Senay Yitbarek

AI Keeps Failing at Microbiome Prediction Why simple models keep winning, where deep learning still shines, and where the field is headed

AI has huge promise for genomics -- but it has consistently failed at microbiome-based prediction.

My new post on why simple models keep winning, where deep learning actually earns its place, and where the field is headed

blekhman.substack.com/p/ai-keeps-f...

UNC-CH Will ‘Scrap’ New Recording Policy, Chancellor Says The move comes less than three weeks after the controversial rules were enacted.

Congrats to @ncaaup.bsky.social & all who fought against this surveillance policy that would've allowed admin to hijack microphones in the classroom for secret recordings.

This move would've chilled classroom discussion & suppressed students' willingness to ask questions & take intellectual risks.

Back in the 1980s-2000s, there was an organization called
Computer Professionals for Social Responsibility that worked to oppose irresponsible and dangerous uses of computers in warfare. Maybe it needs a reboot, in our new age of AI.

en.wikipedia.org/wiki/Compute...

🦋✂️🧬 🧪 New preprint! Led by @donyaniyaz.bsky.social CRISPR‑Cas9 knockouts of ABCG transporters across butterflies & moths reveal how pigment pathways shape color during development. #CRISPR #Lepidoptera #pigmentation
Feedback welcome 👩‍🔬
www.biorxiv.org/content/10.6...

Genomic Perplexity and the Evolution of Context-Dependent Function Abstract. The fundamental principle that selection acts on a gene’s function often assumes implicitly that this function is fixed and intrinsic. However, e

New paper out in MBE! 🧵
"Genomic Perplexity and the Evolution of Context-Dependent Function"
The big idea: genes don't have fixed functions. Function emerges from context - genomic, cellular, environmental. And we can quantify this. academic.oup.com/mbe/article/...

Generalized dynamics of cross-feeding bacteria Abstract. Bacterial cooperation involves the exchange of metabolites, which can range from costless byproducts of metabolism to intentionally produced and

Check out our new paper on cooperating bacteria led by @janamassing.bsky.social w/ @thilogross.bsky.social and @akfbio.bsky.social, where we explore the costs and benefits of metabolitic trade on stability in non-spatial and spatial contexts... exciting! royalsocietypublishing.org/rsif/article...

Faculty Positions

We are hiring an Assistant or Associate Professor in Indigenous Environmental Governance and Management. Very excited for this position.

Please circulate widely among your networks:
www.sfu.ca/rem/about/em...

#academia #HigherEd #AcademicSky

In case you missed it: our review titled "Spatial structure: shaping the ecology and evolution of microbial communities" is out! 🚨

Let me hit you with some highlights on why spatial structure matters. (and why you should care!)

Sharing is appreciated 🙏 🧵👇

doi.org/10.1093/fems...

🗓️Complete schedule for this term, where we will have speakers covering higher-order interactions, metabolic scaling, niche dimensionalty, coexistence and more!

Look forward to seeing you there! All details and Zoom link: iite.info/seminar/

Excited to share a preprint of work from my postdoc with @paulturnerlab.bsky.social exploring how prophages can impact host thermal ecology and evolution. www.biorxiv.org/content/10.6...

Group photo of participants at conference held at Banff International Research Station

Had a great time at the “New mathematical theory in eco evolutionary modeling of host symbiont communities” workshop/conference at Banff International Research Station 🥳

Spatial structure: shaping the ecology and evolution of microbial communities Spatial structure naturally emerges in microbial communities, shaping growth, interactions, and evolution, and revealing how microscale processes scale up

Most microbes don't live in shaking flasks; spatial structure shapes how microbes interact and evolve at every scale, as we discuss in our recent review @jeroenmeijer.bsky.social @simonvanvliet.bsky.social @bedutilh.bsky.social @bramvandijk.bsky.social and others
academic.oup.com/femsre/artic... 🧵👇

UNC Admin Can Now, Officially, Secretly Record Faculty The new policy prohibits students from recording class without permission but explicitly allows administrators to surveil professors for any “lawful purpose.”

UNC Admin Can Now, Officially, Secretly Record Faculty

I am SO incredibly excited to announce the launch of a global list of Inspiring Black Scientists. You can use this list to nominate and connect with researchers. Please share and join us in highlighting these outstanding scientists for #BlackHistoryMonth and beyond!

www.wiley.com/en-us/resear...

Black scientists’ contributions to research throughout history This Black History Month, we’re recognizing Black scientists’ contributions to science throughout history.

STEM Black History Fact 5/28

Dr. Ruth Ella Moore was the first Black scientist to earn a PhD in microbiology and conducted key research on tuberculosis when TB was a leading cause of death.

