Jesse Raab

Benchmarking of proximity-dependent biotinylation enzymes across cellular compartments and time windows Proximity-dependent biotinylation has become a powerful approach for mapping protein interactions and subcellular organization in living cells. Although a growing number of engineered biotin ligases h...

🧪
@gingraslab.bsky.social
compared 10 enzymes used for proximity biotinylation proteomics experiments. UltraID is the winner.

www.biorxiv.org/content/10.1...

Unreal, the impact this is having on scientists. I spent over 700 hrs writing 4 grants submitted Apr-Sept that *might* have been funded next Apr; 2 abt to be 3 apps missed review bc of shutdown. In normal times takes 9-24 mo to get a grant funded. No hope for labs like mine. Literally no hope.

The scientific publishing is broken and open-access not only failed to fix it, it made it worse.
If we do not address the parasitic nature of the for-profit (>30% margins!) publishing, we will not solve the problem. And if the funders (universities) do not intervene, it won't change.

A must read:

Up to 323 cancelled CSR study sections. That's more than the 204 sections cancelled earlier this year. Rescheduling is going to be a hot mess with NIH staff reductions and study section members heading into finals and holidays that limit availability. 🧪

My reviewing style has changed over time. Rather than litigate every little thing, and pushing my own ideas, I focus only on 2 things:
(1) Are the claims interesting/important?
(2) Does the evidence support the claims?

Most of my reviews these days are short and focused.

The origin of hepatocellular carcinoma depends on metabolic zonation The origin of cancer is poorly understood because premalignant cells are rarely followed in their native environments. While the spatial compartmentalization of metabolic functions is critical for pro...

very cool paper on the location of tumor mutations within the liver changing cancer initiation www.science.org/doi/10.1126/...

PUT HER IN THE HALL AS A CONTRIBUTOR YOU COWARDS

oh. alright. two R01 at 5 years. 268 funded for 4 years, 57 for 3 years, 48 for 2 years. 8+804+114+48=974 excess new R01 years. Therefore something around 974 (some wobble based on actual budget amount of each grant) R01 grants that will not be funded FY2025 onward.

Tariffs are currently thwarting my plans for a second moonlander

Mechanisms of DNMT3A–3L-mediated de novo DNA methylation on chromatin - Nature Structural & Molecular Biology Yan et al. use cryo-EM to obtain structures that reveal how DNMT3A2 and DNMT3L cooperate to read histone signals and bind chromatin, illustrating a mechanism that controls DNA methylation and shapes e...

Some hardcore mechanism, for the aficionados (from Peter Jones @vai.org and Ting-Hai Xu @slu-official.bsky.social labs) @natsmb.nature.com www.nature.com/articles/s41...

oh wow, this is amazing

Spread the word! There is a professor position opening at our University @upcite.bsky.social. There are several possible (great) labs to join, but if you are interested in DNA methylation and epigenetics in mammals, don't hesitate to contact me directly!

imgs.xkcd.com/comics/compi...

Assessing molecular gene by treatment interactions using a population of neural progenitors exposed to valproic acid and lithium Gene by treatment (GxT) interactions likely contribute to variability in clinical response, but are difficult to identify in population studies. Here, we applied psychiatric and neurological disorder ...

Excited to share our new preprint on molecular gene x treatment interactions led by Jordan Valone, Brandon Le, and @nanamatoba.bsky.social. www.medrxiv.org/content/10.1.... Here, we tried to further develop the "pharmacogenomics in a dish" approach for psychiatry.

YEATS4 reads histone crotonylation to promote fatty acid metabolism and cancer cell stemness Peng et al. identify YEATS4 as a reader of H3K14cr, by which it activates genes in fatty acid metabolism and enhances the self-renewal of breast cancer stem cells, highlighting the role of YEATS4 as an amplifier in the circuit of histone crotonylation and fatty acid metabolism in breast cancer.

