@danapeer.bsky.social
Reposted
Meet the keynote speakers for the 2025 scverse conference!
John Marioni, Head of Computation at Genentech Research and Early Development and former head of EBI
🧵
#scverse #scverse2025 #AI #DrugDevelopment #MachineLearning #ComputationalBiology #Biotech #Pharma #Genentech
John Marioni, Head of Computation at Genentech Research and Early Development and former head of EBI
🧵
#scverse #scverse2025 #AI #DrugDevelopment #MachineLearning #ComputationalBiology #Biotech #Pharma #Genentech
October 30, 2025 at 3:18 PM
Meet the keynote speakers for the 2025 scverse conference!
John Marioni, Head of Computation at Genentech Research and Early Development and former head of EBI
🧵
#scverse #scverse2025 #AI #DrugDevelopment #MachineLearning #ComputationalBiology #Biotech #Pharma #Genentech
John Marioni, Head of Computation at Genentech Research and Early Development and former head of EBI
🧵
#scverse #scverse2025 #AI #DrugDevelopment #MachineLearning #ComputationalBiology #Biotech #Pharma #Genentech
Reposted
@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
A great read for anyone interested in perturbations and cell-fate decisions. Top notch work.
Our paper is now out in final form at Nature Genetics! For those who missed the preprint, we used large-scale Perturb-seq targeting transcription factors to push primary fibroblasts into diverse transcriptional states, including those observed in cell atlas studies.
August 6, 2025 at 4:59 PM
A great read for anyone interested in perturbations and cell-fate decisions. Top notch work.
Reposted
New paper from @elhamazizi.bsky.social, @bleilab.bsky.social & @danapeer.bsky.social labs: Decipher, a deep generative model to track disease trajectories in single-cell data.
📖 Read: bit.ly/4mufVnZ @columbiaseas.bsky.social @columbiacancer.bsky.social @mskcancercenter.bsky.social
📖 Read: bit.ly/4mufVnZ @columbiaseas.bsky.social @columbiacancer.bsky.social @mskcancercenter.bsky.social
Joint representation and visualization of derailed cell states with Decipher - Genome Biology
Biological insights often depend on comparing conditions such as disease and health. Yet, we lack effective computational tools for integrating single-cell genomics data across conditions or character...
bit.ly
August 5, 2025 at 4:11 PM
New paper from @elhamazizi.bsky.social, @bleilab.bsky.social & @danapeer.bsky.social labs: Decipher, a deep generative model to track disease trajectories in single-cell data.
📖 Read: bit.ly/4mufVnZ @columbiaseas.bsky.social @columbiacancer.bsky.social @mskcancercenter.bsky.social
📖 Read: bit.ly/4mufVnZ @columbiaseas.bsky.social @columbiacancer.bsky.social @mskcancercenter.bsky.social
Reposted
Excited to share our paper on deciphering the design & control principles of tissue scaling w/ Luisa Arispe! Amazing work by co-first authors Danielle Pi and Jonas Braun. We show *differentiated* endothelial cell proliferate in waves with ultrafast cell cycle time of ~5h
www.cell.com/cell-systems...
www.cell.com/cell-systems...
July 7, 2025 at 5:27 PM
Excited to share our paper on deciphering the design & control principles of tissue scaling w/ Luisa Arispe! Amazing work by co-first authors Danielle Pi and Jonas Braun. We show *differentiated* endothelial cell proliferate in waves with ultrafast cell cycle time of ~5h
www.cell.com/cell-systems...
www.cell.com/cell-systems...
This is brilliant!
New in @natbiotech.nature.com: a team led by scientists at MSK and University of Toronto have developed a new platform to facilitate the study of RNA-biding proteins (RBPs) across hundreds of species of plants, insects, and animals.
A resource of RNA-binding protein motifs across eukaryotes reveals evolutionary dynamics and gene-regulatory function - Nature Biotechnology
RNA-binding motifs in eukaryotic proteins are presented in a comprehensive resource.
www.nature.com
July 28, 2025 at 10:38 PM
This is brilliant!
Again I would like to thank the Pezcoller Foundation for inviting me to the 36th Pezcoller Symposium in beautiful Trento. They were warm, pampering and wonderful hosts and science was top notch and delightful. I had fabulous time!
July 28, 2025 at 5:13 PM
Again I would like to thank the Pezcoller Foundation for inviting me to the 36th Pezcoller Symposium in beautiful Trento. They were warm, pampering and wonderful hosts and science was top notch and delightful. I had fabulous time!
A huge congratulations to my better half, Itsik Pe'er, @iscb.bsky.social
July 21, 2025 at 11:54 PM
A huge congratulations to my better half, Itsik Pe'er, @iscb.bsky.social
This is a great tool!
@elihei.bsky.social is gonna present our new tool segger, developed in collaboration with Moritz Gerstung and @danapeer.bsky.social, for fast and accurate segmentation of spatial transcriptomics using attention-based graph neural networks. #MLCSB
📅 July 22 | 🕑 15:50 | 📍 Room 01A
📅 July 22 | 🕑 15:50 | 📍 Room 01A
July 20, 2025 at 1:36 PM
This is a great tool!
