An interesting little side bit as I make my way through this: "[...] the majority of peaks were distal to promoter regions: only 4.0% were within 200 bp of a transcription start site (TSS), and most were > 2 kb from the nearest TSS (Fig. 1G)"

This headline is headed straight to Wait Wait Don't Tell Me...and is also a microcosm of many of the things wrong with this country

We need this in Boston @mbta.com @mayorwu.boston.gov

For me, it was watching sigourney weaver handle the micropipette in Avatar. Ruined the movie.

Hi @benforward3.bsky.social whose jurisdiction is it to get the @mbta.com huge escalators (and elevators) at Porter working again, and keep them working for more than a few weeks at a time? Asking for a friend 🙃😅

I have an academic publishing joke but you have to review these 3 articles for free, pay $4,000 in open access fees, sign in through your library proxy, and sacrifice a goat to get through the paywall to hear more than the first 150 words

🔔 I’m thrilled to announce that I’m running for State Rep! We have accomplished an enormous amount of progressive change in Somerville over the past eight years, and I am fired up to bring this work to the State House. I’m so excited to start knocking doors and earning your votes. Press release 👇

PSA to anyone trying: it seems the GEO FTP servers are down to new submissions due to the partial government shutdown. Keep this in mind if you have a manuscript in prep- or submit to @ebi.embl.org ArrayExpress instead!

Sunsets in Boston are after 5pm starting *tomorrow*. In just over 1 month we'll have daylight at 7pm again. #wbz

The elderly lobsterwoman who was the subject of the best photo ever has passed away. www.bostonglobe.com/2026/01/27/m...

Just looked into data access for a recent cancer single-cell multi-omics study. ~100 biopsies, ~500k cells--potentially an amazing resource for the field Only the raw FASTQs in dbGaP alongside 8 pgs of Methods describing how the data were analyzed; no code, no processed data. We have to do better!

I am looking for a postdoc to develop high-performance algorithms in computational genomics. Email or DM me if interested. For more information, see hlilab.github.io/vacancies. RTs appreciated!

579 high-quality human genomes from @humanpangenome.bsky.social, Arab Pangenome and individual papers (CHM13, CN1, KSA001, I002C, YAO and KOREF1). Sequences available in the AGC format (3.7GB) and FM-index in the ropebwt3 format (20.3GB). For details, see github.com/lh3/human-asm

It’s the “season of love and giving”…but this year, doesn’t it seem more like a “season of fear and taking”? Like many of you, I’ve been saddened by the human impact of draconian government budget cuts and how angry many housed Americans are at unhoused Americans. 🧵 1 of 9

We are thrilled to announce the first official release (v0.1.8) of #𝗯𝗲𝗱𝗱𝗲𝗿, the successor to one of our flagship tool, #𝗯𝗲𝗱𝘁𝗼𝗼𝗹𝘀! Based on ideas we conceived of long ago (!), this was achieved thanks to the dedication of Brent Pedersen. 1/n

📢 We are taking applications for our Postdoctoral Fellows Program at Harvard/DFCI! 🔹Join a research group in our department 🔹Co-mentoring opportunities with 2+ faculty 🔹Collaborate with investigators beyond our department 🔹Salary starts at $75K Apply here: t.co/B7SLZzQFKu

Many people hours, calls and messages later: OSTA is now “in (pre)print”, though the real thing lives at bioconductor.org/books/OSTA. Check it out, get in touch. We welcome any feedback, suggestions, wishes (& contributions). It’s been a joy working with you @estellayixingdong.bsky.social!

Despite city lights and buildings, clearest view of the Aurora from Somerville I've ever seen!

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.

PSA: Many of you may have noticed a website floating around called formatmypaper(dot)com. People rightly noted something was fishy. I dig into what happened here: open.substack.com/pub/ubadah/p...

Online now: Pan-cancer spatial characterization of key immune biomarkers in the tumor microenvironment

Today at #ASHG25 I will talk about the work of a talented graduate student Dev Raj Bhattarai on cell type-specific isoform expression in Alzheimer's disease at the @nanoporetech.com Education Session (12pm Rm 153). Dev will also present his work today at poster 9228T.

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

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.

🧬🖥️ 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

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.

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

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!

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

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

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

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!

🚀 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

📢 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

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 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/

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/

Implement a 100% tarrif and ruin a movie Four⊢een

Online now in Cancer Discovery concurrent with the #AACR25 Opening Plenary, by plenary speaker Catherine Wu: The Future of Personalized Cancer Vaccines doi.org/10.1158/2159...#AACR25

longcallD is a new variant caller for genomic long reads. It jointly calls phased small and structural variants. Single binary, one command line for the whole process. Comparable accuracy to mainstream callers. Great work by Yan Gao. github.com/yangao07/lon...