Deniz Gökbuget
@denizgoekbuget.bsky.social
Principal Scientist @Genentech | Translational research & biomarker development in prostate cancer. Passionate about bridging science and patient impact.
Pinned
KMT2C/KMT2D-dependent H3K4me1 mediates changes in DNA replication timing and origin activity during a cell fate transition
Gökbuget et al. use machine learning to quantify chromatin state changes that predict
DNA replication timing changes during cell differentiation. By following up on top
predictors through functional v...
www.cell.com
🚨 New Paper Alert! 🚨
Our latest study on KMT2C/KMT2D (mutated in 20% of cancers) reveals a new function for H3K4me1 in regulating DNA replication timing (RT) and origin activity during cell state transitions. Check it out: www.cell.com/cell-reports.... More info ⬇️
Our latest study on KMT2C/KMT2D (mutated in 20% of cancers) reveals a new function for H3K4me1 in regulating DNA replication timing (RT) and origin activity during cell state transitions. Check it out: www.cell.com/cell-reports.... More info ⬇️
I’m excited to share that I’ve joined Genentech as a Principal Scientist in Translational Medicine, where I’ll focus on biomarker development and translational research in prostate cancer. I’m looking forward to working with incredible colleagues to advance innovative therapies for patients.
October 28, 2025 at 4:50 AM
I’m excited to share that I’ve joined Genentech as a Principal Scientist in Translational Medicine, where I’ll focus on biomarker development and translational research in prostate cancer. I’m looking forward to working with incredible colleagues to advance innovative therapies for patients.
Check out our new BioRepli-seq technique in this invited article related to our recent KMT2C/KMT2D replication timing study ⬇️. We use click chemistry–based biotinylation and on-bead library prep to comprehensively profile genome-wide DNA replication timing.
🔗 star-protocols.cell.com/protocols/4439
🔗 star-protocols.cell.com/protocols/4439
September 4, 2025 at 9:35 PM
Check out our new BioRepli-seq technique in this invited article related to our recent KMT2C/KMT2D replication timing study ⬇️. We use click chemistry–based biotinylation and on-bead library prep to comprehensively profile genome-wide DNA replication timing.
🔗 star-protocols.cell.com/protocols/4439
🔗 star-protocols.cell.com/protocols/4439
Reposted by Deniz Gökbuget
Summary Table of the massive defunding of biomedical research in the United States
www.nytimes.com/interactive/...
www.nytimes.com/interactive/...
July 6, 2025 at 3:13 PM
Summary Table of the massive defunding of biomedical research in the United States
www.nytimes.com/interactive/...
www.nytimes.com/interactive/...
Reposted by Deniz Gökbuget
Dr. Cooperberg receives ASPI’s 2025 Special Award for Patient Advocacy for leading a successful campaign to restore Active Surveillance in prostate cancer guidelines. youtu.be/ZHQIkIze6k8?...
Check out his presentation on "Active Surveillance: Past, Present, and Future":
youtu.be/ev1WcQ1Ucic?...
Check out his presentation on "Active Surveillance: Past, Present, and Future":
youtu.be/ev1WcQ1Ucic?...
Active Surveillance: Past, Present, and Future
YouTube video by ASPI: Active Surveillance Patients International
youtu.be
July 3, 2025 at 4:10 PM
Dr. Cooperberg receives ASPI’s 2025 Special Award for Patient Advocacy for leading a successful campaign to restore Active Surveillance in prostate cancer guidelines. youtu.be/ZHQIkIze6k8?...
Check out his presentation on "Active Surveillance: Past, Present, and Future":
youtu.be/ev1WcQ1Ucic?...
Check out his presentation on "Active Surveillance: Past, Present, and Future":
youtu.be/ev1WcQ1Ucic?...
Race for the Prize (2017 Remaster)
YouTube video by The Flaming Lips - Topic
www.youtube.com
June 18, 2025 at 5:49 PM
Reposted by Deniz Gökbuget
Dress to kill. Come to see how I created a novel cancer vaccine by transferring MHC-peptide complexes from tumor cells to universal iPSC-derived Dendritic cells.
#ISSCR2025
AI and Cancer Evolution Session, Friday 8:30am, Convention Hall B, level 1
@ucsfcancer.bsky.social
@ucsfstemcell.bsky.social
#ISSCR2025
AI and Cancer Evolution Session, Friday 8:30am, Convention Hall B, level 1
@ucsfcancer.bsky.social
@ucsfstemcell.bsky.social
June 11, 2025 at 3:38 AM
Dress to kill. Come to see how I created a novel cancer vaccine by transferring MHC-peptide complexes from tumor cells to universal iPSC-derived Dendritic cells.
