Derrick Fouts is a Professor at the Rockville Campus. Dr. Fouts has extensive experience in viral and bacteriophage genomics, bacterial genomics, comparative genomics, and metagenomics of bacterial and viral communities.

Since joining Dr. Karen Nelson's group at TIGR/51ݶ in 2001, Dr. Fouts has led several microbial sequencing projects, including animal, plant and human pathogens. Many of these projects were among the first to compare multiple strains. In addition to leading projects, Dr. Fouts has developed various software tools, including applications to perform multi-genome comparisons and heuristic software (Phage Finder) to identify prophage regions in bacterial genomes. He is currently leading the effort to sequence the human virome and reference viral and bacteriophage genomes as part of the NIH sponsored, Human Microbiome Project.

Dr. Fouts received his B.S. degree (1992) in Biology with honors from Indiana University, Bloomington, and his M.S. (1994) and PhD (1997) degrees in Microbiology from the University of Illinois Urbana/Champaign Department of Microbiology. In 1997, he began postdoctoral work in Dr. Alan Collmer's lab at Cornell University.


Gut microbes. 2024-02-01; 16.1: 2307586.
Fungal signature differentiates alcohol-associated liver disease from nonalcoholic fatty liver disease
Viebahn G, Hartmann P, Lang S, Demir M, Zhang X, Fouts DE, Stärkel P, Schnabl B
PMID: 38298161
BMC infectious diseases. 2023-08-28; 23.1: 556.
Characteristics and genomic epidemiology of colistin-resistant Enterobacterales from farmers, swine, and hospitalized patients in Thailand, 2014-2017
Boonyasiri A, Brinkac LM, Jauneikaite E, White RC, Greco C, Seenama C, Tangkoskul T, Nguyen K, Fouts DE, Thamlikitkul V
PMID: 37641085
Journal of clinical microbiology. 2023-07-20; 61.7: e0019923.
Escherichia coli ST131 Associated with Increased Mortality in Bloodstream Infections from Urinary Tract Source
Brumwell A, Sutton G, Lantos PM, Hoffman K, Ruffin F, Brinkac L, Clarke TH, Adams MD, Fowler VG, Fouts DE, Thaden JT
PMID: 37338371
Hepatology (Baltimore, Md.). 2023-06-01; 77.6: 2073-2083.
Any alcohol use in NAFLD patients is associated with significant changes to the intestinal virome
Hsu CL, Lang S, Demir M, Fouts DE, Stärkel P, Schnabl B
PMID: 36631002
Hepatology communications. 2023-02-01; 7.2: e0029.
Malassezia restricta promotes alcohol-induced liver injury
Zeng S, Hartmann P, Park M, Duan Y, Lang S, Llorente C, Wang Y, Cabré N, Fouts DE, Bacher P, Jung WH, Stärkel P, Schnabl B
PMID: 36706195
Antibiotics (Basel, Switzerland). 2022-11-19; 11.11:
Design of a Bacteriophage Cocktail Active against Shigella Species and Testing of Its Therapeutic Potential in Galleria mellonella
Filippov AA, Su W, Sergueev KV, Kevorkian RT, Snesrud EC, Srijan A, He Y, Fouts DE, Lurchachaiwong W, McGann PT, Ellison DW, Swierczewski BE, Nikolich MP
PMID: 36421303
Hepatology communications. 2022-08-01; 6.8: 2058-2069.
Intestinal virome in patients with alcohol use disorder and after abstinence
Hsu CL, Zhang X, Jiang L, Lang S, Hartmann P, Pride D, Fouts DE, Stärkel P, Schnabl B
PMID: 35368152
JAC-antimicrobial resistance. 2022-06-01; 4.3: dlac040.
Clinical challenges treating Stenotrophomonas maltophilia infections: an update