Reposted
And just like that @katharinaweins.bsky.social and Elvira Isenring managed to make us look cooler than we'll ever be:
www.youtube.com/watch?v=8t8R...
www.youtube.com/watch?v=8t8R...
Bioimaging | UZH Research Spotlight
YouTube video by Universität Zürich
www.youtube.com
June 24, 2025 at 5:39 PM
And just like that @katharinaweins.bsky.social and Elvira Isenring managed to make us look cooler than we'll ever be:
www.youtube.com/watch?v=8t8R...
www.youtube.com/watch?v=8t8R...
The line up for this conference is amazing and I am really looking forward to all the talks and discussions tomorrow!
Computational Approaches to Mapping Cells, Tissues, and Tumor Progression: Where Does AI Help? #AACRFellows Dana Pe’er addressed this question in a keynote lecture to open the AACR Special Conference on Artificial Intelligence and Machine Learning. #AACRai25
July 11, 2025 at 2:25 AM
The line up for this conference is amazing and I am really looking forward to all the talks and discussions tomorrow!
Reposted
Deadline in 9 days - apply now!
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
July 4, 2025 at 9:36 AM
Deadline in 9 days - apply now!
Reposted
For ESIs dealing with grants being rescinded: if an investigator’s 1st substantial independent research award is terminated within the first 3 years of the project period (not due to scientific misconduct ) they can request the reinstatement of ESI status
grants.nih.gov/news-events/...
grants.nih.gov/news-events/...
July 2, 2025 at 7:27 PM
For ESIs dealing with grants being rescinded: if an investigator’s 1st substantial independent research award is terminated within the first 3 years of the project period (not due to scientific misconduct ) they can request the reinstatement of ESI status
grants.nih.gov/news-events/...
grants.nih.gov/news-events/...
I am thrilled to share with the world a new preprint, spearheaded by the truly amazing Jose Reyes in partnership with the Lowe lab. The paper sheds light on benign to malignant transition in PDAC, uncovering roles of plasticity, tissue remodeling and P53. -> www.biorxiv.org/content/10.1...
Oncogenic and tumor-suppressive forces converge on a progenitor-orchestrated niche to shape early tumorigenesis
The transition from benign to malignant growth is a pivotal yet poorly understood step in cancer progression that marks the shift from a pathologically inert condition to a clinically lethal disease. ...
www.biorxiv.org
July 3, 2025 at 1:12 PM
I am thrilled to share with the world a new preprint, spearheaded by the truly amazing Jose Reyes in partnership with the Lowe lab. The paper sheds light on benign to malignant transition in PDAC, uncovering roles of plasticity, tissue remodeling and P53. -> www.biorxiv.org/content/10.1...
I am so honored to be an awardee from a foundation that recognizes and funds innovation. I wish more foundations shared the Mark foundations vision. Also, the Pezcoller meeting was so fantastic this year, we were hardly the only highlights.
Of course, hearing from our awardees is always a highlight! Today’s presenters included Endeavor Award team member @danapeer.bsky.social, who discussed tissue architecture, and Emerging Leader Award winner
@vanallenlab.bsky.social, who shared his work using AI to enhance precision cancer medicine.
@vanallenlab.bsky.social, who shared his work using AI to enhance precision cancer medicine.
June 27, 2025 at 1:58 PM
I am so honored to be an awardee from a foundation that recognizes and funds innovation. I wish more foundations shared the Mark foundations vision. Also, the Pezcoller meeting was so fantastic this year, we were hardly the only highlights.
Reposted
Please check out our new approach to modeling somatic mutation signatures.
DAMUTA has independent Damage and Misrepair signatures whose activities are more interpretable and more predictive of DNA repair defects, than COSMIC SBS signatures 🧬🖥️🧪
www.biorxiv.org/content/10.1...
DAMUTA has independent Damage and Misrepair signatures whose activities are more interpretable and more predictive of DNA repair defects, than COSMIC SBS signatures 🧬🖥️🧪
www.biorxiv.org/content/10.1...
Damage and Misrepair Signatures: Compact Representations of Pan-cancer Mutational Processes
Mutational signatures of single-base substitutions (SBSs) characterize somatic mutation processes which contribute to cancer development and progression. However, current mutational signatures do not ...
www.biorxiv.org
June 3, 2025 at 12:34 AM
Please check out our new approach to modeling somatic mutation signatures.
DAMUTA has independent Damage and Misrepair signatures whose activities are more interpretable and more predictive of DNA repair defects, than COSMIC SBS signatures 🧬🖥️🧪
www.biorxiv.org/content/10.1...
DAMUTA has independent Damage and Misrepair signatures whose activities are more interpretable and more predictive of DNA repair defects, than COSMIC SBS signatures 🧬🖥️🧪
www.biorxiv.org/content/10.1...
