Weekly reads 13/07/26: From neural memory to microbial manipulation: how sex, epigenetics, and bacteria redefine resilience and disease open.substack.com/pub/behindth... #Epigenetics #CancerResearch #SpatialTranscriptomics #Microbiome #AntibioticResistance

1/ I'm excited to share that we're launching NECB 2026, the inaugural New England Computational Biology Symposium. Oct 1-2 at Microsoft Research New England, Cambridge. Two days of keynotes,talks, and posters to bring our community together across institutions.Space is limited. newenglandcompbio.org

Single cell multiomics unravel the transcription networks controlling the different EMT tumor states www.nature.com/articles/s4...

Beyond proud to share our new paper, out in @natcomms.nature.com, where I'm co-last author 🎉 We mapped the transcription factors that control distinct EMT states in cancer and found some surprising new regulators along the way. 🧵 www.nature.com/articles/s41... (1/20)

Weekly reads 06/07/26: From cell competition to genetic edges: how intercellular interactions redefine disease and discovery open.substack.com/pub/behindth... #CellBiology #Neuroscience #ComputationalBiology #Alzheimers #CancerResearch

Weekly reads 22/6/26 How spatial context, summary statistics, and scalable frameworks are transforming biology open.substack.com/pub/behindth... #SpatialTranscriptomics #SingleCell #ComputationalBiology #DrugDiscovery #Genomics

Weekly reads 15/06/26: From spatial counterfactuals to tumor microbiomes: how context reshapes biology open.substack.com/pub/behindth... #SpatialTranscriptomics #SingleCell #CancerResearch #ComputationalBiology #Microbiome

Weekly reads 8/06/26: The invisible foundations of cancer: early malignancy, epigenetic plasticity, and the tools to see it all open.substack.com/pub/behindth... #CancerResearch #SingleCell #Epigenetics #SpatialOmics #ComputationalBiology

Weekly reads 1/06/26 : Spatial screens, communication maps, and a pancreatic cancer milestone open.substack.com/pub/behindth... #SpatialBiology #SingleCell #CancerResearch #SpatialOmics

Weekly reads 25/05/26: Mapping biology across space, time, and scale with AI-powered discovery open.substack.com/pub/behindth... #CancerResearch #SpatialBiology #SingleCell #ComputationalBiology #SystemsBiology

Weekly reads 18/05/26 : Twin tumors, spatial maps, and stromal rewiring open.substack.com/pub/behindth... #SpatialTranscriptomics #CancerResearch #SingleCell #ComputationalBiology

Weekly reads 11/05/26: How cells communicate, adapt, and age across space and time open.substack.com/pub/behindth... #SpatialOmics #CancerResearch #SingleCell #ComputationalBiology

📢 We are recruiting! We are looking for postdoctoral researchers to join my team at @pasteur.fr (research.pasteur.fr/en/team/mach...). We develop AI methods to infer cellular dynamics and gene regulation. If you are interested, send me an email with your CV. We look forward to hearing from you!

InterScale reveals multi-scale cellular interaction programs in spatial transcriptomics https://www.biorxiv.org/content/10.64898/2026.05.07.723456v1

Weekly reads 04/05/26: Virtual spatial transcriptomes, tumor ecotypes, and the hidden logic of cell communication open.substack.com/pub/behindth... #SpatialTranscriptomics #CancerResearch #SingleCell #ComputationalBiology (1/3)

Weekly reads 27/4/36: Reference-free discovery, spatial resolution, and targeting tumor states open.substack.com/pub/behindth... #SingleCell #SpatialOmics #CancerResearch #ComputationalBiology

Weekly reads 20/4/26: From metastatic clones to synthetic DNA: how cell fate is written and rewritten open.substack.com/pub/behindth... #CancerResearch #SingleCell #SpatialOmics #Immunology #Genomics

Weekly reads 13/04/26: From mutation mapping to mitochondrial therapy: rethinking cell State and resistance open.substack.com/pub/behindth... #CancerResearch #SingleCell #SpatialOmics #PrecisionMedicine

Very proud of this and so cool that enhancer-level models can predict the effect of genetic variation. There is so much personal variation in terms of gene regulation in the human brain, it is fantastic to uncover this thanks to technology (whole-genome sequencing and single-cell multiomics) and AI

What does it take to truly understand #cancer in all of its complexity? Delighted to share our Review in Cell "Cancer ecosystems: A dynamic interplay across scales" with Daniela Quail, where we propose a multi-scale framework connecting tumor ecology with physiology 🧪⚕️ www.cell.com/cell/fulltex...

