Reposted by Yuanhua HuangbioRxiv Bioinfo @biorxiv-bioinfo.bsky.social · 29/05/2026TopOmics: Topic Modelling for All Omics www.biorxiv.org/content/10.64898/20… 021
Yuanhua Huang @yuanhuahuang.bsky.social · 30/04/2026Call for full paper at iscbAI 2026; deadline May 22. iscbAI 2026: the 2nd International Symposium on Computational Biology with AI (www.iscb-cn.org.cn/web/64/list....) 📅 Date: August 21st-August 24th , 2026 📍 Location: Bali Island, Indonesia 000
Reposted by Yuanhua HuangHKU School of Biomedical Sciences @hkusbms.bsky.social · 30/12/2025Enjoy Newsletter Issue 22 feature stories and research highlight “Exploring Neuronal Influences on Cancer via CRISPR Screens in Organoids” contributed by Professor Alan Wong at online.flippingbook.com/view/6892878...online.flippingbook.comHKU SBMS Newsletter Issue 22This interactive flipbook is created with FlippingBook, a service for streaming PDFs online. No download, no waiting. Open and start reading right away! 021
Reposted by Yuanhua HuangStegle Lab @steglelab.bsky.social · 19/12/2025We’re excited to announce the "Toward Trustworthy AI Modeling for Computational Healthcare" @elsa-ai.eu workshop, a one-day in-person event focused on building private, fair, robust, reliable, and accountable AI systems for healthcare. Register now. 📅 March 9, 2026 📍 EMBL, Heidelberg, Germany 053
Reposted by Yuanhua HuangRio Sugimura @riosugimura.bsky.social · 22/11/2025We are thrilled to host Human Embryo Biology and Modeling symposium at @hkusbms.bsky.social . Human embryos, stem cell embryos, model organisms, single-cell atlas Nov 26, 2pm-6:30pm Guojun Sheng, @liliulab.bsky.social , Angela Wu, Rio Sugimura, Tiago Rito, Pentao Liu 043
Reposted by Yuanhua HuangStegle Lab @steglelab.bsky.social · 07/11/2025Are 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 13412
Reposted by Yuanhua HuangDenis Wirtz @deniswirtz.bsky.social · 02/10/2025We 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... 0142
Reposted by Yuanhua HuangHKU School of Biomedical Sciences @hkusbms.bsky.social · 30/09/2025Enjoy 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.comHKU SBMS Newsletter Issue 21This interactive flipbook is created with FlippingBook, a service for streaming PDFs online. No download, no waiting. Open and start reading right away! 032
Reposted by Yuanhua HuangAnshul Kundaje @anshulkundaje.bsky.social · 19/08/2025@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 16866
Reposted by Yuanhua HuangJames Briscoe @jamesbriscoe.bsky.social · 14/08/2025Latest 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...biorxiv.orgReconstructing Waddington's Landscape from DataThe 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... 26724
Reposted by Yuanhua HuangStegle Lab @steglelab.bsky.social · 19/07/2025This 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. 👇 174
Reposted by Yuanhua HuangPablo Meyer @oldbap.bsky.social · 20/07/2025ISMB/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 163
Yuanhua Huang @yuanhuahuang.bsky.social · 21/07/2025New 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...biorxiv.orgAssessing large-scale genomic language models in predicting personal gene expression: promises and limitationsLarge-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-... 131
Reposted by Yuanhua HuangJames Briscoe @jamesbriscoe.bsky.social · 17/07/2025Just 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...authors.elsevier.comScienceDirect.com | Science, health and medical journals, full text articles and books. 14923
Reposted by Yuanhua HuangNature Biotechnology @natbiotech.nature.com · 16/07/2025Topological velocity inference from spatial transcriptomic data go.nature.com/4lyR02wgo.nature.comTopological velocity inference from spatial transcriptomic data - Nature BiotechnologyTopoVelo infers cell differentiation stages and rate parameters of gene expression using spatially coupled differential equations. 165
Reposted by Yuanhua HuangbioRxiv Bioinfo @biorxiv-bioinfo.bsky.social · 12/07/2025CNA detection from spatial transcriptomics using SpaCNA www.biorxiv.org/content/10.1101/202… 011
Reposted by Yuanhua HuangJames Briscoe @jamesbriscoe.bsky.social · 08/07/2025Useful 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...cell.comThe cellular substrate of evolutionary noveltyJoseph 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 ... 26020
Reposted by Yuanhua HuangRio Sugimura @riosugimura.bsky.social · 27/06/2025Received a major funding. We will be recruiting a postdoc soon. Synthetic immune organ 021
Reposted by Yuanhua HuangOliver Stegle @oliverstegle.bsky.social · 26/06/2025Job 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.comPostdoctoral Researcher in Computational GeneticsThe 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... 01518
