Keerthana Arun

Massively parallel interrogation of the fitness of natural variants in ancient signaling pathways reveals pervasive local adaptation The nature of standing genetic variation remains a central debate in population genetics, with differing perspectives on whether common variants are almost always neutral as suggested by neutral and n...

One of the most exciting works of my career, years in the making. We used high-throughput precision genome editing to test the fitness effects of thousands of natural variants. Our findings challenge the long-held assumption that common variants are inconsequential.

www.biorxiv.org/content/10.1...

Lab’s 1st preprint!

Menstruation is understudied due to societal taboos + a biological challenge: mice (a key system for research + drug discovery) don’t menstruate.

@cagricevrim.bsky.social made menstruating mice + used them to discover early events in menstruation.

He is on the job market!

To a Life in Despair Don't. Don't go to the bridge. Don't wake in your coat in the morning light and carry those stones into the river. Don't find your father's pistol in the attic, hidden in the family albums. Don't. Don't pour the pills into the whiskey, the walls dissolving like your childhood. Don't, just don't choose not to wake. Stay. Just stay. Tell yourself you'll do it tomorrow. You can always walk alone into the darkness. But not yet. Not yet. Not this soon. I don't have a reason to give you. All I have is the morning, and the autumn wind, and the child you once were in the darkness, looking at the new moon through the ruins, saying save me, save me, save me, and the moon looking back with her vacant face saying I promise, I stone- cold promise that the face of utter hopelessness is the face of something just about to change. —Joseph Fasano

I hope this reaches you.

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!

Goyal Lab

**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

Combinatorial BMP4 and activin direct the choice between alternate routes to endoderm in a stem cell model of human gastrulation Inge et al. show that human endoderm originates from two converging developmental routes with distinct dynamics and efficiencies yet similar developmental potential. Combinatorial activin and BMP4 sig...

1/7 Really happy to see my PhD work published in ✨Developmental Cell✨ today! We find human endoderm is specified by two developmental trajectories 🔀, and the choice between alternate routes is dictated by the combinatorial BMP4/Activin signalling. www.cell.com/developmenta...

Excited to share our paper on deciphering the design & control principles of tissue scaling w/ Luisa Arispe! Amazing work by co-first authors Danielle Pi and Jonas Braun. We show *differentiated* endothelial cell proliferate in waves with ultrafast cell cycle time of ~5h
www.cell.com/cell-systems...

Excited to share our latest by my postdoc Ben KS: we use statistical physics & Bayesian inference to model genome-wide perturbation outcomes. Remarkably, perturbation responses are encoded in gene "chatter" even before the perturbation–a fundamental insight with broad implications
shorturl.at/2LHbw

This was a great collaboration with Michael Kosicki @axelvisel.bsky.social and Len

Thanks to Boyang (ex-PD) and Vivian (staff scientist) from my lab who helped train & interpret ChromBPNet models.

Non-canonical enhancers control gene expression and cell fate in human pluripotent stem cells Enhancers are key gene regulatory elements that ensure the precise spatiotemporal execution of developmental gene expression programmes. However recent findings indicate that approaches to identify en...

Delighted & excited to share our latest preprint on non-canonical enhancers in human pluripotent stem cells, the result of a fantastic and fun collaboration with @guenesdoganlab.bsky.social‬:
www.biorxiv.org/content/10.1...

🧵 below

New preprint! We found dynamic signal processing (IFFL) in a single protein, which pulses in response to step inputs. New insights for capability of protein computation + implications for new opto and thermo probes

www.biorxiv.org/content/10.1...

Check out the 🧵 from first author Dennis Huang:

Predictable Engineering of Signal-Dependent Cis-Regulatory Elements

Excited to share my latest work with @joadelas.bsky.social and @jamesbriscoe.bsky.social

Predictable Engineering of Signal-Dependent Cis-Regulatory Elements

www.biorxiv.org/content/10.1...
1/11

Legitmately thrilled to share our latest work, in which @fernpizza.bsky.social solved an experimental challenge in plasmid biology as old as the field: measuring how plasmids compete and evolve within individual cells!

