Benjamin Callahan

Our latest: The taxonomic resolution of 16S sequencing doesn't stop at the species level when using modern long-read techniques. Serovars from 16S... biorxiv.org/content/10.110… #NCStateMicrobiome

Love that @bejcal called using data only in the original paper “a crime against data” - make it findable & usable so it has many lives/uses! #NMDC #ASMicrobe

decontam functionality is now available through QIIME2. Thanks Jorden Rabasco and QIIME team.

Excited to finally share our work showing the diversity of Gardnerella in the vaginal microbiome! When I started this project a few years ago, all Gardnerella was considered a single species. Here we add to the rapidly expanding knowledge of the diversity of this genus.

Did you know: It is not rare for every known genomospecies of Gardnerella (all 14!) to be present in a vaginal microbiome sample? And how ecologically different are these Gardnerellas? Our latest preprint, led by Hanna Berman: biorxiv.org/content/10.110… #NCStateMicrobiome

STAMPS @ MBL is back in 2023! Jul 19-29 in Woods Hole ☀️🏖️💻 STAMPS has trained thousands of microbial ecologists (of all stripes!) in the bioinformatic and statistical analysis of microbiome data 🌟🧠🦠 Join us for #STAMPS2023 and be one of them! 😻🥳📈

DADA2 1.26 release is live on Bioconductor. The package now natively compiles and runs on ARM architectures like the Apple M1/M2 chips. bioconductor.org/packages/relea…

@JTNearing @IMMSAStandards I think the mailing list should carryover

@IMMSAStandards @bejcal Do we need to resign up if we were in the previous group?

Calling all students and microbiome professionals! Join the IMMSA Bioinformatics Working Group to address "How do we define how accurate a microbiome profile is?" forms.gle/TAA39T1fLxrCMA…. Meeting will be on zoom Thursday Nov 10, 2022 at Noon eastern time!

Our researchers aren’t just solving problems, but also sharing their expertise with early-career scientists! Yesterday, @bejcal and @buchler_nicolas gave a fantastic seminar to our postdocs on the skills and importance of peer reviewing!

@bejcal This manuscript addresses the mixed and inconsistent findings related to the associations between the vaginal microbiome and preterm birth in current literature. 1/

The Nucleic Acid Observatory project at MIT is hiring an experimental scientist to help lead our efforts to develop an environmental metagenomics monitoring system to detect catastrophic biothreats linkedin.com/posts/michael-…

Thanks to @CraigGin for help all along the way, and our co-authors who helped us understand and effectively use their primary research. (and apologies for not knowing your twitter handles!)

Out latest work led by @DavidHuangCZ1 is out on medRxiv: "Meta-Analysis Reveals the Vaginal Microbiome is a Better Predictor of Earlier Than Later Preterm Birth" medrxiv.org/content/10.110…

Congrats to CVM's Dr. Ben Callahan (@bejcal), Assistant Professor of Microbiomes and Complex Microbial Communities, on being awarded the American Society for Microbiology's Microbiome Data Prize!

@Manuel_Kleiner Thanks Manuel.

New preprint alert! 🚨🥳😻 When we first put out the “MWC model” paper, there was a lot of concern about how negatively impactful the problem of unequal detection efficiencies in microbiome taxonomic profiling is. A thread🧵… 1/

This preprint builds on our previous work developing a quantitative model for taxonomic bias in metagenomic sequencing: doi.org/10.7554/eLife.… Thanks to our collaborators @AmyDWillis @archaearama and @JTNearing

A few quick hits: There are right(er) and wrong(er) ways to measure absolute abundances. Great care is needed to correctly estimate small non-zero differential abundances. And while taxonomic bias can interfere with DA analyses, it doesn't make all such results invalid. 6/

Our latest work led by @mikemc423 on bioRxiv goes deep on "Implications of taxonomic bias for microbial differential-abundance analysis": biorxiv.org/content/10.110… Metagenomic sequencing is biased. When are differential abundance (DA) results still valid? #NCStateMicrobiome 1/