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David Fischer

@davidsebfischer.bsky.social
1.2K followers 1.1K following 24 posts

I develop mechanistic machine learning tools for single-cell and spatial omics data to understand the regulatory patterns underlying human disease dynamics. ai4biomedicine.org

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David Fischer @davidsebfischer.bsky.social · 26/11/2025
Agentic AI systems are becoming available for use in science – but can we trust them?
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Nature Reviews Genetics @natrevgenet.nature.com · 18/07/2025
Our featured article: Adapting systems biology to address the complexity of human disease in the single-cell era go.nature.com/3XBo6Vh #Review by @davidsebfischer.bsky.social, Martin A. Villanueva, Peter S. Winter & ‪@shaleklab.bsky.social‬ @broadinstitute.org @mit.edu @ragoninstitute.bsky.social
go.nature.com
Adapting systems biology to address the complexity of human disease in the single-cell era - Nature Reviews Genetics
Differences between humans and experimental models create a translational gap that makes it difficult to extrapolate research findings. The authors review systems-focused approaches to identify and co...
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Sten Linnarsson @sten.linnarsson.org · 25/06/2025
A major KI initiative to recruit new assistant professors with outstanding proposals in all areas of medicine, biomedicine and public health. We offer an amazing research environment, great colleagues and generous startup packages. Check it out and get working on your applications! (repost please!)
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David Fischer @davidsebfischer.bsky.social · 06/05/2025
Check out this drone footage of our institute!
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David Fischer @davidsebfischer.bsky.social · 02/05/2025
Cool positions for AI x biology in Belgium!
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David Fischer @davidsebfischer.bsky.social · 13/03/2025
Currently, there's a lot of interest in quantitative models that would help us understand and predict features of the complex cellular systems that underlie human health and disease - think about virtual cells, for example. On can trace some of these ideas back to the early days of systems biology.
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Ty Miller Lab @tymillerlab.bsky.social · 27/02/2025
Proud to share our @nature.com paper, co-led by Chadi El Farran & Charles Couturier under mentorship of Brad Bernstein where we develop a new framework to understand immunomodulatory myeloid cells in #glioma & lay a foundation to develop more effective immunotherapies. www.nature.com/articles/s41...
nature.com
Programs, origins and immunomodulatory functions of myeloid cells in glioma - Nature
A study of myeloid cells in gliomas, a type of brain tumour, used a factor-based computational framework to reveal four immunomodulatory gene-expression programs that are expressed across myeloid cell...
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David Fischer @davidsebfischer.bsky.social · 07/01/2025
Read about self-supervision in models of scRNA-seq data in this deep dive!
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Kristina Ulicna @kristinaulicna.bsky.social · 19/12/2024
Exciting news! 🚀 The Learning Meaningful Representations of Life ( #LMRL 🌟) workshop is returning at #ICLR2025! 🎉 On 27th / 28th April 2025 in Singapore 🇸🇬, this popular event returns with a fresh organizing team 👇 & bold new ideas 🧠 to explore bridging AI & life sciences 🧬
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Anshul Kundaje @anshulkundaje.bsky.social · 25/12/2024
Our ChromBPNet preprint out! www.biorxiv.org/content/10.1... Huge congrats to Anusri! This was quite a slog (for both of us) but we r very proud of this one! It is a long read but worth it IMHO. Methods r in the supp. materials. Bluetorial coming soon below 1/
biorxiv.org
ChromBPNet: bias factorized, base-resolution deep learning models of chromatin accessibility reveal cis-regulatory sequence syntax, transcription factor footprints and regulatory variants
Despite extensive mapping of cis-regulatory elements (cREs) across cellular contexts with chromatin accessibility assays, the sequence syntax and genetic variants that regulate transcription factor (T...
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David Fischer @davidsebfischer.bsky.social · 19/12/2024
What cellular & multicellular changes underpin aging of ovaries? We used spatial transcriptomics to study this process in mice, capturing dynamic changes in cells, follicles, and tissue across the estrous cycle. Read about the age-related changes in these dynamics we discovered!
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Rita Strack @ritastrack.bsky.social · 06/12/2024
I could not be more thrilled to announce the Nature Methods @naturemethods.bsky.social Method of the Year is Spatial Proteomics! Please see our editorial as a roadmap to the fantastic content in this special issue! www.nature.com/articles/s41...
nature.com
Method of the Year 2024: spatial proteomics - Nature Methods
Approaches for profiling the spatial proteome in tissues are the basis of atlas-scale projects that are delivering on their promise for understanding biological complexity in health and disease.
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Leander @le-and-er.bsky.social · 21/11/2024
Super excited to share our Human Neural Organoid Atlas, now out in Nature! Led by @zhisonghe.bsky.social @josch1.bsky.social, and myself, this resource was created from 36 scRNA-seq datasets—totalling over 1.7 million cells! 🔬✨
 www.nature.com/articles/s41...
 Find out how it can serve you ⏬
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nature.com
An integrated transcriptomic cell atlas of human neural organoids - Nature
A human neural organoid cell atlas integrating 36 single-cell transcriptomic datasets shows cell types and states and estimates transcriptomic similarity between primary and organoid counterparts, sho...
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Kevin K. Yang 楊凱筌 @kevinkaichuang.bsky.social · 20/11/2024
I think Pack 2 is up to 135/150 now, so between the two you can follow 285 bioml researchers in about 4 clicks!
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David Fischer @davidsebfischer.bsky.social · 20/11/2024
To expedite the development of a network focussed on single-cell and spatial genomics on this platform, I started to collect accounts of scientists & groups that are broadly active in these fields. This is work in progress, DM if you want to be added or have suggestions! go.bsky.app/HZTJxbZ
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Jacob Schreiber @jmschreiber91.bsky.social · 18/11/2024
My goal is to understand the regulatory role of every nucleotide in the genome, and how this changes across every cell in the human body. If you are interested in doing a Ph.D. with me at UMass Chan Medical (Genomics and Comp Bio Department), see the links below. Deadline is Dec 1st.
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Kevin K. Yang 楊凱筌 @kevinkaichuang.bsky.social · 18/11/2024
Two BioML starter packs now: Pack 1: go.bsky.app/2VWBcCd Pack 2: go.bsky.app/Bw84Hmc DM if you want to be included (or nominate people who should be!)
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Andre Rendeiro @andre-rendeiro.com · 16/11/2024
What if we could look at a human tissue image🔬and quantify its biological age?🧬 And how could we get the same insights without collecting the tissue sample? In our new @biorxivpreprint, we create "tissue clocks" ⏳to do just that! www.biorxiv.org/content/10.1... 📝 #aging #tissue thread below⬇️
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