Little gist for getting coauthor list from PubMed for NSF COA list. Thanks to coauthors gpt5 and claude. gist.github.com/davidaknowle...

The 21st Century version of corvée work for academics is reviewing papers or grants, writing letters of recommendation, giving public outreach lectures.

@brielin.bsky.social's fantastic work on causal gene network inference from Perturb-seq is published! We estimate total causal effects using guides as instruments, then deconvolve into direct & mediated effects with a directed analog of graphical lasso. Deets: nature.com/articles/s41467-025-64353-7

Anyone else not able to log into dbGaP? Can't tell if it's shutdown-related or just the usual struggles. eRA commons seems fine.

MLCB2025 day 2 kicking off with Jacob Schreiber on DL for interpreting and designing regulatory DNA sequence. youtube.com/@mlcbconf

YouTube link for MLCB2025 is up! Starting in 30 min. www.youtube.com/live/19I7xTh...

#MLCB2025 is tomorrow & Thursday with a fantastic lineup of keynotes & contributed talks www.mlcb.org/schedule. We'll be livestreaming through our YouTube channel www.youtube.com/@mlcbconf. Thanks to www.corteva.com, instadeep.com, the Simons Center at CSHL & NYGC for generous support!

Shiny new probabilistic model, gruyere 🧀, for powering up rare variant associations w/ DL effect prediction! We find novel associations for Alzheimer's disease, e.g. nuclear pore protein NUP93 in microglia. Big thanks to NIH/NIA/ADSP and Anjali for the hard work! authors.elsevier.com/a/1ldzwgeXDzHj

Excited for this to be out officially! It was a great team effort and has a lot of useful tidbits for studying isoform function. www.nature.com/articles/s41...

New work from the lab trying to wrap our heads around the massive complexity of the human transcriptome revealed by long-read RNA-seq! Fun collab with Gloria Sheynkman. www.biorxiv.org/content/10.1...

We had a bunch of requests so we're extending the #MLCB2025 deadline to June 3rd (anywhere on earth)! cmt3.research.microsoft.com/MLCB2025 to submit.

Just under a week until the #MLCB2025 paper/abstract deadline on June 1st! In-person registration is full but you can join the wait list forms.gle/gnj6AAV7oWj6... or watch online at youtube.com/@mlcbconf. Sept 10-11 at @nygenome.org. Full deets at mlcb.org! Please RP.

Free in-person registration is open for #MLCB2025! Sept 10-11 at @nygenome.org and online at youtube.com/@mlcbconf. Paper/abstract deadline is June 1, more deets including our fantastic invited speaker lineup at mlcb.org! Please RP.

What drives cytoplasmic mRNA organization? We created unbiased, genome-wide maps of mesoscale RNA-RNA spatial proximity, revealing impact of encoded protein function. Fantastic work from @lindsayabecker.bsky.social @sofiquinodoz.bsky.social @davidaknowles.bsky.social www.biorxiv.org/content/10.1...

Did you know that science labs work like small business entrepreneurs? Faculty hired on strength of ideas, get some startup $ to last 3-4 yrs. After that is grants- grants pay all our + our trainees’ salaries + scientific work. Funding in this country is frozen. That means scientific work stops

Wow. "NIH" canceled my co-mentored (with Dave Sulzer) PhD student's F31 funding. His work is on understanding the genetics and neuroscience of language learning disorders. F31 provides no indirect $ to Columbia, just pays his salary. Not that it should matter, but he's an American citizen. W.T.F.

This is dangerously irresponsible on every level. Indiscriminately slashing this funding will cripple lifesaving research on everything from cancer to opioid addiction.

Thinking back on all this I better understand the pain I feel to see science under devastating attack here. It’s not just about my livelihood or my university. It’s about my identity. And it’s about a pursuit that I see as standing along with art, literature, and music as among our highest callings.

@ygilad.bsky.social has what looks like a useful book just released: An Intuitive Primer on Effective Functional Genomics Study Design www.amazon.com/Intuitive-Pr... I just bought a copy for the lab.

It's been 3 weeks since Congestion Relief Zone tolling went into effect, and the program is working! We're seeing traffic move quicker into and within Manhattan, which benefits all New Yorkers—drivers, bus riders, emergency vehicle operators, pedestrians, and more.

#MLCB2025 will be Sept 10-11 at @nygenome.org in NYC! Paper deadline June 1st & in-person registration will open in May. Please sign up for our mailing list groups.google.com/g/mlcb/ for future announcements. More details at mlcb.github.io. Please RP!

First post in the Good Place! Our preprint on cellular behavior analysis in TCR T cells & cancer cell live-cell imaging data is out! This 3-year collaboration led by pd Archit Verma w/ Alex Marson & Julia Carnevale, with segmentation & tracking by @davidvv & team! www.biorxiv.org/content/10.1...

