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Reposted by Emre Kocakavuk

Nuria Lopez-Bigas @nlbigas.bsky.social · 19h

🚨 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)

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.

www.nature.com

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Reposted by Emre Kocakavuk

zaira seferbekova 👩🏻‍💻 @zaira-sef.bsky.social · 2d

🚨 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/

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Reposted by Emre Kocakavuk

Thomas Norman @normanlab.bsky.social · Aug 6

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.

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Reposted by Emre Kocakavuk

ESMO - European Society for Medical Oncology @myesmo.bsky.social · Jun 30

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

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Emre Kocakavuk @ekocakavuk.bsky.social · Jun 12

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.

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Reposted by Emre Kocakavuk

Fran Supek @fransupek.bsky.social · May 14

🧵 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

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

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Emre Kocakavuk @ekocakavuk.bsky.social · May 7

🧪 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

Job Finder - Karriereportal - Universitätsklinikum Essen

Finden Sie eine Stelle am Universitätsklinikum Essen

karriere.ume.de

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Emre Kocakavuk @ekocakavuk.bsky.social · Apr 9

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

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

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Emre Kocakavuk @ekocakavuk.bsky.social · Mar 6

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

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 ...

www.nature.com

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Reposted by Emre Kocakavuk

Emre Kocakavuk @ekocakavuk.bsky.social · Feb 19

📣 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

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Reposted by Emre Kocakavuk

Roel Verhaak @roelverhaak.bsky.social · Mar 1

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

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...

www.biorxiv.org

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Reposted by Emre Kocakavuk

Konrad Wagstyl @konradwagstyl.bsky.social · Feb 27

🚀 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: [email protected]

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Emre Kocakavuk @ekocakavuk.bsky.social · Feb 26

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

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

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...

www.nature.com

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Emre Kocakavuk @ekocakavuk.bsky.social · Feb 19

📣 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

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Reposted by Emre Kocakavuk

Eric Topol @erictopol.bsky.social · Feb 17

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...

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...

www.nature.com

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Reposted by Emre Kocakavuk

Nature Genetics @natgenet.nature.com · Feb 11

📢ONLINE @naturegenet.bsky.social

📰Quantifying cell divisions along evolutionary lineages in #cancer.

By Martin Blohmer, Kamila Naxerova and colleagues.

⬇️

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...

www.nature.com

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Reposted by Emre Kocakavuk

Christian Reinhardt @chr-reinhardt.bsky.social · Feb 10

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!

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Reposted by Emre Kocakavuk

Francisca Vazquez PhD @vazquezf.bsky.social · Feb 6

(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

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...

nature.com

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Emre Kocakavuk @ekocakavuk.bsky.social · Feb 4

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.

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Reposted by Emre Kocakavuk

Fabian Theis @fabiantheis.bsky.social · Jan 22

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...

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...

www.nature.com

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Reposted by Emre Kocakavuk

Nature Reviews Cancer @natrevcancer.nature.com · Jan 17

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

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...

bit.ly

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Reposted by Emre Kocakavuk

Eli Van Allen @vanallenlab.bsky.social · Jan 2

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/...

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...

www.science.org

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Reposted by Emre Kocakavuk

Nuria Lopez-Bigas @nlbigas.bsky.social · Nov 25

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

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Reposted by Emre Kocakavuk

Anna Obenauf @obenaufa.bsky.social · Nov 27

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...

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Jon Lim, MRCP PhD @drjonlim.bsky.social · Nov 23

🎨 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

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