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Food authentication from shotgun sequencing reads with an application on high protein powders.

Haiminen N, Edlund S, Chambliss D, Kunitomi M, Weimer BC, Ganesan B, Baker R, Markwell P, Davis M, Huang BC, Kong N, Prill RJ, Marlowe CH, Quintanar A, Pierre S, Dubois G, Kaufman JH, Parida L, Beck KL.

NPJ Sci Food. 2019 Nov 19;3:24. doi: 10.1038/s41538-019-0056-6. eCollection 2019.


Insular Microbiogeography: Three Pathogens as Exemplars.

Kaufman JH, Elkins CA, Davis M, Weis AM, Huang BC, Mammel MK, Patel IR, Beck KL, Edlund S, Chambliss D, Douglas J, Bianco S, Kunitomi M, Weimer BC.

Curr Issues Mol Biol. 2019 Oct 9;36:89-108. doi: 10.21775/cimb.036.089. [Epub ahead of print]


Draft Genome Sequence of Bacillus velezensis CE2, Which Genetically Encodes a Novel Multicomponent Lantibiotic.

Campbell E, Gerst M, Huang BC, Kong N, Weimer BC, Yousef AE.

Microbiol Resour Announc. 2019 Jan 17;8(3). pii: e01420-18. doi: 10.1128/MRA.01420-18. eCollection 2019 Jan.


Nitrogen fixation in a landrace of maize is supported by a mucilage-associated diazotrophic microbiota.

Van Deynze A, Zamora P, Delaux PM, Heitmann C, Jayaraman D, Rajasekar S, Graham D, Maeda J, Gibson D, Schwartz KD, Berry AM, Bhatnagar S, Jospin G, Darling A, Jeannotte R, Lopez J, Weimer BC, Eisen JA, Shapiro HY, Ané JM, Bennett AB.

PLoS Biol. 2018 Aug 7;16(8):e2006352. doi: 10.1371/journal.pbio.2006352. eCollection 2018 Aug.


Whole Cell Cross-Linking to Discover Host-Microbe Protein Cognate Receptor/Ligand Pairs.

Weimer BC, Chen P, Desai PT, Chen D, Shah J.

Front Microbiol. 2018 Jul 19;9:1585. doi: 10.3389/fmicb.2018.01585. eCollection 2018.


Effect of temperature control on the metabolite content in exhaled breath condensate.

Zamuruyev KO, Borras E, Pettit DR, Aksenov AA, Simmons JD, Weimer BC, Schivo M, Kenyon NJ, Delplanque JP, Davis CE.

Anal Chim Acta. 2018 May 2;1006:49-60. doi: 10.1016/j.aca.2017.12.025. Epub 2017 Dec 30.


Comparative analysis of Campylobacter isolates from wild birds and chickens using MALDI-TOF MS, biochemical testing, and DNA sequencing.

Lawton SJ, Weis AM, Byrne BA, Fritz H, Taff CC, Townsend AK, Weimer BC, Mete A, Wheeler S, Boyce WM.

J Vet Diagn Invest. 2018 May;30(3):354-361. doi: 10.1177/1040638718762562. Epub 2018 Mar 12.


Prebiotic Oligosaccharides Potentiate Host Protective Responses against L. Monocytogenes Infection.

Chen P, Reiter T, Huang B, Kong N, Weimer BC.

Pathogens. 2017 Dec 19;6(4). pii: E68. doi: 10.3390/pathogens6040068.


Exhaled breath condensate methods adapted from human studies using longitudinal metabolomics for predicting early health alterations in dolphins.

Borras E, Aksenov AA, Baird M, Novick B, Schivo M, Zamuruyev KO, Pasamontes A, Parry C, Foutouhi S, Venn-Watson S, Weimer BC, Davis CE.

Anal Bioanal Chem. 2017 Nov;409(28):6523-6536. doi: 10.1007/s00216-017-0581-6. Epub 2017 Oct 23.


Draft Genome Sequences of Salmonella enterica Serovar Typhimurium LT2 with Deleted Chitinases That Are Emerging Virulence Factors.

Arabyan N, Huang BC, Weimer BC.

