Kadir Akdemir
@kcakdemir.bsky.social
Husband & father | Asst prof at MD Anderson Cancer Center | Our lab focuses on tumor evolution, chromatin folding & instability
akdemirlab.github.io
akdemirlab.github.io
Pinned
Kadir Akdemir
@kcakdemir.bsky.social
· Feb 28
Really excited to share our lab's first manuscript! I cant be more proud of our team, especially @nora-mae.bsky.social who diligently worked on this project.
It will be a long thread but I promise it's worth it!
#Oncology #BrainMets
It will be a long thread but I promise it's worth it!
#Oncology #BrainMets
Reposted by Kadir Akdemir
The Kim Lab (sskimlab.org) at UC Irvine is recruiting motivated grad students interested in uncovering how transcriptional regulators direct cell fates. We accept students through the CMB (cmb.uci.edu) and MCSB (ccbs.uci.edu/education/mcsb/) PhD programs. Please share with prospective grad students!
Kim Lab at UC Irvine
Visit the post for more.
sskimlab.org
October 30, 2025 at 3:37 PM
The Kim Lab (sskimlab.org) at UC Irvine is recruiting motivated grad students interested in uncovering how transcriptional regulators direct cell fates. We accept students through the CMB (cmb.uci.edu) and MCSB (ccbs.uci.edu/education/mcsb/) PhD programs. Please share with prospective grad students!
Reposted by Kadir Akdemir
Less than 70% of science Nobel prize winners awarded this century hail from the country in which they were awarded their prize.
“Mobility benefits everyone. Each newcomer brings fresh ideas, new techniques & different ways of looking at old problems”
🧪 #academicSky
www.nature.com/articles/d41...
“Mobility benefits everyone. Each newcomer brings fresh ideas, new techniques & different ways of looking at old problems”
🧪 #academicSky
www.nature.com/articles/d41...
More than 30% of this century’s science Nobel prizewinners immigrated: see their journeys
The most common destination for eventual Nobel laureates in physics, chemistry and medicine since 2000 is the United States, Nature has found.
www.nature.com
October 9, 2025 at 10:58 PM
Less than 70% of science Nobel prize winners awarded this century hail from the country in which they were awarded their prize.
“Mobility benefits everyone. Each newcomer brings fresh ideas, new techniques & different ways of looking at old problems”
🧪 #academicSky
www.nature.com/articles/d41...
“Mobility benefits everyone. Each newcomer brings fresh ideas, new techniques & different ways of looking at old problems”
🧪 #academicSky
www.nature.com/articles/d41...
Reposted by Kadir Akdemir
Very happy that the review article by @magnushaughey.bsky.social and Imran Noorani on the evolutionary role of extra-chromosomal DNA in cancers just came out.
authors.elsevier.com/sd/article/S...
authors.elsevier.com/sd/article/S...
ScienceDirect.com | Science, health and medical journals, full text articles and books.
authors.elsevier.com
July 9, 2025 at 1:43 PM
Very happy that the review article by @magnushaughey.bsky.social and Imran Noorani on the evolutionary role of extra-chromosomal DNA in cancers just came out.
authors.elsevier.com/sd/article/S...
authors.elsevier.com/sd/article/S...
Reposted by Kadir Akdemir
🚨The formation of 3D chromatin hubs is a poorly understood
phenomenon.
I wrote a N&V about the excellent work Karpinska, Zhu and colleagues, from @mariekeoudelaar.bsky.social lab, who shed new light on the formation and function of these structures.
rdcu.be/elPt3
phenomenon.
I wrote a N&V about the excellent work Karpinska, Zhu and colleagues, from @mariekeoudelaar.bsky.social lab, who shed new light on the formation and function of these structures.
rdcu.be/elPt3
Decoupling chromatin hubs from gene control
Nature Structural & Molecular Biology - Chromatin hubs, which are formed during cell differentiation, are characterized by simultaneous interactions between multiple regulatory elements and...
www.nature.com
May 13, 2025 at 10:13 AM
🚨The formation of 3D chromatin hubs is a poorly understood
phenomenon.
