Works (44)

Updated: September 2nd, 2023 05:01

2023 article

A pile of pipelines: An overview of the bioinformatics software for metabarcoding data analyses

Hakimzadeh, A., Abdala Asbun, A., Albanese, D., Bernard, M., Buchner, D., Callahan, B., … Anslan, S. (2023, August 7). MOLECULAR ECOLOGY RESOURCES, Vol. 8.

author keywords: amplicon data analysis; bioinformatics; environmental DNA; metabarcoding; pipeline; review
Sources: Web Of Science, ORCID
Added: August 28, 2023

2023 journal article

Gallbladder microbiota in healthy dogs and dogs with mucocele formation

PLOS ONE, 18(2).

By: J. Gookin n, A. Hartley n, K. Aicher n, K. Mathews n, R. Cullen n, J. Cullen n, B. Callahan n, D. Stowe n ...

MeSH headings : Dogs; Animals; Gallbladder / pathology; Mucocele / veterinary; RNA, Ribosomal, 16S / genetics; Bile / microbiology; Gallbladder Diseases / veterinary; Microbiota / genetics; Bile Duct Diseases; Dog Diseases / diagnosis
Sources: Web Of Science, ORCID
Added: April 24, 2023

2023 article

GardnerellaDiversity and Ecology in Pregnancy and Preterm Birth

Berman, H. L., Goltsman, D. S. A., Anderson, M., Relman, D. A., & Callahan, B. J. (2023, February 4).

By: H. Berman n, D. Goltsman*, M. Anderson n, D. Relman* & B. Callahan n

Source: ORCID
Added: February 5, 2023

2023 article

Rookery through rehabilitation: Microbial community assembly in newborn harbour seals after maternal separation

Switzer, A. D., Callahan, B. J., Costello, E. K., Bik, E. M., Fontaine, C., Gulland, F. M. D., & Relman, D. A. (2023, June 16). ENVIRONMENTAL MICROBIOLOGY, Vol. 6.

By: A. Switzer*, B. Callahan n, E. Costello*, E. Bik*, C. Fontaine*, F. Gulland*, D. Relman*

Sources: Web Of Science, ORCID
Added: July 10, 2023

2022 journal article

Identification of microbial taxa present in Ctenocephalides felis (cat flea) reveals widespread co-infection and associations with vector phylogeny

PARASITES & VECTORS, 15(1).

By: C. Manvell, H. Berman n, B. Callahan n, E. Breitschwerdt n, W. Swain n, K. Ferris n, R. Maggi n, E. Lashnits n

author keywords: Flea microbiome; Bartonella; Wolbachia; Rickettsia; Flea phylogenetics; Flea diversity; DNA barcoding; 16S NGS
MeSH headings : Animals; Cats; Bartonella / genetics; Cat Diseases / parasitology; Coinfection; Ctenocephalides / microbiology; Flea Infestations / epidemiology; Flea Infestations / veterinary; Phylogeny; Rickettsia / genetics
Sources: Web Of Science, ORCID
Added: November 14, 2022

2022 article

Implications of taxonomic bias for microbial differential-abundance analysis

McLaren, M. R., Nearing, J. T., Willis, A. D., Lloyd, K. G., & Callahan, B. J. (2022, August 19).

By: M. McLaren*, J. Nearing*, A. Willis*, K. Lloyd* & B. Callahan n

Source: ORCID
Added: August 24, 2022

2022 article

Meta-Analysis Reveals the Vaginal Microbiome is a Better Predictor of Earlier Than Later Preterm Birth

Huang, C., Gin, C., Fettweis, J., Foxman, B., Gelaye, B., MacIntyre, D. A., … Callahan, B. (2022, September 27).

By: C. Huang n, C. Gin n, J. Fettweis*, B. Foxman*, B. Gelaye*, D. MacIntyre*, A. Subramaniam*, W. Fraser*, N. Tabatabaei*, B. Callahan n

Source: ORCID
Added: October 20, 2022

2022 journal article

Phylogeny-guided microbiome OTU-specific association test (POST)

MICROBIOME, 10(1).