#ISSCR2025
AI and Cancer Evolution Session, Friday 8:30am, Convention Hall B, level 1
@ucsfcancer.bsky.social
@ucsfstemcell.bsky.social
#ISSCR2025
AI and Cancer Evolution Session, Friday 8:30am, Convention Hall B, level 1
@ucsfcancer.bsky.social
@ucsfstemcell.bsky.social
Reposted by Deniz Gökbuget
great start to ISSCR annual meeting. great session on immune engineering this morning @isscr.org #isscr2025
June 11, 2025 at 4:14 AM
great start to ISSCR annual meeting. great session on immune engineering this morning @isscr.org #isscr2025
Reposted by Deniz Gökbuget
We just got an email that Hopkins is freezing salaries, hiring, and some construction projects. In addition to the 800 million USAID we lost, we’ve had another 50 million in grants canceled so far. And a 2/3 year over year decline in funded grants despite an increase in submissions
June 2, 2025 at 9:02 PM
We just got an email that Hopkins is freezing salaries, hiring, and some construction projects. In addition to the 800 million USAID we lost, we’ve had another 50 million in grants canceled so far. And a 2/3 year over year decline in funded grants despite an increase in submissions
Reposted by Deniz Gökbuget
Cell cycle duration determines oncogenic transformation capacity
Tumours usually originate from a specific cell type in a given tissue; cell types that have faster cycles are more likely to become cancerous
🧪
www.nature.com/articles/s41...
Tumours usually originate from a specific cell type in a given tissue; cell types that have faster cycles are more likely to become cancerous
🧪
www.nature.com/articles/s41...
Cell cycle duration determines oncogenic transformation capacity - Nature
Total cell cycle duration is a key hallmark of cancer initiation, and determines whether defects in apoptosis, senescence, immune surveillance, angiogenesis, DNA repair, polarity and proliferation lea...
www.nature.com
May 2, 2025 at 6:01 AM
Cell cycle duration determines oncogenic transformation capacity
Tumours usually originate from a specific cell type in a given tissue; cell types that have faster cycles are more likely to become cancerous
🧪
www.nature.com/articles/s41...
Tumours usually originate from a specific cell type in a given tissue; cell types that have faster cycles are more likely to become cancerous
🧪
www.nature.com/articles/s41...
Reposted by Deniz Gökbuget
A tour de force study from Taipale&Yin labs. It expands the vocabulary of the Regulatory Code by adding 1131 TF:TF composite motifs that are different from the individual TF motifs. The new composite motifs are enriched in cell-type specific elements and active in vivo
www.nature.com/articles/s41...
www.nature.com/articles/s41...
DNA-guided transcription factor interactions extend human gene regulatory code - Nature
A large-scale analysis of DNA-bound transcription factors (TFs) shows how the presence of DNA markedly affects the landscape of TF interactions, and identifies composite motifs that are recognized by ...
www.nature.com
April 9, 2025 at 4:51 PM
A tour de force study from Taipale&Yin labs. It expands the vocabulary of the Regulatory Code by adding 1131 TF:TF composite motifs that are different from the individual TF motifs. The new composite motifs are enriched in cell-type specific elements and active in vivo
www.nature.com/articles/s41...
www.nature.com/articles/s41...
For decades, NIH funding has fueled breakthroughs in cancer, heart disease and more. But a new policy puts progress at risk. We need Congress to oppose this abrupt change. Join me in emailing lawmakers today! #SaveNIHresearch bit.ly/4hxmfsK
Protect research funding
Federal funding for biomedical research is under threat.
bit.ly
February 14, 2025 at 12:03 AM
For decades, NIH funding has fueled breakthroughs in cancer, heart disease and more. But a new policy puts progress at risk. We need Congress to oppose this abrupt change. Join me in emailing lawmakers today! #SaveNIHresearch bit.ly/4hxmfsK
Reposted by Deniz Gökbuget
Trump & Musk are making massive cuts to the National Institutes of Health.
I know there is a lot going on right now, but this is one of worst things they have done so far, will affect cancer research and trials, the search for cures, innovation and competitiveness, our universities. Your lives.
I know there is a lot going on right now, but this is one of worst things they have done so far, will affect cancer research and trials, the search for cures, innovation and competitiveness, our universities. Your lives.
February 8, 2025 at 11:16 PM
Trump & Musk are making massive cuts to the National Institutes of Health.