I wrote a N&V about the excellent work Karpinska, Zhu and colleagues, from @mariekeoudelaar.bsky.social lab, who shed new light on the formation and function of these structures.
rdcu.be/elPt3
phenomenon.
I wrote a N&V about the excellent work Karpinska, Zhu and colleagues, from @mariekeoudelaar.bsky.social lab, who shed new light on the formation and function of these structures.
rdcu.be/elPt3
Excited to share our latest manuscript www.biorxiv.org/content/10.1...
This was a great collaboration with Drs. Huse, Lang, @jesserdixon.bsky.social
This was a great collaboration with Drs. Huse, Lang, @jesserdixon.bsky.social
May 22, 2025 at 5:37 PM
Excited to share our latest manuscript www.biorxiv.org/content/10.1...
This was a great collaboration with Drs. Huse, Lang, @jesserdixon.bsky.social
This was a great collaboration with Drs. Huse, Lang, @jesserdixon.bsky.social
Reposted by Kadir Akdemir
Incoming - new preprint alert from the Parkes lab led by @brunobeernaert.bsky.social Full bluetutorial follows! 1/ 11 www.biorxiv.org/content/10.1...
May 12, 2025 at 12:08 PM
Incoming - new preprint alert from the Parkes lab led by @brunobeernaert.bsky.social Full bluetutorial follows! 1/ 11 www.biorxiv.org/content/10.1...
Reposted by Kadir Akdemir
🧪 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
Reposted by Kadir Akdemir
that’s right
I knew the U.S. higher education system was a massive draw for foreigners, but I did not know the U.S. sold more educational services to the rest of the world than it did natural gas and coal combined. Great piece by @crampell.bsky.social
April 26, 2025 at 1:55 AM
that’s right
Reposted by Kadir Akdemir
Huge opportunity for postdocs gearing up for an academic job search, hosted by @stanford-chemh.bsky.social @berkeleymcb.bsky.social and UCSF!
Hello Community!
Are you a postdoc/grad student preparing to launch a faculty search? Do you have a track record of excellence in research, leadership, mentorship & community engagement? Apply to the 2025 Next Generation Faculty Symposium: www.berkeleystanfordnextgensymposium.com! Pls repost! (1/3)
Are you a postdoc/grad student preparing to launch a faculty search? Do you have a track record of excellence in research, leadership, mentorship & community engagement? Apply to the 2025 Next Generation Faculty Symposium: www.berkeleystanfordnextgensymposium.com! Pls repost! (1/3)
April 25, 2025 at 11:46 PM
Huge opportunity for postdocs gearing up for an academic job search, hosted by @stanford-chemh.bsky.social @berkeleymcb.bsky.social and UCSF!
Reposted by Kadir Akdemir
Nature Genetics is looking to hire a new editor!
Come join our team and help publish the most exciting research in genetics and genomics! Deadline is April 25th.
springernature.wd3.myworkdayjobs.com/en-US/Spring...
Come join our team and help publish the most exciting research in genetics and genomics! Deadline is April 25th.
springernature.wd3.myworkdayjobs.com/en-US/Spring...
Associate or Senior Editor Nature Genetics and Nature Communication
Job Title: Associate or Senior Editor Nature Genetics and Nature Communication Organisation: Nature Portfolio Location: New York/Philadelphia, Shanghai/Beijing, Madrid or Milan Application Deadline: A...
springernature.wd3.myworkdayjobs.com
April 11, 2025 at 5:17 PM
Nature Genetics is looking to hire a new editor!
Come join our team and help publish the most exciting research in genetics and genomics! Deadline is April 25th.
springernature.wd3.myworkdayjobs.com/en-US/Spring...
Come join our team and help publish the most exciting research in genetics and genomics! Deadline is April 25th.
springernature.wd3.myworkdayjobs.com/en-US/Spring...
