Benjamin J Callahan
Associate Professor Dept of Population Health & Pathobiology North Carolina State University Raleigh, NC 27607 | Email: bcallah@ncsu.edu Phone: (919) 515-8536 Web: callahanlab.org |
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, Minor in Linguistics Iowa State University |
Positions
2022 - | Associate Professor, Microbiomes and Complex Microbial Communities Department of Population Health & Pathobiology North Carolina State University, College of Veterinary Medicine |
2017 - 2022 | Assistant Professor, Microbiomes and Complex Microbial Communities Department of Population Health & Pathobiology North Carolina State University, College of Veterinary Medicine |
2014 - 2016 | Research Associate Stanford University, Department of Statistics |
2010 - 2013 | Postdoctoral Scholar Stanford University, Department of Applied Physics |
Publications
Google Scholar profile: https://scholar.google.com/citations?user=zGifBvwAAAAJ
Maier JL#, Gin C#, Callahan B, Sheriff EK, Duerkop BA, Kleiner M (2024). Pseudo-pac site sequences used by phage P22 in generalized transduction of Salmonella. PLoS Pathogens, 20 (6), e1012301. https://doi.org/10.1371/journal.ppat.1012301
Berman HL#, Goltsman DS, Anderson M, Relman DA, Callahan BJ^ (2024). Gardnerella Diversity and Ecology in Pregnancy and Preterm Birth. mSystems, 9, e01339-23. https://doi.org/10.1128/msystems.01339-23
Belotserkovsky I, Stabryla LM, Hunter M, Allegretti J, Callahan BJ, Carlson PE, Daschner PJ, Goudarzi M, Guyard C, Jackson SA, Rao K, Servetas SL, Sokol H, Wargo JA, Novick S (2024). Standards for fecal microbiota transplant: Tools and therapeutic advances. Biologicals, 86, 101758. https://doi.org/10.1016/j.biologicals.2024.101758
Scheible M, Stinson TL, Breen M, Callahan BJ, Thomas R, Meiklejohn KA^ (2024). The development of non-destructive sampling methods of parchment skins for genetic species identification. PLoS One, 19(3), e0299524. https://doi.org/10.1371/journal.pone.0299524
Halleran J^, Sylvester H, Jacob M, Callahan B, Baynes R, Foster D. Impact of florfenicol dosing regimen on the phenotypic and genotypic resistance of enteric bacteria in steers (2024). Scientific Reports, 14, 4920. https://doi.org/10.1038/s41598-024-55591-8
Grinevich D#, Harden L, Thakur S, Callahan BJ^ (2024). Serovar-level Identification of Bacterial Foodborne Pathogens from Full-length 16S rRNA Gene Sequencing. mSystems, e00757-23. https://doi.org/10.1128/msystems.00757-23
Hakimzadeh A, Abdala Asbun A, Albanese D, Bernard M, Buchner D, Callahan B, Caporaso JG, Curd E, Djemiel C, Brandström Durling M, Elbrecht V, Gold Z, Gweon HS, Hajibabaei M, Hildebrand F, Mikryukov V, Normandeau E, Özkurt E, Palmer JM, Pascal G, Porter TM, Straub D, Vasar M, Větrovský T, Zafeiropoulos H, Anslan S^ (2024). A pile of pipelines: An overview of the bioinformatics software for metabarcoding data analyses. Molecular Ecology Resources, 24 (5), e13847. https://doi.org/10.1111/1755-0998.13847
Templeton GB, Fefer G, Case BC, Roach J, Azcarate-Peril MA, Gruen ME, Callahan BJ, Olby NJ^. Longitudinal Analysis of Canine Oral Microbiome Using Whole Genome Sequencing in Aging Companion Dogs (2023). Animals, 13(24), 3846. https://doi.org/10.3390/ani13243846
Slead TS, Callahan BJ, Schreeg ME, Seiler GS, Stowe DM, Azcarate‐Peril MA, Jacob ME, Gookin JL^ (2023). Microbiome analysis of bile from apparently healthy cats and cats with suspected hepatobiliary disease. Journal of Veterinary Internal Medicine, 37(6), 2178-2187. https://doi.org/10.1111/jvim.16852
Gin TE#^, Petzold EA, Uthappa DM, Neighbors CE, Borough AR, Gin C#, Lashnits E, Sempowski GD, Denny T, Bienzle D, Weese JS, Callahan BJ, Woods CW (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, e16310. https://doi.org/10.7717/peerj.16310
Huang C#, Gin C#, Fettweis J, Foxman B, Gelaye B, MacIntyre DA, Subramaniam A, Fraser W, Tabatabaei N, Callahan B^ (2023). Meta-Analysis Reveals the Vaginal Microbiome is a Better Predictor of Earlier Than Later Preterm Birth. BMC Biology, 21, 199. https://doi.org/10.1186/s12915-023-01702-2
Switzer AD, Callahan BJ, Costello EK, Bik EM, Fontaine C, Gulland FM, Relman DA^ (2023). Rookery through rehabilitation: Microbial community assembly in newborn harbour seals after maternal separation. Environmental Microbiology, 25(11), 2182-2202. https://doi.org/10.1111/1462-2920.16444