Evidence for toxin-encoding coinfections driving intransitive dynamics between allelopathic phenotypes in natural yeast populations Abstract. Competitive intransitivity, or non-hierarchical competitive interactions, such as those exemplified by the rock-paper-scissors game where no sing

Evidence for toxin-encoding coinfections driving intransitive dynamics between allelopathic phenotypes in natural #yeast populations:

@tommytraverscook.bsky.social et al.

doi.org/10.1093/jeb/...

Awesome opportunity for a 2 year mentored fellowship that transitions to a TT line at Stony Brook in ecological and/or evolutionary responses to global change through the SUNY Prodigy+ program: apply.interfolio.com/178040

The Importance of Biological Theory - Biological Theory Biological Theory -

I am happy to share this article, entitled "The importance of Biological Theory". It is my inaugural editorial as the new Editor-in-Chief of @biologicaltheory.bsky.social . In these complex and challenging times, theory is more important now than ever. Enjoy!

doi.org/10.1007/s137...

How MAHA Exploits the Flaws of Modern Science Opinion | The weaknesses in science’s processes have been weaponized against it. It’s time to confront those flaws and fix them.

"Take away college football tomorrow & watch college towns descend into chaos. But when they came for our pipettes & microscopes, almost nothing happened. "

New thoughts on the War on Science, 1 yr later, for @undark.org:

'How MAHA Exploits the Flaws of Modern Science '
undark.org/2026/01/28/o...

Koolstof opslaan in landbouwgrond: iedereen wil het, maar het werkt niet Landbouwexperts, beleidsmakers, boeren, van rechts tot links en van intensief tot biodynamisch: over één klimaatmaatregel zijn ze allemaal enthousiast. Sla koolstof op in landbouwgrond, en iedereen wi...

Hoogleraar bodemecologie Franciska de Vries: Het verhogen van de hoeveelheid koolstof via organisch materiaal in landbouwbodems is heel belangrijk, maar gaat klimaatopwarming niet effectief tegen.
Wat wél werkt: meer natuur en minder vee.
decorrespondent.nl/16694/koolst...
@frantecol.bsky.social

I remain absolutely furious that all this shit in Minneapolis started because a barely-literate homeschooled mormon made a video trying to run up in daycare centers trying to find people of Somalian descent doing fraud despite the ringleader (a white woman) being in jail since March. Demonic.

UC Board of Regents approves dismissal of tenured ecology professor - Daily Bruin The UC Board of Regents approved the dismissal of a tenured UCLA professor Wednesday. Priyanga Amarasekare, an ecology and evolutionary biology professor who began at UCLA in 2005, was initially suspe...

😢 dailybruin.com/2026/01/22/u...

network showing more diverse connections over time for editors and reviewers

cover of the paper with title and authors

last paragraph of the abstract: Synthesis and applications. Our results show that editorial diversification is a practical lever for making peer review more inclusive and better aligned with the global distribution of ecological research. These changes make the publication process fairer and improve the quality and global impact of the papers published.

New paper, Great news:
We have been saying for years that making the editorial board more diverse was needed
We now show that diverse team of editors makes for more diverse reviewers
More Inclusive=Better Science
Things are getting better on this❤️
besjournals.onlinelibrary.wiley.com/doi/10.1111/...

Dr. Gladys West, Mathematician Whose Work Made GPS Possible, Dies at 95 ALEXANDRIA, VA — Dr. Gladys West, the pioneering mathematician whose work laid the foundation for modern GPS technology, has died. She passed away

thezebra.org/2026/01/18/d...

#Blacksky #WomeninSTEM

Can interactive web apps help biology students become better modellers?

peischllab.github.io/MEEW.html
We're running an ethics-approved, pre-registered study thanks to funding from the University of Bern.

Are you lecturing in the Spring?
Contact me to receive the survey link!

Evolutionary game theory researches: Join us for the ‘Evolutionary Games: Mathematical Theory and Biological Insights’ workshop at NITMB!

Travel applications are due Wednesday, March 11th - www.nitmb.org/evolutionary...

Is there a mathematics of discontinuous behavior? Christopher Zeeman was a leading proponent of Catastrophe Theory, a topological approach to sudden change that underpins much of today’s work on tipping points. This is his beautiful 1976 paper in @sciam.bsky.social www.jstor.org/stable/pdf/2...

Can microbial partners reduce agrochemical harm? In clover–rhizobia mutualisms, herbicide effects depend strongly on rhizobial strain, highlighting symbionts as potential buffers against stress. Image Matt Lavin @wikimedia
academic.oup.com/evlett/advan...

This Diminutive Reptile Plays Rock-Paper-Scissors

Thanks to Barry Sinervo for leading decades-long research on the amazing side-blotched lizards. www.nytimes.com/2026/01/01/s...