Excited to share our latest work in Nature. Applying single-molecule and single-cell DNA sequencing methods, we uncover an extraordinary landscape of somatic mutations in immune checkpoint genes in autoimmune B cells, suggesting that somatic mutations may be key to autoimmunity [1/n] rdcu.be/fdqbr

Weekly reads 06/04/26: When cells compete, learn, and communicate open.substack.com/pub/behindth... #SingleCell #CancerResearch #SpatialBiology #ComputationalBiology

Why bioRxiv exhibit 10000001

We launched a new Group Leader vacancy in our Center for AI & Computational Biology - VIB.AI @vibai.bsky.social - with a Professorship at Ghent University. Join us with your most creative AI+Biology research plan! Apply before 31st May vib.ai/en/group-lea...

Weekly reads 30/3/26 : From synthetic genomes to multi-omics cells: integrating and rewriting biology open.substack.com/pub/behindth... #SyntheticBiology #SingleCell #SpatialOmics #Genomics #ComputationalBiology

Join us for a postdoc in AI in human genetics at @embl.org in close collaboration with Adrian Cortes (GSK) and @brianfclarke.bsky.social - exploring the effects of rare variants using population-scale cohorts and single-cell readouts. 🔗 Apply now: embl.wd103.myworkdayjobs.com/en-US/EMBL/d...

We are recruiting! We are searching for an exceptional postdoctoral fellow to lead the single-cell phenoscaping efforts of the REWIRE-CAN Cancer Grand Challenge @cancergrand.bsky.social For more information and to apply please visit: www.ucl.ac.uk/work-at-ucl/...

In my latest column, I explain some of my reasons for being deeply skeptical about AI models that claim to understand DNA, genes, and genomes: stevensalzberg.substack.com/p/ai-is-star...

Weekly reads 23/3/26: Memory, models, and massive data: rethinking cancer across scales open.substack.com/pub/behindth... #CancerResearch #SingleCell #SpatialOmics #ComputationalBiology #SystemsBiology

Weekly reads 16/3/26: Rewiring cancer biology across scales: from 3D genomes to microbial niches open.substack.com/pub/behindth... #CancerResearch #SingleCell #SpatialOmics #Immunology #ComputationalBiology #AI

Weekly reads 9/3/26: How tumors adapt and how new tools are helping us see it open.substack.com/pub/behindth... #Cancer #SingleCell #Immunotherapy #ComputationalBiology

Weekly reads 23/2/26: When context controls cancer: oxygen, space, niches and chromatin open.substack.com/pub/behindth... Cancer isn’t just mutations: it’s metabolism, space, niches, and chromatin. #CancerResearch #SingleCell #SpatialBiology #TumorMicroenvironment #PrecisionOncology

🚨 New paper from our lab just published in Nature🚨 www.nature.com/articles/s41... Discover how 🌱 tumour formation is shaped by tissue context from the very beginning. Cancer is not driven by genetics alone ✨Fantastic team led by Greta Skrupskelyte, Eduardo Rojo, @hariajith.bsky.social

As an alternative to the h-index, I made the Mentorship Index (M-index) to proxy a scientist's contribution to mentoring junior scientists. Ex. M10-index = # last-author publications where the first author had < 10 pubs. Calculate yours: jef.works/Mentorship-I... Blog: jef.works/blog/2026/03... 🧵👇

This week I’ve been thinking about what matters most in science. For me, it’s mentoring. I wrote a short reflection on the people who shaped me, and the lessons I hope to pass forward someday: open.substack.com/pub/behindth...

