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Reposted by Yogesh Goyal

Rita Strack @ritastrack.bsky.social · 14d

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...

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Reposted by Yogesh Goyal

Yun S. Song @yun-s-song.bsky.social · 16d

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)

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Anders Sejr Hansen @andersshansen.bsky.social · 17d

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...

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Reposted by Yogesh Goyal

Vijay Ramani @vram142.bsky.social · 18d

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...

www.biorxiv.org

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Reposted by Yogesh Goyal

Jaehyuk Choi @jaehyukchoimd.bsky.social · 19d

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

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Reposted by Yogesh Goyal

Ian Mellis @ianmellis.bsky.social · 19d

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 · 19d

**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

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Yogesh Goyal @goyallab.bsky.social · 19d

**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

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Yogesh Goyal @goyallab.bsky.social · 26d

Congrats Anna!

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Reposted by Yogesh Goyal

Michael Baym @baym.lol · Sep 1

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...

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

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Reposted by Yogesh Goyal

Stefano Di Talia @ditalialab.bsky.social · Sep 2

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!

Priyom Adhyapok @priyomadhyapok.bsky.social · Sep 2

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

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Reposted by Yogesh Goyal

Michael Baym @baym.lol · Sep 1

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

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Reposted by Yogesh Goyal

Anshul Kundaje @anshulkundaje.bsky.social · Aug 19

@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

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Reposted by Yogesh Goyal

Itai Yanai @itaiyanai.bsky.social · Aug 25

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

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Reposted by Yogesh Goyal

Colin Conine @colinconine.bsky.social · Aug 23

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

bioRxivpreprint @biorxivpreprint.bsky.social · Aug 22

Epididymal extracellular vesicles harbor and convey mRNA to sperm for transfer to zygotes https://www.biorxiv.org/content/10.1101/2025.08.18.670952v1

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Yogesh Goyal @goyallab.bsky.social · Aug 22

Exciting news!

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Yogesh Goyal @goyallab.bsky.social · Aug 21

I’m so sorry…

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Yogesh Goyal @goyallab.bsky.social · Aug 19

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...

Ben-Zion Shilo (1951–2025)

www.sciencedirect.com

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Yogesh Goyal @goyallab.bsky.social · Aug 19

Batch effects

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Yogesh Goyal @goyallab.bsky.social · Aug 18

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!

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Yogesh Goyal @goyallab.bsky.social · Aug 16

Wooo!! Congrats Mo, super deserving!

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Reposted by Yogesh Goyal

James Briscoe @jamesbriscoe.bsky.social · Aug 14

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...

Reconstructing Waddington's Landscape from Data

The development of a zygote into a functional organism requires that this single progenitor cell gives rise to numerous distinct cell types. Attempts to exhaustively tabulate the interactions within d...

www.biorxiv.org

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Reposted by Yogesh Goyal

Anshul Kundaje @anshulkundaje.bsky.social · Aug 12

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.

Stealth genomics startup focused on non-cancer diagnostic applications

Senior Deep Learning Engineer
• Ph.D. in relevant field with 3+ years practical experience in deep learning for biology
• Demonstrated proficiency in building DL architectures using Pytorch or TensorFlow+Keras.
• Substantial expertise in training lightweight deep learning models and tuning large foundation models.
• Substantial expertise with developing efficient data loaders for large datasets and optimizing training workflows.
• Deep expertise training and deploying models in Cloud-based compute environments and local hardware.
• Sufficient knowledge of the genomics of gene regulation to ask the right questions for the specific information to be gained.
• Expertise in developing models of gene regulation and sequence-to-function models is a plus.
• Interactive team player in highly collaborative small setting. Experience collaborating and communicating with biologists.

Interested candidates can send their CV to anshul @ kundaje . net

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Yogesh Goyal @goyallab.bsky.social · Aug 8

Indeed! Many more to come

Reposted by Yogesh Goyal

Tera Levin @teralevin.bsky.social · Aug 5

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...

Hypermutable hotspot enables the rapid evolution of self/non-self recognition genes in Dictyostelium

Cells require highly polymorphic receptors to perform accurate self/non-self recognition. In the amoeba Dicytostelium discoideum, polymorphic TgrB1 & TgrC1 proteins are used to bind sister cells and e...

www.biorxiv.org

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Yogesh Goyal @goyallab.bsky.social · Aug 2

wrong answers only

umap artwork from @biophysben.bsky.social

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