Genome Announc. 2017 Aug 3;5(31). pii: e00659-17. doi: 10.1128/genomeA.00659-17.


SigTree: A Microbial Community Analysis Tool to Identify and Visualize Significantly Responsive Branches in a Phylogenetic Tree.

Stevens JR, Jones TR, Lefevre M, Ganesan B, Weimer BC.

Comput Struct Biotechnol J. 2017 Jul 6;15:372-378. doi: 10.1016/j.csbj.2017.06.002. eCollection 2017. Review.


100K Pathogen Genome Project.

Weimer BC.

Genome Announc. 2017 Jul 13;5(28). pii: e00594-17. doi: 10.1128/genomeA.00594-17.


Draft Genome Sequences of 1,183 Salmonella Strains from the 100K Pathogen Genome Project.

Kong N, Davis M, Arabyan N, Huang BC, Weis AM, Chen P, Thao K, Ng W, Chin N, Foutouhi S, Foutouhi A, Kaufman J, Xie Y, Storey DB, Weimer BC.

Genome Announc. 2017 Jul 13;5(28). pii: e00518-17. doi: 10.1128/genomeA.00518-17.


Analytical methodologies for broad metabolite coverage of exhaled breath condensate.

Aksenov AA, Zamuruyev KO, Pasamontes A, Brown JF, Schivo M, Foutouhi S, Weimer BC, Kenyon NJ, Davis CE.

J Chromatogr B Analyt Technol Biomed Life Sci. 2017 Sep 1;1061-1062:17-25. doi: 10.1016/j.jchromb.2017.06.038. Epub 2017 Jun 27.


A Syst-OMICS Approach to Ensuring Food Safety and Reducing the Economic Burden of Salmonellosis.

Emond-Rheault JG, Jeukens J, Freschi L, Kukavica-Ibrulj I, Boyle B, Dupont MJ, Colavecchio A, Barrere V, Cadieux B, Arya G, Bekal S, Berry C, Burnett E, Cavestri C, Chapin TK, Crouse A, Daigle F, Danyluk MD, Delaquis P, Dewar K, Doualla-Bell F, Fliss I, Fong K, Fournier E, Franz E, Garduno R, Gill A, Gruenheid S, Harris L, Huang CB, Huang H, Johnson R, Joly Y, Kerhoas M, Kong N, Lapointe G, Larivière L, Loignon S, Malo D, Moineau S, Mottawea W, Mukhopadhyay K, Nadon C, Nash J, Ngueng Feze I, Ogunremi D, Perets A, Pilar AV, Reimer AR, Robertson J, Rohde J, Sanderson KE, Song L, Stephan R, Tamber S, Thomassin P, Tremblay D, Usongo V, Vincent C, Wang S, Weadge JT, Wiedmann M, Wijnands L, Wilson ED, Wittum T, Yoshida C, Youfsi K, Zhu L, Weimer BC, Goodridge L, Levesque RC.

Front Microbiol. 2017 Jun 2;8:996. doi: 10.3389/fmicb.2017.00996. eCollection 2017.


Draft Genome Sequences of Salmonella Lysozyme Gene Knockout Mutants.

Arabyan N, Huang BC, Weimer BC.

Genome Announc. 2017 Jun 8;5(23). pii: e00519-17. doi: 10.1128/genomeA.00519-17.


Amylases and Their Importance during Glycan Degradation: Genome Sequence Release of Salmonella Amylase Knockout Strains.

Arabyan N, Huang BC, Weimer BC.

Genome Announc. 2017 May 18;5(20). pii: e00355-17. doi: 10.1128/genomeA.00355-17.


Implication of Sialidases in Salmonella Infection: Genome Release of Sialidase Knockout Strains from Salmonella enterica Serovar Typhimurium LT2.

Arabyan N, Weis AM, Huang BC, Weimer BC.

Genome Announc. 2017 May 11;5(19). pii: e00341-17. doi: 10.1128/genomeA.00341-17.


Shigella Draft Genome Sequences: Resources for Food Safety and Public Health.

Weis AM, Gilpin B, Huang BC, Kong N, Chen P, Weimer BC.

