Emre Kocakavuk
@ekocakavuk.bsky.social
Emmy Noether Group Leader | Forbeck Scholar | Clinician Scientist in Hematology/Oncology
kocakavuklab.com
kocakavuklab.com
Reposted by Emre Kocakavuk
🚨 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
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
October 8, 2025 at 4:44 PM
🚨 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
www.nature.com/articles/s41...
by @raquelbmi.bsky.social, @ferriol.bsky.social et al (in collaboration with Rosana Risques lab in @uwmedicine.bsky.social)
Reposted by Emre Kocakavuk
🚨 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/
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/
October 6, 2025 at 12:41 PM
🚨 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/
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/
Reposted by Emre Kocakavuk
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.
August 6, 2025 at 3:14 PM
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.
Reposted by Emre Kocakavuk
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
How to move from bedside to bench to biotech
📅 8 July 2025
🕒 15:00–16:00 CEST
🔗 buff.ly/Qgnebwk
June 30, 2025 at 8:01 AM
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
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.
June 12, 2025 at 5:15 AM
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.
Reposted by Emre Kocakavuk
🧵 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 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
May 14, 2025 at 8:08 AM
🧵 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 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
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
May 7, 2025 at 8:32 PM
🧪 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
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
Evolutionary fingerprints of epithelial-to-mesenchymal transition | @nature.com
www.nature.com/articles/s41...
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
March 6, 2025 at 8:31 AM
Evolutionary fingerprints of epithelial-to-mesenchymal transition | @nature.com
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Reposted by Emre Kocakavuk
📣 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
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
February 19, 2025 at 2:42 PM
📣 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
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
Reposted by Emre Kocakavuk
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
March 1, 2025 at 11:00 PM
New preprint from the lab - Selective depletion of cancer cells with extrachromosomal DNA via lentiviral infection www.biorxiv.org/content/10.1...
Reposted by Emre Kocakavuk
🚀 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
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
February 27, 2025 at 2:13 PM
🚀 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
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.com
www.nature.com/articles/s41...
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
February 26, 2025 at 5:32 PM
Programs, origins and immunomodulatory functions of myeloid cells in glioma | @nature.com
www.nature.com/articles/s41...
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
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
February 19, 2025 at 2:42 PM
📣 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
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
Reposted by Emre Kocakavuk
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...
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
February 17, 2025 at 3:47 PM
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...
www.nature.com/articles/s41...
Reposted by Emre Kocakavuk
📢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.
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
February 11, 2025 at 7:42 AM
📢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.
By Martin Blohmer, Kamila Naxerova and colleagues.
⬇️
www.nature.com/articles/s41...
Reposted by Emre Kocakavuk
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!
karriere.ume.de/job-finder/?...
karriere.ume.de/job-finder/?...
Bei Interesse melden Sie sich bitte sehr gerne bei uns!
February 10, 2025 at 11:54 AM
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!
karriere.ume.de/job-finder/?...
karriere.ume.de/job-finder/?...
Bei Interesse melden Sie sich bitte sehr gerne bei uns!
Reposted by Emre Kocakavuk
(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
@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
February 6, 2025 at 1:07 PM
(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
@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.
February 4, 2025 at 4:44 PM
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.
Reposted by Emre Kocakavuk
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
January 22, 2025 at 10:46 PM
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...
Reposted by Emre Kocakavuk
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
📖👉 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
January 17, 2025 at 2:15 PM
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
📖👉 bit.ly/3C53w8g
Reposted by Emre Kocakavuk
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/...
@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
January 2, 2025 at 11:38 PM
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/...
@danafarber.bsky.social @bostonchildrens.bsky.social @broadinstitute.org @science.org
www.science.org/doi/10.1126/...
Reposted by Emre Kocakavuk
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
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
November 25, 2024 at 3:37 AM
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
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
Reposted by Emre Kocakavuk
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...
November 27, 2024 at 5:58 PM
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...
Reposted by Emre Kocakavuk
🎨 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
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
November 23, 2024 at 3:50 PM
🎨 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
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