, Casjens SR, Bruno JF, Xu Y, Drabek EF, Riley DR, Cantarel BL, Pagan PE, Hernandez YA, Vargas LC, Dunn JJ, Schutzer SE, Fraser CM, Qiu WG, Luft BJ. Inter- and intra-specific pan-genomes of Borrelia burgdorferi sensu lato: genome stability and adaptive radiation. BMC Genomics. 2013 Oct 10;14:693. PMID: 24112474

Hosgood HD 3rd, Sapkota AR, Rothman N, Rohan T, Hu W, Xu J, Vermeulen R, He X, White JR, Wu G, Wei F, Mongodin EF, Lan Q. The potential role of lung microbiota in lung cancer attributed to household coal burning exposures. Environ Mol Mutagen. 2014 Jun 3. PMID: 24895247.

Mongodin EF, Casjens SR, Bruno JF, Xu Y, Drabek EF, Riley DR, Cantarel BL, Pagan PE, Hernandez YA, Vargas LC, Dunn JJ, Schutzer SE, Fraser CM, Qiu WG, Luft BJ. Inter- and intra-specific pan-genomes of Borrelia burgdorferi sensu lato: genome stability and adaptive radiation. BMC Genomics. 2013 Oct 10;14:693. PMID: 24112474

Alaish SM, Smith AD, Timmons J, Greenspon J, Eyvazzadeh D, Murphy E, Shea-Donahue T, Cirimotich S, Mongodin E, Zhao A, Fasano A, Nataro JP, Cross A. Gut microbiota, tight junction protein expression, intestinal resistance, bacterial translocation and mortality following cholestasis depend on the genetic background of the host. Gut Microbes. 2013 Jul-Aug;4(4):292-305. PMID: 23652772

Erickson AR, Cantarel BL, Lamendella R, Darzi Y, Mongodin EF, Pan C, Shah M, Halfvarson J, Tysk C, Henrissat B, Raes J, Verberkmoes NC, Fraser CM, Hettich RL, Jansson JK. Integrated metagenomics/metaproteomics reveals human host-microbiota signatures of Crohn's disease. PLoS One. 2012;7(11):e49138. PMID: 23209564 

Additional Publication Citations

Dennison NJ, Saraiva RG, Cirimotich CM, Mlambo G, Mongodin EF, Dimopoulos G. Functional genomic analyses of Enterobacter, Anopheles and Plasmodium reciprocal interactions that impact vector competence. Malar J. 2016 Aug 22;15(1):425. doi: 10.1186/s12936-016-1468-2. PMID: 27549662; PMCID: PMC4994321.


MetaSUB International Consortium. The Metagenomics and Metadesign of the Subways and Urban Biomes (MetaSUB) International Consortium inaugural meeting report. Microbiome. 2016 Jun 3;4(1):24. doi: 10.1186/s40168-016-0168-z. PMID: 27255532; PMCID: PMC4894504.


Fricke WF, Song Y, Wang AJ, Smith A, Grinchuk V, Mongodin E, Pei C, Ma B, Lu N, Urban JF Jr, Shea-Donohue T, Zhao A. Type 2 immunity-dependent reduction of segmented filamentous bacteria in mice infected with the helminthic parasite Nippostrongylus brasiliensis. Microbiome. 2015 Sep 17;3:40. doi:10.1186/s40168-015-0103-8. PMID: 26377648; PMCID: PMC4574229.


Bromberg JS, Fricke WF, Brinkman CC, Simon T, Mongodin EF. Microbiota—implications for immunity and transplantation. Nat Rev Nephrol. 2015. Jun;11(6):342-53. doi: 10.1038/nrneph.2015.70. Epub 2015 May 12. Review. PMID: 25963591.


Sharma-Kuinkel BK, Mongodin EF, Myers JR, Vore KL, Canfield GS, Fraser CM, Rude TH, Fowler VG Jr, Gill SR. Potential Influence of Staphylococcus aureus Clonal Complex 30 Genotype and Transcriptome on Hematogenous Infections. Open Forum Infect Dis. 2015 Jun 24;2(3):ofv093. PMID: 26213692; PMCID: PMC4512144.