Genome Announc. 2017 Apr 20;5(16). pii: e00176-17. doi: 10.1128/genomeA.00176-17.


Draft Genome Sequence of Multidrug-Resistant Abortive Campylobacter jejuni from Northern California.

Weis AM, Clothier KA, Huang BC, Kong N, Weimer BC.

Genome Announc. 2017 Apr 13;5(15). pii: e00171-17. doi: 10.1128/genomeA.00171-17.


Automation of PacBio SMRTbell NGS library preparation for bacterial genome sequencing.

Kong N, Ng W, Thao K, Agulto R, Weis A, Kim KS, Korlach J, Hickey L, Kelly L, Lappin S, Weimer BC.

Stand Genomic Sci. 2017 Mar 23;12:27. doi: 10.1186/s40793-017-0239-1. eCollection 2017.


Fallacy of the Unique Genome: Sequence Diversity within Single Helicobacter pylori Strains.

Draper JL, Hansen LM, Bernick DL, Abedrabbo S, Underwood JG, Kong N, Huang BC, Weis AM, Weimer BC, van Vliet AH, Pourmand N, Solnick JV, Karplus K, Ottemann KM.

mBio. 2017 Feb 21;8(1). pii: e02321-16. doi: 10.1128/mBio.02321-16.


100K Pathogen Genome Project: 306 Listeria Draft Genome Sequences for Food Safety and Public Health.

Chen P, Kong N, Huang B, Thao K, Ng W, Storey DB, Arabyan N, Foutouhi A, Foutouhi S, Weimer BC.

Genome Announc. 2017 Feb 9;5(6). pii: e00967-16. doi: 10.1128/genomeA.00967-16.


Large-Scale Release of Campylobacter Draft Genomes: Resources for Food Safety and Public Health from the 100K Pathogen Genome Project.

Weis AM, Huang BC, Storey DB, Kong N, Chen P, Arabyan N, Gilpin B, Mason C, Townsend AK, Smith WA, Byrne BA, Taff CC, Weimer BC.

Genome Announc. 2017 Jan 5;5(1). pii: e00925-16. doi: 10.1128/genomeA.00925-16.


Human breath metabolomics using an optimized non-invasive exhaled breath condensate sampler.

Zamuruyev KO, Aksenov AA, Pasamontes A, Brown JF, Pettit DR, Foutouhi S, Weimer BC, Schivo M, Kenyon NJ, Delplanque JP, Davis CE.

J Breath Res. 2016 Dec 22;11(1):016001. doi: 10.1088/1752-7163/11/1/016001.


Draft Genome Sequences of Campylobacter jejuni Strains That Cause Abortion in Livestock.

Weis AM, Clothier KA, Huang BC, Kong N, Weimer BC.

Genome Announc. 2016 Dec 1;4(6). pii: e01324-16. doi: 10.1128/genomeA.01324-16.


Comparative Genomics Reveals the Diversity of Restriction-Modification Systems and DNA Methylation Sites in Listeria monocytogenes.

Chen P, den Bakker HC, Korlach J, Kong N, Storey DB, Paxinos EE, Ashby M, Clark T, Luong K, Wiedmann M, Weimer BC.

Appl Environ Microbiol. 2017 Jan 17;83(3). pii: e02091-16. doi: 10.1128/AEM.02091-16. Print 2017 Feb 1.


Genomic Comparison of Campylobacter spp. and Their Potential for Zoonotic Transmission between Birds, Primates, and Livestock.

Weis AM, Storey DB, Taff CC, Townsend AK, Huang BC, Kong NT, Clothier KA, Spinner A, Byrne BA, Weimer BC.

Appl Environ Microbiol. 2016 Nov 21;82(24):7165-7175. Print 2016 Dec 15.


The Bacterial Mobile Resistome Transfer Network Connecting the Animal and Human Microbiomes.

Hu Y, Yang X, Li J, Lv N, Liu F, Wu J, Lin IY, Wu N, Weimer BC, Gao GF, Liu Y, Zhu B.

Appl Environ Microbiol. 2016 Oct 27;82(22):6672-6681. Print 2016 Nov 15.


