Lightnews — Scholar-powered news

David A Knowles @davidaknowles.bsky.social · 27d

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

3

David A Knowles @davidaknowles.bsky.social · 27d

Back up again now, sorry for the interruption after lunch!

1

David A Knowles @davidaknowles.bsky.social · 28d

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

Machine Learning in Computational Biology 2025

YouTube video by Machine Learning in Computational Biology

www.youtube.com

1 5 19

David A Knowles @davidaknowles.bsky.social · 28d

#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!

MLCB - Schedule

The in-person component will be held at the New York Genome Center, 101 6th Ave, New York, NY 10013.

www.mlcb.org

2 8

David A Knowles @davidaknowles.bsky.social · Aug 20

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

authors.elsevier.com

5 15

David A Knowles @davidaknowles.bsky.social · Aug 20

That is one hell of a recruitment photo!

David A Knowles @davidaknowles.bsky.social · Jul 29

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...

Cas13d-mediated isoform-specific RNA knockdown with a unified computational and experimental toolbox - Nature Communications

The majority of human genes can produce multiple isoforms, but studying their functional relevance requires tools to target specific isoforms. Here, the authors develop a CRISPR-based exon-exon juncti...

www.nature.com

2 18 41

David A Knowles @davidaknowles.bsky.social · Jul 8

Good question. Certainly trickier - you could assume independence across splicing events (quantified via SR) within in a gene and see how well that matches what you get from LR for a matched sample.

David A Knowles @davidaknowles.bsky.social · Jul 2

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...

Perplexity as a Metric for Isoform Diversity in the Human Transcriptome

Long-read sequencing (LRS) has revealed a far greater diversity of RNA isoforms than earlier technologies, increasing the critical need to determine which, and how many, isoforms per gene are biologic...

www.biorxiv.org

2 22 55

David A Knowles @davidaknowles.bsky.social · May 31

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.

2 9

David A Knowles @davidaknowles.bsky.social · May 26

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.

Machine Learning in Computational Biology

Youtube channel for the Machine Learning in Computational Biology conference.

youtube.com

4 10

David A Knowles @davidaknowles.bsky.social · May 15

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.

Machine Learning in Computational Biology

Youtube channel for the Machine Learning in Computational Biology conference: https://mlcb.github.io/

youtube.com

22 42

Reposted by David A Knowles

brangwynnelab.bsky.social @brangwynnelab.bsky.social · Apr 21

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...

Genome-wide mapping of mesoscale neuronal RNA organization and condensation

Subcellular RNA organization can affect critical cellular functions. However, our understanding of RNA microenvironments, particularly biomolecular condensates, remains limited, largely due to a lack ...

www.biorxiv.org

1 26 55

David A Knowles @davidaknowles.bsky.social · Apr 7

Dire wolf cosplay.

1 3

Reposted by David A Knowles

Rachael Sirianni, PhD @docsirianni.bsky.social · Mar 15

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

4 89 210

David A Knowles @davidaknowles.bsky.social · Mar 11

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.

21 220 520

David A Knowles @davidaknowles.bsky.social · Feb 16

Just anti funding any science, completely different!

1

Reposted by David A Knowles

Congressman Bill Foster @repbillfoster.bsky.social · Feb 8

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

NIH cuts billions of dollars in biomedical funding, effective immediately

The move halts a large slice of money for most universities and research institutions virtually overnight, imperiling vital research in everything from cancer to heart disease.

www.washingtonpost.com

170 640 2.5K

Reposted by David A Knowles

Carl T. Bergstrom @carlbergstrom.com · Feb 8

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.

48 200 1.5K

Reposted by David A Knowles

John Greally @greally.bsky.social · Jan 31

@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.

An Intuitive Primer on Effective Functional Genomics Study Design

Amazon.com: An Intuitive Primer on Effective Functional Genomics Study Design: 9798218585952: Gilad, Yoav: Books

www.amazon.com

2 4 14

David A Knowles @davidaknowles.bsky.social · Jan 31

It's been very helpful around NYGC in Soho, no more stationary honking cars trying to squeeze into the Holland tunnel.

4

Reposted by David A Knowles

Metropolitan Transportation Authority @mta.info · Jan 30

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.

25 200 1.2K

David A Knowles @davidaknowles.bsky.social · Jan 27

#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!

14 33

Reposted by David A Knowles

Engelhardt Research Group @thebeehive.bsky.social · Nov 26

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...

Cellular behavior analysis from live-cell imaging of TCR T cell–cancer cell interactions

T cell therapies, such as chimeric antigen receptor (CAR) T cells and T cell receptor (TCR) T cells, are a growing class of anti-cancer treatments. However, expansion to novel indications and beyond l...

www.biorxiv.org

1 7 18

Reposted by David A Knowles

Green Hombre @greenhombre.bsky.social · Jan 20

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

1 14 40