By: C. Huang n, B. Callahan n, M. Wu*, S. Holloway n, H. Brochu n, W. Lu n, X. Peng n, J. Tzeng n

author keywords: Association test; Phylogenetic tree; Kernel machine regression
MeSH headings : Computational Biology / methods; Computer Simulation; Female; Humans; Infant, Newborn; Microbiota / genetics; Phylogeny; Premature Birth
Sources: Web Of Science, ORCID
Added: June 20, 2022

2021 journal article

Effects of danofloxacin dosing regimen on gastrointestinal pharmacokinetics and fecal microbiome in steers

SCIENTIFIC REPORTS, 11(1).

By: J. Halleran n, B. Callahan n, M. Jacob n, H. Sylvester n, T. Prange n, M. Papich n, D. Foster n

MeSH headings : Animals; Anti-Bacterial Agents / pharmacology; Cattle; Enterococcus / drug effects; Escherichia coli / drug effects; Fluoroquinolones / pharmacology; Gastrointestinal Microbiome / drug effects; Gastrointestinal Tract / drug effects; Gastrointestinal Tract / microbiology; Male
Sources: Web Of Science, ORCID
Added: July 26, 2021

2021 journal article

Ultra-accurate microbial amplicon sequencing with synthetic long reads

MICROBIOME, 9(1).

By: B. Callahan n, D. Grinevich n, S. Thakur n, M. Balamotis* & T. Ben Yehezkel*

author keywords: Synthetic long reads; Amplicon sequencing; Metagenomics; Long-read sequencing
MeSH headings : High-Throughput Nucleotide Sequencing; Metagenome; Microbiota / genetics; RNA, Ribosomal, 16S / genetics; Sequence Analysis, DNA
Sources: ORCID, Web Of Science
Added: June 6, 2021

2020 journal article

Clostridioides difficile carriage in animals and the associated changes in the host fecal microbiota

ANAEROBE, 66.

By: R. Thanissery n, M. McLaren n, A. Rivera n, A. Reed n, N. Betrapally n, T. Burdette n, J. Winston n, M. Jacob n, B. Callahan n, C. Theriot n

author keywords: C. difficile; C. hiranonis; Microbiome; Ribotype; Antibiotic resistance; Animal; Canine; Equine; Feline
MeSH headings : Animals; Anti-Bacterial Agents / pharmacology; Bacterial Toxins / genetics; Bacterial Toxins / metabolism; Bacterial Typing Techniques; Cats; Chlorocebus aethiops; Clostridioides difficile / classification; Clostridioides difficile / drug effects; Clostridioides difficile / physiology; Clostridium Infections / epidemiology; Clostridium Infections / microbiology; Clostridium Infections / veterinary; Coculture Techniques; Dogs; Feces / microbiology; Female; Gastrointestinal Microbiome; Horses; Hospitals, Animal; Host-Pathogen Interactions; Male; Microbial Interactions; Microbial Sensitivity Tests; North Carolina; Polymerase Chain Reaction; Prevalence; RNA, Ribosomal, 16S; Ribotyping; Risk Factors; Tertiary Healthcare; Vero Cells
Sources: Web Of Science, ORCID
Added: January 11, 2021

2020 journal article

Pathogen resistance may be the principal evolutionary advantage provided by the microbiome

Philosophical Transactions of the Royal Society B: Biological Sciences, 375(1808), 20190592.

By: M. McLaren n & B. Callahan n

author keywords: colonization resistance; commensal bacteria; defensive symbionts; evolution of immunity; host-microbiome interactions; microbiome
MeSH headings : Animals; Biological Evolution; Disease Resistance; Host Microbial Interactions; Invertebrates / microbiology; Plant Diseases; Plants / microbiology; Symbiosis; Vertebrates / microbiology
Source: ORCID
Added: August 12, 2020

2020 journal article

The role of the microbiome in host evolution

Philosophical Transactions of the Royal Society B: Biological Sciences, 375(1808), 20190588.