Mojica MF, Humphries R, LiPuma JJ, Mathers AJ, Rao GG, Shelburne SA, Fouts DE, van Duin D, Bonomo RA
PMID: 35529051
Antimicrobial agents and chemotherapy. 2022-05-17; 66.5: e0179021.
Imipenem/Relebactam Resistance in Clinical Isolates of Extensively Drug Resistant Pseudomonas aeruginosa: Inhibitor-Resistant β-Lactamases and Their Increasing Importance
Hujer AM, Bethel CR, Taracila MA, Marshall SH, Rojas LJ, Winkler ML, Painter RE, Domitrovic TN, Watkins RR, Abdelhamed AM, D'Souza R, Mack AR, White RC, Clarke T, Fouts DE, Jacobs MR, Young K, Bonomo RA
PMID: 35435707
Journal of hepatology. 2022-04-01; 76.4: 788-799.
The fecal mycobiome in non-alcoholic fatty liver disease
Demir M, Lang S, Hartmann P, Duan Y, Martin A, Miyamoto Y, Bondareva M, Zhang X, Wang Y, Kasper P, Bang C, Roderburg C, Tacke F, Steffen HM, Goeser T, Kruglov A, Eckmann L, Stärkel P, Fouts DE, Schnabl B
PMID: 34896404
Viruses. 2022-03-29; 14.4:
Identification and Characterization of vB_PreP_EPr2, a Lytic Bacteriophage of Pan-Drug Resistant Providencia rettgeri
Mencke JL, He Y, Filippov AA, Nikolich MP, Belew AT, Fouts DE, McGann PT, Swierczewski BE, Getnet D, Ellison DW, Margulieux KR
PMID: 35458437
Applied and environmental microbiology. 2022-02-08; 88.3: e0148621.
Cross-Genus "Boot-Up" of Synthetic Bacteriophage in Staphylococcus aureus by Using a New and Efficient DNA Transformation Method
Assad-Garcia N, D'Souza R, Buzzeo R, Tripathi A, Oldfield LM, Vashee S, Fouts DE
PMID: 34818102
Metabolites. 2022-01-05; 12.1:
Machine Learning Applied to Omics Datasets Predicts Mortality in Patients with Alcoholic Hepatitis
Gao B, Wu TC, Lang S, Jiang L, Duan Y, Fouts DE, Zhang X, Tu XM, Schnabl B
PMID: 35050163
Journal of hepatology. 2021-12-01; 75.6: 1465-1475.
Intestinal virome and therapeutic potential of bacteriophages in liver disease
Hsu C, Hsu CL, Duan Y, Fouts DE, Schnabl B
PMID: 34437908
Frontiers in physiology. 2021-07-19; 12.699253.
Dynamic Changes of the Fungal Microbiome in Alcohol Use Disorder
Hartmann P, Lang S, Zeng S, Duan Y, Zhang X, Wang Y, Bondareva M, Kruglov A, Fouts DE, Stärkel P, Schnabl B
PMID: 34349667
The Journal of antimicrobial chemotherapy. 2021-07-15; 76.8: 2017-2023.
Apramycin resistance in epidemic carbapenem-resistant Klebsiella pneumoniae ST258 strains
Hao M, Schuyler J, Zhang H, Shashkina E, Du H, Fouts DE, Satlin M, Kreiswirth BN, Chen L
PMID: 33942093
Cellular and molecular gastroenterology and hepatology. 2021-02-22; 12.1: 293-320.
Intestinal α1-2-Fucosylation Contributes to Obesity and Steatohepatitis in Mice
Zhou R, Llorente C, Cao J, Zaramela LS, Zeng S, Gao B, Li SZ, Welch RD, Huang FQ, Qi LW, Pan C, Huang Y, Zhou P, Beussen I, Zhang Y, Bryam G, Fiehn O, Wang L, Liu EH, Yu RT, Downes M, Evans RM, Goglin K, Fouts DE, Brenner DA, Bode L, Fan X, Zengler K, Schnabl B
PMID: 33631374
BMC infectious diseases. 2021-02-04; 21.1: 142.
Genomic and clinical characterisation of multidrug-resistant carbapenemase-producing ST231 and ST16 Klebsiella pneumoniae isolates colonising patients at Siriraj hospital, Bangkok, Thailand from 2015 to 2017
Boonyasiri A, Jauneikaite E, Brinkac LM, Greco C, Lerdlamyong K, Tangkoskul T, Nguyen K, Thamlikitkul V, Fouts DE
PMID: 33541274
Diagnostic microbiology and infectious disease. 2021-02-01; 99.2: 115242.
