iiinova — where your digital self keeps evolving

Reposted by Deniz Gökbuget

UCSF Broad Stem Cell Center @ucsfstemcell.bsky.social · 25/08/2026

@robertblelloch.bsky.social + team engineered iPSC-derived dendritic cells coated w/ patient tumor membranes to present multiple cancer antigens to T cells. The approach induced tumor-specific T cell responses in patient samples and slowed tumor growth in humanized mice. www.cell.com/cell-stem-ce...

cell.com

Engineered human iPSC-derived dendritic cells dressed with tumor MHC complexes as a cancer vaccine

Blelloch and colleagues create genetically engineered universal human iPSCs, differentiate them into CCR7+ migratory dendritic cells, and dress them with tumor-derived MHC class I-antigen complexes to...

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Reposted by Deniz Gökbuget

Meghan Bartels @meghanbartels.bsky.social · 24/06/2026

I’m so sad to share that yesterday was my last day at Scientific American. It was an honor to work alongside my incredible colleagues and to speak with researchers across the sciences. If you’re looking to hire staff or freelance, please consider me and my other laid off coworkers (🧵)

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Deniz Gökbuget @denizgoekbuget.bsky.social · 10/12/2025

We’re hiring now: 2026 Translational Medicine – Oncology Intern (Genentech, SSF). Work on epigenetics, multi-omics, and biomarker discovery for targeted therapies. PhD students in relevant fields encouraged to apply. Details and how to apply: roche.wd3.myworkdayjobs.com/ROG-A2O-GENE...

roche.wd3.myworkdayjobs.com

2026 Summer Intern - Translational Medicine

2026 Summer Intern - Translational Medicine Department Summary In Translational Medicine, our vision is to create the future of medicine by applying borderless, rigorous translational science to radic...

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Deniz Gökbuget @denizgoekbuget.bsky.social · 28/10/2025

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.

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Deniz Gökbuget @denizgoekbuget.bsky.social · 04/09/2025

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

Cell Press: STAR Protocols

STAR Protocols is an open access, peer-reviewed journal from Cell Press. We offer structured, transparent, accessible, and repeatable step-by-step experimental and computational protocols from all are...

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Reposted by Deniz Gökbuget

Eric Topol @erictopol.bsky.social · 06/07/2025

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 · 03/07/2025

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?...

youtu.be

Active Surveillance: Past, Present, and Future

YouTube video by ASPI: Active Surveillance Patients International

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Deniz Gökbuget @denizgoekbuget.bsky.social · 11/06/2025

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 · 11/06/2025

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 · 11/06/2025

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 · 02/06/2025

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 · 16/05/2025

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 · 02/05/2025

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...

nature.com

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...

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Reposted by Deniz Gökbuget

Evgeny Kvon @evgenykvon.bsky.social · 09/04/2025

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...

nature.com

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 ...

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Deniz Gökbuget @denizgoekbuget.bsky.social · 14/02/2025

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

bit.ly

Protect research funding

Federal funding for biomedical research is under threat.

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Reposted by Deniz Gökbuget

Sen. Adam Schiff @schiff.senate.gov · 08/02/2025

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 · 05/02/2025

Thanks for the shout-out, we appreciate it.

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Deniz Gökbuget @denizgoekbuget.bsky.social · 05/02/2025

Thanks for your kind words, and your amazing contributions!

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Deniz Gökbuget @denizgoekbuget.bsky.social · 04/02/2025

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.

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Deniz Gökbuget @denizgoekbuget.bsky.social · 04/02/2025

6/ • 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 · 04/02/2025

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

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Deniz Gökbuget @denizgoekbuget.bsky.social · 04/02/2025

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

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Deniz Gökbuget @denizgoekbuget.bsky.social · 04/02/2025

3/ 📊 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 · 04/02/2025

2/ 🔬 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.

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Deniz Gökbuget @denizgoekbuget.bsky.social · 04/02/2025

1/ 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). 🙏

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Deniz Gökbuget @denizgoekbuget.bsky.social · 04/02/2025

🚨 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 ⬇️

cell.com

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...

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Reposted by Deniz Gökbuget

Matt Cooperberg @dr-coops.bsky.social · 16/01/2025

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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Reposted by Deniz Gökbuget

Blelloch Lab UCSF @rblellochlab.bsky.social · 14/11/2024

Huaigeng is presenting his exciting work on developing cancer vaccines today at the UCSF Prostate Program retreat.

Huaigeng Xu at the podium ready to give his presentation.

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Reposted by Deniz Gökbuget

Jiuling Yang @jiulingy.bsky.social · 13/11/2024

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....

pubs.acs.org

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...

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Deniz Gökbuget @denizgoekbuget.bsky.social · 13/11/2024

Thanks so much, Oliver. Also, I would recommend adding: @robertblelloch.bsky.social

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Deniz Gökbuget @denizgoekbuget.bsky.social · 13/11/2024

Glad to see @robertblelloch.bsky.social over here, outstanding mentor and scientist. Follow him, and also check out his lab account: @rblellochlab.bsky.social

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Deniz Gökbuget @denizgoekbuget.bsky.social · 12/11/2024

Mind adding me as well? Much appreciated!

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Reposted by Deniz Gökbuget

Tatiana Moiseeva @tat1anamoiseeva.bsky.social · 12/11/2024

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

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Reposted by Deniz Gökbuget

Blelloch Lab UCSF @rblellochlab.bsky.social · 11/11/2024

The Blelloch Lab held a retreat in the Tahoe National Forest this weekend. We decided to join the Bluesky Science Community.

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Reposted by Deniz Gökbuget

Benoit Bruneau @benoitbruneau.bsky.social · 10/11/2024

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!

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Reposted by Deniz Gökbuget

Phil Ewels @ewels.bsky.social · 14/05/2024

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!

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Deniz Gökbuget @denizgoekbuget.bsky.social · 12/02/2024

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...

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Deniz Gökbuget @denizgoekbuget.bsky.social · 11/12/2023

compbio.mit.edu/ChromHMM/ Iteratively tuning the parameters should get you closer to the desired domain-sized segments.

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Deniz Gökbuget @denizgoekbuget.bsky.social · 11/12/2023

Could try ChromHMM-like approaches.

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Deniz Gökbuget @denizgoekbuget.bsky.social · 09/12/2023

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

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