Benjamin J Callahan
Assistant Professor Dept of Population Health & Pathobiology North Carolina State University Raleigh, NC 27607 | Email: bcallah@ncsu.edu Phone: (319) 621-2743 Web: www.callahanlab.org Twitter: @bejcal |
Education
2009 | PhD in Physics University of California, Santa Barbara Evolution on an interacting fitness landscape: The effects of the interplay of epistasis and recombination on genetic structure |
2002 | BS in Physics and Math, With distinction Minor in Linguistics Iowa State University |
Positions
2017 - | Assistant Professor, Microbiomes and Complex Microbial Communities Department of Population Health & Pathobiology College of Veterinary Medicine |
2014 - 2016 | Research Associate Department of Statistics Stanford University |
2010 - 2013 | Postdoctoral Scholar Department of Applied Physics Stanford University |
Publications
Berman HL#, McLaren MR#, Callahan BJ^ (2019). Understanding and Interpreting Community Sequencing Measurements of the Vaginal Microbiome. BJOG: An International Journal of Obstetrics & Gynaecology, in press.
McLaren MR#, Willis AD, Callahan BJ^ (2019). Consistent and correctable bias in metagenomic sequencing experiments. eLife, 8, e46923.
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, gkz569. 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 (2019). dada2: Accurate, high-resolution sample inference from amplicon sequencing data. R package version 1.12.1.
Top 10% most downloaded Bioconductor packages.
Callahan BJ, Davis NM (2018). decontam: Identify contaminants in marker-gene and metagenomics sequencing data. R package version 1.4.0.
Grants
2019 | NIH NIGMS (PI) Quantitative Metagenomics and the Vaginal Microbiome of Preterm Birth $1,442,610 |
2019 | USDA National Institute of Food and Agriculture (PI) FACT: Rapid Detection and Tracking of Foodborne Pathogens with Long-read Amplicon Sequencing $493,921 |
2019 | American Kennel Club (Co-I, PI: Munana) Is Gut Dysbiosis Associated with Canine Idiopathic Epilepsy? $104,453 |
2017 | Plant Soil Microbial Community Consortium (PI) Extension and validation of maximum resolution amplicon bioinformatics methods to fungal marker-gene data $55,000 |
2015 | Samarth Foundation (Postdoc) The microbiome of preterm birth in high resolution $30,000 |
Invited Talks
2019 | Microbiome Movement - Maternal & Infant Health Summit, Boston MA |
2019 | Simons Foundation 3rd Workshop on Statistical and Algorithmic Challenges in Microbiome Data Analysis, New York City NY |
2019 | Triangle Microbial Interactions Meeting, Chapel Hill NC |
2019 | UNC-Charlotte Bioinformatics Seminar Series, Charlotte NC |
2019 | UNC Bioinformatics & Computational Biology Seminar, Chapel Hill NC |
2018 | VCU Microbiology & Immunology Research Seminar, Richmond VA |
2018 | International Metagenomics and Microbiome Standards Alliance, Webinar |
2018 | Physical Principles Governing the Organization of Microbial Communities, Aspen Center for Physics, Aspen CO |
2018 | Symposium on the Microbiome: Hype and Hope, Fred Hutchinson Cancer Research Center, Seattle WA |
2018 | Kavli Foundation Microbiome Seminar, Ohio State, Columbus OH |
2017 | UNC First Friday Microbiome Seminar, Chapel Hill NC |
2017 | BASF Seminar, Research Triangle Park NC |
2017 | Joint Statistical Meetings, Baltimore MD |
2017 | University of Idaho Seminar for the Center for Modeling Complex Interactions (CMCI) and the Institute for Bioinformatics and Evolutionary Studies (IBEST) |
2017 | UNC Biostatistics Department Seminar, Chapel Hill NC |
2016 | Bioinformatics for the Microbiome Symposium, Stanford CA |
2016 | Challenges in Microbiome Data Analysis, Simons Foundation, NYC NY |
2015 | Microbiome Workshop, Johnson & Johnson, Webinar |
2012 | REvolution - Transcending the Past Symposium, Stanford CA |
2011 | Seminar, Vienna Institute of Science and Technology, Vienna Austria |
2010 | Bay Area Population Genomics Meeting, UC Berkeley |
2009 | Seminar, Princeton University, Princeton NJ |
Honors and Awards
2015 | Pacific Symposium on Biocomputing Travel Award |
2014 | American Society of Naturalists Conference Best Postdoc Talk (2nd place) |
2003 - 2005 | Broida Fellowship for Graduate Studies in Physics |
before 2002 | Phi Beta Kappa, Tau Beta Pi, National Merit Scholarship |
Professional Activities
Reviewer: Bioinformatics, Environmental Microbiology, Frontiers in Genetics, Genetics, Microbiome, mSphere, mSystems, Nature, Nature Communications, Nature Ecology & Evolution, Nature Methods, New Phytologist, PeerJ, PLoS One, PNAS, Proceedings of the Royal Society B, Science, Theoretical Population Biology
Mentor: Naga Betrapally (postdoc), Michael McLaren (postdoc), Hanna Berman (PhD), Michael Rosen (PhD), Joel Thompson (MS), Katie Lund (undergraduate)
Workshop Instruction: Strategies and Techniques for Analyzing Microbial Population Structures at Woods Hole (2015, 2017, 2019), 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)