Benjamin Callahan

Halleran, J., Sylvester, H., Jacob, M., Callahan, B., Baynes, R., & Foster, D. (2024). Impact of florfenicol dosing regimen on the phenotypic and genotypic resistance of enteric bacteria in steers. SCIENTIFIC REPORTS, 14(1). https://doi.org/10.1038/s41598-024-55591-8

Grinevich, D., Harden, L., Thakur, S., & Callahan, B. (2024, February 6). Serovar-level identification of bacterial foodborne pathogens from full-length 16S rRNA gene sequencing (M. G. I. Langille, Ed.). MSYSTEMS, Vol. 2. https://doi.org/10.1128/msystems.00757-23

Scheible, M., Stinson, T. L., Breen, M., Callahan, B. J., Thomas, R., & Meiklejohn, K. A. (2024). The development of non-destructive sampling methods of parchment skins for genetic species identification. PLOS ONE, 19(3). https://doi.org/10.1371/journal.pone.0299524

Hakimzadeh, A., Abdala Asbun, A., Albanese, D., Bernard, M., Buchner, D., Callahan, B., … Anslan, S. (2023, August 7). A pile of pipelines: An overview of the bioinformatics software for metabarcoding data analyses. MOLECULAR ECOLOGY RESOURCES, Vol. 8. https://doi.org/10.1111/1755-0998.13847

Gin, T. E., Petzold, E. A., Uthappa, D. M., Neighbors, C. E., Borough, A. R., Gin, C., … Woods, C. W. (2023). Evaluation of SARS-CoV-2 identification methods through surveillance of companion animals in SARS-CoV-2-positive homes in North Carolina, March to December 2020. PEERJ, 11. https://doi.org/10.7717/peerj.16310

Gookin, J. L., Hartley, A. N., Aicher, K. M., Mathews, K. G., Cullen, R., Cullen, J. M., … Stauffer, S. H. (2023). Gallbladder microbiota in healthy dogs and dogs with mucocele formation. PLOS ONE, 18(2). https://doi.org/10.1371/journal.pone.0281432

Berman, H. L., Goltsman, D. S. A., Anderson, M., Relman, D. A., & Callahan, B. J. (2023, February 4). GardnerellaDiversity and Ecology in Pregnancy and Preterm Birth. https://doi.org/10.1101/2023.02.03.527032

Templeton, G. B., Fefer, G., Case, B. C., Roach, J., Azcarate-Peril, M. A., Gruen, M. E., … Olby, N. J. (2023). Longitudinal Analysis of Canine Oral Microbiome Using Whole Genome Sequencing in Aging Companion Dogs. ANIMALS, 13(24). https://doi.org/10.3390/ani13243846

Huang, C., Gin, C., Fettweis, J., Foxman, B., Gelaye, B., MacIntyre, D. A., … Callahan, B. (2023). Meta-analysis reveals the vaginal microbiome is a better predictor of earlier than later preterm birth. BMC Biology. https://doi.org/10.1186/s12915-023-01702-2

Slead, T. S., Callahan, B. J., Schreeg, M. E., Seiler, G. S., Stowe, D. M., Azcarate-Peril, M. A., … Gookin, J. L. (2023, September 13). Microbiome analysis of bile from apparently healthy cats and cats with suspected hepatobiliary disease. JOURNAL OF VETERINARY INTERNAL MEDICINE, Vol. 9. https://doi.org/10.1111/jvim.16852

Switzer, A. D., Callahan, B. J., Costello, E. K., Bik, E. M., Fontaine, C., Gulland, F. M. D., & Relman, D. A. (2023, June 16). Rookery through rehabilitation: Microbial community assembly in newborn harbour seals after maternal separation. ENVIRONMENTAL MICROBIOLOGY, Vol. 6. https://doi.org/10.1111/1462-2920.16444

Grinevich, D., Harden, L., Thakur, S., & Callahan, B. J. (2023, June 28). Serovar-level Identification of Bacterial Foodborne Pathogens From Full-length 16S rRNA Gene Sequencing. https://doi.org/10.1101/2023.06.28.546915