Reposted by Kadir Akdemir
Earnshaw, Goloborodko, Dekker & Mirny labs are excited to present our latest work, "Rules of engagement for condensins and cohesins guide mitotic chromosome formation" - now accepted!!
www.science.org/doi/10.1126/...
A short clip describing the key results:
www.youtube.com/watch?v=pmvO...
www.science.org/doi/10.1126/...
A short clip describing the key results:
www.youtube.com/watch?v=pmvO...
Rules of Engagement
YouTube video by Johan Gibcus
www.youtube.com
April 11, 2025 at 7:45 AM
Earnshaw, Goloborodko, Dekker & Mirny labs are excited to present our latest work, "Rules of engagement for condensins and cohesins guide mitotic chromosome formation" - now accepted!!
www.science.org/doi/10.1126/...
A short clip describing the key results:
www.youtube.com/watch?v=pmvO...
www.science.org/doi/10.1126/...
A short clip describing the key results:
www.youtube.com/watch?v=pmvO...
Reposted by Kadir Akdemir
Lookin for a good read in between experiments? Check out the commentary article in @neuroonc.bsky.social @dbayik.bsky.social and I wrote on an insightful study on myeloid cells in gliomas 🙂↔️ link here: academic.oup.com/neuro-oncolo...
An in-depth survey of immunosuppressive myeloid cell heterogeneity in GBM
Brandon Emanuel León, Defne Bayik; An in-depth survey of immunosuppressive myeloid cell heterogeneity in GBM, Neuro-Oncology, , noaf080, https://doi.org/10
academic.oup.com
March 27, 2025 at 12:07 AM
Lookin for a good read in between experiments? Check out the commentary article in @neuroonc.bsky.social @dbayik.bsky.social and I wrote on an insightful study on myeloid cells in gliomas 🙂↔️ link here: academic.oup.com/neuro-oncolo...
This is truly heartbreaking!
I don’t understand the “logic” behind all this. Hurting the US science will only make scientific enterprises of other countries stronger. Why an administration would want that?
I don’t understand the “logic” behind all this. Hurting the US science will only make scientific enterprises of other countries stronger. Why an administration would want that?
There are days in life that shake you.
I’m shattered 💔 to share that I just found out that the US Government terminated my 2024 NIH Director’s Early Independence Award (~$2 million), threatening my long-promised assistant professor job at Columbia University
& academic career... 1/🧵
I’m shattered 💔 to share that I just found out that the US Government terminated my 2024 NIH Director’s Early Independence Award (~$2 million), threatening my long-promised assistant professor job at Columbia University
& academic career... 1/🧵
March 19, 2025 at 12:26 PM
This is truly heartbreaking!
I don’t understand the “logic” behind all this. Hurting the US science will only make scientific enterprises of other countries stronger. Why an administration would want that?
I don’t understand the “logic” behind all this. Hurting the US science will only make scientific enterprises of other countries stronger. Why an administration would want that?
Reposted by Kadir Akdemir
Cancer knows no borders, and setbacks in one part of the world can have lasting consequences for #patients everywhere
The #EACR, and all co-signing national #cancer societies & foundations, stand in solidarity and offer our full support to our friends and colleagues in the US
#StandUpForScience 🧪
The #EACR, and all co-signing national #cancer societies & foundations, stand in solidarity and offer our full support to our friends and colleagues in the US
#StandUpForScience 🧪
March 10, 2025 at 12:06 PM
Cancer knows no borders, and setbacks in one part of the world can have lasting consequences for #patients everywhere
The #EACR, and all co-signing national #cancer societies & foundations, stand in solidarity and offer our full support to our friends and colleagues in the US
#StandUpForScience 🧪
The #EACR, and all co-signing national #cancer societies & foundations, stand in solidarity and offer our full support to our friends and colleagues in the US
#StandUpForScience 🧪
Reposted by Kadir Akdemir
Happy to share our review with @akispapantonis.bsky.social in which we summarise and discuss our current understanding of enhancer-mediated gene activation in the context of the 3D genome:
www.annualreviews.org/content/jour...
www.annualreviews.org/content/jour...
