Emre Kocakavuk

Sex and smoking bias in the selection of somatic mutations in human bladder - Nature Sex bias and association with smoking history identified in the landscape of driver mutations and clonal expansions in normal human bladder tissue may explain the higher bladder cancer risk in men and smokers.

🚨 New paper alert!

Sex and smoking bias in the selection of somatic mutations in human bladder

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

by @raquelbmi.bsky.social, @ferriol.bsky.social et al (in collaboration with Rosana Risques lab in @uwmedicine.bsky.social)

🚨 new glioblastoma preprint alert!

we present the first spatially resolved single cell atlas comparing radionecrotic changes (RN) and recurrent IDH-wildtype glioblastoma (GB) –– shedding light on a long-standing diagnostic challenge.

🧵 1/

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.

Don’t miss the YO4YO Virtual Session with Ranjit Bindra & @ekocakavuk.bsky.social
How to move from bedside to bench to biotech

📅 8 July 2025
🕒 15:00–16:00 CEST

🔗 buff.ly/Qgnebwk

I am deeply saddened by the passing of Prof. Gazi Yaşargil (1925–2025), the father of microneurosurgery. What an inspirational career devoted to the betterment of medicine and humankind, a legacy that will be carried onward. Rest in peace, Gazi Hocam.

AI-generated illustration of DNA with mutations, cancer cells, and drugs applied to them

🧵 Ahmed’s @genomedatalab.bsky.social paper on evolution of chemotherapy resistance is out @natcomms.nature.com!

We developed DiffInvex - a method tracking how #cancer driver genes change under therapy using ~10k whole-genomes. Key insight: drug resistance often emerges through existing pathways 1/5

🧪 We’re Hiring: Lab Technician 🧪

I’m happy to share that our newly established Emmy Noether Group in Essen is looking for a Lab Technician to join our team!

🔗 Apply here: karriere.ume.de/job-finder/?...
📅 Start: At the earliest possible date
💻 Homepage: kocakavuklab.vercel.app/overview

Comprehensive interrogation of synthetic lethality in the DNA damage response - Nature Combinatorial CRISPRi screening was used to map genetic interactions in DNA damage response pathways, revealing known and new connections, including the roles of WDR48 and USP1 in preventing under-rep...

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

Evolutionary fingerprints of epithelial-to-mesenchymal transition - Nature Malignant cells with mesenchymal features display increased chromatin accessibility, particularly in the pericentromeric and centromeric regions, in turn resulting in delayed mitosis and catastrophic ...

Evolutionary fingerprints of epithelial-to-mesenchymal transition | @nature.com

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

📣 Open computational PhD & Postdoc positions!

Excited about the open positions as part of our newly funded Emmy Noether Group are online now under
kocakavuklab.vercel.app/joinus

📢 Please RT (what's the bsky equivalent here?) and distribute !

👇A quick instruction on how to apply

Selective depletion of cancer cells with extrachromosomal DNA via lentiviral infection Extrachromosomal DNA (ecDNA), a major focal oncogene amplification mode found across cancer, has recently regained attention as an emerging cancer hallmark, with a pervasive presence across cancers. W...

New preprint from the lab - Selective depletion of cancer cells with extrachromosomal DNA via lentiviral infection www.biorxiv.org/content/10.1...

🚀 Fully Funded PhD – AI & Neurodevelopment @ KCL! 🧠💡

Come join us in the IMAGINE lab to develop AI tools for imaging and genetics in neurodevelopmental disorders!

Apply here: shorturl.at/Zb4GX
For more info, get in touch: konrad.wagstyl@kcl.ac.uk

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...

Programs, origins and immunomodulatory functions of myeloid cells in glioma | @nature.com

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

📣 Open computational PhD & Postdoc positions!

Excited about the open positions as part of our newly funded Emmy Noether Group are online now under
kocakavuklab.vercel.app/joinus

📢 Please RT (what's the bsky equivalent here?) and distribute !

👇A quick instruction on how to apply

Functional analysis of cancer-associated germline risk variants - Nature Genetics Analysis of 4,041 single-nucleotide variants (SNVs) linked to 13 cancers performed in primary human cell types identifies 380 potentially regulatory SNVs and their putative target genes. Editing one S...

Assessing the functionality of over 4,000 genome variants for their role in cancer, with prominence of impact for those related to the immune system and chronic inflammation
www.nature.com/articles/s41...

Quantifying cell divisions along evolutionary lineages in cancer - Nature Genetics This work presents a framework for estimating cell division numbers using DNA replication-associated polyguanine tract mutations, with applications for understanding tumor natural histories and origin...