Manvell, C., Berman, H., Callahan, B., Breitschwerdt, E., Swain, W., Ferris, K., … Lashnits, E. (2022). Identification of microbial taxa present in Ctenocephalides felis (cat flea) reveals widespread co-infection and associations with vector phylogeny. PARASITES & VECTORS, 15(1). https://doi.org/10.1186/s13071-022-05487-1

McLaren, M. R., Nearing, J. T., Willis, A. D., Lloyd, K. G., & Callahan, B. J. (2022, August 19). Implications of taxonomic bias for microbial differential-abundance analysis. https://doi.org/10.1101/2022.08.19.504330

Huang, C., Gin, C., Fettweis, J., Foxman, B., Gelaye, B., MacIntyre, D. A., … Callahan, B. (2022, September 27). Meta-Analysis Reveals the Vaginal Microbiome is a Better Predictor of Earlier Than Later Preterm Birth. https://doi.org/10.1101/2022.09.26.22280389

Huang, C., Callahan, B. J., Wu, M. C., Holloway, S. T., Brochu, H., Lu, W., … Tzeng, J.-Y. (2022). Phylogeny-guided microbiome OTU-specific association test (POST). MICROBIOME, 10(1). https://doi.org/10.1186/s40168-022-01266-3

Halleran, J. L., Callahan, B. J., Jacob, M. E., Sylvester, H. J., Prange, T., Papich, M. G., & Foster, D. M. (2021). Effects of danofloxacin dosing regimen on gastrointestinal pharmacokinetics and fecal microbiome in steers. SCIENTIFIC REPORTS, 11(1). https://doi.org/10.1038/s41598-021-90647-z

Callahan, B. J., Grinevich, D., Thakur, S., Balamotis, M. A., & Ben Yehezkel, T. (2021). Ultra-accurate microbial amplicon sequencing with synthetic long reads. MICROBIOME, 9(1). https://doi.org/10.1186/s40168-021-01072-3

Thanissery, R., McLaren, M. R., Rivera, A., Reed, A. D., Betrapally, N. S., Burdette, T., … Theriot, C. M. (2020). Clostridioides difficile carriage in animals and the associated changes in the host fecal microbiota. ANAEROBE, 66. https://doi.org/10.1016/j.anaerobe.2020.102279

McLaren, M. R., & Callahan, B. J. (2020). Pathogen resistance may be the principal evolutionary advantage provided by the microbiome. Philosophical Transactions of the Royal Society B: Biological Sciences, 375(1808), 20190592. https://doi.org/10.1098/rstb.2019.0592

Kolodny, O., Callahan, B. J., & Douglas, A. E. (2020). The role of the microbiome in host evolution. Philosophical Transactions of the Royal Society B: Biological Sciences, 375(1808), 20190588. https://doi.org/10.1098/rstb.2019.0588

Callahan, B. J., Grinevich, D., Thakur, S., Balamotis, M. A., & Yehezkel, T. B. (2020, July 7). Ultra-accurate Microbial Amplicon Sequencing Directly from Complex Samples with Synthetic Long Reads (Vol. 7). Vol. 7. https://doi.org/10.1101/2020.07.07.192286

Berman, H. L., McLaren, & Callahan, B. J. (2020). Understanding and interpreting community sequencing measurements of the vaginal microbiome. BJOG: An International Journal of Obstetrics & Gynaecology, 127(2), 139–146. https://doi.org/10.1111/1471-0528.15978

Foster, D. M., Jacob, M. E., Farmer, K. A., Callahan, B. J., Theriot, C. M., Kathariou, S., … Papich, M. G. (2019). Ceftiofur formulation differentially affects the intestinal drug concentration, resistance of fecal Escherichia coli, and the microbiome of steers. PLOS ONE, 14(10). https://doi.org/10.1371/journal.pone.0223378