A comprehensive and contemporary "snapshot" of β-lactamases in carbapenem resistant Acinetobacter baumannii
Hujer AM, Hujer KM, Leonard DA, Powers RA, Wallar BJ, Mack AR, Taracila MA, Rather PN, Higgins PG, Prati F, Caselli E, Marshall SH, Clarke T, Greco C, Venepally P, Brinkac L, Kreiswirth BN, Fouts DE, Bonomo RA, Antibacterial Resistance Leadership Group (ARLG)
PMID: 33248392
Hepatology (Baltimore, Md.). 2020-12-01; 72.6: 2182-2196.
Intestinal Virome in Patients With Alcoholic Hepatitis
Jiang L, Lang S, Duan Y, Zhang X, Gao B, Chopyk J, Schwanemann LK, Ventura-Cots M, Bataller R, Bosques-Padilla F, Verna EC, Abraldes JG, Brown RS, Vargas V, Altamirano J, Caballería J, Shawcross DL, Ho SB, Louvet A, Lucey MR, Mathurin P, Garcia-Tsao G, Kisseleva T, Brenner DA, Tu XM, Stärkel P, Pride D, Fouts DE, Schnabl B
PMID: 32654263
Gut microbes. 2020-11-09; 12.1: 1785251.
Changes in the fecal bacterial microbiota associated with disease severity in alcoholic hepatitis patients
Lang S, Fairfied B, Gao B, Duan Y, Zhang X, Fouts DE, Schnabl B
PMID: 32684075
Gut microbes. 2020-11-09; 12.1: 1782157.
Intestinal permeability, microbial translocation, changes in duodenal and fecal microbiota, and their associations with alcoholic liver disease progression in humans
Maccioni L, Gao B, Leclercq S, Pirlot B, Horsmans Y, De Timary P, Leclercq I, Fouts D, Schnabl B, Stärkel P
PMID: 32588725
Gastroenterology. 2020-11-01; 159.5: 1839-1852.
Intestinal Virome Signature Associated With Severity of Nonalcoholic Fatty Liver Disease
Lang S, Demir M, Martin A, Jiang L, Zhang X, Duan Y, Gao B, Wisplinghoff H, Kasper P, Roderburg C, Tacke F, Steffen HM, Goeser T, Abraldes JG, Tu XM, Loomba R, Stärkel P, Pride D, Fouts DE, Schnabl B
PMID: 32652145
The Journal of antimicrobial chemotherapy. 2020-10-01; 75.10: 2760-2768.
AbGRI4, a novel antibiotic resistance island in multiply antibiotic-resistant Acinetobacter baumannii clinical isolates
Chan AP, Choi Y, Clarke TH, Brinkac LM, White RC, Jacobs MR, Bonomo RA, Adams MD, Fouts DE
PMID: 32681170
Journal of clinical microbiology. 2020-08-24; 58.9:
Newly Named Klebsiella aerogenes (formerly Enterobacter aerogenes) Is Associated with Poor Clinical Outcomes Relative to Other Enterobacter Species in Patients with Bloodstream Infection
Wesevich A, Sutton G, Ruffin F, Park LP, Fouts D, Fouts DE, Fowler VG, Thaden JT
PMID: 32493786
Clinical infectious diseases : an official publication of the Infectious Diseases Society of America. 2020-08-14; 71.4: 1095-1098.
Monitoring Ceftazidime-Avibactam and Aztreonam Concentrations in the Treatment of a Bloodstream Infection Caused by a Multidrug-Resistant Enterobacter sp. Carrying Both Klebsiella pneumoniae Carbapenemase-4 and New Delhi Metallo-β-Lactamase-1
Yasmin M, Fouts DE, Jacobs MR, Haydar H, Marshall SH, White R, D'Souza R, Lodise TP, Rhoads DD, Hujer AM, Rojas LJ, Hoyen C, Perez F, Edwards A, Bonomo RA
PMID: 31802119
Gut microbes. 2020-05-03; 11.3: 265-275.
Intestinal and hepatic microbiota changes associated with chronic ethanol administration in mice
Bluemel S, Wang L, Kuelbs C, Moncera K, Torralba M, Singh H, Fouts DE, Schnabl B
PMID: 30982395
Antimicrobial agents and chemotherapy. 2020-04-21; 64.5:
ARGONAUT II Study of the In Vitro Activity of Plazomicin against Carbapenemase-Producing Klebsiella pneumoniae
