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)

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!

**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

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...

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!

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

@jengreitz.bsky.social l & my lab want to co-hire a computational biologist/biostatistician with project management expertise to help map the regulatory code of the human genome and discover genetic mechanisms of disease. Details below careersearch.stanford.edu/jobs/computa... Plz RT

Good ideas come from having lots of experience. And experience comes from having lots of bad ideas.

New from the lab led by @natrigg.bsky.social. We started by characterizing mRNA in sperm, EVs, and the epithelium across epididymal transit. This revealed evidence that sperm acquire specific mRNAs through fusion with epididymal EVs, which we further established with in vitro co-incubation assays

Nice writeup by Stas capturing Benny Shilo, who passed away untimely. To me as a young graduate student and to others in our lab, Benny was fondly referred to as the “EGFR Uncle.” Benny was kind and I loved how he always had time for young trainees www.sciencedirect.com/science/arti...

QUESTION: What are the best ways currently to integrate scRNAseq samples (same cell line, drug treated vs untreated) for comparitive analysis? We are aware of scTransfrom, scanorama, harmony, scVI. Any suggestions would be great!

Latest on Waddington Landscapes: Computational methods to fit dynamical landscapes directly to single cell data Applied to neural tube patterning shows morphogen-signalling landscapes can be linearly interpolated Connects interpretable landscape models with data www.biorxiv.org/content/10.1...

Job Alert: A stealth startup focused on non-cancer diagnostics is keen to hire a deep learning for genomics/bio engineer. I am an advisor for the startup & closely involved. Please see the job description below and get in touch if interested. Plz forward.

I'm excited to announce our new biorxiv preprint, wherein we investigate the evolution of the weirdest genetic locus I've ever seen! Behold the tgr genes of the social amoeba, which mediate self/non-self discrimination during facultative multicellularity 🐅 🧵 1/ www.biorxiv.org/content/10.1...

wrong answers only umap artwork from @biophysben.bsky.social

How challenging is the prediction of transcriptional responses to CRISPR gene perturbations ? A simple model, just scaling RNA correlation vectors, results in accurate predictions for many perturbations. The model is intuitive & grounded in a simple approximation. 1/2

New preprint! We solve a mystery you didn't know existed. Mitotic cells lack new transcription but require ongoing translation. Interphase mRNA half life is only 2-4 hrs. So how do cells arrest in mitosis for hours without depleting their transcriptomes? www.biorxiv.org/content/10.1...

Delighted to have our preprint led by @lvchosen1.bsky.social up: Genetic variation reveals a homeotic long noncoding RNA that modulates human hematopoietic stem cells biorxiv.org/content/10.1... 🧵 below ...

Just noticed a super nice preview of our paper by @ditalialab.bsky.social and Alexandra Hiestand. As always, good editorial experience with @cp-cellsystems.bsky.social www.cell.com/cell-systems...

genomebiology.biomedcentral.com/articles/10.... Quite an indictment of some of the current single cell "virtual cell" foundation models. Even for the relatively mundane applications, cell labeling, batch correction etc, they are poor compared to much simpler & cheaper methods.

Come work at Nature Methods! A dream job. I know from experience 😄

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...

looks useful

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