Format
Sort by
Items per page

Send to

Choose Destination

Search results

Items: 1 to 50 of 84

1.

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.

MBio. 2019 Jul 2;10(4). pii: e00405-19. doi: 10.1128/mBio.00405-19.

2.

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 Jr, 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.

Hepatology. 2019 Jun 22. doi: 10.1002/hep.30832. [Epub ahead of print]

PMID:
31228214
3.

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.

J Infect Dis. 2019 May 17. pii: jiz149. doi: 10.1093/infdis/jiz149. [Epub ahead of print]

PMID:
31099835
4.

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.

Gut Microbes. 2019 Apr 14:1-11. doi: 10.1080/19490976.2019.1595300. [Epub ahead of print]

PMID:
30982395
5.

Bacteriophage φEf11 ORF28 Endolysin, a Multifunctional Lytic Enzyme with Properties Distinct from All Other Identified Enterococcus faecalis Phage Endolysins.

Zhang H, Buttaro BA, Fouts DE, Sanjari S, Evans BS, Stevens RH.

Appl Environ Microbiol. 2019 Jun 17;85(13). pii: e00555-19. doi: 10.1128/AEM.00555-19. Print 2019 Jul 1.

PMID:
30979842
6.

Rapid Replacement of Acinetobacter baumannii Strains Accompanied by Changes in Lipooligosaccharide Loci and Resistance Gene Repertoire.

Adams MD, Wright MS, Karichu JK, Venepally P, Fouts DE, Chan AP, Richter SS, Jacobs MR, Bonomo RA.

MBio. 2019 Mar 26;10(2). pii: e00356-19. doi: 10.1128/mBio.00356-19.

7.

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.

mSphere. 2019 Mar 13;4(2). pii: e00685-18. doi: 10.1128/mSphere.00685-18.

8.

Closed Genome Sequences of Clinical Neisseria gonorrhoeae Strains Obtained from Combined Oxford Nanopore and Illumina Sequencing.

White RC, Torralba M, Colt K, Harrison F, Goglin K, Nguyen K, D'Souza R, Bristow CC, Ellis O, Soge OO, Klausner JD, Fouts DE.

Microbiol Resour Announc. 2019 Feb 28;8(9). pii: e00072-19. doi: 10.1128/MRA.00072-19. eCollection 2019 Feb.

9.

OMeta: an ontology-based, data-driven metadata tracking system.

Singh I, Kuscuoglu M, Harkins DM, Sutton G, Fouts DE, Nelson KE.

BMC Bioinformatics. 2019 Jan 7;20(1):8. doi: 10.1186/s12859-018-2580-9.

11.

ARGONAUT-I: Activity of Cefiderocol (S-649266), a Siderophore Cephalosporin, against Gram-Negative Bacteria, Including Carbapenem-Resistant Nonfermenters and Enterobacteriaceae with Defined Extended-Spectrum β-Lactamases and Carbapenemases.

Jacobs MR, Abdelhamed AM, Good CE, Rhoads DD, Hujer KM, Hujer AM, Domitrovic TN, Rudin SD, Richter SS, van Duin D, Kreiswirth BN, Greco C, Fouts DE, Bonomo RA.

Antimicrob Agents Chemother. 2018 Dec 21;63(1). pii: e01801-18. doi: 10.1128/AAC.01801-18. Print 2019 Jan.

12.

Large-scale comparative analysis of microbial pan-genomes using PanOCT.

Inman JM, Sutton GG, Beck E, Brinkac LM, Clarke TH, Fouts DE.

Bioinformatics. 2019 Mar 15;35(6):1049-1050. doi: 10.1093/bioinformatics/bty744.

13.

Characterization of the AmpC β-Lactamase from Burkholderia multivorans.

Becka SA, Zeiser ET, Barnes MD, Taracila MA, Nguyen K, Singh I, Sutton GG, LiPuma JJ, Fouts DE, Papp-Wallace KM.

Antimicrob Agents Chemother. 2018 Sep 24;62(10). pii: e01140-18. doi: 10.1128/AAC.01140-18. Print 2018 Oct.

