Benjamin J Callahan

Education

Positions

Publications

Google Scholar profile: https://scholar.google.com/citations?user=zGifBvwAAAAJ

Thanissery R, McLaren MR#, Rivera A, Reed AD, Betrapally NS, Burdette T, Winston JA, Jacob M, Callahan BJ, Theriot CM^ (2020). C. difficile carriage in animals and the associated changes in the host fecal microbiota. Anaerobe, 66, 102279. https://doi.org/10.1016/j.anaerobe.2020.102279 

McLaren MR#, Callahan BJ^ (2020). Pathogen resistance may be the principal evolutionary advantage provided by the microbiome. Phil. Trans. R. Soc. B, 375, 20190592. https://doi.org/10.1098/rstb.2019.0592 

Kolodny O, Callahan BJ, Douglas AE (2020). The role of the microbiome in host evolution. Phil. Trans. R. Soc. B, 375, 20190588. https://doi.org/10.1098/rstb.2019.0588 

Callahan BJ^, Grinevich D#, Thakur S, Balamotis MA, Yehezkel TB (2020). Ultra-accurate Microbial Amplicon Sequencing with Synthetic Long Reads. bioRxiv, 192286. https://doi.org/10.1101/2020.07.07.192286 

Muñana K^, Jacob J, Callahan BJ (2020). Evaluation of fecal Lactobacillus populations in dogs with idiopathic epilepsy: A pilot study. Animal Microbiome,  2, 19. https://doi.org/10.1186/s42523-020-00036-6 

Berman HL#, McLaren MR#, Callahan BJ^ (2020). Understanding and Interpreting Community Sequencing Measurements of the Vaginal Microbiome. BJOG: An International Journal of Obstetrics & Gynaecology, 127, 139-146. https://doi.org/10.1111/1471-0528.15978 

Foster DM^, Jacob M, Farmer K, Callahan B, Theriot C, Kathariou S, Cernicchiaro N, Prange T, Papich M (2019). Ceftiofur formulation differentially affects the intestinal drug concentrations, resistance of fecal Escherichia coli, and the microbiome of steers. PLoS One, 14(10), e0223378. https://doi.org/10.1371/journal.pone.0223378 

McLaren MR#, Willis AD, Callahan BJ^ (2019). Consistent and correctable bias in metagenomic sequencing experiments. eLife, 8, e46923. https://doi.org/10.7554/eLife.46923.001 

Bolyen E*, Rideout JR*, Dillon MR*, Bokulich NA*, [......12 authors......], Callahan BJ, [......91 authors......], JG Caporaso^ (2019). Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2. Nature Biotechnology, 37, 852–857. https://doi.org/10.1038/s41587-019-0209-9 

Callahan BJ^, Wong J, Heiner C, Oh S, Theriot CM, Gulati AS, McGill SK, Dougherty MK (2019). High-throughput amplicon sequencing of the full-length 16S rRNA gene with single-nucleotide resolution. Nucleic Acids Research, 47, e103. https://doi.org/10.1093/nar/gkz569 

Davis NM*, Proctor D*, Holmes SP, Relman DA, Callahan BJ^ (2018). Simple statistical identification and removal of contaminant sequences in marker-gene and metagenomics data. Microbiome, 6, 226. https://doi.org/10.1186/s40168-018-0605-2 

Jeganathan P, Callahan BJ, Proctor DM, Relman DA, Holmes SP^ (2018). The Block Bootstrap Method for Longitudinal Microbiome Data. arXiv, 1809.01832 [stat.ME].