Mechanisms of Enhancer-Mediated Gene Activation in the Context of the 3D Genome | Annual Reviews
Precise spatiotemporal regulation of gene expression is critical for the development and functioning of complex, multicellular organisms. Enhancers play a fundamental role in the regulation of gene ex...
www.annualreviews.org
March 10, 2025 at 7:54 AM
Happy to share our review with @akispapantonis.bsky.social in which we summarise and discuss our current understanding of enhancer-mediated gene activation in the context of the 3D genome:
www.annualreviews.org/content/jour...
www.annualreviews.org/content/jour...
Reposted by Kadir Akdemir
Review alert - "Modelling and design of transcriptional enhancers" by Seppe and Vasilis 👇
We wrote a review article on modelling and design of transcriptional enhancers using sequence-to-function models.
From conventional machine learning methods to CNNs and using models as oracles/generative AI for synthetic enhancer design!
@natrevbioeng.bsky.social
www.nature.com/articles/s44...
From conventional machine learning methods to CNNs and using models as oracles/generative AI for synthetic enhancer design!
@natrevbioeng.bsky.social
www.nature.com/articles/s44...
Modelling and design of transcriptional enhancers - Nature Reviews Bioengineering
Enhancers are genomic elements critical for regulating gene expression. In this Review, the authors discuss how sequence-to-function models can be used to unravel the rules underlying enhancer activit...
www.nature.com
February 28, 2025 at 4:53 PM
Review alert - "Modelling and design of transcriptional enhancers" by Seppe and Vasilis 👇
Really excited to share our lab's first manuscript! I cant be more proud of our team, especially @nora-mae.bsky.social who diligently worked on this project.
It will be a long thread but I promise it's worth it!
#Oncology #BrainMets
It will be a long thread but I promise it's worth it!
#Oncology #BrainMets
February 28, 2025 at 2:27 PM
Really excited to share our lab's first manuscript! I cant be more proud of our team, especially @nora-mae.bsky.social who diligently worked on this project.
It will be a long thread but I promise it's worth it!
#Oncology #BrainMets
It will be a long thread but I promise it's worth it!
#Oncology #BrainMets
Reposted by Kadir Akdemir
Timothy A. Yap, MBBS, PhD, has been appointed editor-in-chief of the AACR journal Clinical Cancer Research. Dr. Yap is co-director for the AACR/ASCO Methods in Clinical Cancer Research Workshop and a past cochair of the AACR Annual Meeting Clinical Trials Committee. www.aacr.org/about-the-aa...
February 24, 2025 at 9:58 PM
Timothy A. Yap, MBBS, PhD, has been appointed editor-in-chief of the AACR journal Clinical Cancer Research. Dr. Yap is co-director for the AACR/ASCO Methods in Clinical Cancer Research Workshop and a past cochair of the AACR Annual Meeting Clinical Trials Committee. www.aacr.org/about-the-aa...
Here is how random things affect your career: in Oct, I applied for my 1st R01. For study sections I recommended CG first and then GRIC. My grant was assigned to GRIC. It seems CG met last week but GRIC was cancelled today. Where should I put this information on my CV/biosketch?!
Wondering if your study section cancelled? I update this sheet daily. As of today, 56/124 study sections that should have met since Jan 2, 2025 have "not met as scheduled." docs.google.com/spreadsheets...
2025 Study section tracking
docs.google.com
February 24, 2025 at 10:39 PM
Here is how random things affect your career: in Oct, I applied for my 1st R01. For study sections I recommended CG first and then GRIC. My grant was assigned to GRIC. It seems CG met last week but GRIC was cancelled today. Where should I put this information on my CV/biosketch?!