By: O. Kolodny*, B. Callahan n & A. Douglas*

author keywords: beneficial microbes; coevolution; commensals; eco-evolutionary dynamics
MeSH headings : Animals; Biological Evolution; Communicable Disease Control; Crops, Agricultural / microbiology; Host Microbial Interactions; Humans; Microbiota; Nutritive Value; Pest Control
Source: ORCID
Added: August 12, 2020

2020 article

Ultra-accurate Microbial Amplicon Sequencing Directly from Complex Samples with Synthetic Long Reads

Callahan, B. J., Grinevich, D., Thakur, S., Balamotis, M. A., & Yehezkel, T. B. (2020, July 7). (Vol. 7). Vol. 7.

By: B. Callahan n, D. Grinevich n, S. Thakur n, M. Balamotis* & T. Yehezkel*

Source: ORCID
Added: July 9, 2020

2020 journal article

Understanding and interpreting community sequencing measurements of the vaginal microbiome

BJOG: An International Journal of Obstetrics & Gynaecology, 127(2), 139–146.

By: H. Berman n, . McLaren n & B. Callahan n

author keywords: 16S rRNA gene; amplicon sequencing; metagenomics; metatranscriptomics; vaginal microbiome
MeSH headings : Female; Humans; Microbiota / genetics; RNA, Ribosomal, 16S; Reproducibility of Results; Sequence Analysis, DNA; Vagina / microbiology
Source: ORCID
Added: November 2, 2019

2019 journal article

Ceftiofur formulation differentially affects the intestinal drug concentration, resistance of fecal Escherichia coli, and the microbiome of steers

PLOS ONE, 14(10).

MeSH headings : Animals; Anti-Bacterial Agents / administration & dosage; Anti-Bacterial Agents / chemistry; Anti-Bacterial Agents / pharmacokinetics; Cattle; Cattle Diseases / drug therapy; Cattle Diseases / microbiology; Cephalosporins / administration & dosage; Cephalosporins / chemistry; Cephalosporins / pharmacokinetics; Drug Resistance, Bacterial; Escherichia coli / classification; Escherichia coli / drug effects; Escherichia coli / genetics; Feces / microbiology; Microbial Sensitivity Tests; Microbiota; RNA, Ribosomal, 16S / genetics
Sources: Web Of Science, ORCID
Added: June 1, 2020

2019 article

Consistent and correctable bias in metagenomic sequencing experiments

McLaren, M. R., Willis, A. D., & Callahan, B. J. (2019, February 25). BioRxiv, Vol. 2, p. 559831.

By: M. McLaren n, A. Willis* & B. Callahan n

Source: ORCID
Added: February 26, 2019

2019 journal article

Consistent and correctable bias in metagenomic sequencing experiments

ELife.

By: M. McLaren n, A. Willis* & B. Callahan n

MeSH headings : Bacteria / classification; Bacteria / genetics; Bias; Biota; Cluster Analysis; DNA, Ribosomal / chemistry; DNA, Ribosomal / genetics; Metagenomics / methods; Models, Theoretical; Phylogeny; RNA, Ribosomal, 16S / genetics; Sequence Analysis, DNA / methods
Source: ORCID
Added: September 10, 2019

2019 journal article

High-throughput amplicon sequencing of the full-length 16S rRNA gene with single-nucleotide resolution

Nucleic Acids Research, 7.

By: B. Callahan n, J. Wong*, C. Heiner*, S. Oh*, C. Theriot n, A. Gulati*, S. McGill*, M. Dougherty*

MeSH headings : Escherichia coli K12 / classification; Escherichia coli K12 / genetics; Escherichia coli O157 / classification; Escherichia coli O157 / genetics; Feces / microbiology; High-Throughput Nucleotide Sequencing; Humans; Microbiota / genetics; Phylogeny; Polymerase Chain Reaction / methods; Polymorphism, Single Nucleotide / genetics; RNA, Ribosomal, 16S / genetics; Sequence Analysis, DNA
Source: ORCID
Added: August 21, 2019

2019 journal article

Multiomics modeling of the immunome, transcriptome, microbiome, proteome and metabolome adaptations during human pregnancy

BIOINFORMATICS, 35(1), 95–103.

By: M. Ghaemi*, D. DiGiulio*, K. Contrepois*, B. Callahan n, T. Ngo*, B. Lee-McMullen*, B. Lehallier*, A. Robaczewska* ...