Goldberg BE, Mongodin EF, Jones CE, Chung M, Fraser CM, Tate A, Zeichner SL. The Oral Bacterial Communities of Children with Well-Controlled HIV Infection and without HIV Infection. PLoS One. 2015 Jul 6;10(7):e0131615. PMID: 26146997; PMCID: PMC4492946.


Anton BP, Mongodin EF, Agrawal S, Fomenkov A, Byrd DR, Roberts RJ, Raleigh EA. Complete Genome Sequence of ER2796, a DNA Methyltransferase-Deficient Strain of Escherichia coli K-12. PLoS One. 2015 May 26;10(5). PMID: 26010885; PMCID: PMC4444293.


Hosgood HD 3rd, Sapkota AR, Rothman N, Rohan T, Hu W, Xu J, Vermeulen R, He X, White JR, Wu G, Wei F, Mongodin EF, Lan Q. The potential role of lung microbiota in lung cancer attributed to household coal burning exposures. Environ Mol Mutagen. 2014 Jun 3. PMID: 24895247.


Martin CL, Sukarna TY, Akther S, Ramrattan G, Pagan P, Di L, Mongodin EF, Fraser CM, Schutzer SE, Luft BJ, Casjens SR, Qiu WG. Phylogenomic identification of regulatory sequences in bacteria: an analysis of statistical power and an application to Borrelia burgdorferi sensu lato. MBio. 2015 Apr 14;6(2). Erratum in: MBio. 2015;6(4):e00999.


Brotman RM, He X, Gajer P, Fadrosh D, Sharma E, Mongodin EF, Ravel J, Glover ED, Rath JM. Association between cigarette smoking and the vaginal microbiota: a pilot study. BMC Infect Dis. 2014 Aug 28;14:471. PMID: 25169082


Di L, Pagan PE, Packer D, Martin CL, Akther S, Ramrattan G, Mongodin EF, Fraser CM, Schutzer SE, Luft BJ, Casjens SR, Qiu WG. BorreliaBase: a phylogeny-centered browser of Borrelia genomes. BMC Bioinformatics. 2014 Jul 3;15:233. PMID: 24895247.


Dugan VG, Emrich SJ, Giraldo-Calderón GI, Harb OS, Newman RM, Pickett BE, Schriml LM, Stockwell TB, Stoeckert CJ Jr, Sullivan DE, Singh I, Ward DV, Yao A, Zheng J, Barrett T, Birren B, Brinkac L, Bruno VM, Caler E, Chapman S, Collins FH, Cuomo CA, Di Francesco V, Durkin S, Eppinger M, Feldgarden M, Fraser C, Fricke WF, Giovanni M, Henn MR, Hine E, Hotopp JD, Karsch-Mizrachi I, Kissinger JC, Lee EM, Mathur P, Mongodin EF, Murphy CI, Myers G, Neafsey DE, Nelson KE, Nierman WC, Puzak J, Rasko D, Roos DS, Sadzewicz L, Silva JC, Sobral B, Squires RB, Stevens RL, Tallon L, Tettelin H, Wentworth D, White O, Will R, Wortman J, Zhang Y, Scheuermann RH. Standardized metadata for human pathogen/vector genomic sequences. PLoS One. 2014 Jun 17;9(6):e99979. PMID: 24936976.


Jackson HT*, Mongodin EF*, Davenport KP, Fraser CM, Sandler AD, Zeichner SL. Culture-independent evaluation of the appendix and rectum microbiomes in children with and without appendicitis. PLoS One. 2014 Apr 23;9(4):e95414. PMID: 24759879.


