Excited to share my first preprint on federated conditional analysis of rare single variant and aggregate association tests across six genetically-inferred ancestry groups in All of Us and UK Biobank doi.org/10.64898/202...

Preprint from @lpachter.bsky.social lab argues journals should treat results as machine-readable objects, not just PDFs. Narratives stay for humans, but claims, evidence, and evaluations should ship in structured form so machines can index and verify. www.biorxiv.org/content/10.6... 1/ 🧵

Re-analysis of human population-scale whole genome seq data elucidates genetic architecture of EBV DNA persistence, a framework for the broader human virome @nature.com @caleblareau.bsky.social @sherrynyeo.bsky.social @erinmayc.bsky.social @ryandhindsa.bsky.social www.nature.com/articles/s41...

This was a fun and rewarding collaboration! A great example of extracting biological signal from data hiding in plain sight

Today in @nature.com, we describe how discarded reads in biobank-scale WGS can help resolve the genetic predictors and consequences of Epstein-Barr Virus (EBV) infection. Wonderful working with @ryandhindsa.bsky.social @sherrynyeo.bsky.social @erinmayc.bsky.social www.nature.com/articles/s41...

The Cancer Signaling & Microenvironment Program at Fox Chase Cancer Center is looking for tenure track faculty (assist./assoc./full) in computational & experimental protein design. CV & 3-page research statement by Feb 15. More info here: www.linkedin.com/feed/update/... Questions: DM/Email me.

i see this all the time with no mention of structural suppression: - Electoral College winner-take-all - working day elections - voter registration burden turnout in battleground states is fairly high. people aren't lazy. they are responding to disincentivization and disenfranchisement.

We are very excited to share the first preprint of a new direction for our group. Led by the fearless duo of @arthurwchow.bsky.social and @hoyinchu.bsky.social, our foray into computational protein design—

I had an unbelievable first time running the NYC Marathon with @fredsteammskcc.bsky.social and @mskcancercenter.bsky.social! Shout out to the lab for supporting us!

We have some BIG PLANS TONIGHT!!! with @ronanchaligne.bsky.social @mskcancercenter.bsky.social

We're excited to share that Dr. Omar Abdel-Wahab, a leukemia specialist at MSK, has been elected to the @nam.edu. With Dr. Abdel-Wahab’s appointment, a total of 28 MSK faculty members have been conferred with this recognition. Congratulations, Dr. Abdel-Wahab! bit.ly/49ezKw0

Zero arrests. 100,000 people. No violence. This who we are.

#nokings #nyc #weareallthefrog

Penn and USC have also rejected the Compact! That makes 4 - stronger together. www.insidehighered.com/news/faculty...

The data is from April but holy moly

How can mitophagy be an effective quality control mechanism if mtDNA mutations reach high enough levels to cause disease? This question led us into a dark path, full of concepts of evolutionary genetics, germline stem cell biology and mito-nuclear compatibility. www.science.org/doi/10.1126/...

Now that I'm settled in at @umasschan.bsky.social, I'm hiring at all levels: grad students, post-docs, and software engineers/bioinformaticians! The goal of my lab is to understand the regulatory role of every nucleotide in our genomes and how this changes across every cell in our bodies.

Two group leader positions available in the broader areas of RNA science, RNA technologies, and RNA medicine. Attractive packages and a great environment. Come and join us at Helmholtz RNA Würzburg, Bavaria.

We’re excited to report work led by postdoc Jennifer Porat in the lab, finding that DNA accumulates on the surface of living cells and that the secreted extracellular protein DNASE1L3 can modulate its levels on B and T cells. With a new twist for ATAC-seq as well www.biorxiv.org/content/10.1...

A new Nature Medicine study analyzing health records from >100 million people in the US offers compelling evidence that reactivation of varicella-zoster virus (VZV) ,the same virus that causes chickenpox and shingles may contribute to dementia risk. www.nature.com/articles/s41...

BREAKING: The Nobel Prize in Physiology or Medicine has been awarded jointly to Mary E. Brunkow, Fred Ramsdell, and Shimon Sakaguchi "for their discoveries concerning peripheral immune tolerance" Stay tuned for more. #NobelPrize

Great article from @stephaniemlee.bsky.social at @chronicle.com on the NIH Autism Data Science Initiative (ADSI) www.chronicle.com/article/what... ADSI funding went to reputable scientists because and only because dedicated NIH civil servants fought hard to ensure a rigorous, science-based process.

Does anyone have a good, reasonably up-to-date review of cryo-EM uses and methodology for (relatively) high-resolution protein structure determination? For someone who doesn't have a cryo-EM background.

Reminder starting in October NIH NOFOs won’t be posted in the Guide for grants and contracts. Tips on how to search for opportunities & set up a subscription for custom searches here: grants.nih.gov/news-events/...

Introducing Spacelink, a unified framework for identifying and prioritizing spatially variable gene programs at tissue and cell type resolution and linking them to disease GWAS studies. Led by Hanbyul Lee & Haochen Sun www.biorxiv.org/content/10.1...

🚨 New preprints from our lab!
First, we introduce Cryo-mtscATAC-seq, led by Maren (@ms-maren.bsky.social ), enabling high-throughput clonal tracing from frozen human samples by isolating nuclei with their mitochondria (“CryoCells”).
👉 www.biorxiv.org/content/10.1...

