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
North Carolina State University

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)