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Deniz Gökbuget

@denizgoekbuget.bsky.social

1.6K followers 340 following 24 posts

Principal Scientist @Genentech | Translational research & biomarker development in prostate cancer. Passionate about bridging science and patient impact.

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Deniz Gökbuget @denizgoekbuget.bsky.social · Feb 4

🚨 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 ⬇️

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

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Deniz Gökbuget @denizgoekbuget.bsky.social · 6d

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.

Deniz Gökbuget @denizgoekbuget.bsky.social · Sep 4

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

Reposted by Deniz Gökbuget

Eric Topol @erictopol.bsky.social · Jul 6

Summary Table of the massive defunding of biomedical research in the United States
www.nytimes.com/interactive/...

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Reposted by Deniz Gökbuget

UCSF Department of Urology @ucsfurology.bsky.social · Jul 3

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?...

Active Surveillance: Past, Present, and Future

YouTube video by ASPI: Active Surveillance Patients International

youtu.be

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Deniz Gökbuget @denizgoekbuget.bsky.social · Jun 18

This one hits different these days: www.youtube.com/watch?v=MBH-... #TheFlamingLips #ResearchLife

Race for the Prize (2017 Remaster)

YouTube video by The Flaming Lips - Topic

www.youtube.com

Deniz Gökbuget @denizgoekbuget.bsky.social · Jun 11

Really cool work led by @huaigengxu.bsky.social. Too bad, I don't get to see it live. 🤞

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Reposted by Deniz Gökbuget

HuaigengXu @huaigengxu.bsky.social · Jun 11

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

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Reposted by Deniz Gökbuget

Robert Blelloch @robertblelloch.bsky.social · Jun 11

great start to ISSCR annual meeting. great session on immune engineering this morning @isscr.org #isscr2025

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Reposted by Deniz Gökbuget

Sarah Hörst @planetdr.bsky.social · Jun 2

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

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Reposted by Deniz Gökbuget

Ryan Boileau @bffswithbiology.bsky.social · May 16

Oof, just got notice HHMI is not even doing Hanna Gray Fellows, or any competition, this year due to the challenging times in science funding rn 😬 Understandable. On the bright side, I was really proud my application🌈 #science #nih #hhmi

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Reposted by Deniz Gökbuget

Magdalena Skipper @magdalenaskipper.bsky.social · May 2

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...

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

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Reposted by Deniz Gökbuget

Evgeny Kvon @evgenykvon.bsky.social · Apr 9

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...

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

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Deniz Gökbuget @denizgoekbuget.bsky.social · Feb 14

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

Reposted by Deniz Gökbuget

Sen. Adam Schiff @schiff.senate.gov · Feb 8

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.

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Deniz Gökbuget @denizgoekbuget.bsky.social · Feb 5

Thanks for the shout-out, we appreciate it.

Deniz Gökbuget @denizgoekbuget.bsky.social · Feb 5

Thanks for your kind words, and your amazing contributions!

Deniz Gökbuget @denizgoekbuget.bsky.social · Feb 4

7/
This experience underscores the need for a more supportive review process to effectively promote the next generation of scientists.
We thank those reviewers and editors who were tough but fair sports, providing constructive feedback that helped improve our work. Also, we thank NIH for support.

Deniz Gökbuget @denizgoekbuget.bsky.social · Feb 4

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• Reviewer defamatory language 😔
• Lack of reviewer argumentation (claim, reason, support, and warrant)
• De novo concerns in 2nd round review
• Lack of support from journal team despite 8 months of costly revision experiments

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Deniz Gökbuget @denizgoekbuget.bsky.social · Feb 4

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However, our journey wasn’t without challenges. Previous submission to a major NPG journal faced:

Deniz Gökbuget @denizgoekbuget.bsky.social · Feb 4

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📃 Our findings highlight critical new functions of KMT2C/KMT2D beyond transcriptional regulation, essential for understanding diseases associated with mutations in these genes.

Deniz Gökbuget @denizgoekbuget.bsky.social · Feb 4

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📊 Key Findings:
• Chromatin state predicts local RT in steady state and its changes during differentiation.
• H3K4me1 emerges as a top predictor.
• Loss of H3K4me1 locally impairs RT changes independent of transcription.
• H3K4me1 locally promotes replication origin activation.

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Deniz Gökbuget @denizgoekbuget.bsky.social · Feb 4

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🔬 Approach:
• Developed an improved biotin-based DNA RT profiling method.
• Profiled 21 chromatin features by CUT&Tag during early pluripotency cell state transition.
• Used machine learning to identify chromatin features predictive of RT in steady state and during differentiation.

Deniz Gökbuget @denizgoekbuget.bsky.social · Feb 4

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I am grateful to have led this research, working alongside an incredible team: Liana Goehring (@lianagoehring.bsky.social), Ryan Boileau (@bffswithbiology.bsky.social), Kayla Lenshoek (@klenshoek.bsky.social), Tony Huang, and Robert Blelloch (@robertblelloch.bsky.social). 🙏

Deniz Gökbuget @denizgoekbuget.bsky.social · Feb 4

KMT2C/KMT2D-dependent H3K4me1 mediates changes in DNA replication timing and origin activity during a cell fate transition

www.cell.com

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Reposted by Deniz Gökbuget

Matt Cooperberg @dr-coops.bsky.social · Jan 16

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....

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