Jacobs MR, Good CE, Hujer AM, Abdelhamed AM, Rhoads DD, Hujer KM, Rudin SD, Domitrovic TN, Connolly LE, Krause KM, Patel R, Arias CA, Kreiswirth BN, Rojas LJ, D'Souza R, White RC, Brinkac LM, Nguyen K, Singh I, Fouts DE, van Duin D, Bonomo RA, Antibacterial Resistance Leadership Group
PMID: 32152078
Hepatology (Baltimore, Md.). 2020-02-01; 71.2: 522-538.
Intestinal Fungal Dysbiosis and Systemic Immune Response to Fungi in Patients With Alcoholic Hepatitis
Lang S, Duan Y, Liu J, Torralba MG, Kuelbs C, Ventura-Cots M, Abraldes JG, Bosques-Padilla F, Verna EC, Brown RS, Vargas V, Altamirano J, Caballería J, Shawcross D, Lucey MR, Louvet A, Mathurin P, Garcia-Tsao G, Ho SB, Tu XM, Bataller R, Stärkel P, Fouts DE, Schnabl B
PMID: 31228214
Alcoholism, clinical and experimental research. 2020-01-01; 44.1: 87-101.
A Novel Mouse Model of Acute-on-Chronic Cholestatic Alcoholic Liver Disease: A Systems Biology Comparison With Human Alcoholic Hepatitis
Furuya S, Argemi J, Uehara T, Katou Y, Fouts DE, Schnabl B, Dubuquoy L, Belorkar A, Vadigepalli R, Kono H, Bataller R, Rusyn I
PMID: 31710124
Nature. 2019-11-13; 575.7783: 505-511.
Bacteriophage targeting of gut bacterium attenuates alcoholic liver disease
Duan Y, Llorente C, Lang S, Brandl K, Chu H, Jiang L, White RC, Clarke TH, Nguyen K, Torralba M, Shao Y, Liu J, Hernandez-Morales A, Lessor L, Rahman IR, Miyamoto Y, Ly M, Gao B, Sun W, Kiesel R, Hutmacher F, Lee S, Ventura-Cots M, Bosques-Padilla F, Verna EC, Abraldes JG, Brown RS, Vargas V, Altamirano J, Caballería J, Shawcross DL, Ho SB, Louvet A, Lucey MR, Mathurin P, Garcia-Tsao G, Bataller R, Tu XM, Eckmann L, van der Donk WA, Young R, Lawley TD, Stärkel P, Pride D, Fouts DE, Schnabl B
PMID: 31723265
The Journal of infectious diseases. 2019-07-19; 220.4: 666-676.
Ceftazidime-Avibactam in Combination With Fosfomycin: A Novel Therapeutic Strategy Against Multidrug-Resistant Pseudomonas aeruginosa
Papp-Wallace KM, Zeiser ET, Becka SA, Park S, Wilson BM, Winkler ML, D'Souza R, Singh I, Sutton G, Fouts DE, Chen L, Kreiswirth BN, Ellis-Grosse EJ, Drusano GL, Perlin DS, Bonomo RA
PMID: 31099835
mBio. 2019-07-02; 10.4:
Population Structure, Molecular Epidemiology, and β-Lactamase Diversity among Stenotrophomonas maltophilia Isolates in the United States
Mojica MF, Rutter JD, Taracila M, Abriata LA, Fouts DE, Papp-Wallace KM, Walsh TJ, LiPuma JJ, Vila AJ, Bonomo RA
PMID: 31266860
mSphere. 2019-03-13; 4.2:
Emergence of New Delhi Metallo-β-Lactamase (NDM-5) in Klebsiella quasipneumoniae from Neonates in a Nigerian Hospital
Brinkac LM, White R, D'Souza R, Nguyen K, Obaro SK, Fouts DE
PMID: 30867330
BMC bioinformatics. 2019-01-07; 20.1: 8.
OMeta: an ontology-based, data-driven metadata tracking system
Singh I, Kuscuoglu M, Harkins DM, Sutton G, Fouts DE, Nelson KE
PMID: 30612540
BMC bioinformatics. 2018-06-27; 19.1: 246.
PanACEA: a bioinformatics tool for the exploration and visualization of bacterial pan-chromosomes
Clarke TH, Brinkac LM, Inman JM, Sutton G, Fouts DE
PMID: 29945570
Frontiers in cellular and infection microbiology. 2018-06-19; 8.193.
Genomic Comparison Among Global Isolates of L. interrogans Serovars Copenhageni and Icterohaemorrhagiae Identified Natural Genetic Variation Caused by an Indel