Ed(s): J. Wren

MeSH headings : Computational Biology; Female; Humans; Metabolome; Microbiota; Pregnancy; Proteome; Transcriptome
Sources: Web Of Science, ORCID
Added: March 11, 2019

2018 article

High-throughput amplicon sequencing of the full-length 16S rRNA gene with single-nucleotide resolution

Callahan, B. J., Wong, J., Heiner, C., Oh, S., Theriot, C. M., Gulati, A. S., … Dougherty, M. K. (2018, August 15). (Vol. 8). Vol. 8.

By: B. Callahan n, J. Wong*, C. Heiner*, S. Oh*, C. Theriot n, A. Gulati*, S. McGill*, M. Dougherty*

Source: ORCID
Added: August 21, 2019

2018 article

In Nature, There Is Only Diversity

MBIO, Vol. 9.

By: M. McLaren n & B. Callahan n

author keywords: metagenomics; microbial ecology; microbiome
MeSH headings : Metagenomics; RNA, Ribosomal, 16S
Sources: Web Of Science, ORCID
Added: August 6, 2018

2018 journal article

Simple statistical identification and removal of contaminant sequences in marker-gene and metagenomics data

MICROBIOME, 6(1).

By: N. Davis*, D. Proctor*, S. Holmes*, D. Relman* & B. Callahan n

author keywords: Microbiome; Metagenomics; Marker-gene; 16S rRNA gene; DNA contamination
MeSH headings : Bacteria / classification; Bacteria / genetics; DNA Contamination; DNA, Bacterial / genetics; DNA, Ribosomal / genetics; Databases, Genetic; Genetic Markers; Humans; Internet; Metagenomics / methods; Models, Statistical; Mouth / microbiology; RNA, Ribosomal, 16S / genetics; Sequence Analysis, DNA / methods; Software
Sources: Web Of Science, ORCID
Added: January 7, 2019

2017 journal article

Exact sequence variants should replace operational taxonomic units in marker-gene data analysis

The ISME Journal, 11(12), 2639–2643.

By: B. Callahan n, P. McMurdie & S. Holmes*

MeSH headings : Bacteria / classification; Bacteria / genetics; Bacteria / isolation & purification; Classification / methods; Databases, Nucleic Acid; Genetic Variation; Sequence Analysis, DNA
Sources: Crossref, ORCID
Added: July 21, 2019

2017 journal article

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 OF THE UNITED STATES OF AMERICA, 114(37), 9966–9971.

By: B. Callahan n, D. DiGiulio*, D. Goltsman*, C. Sun*, E. Costello*, P. Jeganathan*, J. Biggio*, R. Wong* ...

author keywords: pregnancy; prematurity; vaginal microbiota; Lactobacillus; Gardnerella
MeSH headings : Adult; Black or African American; Case-Control Studies; Cohort Studies; DNA Replication; Female; Gardnerella vaginalis / classification; Humans; Lactobacillus / classification; Microbiota / genetics; Microbiota / immunology; Pregnancy; Premature Birth / etiology; Premature Birth / microbiology; RNA, Ribosomal, 16S / genetics; United States / epidemiology; Vagina / microbiology; White People
Source: Web Of Science
Added: August 6, 2018

2017 journal article

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, 201705899.

By: B. Callahan, D. DiGiulio, D. Goltsman, C. Sun, E. Costello, P. Jeganathan, J. Biggio, R. Wong ...

Source: ORCID
Added: August 21, 2019

2017 article

Simple statistical identification and removal of contaminant sequences in marker-gene and metagenomics data

Davis, N. M., Proctor, D. M., Holmes, S. P., Relman, D. A., & Callahan, B. J. (2017, November 17). (Vol. 11). Vol. 11.

By: N. Davis*, D. Proctor*, S. Holmes*, D. Relman* & B. Callahan n

Source: ORCID
Added: August 21, 2019

2016 journal article

1,2-Dichloroethane Exposure Alters the Population Structure, Metabolism, and Kinetics of a Trichloroethene-Dechlorinating Dehalococcoides mccartyi Consortium

Environmental Science & Technology, 50(22), 12187–12196.

