Lightnews — Scholar-powered news

Reposted by Yuanhua Huang

PHD Comics @phdcomics.com · 1d

Study for life

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Reposted by Yuanhua Huang

Denis Wirtz @deniswirtz.bsky.social · 9d

We have developed a new workflow to map whole human organs in 3D & at single-cell resolution

Colleague Prof. Luciane Kagohara mapped out the transcriptomic profile + aneuploidy of ovarian precancerous lesions (STIC) in healthy fallopian tube.

More here: www.biorxiv.org/content/10.1...

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Reposted by Yuanhua Huang

HKU School of Biomedical Sciences @hkusbms.bsky.social · 11d

Enjoy feature stories about the revamped BBiomedSc programme in the academic year 2025/26, as well as the Croucher Summer Course – Precision Genome Engineering; and check out the research highlight contributed by Dr. Yan Xue!

online.flippingbook.com/view/7447824...

HKU SBMS Newsletter Issue 21

This interactive flipbook is created with FlippingBook, a service for streaming PDFs online. No download, no waiting. Open and start reading right away!

online.flippingbook.com

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Reposted by Yuanhua Huang

PennMedCSO @pennmedcso.bsky.social · 15d

Scaling up spatial transcriptomics for large-sized tissues with iSCALE ft. @AmeliaSchroed, Melanie Loth, Chunyu Luo, Sicong Yao, Hanying Yan, Daiwei Zhang & @drmingyaoli.bsky.social (@dbei-upenn.bsky.social) @pennpathlabmed.bsky.social @natmethods.nature.com www.nature.com/articles/s41...

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Reposted by Yuanhua Huang

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 Yuanhua Huang

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 Yuanhua Huang

Stegle Lab @steglelab.bsky.social · Jul 19

This year, our lab has a great representation at the ISMB/ECCB 2025 conference in Liverpool! Every day at the conference, you’ll have the chance to hear at least one talk or explore a poster by one of our incredible lab members.
More details below. 👇

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Yuanhua Huang @yuanhuahuang.bsky.social · Jul 21

It's a pity to miss #ISMBECCB2025 & this exciting event. Just want to share a bit on our recent try with genomic language models for personal gene expression prediction.
bsky.app/profile/yuan...

Yuanhua Huang @yuanhuahuang.bsky.social · Jul 21

New preprint: A big headache for sequence models is to predict cross-person variability of RNA levels from DNA in zero-shot genes. Our gLM2X-Tower shows the problem remains unsolved, incl Evo2 & AlphaGenome. However, few-shot setting is promising & can be a new focus.
www.biorxiv.org/content/10.1...

Assessing large-scale genomic language models in predicting personal gene expression: promises and limitations

Large-scale genomic language models (gLMs) hold promise for modeling gene regulation, yet their ability to predict personal gene expression remains largely unexplored. We developed a framework, gLM2X-...

www.biorxiv.org

Reposted by Yuanhua Huang

Pablo Meyer @oldbap.bsky.social · Jul 20

ISMB/ECCB 2025:
Join us for the DREAM Challenges session on Monday, 21 July, 14:00 Explore community-driven benchmarking for Foundation Models—run a live experiment for LLMs.
@bowang87.bsky.social @anshulkundaje.bsky.social @cziscience.bsky.social @mariabrbic.bsky.social @juliosaezrod.bsky.social

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Yuanhua Huang @yuanhuahuang.bsky.social · Jul 21

@ShuminLi led the development of the gLM2X-Tower framework and all benchmarking analysis, with computing support from @RuibangLuo!
This work was also used for our Genomic AI hackathon, supported by @hkusbms.bsky.social and @CPOS!
bsky.app/profile/yuan...

Yuanhua Huang @yuanhuahuang.bsky.social · Apr 2

Our full-day mini AI hackathon on genomic language models starts soon: 8.30am-8.30pm! With a whole team, we aim to test how gLMs work for two tasks:
1. SNP2GEX: personal variants to gene expression (unseen individuals & genes);
2. Seq2CellxTF: short regulatory to TF binding (unseen cell & TFs).

Yuanhua Huang @yuanhuahuang.bsky.social · Jul 21

New preprint: A big headache for sequence models is to predict cross-person variability of RNA levels from DNA in zero-shot genes. Our gLM2X-Tower shows the problem remains unsolved, incl Evo2 & AlphaGenome. However, few-shot setting is promising & can be a new focus.
www.biorxiv.org/content/10.1...

Assessing large-scale genomic language models in predicting personal gene expression: promises and limitations

Large-scale genomic language models (gLMs) hold promise for modeling gene regulation, yet their ability to predict personal gene expression remains largely unexplored. We developed a framework, gLM2X-...

www.biorxiv.org

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Reposted by Yuanhua Huang

James Briscoe @jamesbriscoe.bsky.social · Jul 17

Just published: The cis-regulatory logic integrating spatial and temporal patterning in the vertebrate neural tube

A global temporal chromatin program, operating across the CNS, directs binding of specific spatial TFs & hence when/where neurons & glia are born

authors.elsevier.com/sd/article/S...

