Manuscripts

This page reflects manuscripts for the last 5 years. For a full list see Google Scholar, ResearchGate, Orcid, or ReseacherID

2022

  • Monteiro, H. F., Z. Zhou, M. S. Gomes, P. M. G. Peixoto, E. C. R. Bonsaglia, I. F. Canisso, B. C. Weimer, and F. S. Lima. 2022. Rumen and lower gut microbiomes relationship with feed efficiency and production traits throughout the lactation of Holstein dairy cows. Sci Report 12:4904. (DOI:10.1038/s41598-022-08761-5).
  • Aguilar-Zamora, Emmanuel, Bart C. Weimer, Roberto C. Torres, Alejandro Gomez-Delgado, Nayeli Ortiz-Olvera, Varenka Barbero-Becerro, Gerardo Aparicio-Ozores, Javier Torres, and Margarita Camorlinga-Ponce. 2022. Molecular epidemiology and antimicrobial resistance in hospitalized patients from Mexico. Frontiers in Microbiology 12:787451. (DOI:10.3389/fmicb.2021.787451).  
  • Weimer, B.C., 2022. Lactic Acid Bacteria: Physiology and Stress Responses. In: McSweeney, P.L.H., McNamara, J.P. (Eds.), Encyclopedia of Dairy Sciences (3rd edition), vol. 4. Academic Press, pp. 238–248. (DOI:10.1016/B978-0-12-818766-1.00377-9; ISBN: 9780128187661).

2021

  • Wang, Yi, Pramod K. Pandey, Colleen Chiu, Richard Jeannotte, Sundaram Kuppu, Ruihong Zhang, Richard Pereira, Bart C. Weimer, Nitin Nitin, Sharif Aly. 2021. Quantification of antibiotic resistance genes and mobile gene elements in manure from dairy farms in California. PeerJ 9:e12408 (DOI: 10.7717/peerj.12408).
  • Weimer, Bart C. 2021. Bacteria: A journal for the new developments and management of challenging area of microbiology. Bacteria 1:1-2 (DOI: 10.3390/bacteria1010001).
  • van Oosterhout, Cock, Jessica F. Stephenson, Bart C. Weimer, Hinh Ly, Neil Hall, Kevin M. Tyler.COVID-19 adaptive evolution during the pandemic – Implications of new SARS-CoV-2 variants on public health policies. Virulence 12:2013-2016 (DOI: 10.1080/21505594.2021.1960109).
  • Hernández-Juárez, Laura E., Margarita Camorlinga, Alfonso Méndez-Tenorio, Judith Flores Calderón, B. Carol Huang, DJ Darwin R. Bandoy, Bart C. Weimer, and Javier Torres. 2021. Analyses of publicly available Hungatella hathewayi genomes revealed genetic distances indicating they belong to more than one species. Virulence 12:1950-1964. (DOI:10.1080/21505594.2021.1950955).
  • Flores-Valdez, Mauricio, Miguel A. Ares, Roberto Rosales-Reyes, Javier Torres, Jorge A Girón, Bart C. Weimer, Alfonso Mendez Tenorio, and Miguel A. De la Cruz. 2021. Whole genome sequencing of pediatric Klebsiella pneumoniae strains reveals important insights into their virulence-associated traits. Frontiers in Microbiology 12:711577 (DOI: 10.3389/fmicb.2021.711577).