Reposted by Kadir Akdemir
For all the gains AI affords in compound design and discovery, experimental validation still remains a bottleneck. But we're making that part easy for the cancer target TBXT with a suite of biophysical, in vitro and in vivo assay capabilities—plus prizes for potent binders: tbxtchallenge.org
February 22, 2025 at 8:16 PM
For all the gains AI affords in compound design and discovery, experimental validation still remains a bottleneck. But we're making that part easy for the cancer target TBXT with a suite of biophysical, in vitro and in vivo assay capabilities—plus prizes for potent binders: tbxtchallenge.org
Reposted by Kadir Akdemir
Multiscale footprints reveal the organization of cis-regulatory elements www.nature.com/articles/s41...
▶️Footprints of DNA–protein interactions from bulk & single-cell ATAC-seq ⤵️
▶️Deep learning to infer transcription factor and nucleosome binding
▶️Age-associated reduction of nucleosome footprints
▶️Footprints of DNA–protein interactions from bulk & single-cell ATAC-seq ⤵️
▶️Deep learning to infer transcription factor and nucleosome binding
▶️Age-associated reduction of nucleosome footprints
January 23, 2025 at 12:49 AM
Multiscale footprints reveal the organization of cis-regulatory elements www.nature.com/articles/s41...
▶️Footprints of DNA–protein interactions from bulk & single-cell ATAC-seq ⤵️
▶️Deep learning to infer transcription factor and nucleosome binding
▶️Age-associated reduction of nucleosome footprints
▶️Footprints of DNA–protein interactions from bulk & single-cell ATAC-seq ⤵️
▶️Deep learning to infer transcription factor and nucleosome binding
▶️Age-associated reduction of nucleosome footprints
Reposted by Kadir Akdemir
All NIH study sections canceled indefinitely. This will halt science and devastate research budgets in universities.
January 22, 2025 at 8:46 PM
All NIH study sections canceled indefinitely. This will halt science and devastate research budgets in universities.
Reposted by Kadir Akdemir
Snow day at the Zoo! ❄️ Lisa our Amur Leopard is choosing to explore the snow this morning.
All animals are healthy and doing well. During the wintery weather, our animals have access to their heated barns prepped with extra hay.
📸: John R., Hoofstock & Carnivore Curator
All animals are healthy and doing well. During the wintery weather, our animals have access to their heated barns prepped with extra hay.
📸: John R., Hoofstock & Carnivore Curator
January 21, 2025 at 4:44 PM
Snow day at the Zoo! ❄️ Lisa our Amur Leopard is choosing to explore the snow this morning.
All animals are healthy and doing well. During the wintery weather, our animals have access to their heated barns prepped with extra hay.
📸: John R., Hoofstock & Carnivore Curator
All animals are healthy and doing well. During the wintery weather, our animals have access to their heated barns prepped with extra hay.
📸: John R., Hoofstock & Carnivore Curator
Reposted by Kadir Akdemir
Thrilled to welcome Ziya Gokaslan, M.D., from Brown University to deliver the 29th Annual Leavens Lecture at @mdanderson.bsky.social today!
Dr. Gokaslan spoke on spinal surgery and #chordoma.
Dr. Gokaslan spoke on spinal surgery and #chordoma.
January 17, 2025 at 1:33 PM
Thrilled to welcome Ziya Gokaslan, M.D., from Brown University to deliver the 29th Annual Leavens Lecture at @mdanderson.bsky.social today!
Dr. Gokaslan spoke on spinal surgery and #chordoma.
Dr. Gokaslan spoke on spinal surgery and #chordoma.
Hopefully 2025 will be as fun/interesting as it’s mathematically. Happy New Year!!! (Credit: Moshe Verdi - I couldn’t find him here)
January 1, 2025 at 11:12 PM
Hopefully 2025 will be as fun/interesting as it’s mathematically. Happy New Year!!! (Credit: Moshe Verdi - I couldn’t find him here)