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Jeremy Simon @jeremymsimon.bsky.social · 1d

Years ago when I was at UNC (now at DFCI) we were looking at environmental chemicals and came across this class of fungicides that induced a lot of transcriptional changes in neurons:
www.nature.com/articles/nco...
Curious if there could be something additive here..?

Identification of chemicals that mimic transcriptional changes associated with autism, brain aging and neurodegeneration - Nature Communications

This study presents gene expression responses of cultured brain cells to hundreds of chemicals found in the environment and in food. The authors identified chemicals that induce transcriptomic profiles that overlap those seen in human brains affected with autism, aging, and neurodegeneration.

www.nature.com

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Jeremy Simon @jeremymsimon.bsky.social · 1d

Super interesting results! Do you think this proximity could lead to secondary problems, in that if these mitochondria are also dysfunctional and producing ROS, their proximity to the nucleus increases the probability of DNA damage?

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Jeremy Simon @jeremymsimon.bsky.social · 2d

Incredible opportunity to go train with the Patro lab @umdscience.bsky.social and develop new genomic methods!

Rob Patro @robp.bsky.social · 2d

Hi bioinformatics, genomics and CS friends! Please help me spread the word. I'm hiring a postdoc! Come work on cutting edge method development in algorithmic genomics with me and my group at @umdscience.bsky.social! 🖥️🧬

Rob Patro @robp.bsky.social · 4d

And it's posted! If you're interested and eligible, please consider applying through the UMD portal: umd.wd1.myworkdayjobs.com/en-US/UMCP/j....

If you're a PI working in algorithmic genomics (& you can recommend my lab to your top graduating students ;P), please let them know!

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Jeremy Simon @jeremymsimon.bsky.social · 16d

Got it, thanks! It's less clear to me whether there's any benefit to this cohort-level approach if you're dealing with patient samples but curious if you or others have thoughts on that

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Jeremy Simon @jeremymsimon.bsky.social · 16d

but maybe it doesn't add much in this context? e.g. I have n=6 treated and control cell lines and I'm looking to predict antigens enriched in the treated cells. This workflow may find antigens enriched in any one replicate, but could/should we merge splice/transcript assemblies and quantify across?

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Jeremy Simon @jeremymsimon.bsky.social · 16d

This looks great! One question I have is whether each sample in a cohort gets processed completely independently, or whether there is any cohort-level discovery and quantification? I've always thought a 2-pass approach to assemble and quantify across samples was preferred if the data were available

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Reposted by Jeremy Simon

Boston Public Health Commission @publichealth.boston.gov · 18d

We’re offering free vaccine clinics in Boston. Vaccines are safe, effective, and protect against serious illness. Getting vaccinated keeps you healthy and helps protect your family, friends, and community.

Learn more at boston.gov/vaccine-clinics.

A group of young people sit on a bench behind a fence at a baseball diamond. Text reads, “FREE Vaccine Clinics in Boston. Get your flu and COVID-19 vaccines for free. No appointment necessary, walk-ins welcome. Find dates, times, and locations at boston.gov/vaccine-clinics.” The logos for the City of Boston, Boston Public Health Commission, Boston Public Schools, Boston Centers for Youth and Families, Legacy Care Group, and Shaw’s Star Market are at the bottom.

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Jeremy Simon @jeremymsimon.bsky.social · Sep 12

Pretty sure original authors say attack-seek

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Jeremy Simon @jeremymsimon.bsky.social · Sep 8

"Healthcare access" is not healthcare

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Jeremy Simon @jeremymsimon.bsky.social · Sep 8

This is a test run, they'll employ this same model to polling places in NC for the next election

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Jeremy Simon @jeremymsimon.bsky.social · Sep 2

I also will often work backwards for an entire analysis: figure out what question I'm trying to answer, what the key conclusion is, sketch an idealized figure that would support that conclusion, then figure out the steps to make that figure. Then cry and repeat when it doesn't match my sketch