McLaren, M. R., Willis, A. D., & Callahan, B. J. (2019, February 25). Consistent and correctable bias in metagenomic sequencing experiments. BioRxiv, Vol. 2, p. 559831. https://doi.org/10.1101/559831

McLaren, M. R., Willis, A. D., & Callahan, B. J. (2019). Consistent and correctable bias in metagenomic sequencing experiments. ELife. https://doi.org/10.7554/eLife.46923

Callahan, B. J., Wong, J., Heiner, C., Oh, S., Theriot, C. M., Gulati, A. S., … Dougherty, M. K. (2019). High-throughput amplicon sequencing of the full-length 16S rRNA gene with single-nucleotide resolution. Nucleic Acids Research, 7. https://doi.org/10.1093/nar/gkz569

Ghaemi, M. S., DiGiulio, D. B., Contrepois, K., Callahan, B., Ngo, T. T. M., Lee-McMullen, B., … Aghaeepour, N. (2019). Multiomics modeling of the immunome, transcriptome, microbiome, proteome and metabolome adaptations during human pregnancy. BIOINFORMATICS, 35(1), 95–103. https://doi.org/10.1093/bioinformatics/bty537

Callahan, B. J., Wong, J., Heiner, C., Oh, S., Theriot, C. M., Gulati, A. S., … Dougherty, M. K. (2018, August 15). High-throughput amplicon sequencing of the full-length 16S rRNA gene with single-nucleotide resolution (Vol. 8). Vol. 8. https://doi.org/10.1101/392332

McLaren, M. R., & Callahan, B. J. (2018). In Nature, There Is Only Diversity. MBIO, Vol. 9. https://doi.org/10.1128/mbio.02149-17

Davis, N. M., Proctor, D. M., Holmes, S. P., Relman, D. A., & Callahan, B. J. (2018). Simple statistical identification and removal of contaminant sequences in marker-gene and metagenomics data. MICROBIOME, 6(1). https://doi.org/10.1186/s40168-018-0605-2

Callahan, B. J., McMurdie, P. J., & Holmes, S. P. (2017). Exact sequence variants should replace operational taxonomic units in marker-gene data analysis. The ISME Journal, 11(12), 2639–2643. https://doi.org/10.1038/ismej.2017.119

Callahan, B. J., DiGiulio, D. B., Goltsman, D. S. A., Sun, C. L., Costello, E. K., Jeganathan, P., … Relman, D. A. (2017). Replication and refinement of a vaginal microbial signature of preterm birth in two racially distinct cohorts of US women. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 114(37), 9966–9971. https://doi.org/10.1073/pnas.1705899114

Callahan, B. J., DiGiulio, D. B., Goltsman, D. S. A., Sun, C. L., Costello, E. K., Jeganathan, P., … others. (2017). Replication and refinement of a vaginal microbial signature of preterm birth in two racially distinct cohorts of US women. Proceedings of the National Academy of Sciences, 201705899.

Davis, N. M., Proctor, D. M., Holmes, S. P., Relman, D. A., & Callahan, B. J. (2017, November 17). Simple statistical identification and removal of contaminant sequences in marker-gene and metagenomics data (Vol. 11). Vol. 11. https://doi.org/10.1101/221499

Mayer-Blackwell, K., Fincker, M., Molenda, O., Callahan, B., Sewell, H., Holmes, S., … Spormann, A. M. (2016). 1,2-Dichloroethane Exposure Alters the Population Structure, Metabolism, and Kinetics of a Trichloroethene-Dechlorinating Dehalococcoides mccartyi Consortium. Environmental Science & Technology, 50(22), 12187–12196. https://doi.org/10.1021/acs.est.6b02957

Callahan, B. J., Sankaran, K., Fukuyama, J. A., McMurdie, P. J., & Holmes, S. P. (2016). Bioconductor Workflow for Microbiome Data Analysis: from raw reads to community analyses. F1000Research, 5, 1492. https://doi.org/10.12688/f1000research.8986.2