I'd like to announce the medRxiv preprint of our latest work: A multimodal atlas of COVID-19 severity identifies hallmarks of dysregulated immunity. www.medrxiv.org/content/10.1...

my mom took tylenol when she was pregnant, which made me super focused on menswear and now i have a million followers on twitter

Mapping transcriptional responses to cellular perturbation dictionaries with RNA fingerprinting https://www.biorxiv.org/content/10.1101/2025.09.19.676866v1

New preprint from our lab! What can we learn about the properties of gene regulatory elements by CRISPR’ing a random set of accessible sites in human cells? Find out here: www.biorxiv.org/content/10.1... 👇 1/

GPU-accelerated MMseqs2 offers tremendous speedup for homology retrieval, protein structure prediction with ColabFold, and protein structure search with Foldseek. @martinsteinegger.bsky.social @milot.bsky.social @machine.learning.bio www.nature.com/articles/s41...

Today 62 National Cancer Institute (NCI)-Designated Cancer Centers released a statement reinforcing the importance of HPV vaccination. HPV vaccination is safe and protects against six types of cancer – including oropharyngeal, cervical, and anal cancers. #HPVvaccine #HPVvax #EndHPVCancers

📢We are hiring! The Collins Genomics Lab @danafarber.bsky.social is looking to hire two postdoctoral fellows One in hereditary and early-onset adult cancers: careers.dana-farber.org/job/12158/po... 1/2🧵

🎉 Congratulations to our 10 MSK Postdoc Slam finalists! 👏 You were all fantastic and it was truly inspiring to learn about the incredible and diverse work happening at @mskcancercenter.bsky.social. Our #MSKPostdocs gave the judges a real challenge… choosing winners was no easy task! 🤗 #NPAW2025

Now accepting applications for our 2026 Cancer Biology & Cancer Engineering programs. Aspiring scientists & engineers will solve fundamental problems in biology & conduct research & develop technology that will help understand, diagnose, & treat cancer. bit.ly/3WUiuo1

MSK’s Gerstner Sloan Kettering Graduate School of Biomedical Sciences is now accepting applications for its Cancer Biology and Cancer Engineering #PhD programs for the 2026 academic year. Apply below:

The totality of humanity’s (public) sequencing data is now at your fingertips. This is an absolutely monumental resource for genomics research! Congratulations @rayanchikhi.bsky.social @rnalab.bsky.social on this incredible feat!!!

Logan rapidly accesses the tapestry of Life’s genetic diversity and can help solve global issues. To tackle the microplastic crisis, we searched Logan for new versions of the 213 known plastic-degrading enzymes. We identified 200+ million homologs 🤯, including new high-efficiency enzymes 🥤🔥

🌎👩‍🔬 For 15+ years biology has accumulated petabytes (million gigabytes) of🧬DNA sequencing data🧬 from the far reaches of our planet.🦠🍄🌵 Logan now democratizes efficient access to the world’s most comprehensive genetics dataset. Free and open. doi.org/10.1101/2024...

Banking fixed samples before sorting improves experiment planning & instrument scheduling. 10x GEM-X DSP-based fixation recommends sorting before fixing cells. We attempted to stain, fix, and freeze cells before sorting & generating GEMs for 5' libraries. SFFS = STAIN FIX FREEZE SORT (1/7)

Love thy neighbor.

Exciting to see our protein binder design pipeline BindCraft published in its final form in @Nature ! This has been an amazing collaborative effort with Lennart, Christian, @sokrypton.org, Bruno and many other amazing lab members and collaborators. www.nature.com/articles/s41...

@jengreitz.bsky.social l & my lab want to co-hire a computational biologist/biostatistician with project management expertise to help map the regulatory code of the human genome and discover genetic mechanisms of disease. Details below careersearch.stanford.edu/jobs/computa... Plz RT

This preprint from Helen Sakharova is one of the coolest things to come out of my lab: “Protein language models reveal evolutionary constraints on synonymous codon choice.” Codon choice is a big puzzle in how information is encoded in genomes, and we have a new angle. www.biorxiv.org/content/10.1...

Stoked to finally have a preprint out for Phold, our tool that uses protein structural information to enhance phage genome annotation #phagesky 1/n www.biorxiv.org/content/10.1...

🧬🖥️ I am strongly of the opinion that bioinformatics needs to move away entirely from text-based and "loosely" structured file formats for essentially any type of data. File formats should be binary-first, and designed for *correct* and *efficient* machine parsing 1/3

Had a blast this weekend at the Badger Trail Races— super ULTRA mega congrats to @colehoneycutt.bsky.social and @paulklauser.bsky.social on their first 100M finishes!!!! Together, we ran 303.3 miles in under 75 hours, burning 50,000+ calories along the way!

The NIH can’t award ANY grants to outside researchers under new WH restriction, reports @wsj.com. The pause came in the form of a footnote from OMB Director Vought, in a document that doles out federal funds to the NIH. Prelude to rescissions, especially after his comments over the weekend?

🚨Today, in #NatureCancer, we show that #CAR-T cells and #CAR-NK cells contain the seeds of their own self-destruction. Disruption of a FAS-L/FAS enhances CAR potency against liquid and solid cancers. rdcu.be/exjEy. @mskcancercenter.bsky.social @parkerici.bsky.social

We're excited to announce major upgrades to the HCR™ platform! 🧬 HiFi Architecture enables miRNA/siRNA detection with unmatched clarity. 🧪 RTU Dispensers now ship for DISCOVERY ULTRA, enabling scalable, low-variability workflows. Explore the full announcement: tinyurl.com/39je4x8x