  • Weimer, Bart C., and DJ Darwin Bandoy. 2021. Where coronavirus variants emerge, surges follow – new research suggests how genomic surveillance can be an early warning system. TheConversation.com (https://theconversation.com/where-coronavirus-variants-emerge-surges-follow-new-research-suggests-how-genomic-surveillance-can-be-an-early-warning-system-158733)
  • Santos-Medellin, Christian, Zachary Liechty, Joseph Edwards, Bao Nguyen, Bihua Huang, Bart C. Weimer, and Venkatesan Sundaresan. 2021. Drought duration determines the recovery dynamics of rice root microbiomes. Nature Plants (DOI:10.1038/s41477-021-00967-1).
  • Borras, Eva, Leah Schrumpf, Noelle Stephens, Bart C. Weimer, Cristina E. Davis, and Edward S. Schelegle. 2021. Novel LC-MS methodology to detect and quantify ascorbic and uric acid simultaneously using different biological matrices. J. Chrom B:122588 (DOI:10.1016/j.jchromb.2021.122588).
  • Miller, John J.,Bart C. Weimer, Ruth Timme, Catharina Lüdeke, James Pettengill, DJ Darwin Bandoy, Allison Weis, James Kaufman, Bihua Huang, Justin Payne, Errol Strain, and Jessica Jones. 2021. Phylogenetic and biogeographic patterns of
    Vibrio parahaemolyticus from North America inferred from whole-genome sequence data. Appl. Environ. Microbiol. 87:e01403-20 (DOI:10.1128/AEM.01403-20; PMID: 33187991)
  • Bandoy, DJ Darwin, and Bart C. Weimer. 2021. Analysis of SARS-CoV-2 genomic epidemiology reveals disease transmission coupled to variant emergence and allelic variation. Nature Scientific Reports 11:7380-92 (DOI:10.1038/s41598-021-86265-4)
  • Hurley, Karyl, Caroline Mansfield, Ilze Matīse VanHoutan, Lauren Lacorcia, Karin Allenspach, Geoffrey Hebbard, Stanley L. Marks, Bob Poppenga, James H. Kaufman,
    Bart C. Weimer, Kevin Douglas Woolard,Joe Bielitzki,Derek Lulham, and Jerome Naar. 2021. A comparative analysis of two unrelated incidents of food-associated megaesophagus outbreaks in dogs: Latvia 2014-2016 and Australia 2017-2018. JAVMA 259:172-183. (DOI:10.2460/javma.259.2.172).
  • Beck, Kristen L., Niina Haiminen, David Chambliss, Stefan Edlund, Mark Kunitomi, Robert Baker, Peter Markwell, Bala Ganesan, Laxmi Parida, Ban Kawas, Matthew Davis, Robert Prill, Carol Huang, Nguyet Kong, Trey Marlowe, Steven Binder, Geraud Dubois, James Kaufman, and Bart C. Weimer. 2021. Characterizing the microbiome in factory ingredient samples using metatranscriptome deep sequencing data. npj Sci Food5. (DOI:10.1038/s41538-020-00083-y)

