Benjamin Callahan

Microbes, Evolution, Stats, Physics

[Benjamin Callahan @bejcal]

Our latest: The taxonomic resolution of 16S sequencing doesn't stop at the species level when using modern long-read techniques. Serovars from 16S...

https://t.co/PIWBigas4l

#NCStateMicrobiome

[Chris @DrChrisKellogg]

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

[Benjamin Callahan @bejcal]

Our latest: The taxonomic resolution of 16S sequencing doesn't stop at the species level when using modern long-read techniques. Serovars from 16S...

https://t.co/PIWBigas4l

#NCStateMicrobiome

[Benjamin Callahan @bejcal]

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

[QIIME 2 @qiime2]

@QIIME2 2023.5 is now available & includes new parallel computing support w @ParslProject, ability to resume failed pipeline runs, provenance replay, decontam actions, and much more. Thank you to all who contributed! #microbiome #bioinformatics https://t.co/KBaEQ37oPB

[Hanna Berman @hannalberman]

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.

[Benjamin Callahan @bejcal]

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:

https://t.co/uzz0LTamAI

#NCStateMicrobiome

[Amy Willis 😻 amydwillis.bsky.social @AmyDWillis]

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! 😻🥳📈

[Benjamin Callahan @bejcal]

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

https://t.co/XoV26hl0dR

[Benjamin Callahan @bejcal]

@JTNearing @IMMSAStandards I think the mailing list should carryover

[IMMSA @IMMSAStandards]

Calling all students and microbiome professionals! Join the IMMSA Bioinformatics Working Group to address "How do we define how accurate a microbiome profile is?" https://t.co/9rRZnRE72x. Meeting will be on zoom Thursday Nov 10, 2022 at Noon eastern time!

[NCSU CVM Research @CVMResearch]

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!

[David Huang @DavidHuangCZ1]

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

[Mike McLaren @mikemc423]

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
https://t.co/bZ00GXyIDN

[Benjamin Callahan @bejcal]

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!)

[Benjamin Callahan @bejcal]

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"

https://t.co/XkbtGYqYU7

[NCSU CVM Research @CVMResearch]

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!

[Benjamin Callahan @bejcal]

@Manuel_Kleiner Thanks Manuel.

[Amy Willis 😻 amydwillis.bsky.social @AmyDWillis]

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/

[Benjamin Callahan @bejcal]

This preprint builds on our previous work developing a quantitative model for taxonomic bias in metagenomic sequencing: https://t.co/r3hA34uZlp

Thanks to our collaborators @AmyDWillis @archaearama and @JTNearing

[Benjamin Callahan @bejcal]

Our latest work led by @mikemc423 on bioRxiv goes deep on "Implications of taxonomic bias for microbial differential-abundance analysis": https://t.co/JIuwpvteoh

Metagenomic sequencing is biased. When are differential abundance (DA) results still valid?

#NCStateMicrobiome 1/

[Benjamin Callahan @bejcal]

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/