Special thanks to @goyallab.bsky.social @vaikuntsuri.bsky.social for their guidance over the last two years, Mike Hinczewski, and to all my advisors throughout my time in science so far!

So happy to see one of my first postdocs Ben starting his own group at Fred Hutch! Ben has been central to our perturbation modeling efforts and I’m excited to see what he does in his own group.

Ben Kuznets-Speck@biophysben.bsky.social · 4w ago

Thrilled to announce I'll starting my lab in Biostatistics at Fred Hutch Cancer Center, where we'll fearlessly cross the boundaries of statistical physics, AI, and single-cell biology to study drug resistance, metastasis, and immune exhaustion! Huge thanks to everyone who made this possible.

A preview from my group on @rongfan8.bsky.social 's excellent new technology and the broader spatial CRISPR screens in @natbiotech.nature.com

Nature Biotechnology@natbiotech.nature.com · 2mo ago

Spatial CRISPR screens map total RNA in tissue #NBTNV www.nature.com/articles/s41...

#TwINFER by Yogesh Goyal et al for analyzing recently divided cells (aka “twins”) seems interesting Gotta read later the preprint from doi.org/10.64898/202... #BoG2026 @cshlmeetings.bsky.social

Delighted to share our lab's latest (w/ inimitable @genophoria.bsky.social) in final form at @nature.com. Enormous lift by Sean Wang, @palindromephd.bsky.social & @martyyang.bsky.social to address extensive & constructive reviewer comments & see this through. (1/n) www.nature.com/articles/s41...

Pervasive and programmed nucleosome distortion on single chromatin fibres - Nature

An analytical pipeline called Iteratively Defined Lengths of Inaccessibility (IDLI) maps the genome-wide occupancy of a range of nucleosome types and shows that most nucleosomes exhibit programmed ‘di...

nature.com

*POSTDOC Positions* Multiple positions open in my group at @biohub.org & @feinberg.northwestern.edu / @nitmb.bsky.social We welcome PhDs from diverse disciplines interested in QBio & BioE job-boards.greenhouse.io/biohub/jobs/... job-boards.greenhouse.io/biohub/jobs/... www.goyallab.org/positions

For decades, molecular biology and human genetics have been built around measurements of average gene expression. That was partly conceptual, but also technological: for a long time, the mean was the quantity we could measure most reliably. Our new preprint argues that this framework is incomplete.

Delighted to have our work on 🧬 resilience to 🩸cancer led by @g-agarwal.bsky.social & amazing collaborators, including @kharaslab.bsky.social, published in @science.org: www.science.org/doi/10.1126/... 🧵

New online! Revisiting the molecular workhorse: plasmids in evolutionary conflict

Super happy to be associated with this work !!

Ben Kuznets-Speck@biophysben.bsky.social · 8mo ago

Today we’re excited to share Keeping SCORE, a framework that turns any diffusion model into a thermodynamic inference machine. Using only a model’s score function, we compute exact class likelihoods and uncertainty—and even decompose which features drove the decision. www.biorxiv.org/content/10.1...

Excited for this work by Michael Cortazar, an @JagannathanLab Postdoc, to be out as a preprint. So much hard work went into it, but it was well worth it 🤓

bioRxiv Genomics@biorxiv-genomic.bsky.social · 8mo ago

Genomic stop codon scanning reveals quantitative principles of nonsense-mediated mRNA decay https://www.biorxiv.org/content/10.64898/2025.12.20.695734v1

Excited to share new work by Daiki and Hector in collaboration with Monika: arxiv.org/abs/2512.13859 We introduce a gating mechanism in classic associative memory models and find capacity is increased far above the Hopfield limit without the usual catastrophic breakdown.

Neuromodulation-inspired gated associative memory networks:extended memory retrieval and emergent multistability

Classical autoassociative memory models have been central to understanding emergent computations in recurrent neural circuits across diverse biological contexts. However, they typically neglect neurom...

arxiv.org

NEW PREPRINT led by stellar postdoc @biophysben.bsky.social We turn diffusion models into inference machines. Score function→exact likelihoods, uncertainty estimate & interpretablity. Diffusion models generate. But classify? Untapped—until now @chanzuckerberg.bsky.social shorturl.at/s32uX

Interpretable Thermodynamic Score-based Classification of Relaxation Excursions

Classification and regression are cornerstones of computational biology and science at large, from identifying cell types to stratifying patients by disease state. Current deep learning classifiers pr...

shorturl.at

Ben Kuznets-Speck@biophysben.bsky.social · 8mo ago

Today we’re excited to share Keeping SCORE, a framework that turns any diffusion model into a thermodynamic inference machine. Using only a model’s score function, we compute exact class likelihoods and uncertainty—and even decompose which features drove the decision. www.biorxiv.org/content/10.1...

Guaranteed funding for five years and a 20% increase in a $39K base stipend if you haul in a fellowship. World class facilities and faculty in metabolism, structural biology, epigenetics, and beyond. Grand Rapids is half the cost of living of California or Boston. Apply by December 1st if interested

Eric Swindell@gradschooldean.bsky.social · 10mo ago

Van Andel Institute PhD program application is OPEN! youtu.be/o79eqd1Ui0s?...

Hot off the press! Our latest paper led by @fernpizza.bsky.social, understanding how plasmids evolve inside cells. These small, self-replicating DNA circles live inside bacteria and carry antibiotic resistance genes, but also compete with one another to replicate. 1/ www.science.org/doi/10.1126/...