Mongodin EF, Casjens SR, Bruno JF, Xu Y, Drabek EF, Riley DR, Cantarel BL, Pagan PE, Hernandez YA, Vargas LC, Dunn JJ, Schutzer SE, Fraser CM, Qiu WG, Luft BJ. Inter- and intra-specific pan-genomes of Borrelia burgdorferi sensu lato: genome stability and adaptive radiation. BMC Genomics. 2013 Oct 10;14:693. PMID: 24112474


Alaish SM, Smith AD, Timmons J, Greenspon J, Eyvazzadeh D, Murphy E, Shea-Donahue T, Cirimotich S, Mongodin E, Zhao A, Fasano A, Nataro JP, Cross A. Gut microbiota, tight junction protein expression, intestinal resistance, bacterial translocation and mortality following cholestasis depend on the genetic background of the host. Gut Microbes. 2013 Jul-Aug;4(4):292-305. PMID: 23652772


Erickson AR, Cantarel BL, Lamendella R, Darzi Y, Mongodin EF, Pan C, Shah M, Halfvarson J, Tysk C, Henrissat B, Raes J, Verberkmoes NC, Fraser CM, Hettich RL, Jansson JK. Integrated metagenomics/metaproteomics reveals human host-microbiota signatures of Crohn's disease. PLoS One. 2012;7(11):e49138. PMID: 23209564


Kos VN, Desjardins CA, Griggs A, Cerqueira G, Van Tonder A, Holden MT, Godfrey P, Palmer KL, Bodi K, Mongodin EF, Wortman J, Feldgarden M, Lawley T, Gill SR, Haas BJ, Birren B, Gilmore MS. Comparative genomics of vancomycin-resistant Staphylococcus aureus strains and their positions within the clade most commonly associated with Methicillin-resistant S. aureus hospital-acquired infection in the United States. MBio. 2012 May 22;3(3).


Zupancic ML, Cantarel BL, Liu Z, Drabek EF, Ryan K, Cirimotich S, Jones C, Knight R, Mongodin EF, Horenstein R, Mitchell BD, Steinle N, Snitker S, Shuldiner AR, Fraser-Liggett CM. Analysis of the gut microbiota in the Old Order Amish identifies three enterotypes and bacterial species correlated with obesity and the metabolic syndrome. PLoS One, 2012, 2012;7(8):e43052.


Schutzer SE, Fraser-Liggett CM, Qiu WG, Kraiczy P, Mongodin EF, Dunn JJ, Luft BJ, Casjens SR. Whole genome sequences of Borrelia bissettii, Borrelia valaisiana and Borrelia spielmanii". J Bacteriol. 2012 Jan;194(2):545-6.


Cantarel BL, Erickson AR, Verberkmoes NC, Erickson BK, Carey PA, Pan C, Shah M, Mongodin EF, Jansson JK, Fraser-Liggett CM, Hettich RL. Strategies for Metagenomic-Guided Whole-Community Proteomics of Complex Microbial Environments. PLoS One 2011; 6 (11): e27173.


Casjens SR, Mongodin EF, Qiu WG, Dunn JJ, Luft BJ, Fraser-Liggett CM, Schutzer SE. Whole-Genome Sequences of Two Borrelia afzelii and Two Borrelia garinii Lyme Disease Agent Isolates. J Bacteriol 2011; 193 (24): 6995-6.


Han A, Zenilman JM, Melendez JH, Shirtliff ME, Agostinho A, James G, Stewart PS, Mongodin EF, Rao D, Rickard AH, Lazarus GS. The importance of a multifaceted approach to characterizing the microbial flora of chronic wounds. Wound Repair and Regeneration, 2011; 19 (5): 532-41.


Haven J, Vargas LC, Mongodin EF, Xue V, Hernandez Y, Pagan P, Fraser-Liggett CM, Schutzer SE, Luft BJ, Casjens SR, Qiu WG. Pervasive Recombination and Sympatric Genome Diversification Driven by Frequency-Dependent Selection in Borrelia burgdorferi, the Lyme disease Bacterium. Genetics 2011; Sept. 2 . PMID: 21890743


Casjens SR, Fraser-Liggett CM, Mongodin EF, Qiu WG, Dunn JJ, Luft BJ, Schutzer SE. Whole Genome Sequence of an Unusual Borrelia burgdorferi Sensu Lato Isolate. J Bacteriol 2011; 193 (6): 1489-90. PMID: 21217002.