Gookin JL, Hartley AN, Aicher KM, Mathews KG, Cullen R, Cullen JM, Callahan BJ, Stowe DM, Seiler GS, Jacob ME, Arnold JW (2023). Gallbladder microbiota in healthy dogs and dogs with mucocele formation. Plos one, 18(2):e0281432. https://doi.org/10.1371/journal.pone.0281432
Manvell C, Berman H#, Callahan B, Breitschwerdt E, Swain W, Ferris K, Maggi R, Lashnits E^. Identification of microbial taxa present in Ctenocephalides felis (cat flea) reveals widespread co-infection and associations with vector phylogeny (2022). Parasites & Vectors, 15, 398. https://doi.org/10.1186/s13071-022-05487-1
McLaren MR#, Nearing JT, Willis AD, Lloyd KG, Callahan BJ^ (2022). Implications of taxonomic bias for microbial differential-abundance analysis. bioRxiv, 2022.08.19.504330 [PREPRINT]. https://doi.org/10.1101/2022.08.19.504330
Huang C#, Callahan BJ, Wu MC, Holloway ST, Brochu H, Lu W, Peng X, Tzeng JY^ (2022). Phylogeny-Guided Microbiome OTU-Specific Association Test (POST). Microbiome, 10, 86. https://doi.org/10.1186/s40168-022-01266-3
Tedersoo L^, Albertsen M, Anslan S, Callahan B (2021). Perspectives and benefits of high-throughput long-read sequencing in microbial ecology. Applied and Environmental Microbiology, 87(17), e00626-21. https://doi.org/10.1128/AEM.00626-21
Callahan BJ^, Grinevich D#, Thakur S, Balamotis MA, Yehezkel TB (2021). Ultra-accurate Microbial Amplicon Sequencing with Synthetic Long Reads. Microbiome, 9, 130. https://doi.org/10.1186/s40168-021-01072-3
Halleran JL^, Callahan BJ, Jacob ME, Sylvester HJ, Prange T, Papich MG, Foster DM (2021). Effects of danofloxacin dosing regimen on gastrointestinal pharmacokinetics and fecal microbiome in steers. Scientific Reports, 11(1), 1-3. https://doi.org/10.1038/s41598-021-90647-z
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
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 (2024). dada2: Accurate, high-resolution sample inference from amplicon sequencing data. R package version 1.32.0.
Over 25,000 citations (Google Scholar, Dec 2024)
Top 5% most downloaded Bioconductor packages.
Callahan BJ, Davis NM (2024). decontam: Identify contaminants in marker-gene and metagenomics sequencing data. R package version 1.22.0.
Over 2,400 citations (Google Scholar, Dec 2024)
Funded Grants
2019 - 2024 | NIH NIGMS R35GM133745 (Role: PI) Quantitative Metagenomics and the Vaginal Microbiome of Preterm Birth Total Costs: $1,442,610 |
2022 - 2027 | NSF Engineering Research Center (Role: Co-I) Engineering Research Center for Precision Microbiome Engineering (PreMiEr) Total Costs (my segment): $449,335 |
2024 - 2028 | NIH NIAID R01AI171046 (Role: Co-I) DNA transduction in intestinal microbiomes and the spread of pathogenicity traits Total Costs (my segment): ~$250,000 |
2024 – 2025 | Triangle Center for Evolutionary Medicine (Role: Co-Lead; Trainee is PI) Microbiome sharing between humans and their pet dogs Total Costs: $7,500 |
2021 – 2023 (completed) | NIH NICHD F31HD104353 (Role: Sponsor; Trainee is PI) Understanding Intraspecific Diversity of Gardnerella vaginalis in the Vaginal Microbiome (Hanna Berman) Total Costs: $111,672 |
2021 – 2024 (completed) | US Army Research Office (Role: Co-I) Validating DNA Metabarcoding for Characterization of Pollen from Surface Soils Total Costs: $450,000.00 |
2022 – 2023 (completed) | NCSU Data Science Academy (DSA) Seed Grant (Role: Co-PI) Using Machine Learning to Automate the Identification of Transducing Events from Metagenomic Data Total Costs: $41,712 |
2021 – 2023 (completed) | NCSU Research and Innovation Seed Funding Program (Role: Co-I) Medieval Monks Meet Modern Science: Using Genetics to Unlock the Secrets of Medieval Parchment Books and their Makers Total Costs: $18,750 (plus $6,250 matching funds from the CVM) |
2019 - 2022 (completed) | American Kennel Club (Role: Co-I) Is Gut Dysbiosis Associated with Canine Idiopathic Epilepsy? Total Costs: $104,453 |
2019 – 2020 (completed) | Triangle Center for Evolutionary Medicine (Role: Co-Lead; Trainee is PI) Exploring connections between Gardnerella vaginalis diversity and preterm birth Total Costs: $6,000 |
2017 - 2019 (completed) | Plant Soil Microbial Community Consortium (Role: PI) Extension and validation of maximum resolution amplicon bioinformatics methods to fungal marker-gene data Total Costs: $55,000 |
Pending Grants
2025 - 2029 | NIH NIGMS 2R35GM133745 (Role: PI) Improving Microbiome Science by Modeling the Measurement Process Total Costs: $2,062,945 Impact Score: 20 |