Santos LA, Adhikarla H, Yan X, Wang Z, Fouts DE, Vinetz JM, Alcantara LCJ, Hartskeerl RA, Goris MGA, Picardeau M, Reis MG, Townsend JP, Zhao H, Ko AI, Wunder EA
PMID: 29971217
Nature communications. 2017-10-16; 8.1: 837.
Gastric acid suppression promotes alcoholic liver disease by inducing overgrowth of intestinal Enterococcus
Llorente C, Jepsen P, Inamine T, Wang L, Bluemel S, Wang HJ, Loomba R, Bajaj JS, Schubert ML, Sikaroodi M, Gillevet PM, Xu J, Kisseleva T, Ho SB, Depew J, Du X, Sørensen HT, Vilstrup H, Nelson KE, Brenner DA, Fouts DE, Schnabl B
PMID: 29038503
The Journal of clinical investigation. 2017-06-30; 127.7: 2829-2841.
Intestinal fungi contribute to development of alcoholic liver disease
Yang AM, Inamine T, Hochrath K, Chen P, Wang L, Llorente C, Bluemel S, Hartmann P, Xu J, Koyama Y, Kisseleva T, Torralba MG, Moncera K, Beeri K, Chen CS, Freese K, Hellerbrand C, Lee SM, Hoffman HM, Mehal WZ, Garcia-Tsao G, Mutlu EA, Keshavarzian A, Brown GD, Ho SB, Bataller R, Stärkel P, Fouts DE, Schnabl B
PMID: 28530644
Journal of neurovirology. 2017-04-01; 23.2: 171-185.
HSV-1 clinical isolates with unique in vivo and in vitro phenotypes and insight into genomic differences
Danaher RJ, Fouts DE, Chan AP, Choi Y, Depew J, McCorrison JM, Nelson KE, Wang C, Miller CS
PMID: 27739035
PLoS neglected tropical diseases. 2016-02-18; 10.2: e0004403.
What Makes a Bacterial Species Pathogenic?:Comparative Genomic Analysis of the Genus Leptospira
Fouts DE, Matthias MA, Adhikarla H, Adler B, Amorim-Santos L, Berg DE, Bulach D, Buschiazzo A, Chang YF, Galloway RL, Haake DA, Haft DH, Hartskeerl R, Ko AI, Levett PN, Matsunaga J, Mechaly AE, Monk JM, Nascimento AL, Nelson KE, Palsson B, Peacock SJ, Picardeau M, Ricaldi JN, Thaipandungpanit J, Wunder EA, Yang XF, Zhang JJ, Vinetz JM
PMID: 26890609
Cell host & microbe. 2016-02-10; 19.2: 227-39.
Intestinal REG3 Lectins Protect against Alcoholic Steatohepatitis by Reducing Mucosa-Associated Microbiota and Preventing Bacterial Translocation
Wang L, Fouts DE, Stärkel P, Hartmann P, Chen P, Llorente C, Depew J, Moncera K, Ho SB, Brenner DA, Hooper LV, Schnabl B
PMID: 26867181
Genome announcements. 2015-01-22; 3.1:
Genome Sequences of the Listeria ivanovii subsp. ivanovii Type Strain and Two Listeria ivanovii subsp. londoniensis Strains
Hupfeld M, Fouts DE, Loessner MJ, Klumpp J
PMID: 25614561
Gastroenterology. 2015-01-01; 148.1: 203-214.e16.
Supplementation of saturated long-chain fatty acids maintains intestinal eubiosis and reduces ethanol-induced liver injury in mice
Chen P, Torralba M, Tan J, Embree M, Zengler K, Stärkel P, van Pijkeren JP, Depew J, Loomba R, Ho SB, Bajaj JS, Mutlu EA, Keshavarzian A, Tsukamoto H, Nelson KE, Fouts DE, Schnabl B
PMID: 25239591
Pathogens (Basel, Switzerland). 2014-04-10; 3.2: 280-308.
Leptospiral pathogenomics
Lehmann JS, Matthias MA, Vinetz JM, Fouts DE
PMID: 25437801
Bacteriophage. 2012-07-01; 2.3: 190-199.
Next generation sequencing technologies and the changing landscape of phage genomics
Klumpp J, Fouts DE, Sozhamannan S
PMID: 23275870
Journal of hepatology. 2012-06-01; 56.6: 1283-92.
Bacterial translocation and changes in the intestinal microbiome in mouse models of liver disease
Fouts DE, Torralba M, Nelson KE, Brenner DA, Schnabl B
PMID: 22326468
Archives of virology. 2011-01-01; 156.1: 25-35.