Schutzer SE, Fraser-Liggett CM, Casjens SR, Qiu WG, Dunn JJ, Mongodin EF, Luft BJ. Whole-genome sequences of thirteen isolates of Borrelia burgdorferi. J Bacteriol 2011; 193 (4): 1018-20. PMID: 20935092.


Purushe J, Fouts DE, Morrison M, White BA, Mackie RI, North American Consortium for Fibrolytic Ruminal Bacteria*, Coutinho PM, Henrissat B, Nelson KE. Comparative Genome Analysis of Prevotella ruminicola and Prevotella bryantii: Insights into Their Environmental Niche. Microb Ecol 2010. PMID: 20585943.


Li L, Hsiao WW, Nandakumar R, Barbuto SM, Mongodin EF, Paster BJ, Fraser-Liggett CM, Fouad AF. Analyzing Endodontic Infections by Deep Coverage Pyrosequencing. J Dent Res, 2010; Jun 2 [Epub ahead of print]. PMID: 20519493.


Bik EM, Davis Long C, Armitage GC, Loomer P, Emerson J, Mongodin EF, Nelson KE, Gill SR, Fraser-Liggett CM, Relman DA. Bacterial diversity in the human oral cavity of ten healthy individuals. ISME Journal, 2010; March 25 [Epub ahead of print]. PMID: 20336157.


Morrison M, Daugherty SC, Nelson WC, Davidsen T, Nelson KE; North American Consortium for Fibrolytic Ruminal Bacteria*. The FibRumBa database: a resource for biologists with interests in gastrointestinal microbial ecology, plant biomass degradation, and anaerobic microbiology. Microbial Ecology. 2010 Feb;59(2):212-3. PMID: 19609599


Wywial E, Haven J, Casjens SR, Hernandez YA, Singh S, Mongodin EF, Fraser-Liggett CM, Luft BJ, Schutzer SE, Qiu WG. Fast, adaptive evolution at a bacterial host-resistance locus: the PFam54 gene array in Borrelia burgdorferi. Gene. 2009 Sep 15; 445(1-2) : 26-37. PMID: 19505540.


Emami K, Topakas E, Nagy T, Henshaw J, Jackson KA, Nelson KE, Mongodin EF, Murray JW, Lewis RJ, Gilbert HJ. Regulation of the xylan degrading apparatus of Cellvibrio japonicus by a novel two-component system. Journal of Biological Chemistry, 2009; 284(2) : 1086-96. PMID: 18922794.


van de Werken HJ, Verhaart MR, Vanfossen AL, Willquist K, Lewis DL, Nichols JD, Goorissen HP, Mongodin EF, Nelson KE, van Niel EW, Stams AJ, Ward DE, de Vos WM, van der Oost J, Kelly RM, Kengen SW. Hydrogenomics of the extremely thermophilic bacterium Caldicellulosiruptor saccharolyticus. Applied and Environmental Microbiology, 2008; 74(21) : 6720-9. PMID: 18776029.


White JR, Escobar-Paramo P, Mongodin EF, Nelson KE, Jocelyne DiRuggiero J. Extensive Genome Rearrangements and Multiple Horizontal Gene Transfers in a Population of Pyrococcus Isolates from Vulcano Island, Italy. Applied and Environmental Microbiology, 2008; 74(20) : 6447-51. PMID: 18723649.


Rasko DA, Rosovitz MJ, Myers GSA, Mongodin EF, Fricke WF, Gajer P, Crabtree J, Sperandio V, Ravel J. The pan-genome structure of Escherichia coli: comparative genomic analysis of E. coli commensal and pathogenic isolates. Journal of Bacteriology, 2008; 190 (20): 6881-93. PMID: 18676672.