Salmonella Typhimurium Enzymatically Landscapes the Host Intestinal Epithelial Cell (IEC) Surface Glycome to Increase Invasion.

Park D, Arabyan N, Williams CC, Song T, Mitra A, Weimer BC, Maverakis E, Lebrilla CB.

Mol Cell Proteomics. 2016 Dec;15(12):3653-3664. Epub 2016 Oct 17.


Enhanced non-invasive respiratory sampling from bottlenose dolphins for breath metabolomics measurements.

Zamuruyev KO, Aksenov AA, Baird M, Pasamontes A, Parry C, Foutouhi S, Venn-Watson S, Weimer BC, Delplanque JP, Davis CE.

J Breath Res. 2016 Sep 30;10(4):046005. doi: 10.1088/1752-7155/10/4/046005.


Salmonella Degrades the Host Glycocalyx Leading to Altered Infection and Glycan Remodeling.

Arabyan N, Park D, Foutouhi S, Weis AM, Huang BC, Williams CC, Desai P, Shah J, Jeannotte R, Kong N, Lebrilla CB, Weimer BC.

Sci Rep. 2016 Jul 8;6:29525. doi: 10.1038/srep29525.


Influence of Host Ecology and Behavior on Campylobacter jejuni Prevalence and Environmental Contamination Risk in a Synanthropic Wild Bird Species.

Taff CC, Weis AM, Wheeler S, Hinton MG, Weimer BC, Barker CM, Jones M, Logsdon R, Smith WA, Boyce WM, Townsend AK.

Appl Environ Microbiol. 2016 Jul 15;82(15):4811-20. doi: 10.1128/AEM.01456-16. Print 2016 Aug 1.


Metabolome searcher: a high throughput tool for metabolite identification and metabolic pathway mapping directly from mass spectrometry and using genome restriction.

Dhanasekaran AR, Pearson JL, Ganesan B, Weimer BC.

BMC Bioinformatics. 2015 Feb 25;16:62. doi: 10.1186/s12859-015-0462-y.


Complete Genome Sequences of a Clinical Isolate and an Environmental Isolate of Vibrio parahaemolyticus.

Lüdeke CH, Kong N, Weimer BC, Fischer M, Jones JL.

Genome Announc. 2015 Mar 26;3(2). pii: e00216-15. doi: 10.1128/genomeA.00216-15.


Enhanced cardiac Akt/protein kinase B signaling contributes to pathological cardiac hypertrophy in part by impairing mitochondrial function via transcriptional repression of mitochondrion-targeted nuclear genes.

Wende AR, O'Neill BT, Bugger H, Riehle C, Tuinei J, Buchanan J, Tsushima K, Wang L, Caro P, Guo A, Sloan C, Kim BJ, Wang X, Pereira RO, McCrory MA, Nye BG, Benavides GA, Darley-Usmar VM, Shioi T, Weimer BC, Abel ED.

Mol Cell Biol. 2015 Mar;35(5):831-46. doi: 10.1128/MCB.01109-14. Epub 2014 Dec 22.


Gut microbiota-produced succinate promotes C. difficile infection after antibiotic treatment or motility disturbance.

Ferreyra JA, Wu KJ, Hryckowian AJ, Bouley DM, Weimer BC, Sonnenburg JL.

Cell Host Microbe. 2014 Dec 10;16(6):770-7. doi: 10.1016/j.chom.2014.11.003.


Genetic mechanisms underlying the pathogenicity of cold-stressed Salmonella enterica serovar typhimurium in cultured intestinal epithelial cells.

Shah J, Desai PT, Weimer BC.

Appl Environ Microbiol. 2014 Nov;80(22):6943-53. doi: 10.1128/AEM.01994-14. Epub 2014 Sep 5.


Genomic epidemiology of Salmonella enterica serotype Enteritidis based on population structure of prevalent lineages.

Deng X, Desai PT, den Bakker HC, Mikoleit M, Tolar B, Trees E, Hendriksen RS, Frye JG, Porwollik S, Weimer BC, Wiedmann M, Weinstock GM, Fields PI, McClelland M.