ScienceDirect.com | Science, health and medical journals, full text articles and books.

authors.elsevier.com

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Reposted by Yuanhua Huang

Nature Biotechnology @natbiotech.nature.com · Jul 16

Topological velocity inference from spatial transcriptomic data go.nature.com/4lyR02w

Topological velocity inference from spatial transcriptomic data - Nature Biotechnology

TopoVelo infers cell differentiation stages and rate parameters of gene expression using spatially coupled differential equations.

go.nature.com

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Reposted by Yuanhua Huang

bioRxiv Bioinfo @biorxiv-bioinfo.bsky.social · Jul 12

CNA detection from spatial transcriptomics using SpaCNA https://www.biorxiv.org/content/10.1101/2025.07.08.663688v1

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Reposted by Yuanhua Huang

James Briscoe @jamesbriscoe.bsky.social · Jul 8

Useful perspective incorporating GRNs & gene modules into theory of evolutionary novelty

Parker & Pennell emphasise gene modules, not individual genes, as fundamental units of phenotypic evolution

Provides a needed evolutionary lens for analysing scRNAseq & cell types

www.cell.com/current-biol...

The cellular substrate of evolutionary novelty

Joseph Parker and Matt Pennell propose gene expression programs — sets of co-expressed transcripts that collectively encode cellular subfunctions — as fundamental entities from which novel organismal ...

www.cell.com

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Reposted by Yuanhua Huang

Rio Sugimura @riosugimura.bsky.social · Jun 27

Received a major funding. We will be recruiting a postdoc soon.
Synthetic immune organ

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Reposted by Yuanhua Huang

Oliver Stegle @oliverstegle.bsky.social · Jun 26

Job alert: Join us for a postdoc in AI in genetics at @EMBL Heidelberg! Great collaboration with @Adrian Cortes @GSK, aiming to develop new tools to elucidate genetic effects using population-scale cohorts and single-cell readouts. Please share!

embl.wd103.myworkdayjobs.com/de-DE/EMBL/d...

Postdoctoral Researcher in Computational Genetics

The research group of Oliver Stegle looks for a postdoctoral researcher to join a collaborative project with GSK with the goal to apply computational methods to investigate the effects of rare variant...

embl.wd103.myworkdayjobs.com

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Reposted by Yuanhua Huang

Tissue Design Lab @HKU @ritolab.bsky.social · Jun 11

🚀🚀 I'm starting my own lab @ HKU ! !
The lab will be investigating how cells build complex tissues — with a focus on tissue boundaries, niche establishment, and many open questions sparked by our recent work on trunk-organoids rdcu.be/eqsho 🫡🫡

Timely TGFβ signalling inhibition induces notochord

Nature - Through analysis of developing chick embryos and in vitro differentiation of embryonic stem cells, a study develops a method to generate a model of the human trunk with a notochord.

rdcu.be

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Reposted by Yuanhua Huang

Rio Sugimura @riosugimura.bsky.social · Jun 8

One day ahead of our Hematology & Immunology Symposium at CUHKMedicine

Kathy Lui and I host impressive speaker lineups
Filipe Pereira, Mingxia Gu, Lizhong Li, @liliyanglab.bsky.social Giulia Adriani, Bin Zhou, Jun Shen, Li Qian, Andras Nagy, Lika Drakhlis, Albert Cheung

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Reposted by Yuanhua Huang

Rio Sugimura @riosugimura.bsky.social · Jun 8

We CTSCB_HK are elated to host Mingxia Gu from UCLA to our invited seminar series on stem cells

Vascularized organoids

Exciting start of the ISSCR week at HK

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Reposted by Yuanhua Huang

HKU School of Biomedical Sciences @hkusbms.bsky.social · May 27

We are delighted to have Dr. Yi-Ping Hsueh as our guest speaker for the recent #HKUSBMS RPG Symposium 2025. Dr. Hsueh discussed her Autism Research in Mouse Models while #SBMS RPG students gave excellent oral presentations and poster presentations. Thank you all for joining us🎉!

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Reposted by Yuanhua Huang

Julio Saez-Rodriguez @juliosaezrod.bsky.social · May 16

join us at ISMB iscb.bsky.social & @dreamchallenges.bsky.social - benchmarking foundation models w. @anshulkundaje.bsky.social @oldbap.bsky.social G. Stolovitzky @bowang87.bsky.social @mariabrbic.bsky.social K. Kalantar, J. Guinney supported by @ebi.embl.org @cziscience.bsky.social Tempus AI

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Reposted by Yuanhua Huang

Stegle Lab @steglelab.bsky.social · May 16

🚨 Impressive PhD work by Manu!

Our new method scDORI decodes plasticity regulators at single-cell multi-omic resolution — scaling to millions of cells and uncovering the regulatory logic driving glioblastoma heterogeneity.

🔍 Dive into the thread below and the preprint for all the insights!

Manu Saraswat @manusaraswat.bsky.social · May 16

🧠 Excited to share my main PhD project! We mapped the regulatory rules governing Glioblastoma plasticity using single-cell multi-omics and deep learning. This work is part of a two-paper series with @bayraktarlab.bsky.social @oliverstegle.bsky.social and @moritzmall.bsky.social, Preprint at end🧵👇

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Reposted by Yuanhua Huang

Omer Ali Bayraktar @bayraktarlab.bsky.social · May 16

Over the past 3 years, we led a fantastic @wellcomeleap.bsky.social collaboration w. @oliverstegle.bsky.social, Behjati, Mall, Mair, @jamesbriscoe.bsky.social & @juliosaezrod.bsky.social labs. We created a massive multiomic atlas & new comp models to discover human GB biology www.gbmspace.org

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