Weekly reads 16/2/26: From ecDNA to epigenomic priming: modeling what averages miss open.substack.com/pub/behindth... Overall theme: Averages hide, structure reveals. #SingleCell #SpatialOmics #CancerBiology #ComputationalBiology #MultiOmics #AIinBiology

Weekly reads 9/2/25: Systemic programs and structured models across cancer and aging open.substack.com/pub/behindth... Mechanism + structure > scale alone. #CancerBiology #SingleCell #Genomics #Aging #Immunology #AIinBiology #LineageTracing

🧬 We're hiring a postdoc! Come chart somatic evolution with us using cutting-edge long-read & single-cell tech 🔬 Computational bio background + love for complex cancer genomics = perfect fit 📍 Leuven, Belgium 📧 jobs.vib.be/j/129915/ #postdoc #genomics #hiring

Weekly reads 2/2/26 : How space, context, and uncertainty reshape cancer and single-cell biology open.substack.com/pub/behindth... Big theme: space + context + mechanism > black-box scale alone. #SpatialOmics #SingleCell #CancerBiology #TumorMicroenvironment #AIinBiology #Immunology

🚀 Interested in a postdoc in computational biology & AI for neuroscience? The NOMIS Synergy Fellowship offers a great opportunity to develop such a position in my lab within the interdisciplinary Synergy excellence cluster. 🔗 www.synergy-munich.de/news-events/...

🧬 2026 Internship: Marioni Group @genentech.bsky.social Seeking PhD intern for Deep Learning on large-scale genetic screens (Perturb-seq/Optical). Focus: ML for single-cell + imaging to decode phenotypes. 📍 SSF (On-site) | 12-wk paid ⚠️ Apply via portal only: 🔗 bit.ly/45P7TQB #CompBio #AI #Genetics

Weekly reads 26/1/26: When Simple Representations Outperform Complex Models in Biology open.substack.com/pub/behindth... Big takeaway: biology gets clearer when models respect geometry, hierarchy, and context. #SingleCell #SpatialOmics #CancerBiology #ComputationalBiology #Genomics

Turns out that if you use a broom to scratch yourself everyone thinks you're a weirdo but if a cow does it they end up in the cover of Current Biology

Two postdoc positions opened in my team @pasteur.fr in Paris on the development of machine learning methods for single-cell multi-omics spatiotemporal data. See the announcement for all details emploi.cnrs.fr/Offres/CDD/U...

I am just reading this paper, and it is absolutely wild. Tumor cells acquire mutations in mitochondria, and then transfer them to T-cells, and the mutant mitochondria drives dysfunction in the T-cells?! www.nature.com/articles/s41...

Weekly reads 19/1/26: Multimodal integration, interpretability, and robustness in spatial biology open.substack.com/pub/behindth... Main theme: multimodal data is powerful, but only if it’s aligned, interpretable, and batch-aware. #SpatialOmics #SingleCell #RegulatoryGenomics #AI

Weekly reads 12/1/25: Context, benchmarks and reality checks for single-cell foundation models open.substack.com/pub/behindth... Big takeaway: scale helps,but context, benchmarks, and classical baselines still matter. #SpatialTranscriptomics #scRNAseq #AIinBiology #ComputationalBiology

TF-MINDI is out! A new method to learn cis-regulatory codes through rich embeddings of TF binding sites. TF-MINDI decomposes motif neighbourhoods, and works downstream of any sequence-to-function deep learning model. We deeply study the enhancer code in human neural development, check out the thread

Weekly reads 5/1/26: Standardizing, disentangling, and interpreting cells in space open.substack.com/pub/behindth... #SingleCel #Epigenomics #SpatialBiology #CRISPR #CellCellCommunication #AIinBiology #SpatialOmics

We are looking for a new colleague in the lab of @jdemeul.bsky.social! If you are looking for a Postdoctoral position in Cancer Genomics,check the position here: jobso.id/pbgr