14.

Sequence heterogeneity of the PenA carbapenemase in clinical isolates of Burkholderia multivorans.

Becka SA, Zeiser ET, Marshall SH, Gatta JA, Nguyen K, Singh I, Greco C, Sutton GG, Fouts DE, LiPuma JJ, Papp-Wallace KM.

Diagn Microbiol Infect Dis. 2018 Nov;92(3):253-258. doi: 10.1016/j.diagmicrobio.2018.06.005. Epub 2018 Jun 18.

15.

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 Jr.

Front Cell Infect Microbiol. 2018 Jun 19;8:193. doi: 10.3389/fcimb.2018.00193. eCollection 2018.

16.

PanACEA: a bioinformatics tool for the exploration and visualization of bacterial pan-chromosomes.

Clarke TH, Brinkac LM, Inman JM, Sutton G, Fouts DE.

BMC Bioinformatics. 2018 Jun 27;19(1):246. doi: 10.1186/s12859-018-2250-y.

17.

Multidrug resistant pathogens respond differently to the presence of co-pathogen, commensal, probiotic and host cells.

Chan AP, Choi Y, Brinkac LM, Krishnakumar R, DePew J, Kim M, Hinkle MK, Lesho EP, Fouts DE.

Sci Rep. 2018 Jun 5;8(1):8656. doi: 10.1038/s41598-018-26738-1.

18.

GGRaSP: a R-package for selecting representative genomes using Gaussian mixture models.

Clarke TH, Brinkac LM, Sutton G, Fouts DE.

Bioinformatics. 2018 Sep 1;34(17):3032-3034. doi: 10.1093/bioinformatics/bty300.

19.

Dysregulation of serum bile acids and FGF19 in alcoholic hepatitis.

Brandl K, Hartmann P, Jih LJ, Pizzo DP, Argemi J, Ventura-Cots M, Coulter S, Liddle C, Ling L, Rossi SJ, DePaoli AM, Loomba R, Mehal WZ, Fouts DE, Lucey MR, Bosques-Padilla F, Mathurin P, Louvet A, Garcia-Tsao G, Verna EC, Abraldes JG, Brown RS Jr, Vargas V, Altamirano J, Caballería J, Shawcross D, Stärkel P, Ho SB, Bataller R, Schnabl B.

J Hepatol. 2018 Aug;69(2):396-405. doi: 10.1016/j.jhep.2018.03.031. Epub 2018 Apr 12.

20.

Publisher Correction: 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.

Nat Commun. 2017 Dec 12;8(1):2137. doi: 10.1038/s41467-017-01779-8.

21.

Modulation of the intestinal bile acid/farnesoid X receptor/fibroblast growth factor 15 axis improves alcoholic liver disease in mice.

Hartmann P, Hochrath K, Horvath A, Chen P, Seebauer CT, Llorente C, Wang L, Alnouti Y, Fouts DE, Stärkel P, Loomba R, Coulter S, Liddle C, Yu RT, Ling L, Rossi SJ, DePaoli AM, Downes M, Evans RM, Brenner DA, Schnabl B.

Hepatology. 2018 Jun;67(6):2150-2166. doi: 10.1002/hep.29676. Epub 2018 Apr 16.

22.

Amplification for Whole Genome Sequencing of Bacteriophages from Single Isolated Plaques Using SISPA.

Fouts DE.

Methods Mol Biol. 2018;1681:165-178. doi: 10.1007/978-1-4939-7343-9_12.

PMID:
29134594
23.

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.

Nat Commun. 2017 Oct 16;8(1):837. doi: 10.1038/s41467-017-00796-x. Erratum in: Nat Commun. 2017 Dec 12;8(1):2137.

24.

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.

J Clin Invest. 2017 Jun 30;127(7):2829-2841. doi: 10.1172/JCI90562. Epub 2017 May 22.

25.

LOCUST: a custom sequence locus typer for classifying microbial isolates.

Brinkac LM, Beck E, Inman J, Venepally P, Fouts DE, Sutton G.