Callahan, B. J., McMurdie, P. J., Rosen, M. J., Han, A. W., Johnson, A. J. A., & Holmes, S. P. (2016). DADA2: High-resolution sample inference from Illumina amplicon data. Nature Methods, 13(7), 581–583. https://doi.org/10.1038/nmeth.3869

Bik, E. M., Costello, E. K., Switzer, A. D., Callahan, B. J., Holmes, S. P., Wells, R. S., … Relman, D. A. (2016). Marine mammals harbor unique microbiotas shaped by and yet distinct from the sea. Nature Communications, 7(1), 10516. https://doi.org/10.1038/ncomms10516

Callahan, B. J., Proctor, D., Relman, D. A., Fukuyama, J., & Holmes, S. P. (2016). Reproducible research workflow in R for the analysis of personalized human microbiome data. Pacific Symposium on Biocomputing, 21, 183–194.

Callahan, B., Proctor, D., Relman, D., Fukuyama, J., & Holmes, S. (2016). Reproducible research workflow in R for the analysis of personalized human microbiome data. Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing, 21, 183.

DiGiulio, D. B., Callahan, B. J., McMurdie, P. J., Costello, E. K., Lyell, D. J., Robaczewska, A., … Relman, D. A. (2015). Temporal and spatial variation of the human microbiota during pregnancy. Proceedings of the National Academy of Sciences, 112(35), 11060–11065. https://doi.org/10.1073/pnas.1502875112

DiGiulio, D. B., Callahan, B. J., McMurdie, P. J., Costello, E. K., Lyell, D. J., Robaczewska, A., … others. (2015). Temporal and spatial variation of the human microbiota during pregnancy. Proceedings of the National Academy of Sciences, 112(35), 11060–11065.

Callahan, B. J., Fukami, T., & Fisher, D. S. (2014). Rapid evolution of adaptive niche construction in experimental microbial populations. Evolution, 68(11), 3307–3316. https://doi.org/10.1111/evo.12512

Walker, S. I., Callahan, B. J., Arya, G., Barry, J. D., Bhattacharya, T., Grigoryev, S., … Rosenberg, S. M. (2013). Evolutionary dynamics and information hierarchies in biological systems. Annals of the New York Academy of Sciences, 1305(1), 1–17. https://doi.org/10.1111/nyas.12140

Rosen, M. J., Callahan, B. J., Fisher, D. S., & Holmes, S. P. (2012). Denoising PCR-amplified metagenome data. BMC Bioinformatics, 13(1), 283.

Callahan, B. J. (2012). The length scale of selection in protein evolution. Fly, 6(1), 16–20. https://doi.org/10.4161/fly.18305

Callahan, B., Neher, R. A., Bachtrog, D., Andolfatto, P., & Shraiman, B. I. (2011). Correlated Evolution of Nearby Residues in Drosophilid Proteins. PLoS Genetics, 7(2), e1001315. https://doi.org/10.1371/journal.pgen.1001315

Sellis, D., Callahan, B. J., Petrov, D. A., & Messer, P. W. (2011). Heterozygote advantage as a natural consequence of adaptation in diploids. Proceedings of the National Academy of Sciences, 108(51), 20666–20671. https://doi.org/10.1073/pnas.1114573108

Callahan, B., Thattai, M., & Shraiman, B. I. (2009). Emergent gene order in a model of modular polyketide synthases. Proceedings of the National Academy of Sciences, 106(46), 19410–19415. https://doi.org/10.1073/pnas.0902364106

Callahan, B. J. (2009). Evolution on an interacting fitness landscape: The effects of the interplay of epistasis and recombination on genetic structure. University of California, Santa Barbara.

Cheung, M. S., Finke, J. M., Callahan, B., & Onuchic, J. N. (2003). Exploring the Interplay between Topology and Secondary Structural Formation in the Protein Folding Problem. The Journal of Physical Chemistry B, 107(40), 11193–11200. https://doi.org/10.1021/jp034441r