2020

  • Higdon, Shawn M., Tania Pozzo, Nguyet Kong, Bihua C. Huang, Mai Lee Yang, Richard Jeannotte, C. Titus Brown, Alan Bennett, and Bart C. Weimer. 2020. Genomic characterization of a diazotrophic microbiota associated with maize aerial root mucilage. PLoS One 15:e0239677 (DOI:10.1371/journal.pone.0239677)
  • Higdon, Shawn M., Bihua C. Huang, Alan B. Bennett, and Bart C. Weimer. 2020. Identification of nitrogen fixation genes in Lactococcus isolated from maize using population genomics and machine learning. Microorganisms8:2043 (DOI:10.3390/microorganisms8122043) (Special Issue – Plant microbe interactions)
  • Higdon, Shawn M., Tania Pozzo, Emily Tibbett, Colleen Chiu, Richard Jeannotte, Bart C. Weimer, and Alan B. Bennett. 2020. Diazotrophic bacteria from maize exhibit multifaceted plant growth promotion traits in multiple hosts. PLoS One 15:e0239081 (DOI:10.1371/journal.pone.0239081; PMID: 32925972)
  • Santos-Medellin, Christian, Zachary Liechty, Joseph Edwards, Bao Nguyen, Bihua Huang, Bart C. Weimer, Venkatesan Sundaresan. 2020. Drought duration determines the recovery dynamics of rice root microbiomes. BioRxiv (DOI:10.1101/2020.09.29.314781)
  • Nayfach, Stephen, Simon Roux, Rekha Seshadri, Daniel Udwary, Neha Varghese, Frederik Schulz, Dongying Wu, David Paez-Espino, I-Min Chen, Marcel Huntemann, Krishna Palaniappan, Joshua Ladau, Supratim Mukherjee, T.B.K. Reddy, Torben Nielsen, Edward Kirton, José P. Faria, Janaka N. Edirisinghe, Christopher S. Henry, Sean P. Jungbluth, Dylan Chivian, Paramvir Dehal, Elisha M. Wood-Charlson, Adam P. Arkin, Susannah Tringe, Axel Visel, IMG/M Data Consortium (Bart C. Weimer), Tanja Woyke, Nigel J. Mouncey, Natalia N. Ivanova, Nikos C. Kyrpides, Emiley A. Eloe-Fadrosh. 2020. A Genomic Catalogue of Earth’s Microbiomes. Nature Biotechnology (DOI:10.1038/s41587-020-0718-6
  • Chang, Ruixue, Pramod Pandey, Yanming Li, Chandrasekar Venkitasamy, Zhao Chen, Rodrigo Gallardo,Bart C. Weimer, Michele Jay-Russell. 2020. Assessment of Gaseous Ozone Treatment on Salmonella Typhimurium and Escherichia coli O157:H7. Reductions in Poultry Litter. Waste Management 117:42-47 DOI:10.1016/j.wasman.2020.07.039
  • Beck, Kristen L., Niina Haiminen, David Chambliss, Stefan Edlund, Mark Kunitomi, Robert Baker, Peter Markwell, Bala Ganesan, Laxmi Parida, Ban Kawas, Matthew Davis, Robert Prill, Carol Huang, Nguyet Kong, Trey Marlowe, Steven Binder, Geraud Dubois, James Kaufman, Bart C. Weimer. 2020. Characterizing the microbiome in factory ingredient samples using metatranscriptome deep sequencing data. BioRxiv DOI:10.1101/2020.05.18.102574
  • Higdon, Shawn M., Tania Pozzo, Emily Tibbett, Colleen Chiu, Richard Jeannotte, Bart C. Weimer, and Alan B. Bennett. 2020. Diazotrophic bacteria from maize exhibit multifaceted plant growth promotion traits and host adaptability. BioRxiv doi: https://doi.org/10.1101/2020.04.27.064337
  • Higdon, Shawn M., Tania Pozzo, Nguyet Kong, Bihua C. Huang, Mai Lee Yang, Richard Jeannotte, C. Titus Brown, Alan B. Bennett, Bart C. Weimer. 2020. Genomic characterization of a diazotrophic microbiota associated with maize aerial root mucilage. BioRxiv DOI:10.1101/2020.04.27.064337
  • Chen, Poyin, DJ Darwin Bandoy, Bart C. Weimer. 2020. Bacterial epigenomics: epigenetics in the age of population genomics. InThe Pan-Genome – Diversity, Dynamics, and Evolution of Genomes. Ed.Duccio Medini and Hervé Tettelin. Springer, NYC, NY. ISBN 978-3-030-38281-0 (eBook); 978-3-030-38280-3 (hardback); DOI: 10.1007/978-3-030-38281-0
  • Pandey, Pramod, Sriram K Vidyarthi, Venkata Vaddella, Chandrasekar Venkitasamy, Maurice Pitesky, Bart C. Weimer, Alda F. A. Pires. 2020. Improving biosecurity procedures to minimize the risk of spreading pathogenic infections agents after carcass recycling. Front in Food Micro 11:623 DOI:10.3389/fmicb.2020.00623
  • Bandoy, DJ Darwin and Bart C. Weimer. 2020. Biological Machine Learning Combined with Campylobacter Population Genomics Reveals Virulence Gene Allelic Variants Cause Disease. DOI:10.3390/microorganisms8040549
  • Bandoy, DJ Darwin and Bart C. Weimer. 2020. Pandemic dynamics of COVID-19 using epidemic stage, instantaneous reproductive number, and pathogen genome identity (GENI) score: modeling molecular epidemiology. DOI:10.1101/2020.03.17.20037481
  •  Coolbear, T., Martin G. Wilkinson, Bart C. Weimer. 2020. Lactic Acid Bacteria in Flavor Development. DOI:10.1016/B978-0-12-818766-1.00019-2

