Jeremy Simon

A lovely meditation on community.

(Go there, the food is really good!)

This one hurts, truly a legend

Files referring to coordinates without genome info should be gone

we should always include genome digests

According to Google search trends, it was in the vernacular since at least Jan 1 2008

Rowboats and a boathouse on a blue-green lake in front of mountains

A refuge dwarfed by huge mountains in northern Italy

The Seceda ridgeline in the Dolomites

A gondola on the main canal of Venice at dusk

And for an added bonus, here are some photos I took highlighting the incredible places seen in recent weeks

I really hope this becomes a standard for publications with complex analyses as it is essential for reproducibility. Quarto makes this quite easy (and beautiful!)

Far too many papers have no code at all or simply state "custom code for analysis is available upon reasonable request" (or similar)

Was out of town when this first dropped, so following up now to call attention to our *extensive* github repo consisting of 7 quarto books (written by Chloe Tu and me) that contain all code to produce the figures shown in this paper:
github.com/jeremymsimon...

Very excited this is finally published in the ISMB proceedings. This was @noorpratap.bsky.social's last conference-related paper in my lab (but look out for a new Genome Research paper soon), & a monumental effort. It's already integrated into simpleaf. Noor will be presenting it at ISMB next week!

A multi-adjuvant personal neoantigen vaccine generates potent immunity in melanoma A personalized neoantigen peptide vaccine formulated with Montanide plus poly-ICLC and administered with local ipilimumab plus systemic nivolumab induces robust neoepitope-specific T cell responses and reshapes the T cell repertoire in blood and tumor.

Now online! A multi-adjuvant personal neoantigen vaccine generates potent immunity in melanoma

Dana-Farber Cancer Institute in Cell

In a study published in @cellpress.bsky.social, @danafarber.bsky.social researchers showed that a modified NeoVax cancer vaccine triggered strong immune responses in melanoma.

Read more: bit.ly/44nz5Wp

A multi-adjuvant personal neoantigen vaccine generates potent immunity in melanoma A personalized neoantigen peptide vaccine formulated with Montanide plus poly-ICLC and administered with local ipilimumab plus systemic nivolumab induces robust neoepitope-specific T cell responses an...

The more potent and bespoke immunotherapy vs cancer, the better. Today's example is a neoantigen vaccine vs melanoma
cell.com/cell/fulltex...

A multi-adjuvant personal neoantigen vaccine generates potent immunity in melanoma A personalized neoantigen peptide vaccine formulated with Montanide plus poly-ICLC and administered with local ipilimumab plus systemic nivolumab induces robust neoepitope-specific T cell responses an...

Our new study investigating combination neoantigen vaccine plus montanide and Ipi in melanoma is now online in @cellpress.bsky.social !

A multi-adjuvant personal neoantigen vaccine generates potent immunity in melanoma: www.cell.com/cell/fulltex...

This is the message. Everyone in the US should have access to life-saving treatments in their state. The value is immense, and we would be throwing away a half century of investment to lose these centers and research hospitals. The risk of losing these is real as we look to a 2026 budget.

From @kimrynrathmell.bsky.social

Much of my work since joining @danafarber.bsky.social has been focused on this exciting field of personalized immunotherapy and its potential to treat many forms of cancer

Stay tuned as one of these newest stories is in press!

GitHub - COMBINE-lab/QCatch: Quality Control downstream of alevin-fry / simpleaf Quality Control downstream of alevin-fry / simpleaf - COMBINE-lab/QCatch

🚀 We are thrilled to introduce QCatch — a fast, command-line QC reporting tool built for alevin-fry & simpleaf single-cell data! Led by @ygao61.bsky.social & in collaboration with Dongze He 🧬🖥️ . The Preprint 📖 is available at bit.ly/4neSznl. Read more below: 1/3

A very large proportion of these are HIV related. And many terminated on this list relate to cancer, Alzheimer's, diabetes, etc- despite what some politicians may be saying

Research Officer - Bioinformatics Job in Fitzroy, Melbourne VIC - SEEK Seeking a Postdoc to develop computational toolkits to enable large-scale studies of single-cell and spatial 'omics and statistical genetics

📢 PostDoc opportunity in our Bioinformatics & Cellular Genomics lab at SVI! 🧬

You’d join a welcoming, supportive, and brilliant team.

Why not spend a few years in Melbourne and be part of something exciting?

Apply here: www.seek.com.au/job/84737876

#ScienceCareers #PostDoc #Bioinformatics

Or..perhaps it broadens it? Is there a package you can cook up called "tximitxurri", or "txistu"?

This was such a funny thing to me- in Basque country in Spain, so many business names began with "txi". @mikelove.bsky.social had no idea but it really limits his potential for universal brand awareness 😆

Spanish reticulated dumptruck brand Tximela got a re-brand to Tximeta, and is carrying a large photoshopped fish in its bed

Reminds me of an oldie but a goodie

Or if the tracking of novel txps is itself optional, you can instead make synonyms on the executable itself, ie oarfish (known only) and moarfish (both) 😂

I personally like --known and --novel

#opentowork | Bryan Quach #opentowork So far this year, RTI International has reduced its workforce by 35%. This week I became part of that 35% as the institute adjusts to the ongoing changes in federal funding. Feel free to r...

My former lab mate, Bryan Quach, is an amazing scientist! Unfortunately due ongoing changes in federal funding he's part of RTI's reduction in workforce. If you're looking for a data scientist or bioinformatician? Hire him! www.linkedin.com/posts/bryanq...

My local shop used to sell watermelon pre-cut into quarters but I refused to buy it because they failed to appropriately label it "Quartermelon"

It must be Open Eye then 😅

My sympathy and support for all the international students and postdocs at Harvard. I can only imagine how scary this must feel. Stay strong. And if there's anything I can do to help those in compbio, please reach out. All of us need to rally to help them out. 1/

Stephanie Hicks named fellow of the American Statistical Association Hicks was recognized for her professional contributions, leadership, and commitment to the field of statistics.

Congratulations to Malone Center affiliate member @stephaniehicks.bsky.social on this distinction from @amstatnews.bsky.social!

Tag yourself, I'm 2016 👋

Very interesting result here! I wonder if anything parallel to what we found in renal cell carcinoma applies here? We previously found that JMJD6 regulates DGAT1 and lipid droplet formation
pubmed.ncbi.nlm.nih.gov/35764091/

I will never forget this, especially because it came on the heels of your reluctance to admit you were a hipster 😂😂