Some thoughts on where AI in genomics stands right now, building on a symposium we recently hosted at UChicago.
Seven points, ranging from why scaling DNA models hasn't delivered, to why metadata is the real bottleneck, to the weird backlash against AI in academia
open.substack.com/pub/blekhman...
open.substack.com
A grounded take from the messy middle of an AI revolution
My letter to Minister Lawless about Research Ireland's decision to devolve the awarding of doctoral scholarships & postdoctoral fellowships to universities. A disastrous move. Please consider raising this issue in your own institutions and with elected representatives and the media.
Our thoughts, impressions, and presentations of the "2nd EuroDepMap symposium" in Milan (Nov 2025) are online at
@febsletters.bsky.social.
febs.onlinelibrary.wiley.com/doi/10.1002/...
Held on 20 November 2025 at Human Technopole in Milan, the 2nd European Cancer Dependency Map Symposium convened experimental and computational scientists to discuss how cancer dependency mapping in ...
We are very happy to see our study finally appear online @nature.com! This has been work of nearly 10 years in collaboration with the National Institute of Genome Medicine 🇲🇽, the National Cancer Institute 🇲🇽, the @sangerinstitute.bsky.social and others ⬇️
www.nature.com/articles/s41...
Our preprint is now published in MSB. link.springer.com/article/10.1...
We decompose multi-omics into distinct phenotypic axes (drug response vs ARID1A-driven cell state), improving interpretation and revealing how baseline cell state rewires signaling and shapes MAPK inhibitor resistance.
We have started a project trying to predic the interactions/structures of all yeast protein pairs using an AlphaFold pooling approach. We are making the current dataset open and we welcome collaborations.
www.evocellnet.com/2026/03/mapp...
The past two decades of PARP inhibitor synthetic lethality in cancer is explored.
Analysis of the somatic and transcriptomic profile of 123 acral melanoma samples from Mexican patients helps understand tumour origins and prognosis, and highlights the importance of including samples...
We are excited to announce the early-stage release of our S. cerevisiae structural interactome mapping project. Using AlphaFold3 (AF3), w...
www.evocellnet.com
Resistance to BRAF/MAPK inhibitors is a significant challenge in melanoma treatment, driven by adaptive and acquired mechanisms allowing tumor cells to evade therapy. We explored early signaling respo...
Thinking about applying for an MSCA postdoctoral fellowship? The UCD School of Medicine has a list of academics keen to support applicants. I'm one – looking for people interested in synthetic lethality, paralogs in disease, or LLMs for genotype-phenotype analysis.
www.ucd.ie/medicine/res...
Rob Kitchin
Daniela Robles-Espinoza
Chris Lord and Andrew Tutt’s Lab Institute of Cancer Research
Another genetic interaction map of the DNA Damage Response. That makes six maps now! www.biorxiv.org/content/10.6...
Now out in Genome Medicine link.springer.com/article/10.1...
Work led by the brilliant Elle Loughran (not on bsky) on the evolution of hypodiploid tumours, who is heading to Montpellier this week to start a postdoc with @aline-muyle.bsky.social!
The DNA damage response (DDR) is a complex network of cellular pathways that ensures the faithful maintenance of our genomes upon a wide array of genomic insults. To elucidate the functional architect...
New preprint from our group @ebi.embl.org and the Vidal-Puig group! We combined pseudotemporal ordering of cross sectional MASLD patient data with network analysis to describe the disease progression and identify a signature of 24 plasma biomarkers for patient staging www.biorxiv.org/content/10.1...
Pervasive Chromosomal Instability Drives the Karyotypic Evolution of Hypodiploid Tumours https://www.biorxiv.org/content/10.1101/2025.08.08.668983v1