Reposted by Yuanhua HuangTissue Design Lab @HKU @ritolab.bsky.social · 11/06/2025🚀🚀 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 🫡🫡rdcu.beTimely TGFβ signalling inhibition induces notochordNature - 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. 32612
Reposted by Yuanhua HuangRio Sugimura @riosugimura.bsky.social · 09/06/2025One 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 031
Reposted by Yuanhua HuangRio Sugimura @riosugimura.bsky.social · 09/06/2025We 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 152
Reposted by Yuanhua HuangHKU School of Biomedical Sciences @hkusbms.bsky.social · 27/05/2025We 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🎉! 021
Reposted by Yuanhua HuangJulio Saez-Rodriguez @juliosaezrod.bsky.social · 16/05/2025join 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 AIiscb.bsky.socialISCB News (@iscb.bsky.social)Empowering Computational Biology, Transforming Global Science! The International Society for Computational Biology is a scholarly society for advancing understanding of living systems through comput... 01810
Reposted by Yuanhua HuangStegle Lab @steglelab.bsky.social · 16/05/2025🚨 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! 0205
Reposted by Yuanhua HuangOmer Ali Bayraktar @bayraktarlab.bsky.social · 16/05/2025Over 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 1166
Reposted by Yuanhua HuangRio Sugimura @riosugimura.bsky.social · 14/05/2025kathyLui & 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 012
Reposted by Yuanhua HuangAnshul Kundaje @anshulkundaje.bsky.social · 20/04/2025genomebiology.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.genomebiology.biomedcentral.comZero-shot evaluation reveals limitations of single-cell foundation models - Genome BiologyFoundation models such as scGPT and Geneformer have not been rigorously evaluated in a setting where they are used without any further training (i.e., zero-shot). Understanding the performance of mode... 615747
Reposted by Yuanhua HuangHKU School of Biomedical Sciences @hkusbms.bsky.social · 16/04/2025Join us in-person on May 12 for a stimulating KE seminar by #HKU Prof Benjamin Becker on AI-inspired mind reading, brain scans and mental health, hosted by Prof Ralf Jauch @ralfhku.bsky.social. Do stay behind to network. Register today: hku.au1.qualtrics.com/jfe/form/SV_... 032
Yuanhua Huang @yuanhuahuang.bsky.social · 02/04/2025Our 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). 152
Reposted by Yuanhua HuangJason Wong @jwhwong.bsky.social · 27/03/2025Great to finally see LocusMasterTE in print by PhD student, Sojung Lee. We developed a bioinformatics method to leverage long read sequencing data to improve expression quantification of transposable elements genomebiology.biomedcentral.com/articles/10.... #GenomeBiologygenomebiology.biomedcentral.comLocusMasterTE: integrating long-read RNA sequencing improves locus-specific quantification of transposable element expression - Genome BiologyTransposable elements (TEs) can influence human diseases by disrupting genome integrity, yet their quantification has been challenging due to the repetitive nature of these sequences across the genome... 1198
Reposted by Yuanhua HuangStegle Lab @steglelab.bsky.social · 18/03/20251/ New preprint! 🍳 @elihei.bsky.social and our team at @embl.org , @dkfz.bsky.social, and @mskcancercenter.bsky.social built #segger - a fast, accurate cell segmentation tool for spatial transcriptomics that assigns transcripts to their cell origins! doi.org/10.1101/2025... 36422
Reposted by Yuanhua HuangHKU School of Biomedical Sciences @hkusbms.bsky.social · 20/03/2025Three Co-Chairs of the ISSCR Program Committee discussed the upcoming #ISSCR2025 meeting in #HK on The Stem Cell Podcast, and #HKUSBMS Prof. Kathryn Cheah emphasised the importance of international participation and diversity among speakers and attendees. Take a listen. 031
Reposted by Yuanhua HuangHuman Cell Atlas @humancellatlas.org · 20/12/2024Super to see this work on the Asian Immune Diversity Atlas featured on the December Nature Genetic cover and part of the @natureportfolio.bsky.social HCA 2024 Collection. Congratulations to everyone involved in this analysis of blood cells from people with diverse Asian ancestries.buff.lyNature Genetics - An Asian Immune Diversity AtlasAnalysis of single-cell RNA sequencing data from peripheral blood of 474 individuals of diverse Asian ancestries links cell-type-specific splicing variation... 096
Reposted by Yuanhua HuangbioRxiv Bioinfo @biorxiv-bioinfo.bsky.social · 17/03/2025Segger: Fast and accurate cell segmentation of imaging-based spatial transcriptomics data www.biorxiv.org/content/10.1101/202… 011
Yuanhua Huang @yuanhuahuang.bsky.social · 18/03/2025Excellent example of how alternative transcription start site usage links to cancer types: see the detailed study below about this HERV gene ERVK-7 and its cell type-specific TSS regulations! Well done Jason and team. 010