Bioinformatics. 2017 Jun 1;33(11):1725-1726. doi: 10.1093/bioinformatics/btx045.

26.

Structural proteins of Enterococcus faecalis bacteriophage ϕEf11.

Stevens RH, Zhang H, Hsiao C, Kachlany S, Tinoco EM, DePew J, Fouts DE.

Bacteriophage. 2016 Nov 4;6(4):e1251381. doi: 10.1080/21597081.2016.1251381. eCollection 2016.

27.

Comprehensive Genome Analysis of Carbapenemase-Producing Enterobacter spp.: New Insights into Phylogeny, Population Structure, and Resistance Mechanisms.

Chavda KD, Chen L, Fouts DE, Sutton G, Brinkac L, Jenkins SG, Bonomo RA, Adams MD, Kreiswirth BN.

MBio. 2016 Dec 13;7(6). pii: e02093-16. doi: 10.1128/mBio.02093-16.

28.

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.

J Neurovirol. 2017 Apr;23(2):171-185. doi: 10.1007/s13365-016-0485-9. Epub 2016 Oct 13.

PMID:
27739035
29.

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 Jr, Yang XF, Zhang JJ, Vinetz JM.

PLoS Negl Trop Dis. 2016 Feb 18;10(2):e0004403. doi: 10.1371/journal.pntd.0004403. eCollection 2016 Feb.

30.

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.

Cell Host Microbe. 2016 Feb 10;19(2):227-39. doi: 10.1016/j.chom.2016.01.003.

31.

A novel method of consensus pan-chromosome assembly and large-scale comparative analysis reveal the highly flexible pan-genome of Acinetobacter baumannii.

Chan AP, Sutton G, DePew J, Krishnakumar R, Choi Y, Huang XZ, Beck E, Harkins DM, Kim M, Lesho EP, Nikolich MP, Fouts DE.

Genome Biol. 2015 Jul 21;16:143. doi: 10.1186/s13059-015-0701-6.

32.

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.

Genome Announc. 2015 Jan 22;3(1). pii: e01440-14. doi: 10.1128/genomeA.01440-14.

33.

Leptospiral pathogenomics.

Lehmann JS, Matthias MA, Vinetz JM, Fouts DE.

Pathogens. 2014 Apr 10;3(2):280-308. doi: 10.3390/pathogens3020280. Review.

34.

NeatFreq: reference-free data reduction and coverage normalization for De Novo sequence assembly.

McCorrison JM, Venepally P, Singh I, Fouts DE, Lasken RS, Methé BA.

BMC Bioinformatics. 2014 Nov 19;15:357. doi: 10.1186/s12859-014-0357-3.

35.

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.

Gastroenterology. 2015 Jan;148(1):203-214.e16. doi: 10.1053/j.gastro.2014.09.014. Epub 2014 Sep 16.

36.

The odd one out: Bacillus ACT bacteriophage CP-51 exhibits unusual properties compared to related Spounavirinae W.Ph. and Bastille.

Klumpp J, Schmuki M, Sozhamannan S, Beyer W, Fouts DE, Bernbach V, Calendar R, Loessner MJ.

Virology. 2014 Aug;462-463:299-308. doi: 10.1016/j.virol.2014.06.012. Epub 2014 Jul 8.

37.

Genome Sequences of Three Frequently Used Listeria monocytogenes and Listeria ivanovii Strains.

Klumpp J, Staubli T, Schmitter S, Hupfeld M, Fouts DE, Loessner MJ.

Genome Announc. 2014 May 1;2(2). pii: e00404-14. doi: 10.1128/genomeA.00404-14.

38.

Pathogenomic inference of virulence-associated genes in Leptospira interrogans.

Lehmann JS, Fouts DE, Haft DH, Cannella AP, Ricaldi JN, Brinkac L, Harkins D, Durkin S, Sanka R, Sutton G, Moreno A, Vinetz JM, Matthias MA.

PLoS Negl Trop Dis. 2013 Oct 3;7(10):e2468. doi: 10.1371/journal.pntd.0002468. eCollection 2013.

39.

Sequencing viral genomes from a single isolated plaque.