Invited Talks
2024 | Precision Microbiome Engineering Research (PreMiEr) Center seminar series, Virtual |
2024 | Microbiology and Physiological Systems (MaPS) Seminar, UMass Chan Medical School, Worcester MA |
2023 | Microbiome Data Congress 2023 Pre-event Webinar, Virtual |
2023 | ASM Microbe 2023 (session keynote), Houston TX |
2023 | Precision Microbiome Engineering Research Center (PreMiEr) Research seminar series, Virtual |
2022 | Wayne State University, Dept of Biochemistry, Microbiology, and Immunology, Detroit MI |
2022 | PRIME-TR Virtual Monthly Microbiome Meeting, MD Anderson Cancer Center |
2022 | Food Animal Innovation Summit, Raleigh NC |
2022 | NIST/IMMSA Workshop on on Standards for Microbiome and Multi’Omics Measurements, Boulder CO |
2022 | Microbiome Data Congress 2022, Boston MA |
2022 | IABS - BIOASTER Webinar on Standards for Faecal Microbiota Transplant: Tools and Therapeutic Advances |
2022 | Johns Hopkins Microbiome Forum |
2021 | East Carolina University, Dept. of Microbiology and Immunology Seminar, Greenville NC |
2021 | Kavli Institute of Theoretical Physics Program on The Ecology and Evolution of Microbial Communities, Santa Barbara CA |
2021 | Microbiome Data Congress 2021, Boston MA |
2021 | Aarhus University, Denmark |
2021 | Advanced Food Science Seminar, University of Nebraska - Lincoln, Lincoln NE |
2021 | DNAQUA International Conference, Data Analysis & Storage Session Keynote |
2021 | Duke University Marine Laboratory |
2021 | Loop Genomics, Live Webinar |
2020 | University of Innsbruck, Austria |
2020 | Microbiome Movement - Maternal & Infant Health Summit, Virtual Seminar |
2020 | University of South Florida, Virtual Seminar |
2020 | FDA, Virtual Seminar |
2020 | NIEHS, Research Triangle Park NC |
2020 | University of Louisville, Louisville KY |
2019 | NIST Workshop on Standards for Microbiome Measurements, Gaithersburg MD |
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 | Vienna Institute of Science and Technology, Vienna Austria |
2010 | Bay Area Population Genomics Meeting, UC Berkeley |
2009 | Princeton University, Princeton NJ |
Honors and Awards
2023 | University Faculty Scholar, NC State University |
2023 | Microbiome Data Prize, American Society for Microbiology (ASM) |
2022 | Academic Service Award, NC State Genetics & Genomics Academy |
2021 | Goodnight Early Career Innovator Award, NC State University |
2014 | Best Postdoc Talk (2nd place), American Society of Naturalists |
2003 - 2005 | Broida Fellowship for Graduate Studies in Physics, UC Santa Barbara |
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, BMC Biology, BMC Genomics, Environmental Microbiology, Frontiers in Genetics, Genetics, Gigascience, Journal of Computational Biology, Journal of Mathematical Biology, Journal of the American Statistical Association, Microbiome, Molecular Ecology Resources, mSphere, mSystems, mBio, Nature, Nature Communications, Nature Ecology & Evolution, Nature Methods, Nature Microbiology, New Phytologist, PeerJ, PLoS Computational Biology, PLoS One, PNAS, Proceedings of the Royal Society B, Science, Theoretical Population Biology.
Reviewer (grants): Scientific Oversight Committee (SOC) for the Ocular Microbiome Consortium (OMC) (Jun 2024; Jan 2025), NIH MRAF Study Section (Feb 2024), NIH BBBT-02 Study Section (May 2023, Nov 2023, Jul 2024), NIH NEI U24 “Characterization of the Resident Ocular Microbiome” Study Section (Nov 2022), NIH EMNR Study Section (Mar 2022), NIH CHHD-W Study Section (Oct 2021), NIH K99 Study Section (Nov 2020), NIH BDMA Study Section (Feb 2020). NC State CVM Intramural Research Grants (2021-present).
Advisor: Michael McLaren (postdoc - completed, continued in science), Dmitry Grinevich (postdoc - completed, continued in science), Craig Gin (postdoc - completed, continued in data science), Naga Betrapally (postdoc - completed, continued in science), Caizhi Huang (PhD - completed, continued in science), Hanna Berman (PhD - completed, continued in science policy), Taylor Gin (PhD), Ozge Kuddar (PhD), Jorden Rabasco (PhD), Yixuan Yang (PhD).
Workshop Instruction: Strategies and Techniques for Analyzing Microbial Population Structures at Woods Hole (2015, 2017, 2019, 2022, 2023, 2024, 2025), 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 in R Workshop at NC State (2018, 2023 - Lead instructor)