Clostridium perfringens bacteriophages ΦCP39O and ΦCP26F: genomic organization and proteomic analysis of the virions
Seal BS, Fouts DE, Simmons M, Garrish JK, Kuntz RL, Woolsey R, Schegg KM, Kropinski AM, Ackermann HW, Siragusa GR
PMID: 20963614
PLoS genetics. 2008-07-25; 4.7: e1000141.
Complete genome sequence of the N2-fixing broad host range endophyte Klebsiella pneumoniae 342 and virulence predictions verified in mice
Fouts DE, Tyler HL, Deboy RT, Daugherty S, Ren Q, Badger JH, Durkin AS, Huot H, Shrivastava S, Kothari S, Dodson RJ, Mohamoud Y, Khouri H, Roesch LF, Krogfelt KA, Struve C, Triplett EW, Methé BA
PMID: 18654632
Journal of bacteriology. 2007-01-01; 189.1: 52-64.
Complete sequence analysis of novel plasmids from emetic and periodontal Bacillus cereus isolates reveals a common evolutionary history among the B. cereus-group plasmids, including Bacillus anthracis pXO1
Rasko DA, Rosovitz MJ, Økstad OA, Fouts DE, Jiang L, Cer RZ, Kolstø AB, Gill SR, Ravel J
PMID: 17041058
Nucleic acids research. 2006-10-24; 34.20: 5839-51.
Phage_Finder: automated identification and classification of prophage regions in complete bacterial genome sequences
Fouts DE
PMID: 17062630
Journal of bacteriology. 2006-05-01; 188.9: 3402-8.
Sequencing Bacillus anthracis typing phages gamma and cherry reveals a common ancestry
Fouts DE, Rasko DA, Cer RZ, Jiang L, Fedorova NB, Shvartsbeyn A, Vamathevan JJ, Tallon L, Althoff R, Arbogast TS, Fadrosh DW, Read TD, Gill SR
PMID: 16621835
Journal of bacteriology. 2005-04-01; 187.7: 2426-38.
Insights on evolution of virulence and resistance from the complete genome analysis of an early methicillin-resistant Staphylococcus aureus strain and a biofilm-producing methicillin-resistant Staphylococcus epidermidis strain
Gill SR, Fouts DE, Archer GL, Mongodin EF, Deboy RT, Ravel J, Paulsen IT, Kolonay JF, Brinkac L, Beanan M, Dodson RJ, Daugherty SC, Madupu R, Angiuoli SV, Durkin AS, Haft DH, Vamathevan J, Khouri H, Utterback T, Lee C, Dimitrov G, Jiang L, Qin H, Weidman J, Tran K, Kang K, Hance IR, Nelson KE, Fraser CM
PMID: 15774886
PLoS biology. 2005-01-04; 3.1: e15.
Major structural differences and novel potential virulence mechanisms from the genomes of multiple campylobacter species
Fouts DE, Mongodin EF, Mandrell RE, Miller WG, Rasko DA, Ravel J, Brinkac LM, Deboy RT, Parker CT, Daugherty SC, Dodson RJ, Durkin AS, Madupu R, Sullivan SA, Shetty JU, Ayodeji MA, Shvartsbeyn A, Schatz MC, Badger JH, Fraser CM, Nelson KE
PMID: 15660156
PLoS biology. 2004-10-01; 2.10: e303.
Genomic insights into methanotrophy: the complete genome sequence of Methylococcus capsulatus (Bath)
Ward N, Larsen Ø, Sakwa J, Bruseth L, Khouri H, Durkin AS, Dimitrov G, Jiang L, Scanlan D, Kang KH, Lewis M, Nelson KE, Methé B, Wu M, Heidelberg JF, Paulsen IT, Fouts D, Ravel J, Tettelin H, Ren Q, Read T, Deboy RT, Seshadri R, Salzberg SL, Jensen HB, Birkeland NK, Nelson WC, Dodson RJ, Grindhaug SH, Holt I, Eidhammer I, Jonasen I, Vanaken S, Utterback T, Feldblyum TV, Fraser CM, Lillehaug JR, Eisen JA
PMID: 15383840
Nucleic acids research. 2004-04-28; 32.8: 2386-95.
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