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Reposted by Jeremy Simon

Rob Patro @robp.bsky.social · Aug 21

🧬🖥️ Thrilled that our paper "Tree-based differential testing using inferential uncertainty for RNA-seq" genome.cshlp.org/content/earl..., led by @noorpratap.bsky.social, & in collab with @mikelove.bsky.social, @fennecpaaaw.bsky.social and Jason Fan is now accepted at @genomeresearch.bsky.social. 1/4

Tree-based differential testing using inferential uncertainty for RNA-seq

An international, peer-reviewed genome sciences journal featuring outstanding original research that offers novel insights into the biology of all organisms

genome.cshlp.org

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Reposted by Jeremy Simon

Brian Strahl @brianstrahl.bsky.social · Aug 11

Ever wondered what else SETD2 does beyond transcription? 🧬
Check out our new ‪@natcellbio.nature.com‬ study.
Awesome work from Abid Khan in the lab SETD2 moonlights during mitosis to keep the genome safe from chaos.showing how SETD2 moonlights to safeguard the genome during cell division.

SETD2 moonlights during mitosis to keep the genome safe from chaos.https://www.nature.com/articles/s41556-025-01723-9

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Reposted by Jeremy Simon

Damien C-C @dccc-phd.bsky.social · Aug 8

A lovely meditation on community.

(Go there, the food is really good!)

WBUR @wbur.org · Aug 8

Essay: As a Somerville resident, the Palestinian-owned Yafa Bakery & Café quickly became my “third space,” writes Lydia Begag. I’d find myself wandering there for a cup of chai or piece of baklawa, but it was the owner, Abdulla Awad, who really brought me back.

A Palestinian bakery in Somerville that always feels like home

What continues to make Yafa so special is that what might feel sacred elsewhere is the standard here, writes Lydia Begag. Over time, I started paying attention not just to how Abdulla’s practice of ‘a...

www.wbur.org

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Jeremy Simon @jeremymsimon.bsky.social · Aug 7

This one hurts, truly a legend

NPR @npr.org · Aug 7

Grammy-winning bandleader and pianist Eddie Palmieri, whose pounding rhythms forged a new style for Latin music, has died.

Eddie Palmieri, a trailblazer in Latin music, has died at age 88

The bandleader and pianist was one of the leading Latin musicians of his generation. He won multiple Grammys and was recognized as an NEA Jazz Master.

n.pr

Reposted by Jeremy Simon

Michael Love @mikelove.bsky.social · Aug 5

Files referring to coordinates without genome info should be gone

we should always include genome digests

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Jeremy Simon @jeremymsimon.bsky.social · Jul 29

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

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Jeremy Simon @jeremymsimon.bsky.social · Jul 18

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

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

A refuge dwarfed by huge mountains in northern Italy

A gondola on the main canal of Venice at dusk

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Jeremy Simon @jeremymsimon.bsky.social · Jul 18

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)

Jeremy Simon @jeremymsimon.bsky.social · Jul 18

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...

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Reposted by Jeremy Simon

Rob Patro @robp.bsky.social · Jul 18

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!

Davide CIttaro @daweonline.bsky.social · Jul 18

🔥🔥🔥

academic.oup.com/bioinformati...

Alevin-fry-atac enables rapid and memory frugal mapping of single-cell ATAC-seq data using virtual colors for accurate genomic pseudoalignment

AbstractSummary. Ultrafast mapping of short reads via lightweight mapping techniques such as pseudoalignment has significantly accelerated transcriptomic a

academic.oup.com

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Reposted by Jeremy Simon

Cell - a Cell Press journal @cp-cell.bsky.social · Jul 10

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

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.

dlvr.it

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Reposted by Jeremy Simon

Dana-Farber News @danafarbernews.bsky.social · Jul 10

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

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Reposted by Jeremy Simon

Eric Topol @erictopol.bsky.social · Jul 10

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...

cell.com

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Jeremy Simon @jeremymsimon.bsky.social · Jul 10

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...

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...

www.cell.com

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