Ferguson K,  Jacob M, Theriot C, Callahan B, Prange T, Papich M, Foster D^ (2018). Dosing Regimen of Enrofloxacin Impacts Intestinal Pharmacokinetics and the Fecal Microbiota in Steers. Frontiers in Microbiology, 9, 2190. https://doi.org/10.3389/fmicb.2018.02190 

Ghaemi MS, DiGiulio DB, Contrepois K, Callahan B, Ngo T, Lee-McMullen B, Lehallier B, Robaczewska A, Mcilwain D, Rosenberg-Hasson Y, Wong RJ, Quaintance C, Culos A, Stanley N, Tanada A, Tsai A, Gaudilliere D, Ganio E, Han X, Ando K, McNeil L, Tingle M, Wise P, Maric I, Sirota M, Wyss-Coray T, Winn VD, Druzin ML, Gibbs R, Darmstadt GL, Lewis DB, Nia VP, Agard B, Tibshirani R, Nolan G, Snyder MP, Relman DA, Quake SR, Shaw GM, Stevenson DK, Angst MS, Gaudilliere B, Aghaeepour N^ (2018). Multiomics Modeling of the Immunome, Transcriptome, Microbiome, Proteome, and Metabolome Adaptations During Human Pregnancy. Bioinformatics, 35(1), 95-1037. https://doi.org/10.1093/bioinformatics/bty537 

McLaren MR#, Callahan BJ^ (2018). In nature, there is only diversity. mBio, 9:e02149-17. https://doi.org/10.1128/mBio.02149-17 

Callahan BJ*, DiGiulio DB*, Goltsman DSA, Sun CL, Costello EK, Jeganathan P, Biggio JR, Wong RJ, Druzin ML, Shaw GM, Stevenson DK, Holmes SP, Relman DA^ (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 USA, 114(37), 9966–9971. PMCID: PMC5604014. https://doi.org/10.1073/pnas.1705899114 

Callahan BJ^, McMurdie PJ, Holmes SP (2017). Exact sequence variants should replace operational taxonomic units in marker gene data analysis. The ISME Journal, 11, 2639–2643. PMCID: PMC5702726. https://doi.org/10.1038/ismej.2017.119 

Mayer-Blackwell K, Fincker M, Molenda O, Callahan BJ, Sewell H, Holmes S, Edwards E, Spormann A^. 1,2-dichloroethane exposure alters the population structure, metabolism, and kinetics of a trichloroethene-dechlorinating Dehalococcoides mccartyi consortium (2016). Environmental Science & Technology, 50, 12187–12196. PMID: 27809491.

Callahan BJ, Sankaran K, Fukuyama JA, McMurdie PJ, Holmes SP^ (2016). Bioconductor workflow for microbiome data analysis: from raw reads to community analyses. F1000 Research, 5, 1492. PMCID: PMC4955027. https://doi.org/10.12688/f1000research.8986.2 

Callahan BJ^, McMurdie PJ, Rosen MJ, Han AW, Johnson AJ, Holmes SP (2016). DADA2: High resolution sample inference from Illumina amplicon data. Nature Methods, 13, 581–583. PMCID: PMC4927377. https://doi.org/10.1038/nmeth.3869 

Bik EM, Costello EK, Switzer AD, Callahan BJ, Holmes SP, Wells RS, Carlin KP, Jensen ED, Venn-Watson S, Relman DA^ (2016). Marine mammals harbor unique microbiotas shaped by and yet distinct from the sea. Nature Communications, 7, 10516. PMCID: PMC4742810. https://doi.org/10.1038/ncomms10516 

Callahan BJ, Proctor D, Relman DA, Fukuyama J, Holmes SP^ (2016). Reproducible research workflow in R for the analysis of personalized human microbiome data. Pacific Symposium on Biocomputing, 21, 183-194. PMCID: PMC4873301. https://doi.org/10.1142/9789814749411_0018 

DiGiulio DB*, Callahan BJ*, McMurdie PJ, Costello EK, Lyell DJ, Robaczewska A, Sun CL, Goltsman DSA, Wong RJ, Shaw G, Stevenson DK, Holmes SP, Relman DA^ (2015). Temporal and spatial variation of the human microbiota during pregnancy. Proceedings of the National Academy of Sciences USA, 112(35), 11060-11065. PMCID: PMC456827. https://doi.org/10.1073/pnas.1502875112 