I know there is a lot going on right now, but this is one of worst things they have done so far, will affect cancer research and trials, the search for cures, innovation and competitiveness, our universities. Your lives.
I know there is a lot going on right now, but this is one of worst things they have done so far, will affect cancer research and trials, the search for cures, innovation and competitiveness, our universities. Your lives.
🚨 New Paper Alert! 🚨
Our latest study on KMT2C/KMT2D (mutated in 20% of cancers) reveals a new function for H3K4me1 in regulating DNA replication timing (RT) and origin activity during cell state transitions. Check it out: www.cell.com/cell-reports.... More info ⬇️
Our latest study on KMT2C/KMT2D (mutated in 20% of cancers) reveals a new function for H3K4me1 in regulating DNA replication timing (RT) and origin activity during cell state transitions. Check it out: www.cell.com/cell-reports.... More info ⬇️
KMT2C/KMT2D-dependent H3K4me1 mediates changes in DNA replication timing and origin activity during a cell fate transition
Gökbuget et al. use machine learning to quantify chromatin state changes that predict
DNA replication timing changes during cell differentiation. By following up on top
predictors through functional v...
www.cell.com
February 4, 2025 at 5:06 PM
🚨 New Paper Alert! 🚨
Our latest study on KMT2C/KMT2D (mutated in 20% of cancers) reveals a new function for H3K4me1 in regulating DNA replication timing (RT) and origin activity during cell state transitions. Check it out: www.cell.com/cell-reports.... More info ⬇️
Our latest study on KMT2C/KMT2D (mutated in 20% of cancers) reveals a new function for H3K4me1 in regulating DNA replication timing (RT) and origin activity during cell state transitions. Check it out: www.cell.com/cell-reports.... More info ⬇️
Reposted by Deniz Gökbuget
Cancer Statistics 2025 are out! #prostatecancer incidence still on the rise, mortality basically flat. Get screened so you can get treatment _when needed_. #pcsm
acsjournals.onlinelibrary.wiley.com/doi/epdf/10....
acsjournals.onlinelibrary.wiley.com/doi/epdf/10....
January 16, 2025 at 11:25 PM
Cancer Statistics 2025 are out! #prostatecancer incidence still on the rise, mortality basically flat. Get screened so you can get treatment _when needed_. #pcsm
acsjournals.onlinelibrary.wiley.com/doi/epdf/10....
acsjournals.onlinelibrary.wiley.com/doi/epdf/10....
Really enjoyed this rigorous mechanistic study on the multifaceted principles of genome-wide heterochromatin maintenance during pluripotency from the Zaret lab (not on Bsky). Congrats to the authors: www.nature.com/articles/s41...
Distinct H3K9me3 heterochromatin maintenance dynamics govern different gene programmes and repeats in pluripotent cells - Nature Cell Biology
Zhang et al. uncover different dynamics underlying the maintenance and regulation of H3K9me3-enriched heterochromatin domains in mouse embryonic stem cells and propose that loss of H3K9me3 occurs thro...
www.nature.com
December 6, 2024 at 2:30 AM
Really enjoyed this rigorous mechanistic study on the multifaceted principles of genome-wide heterochromatin maintenance during pluripotency from the Zaret lab (not on Bsky). Congrats to the authors: www.nature.com/articles/s41...
Reposted by Deniz Gökbuget
Huaigeng is presenting his exciting work on developing cancer vaccines today at the UCSF Prostate Program retreat.
November 14, 2024 at 8:11 PM
Huaigeng is presenting his exciting work on developing cancer vaccines today at the UCSF Prostate Program retreat.
Reposted by Deniz Gökbuget
I'm excited to share a new publication from my previous lab building on our earlier work on PROTAC degraders targeting MDM2 for cancer therapy. More efficient MDM2 degraders have been developed as we gain deeper insights into their mechanisms. Check it out if interested! pubs.acs.org/doi/full/10....
Discovery of MD-265: A Potent MDM2 Degrader That Achieves Complete Tumor Regression and Improves Long-Term Survival of Mice with Leukemia
MDM2 has been pursued as an attractive therapeutic target for human cancers. Herein, we describe our discovery of MD-265 as a promising PROTAC MDM2 degrader and extensive in vitro and in vivo evaluati...
pubs.acs.org
November 13, 2024 at 7:02 PM
I'm excited to share a new publication from my previous lab building on our earlier work on PROTAC degraders targeting MDM2 for cancer therapy. More efficient MDM2 degraders have been developed as we gain deeper insights into their mechanisms. Check it out if interested! pubs.acs.org/doi/full/10....
