davidaknowles.bsky.social - Profile | ThreadSky | a Reddit-style client for Bluesky

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

submitted 23 days ago • 168 comments

@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.

submitted 32 days ago • 2 comments

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.

submitted 32 days ago • 25 comments

#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!

submitted 35 days ago • 0 comments

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...

submitted 98 days ago • 1 comment

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

submitted 42 days ago • 1 comment

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.

submitted 44 days ago • 3 comments

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

submitted 48 days ago • 0 comments

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

submitted 48 days ago • 0 comments

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. 🫠

submitted 56 days ago • 6 comments

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

submitted 74 days ago • 0 comments

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

submitted 88 days ago • 0 comments

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.

submitted 77 days ago • 1 comment

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!

submitted 76 days ago • 1 comment

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...

submitted 76 days ago • 5 comments

I wish crypto was always short for cryptococcal meningitis

submitted 76 days ago • 11 comments

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

submitted 275 days ago • 0 comments

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.)

submitted 77 days ago • 11 comments

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

submitted 77 days ago • 0 comments

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/

submitted 77 days ago • 1 comment

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.

submitted 77 days ago • 6 comments

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

submitted 78 days ago • 5 comments

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

submitted 84 days ago • 1 comment

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...

submitted 84 days ago • 1 comment

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...

submitted 105 days ago • 4 comments

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

submitted 105 days ago • 176 comments

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!

submitted 105 days ago • 0 comments

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

submitted 109 days ago • 2 comments

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

submitted 189 days ago • 1 comment

"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...

submitted 112 days ago • 0 comments

Fabulous conference, plenty herein to watch & learn

submitted 148 days ago • 0 comments

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

submitted 148 days ago • 0 comments

#MLCB2024 kicks off in 22h (9am PST) with keynote from Jian Zhou on DL for transcriptional initiation! Full schedule at mlcb.github.io and public livestream at youtube.com/live/reqWvNO.... Please RP!

submitted 180 days ago • 0 comments

"In supporting the project further, the university would have risked alienating conservative donors, Silicon Valley figures and members of Congress, who have threatened to stop all federal funding for disinformation research or cut back general support." Well, of course. wapo.st/4b05S3H

submitted 261 days ago • 2 comments

#MLCB2024 submissions are open at cmt3.research.microsoft.com/MLCB2024/! Great lineup of keynotes from @avapamini, @ChikinaLab, @zhou_jian & Nilah Ioannidis. Registration is free & submission deadline is 6/15, more details at mlcb.github.io. Please RP!

submitted 273 days ago • 0 comments

"I still get a lot of engagement on Twitter"

submitted 293 days ago • 4 comments

concerns re #Alphafold3 lack of transparency zenodo.org/records/1117... I note on Pubpeer that this is inconsistent with Nature policy pubpeer.com/publications... #OpenScience #reproducibility

submitted 295 days ago • 1 comment