The Single-cell Analytics Innovation Lab
@mskcancercenter.bsky.social is expanding and looking for ML-oriented computational biologists. Join our team based in NYC to work on cutting-edge single-cell & spatial transcriptomics methods in collaboration with leading research labs. bit.ly/4lTEr2t
@mskcancercenter.bsky.social is expanding and looking for ML-oriented computational biologists. Join our team based in NYC to work on cutting-edge single-cell & spatial transcriptomics methods in collaboration with leading research labs. bit.ly/4lTEr2t
Computational Biologist (Single-cell Genomics / ML) – Single-cell Analytics Innovation LabChaligne Lab Website
bit.ly
May 26, 2025 at 3:13 PM
The Single-cell Analytics Innovation Lab
@mskcancercenter.bsky.social is expanding and looking for ML-oriented computational biologists. Join our team based in NYC to work on cutting-edge single-cell & spatial transcriptomics methods in collaboration with leading research labs. bit.ly/4lTEr2t
@mskcancercenter.bsky.social is expanding and looking for ML-oriented computational biologists. Join our team based in NYC to work on cutting-edge single-cell & spatial transcriptomics methods in collaboration with leading research labs. bit.ly/4lTEr2t
Reposted
David Liu @harvard.edu beautifully articulates the criticality of basic science funding for developing revolutionary therapeutics like life-saving base editors 👏
youtu.be/8YhJM6zxYDw?...
youtu.be/8YhJM6zxYDw?...
Breakthrough Prize-Winning Biochemist on the Deadly Cost of Funding Cuts | Amanpour and Company
YouTube video by Amanpour and Company
youtu.be
May 24, 2025 at 1:13 AM
David Liu @harvard.edu beautifully articulates the criticality of basic science funding for developing revolutionary therapeutics like life-saving base editors 👏
youtu.be/8YhJM6zxYDw?...
youtu.be/8YhJM6zxYDw?...
Reposted
🧠 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 10:05 AM
🧠 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🧵👇
Reposted
🚨 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
How does tumour heterogeneity arise? How can we predict cancer cell plasticity? In 2 new studies, we trace #glioblastoma heterogeneity to a spatial cancer cell trajectory w. multimodal cell atlassing bit.ly/4mkrWgs & predict plasticity w. snRNA/ATAC+deep learning bit.ly/3FbI6Ic 🧵
May 16, 2025 at 11:44 AM
How does tumour heterogeneity arise? How can we predict cancer cell plasticity? In 2 new studies, we trace #glioblastoma heterogeneity to a spatial cancer cell trajectory w. multimodal cell atlassing bit.ly/4mkrWgs & predict plasticity w. snRNA/ATAC+deep learning bit.ly/3FbI6Ic 🧵
I am pleased to share our recent publication, fruit of a wonderful collaboration with truly amazing colleagues @adrienneboire.bsky.social and @meningojan.bsky.social, whose work was a tour de force demonstrating that immunology in the brain is a different beast -> www.nature.com/articles/s41...
Interferon-γ orchestrates leptomeningeal anti-tumour response - Nature
Independent of antigen presentation, migratory CCR7+ dendritic cells orchestrate the influx, proliferation and cytotoxic action of natural killer cells to control cancer cell growth in the leptomening...
www.nature.com
May 14, 2025 at 3:52 PM
I am pleased to share our recent publication, fruit of a wonderful collaboration with truly amazing colleagues @adrienneboire.bsky.social and @meningojan.bsky.social, whose work was a tour de force demonstrating that immunology in the brain is a different beast -> www.nature.com/articles/s41...
Basic science matters!
I am so very proud of our collective work, and of our message: understanding fundamental biology is essential to the understanding of human disease. Basic science matters!
May 14, 2025 at 3:39 PM
Basic science matters!
This collaboration was a true pleasure, with great scientists and wonderful people, leading to amazing science
I am delighted to share that our work focused on anti-tumor immunity in the leptomeningeal space was published today:
www.nature.com/articles/s41...
@meningojan.bsky.social
www.nature.com/articles/s41...
@meningojan.bsky.social
May 14, 2025 at 3:39 PM
This collaboration was a true pleasure, with great scientists and wonderful people, leading to amazing science
Reposted
Delighted to share our latest work deciphering the landscape of chromatin accessibility and modeling the DNA sequence syntax rules underlying gene regulation during human fetal development! www.biorxiv.org/content/10.1... Read on for more: 🧵 1/16 #GeneReg 🧬🖥️
Dissecting regulatory syntax in human development with scalable multiomics and deep learning
Transcription factors (TFs) establish cell identity during development by binding regulatory DNA in a sequence-specific manner, often promoting local chromatin accessibility, and regulating gene expre...
www.biorxiv.org
May 3, 2025 at 6:27 PM
Delighted to share our latest work deciphering the landscape of chromatin accessibility and modeling the DNA sequence syntax rules underlying gene regulation during human fetal development! www.biorxiv.org/content/10.1... Read on for more: 🧵 1/16 #GeneReg 🧬🖥️