Glad to see @robertblelloch.bsky.social over here, outstanding mentor and scientist. Follow him, and also check out his lab account: @rblellochlab.bsky.social
November 13, 2024 at 3:28 AM
Glad to see @robertblelloch.bsky.social over here, outstanding mentor and scientist. Follow him, and also check out his lab account: @rblellochlab.bsky.social
Reposted by Deniz Gökbuget
ok, I tried to make a starter pack on genome stability/DNA replication/DNA repair etc. Sorry if I couldn't find someone, please nominate yourself and your colleagues in comments or DMs, looking forward to connecting with everyone!
go.bsky.app/9jdDNxG
go.bsky.app/9jdDNxG
November 12, 2024 at 1:11 AM
ok, I tried to make a starter pack on genome stability/DNA replication/DNA repair etc. Sorry if I couldn't find someone, please nominate yourself and your colleagues in comments or DMs, looking forward to connecting with everyone!
go.bsky.app/9jdDNxG
go.bsky.app/9jdDNxG
Reposted by Deniz Gökbuget
The Blelloch Lab held a retreat in the Tahoe National Forest this weekend. We decided to join the Bluesky Science Community.
November 11, 2024 at 5:50 AM
The Blelloch Lab held a retreat in the Tahoe National Forest this weekend. We decided to join the Bluesky Science Community.
Reposted by Deniz Gökbuget
Gotta say this place got a billion times more interesting in the last few days. Let’s get everyone who we care about over here!
November 10, 2024 at 10:03 PM
Gotta say this place got a billion times more interesting in the last few days. Let’s get everyone who we care about over here!
Reposted by Deniz Gökbuget
So excited to see this released to the world! We've been talking about a new @nf-co.re manuscript for years - in the end it all came about rather quickly thanks to the collaboration with #EuroFaang!
Have a read and please share widely - this is a great opportunity to reach new audiences!
Have a read and please share widely - this is a great opportunity to reach new audiences!
Delighted to announce that a new @nf-co.re preprint manuscript has just gone live!
A collaboration with #EuroFAANG, the paper covers updates to #Nextflow and @nf-co.re, and describes the experience of the #EuroFaang as they adopted @nf-co.re.
Let's dive in... 🧵
www.biorxiv.org/content/10.1...
A collaboration with #EuroFAANG, the paper covers updates to #Nextflow and @nf-co.re, and describes the experience of the #EuroFaang as they adopted @nf-co.re.
Let's dive in... 🧵
www.biorxiv.org/content/10.1...
Empowering bioinformatics communities with Nextflow and nf-core
bioRxiv - the preprint server for biology, operated by Cold Spring Harbor Laboratory, a research and educational institution
www.biorxiv.org
May 14, 2024 at 10:15 PM
So excited to see this released to the world! We've been talking about a new @nf-co.re manuscript for years - in the end it all came about rather quickly thanks to the collaboration with #EuroFaang!
Have a read and please share widely - this is a great opportunity to reach new audiences!
Have a read and please share widely - this is a great opportunity to reach new audiences!
Thank you to International Society for Stem Cell Research and Kendra Prutton for representing me and my research. I am proud to be part of this impactful and enriching community.
www.isscr.org/isscr-news/m...
www.isscr.org/isscr-news/m...
February 12, 2024 at 7:43 PM
Thank you to International Society for Stem Cell Research and Kendra Prutton for representing me and my research. I am proud to be part of this impactful and enriching community.
www.isscr.org/isscr-news/m...
www.isscr.org/isscr-news/m...
Exciting news! 🧬🎄Our latest preprint on a new MLL3/MLL4 function in DNA replication timing is out: biorxiv.org/content/10.1... Grateful for this teamwork with Ryan Boileau, Kayla Lenshoek, Robert Blelloch.
@UCSF, @UCSFstemcell, @UCSFUrology, @UCSFCancer
@UCSF, @UCSFstemcell, @UCSFUrology, @UCSFCancer
December 9, 2023 at 1:37 AM
Exciting news! 🧬🎄Our latest preprint on a new MLL3/MLL4 function in DNA replication timing is out: biorxiv.org/content/10.1... Grateful for this teamwork with Ryan Boileau, Kayla Lenshoek, Robert Blelloch.
@UCSF, @UCSFstemcell, @UCSFUrology, @UCSFCancer
@UCSF, @UCSFstemcell, @UCSFUrology, @UCSFCancer