Callahan BJ^, Fukami T, Fisher DS (2014). Rapid Evolution of Adaptive Niche Construction in Experimental Microbial Populations. Evolution, 68(11), 3307-3316. PMID: 25138718. https://doi.org/10.1111/evo.12512 

Walker SI*^, Callahan BJ*, Arya G, Barry JD, Bhattacharya T, Grigoryev S, Pellegrini M, Rippe K, Rosenberg SM (2013). Evolutionary Dynamics and Information Hierarchies in Biological Systems. Annals of the New York Academy of Sciences, 1305(1), 1-17. PMID: 23691975

Rosen MJ^, Callahan BJ, Fisher DS, Holmes SP (2012). Denoising PCR-amplified metagenome data. BMC bioinformatics, 13(1), 283. PMCID: PMC3563472. https://doi.org/10.1186/1471-2105-13-283 

Callahan BJ (2012). The length scale of selection in protein evolution. Fly, 6(1), 16-20. PMID: 22198524

Sellis D, Callahan BJ, Petrov DA^, Messer PW (2011). Heterozygote advantage as a natural consequence of adaptation in diploids. Proceedings of the National Academy of Sciences USA, 108(51), 20666-20671. PMCID: PMC3251125. https://doi.org/10.1073/pnas.1114573108 

Callahan BJ^, Neher RA, Bachtrog D, Andolfatto PA, Shraiman BI (2011). Correlated evolution of nearby residues in Drosophilid proteins. PLoS Genetics, 7(2), e1001315. PMCID: PMC3044683. https://doi.org/10.1371/journal.pgen.1001315 

Callahan BJ, Thattai M, Shraiman BI^ (2009). Emergent gene order in a model of modular polyketide synthases. Proceedings of the National Academy of Sciences USA, 106, 19410-19415. PMCID: PMC2780807. https://doi.org/10.1073/pnas.0902364106 

Cheung MS, Finke JM, Callahan BJ, Onuchic JN^ (2003). Exploring the interplay between topology and secondary structural formation in the protein folding problem. Journal of Physical Chemistry B, 107, 1193-11200. https://doi.org/10.1021/jp034441r 

* equal contributions                ^ corresponding                # lab member

Software

Callahan BJ, McMurdie PJ, Holmes SP (2020). dada2: Accurate, high-resolution sample inference from amplicon sequencing data. R package version 1.18.0.

        Over 3,500 citations (Google Scholar, Oct 2020)

        Top 10% most downloaded Bioconductor packages.

Callahan BJ, Davis NM (2020). decontam: Identify contaminants in marker-gene and metagenomics sequencing data. R package version 1.8.0.

        Over 250 citations (Google Scholar, Oct 2020)

Grants

Invited Talks

Honors and Awards

Professional Activities

Editor: Guest editor for Philosophical Transactions B special issue on “The Role of the Microbiome in the Evolution of the Host” (2020).

Reviewer (journals): Bioinformatics, BJOG, Environmental Microbiology, Frontiers in Genetics, Genetics, Gigascience, Microbiome, mSphere, mSystems, Nature, Nature Communications, Nature Ecology & Evolution, Nature Methods, Nature Microbiology, New Phytologist, PeerJ, PLoS Comp Bio, PLoS One, PNAS, Proceedings of the Royal Society B, Science, Theoretical Population Biology.

Reviewer (grants): NIH BDMA Study Section (Feb 2020).

Advisor: Michael McLaren (postdoc), Dmitry Grinevich (postdoc), Craig Gin (postdoc), Naga Betrapally (postdoc), David Huang (PhD), Hanna Berman (PhD), Taylor Gin (PhD).

Workshop Instruction: Strategies and Techniques for Analyzing Microbial Population Structures at Woods Hole (2015, 2017, 2019, 2020-Cancelled), Harvard Workshop on Metagenomics (2015), Microbe Analysis in R at ASM Microbe (2018, 2019), QCBS BIOME Workshop on Metabarcoding at University of Montreal (2018, Lead Instructor), Microbiome Analysis with DADA2 and R Workshop at NC State (2018, Lead Instructor)