2019

  • Foutouhi,Soraya H., Nuradilla Mohamad-Fauzi, Dylan Bobby Storey, Azarene A. Foutouhi, Nguyet Kong, Amir Kol, Dori Borjesson, Prerak Desai, Jigna Shah, James D. Murray, Bart C. Weimer. 2019. Salmonella Enhances Osteogenic Differentiation in Adipose-Derived Mesenchymal Stem Cells      (DOI: https://doi.org/10.1101/795617)
  • Bandoy, DJ Darwin R. and Bart C. Weimer.2019. Biological machine learning combined with bacterial population genomics reveals common and rare allelic variants of genes to cause disease BioRxiv    DOI: https://doi.org/10.1101/739540
  • Haiminen, Niina, Stefan Edlund, David Chambliss, Mark Kunitomi, Bart C. Weimer, Balasubramanian Ganesan, Robert Baker, Peter Markwell, Matthew Davis, B Carol Huang, Nguyet Kong, Robert Prill, Carl H Marlowe, André Quintanar, Sophie Pierre, Geraud Dubois, James Kaufman, Laxmi Parida, Kristen Beck. 2019. Food authentication from metagenome sequencing reads. Nature – Science of Food (DOI 10.1038/s41538-019-0056-6)
  • Kaufman, James H., Christopher A. Elkins, Matthew Davis, Allison M. Weis, Bihua C. Huang, Mark K. Mammel, Isha R. Patel, Kristen L. Beck, Stefan Edlund, David Chambliss, Judith Douglas, Simone Bianco, Mark Kunitomi, Bart C. Weimer. 2019. Insular Microbiogeography. In “Microbial Ecology: Current Advances from Genomics, Metagenomics and Other Omics”, pp. 45-64. Edited by Diana Marco. Caister Academic Press, Poole, UK. (ISBN: 978-1-912530-02-1) (https://doi.org/10.21775/9781912530021; chapter: https://doi.org/10.21775/9781912530021.04)
  • Gerst, Michelle, Emily Campbell, Carol Huang, Nguyet Kong, Bart C. Weimer, and Ahmed E. Yousef. 2018. Draft genome of Bacillus velezensis CE2 which genetically encodes a novel multi-component lantibiotic. Microbiology Resource Announcements (DOI 10.1128/MRA.01420-18)
  • Bandoy, DJ Darwin R., B Carol Huang, and Bart C. Weimer. 2019. Misclassification of a whole-genome sequence reference defined by the Human Microbiome Project: a detrimental carryover effect to microbiome studies. MedRxiv 19000489 (doi.org/10.1101/19000489).

2018

  • Kaufman, James, Ed Seabolt, Mark Kunitomi, Akshay Agarwal, Kristen Beck, Harsha Krishnareddy and Bart C. Weimer. 2018. Exploiting Functional Context in Biology: Reconsidering Classification of Bacterial Life. IEEE Computer Science 9:17-20. (DOI 10.1109/ICDEW.2018.00009)
  • Harness, E. Bart C. Weimer, JD Murray. 2018. Characterization of pig mesenchymal stromal cells for investigation of bacterial association and modification of stem cell function. Transgenic Research 27:485-485.
  • Van Deynze, Allen, Pablo Zamora, Pierre-Marc Delaux, Cristobal Heitmann, Dhileepkumar Jayaraman, Shanmugam Rajasekar, Junko Maeda, Srijak Bhatnagar, Guillaume Jospin, Danielle Graham, Richard Jeannotte, Donald Gibson, Aaron Darling, Kevin D. Schwartz, Alison M. Berry, Javier Lopez, Bart C. Weimer, Jonathan A. Eisen, Howard-Yana Shapiro, Jean-Michel Ané, and Alan B. Bennett. 2018. Nitrogen fixation in a landrace of maize is supported by a mucilage-associated diazotrophic microbiota. PLOS Biology. 16(8): e2006352. (https://doi.org/10.1371/journal.pbio.2006352).
  • Weimer, Bart C., Poyin Chen, Prerak T. Desai, Dong Chen, and Jigna Shah. 2018. Whole cell cross-linking to discover host-microbe protein cognate receptor/ligand pairs. Frontiers in Microbiology 9:1585. (doi: 10.3389/fmicb.2018.01585)
  • Arabyan, Narine and Bart C. Weimer. 2018. Glycosyide Hydrolases: Novel virulence factors during Salmonella infection Atlas of Science. In press.
  • Lawton, Samantha, Allison M. Weis, Barbara A. Byrne, Heather Fritz, Conor Taff, Andrea Townsend, Bart C. Weimer, Asli Mete, Sarah Wheeler, Walter M. Boyce. 2018. Comparative analysis of Campylobacter isolates from wild birds and chickens using MALDI-TOF, biochemical testing, and sequence analysis. Journal of Veterinary Diagnostic Investigation. (PMID: 29528812) (doi.org/10.1177/1040638718762562)
  • Zamuruyev, Konstantin O, Eva Borras, Dayna R Pettit, Alexander A Aksenov, Jason D Simmons, Bart C. Weimer, Michael Schivo, Nicholas J Kenyon, Jean-Pierre Delplanque, Cristina Davis. 2018. Effect of collection temperature on metabolite content in exhaled breath condensate. Analytica Chimica Acta.1006:49-60 https://doi.org/10.1016/j.aca.2017.12.025