Paper out !!🥳big thanks to all authors @marliesoomen.bsky.social @diego-rt.bsky.social @kaessmannlab.bsky.social @jonathangoeke.bsky.social @lorenzamottes.bsky.social & 'bluesky-less'

Lots of interesting new TE (& genes) biology

Data fully browsable💻 👉 embryo.helmholtz-munich.de/shiny_embryo/

KLF2 maintains lineage fidelity and suppresses CD8 T cell exhaustion during acute LCMV infection Naïve CD8 T cells have the potential to differentiate into a spectrum of functional states during an immune response. How these developmental decisions are made and what mechanisms exist to suppress d...

To read: www.science.org/doi/10.1126/...

Thermodynamic principles link in vitro transcription factor affinities to single-molecule chromatin states in cells The molecular details governing transcription factor (TF) binding and the formation of accessible chromatin are not yet quantitatively understood - including how sequence context modulates affinity, h...

Thermodynamic principles link in vitro transcription factor affinities to singlemolecule chromatin states in cells

www.biorxiv.org/content/10.1...

We share a lot of our ideas, code, datasets (that we spend years sanitizing) early. Often way before we release preprints. We do this so that others can use, build on, improve & even "beat" our approaches. But I want to say a few things about some simple expectations 1/

Enhancer scrambling strategy

We are happy to share our enhancer scramble story, a strategy to create hundreds of stochastic deletions, inversions, and duplications within mammalian gene regulatory regions and associate these new architectures with gene expression levels 🧵
www.biorxiv.org/content/10.1...

E. coli prepares for starvation by dramatically remodeling its proteome in the first hours after loss of nutrients It is widely believed that due to nutrient limitations in natural environments, bacteria spend most of their life in non-growing states. However, very little is known about how bacteria change their p...

What do bacterial cells do when they run out of nutrients? Although most bacterial studies focus on cells in exponentially growing states, in the wild bacteria likely spend most of their time slowly starving to death. 1/n
www.biorxiv.org/content/10.1...

Chromatin-based memory as a self-stabilizing influence on cell identity - Genome Biology Cell types are traditionally thought to be specified and stabilized by gene regulatory networks. Here, we explore how chromatin memory contributes to the specification and stabilization of cell states...

Chromatin-based memory as a self-stabilizing influence on cell identity | Genome Biology

#Chromatin #CellFate #Review

genomebiology.biomedcentral.com/articles/10....

How We Can Stop the Next Viral Pandemic A new combo of climate and habitat crises, along with immune system stress, is driving more bat-borne viruses to afflict us

I don't have access to @janeqiu.bsky.social's article in the January @sciam.bsky.social on how to stop the next pandemic, but I have no doubt it will be excellent, as Jane is one of the most informed journalists around on such questions.
www.scientificamerican.com/article/the-...

How Life Really Works Just as I uncovered a new way to understand life, I got news about my own.

For those of us who are not professional biologists, it can be daunting to hear about transcription factors, signaling pathways and non-coding RNA. But this poignant piece from @philipcball.bsky.social opened my eyes to how deep and essential these ideas truly are. nautil.us/how-life-rea...

Excited to share this perspective from the lab on clarifying cell state definitions and possibilities in cancer therapy resistance!!

A figure with six panels (Fig 1B from: doi:10.1101/2024.12.03.626660). Each panel shows the transition path represented by a bifurcation plot of the response B with respect to input signal S. There are four different tristable transition paths indicated by whether or not the intermediate state is accessible, and two bistable transition paths.

Transition paths across the EMT landscape are dictated by network logic.

A 🧵 on the perils of ignoring logic in ODE models of gene regulatory networks (GRNs)

🌟 also read on if you like: EMT, bifurcations, multistability, or Waddington-esque landscapes

www.biorxiv.org/content/10.1...

A preview on the latest work from @robklose.bsky.social lab where Aleks (Not made the bluesky transition yet) used single molecule approaches to address how Polycomb controls transcription. He found that Polycomb limits the frequency with which a promoter can enter a permissive transcribing state.