Emerg Infect Dis. 2014 Sep;20(9):1481-9. doi: 10.3201/eid2009.131095.


Probiotic bacteria survive in Cheddar cheese and modify populations of other lactic acid bacteria.

Ganesan B, Weimer BC, Pinzon J, Dao Kong N, Rompato G, Brothersen C, McMahon DJ.

J Appl Microbiol. 2014 Jun;116(6):1642-56. doi: 10.1111/jam.12482. Epub 2014 Mar 17.


Gastrointestinal microbes interact with canine adipose-derived mesenchymal stem cells in vitro and enhance immunomodulatory functions.

Kol A, Foutouhi S, Walker NJ, Kong NT, Weimer BC, Borjesson DL.

Stem Cells Dev. 2014 Aug 15;23(16):1831-43. doi: 10.1089/scd.2014.0128. Epub 2014 Jun 26.


Exploring bacterial epigenomics in the next-generation sequencing era: a new approach for an emerging frontier.

Chen P, Jeannotte R, Weimer BC.

Trends Microbiol. 2014 May;22(5):292-300. doi: 10.1016/j.tim.2014.03.005. Epub 2014 Apr 8. Review.


Cross-talk between E. coli strains and a human colorectal adenocarcinoma-derived cell line.

He X, Mishchuk DO, Shah J, Weimer BC, Slupsky CM.

Sci Rep. 2013 Dec 4;3:3416. doi: 10.1038/srep03416.


Insulin receptor substrate signaling suppresses neonatal autophagy in the heart.

Riehle C, Wende AR, Sena S, Pires KM, Pereira RO, Zhu Y, Bugger H, Frank D, Bevins J, Chen D, Perry CN, Dong XC, Valdez S, Rech M, Sheng X, Weimer BC, Gottlieb RA, White MF, Abel ED.

J Clin Invest. 2013 Dec;123(12):5319-33. doi: 10.1172/JCI71171. Epub 2013 Nov 1.


Preadaptation to cold stress in Salmonella enterica serovar Typhimurium increases survival during subsequent acid stress exposure.

Shah J, Desai PT, Chen D, Stevens JR, Weimer BC.

Appl Environ Microbiol. 2013 Dec;79(23):7281-9. doi: 10.1128/AEM.02621-13. Epub 2013 Sep 20.


Microbiota-liberated host sugars facilitate post-antibiotic expansion of enteric pathogens.

Ng KM, Ferreyra JA, Higginbottom SK, Lynch JB, Kashyap PC, Gopinath S, Naidu N, Choudhury B, Weimer BC, Monack DM, Sonnenburg JL.

Nature. 2013 Oct 3;502(7469):96-9. doi: 10.1038/nature12503. Epub 2013 Sep 1.


Dissecting the role of milk components on gut microbiota composition.

Maga EA, Weimer BC, Murray JD.

Gut Microbes. 2013 Mar-Apr;4(2):136-9. doi: 10.4161/gmic.23188. Epub 2012 Dec 12.


Consumption of lysozyme-rich milk can alter microbial fecal populations.

Maga EA, Desai PT, Weimer BC, Dao N, Kültz D, Murray JD.

Appl Environ Microbiol. 2012 Sep;78(17):6153-60. doi: 10.1128/AEM.00956-12. Epub 2012 Jun 29.


Intraspecies variation in the emergence of hyperinfectious bacterial strains in nature.

Heithoff DM, Shimp WR, House JK, Xie Y, Weimer BC, Sinsheimer RL, Mahan MJ.

PLoS Pathog. 2012;8(4):e1002647. doi: 10.1371/journal.ppat.1002647. Epub 2012 Apr 12.


Genetic loss of insulin receptors worsens cardiac efficiency in diabetes.

Bugger H, Riehle C, Jaishy B, Wende AR, Tuinei J, Chen D, Soto J, Pires KM, Boudina S, Theobald HA, Luptak I, Wayment B, Wang X, Litwin SE, Weimer BC, Abel ED.

J Mol Cell Cardiol. 2012 May;52(5):1019-26. doi: 10.1016/j.yjmcc.2012.02.001. Epub 2012 Feb 9.

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