Nelson KE, Fouts DE, Mongodin EF, Ravel J, Deboy RT, Kolonay JF, Rasko DA, Angiuoli SV, Gill SR, Paulsen IT, Peterson J, White O, Nelson WC, Nierman W, Beanan MJ, Brinkac LM, Daugherty SC, Dodson RJ, Durkin AS, Madupu R, Haft DH, Selengut J, Van Aken S, Khouri H, Fedorova N, Forberger H, Tran B, Kathariou S, Wonderling LD, Uhlich GA, Bayles DO, Luchansky JB, Fraser CM
PMID: 15115801
Science (New York, N.Y.). 2004-04-02; 304.5667: 66-74.
Environmental genome shotgun sequencing of the Sargasso Sea
Venter JC, Remington K, Heidelberg JF, Halpern AL, Rusch D, Eisen JA, Wu D, Paulsen I, Nelson KE, Nelson W, Fouts DE, Levy S, Knap AH, Lomas MW, Nealson K, White O, Peterson J, Hoffman J, Parsons R, Baden-Tillson H, Pfannkoch C, Rogers YH, Smith HO
PMID: 15001713
Journal of bacteriology. 2003-09-01; 185.18: 5591-601.
Complete genome sequence of the oral pathogenic Bacterium porphyromonas gingivalis strain W83
Nelson KE, Fleischmann RD, Deboy RT, Paulsen IT, Fouts DE, Eisen JA, Daugherty SC, Dodson RJ, Durkin AS, Gwinn M, Haft DH, Kolonay JF, Nelson WC, Mason T, Tallon L, Gray J, Granger D, Tettelin H, Dong H, Galvin JL, Duncan MJ, Dewhirst FE, Fraser CM
PMID: 12949112
Nature. 2003-05-01; 423.6935: 81-6.
The genome sequence of Bacillus anthracis Ames and comparison to closely related bacteria
Read TD, Peterson SN, Tourasse N, Baillie LW, Paulsen IT, Nelson KE, Tettelin H, Fouts DE, Eisen JA, Gill SR, Holtzapple EK, Okstad OA, Helgason E, Rilstone J, Wu M, Kolonay JF, Beanan MJ, Dodson RJ, Brinkac LM, Gwinn M, Deboy RT, Madpu R, Daugherty SC, Durkin AS, Haft DH, Nelson WC, Peterson JD, Pop M, Khouri HM, Radune D, Benton JL, Mahamoud Y, Jiang L, Hance IR, Weidman JF, Berry KJ, Plaut RD, Wolf AM, Watkins KL, Nierman WC, Hazen A, Cline R, Redmond C, Thwaite JE, White O, Salzberg SL, Thomason B, Friedlander AM, Koehler TM, Hanna PC, Kolstø AB, Fraser CM
PMID: 12721629
Molecular plant-microbe interactions : MPMI. 2003-01-01; 16.1: 43-52.
A pseudomonas syringae pv. tomato DC3000 Hrp (Type III secretion) deletion mutant expressing the Hrp system of bean pathogen P. syringae pv. syringae 61 retains normal host specificity for tomato
Fouts DE, Badel JL, Ramos AR, Rapp RA, Collmer A
PMID: 12580281
Proceedings of the National Academy of Sciences of the United States of America. 2002-02-19; 99.4: 2275-80.
Genomewide identification of Pseudomonas syringae pv. tomato DC3000 promoters controlled by the HrpL alternative sigma factor
Fouts DE, Abramovitch RB, Alfano JR, Baldo AM, Buell CR, Cartinhour S, Chatterjee AK, D'Ascenzo M, Gwinn ML, Lazarowitz SG, Lin NC, Martin GB, Rehm AH, Schneider DJ, van Dijk K, Tang X, Collmer A
PMID: 11854524
Gene. 1998-03-27; 210.1: 135-42.
Translationally repressive RNA structures monitored in vivo using temperate DNA bacteriophages
Fouts DE, Celander DW
PMID: 9524249
Nucleic acids research. 1997-11-15; 25.22: 4464-73.
Functional recognition of fragmented operator sites by R17/MS2 coat protein, a translational repressor
Fouts DE, True HL, Celander DW
PMID: 9358153
Biochemistry. 1997-10-28; 36.43: 13256-62.
Site-specific phosphorylation of the human immunodeficiency virus type-1 Rev protein accelerates formation of an efficient RNA-binding conformation
Fouts DE, True HL, Cengel KA, Celander DW
PMID: 9341215
Nucleic acids research. 1996-04-15; 24.8: 1582-4.
Improved method for selecting RNA-binding activities in vivo
Fouts DE, Celander DW
PMID: 8628698