By: K. Mayer-Blackwell*, M. Fincker*, O. Molenda*, B. Callahan*, H. Sewell*, S. Holmes*, E. Edwards*, A. Spormann*

MeSH headings : Biodegradation, Environmental; Chloroflexi / metabolism; Halogenation; Kinetics; Trichloroethylene / metabolism; Vinyl Chloride / metabolism
Sources: Crossref, ORCID
Added: July 21, 2019

2016 journal article

Bioconductor Workflow for Microbiome Data Analysis: from raw reads to community analyses

F1000Research, 5, 1492.

By: B. Callahan*, K. Sankaran*, J. Fukuyama*, P. McMurdie & S. Holmes*

Sources: Crossref, ORCID
Added: July 21, 2019

2016 journal article

DADA2: High-resolution sample inference from Illumina amplicon data

Nature Methods, 13(7), 581–583.

By: B. Callahan*, P. McMurdie*, M. Rosen*, A. Han*, A. Johnson* & S. Holmes*

MeSH headings : Animals; Cohort Studies; Computational Biology / methods; DNA, Bacterial / genetics; False Positive Reactions; Feces / microbiology; Female; High-Throughput Nucleotide Sequencing / methods; Humans; Lactobacillus / classification; Lactobacillus / genetics; Lactobacillus / isolation & purification; Mice; Microbiota / genetics; Pregnancy; RNA, Ribosomal, 16S / genetics; Reproducibility of Results; Sequence Analysis, DNA / methods; Software; Vagina / microbiology
Sources: Crossref, ORCID
Added: July 21, 2019

2016 journal article

Marine mammals harbor unique microbiotas shaped by and yet distinct from the sea

Nature Communications, 7(1), 10516.

By: E. Bik*, E. Costello*, A. Switzer*, B. Callahan*, S. Holmes*, R. Wells*, K. Carlin*, E. Jensen*, S. Venn-Watson*, D. Relman*

MeSH headings : Animals; Bacteroidetes / genetics; Bottle-Nosed Dolphin / microbiology; Gastrointestinal Microbiome / genetics; Microbiota / genetics; Mouth / microbiology; Phylogeny; RNA, Ribosomal, 16S / genetics; Respiratory System / microbiology; Sea Lions / microbiology; Seawater / microbiology; Sequence Analysis, RNA; Tenericutes / genetics; Water Microbiology
Sources: Crossref, ORCID
Added: July 21, 2019

2016 journal article

Reproducible research workflow in R for the analysis of personalized human microbiome data

Pacific Symposium on Biocomputing, 21, 183–194.

By: B. Callahan, D. Proctor, D. Relman, J. Fukuyama & S. Holmes

Source: NC State University Libraries
Added: July 11, 2019

2016 conference paper

Reproducible research workflow in R for the analysis of personalized human microbiome data

Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing, 21, 183.

By: B. Callahan, D. Proctor, D. Relman, J. Fukuyama & S. Holmes

Event: NIH Public Access

Source: ORCID
Added: August 21, 2019

2015 journal article

Temporal and spatial variation of the human microbiota during pregnancy

Proceedings of the National Academy of Sciences, 112(35), 11060–11065.

By: D. DiGiulio*, B. Callahan*, P. McMurdie*, E. Costello*, D. Lyell*, A. Robaczewska*, C. Sun*, D. Goltsman* ...

author keywords: 16S rRNA gene; pregnancy; preterm birth; microbiome; premature labor
MeSH headings : Female; Humans; Intestines / microbiology; Microbiota; Periodontium / microbiology; Pregnancy; Saliva / microbiology; Vagina / microbiology
Source: Crossref
Added: July 21, 2019

2015 journal article

Temporal and spatial variation of the human microbiota during pregnancy

Proceedings of the National Academy of Sciences, 112(35), 11060–11065.

By: D. DiGiulio, B. Callahan, P. McMurdie, E. Costello, D. Lyell, A. Robaczewska, C. Sun, D. Goltsman ...

Source: ORCID
Added: August 21, 2019

2014 journal article

Rapid evolution of adaptive niche construction in experimental microbial populations

Evolution, 68(11), 3307–3316.