YEATS4 reads histone crotonylation to promote fatty acid metabolism and cancer cell stemness

CUT&Tag Overcomes Biases of ChIP and Establishes Chromatin Patterns for Repetitive Genomic Loci New in situ chromatin profiling methods, such as CUT&Tag, have streamlined studies of chromatin features by eliminating the need for up-front purifica…

"Our study reveals that the current understanding of chromatin states is extensively incomplete, and newer in situ chromatin fragmentation-based techniques are preferred for investigating repetitive elements and retrotransposons"

www.sciencedirect.com/science/arti...

Latest version of #depmap added to r2platform.com

R2: academic open online nocode data science platform for biomedical research

#DataScientist #biologist #clinician #genomics #Cancer

AEBP2-Directed H3K27me2 Defines a Specific Vulnerability in EZH2-mutant Lymphoma The catalytic subunit of Polycomb Repressive Complex 2 (PRC2), EZH2, is recurrently mutated in 25% of diffuse large B-cell lymphomas (DLBCL), causing increased H3K27me3 and decreased H3K27me2 levels. ...

🧵1/Exciting news in cancer epigenetics! Our latest research, "AEBP2-Directed H3K27me2 Defines a Specific Vulnerability in EZH2-mutant Lymphoma", is now available on www.biorxiv.org/content/10.1.... Here's a thread summarizing our findings!👇
#CancerResearch #Epigenetics #Chromatin #Lymphoma

Now that the data for fiscal year 2025 are complete, what did NIH's investments in training look like?

There are three mechanism classes to consider: T awards (institutional training grants), F awards (fellowships to individual scientists), and K awards (career development awards)

2/12

🦖 Something HUGE just hatched.

Plasmidsaurus now offers RNA sequencing for gene expression analysis:
• As fast as 3 day turnaround
• $50/sample for academia, $80 for industry
• Up to ~10M unique transcript 3’ end reads per sample
• Interactive results

Explore Plasmidsaurus RNA-Seq today.

UNC Sends Delegation for Capitol Event | Biochemistry and Biophysics Rally for Medical Research – September 18, 2025 | Washington, DC A delegation from UNC joined more than 400 advocates from across the country in Washington DC to urge Congress to prioritize funding fo...

UNC Sends Delegation for Capitol Event
Rally for Medical Research – September 18, 2025 Washington, DC
www.med.unc.edu/biochem/news...

Buffalo peeps! I am hosting a science spooktacular event at the new Third Space venue downtown on Oct 30 at 6PM! Come hear fun stories about science from trainees, all geared towards a non-specialist audience. Check the flyer for all the info! Please RT

YouTube video by Black In Biophys BIBPSSpotlight - 2025 Black In Biophysics Week

We are in this odd climate where people are pretending no barriers exist to careers in science for some groups, but this conversation with 2 outstanding emerging scientists highlights that is just not true.
youtube.com/watch?v=u850...

Picture of Eric

Picture of Rob

Amazing science continues to happen in the US, and we continue to hire remarkable new faculty. Already this term UNC Biology has had terrific promotion seminars from two rising stars: Eric Riddell and Rob Dowen. 1/n

Protein Domain Designer tool for the generation of publication-ready protein domain diagrams

New week, new tool: Find our Protein Domain Designer tool to generate publication-ready protein domain diagrams here: domaindesigner.farnunglab.com

Great department and job opportunity

Hey remember when the CDC dropped 6 of the 8 foodborne illnesses from the nationwide monitoring system in July and one of them was listeria? Mentioning for no particular reason www.nbcnews.com/health/healt...

I think the same thing while I fill out my 800th conflict of interest declaration for submitting a grant

A grant showing the number of projects funded for FY2021 through FY2025. The number for FY2025 lagged behind and did not catch up with 4014 fewer projects funded in FY2025 compared with FY2024.

Here are the results in terms of the number of projects.

The number of funded projects in FY2025 is 4014 fewer than the number for FY2024.

2/3

I believe so