An R-package for selecting representative genomes using Gaussian mixture models.


Phage_Finder is a heuristic computer program written in PERL to identify prophage regions within bacterial genomes.


PanACEA is a tool for Pan-Genome visualization, which utilizes locally-computed interactive web-pages to view ordered pan-genome data.


A custom sequence locus typer for classifying microbial genotypic and phenotypic attributes.

Designer Phage

Synthetic Engineering of Bacteriophage for Treatment of Wound Infections


Viral Synthetic Genomics to Engineer Large dsDNA Viruses

Rapid engineering of large dsDNA viruses using synthetic genomics assembly tools.

Genomics, Biomarkers and Mechanisms of Healing in Chronic Wounds

Utilize genomics approaches to identify the microbial composition and functional elements in non-healing and chronic wounds.

Asymptomatic Bacteriuria: Microbiome and Metaproteome

We use genomics approaches to detect the presence of bacteria with known inflammatory responses in asymptomatic patients. 

Vaginal Microbiome Project

A metagenomics approach to understanding the relationship between the vaginal microbiome, bacterial vaginosis, vaginal health and preterm birth.

Mouse Microbiome

Enteric dysbiosis associated with a mouse model of alcoholic liver disease. The translocation of bacteria and bacterial products into the circulation contributes to alcoholic liver disease.

Toby Clarke, MS
Bioinformatics Engineer
Stephanie Mounaud
Scientific Project Manager
Hayley Nordstrom, MS
Staff Scientist
Lily Velazco
Bacteriophage and Antibacterial Resistant Infections
Press Release

51ݶ scientists awarded five-year, $5.7M grant from NIH to develop phage treatment

Phage research accelerates with the rise of antibiotic resistance to address increasingly prevalent and difficult to treat bacterial infections

Press Release

51ݶ and UC San Diego Develop Phage Treatment as Potential Cure for Alcoholic Liver Disease

Team targeted specific toxin-producing strains of the bacterium, Enterococcus faecalis, which is shown to be responsible for most liver damage

Collaborator Release

Combining Antibiotics, Researchers Deliver One-Two Punch against Ubiquitous Bacterium

CWRU/Cleveland VA findings in mouse models could make inroads against superbugs