2017

  • Chen, Poyin, Taylor Reiter, Bihua Huang, Nguyet Kong, and Bart C. Weimer. 2017. Prebiotic oligosaccharides potentiate host protective responses against Listeria monocytogenes infection. Pathogens 6:68 (invited contribution in – Special issue on Listeria monocytogenes and host interactions; Feature Article).(DOI:10.3390/pathogens6040068; PMID: 29257110)
  • Weis, Allison M., and Bart C. Weimer. 2017. The journey of Campylobacter: a genomic analysis of a successful zoonotic pathogen. Atlas of Science (http://atlasofscience.org/the-journey-of-campylobacter-a-genomic-analysis-of-a-successful-zoonotic-pathogen/#more-22426).
  •  Borras, Eva; Aksenov, Alexander; Baird, Mark; Novick, Brittany; Schivo, Michael; Zamuruyev, Konstantin; Pasamontes, Alberto; Parry, Celeste; Foutouhi, Soraya; Venn-Watson, Stephanie; Weimer, Bart C.; Davis, Cristina. 2017. Exhaled breath metabolomic longitudinal study for an early prediction of health alterations in dolphins. Analytical and Bioanalytical Chemistry. In press. (highlight paper for issue) (PMID: 29063162)
  • Lawton, Samantha, Allison M. Weis, Barbara A. Byrne, Heather Fritz, Conor Taff, Andrea Townsend, Bart C. Weimer, Asli Mete, Sarah Wheeler, Walter M. Boyce. Comparative analysis of Campylobacter isolates from wild birds and chickens using MALDI-TOF, biochemical testing, and sequence analysis. Journal of Veterinary Diagnostic Investigation. In press.
  • Stevens, John R., Todd R. Jones, Michael Lefevre, Balasubramanian Ganesan, and Bart C. Weimer. 2017. SigTree: identifying and visualizing significantly responsive branches in a phylogenetic tree. Computational and Structural Biology Journal 15:372-376. (PMID:28748045)
  • Arabyan, Narine, Bihua C. Huang and Bart C. Weimer. 2017. Draft genomes of Salmonellaentericasv Typhimurium LT2 with deleted chitinases that are emerging virulence factors. Genome Announcements 5:e00659-17 (PMID:28774970).
  • Weimer, Bart C. 2017. 100K Pathogen Genome Project. Genome Announcements 5:e00594-17 (invited commentary)(PMID: 28705971)
  • Kong, Nguyet, Narine Arabyan, Kao Thao, Whitney Ng, Bihua C. Huang, Dylan Bobby Storey, Poyin Chen, Allison M. Weis, Soraya Foutouhi, Azarene Foutouhi, Yi Xie, and Bart C. Weimer. 2017. Draft genome sequences of 1183 Salmonella from the 100K Pathogen Genome Project. Genome Announcements 5:e00518-17. (PMID: 28705963).
  • Arabyan, Narine, Bihua C. Huang and Bart C. Weimer. 2017. Draft Genomes of Salmonellalysozyme knockouts. Genome Announcements 5:e00519-17. (PMID: 28596411).
  • Rheault, Jean-Guillaume Emond, Julie Jeukens, Luca Freschi, Irena Kukavica-Ibrulj, Brian Boyle, Marie-Josée Dupont, Anna Colavecchio, Virginie Barrere, Brigitte Cadieux, Maud Kerhoas, Alanna Crouse, Lei Zhu, Line Larivière, Ana Victoria Pilar, Camille Cavestri, Travis K. Chapin, Denise Tremblay, Caroline Vincent, Eric Fournier, Khadija Youfsi, Ida Ngueng-Feze, Lingqiao Song, Valentine Usongo, Florence Doualla-Bell, Chrystal Berry, Aleisha R. Reimer, Nguyet Kong, Carol B. Huang, Karen Fong, Emily D. Wilson, Kakali Mukhopadhyay, Walid Mottawea, Dele Ogunremi, Hongsheng Huang, Gitanjali Arya, Ann Perets, Catherine Yoshida, James Robertson, Joel Weadge, Michelle D. Danyluk, John Rohde, Rafael Garduno, Siyun Wang, Céline Nadon, Paul Thomassin,Yann Joly, Ismail Fliss, Gisèle Lapointe, Linda Harris, Roger Stephan, Elton Burnett, Sylvain Moineau, Sandeep Tamber, Sadjia Bekal, France Daigle, Samantha Gruenheid, Danielle Malo, Thomas Wittum, Pascal Delaquis, Alexander Gill, Kenneth E. Sanderson, Martin Wiedmann, Eelco Franz, Lucas Wijnands, Bart C. Weimer, Lawrence Goodridge, and Roger C. Levesque. 2017. A Syst-OMICS Approach to Ensuring Food Safety and Reducing the Economic Burden of Salmonellosis. Frontiers in Microbiology 8:996. (PMID: 28626454)Special issue on food safety