DeBoy RT, Mongodin EF, Fouts DE, Tailford LE, Khouri H, Emerson JB, Mohamoud Y, Watkins K, Henrissat B, Gilbert HJ, Nelson NE. Insights into Plant Cell-wall Degradation from the Genome Sequence of the Soil Bacterium Cellvibrio japonicus. Journal of Bacteriology. 2008; 190 (15) : 5455-63. PMID: 18556790.


Ashby MN, Rine J, Mongodin EF, Nelson KE, Dimster-Denk D. Serial Analysis of Ribosomal DNA and the Unexpected Dominance of Rare Members of Microbial Communities. Applied and Environmental Microbiology, 2007 Jul;73(14):4532-42.


Shapir N, Mongodin EF, Sadowsky MJ, Daugherty SC, Nelson KE, Wackett LP. Evolution of Catabolic Pathways: Genomic Insights into Microbial s-Triazine Metabolism. Journal of Bacteriology, 2007, Feb;189(3):674-82.


Mongodin EF, Shapir N, Daugherty SC, Deboy RT, Emerson JB, Shvartzbeyn A, Radune D, Vamathevan J, Riggs F, Grinberg V, Khouri H, Wackett LP, Nelson KE, Sadowsky MJ. Secrets of Soil Survival Revealed by the Genome Sequence of Arthrobacter aurescens TC1. PLoS Genetics, 2006 Dec 22;2(12):e214.


Centeno MS, Guerreiro CI, Dias FM, Morland C, Tailford LE, Goyal A, Prates JA, Ferreira LM, Caldeira RM, Mongodin EF, Nelson KE, Gilbert HJ, Fontes CM. Galactomannan hydrolysis and mannose metabolism in Cellvibrio mixtus. FEMS Microbiology Letters. 2006, Aug;261(1):123-32.


Pieper R, Gatlin T, Parmar P, Huang ST, Clark D, Mongodin EF, Gill SR, Peterson S. Clear protein expression changes comparing three Staphylococcus aureus isolates with different susceptibilities to vancomycin revealed by classical proteomic profiling. Proteomics. 2006, Aug;6(15):4246-58.


DeBoy RT, Mongodin EF, Emerson JB Nelson KE. Genome shuffling in the Thermotogales: involvement of CRISPRs and tRNA genes.  Journal of Bacteriology, 2006, Apr;188(7):2364-74.


Diep BA, Gill SR, Chang RF, Phan TH, Chen JH, Davidson MG, Lin F, Lin J, Carleton HA, Mongodin EF, Sensabaugh GF, Perdreau-Remington F. Complete genome sequence of USA300, an epidemic clone of community-acquired meticillin-resistant Staphylococcus aureus. The Lancet, 2006, Mar 4;367(9512):731-9.


Nesbo CL, Mongodin EF, Nelson KE, Doolittle WF.  The Thermotoga metagenome: lateral gene transfer and recombination. Microbe (formerly known as ASM News), 2006, 1(5), 235-241.


Conners SB, Mongodin EF, Johnson MR, Montero CI, Nelson KE, Kelly RM.  Microbial Biochemistry, Physiology, Ecology and Biotechnology of Hyperthermophilic Thermotoga Species. FEMS Microbiol Rev. 2006, Nov;30(6):872-905.


Gatlin CL, Pieper R, Huang ST, Mongodin EF, Gebregeorgis E, Parmar PP, Clark DJ, Alami H, Papazisi L, Fleischmann RD, Gill SR, Peterson SN. Proteomic Profiling of Cell Envelope-Associated Proteins from Staphylococcus aureus. Proteomics, 2006 Mar;6(5):1530-49.


Mongodin EF, Nelson KE, Daugherty S, Deboy RT, Wister J, Khouri H, Weidman J, Walsh DA, Papke RT, Sanchez Perez G, Sharma AK, Nesbo CL, MacLeod D, Bapteste E, Doolittle WF, Charlebois RL, Legault B, Rodriguez-Valera F. The genome of Salinibacter ruber: convergence and gene exchange among hyperhalophilic bacteria and archaea.  Proc Natl Acad Sci U S A. 2005, 102(50):18147-52.