Who will protect our environment from Trump? Non-profit environmental lawyers. They won hundreds of cases against Trump 45 and have been hiring new lawyers for months. They are ready for this moment. Follow and donate to: @earthjustice.bsky.social @nrdc.org @centerforbiodiv.bsky.social

Reviewing is getting ridiculous. On 7th Jan I agreed to review a manuscript. I just got an email telling me my review was due on 2nd Jan. Adding time travel to the skill set expected of junior faculty.

There are 10 days left to submit abstracts to ProbGen meetings.cshl.edu/meetings.asp...! Fantastic line-up of speakers and topics.

Do any pyro aficionados have insight on what I'm doing wrong here? forum.pyro.ai/t/error-with...

After ~2h of bug hunting: needed to replace lgamma(a+n-y) with lgamma(n-y+a). For tiny a and n=y>0, the former evaluates to +inf and breaks everything, the latter doesn't. 🫠

Gotta love that the only way to give feedback on the reporting burden of NIH's data management & sharing plan template is by 🐌 mail.

Most of the talks from our Oct meeting are now online, with a few more to come: www.precisionmedicine.columbia.edu/videos

A surprising (to me) result! Polygenic score portability across groups does not improve if based on within-family GWAS, which accounts for most forms of environmental confounding. Suggests genetic architecture is main driver and shows within-family GWAS aren't a solution to poor PGS transferability.

Our new (social media) era at @plos.org has officially started - this is the first @plosbiology.org research paper to be posted on Bluesky and *not* on X. Give it some love!

What do GWAS and rare variant burden tests discover, and why? Do these studies find the most IMPORTANT genes? If not, how DO they rank genes? Here we present a surprising result: these studies actually test for SPECIFICITY! A 🧵on what this means... (🧪🧬) www.biorxiv.org/content/10.1...

I wish crypto was always short for cryptococcal meningitis

We have multiple postdoc positions available in my group at NYU. Join us if you're interested in complex trait genetics and biology. More information about the lab on our website: mostafavilab.org

Regularly tempted to write in my NIH grants innovation section: "Funding software that already exists and works well would be highly innovative for the NIH." (I bet half the panel would break down ROFL, but I'm also highly skeptical that I'd get a good score, or that the PO would be amused.)

Specificity, length, and luck: How genes are prioritized by rare and common variant association studies https://www.biorxiv.org/content/10.1101/2024.12.12.628073v1

gaftools: a toolkit for analyzing and manipulating pangenome alignments https://www.biorxiv.org/content/10.1101/2024.12.10.627813v1 🧬🖥️🧪 Source (MIT): https://github.com/marschall-lab/gaftools Docs: https://gaftools.readthedocs.io/en/latest/

Welcome to our Bluesky account where you will find updates on open science publishing, policies and practice. This account will also provide thought leadership posts on scholarly publishing, partnership announcements and updates on PLOS policies and initiatives.

And here is my condensed guide on how to science: top 5 Rules

This « gruyère » software will presumably complement very well the constraint based software Gnocchi ? (I’ll see myself out)

Excited to share our first foray into (noncoding) rare variant association testing: a probabilistic model that learns functional annotation importance and finds associations missed by existing methods. Anjali did a fantastic job with model assessment and scaling! www.medrxiv.org/content/10.1...

Hi all. Just released a fast library (C++/Rust/Python) for performing interval intersections. Uses a novel superset-index that tends to be faster than current libs, and also has a SIMD accelerated counting algorithm 👇 github.com/kcleal/super...

We strongly suggest that academic publishers and other platforms that host research rapidly implement a Share to Bluesky button for their articles. Here's how: docs.bsky.app/docs/advance... #AcademicSky #HigherEd #Altmetrics

The fantastic Machine Learning in CompBio #MLCB2024 papers are up at proceedings.mlr.press/v261/! Reminder that all the talks are available on our yt channel www.youtube.com/@mlcbconf. Please RP!

UPDATE: Nature.com has issued a correction: “Correction 14 November 2024: An earlier version of this article stated that AlphaFold3 is now ‘open source’. This is not the case, as weights for the model can only be accessed upon request, and the code can only be used for non-commercial applications.”

@bowang87.bsky.social is here #machinelearning #biomedicine #genomics folks!

We're hiring for multiple tenure track positions in Genetics, Cell and Developmental Biology.

"Things take longer to happen than you think they will, and then they happen faster than you thought they could." Attributed to Rudi Dornbusch en.wikipedia.org/wiki/Rudi_Do...

Fabulous conference, plenty herein to watch & learn

The fantastic #MLCB2024 talks, spotlights, panel & keynotes are now up on our Youtube channel at www.youtube.com/watch?v=tWzI.... Please RP!