Michele Ceccarelli

MiDNE a tool for multi-omics genes and drugs interactions discovery The availability of models representing molecular interactions in complex pathologies is essential for understanding their molecular setup and identif…

www.sciencedirect.com/science/arti...

Big, beautiful trees!!

SMART-PTA for whole-genome+transcriptome on thousand of single cells from the normal human esophagus 🤯 Massively scaling up the power of scWGS to build deep phylogenies and chart somatic evolution from birth throughout life.

www.biorxiv.org/content/10.1...

#TransposableElements and Homotypic Niches Drive Immune Dynamics and Resistance in #Melanoma Epigenetic-based #immunotherapy
www.biorxiv.org/content/10.1...

Restraint of cancer cell plasticity by spatial homotypic clustering Migliozzi et al. use single-cell resolution spatial transcriptomics of 16 glioblastoma and 2.8 million cells to study tumor architecture. They discover that cell state coherence is maximal in cells or...

Restraint of cancer cell plasticity by spatial homotypic clustering
www.cell.com/cancer-cell/...

Integrated multi-omics profiling reveals the role of the DNA methylation landscape in shaping biological heterogeneity and clinical behaviour of metastatic melanoma.
doi.org/10.1186/s130...

Decoding Plasticity Regulators and Transition Trajectories in Glioblastoma with Single-cell Multiomics Glioblastoma (GB) is one of the most lethal human cancers, marked by profound intratumoral heterogeneity and near-universal treatment resistance. Cellular plasticity, the capacity of cancer cells to t...

Two massive glioblastoma papers, datasets, trajectories, insights, and.. a very cool new method for GRN inference - scDORI -from @steglelab.bsky.social @oliverstegle.bsky.social @bayraktarlab.bsky.social & Moritz Mall www.biorxiv.org/content/10.1... www.biorxiv.org/content/10.1...

Announcing : The 2nd International Summer School on Mathematical Aspects of Data Science
mathsdata2025.github.io
EPFL, Sept 1–5, 2025

Speakers:
Bach @bachfrancis.bsky.social
Bandeira
Mallat
Montanari
Peyré @gabrielpeyre.bsky.social

For PhD students & early-career researchers
Apply before May 15!

The talks from the Post-Bayes workshop are now available online here - youtube.com/playlist?lis... - do take a look!

🚨 New preprint: Topography Aware Optimal Transport for Alignment of Spatial Omics Data

We present our new alignment framework TOAST www.biorxiv.org/content/10.1...

Application deadline for our @wellcometrust.bsky.social #CancerEvolution summer school is tomorrow, 1 April 2025.

coursesandconferences.wellcomeconnectingscience.org/event/evolut...

Our brilliant faculty will cover evo&eco theory, math models, genomics, digital path, clinical trial design & more

Computational analysis of DNA methylation from long-read sequencing - Nature Reviews Genetics Long-read sequencing technologies can directly profile methylation modifications across the genome. In this Review, Fu et al. overview the long-read computational tools to identify and compare methyla...

Computational analysis of DNA methylation from long-read sequencing go.nature.com/3RqrPlc #Review by @yileifu.bsky.social, @timp0.bsky.social & @sedlazeck.bsky.social @bcmhouston.bsky.social @jhu.edu

rdcu.be/efuxT
A detailed guide to assessing #genome-assembly based on #long-read sequencing data using Inspector. @natprot.bsky.social

Comprehensive Profiling of Computational Techniques for Sequencing-Based HLA #ImmuneSignatures Extraction
doi.org/10.1111/tan....

Integrated #multi-omics profiling reveals the role of the DNA methylation landscape in shaping biological heterogeneity and clinical behaviour of metastatic #melanoma
www.biorxiv.org/content/10.1...

Had a terrific time collaborating with Wei Zheng, Sisi Sarkizova (Moderna) and Michele Ceccarelli (Sylvester Cancer Center) for a review on mRNA-based neoantigen-directed cancer immunotherapy (now published in JITC) https://jitc.bmj.com/content/13/1/e010569

Leveraging #mRNA technology for antigen based #immuno-oncology therapies. doi.org/10.1136/jitc...

Method of moments framework for differential expression analysis of single-cell RNA sequencing data: Cell
www.cell.com/cell/fullte...

Only a subset of patients respond to immunotherapy

Why? Which ones?

We conducted an unbiased analysis of response biomarkers and found that hundreds of possible biomarkers collapse into five latent, orthogonal factors that underlie immunotherapy response.

www.nature.com/articles/s41...

I never tire of seeing these progressively improved pediatric ALL survival curves, which represent one of the most remarkable achievements in all of medicine.

Amazing to see even more improvement with bispecific antibody #immunotherapy presented in the #ASH24 Plenary session. #hematology #leukemia

39 cyclic readout with 39 sets of reporters. Because each reporter set contains 4 reporters with 4 different fluorophores (B,G,Y,R), 156 unique reporters are used to bind to the different reporter-landing domains on ISH probes

Deconvolution of omics data in Python with Deconomix -- cellular compositions, cell-type specific gene regulation, and background contributions https://www.biorxiv.org/content/10.1101/2024.11.28.625894v1 Gene expression profiles of heterogeneous bulk samples contain signals from multiple cell population

Deconvolution of omics data in Python with Deconomix -- cellular compositions, cell-type specific gene regulation, and background contributions https://www.biorxiv.org/content/10.1101/2024.11.28.625894v1

YouTube video by Sebastian Raschka Building LLMs from the Ground Up: A 3-hour Coding Workshop

If you find yourself with too much free time over the (long) weekend / holidays, I have ~3h Building an LLM from the Ground Up workshop on YouTube that may come in handy: m.youtube.com/watch?v=quh7...

1/23 Big news for the #ObenaufLab! So excited to finally share our new study providing another puzzle piece, why immunotherapy fails in many tumors, now out in @Nature 🧵👇 www.nature.com/articles/s41...

My deep learning course at the University of Geneva is available on-line. 1000+ slides, ~20h of screen-casts. Full of examples in PyTorch.

fleuret.org/dlc/

And my "Little Book of Deep Learning" is available as a phone-formatted pdf (nearing 700k downloads!)

fleuret.org/lbdl/

Doing good science is 90% finding a science buddy to constantly talk to about the project.

Gliocidin is a nicotinamide-mimetic prodrug that targets glioblastoma - Nature The prodrug gliocidin effectively kills glioblastoma cells by targeting de novo purine synthesis, improving survival in mouse models.

Right on time to discuss at #SNO2024: Gliocidin is a nicotinamide-mimetic prodrug that targets glioblastoma. www.nature.com/articles/s41...

Encouraging data for a neoantigen vaccine vs triple-negative breast cancer, revving up the immune system with favorable outcomes compared with historic controls (Phase 1 trial)
genomemedicine.biomedcentral.com/articles/10....

Interested in #singlecell and #spatial #metabolomics? Then book your calendar for December 10th! – Our online, free event will summarize major achievements of the field in 2024. #metabolism #omics #MALDI #EPFL With Giovanni D'Angelo and our #PhD students we prepared for you a fantastic lineup. 🧵 1/5

If you don’t feel stupid doing science, you’re not trying hard enough.