Haft DA, Selengut J, Mongodin EF and Nelson KE. A guild of forty-five CRISPR-associated (Cas) protein families and multiple CRISPR/Cas subtypes exist in prokaryotic genomes. PLoS Computational Biology, 2005, 1(6):e60.


Mongodin EF, Gill SR, Hance IR, DeBoy RT, Huber R, Stetter K, Nelson KE. Gene transfer in Thermotoga maritima, a model hyperthermophilic species. Journal of Bacteriology, 2005, 187(14):4935-4944.


Mongodin EF, Emerson JB and Nelson KE. Microbial Metagenomics. Microbial Metagenomics. A Report on The American Society for Microbiology 105th Annual Meeting, Atlanta GA, June 5-9, 2005. Genome Biology 2005, 2005, 6:347.


Rasko DA and Mongodin EF. A First Decade of Microbial Genomics: what have we learned and where are we going next ? A report on the International Conference on Microbial Genomics; Halifax, Nova Scotia, Canada, April 13-16 205. Genome Biology, 2005, 6:341.


GillSR, Fouts DE, Archer G, Mongodin EF, DeBoy RT, Ravel J, Paulsen IT, Kolonay JF, Brinkac L, Beanan M, Dodson RJ, Daugherty S, Nelson WC et al.  Insights on evolution of virulence and resistance from the complete genome analysis of an early methicillin resistant Staphylococcus aureus and a biofilm producing methicillin resistant Staphylococcus epidermidis. Journal of Bacteriology, 2005, 187(7):2426-2438.


Fouts DE, Mongodin EF, Mandrell RE, Miller WG, Rasko DA, Ravel J, Brinkac LM, DeBoy RT, Parker CT, Daugherty SC, Dodson RJ, Durkin S, Madupu R, Sullivan S, Shetty J, Ayodeji MA, Shvartsbeyn A, Fraser CM and Nelson KE.  Major structural differences and novel potential virulence mechanisms from the genomes of multiple Campylobacter species.. PLoS Biology, Jan 4th, 2005, e15.


Nelson KE, Fouts DE, Mongodin EF, Ravel J, DeBoy RT, Kolonay JF, Rasko DA, Angiuoli S, Gill SR et al.  Whole genome comparisons of serotype 4b and 1/2a strains of the food-borne pathogen Listeria monocytogenes reveal new insights into the core genome components of this species. Nucleic Acids Research 2004, 32: 2386-2395.


Mongodin E, Finan J, Climo MW, Gill S, Archer GL. Microarray transcription analysis of clinical Staphylococcus aureus isolates resistant to vancomycin. Journal of Bacteriology 2003, 185 : 4638-4643.


Mongodin E, Bajolet O, Cutrona J, Bonnet N, Dupuit F, Puchelle E, de Bentzmann S. Fibronectin-binding proteins of Staphylococcus aureus are involved in adherence to human airway epithelium. Infection and Immunity 2002, 70 : 620-630.


Mongodin E, Bajolet O, Hinnrasky J, Puchelle E, de Bentzmann S. Cell wall-associated protein A as a tool for immunolocalization of Staphylococcus aureus in infected human airway epithelium. Journal of Histochemistry and  Cytochemistry. 2000, 48 : 523-534


Dupuit F, Gaillard D, Hinnrasky J, Mongodin E, de Bentzmann S, Copreni E, Puchelle E. Differentiated and functional human airway epithelium in tracheal xenografts. American Journal of Physiology (Lung Cellular and Molecular Physiology) 2000, 278 : L165-L176.


Le Prigent K, Lagadic-Gossmann D, Mongodin E, Feuvray D. HCO3- dependant alkalinizing transporter in adult rat ventricular myocytes : characterization and modulation. American Journal of Physiology (Heart Circulation and Physiology) 1997, 42 : H2596 – H2603.