  • Arabyan, Narine, Allison M. Weis, Bihua C. Huang and Bart C. Weimer. 2017. Implications of sialidases in diseases: Genome release of Salmonella sialidase knockout strains. Genome Announcements 5:e00341-17. (PMID: 28495784)
  • Arabyan, Narine, Bihua C. Huang and Bart C. Weimer. 2017. Amylases and their importance during glycan degradation: Genome sequence release of Salmonella amylase knockout strains. Genome Announcements 5:e00355-17. (PMID: 28522713)
  • Kaufman, James H., Christopher A. Elkins, Matthew Davis, Allison M Weis, Bihua C. Huang, Mark K Mammel, Isha R. Patel, Kristen L. Beck, Stefan Edlund, David Chambliss, Simone Bianco, Mark Kunitomi, Bart C. Weimer*. 2017. Microbiogeography and microbial genome evolution. arXiv:1703.07454 [q-bio.GN]. *co-corresponding author
  • Weis, Allison M., Brent Gilpin, Bihua C. Huang, Nguyet Kong, Poyin Chen, and Bart C. Weimer. 2017. Shigelladraft genomes: resources for food safety and public health. Genome Announcements 5:e00176-17. (PMID: 28428292)
  • Weis, Allison M., Kristen A. Clothier, Bihua C. Huang, Nguyet Kong, and Bart C. Weimer. 2017. Multidrug-resistant abortive Campylobacter jejuni draft genome from Northern California. Genome Announcements 5:e00171-17. (PMID: 28408683)
  • Draper, Jenny L., Lori M. Hansen, David Bernick, Samar Abedrabbo, Jason G. Underword, Nguyet Kong, Carol B. Huang, Allison M. Weis, Bart C. Weimer, Arnoud Van Vliet, Nader Pourmand, Jay V. Solnick, Kevin Karplus, Karen M. Ottemann. 2017. Fallacy of the unique genome: Sequence diversity within single Helicobacter pylori strains. mBio 8:e02321-16. (PMID: 28223462).
  • Chen, Poyin, Nguyet Kong, Bihua Huang, Kao Thao, Whitney Ng, Dylan Bobby Storey, Narine Arabyan, Azarene Foutouhi, Soraya Foutouhi, and Bart C. Weimer.100K Pathogen Genome Project: 306 Listeria draft genomes for food safety and public health. 2017. Genome Announcements 5:e00967-16. (PMID: 28183778).
  • Aksenov, Alexander, Konstantin Zamuruyev, Alberto Pasamontes, Joshua Brown, Michael Schivo, Soraya Foutouhi, Bart C. Weimer, Nicholas Kenyon, and Cristina Davis. 2017. Analytical methodologies for broad metabolic coverage of exhaled breath condensate. J. Chrom B. 1061-1062:17-25. (PMID: 28697414)
  • Kong, Nguyet, Azarene Foutouhi, B. Carol Huang, Narine Arabyan, Kao Thao, Whitney Ng, Dylan Storey, Lucy Cai, Eric Lee, Richard Jeannotte, Lenore Kelly, Bart C. Weimer. 2017. A Next Generation Sequencing Library Workflow for Foodborne Pathogens with Quality Control Parameters for Quantification and Shearing conditions using the Agilent 2200 TapeStation System. Standards in Genomics (in press).
  • Foutouhi, Soraya H., Nuradilla Mohamad-Fauzi, Dylan Storey, Azarene A. Foutouhi, Nguyet Kong, Amir Kol, Dori Borjesson, Prerak Desai, Jigna Shah, James D. Murray and Bart C. Weimer. 2017. Salmonellaentericassp enterica serotype Typhimurium Enhances Osteogenic Differentiation in Adipose-Derived Mesenchymal Stem Cells. Stem Cells (in press).
