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Benjamin John Callahan, Ph.D.

Assistant Professor, Microbiomes and Complex Microbial Communities


Dr. Benjamin Callahan joined NC State in January 2017 as a Chancellor’s Faculty Excellence Program cluster hire in Microbiomes and Complex Microbial Communities. As an Assistant Professor in the Department of Population Health and Pathobiology and a member of the Bioinformatics Research Center, Dr. Callahan’s research focuses on better understanding various “microbiomes” — the complex microbial communities which inhabit and interact with almost every part of the world around us. He develops new statistical and bioinformatic methods to better characterize microbial communities from high-throughput biological data, and uses those methods to study various interesting problems, for example the relationship between the maternal microbiome and preterm birth.

Dr. Callahan received his Bachelors degree in Physics and Math from Iowa State University, and began to work on problems in quantitative biology while obtaining a Ph.D. in Physics from the University of California, Santa Barbara. After graduation, Dr. Callahan worked as a postdoc in the Applied Physics and Statistics departments at Stanford University, where he studied adaptation in large populations through modeling, comparative genomics and experimental evolution.
CFEP- Assistant Professor, Microbiomes and Complex Microbial Communities
Computational Biology and Bioinformatics, Infectious Diseases
  • (2016) 1,2-dichloroethane exposure alters the population structure, metabolism, and kinetics of a trichloroethene-dechlorinating Dehalococcoides mccartyi consortiumMayer-Blackwell K, Fincker M, Molenda O, Callahan BJ, Sewell H, Holmes S, Edwards E, Spormann A. | Environmental Science & Technology 50:12187–12196.
  • (2016) Bioconductor workflow for microbiome data analysis: from raw reads to community analyses.Callahan BJ, Sankaran K, Fukuyama JA, McMurdie PJ, Holmes SP | F1000 Research 5:1492.
  • (2016) DADA2: High resolution sample inference from Illumina amplicon data.Callahan BJ, McMurdie PJ, Rosen MJ, Han AW, Johnson AJ, Holmes SP | Nature Methods 13 581–583.
  • (2016) Marine mammals harbor novel microbiotas shaped by, yet distinct from, the sea.Bik EM, Costello EK, Switzer AD, Callahan BJ, Holmes SP, Wells RS, Carlin KP, Jensen ED, Venn-Watson S, Relman DA | Nature Communications 7 10516.
  • (2016) Reproducible research workflow in R for the analysis of personalized human microbiome data.Callahan BJ, Proctor D, Relman DA, Fukuyama J, Holmes SP | Pacific Symposium on Biocomputing 21 183-194.
  • (2015) Temporal and spatial variation of the human microbiota during pregnancy.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 | PNAS 112(35), 11060-11065. (*equal contributions)
  • (2014) Rapid Evolution of Adaptive Niche Construction in Experimental Microbial Populations.Callahan BJ, Fukami T, Fisher DS | Evolution 68(11), 3307-3316.
  • (2013) Evolutionary Dynamics and Information Hierarchies in Biological Systems.Walker SI*, Callahan BJ*, Arya G, Barry JD, Bhattacharya T, Grigoryev S, Pellegrini M, Rippe K, Rosenberg SM | Annals of the New York Academy of Sciences 1305(1): 1-17. (*equal contributions)
  • (2012) Denoising PCR-amplified metagenome data.Rosen MJ, Callahan BJ, Fisher DS, Holmes SP | BMC bioinformatics 13(1), 283.
  • (2012) The length scale of selection in protein evolution.Callahan BJ | Fly 6(1), 16-20.
  • (2011) Heterozygote advantage as a natural consequence of adaptation in diploids.Sellis D, Callahan BJ, Petrov DA, Messer PW | PNAS 108:20666-20671.
  • (2011) Correlated evolution of nearby residues in Drosophilid proteins.Callahan BJ, Neher RA, Bachtrog D, Andolfatto PA, Shraiman BI | PLoS Genetics 7(2): e1001315.
  • (2009) Emergent gene order in a model of modular polyketide synthases.Callahan BJ, Thattai M, Shraiman BI | PNAS 106:19410-19415.
  • (2003) Exploring the interplay between topology and secondary structural formation in the protein folding problem.Cheung MS, Finke JM, Callahan BJ, Onuchic JN | Journal of Physical Chemistry B, 107:1193-11200.