📢ONLINE @naturegenet.bsky.social

📰Quantifying cell divisions along evolutionary lineages in #cancer.

By Martin Blohmer, Kamila Naxerova and colleagues.

⬇️

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

Wir suchen 2 Oberärzt:Innen (Akute Leukämien und Allo-TX). Wir bieten das gesamte Spektrum der univ. Hämatologie von mol. Diagnostik bis ICU mit einem fantastischen Team.

karriere.ume.de/job-finder/?...

karriere.ume.de/job-finder/?...

Bei Interesse melden Sie sich bitte sehr gerne bei uns!

SKI complex loss renders 9p21.3-deleted or MSI-H cancers dependent on PELO - Nature Analysis of large-scale CRISPR screening data, combined with experiments in patient-derived tumour organoid models, identifies PELO as a potential therapeutic target in chromosomal 9p21.3-deleted canc...

(1/3) Excited to share our latest work using
@depmap.org to uncover a new synthetic lethality in two distinct patient populations!

We found that SKI complex inactivation through two independent genomic alterations creates a dependency on PELO

#CancerResearch #SyntheticLethality #Genomics #DepMap

What an absolute pleasure to host my mentor @roelverhaak.bsky.social at our West German Cancer Center in Essen today. Fantastic talk in a packed room on #WorldCancerDay2025.

Mapping cells through time and space with moscot - Nature Moscot is an optimal transport approach that overcomes current limitations of similar methods to enable multimodal, scalable and consistent single-cell analyses of datasets across spatial and temporal...

Excited to see Moscot (moscot-tools.org) published in @Nature! We scaled Optimal Transport (OT) in single-cell genomics & added multimodality together with spatiotemporal trajectory inference, finding exciting new biology in the pancreas! 🚀 Read at www.nature.com/articles/s41...

Conventional chemotherapy: millions of cures, unresolved therapeutic index - Nature Reviews Cancer Conventional chemotherapy has successfully cured millions of patients with cancer, yet the mechanisms of action for this remain unclear. In this Perspective, Letai and de The assess the existing mecha...

Conventional chemotherapy has successfully cured millions of cancers, yet its mechanism of action remains unclear. In this #Perspective, Letai & de The assess the proposed existing mechanisms, identify gaps in our understanding & suggest principles to improve chemotherapy utility.

📖👉 bit.ly/3C53w8g

Rare germline structural variants increase risk for pediatric solid tumors Pediatric solid tumors are a leading cause of childhood disease mortality. In this work, we examined germline structural variants (SVs) as risk factors for pediatric extracranial solid tumors using ge...

Here's our latest, led by Drs. Riaz Gillani & Ryan Collins - we studied a type of inherited genetic event (structural variants) + risk of developing certain cancers in kids:
@danafarber.bsky.social @bostonchildrens.bsky.social @broadinstitute.org @science.org

www.science.org/doi/10.1126/...

We recently announced a dual new release of intOGen and boostDM

Computational analysis of 33,218 tumor genomes to identify cancer genes and driver mutations

➡️ Compendium of Cancer Driver Genes - www.intogen.org

➡️ In Silico Saturation Mutagenesis of Cancer Genes - www.intogen.org/boostdm

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...

🎨 In case anyone need…

The NIH BioArt Source is an awesome library of *free* professionally drawn illustrations for scientific presentations or figures. Downloadable in HD. Thank you NIH for this invaluable tool 🙏!

Check it out 👇
bioart.niaid.nih.gov

Somatic mutation and selection at epidemiological scale As we age, many tissues become colonised by microscopic clones carrying somatic driver mutations ([1][1]–[10][2]. Some of these clones represent a first step towards cancer whereas others may contribu...

Resharing here a recent X post. In this preprint, we introduce an improved version of NanoSeq, a duplex sequencing protocol with <5 errors per billion bp in single DNA molecules, and use it to study the somatic mutation landscape of oral epithelium in >1000 people. 1/ www.medrxiv.org/content/10.1...

👉 One click to follow many of the most inspiring researchers around in precision oncology
go.bsky.app/xg4Y26

Comment if you want to join the evolving list

Too often we spend only two weeks choosing a problem and then many years trying solving it, but this limits our potential impact.
A must read for PhD students: Problem choice and decision trees in science and engineering.
pubmed.ncbi.nlm.nih.gov/38608651/

Would love to be added!

Genomics, evolution, and more starter pack!

Help build community with this starter pack.

This list is currently incomplete. Want to be included? Reply and I will remedy that!
go.bsky.app/JjvzkWU