Depew J, Zhou B, McCorrison JM, Wentworth DE, Purushe J, Koroleva G, Fouts DE.

Virol J. 2013 Jun 6;10:181. doi: 10.1186/1743-422X-10-181.

40.

Whole genome sequencing and comparative genomic analyses of two Vibrio cholerae O139 Bengal-specific Podoviruses to other N4-like phages reveal extensive genetic diversity.

Fouts DE, Klumpp J, Bishop-Lilly KA, Rajavel M, Willner KM, Butani A, Henry M, Biswas B, Li M, Albert MJ, Loessner MJ, Calendar R, Sozhamannan S.

Virol J. 2013 May 28;10:165. doi: 10.1186/1743-422X-10-165.

41.
42.

Bacteriophage functional genomics and its role in bacterial pathogen detection.

Klumpp J, Fouts DE, Sozhamannan S.

Brief Funct Genomics. 2013 Jul;12(4):354-65. doi: 10.1093/bfgp/elt009. Epub 2013 Mar 21.

PMID:
23520178
43.

Next generation sequencing technologies and the changing landscape of phage genomics.

Klumpp J, Fouts DE, Sozhamannan S.

Bacteriophage. 2012 Jul 1;2(3):190-199.

44.

Whole genome analysis of Leptospira licerasiae provides insight into leptospiral evolution and pathogenicity.

Ricaldi JN, Fouts DE, Selengut JD, Harkins DM, Patra KP, Moreno A, Lehmann JS, Purushe J, Sanka R, Torres M, Webster NJ, Vinetz JM, Matthias MA.

PLoS Negl Trop Dis. 2012;6(10):e1853. doi: 10.1371/journal.pntd.0001853. Epub 2012 Oct 25.

45.

Next generation sequencing to define prokaryotic and fungal diversity in the bovine rumen.

Fouts DE, Szpakowski S, Purushe J, Torralba M, Waterman RC, MacNeil MD, Alexander LJ, Nelson KE.

PLoS One. 2012;7(11):e48289. doi: 10.1371/journal.pone.0048289. Epub 2012 Nov 7.

46.

Integrated next-generation sequencing of 16S rDNA and metaproteomics differentiate the healthy urine microbiome from asymptomatic bacteriuria in neuropathic bladder associated with spinal cord injury.

Fouts DE, Pieper R, Szpakowski S, Pohl H, Knoblach S, Suh MJ, Huang ST, Ljungberg I, Sprague BM, Lucas SK, Torralba M, Nelson KE, Groah SL.

J Transl Med. 2012 Aug 28;10:174. doi: 10.1186/1479-5876-10-174.

47.

PanOCT: automated clustering of orthologs using conserved gene neighborhood for pan-genomic analysis of bacterial strains and closely related species.

Fouts DE, Brinkac L, Beck E, Inman J, Sutton G.

Nucleic Acids Res. 2012 Dec;40(22):e172. doi: 10.1093/nar/gks757. Epub 2012 Aug 16.

48.

Bacterial translocation and changes in the intestinal microbiome in mouse models of liver disease.

Fouts DE, Torralba M, Nelson KE, Brenner DA, Schnabl B.

J Hepatol. 2012 Jun;56(6):1283-92. doi: 10.1016/j.jhep.2012.01.019. Epub 2012 Feb 9.

49.

Comparative genomic analysis of Vibrio parahaemolyticus: serotype conversion and virulence.

Chen Y, Stine OC, Badger JH, Gil AI, Nair GB, Nishibuchi M, Fouts DE.

BMC Genomics. 2011 Jun 6;12:294. doi: 10.1186/1471-2164-12-294.

50.

Enteric dysbiosis associated with a mouse model of alcoholic liver disease.

Yan AW, Fouts DE, Brandl J, Stärkel P, Torralba M, Schott E, Tsukamoto H, Nelson KE, Brenner DA, Schnabl B.

Hepatology. 2011 Jan;53(1):96-105. doi: 10.1002/hep.24018. Epub 2010 Dec 10.

Supplemental Content

Loading ...
Support Center