  • Kong, Nguyet, Whitney Ng, Kao Thao, Regina Agulto, Allison Weis, Kristi Spittle, and Bart C. Weimer. 2017. Automation of PacBio SMRTbell NGS library preparation for bacterial genome sequencing. Standards in Genomics. 12:27-37 (PMID: 28344744). (highly accessed notation by journal)
  • Weis, Allison M., Bihua C. Huang, Dylan B. Storey, Nguyet Kong, Poyin Chen, Narine Arabyan, Brent Gilpin, Carl Mason, Andrea K. Townsend, Woutrina A. Miller, Barbara A. Byrne, Conor C. Taff, and Bart C. Weimer. 2017. Large-scale release of Campylobacter draft genomes; resources for food safety and public health from the 100K Pathogen Genome Project. Genome Announcements 5(1):e00925-16. (PMID: 28057746).
  • Chen, Poyin, Henk C. den Bakker, Jonas Korlach, Meredith Ashby, Tyson Clark, Khai Luong, R. J. Roberts, Martin Wiedmann, and Bart C. Weimer. 2017. Comparative Genomics Reveals the Diversity of Restriction-Modification Systems and DNA Methylation Sites in Listeria monocytogenes.App. Environ. Microbiol. 83:e02091-16. (PMID: 27836852).
  • Weis, Allison M., Kristin A. Clothier, Bihua C. Huang, Nguyet Kong, Jessica Wasserscheid, Ken Dewar, Bart C. Weimer. 2017. Comparative Genomics of Abortive Campylobacter jejuniIsolates from Multiple Hosts.  AEM
  •  Doherty, Matthew K., Prerak T. Desai, Leslie Woods, Mai Lee Yang, Janneth Pinzon, Nguyet Kong, and Bart C. Weimer. 2017. Vancomycin and aptamer treatment in vivo are synergistic to inhibit Staphylococcus aureus. (in revision) virulence
  • Chen, Poyin, Prerak T. Desai, Dong Chen, Jigna Shah, and Bart C. Weimer. 2017. Whole cell cross-linking to discover host-microbe protein receptor/ligand pairs. Frontiers in Microbiology
  • Chen, Poyin, Taylor Reiter, Bihua Huang, Nguyet Kong, and Bart C. Weimer. 2017. Prebiotic oligosaccharides potentiate host protective responses against Listeria monocytogenes infection. (invited contribution in Special issue on Listeria monocytogenes and host interactions).
  • Kaufman, James*, Huang, Mark K Mammel, Isha R. Patel, Kristen L. Beck, Stefan Edlund, David Chambliss, Simone Bianco, Bart C. Weimer*. 2017. Genomic diversity of microbes. Submitted *co-corresponding author mSphere
  • Zamuruyev, Konstantin O, Eva Borras, Dayna R Pettit, Alexander A Aksenov, Jason D Simmons, Bart C Weimer, Michael Schivo, Nicholas J Kenyon, Jean-Pierre Delplanque, Cristia Davis. 2017. Effect of collection temperature on metabolite content in exhaled breath condensate. (submitted) Analytica Chimica Acta
  • Kong, Nguyet, Whitney Ng, Vivian Lee, Poyin Chen, Lenore Kelly, and Bart C. Weimer.2017. Comparing Various DNA Extraction Methods to Obtain High Molecular Weight Genomic DNA in Listeria monocytogenes for Next Generation Sequencing Pipelines. (submitted). Biotechniques – 1/31/17
  • Kong, Nguyet, Whitney Ng, Lucy Cai, Alvin Leonardo, Patrick Ancheta, B. Carol Huang, Kao Thao, Azarene Foutouhi, Lenore Kelly and Bart C. Weimer. 2017. KAPA Biosystems HTP Library Preparation Kit Using Agilent Electrophoresis Instruments for Quality Control of Library Construction Pipeline. (submitted). Biotechniques – 1/31/17
  • Dhanasekaran, A. Ranjitha, and Bart C. Weimer. 2017. DynaFlux: a software tool to estimate the dynamic state flux of a metabolic network and to perform network analyses. (in revision). mSystems