Benjamin Callahan

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.

Gallbladder microbiota in healthy dogs and dogs with mucocele formation

PLOS ONE, 18(2).

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).

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.

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

PARASITES & VECTORS, 15(1).

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).

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).

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

MICROBIOME, 10(1).

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

SCIENTIFIC REPORTS, 11(1).

Ultra-accurate microbial amplicon sequencing with synthetic long reads

MICROBIOME, 9(1).

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

ANAEROBE, 66.

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

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

The role of the microbiome in host evolution

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

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.

Understanding and interpreting community sequencing measurements of the vaginal microbiome

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

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

PLOS ONE, 14(10).

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.

Consistent and correctable bias in metagenomic sequencing experiments

ELife.

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

Nucleic Acids Research, 7.

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

BIOINFORMATICS, 35(1), 95–103.

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.

In Nature, There Is Only Diversity

MBIO, Vol. 9.

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

MICROBIOME, 6(1).

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

The ISME Journal, 11(12), 2639–2643.

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.

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.

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.

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.

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

F1000Research, 5, 1492.

DADA2: High-resolution sample inference from Illumina amplicon data

Nature Methods, 13(7), 581–583.

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

Nature Communications, 7(1), 10516.

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

Pacific Symposium on Biocomputing, 21, 183–194.

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

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

Temporal and spatial variation of the human microbiota during pregnancy

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

Temporal and spatial variation of the human microbiota during pregnancy

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

Rapid evolution of adaptive niche construction in experimental microbial populations

Evolution, 68(11), 3307–3316.

Evolutionary dynamics and information hierarchies in biological systems

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

Denoising PCR-amplified metagenome data

BMC Bioinformatics, 13(1), 283.

The length scale of selection in protein evolution

Fly, 6(1), 16–20.

Correlated Evolution of Nearby Residues in Drosophilid Proteins

PLoS Genetics, 7(2), e1001315.

Heterozygote advantage as a natural consequence of adaptation in diploids

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

Emergent gene order in a model of modular polyketide synthases

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

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

University of California, Santa Barbara.

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

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