Yogesh Goyal
@goyallab.bsky.social
Single cell systems and synthetic biology lab at Northwestern University and Chan Zuckerberg Biohub Chicago.
https://www.goyallab.org/
https://www.goyallab.org/
Reposted by Yogesh Goyal
New online! Revisiting the molecular workhorse: plasmids in evolutionary conflict
Revisiting the molecular workhorse: plasmids in evolutionary conflict
Nature Reviews Genetics, Published online: 04 February 2026; doi:10.1038/s41576-026-00942-6Campbell and Goyal discuss a recent study by Rossine et al., which introduces a synthetic plasmid system that experimentally separates within-cell from between-cell selection, revealing multilevel evolutionary conflict and addressing questions first posed by Szathmáry and Smith in 1995.
dlvr.it
February 5, 2026 at 3:32 AM
New online! Revisiting the molecular workhorse: plasmids in evolutionary conflict
Reposted by Yogesh Goyal
Super happy to be associated with this work !!
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...
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...
December 17, 2025 at 5:43 PM
Super happy to be associated with this work !!
Reposted by Yogesh Goyal
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 🤓
So much hard work went into it, but it was well worth it 🤓
Genomic stop codon scanning reveals quantitative principles of nonsense-mediated mRNA decay https://www.biorxiv.org/content/10.64898/2025.12.20.695734v1
December 25, 2025 at 1:19 AM
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 🤓
So much hard work went into it, but it was well worth it 🤓
Reposted by Yogesh Goyal
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
December 17, 2025 at 5:45 PM
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.
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
@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
December 2, 2025 at 6:03 PM
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
@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
Reposted by Yogesh Goyal
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
October 22, 2025 at 3:55 PM
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
Reposted by Yogesh Goyal
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/...
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...
www.science.org
November 20, 2025 at 9:42 PM
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/...
www.science.org/doi/10.1126/...
Reposted by Yogesh Goyal
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! ⬇️
November 23, 2025 at 12:27 AM
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! ⬇️
Reposted by Yogesh Goyal
New preprint! We measured temperature- and pH-induced aggregation for over 18,000 natural and de novo designed protein domains!
November 19, 2025 at 9:16 PM
New preprint! We measured temperature- and pH-induced aggregation for over 18,000 natural and de novo designed protein domains!
Reposted by Yogesh Goyal
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...
November 18, 2025 at 5:49 PM
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...
Reposted by Yogesh Goyal
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
November 18, 2025 at 4:15 PM
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
Reposted by Yogesh Goyal
📢 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
apply.interfolio.com/177622
Suggested deadline: 12/15/2025.
@columbiasysbio.bsky.social
November 15, 2025 at 4:02 AM
📢 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
apply.interfolio.com/177622
Suggested deadline: 12/15/2025.
@columbiasysbio.bsky.social
Reposted by Yogesh Goyal
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
His work bridges engineering and biology to advance understanding of cellular plasticity and fate in development and disease. Learn more: tinyurl.com/2rumf48v
October 14, 2025 at 4:15 PM
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
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 !
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)
October 16, 2025 at 5:30 PM
Exciting opportunity to work with @ianmellis.bsky.social who is an excellent mentor and working on cool stuff !
Reposted by Yogesh Goyal
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.
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...
www.biorxiv.org
October 9, 2025 at 10:59 PM
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.
www.biorxiv.org/content/10.1...
My jaw dropped when I heard this presented earlier this year. Incredible.
Reposted by Yogesh Goyal
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...
September 24, 2025 at 6:36 PM
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...
Reposted by Yogesh Goyal
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)
www.biorxiv.org/content/10.1...
(1/n)
September 22, 2025 at 5:29 AM
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)
www.biorxiv.org/content/10.1...
(1/n)
Reposted by Yogesh Goyal
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...
I know of earlier single-locus papers (1982).
www.sciencedirect.com/science/arti...
September 21, 2025 at 6:54 PM
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...
I know of earlier single-locus papers (1982).
www.sciencedirect.com/science/arti...
Reposted by Yogesh Goyal
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)
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...
www.biorxiv.org
September 20, 2025 at 4:10 PM
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)
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)
Reposted by Yogesh Goyal
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
Apply - Interfolio
{{$ctrl.$state.data.pageTitle}} - Apply - Interfolio
apply.interfolio.com
September 20, 2025 at 12:48 AM
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
Reposted by Yogesh Goyal
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!
**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
www.goyallab.org
September 19, 2025 at 1:17 PM
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!
**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
www.goyallab.org
September 19, 2025 at 10:36 AM
**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
Reposted by Yogesh Goyal
What was antibiotic resistance like before we ever used antibiotics? How did we change what antibiotic resistance genes looked like over 100 years?
Our paper looking at resistance genes from a century of NCTC historical isolates now out in mGen:
www.microbiologyresearch.org/content/jour...
Our paper looking at resistance genes from a century of NCTC historical isolates now out in mGen:
www.microbiologyresearch.org/content/jour...
Genomic resistance in historical clinical isolates increased in frequency and mobility after the age of antibiotics
Antibiotic resistance is frequently observed shortly after the clinical introduction of an antibiotic. Whether and how frequently that resistance occurred before the introduction is harder to determin...
www.microbiologyresearch.org
September 1, 2025 at 5:49 PM
What was antibiotic resistance like before we ever used antibiotics? How did we change what antibiotic resistance genes looked like over 100 years?
Our paper looking at resistance genes from a century of NCTC historical isolates now out in mGen:
www.microbiologyresearch.org/content/jour...
Our paper looking at resistance genes from a century of NCTC historical isolates now out in mGen:
www.microbiologyresearch.org/content/jour...
Reposted by Yogesh Goyal
Priyom's preprint is out on biorxiv. See below for a detailed thread. In a nutshell, she has discovered and characterized the oscillator that times notochord and spine segmentation in zebrafish. Turns out that there are uniform Erk oscillations across the entire tissue that act as timekeepers!
Building a spine is no joke, but thankfully zebrafish have their own clocks to keep the pace. Excited to share our preprint on the role of biological oscillators in coordinating notochord development! (www.biorxiv.org/content/10.1...)
Additional thread below
Additional thread below
September 2, 2025 at 5:34 PM
Priyom's preprint is out on biorxiv. See below for a detailed thread. In a nutshell, she has discovered and characterized the oscillator that times notochord and spine segmentation in zebrafish. Turns out that there are uniform Erk oscillations across the entire tissue that act as timekeepers!
Reposted by Yogesh Goyal
Every few months the "good lab hands" thing comes up and it misses a key point: you can learn to have good hands. Training matters.
Good hands aren't some magic gift from the PCR gods, you have to develop them through directed repetitive practice, like any other skill
Good hands aren't some magic gift from the PCR gods, you have to develop them through directed repetitive practice, like any other skill
September 1, 2025 at 6:04 PM
Every few months the "good lab hands" thing comes up and it misses a key point: you can learn to have good hands. Training matters.
Good hands aren't some magic gift from the PCR gods, you have to develop them through directed repetitive practice, like any other skill
Good hands aren't some magic gift from the PCR gods, you have to develop them through directed repetitive practice, like any other skill