Yuanhua Huang
@yuanhuahuang.bsky.social
At the junction between data science and cell biomedicine
Reposted by Yuanhua Huang
Are you using any of our factor models, such as MOFA? 🛵
You might’ve found it challenging to tailor them to your specific use cases - not anymore!
Introducing MOFA-FLEX: a flexible, modular factor analysis framework designed for customizable modeling across diverse multi-omics data scenarios. 1/n
You might’ve found it challenging to tailor them to your specific use cases - not anymore!
Introducing MOFA-FLEX: a flexible, modular factor analysis framework designed for customizable modeling across diverse multi-omics data scenarios. 1/n
November 7, 2025 at 10:29 AM
Are you using any of our factor models, such as MOFA? 🛵
You might’ve found it challenging to tailor them to your specific use cases - not anymore!
Introducing MOFA-FLEX: a flexible, modular factor analysis framework designed for customizable modeling across diverse multi-omics data scenarios. 1/n
You might’ve found it challenging to tailor them to your specific use cases - not anymore!
Introducing MOFA-FLEX: a flexible, modular factor analysis framework designed for customizable modeling across diverse multi-omics data scenarios. 1/n
Reposted by Yuanhua Huang
Reposted by Yuanhua Huang
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...
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...
October 2, 2025 at 2:37 PM
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...
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...
Reposted by Yuanhua Huang
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...
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
September 30, 2025 at 9:23 AM
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...
online.flippingbook.com/view/7447824...
Reposted by Yuanhua Huang
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...
September 25, 2025 at 4:49 PM
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...
Reposted by Yuanhua Huang
@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
Details below
careersearch.stanford.edu/jobs/computa...
Plz RT
August 19, 2025 at 12:29 AM
@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
Details below
careersearch.stanford.edu/jobs/computa...
Plz RT
Reposted by Yuanhua Huang
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...
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
August 14, 2025 at 7:53 AM
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...
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...
Reposted by Yuanhua Huang
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. 👇
More details below. 👇
July 19, 2025 at 5:33 PM
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. 👇
More details below. 👇
Reposted by Yuanhua Huang
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
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
July 20, 2025 at 4:15 PM
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
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
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...
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
July 21, 2025 at 2:23 AM
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...
www.biorxiv.org/content/10.1...
Reposted by Yuanhua Huang
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...
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
July 17, 2025 at 10:07 AM
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...
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...
Reposted by Yuanhua Huang
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
July 16, 2025 at 1:46 PM
Topological velocity inference from spatial transcriptomic data go.nature.com/4lyR02w
Reposted by Yuanhua Huang
CNA detection from spatial transcriptomics using SpaCNA https://www.biorxiv.org/content/10.1101/2025.07.08.663688v1
July 12, 2025 at 7:47 AM
CNA detection from spatial transcriptomics using SpaCNA https://www.biorxiv.org/content/10.1101/2025.07.08.663688v1
Reposted by Yuanhua Huang
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...
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
July 8, 2025 at 9:24 AM
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...
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...
Reposted by Yuanhua Huang
Received a major funding. We will be recruiting a postdoc soon.
Synthetic immune organ
Synthetic immune organ
June 27, 2025 at 3:58 PM
Received a major funding. We will be recruiting a postdoc soon.
Synthetic immune organ
Synthetic immune organ
Reposted by Yuanhua Huang
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...
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
June 26, 2025 at 10:00 AM
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...
embl.wd103.myworkdayjobs.com/de-DE/EMBL/d...
Reposted by Yuanhua Huang
🚀🚀 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 🫡🫡
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
June 11, 2025 at 6:57 AM
🚀🚀 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 🫡🫡
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 🫡🫡
Reposted by Yuanhua Huang
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
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
June 8, 2025 at 11:56 PM
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
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
Reposted by Yuanhua Huang
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
Vascularized organoids
Exciting start of the ISSCR week at HK
June 8, 2025 at 11:57 PM
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
Vascularized organoids
Exciting start of the ISSCR week at HK
Reposted by Yuanhua Huang
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🎉!
May 27, 2025 at 6:50 AM
Reposted by Yuanhua Huang
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
May 16, 2025 at 11:23 AM
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
Reposted by Yuanhua Huang
🚨 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!
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!
🧠 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🧵👇
May 16, 2025 at 11:14 AM
🚨 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!
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!
Reposted by Yuanhua Huang
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
May 16, 2025 at 11:44 AM
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
Reposted by Yuanhua Huang
kathyLui & I host exciting talks of
Blood origin
In vivo lineage tracing
Human embryoid
Vascular organoid
Cardiac organoid
Cardiac Regeneration
Next-gen CAR
Immuno engineering
Immuno reprogramming
Blood origin
In vivo lineage tracing
Human embryoid
Vascular organoid
Cardiac organoid
Cardiac Regeneration
Next-gen CAR
Immuno engineering
Immuno reprogramming
May 14, 2025 at 1:03 AM
kathyLui & I host exciting talks of
Blood origin
In vivo lineage tracing
Human embryoid
Vascular organoid
Cardiac organoid
Cardiac Regeneration
Next-gen CAR
Immuno engineering
Immuno reprogramming
Blood origin
In vivo lineage tracing
Human embryoid
Vascular organoid
Cardiac organoid
Cardiac Regeneration
Next-gen CAR
Immuno engineering
Immuno reprogramming