By: B. Callahan*, T. Fukami* & D. Fisher*

author keywords: Adaptation; mutations; population biology; selection-experimental
MeSH headings : Adaptation, Biological; Directed Molecular Evolution; Environment; Genetic Fitness; Pseudomonas fluorescens / genetics; Pseudomonas fluorescens / physiology
Sources: Crossref, ORCID
Added: July 21, 2019

2013 journal article

Evolutionary dynamics and information hierarchies in biological systems

Annals of the New York Academy of Sciences, 1305(1), 1–17.

author keywords: evolution; information hierarchy; chromatin; epigenetics; viruses; networks
MeSH headings : Animals; Biological Evolution; Chromatin / metabolism; Computational Biology / methods; Epigenomics; Evolution, Molecular; Humans
Sources: Crossref, ORCID
Added: July 21, 2019

2012 journal article

Denoising PCR-amplified metagenome data

BMC Bioinformatics, 13(1), 283.

By: M. Rosen, B. Callahan, D. Fisher & S. Holmes

Sources: NC State University Libraries, ORCID
Added: July 28, 2019

2012 journal article

The length scale of selection in protein evolution

Fly, 6(1), 16–20.

By: B. Callahan*

author keywords: molecular evolution; epistasis; fitness landscape; protein; correlation function; length scale; Drosophila; positive selection; molecular clock; overdispersion
MeSH headings : Animals; Drosophila; Drosophila Proteins / chemistry; Drosophila Proteins / genetics; Drosophila melanogaster; Evolution, Molecular; Selection, Genetic
Sources: Crossref, ORCID
Added: July 21, 2019

2011 journal article

Correlated Evolution of Nearby Residues in Drosophilid Proteins

PLoS Genetics, 7(2), e1001315.

Ed(s): G. McVean

MeSH headings : Amino Acid Substitution; Animals; Drosophila Proteins / genetics; Drosophila melanogaster / genetics; Evolution, Molecular; Multigene Family; Mutation; Phylogeny; Selection, Genetic
Sources: Crossref, ORCID
Added: July 28, 2019

2011 journal article

Heterozygote advantage as a natural consequence of adaptation in diploids

Proceedings of the National Academy of Sciences, 108(51), 20666–20671.

By: D. Sellis, B. Callahan*, D. Petrov & P. Messer

MeSH headings : Adaptation, Physiological / genetics; Alleles; Animal Migration; Animals; Diploidy; Emigration and Immigration; Gene Expression; Genetic Variation; Haploidy; Heterozygote; Humans; Models, Genetic; Mutation; Phenotype; Polymorphism, Genetic; Selection, Genetic
Sources: Crossref, ORCID
Added: July 21, 2019

2009 journal article

Emergent gene order in a model of modular polyketide synthases

Proceedings of the National Academy of Sciences, 106(46), 19410–19415.

By: B. Callahan*, M. Thattai* & B. Shraiman*

author keywords: polyketides; horizontal transfer; evolution; collinearity; evolvability
MeSH headings : Animals; Bacteria / enzymology; Bacteria / genetics; Computer Simulation; Evolution, Molecular; Gene Order; Macrolides / metabolism; Models, Genetic; Plants / enzymology; Plants / genetics; Polyketide Synthases / biosynthesis; Polyketide Synthases / genetics; Protein Biosynthesis / genetics; Selection, Genetic
Sources: Crossref, ORCID
Added: July 28, 2019

2009 thesis

Evolution on an interacting fitness landscape: The effects of the interplay of epistasis and recombination on genetic structure

University of California, Santa Barbara.

By: B. Callahan

Source: ORCID
Added: August 21, 2019

2003 journal article

Exploring the Interplay between Topology and Secondary Structural Formation in the Protein Folding Problem

The Journal of Physical Chemistry B, 107(40), 11193–11200.

By: M. Cheung*, J. Finke*, B. Callahan* & J. Onuchic*

Sources: Crossref, ORCID
Added: July 28, 2019

Employment

Updated: November 17th, 2017 13:45

2017 - present

NC State University, College of Veterinary Medicine Raleigh, NC, US
Assistant Professor Population Health & Pathobiology

Education

Updated: November 17th, 2017 13:44

2003 - 2009

University of California, Santa Barbara Santa Barbara, CA, US
Ph.D. Physics

1998 - 2002

Iowa State University Ames, IA, US
Bachelors of Science Physics, Math