Intracellular competition shapes plasmid population dynamics

From populations of multicellular organisms to selfish genetic elements, conflicts between levels of biological organization are central to evolution. Plasmids are extrachromosomal, self-replicating g...

science.org

PhD students and Postdocs: The Night Science Podcast (@nightsciencepod.bsky.social) is producing an episode highlighting young scientists talking about their creative process. DM me if you'd like us to consider you for this, & read below what PhD student Davis Garner will contribute! ⬇️

New preprint! We measured temperature- and pH-induced aggregation for over 18,000 natural and de novo designed protein domains!

Excited to share our new study, led by @dellaVolpe_L, now out in @natcellbio.nature.com! Blocking #ferroptosis enhances human 🩸 stem cell expansion, with implications for transplantation and gene therapy. www.nature.com/articles/s41...

How do cells adapt morphology to function? In a 🔥 preprint by @zjmaggiexu.bsky.social , with @dudinlab.bsky.social and @amyweeks.bsky.social , we identify a self-organizing single-cell morphology circuit that optimizes the feeding trap structure of the suctorian P. collini. 🧵 tinyurl.com/4k8nv926

📢 Our Dept. of Systems Biology at Columbia University has an open tenure-track Assistant Professor position in the broad area of quantitative biology. Come join our awesome department in NYC! Please circulate. apply.interfolio.com/177622 Suggested deadline: 12/15/2025. @columbiasysbio.bsky.social

Congratulations to Yogesh Goyal, PhD @goyallab.bsky.social, who was named a 2025–2028 Edward Mallinckrodt, Jr. Foundation Grant Fellow! His work bridges engineering and biology to advance understanding of cellular plasticity and fate in development and disease. Learn more: tinyurl.com/2rumf48v

Exciting opportunity to work with @ianmellis.bsky.social who is an excellent mentor and working on cool stuff !

Ian Mellis@ianmellis.bsky.social · 10mo ago

Excited to share a job opportunity to work with me and colleagues at Columbia! If you or someone you know would like to be a Research Technician/Assistant working at the interface of molecular systems biology, virology, immunology, and gene and cell therapies, please reach out! (Links below)

Congratulations @karalmckinley.bsky.social & lab on their groundbreaking recent preprint establishing + characterizing a chemically inducible model of menstruation in mouse: www.biorxiv.org/content/10.1... My jaw dropped when I heard this presented earlier this year. Incredible.

Induction of menstruation in mice reveals the regulation of menstrual shedding

During menstruation, an inner layer of the endometrium is selectively shed, while an outer, progenitor-containing layer is preserved to support repeated regeneration. Progress in understanding this co...

biorxiv.org

Nature Biomedical Engineering is hiring again! This time we're hoping to add an editor with machine learning expertise to the team (although we are open to those with other relevant expertise!) Deadline is Oct 20. Please RT! springernature.wd3.myworkdayjobs.com/SpringerNatu...

We are excited to share GPN-Star, a cost-effective, biologically grounded genomic language modeling framework that achieves state-of-the-art performance across a wide range of variant effect prediction tasks relevant to human genetics. www.biorxiv.org/content/10.1... (1/n)

Asking BlueSky for help: For a review, I am trying to accurately credit the first paper that measured pairwise 3D distances between 2 pieces of DNA on the same chromosome (or cosmid). Is Trask 1989 the first? I know of earlier single-locus papers (1982). www.sciencedirect.com/science/arti...

Some (+)ve news to lighten another heavy weekend: our latest preprint (c/o Mattiroli + Ramani labs) is up! www.biorxiv.org/content/10.1... A tour-de-force by 1st authors Bruna Eckhardt & @palindromephd.bsky.social, focusing on chromatin replication. RTs welcome; tweetorial in 3,2...(1/n)

The eukaryotic replisome intrinsically generates asymmetric daughter chromatin fibers

DNA replication is molecularly asymmetric, due to distinct mechanisms for lagging and leading strand DNA synthesis. Whether chromatin assembly on newly replicated strands is also asymmetric remains un...

biorxiv.org

We have an active search for tenure-track faculty interested in #ImmuneEngineering #ProteinEngineering #GenomeEngineering & #CancerImmunology. Join the newly formed Center for Cellular Therapies and Cancer Immunology #CCTCI. Learn more at apply.interfolio.com/173562. #facultyjobs

Highly productive and innovative group doing elegant quantitative bio spanning theory, experimental and computational methods, and actual applications. If you're interested in a postdoctoral position studying cancer, development, or single cell biology, reach out to Yogesh!

Yogesh Goyal@goyallab.bsky.social · 11mo ago

**POSTDOC POSITION** My lab (www.goyallab.org) at Northwestern and CZ Biohub Chicago looking for a postdoctoc in quantitative biology. We work on a range of topics, including single-cell cancer plasticity, modeling single-cell perturbations, theory, and stem-embryo models. contact via email. Pls RT

**POSTDOC POSITION** My lab (www.goyallab.org) at Northwestern and CZ Biohub Chicago looking for a postdoctoc in quantitative biology. We work on a range of topics, including single-cell cancer plasticity, modeling single-cell perturbations, theory, and stem-embryo models. contact via email. Pls RT

Goyal Lab

goyallab.org