David A Knowles
@davidaknowles.bsky.social
machine learning and functional/statistical genetics. Associate Prof @Columbia and Core Faculty @nygenome. he/him/his. https://daklab.github.io/
Alan's elegant work on evolutionary contrastive learning for understanding promoter regulatory logic out in @GeneticsGSA! academic.oup.com/genetics/art... Was really fun having him visit my lab for his sabbatical & work on this. New bucket list item: write a first-author paper as a PI!
Inferring fungal cis-regulatory networks from genome sequences via unsupervised and interpretable representation learning
Abstract. Gene expression patterns are determined to a large extent by transcription factor (TF) binding to noncoding regulatory regions in the genome. How
academic.oup.com
January 7, 2026 at 9:35 PM
Alan's elegant work on evolutionary contrastive learning for understanding promoter regulatory logic out in @GeneticsGSA! academic.oup.com/genetics/art... Was really fun having him visit my lab for his sabbatical & work on this. New bucket list item: write a first-author paper as a PI!
Reposted by David A Knowles
If you like larger sample sizes, then do check out our reprocessed and fine mapped cis-eQTLs and cis-sQTLs (leafCutter and MAJIQ!) from the INTERVAL cohort (whole blood, n up to 4,729)!
zenodo.org/records/1795...
These will be on the eQTL Catalogue FTP soon as well.
cc @yosephbarash.bsky.social
zenodo.org/records/1795...
These will be on the eQTL Catalogue FTP soon as well.
cc @yosephbarash.bsky.social
Fine mapped eQTL and sQTL summary statistics from the INTERVAL RNA-seq study (part 1)
This repository contains fine mapped eQTL and sQTL summary statistics from the INTERVAL RNA-seq study (Tokolyi et al, 2025). Datasets QTD001000-QTD001002 are based on the whole cohort of 4,729 samples...
zenodo.org
January 7, 2026 at 10:24 AM
If you like larger sample sizes, then do check out our reprocessed and fine mapped cis-eQTLs and cis-sQTLs (leafCutter and MAJIQ!) from the INTERVAL cohort (whole blood, n up to 4,729)!
zenodo.org/records/1795...
These will be on the eQTL Catalogue FTP soon as well.
cc @yosephbarash.bsky.social
zenodo.org/records/1795...
These will be on the eQTL Catalogue FTP soon as well.
cc @yosephbarash.bsky.social
Excited to see this out www.nature.com/articles/s41...! Nonparametric kernel-based tests for spatially variable isoform usage in spatial transcriptomics. So many interesting examples in the CNS and cancer, we're only scratching the surface!
Mapping isoforms and regulatory mechanisms from spatial transcriptomics data with SPLISOSM - Nature Biotechnology
Differential isoform usage is identified with high statistical power from spatial transcriptomics data.
www.nature.com
January 6, 2026 at 7:12 PM
Excited to see this out www.nature.com/articles/s41...! Nonparametric kernel-based tests for spatially variable isoform usage in spatial transcriptomics. So many interesting examples in the CNS and cancer, we're only scratching the surface!
#MLCB2025 proceedings are up at proceedings.mlr.press/v311/ !
Proceedings of Machine Learning Research
Proceedings of the 20th Machine Learning in Computational Biology meeting Held in New York, NY, USA on 10-11 September 2025 Published as Volume 311 by the Proceedings of Machine Learning Research on 3...
proceedings.mlr.press
December 31, 2025 at 10:37 PM
#MLCB2025 proceedings are up at proceedings.mlr.press/v311/ !
I'm a longtime fan of Affinity Designer as an affordable Illustrator-killer for figures, and... it's now free?! www.canva.com/newsroom/new...
Highly recommended if you're sick of paying Adobe $. Maybe Canva can buy NPG too and get rid of the OA fees.
Highly recommended if you're sick of paying Adobe $. Maybe Canva can buy NPG too and get rid of the OA fees.
Why we made Affinity free, and how we’ll keep it that way
We’ve made Affinity completely free, empowering professional designers with studio-grade creative software, supported by Canva’s sustainable ecosystem.
www.canva.com
November 18, 2025 at 11:28 PM
I'm a longtime fan of Affinity Designer as an affordable Illustrator-killer for figures, and... it's now free?! www.canva.com/newsroom/new...
Highly recommended if you're sick of paying Adobe $. Maybe Canva can buy NPG too and get rid of the OA fees.
Highly recommended if you're sick of paying Adobe $. Maybe Canva can buy NPG too and get rid of the OA fees.
Little gist for getting coauthor list from PubMed for NSF COA list. Thanks to coauthors gpt5 and claude. gist.github.com/davidaknowle...
Get COA coauthor list for NSF including affiliations from PUBMED
Get COA coauthor list for NSF including affiliations from PUBMED - coa.py
gist.github.com
November 5, 2025 at 2:50 PM
Little gist for getting coauthor list from PubMed for NSF COA list. Thanks to coauthors gpt5 and claude. gist.github.com/davidaknowle...
Reposted by David A Knowles
The 21st Century version of corvée work for academics is reviewing papers or grants, writing letters of recommendation, giving public outreach lectures.
Academics in Assyria in the 7th c BC complain that admin is preventing them from doing research and teaching
November 3, 2025 at 6:29 PM
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
Large-scale causal discovery using interventional data sheds light on gene network structure in k562 cells - Nature Communications
The authors give a method for learning causal gene networks using Perturb-seq data. In K562 cells, they find a network with small-world and scale-free properties. Analysis shows a relationship between...
nature.com
November 3, 2025 at 7:09 PM
@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.
October 28, 2025 at 3:40 PM
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
September 11, 2025 at 1:45 PM
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...
Machine Learning in Computational Biology 2025
YouTube video by Machine Learning in Computational Biology
www.youtube.com
September 10, 2025 at 1:01 PM
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!
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
September 10, 2025 at 12:16 AM
#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
authors.elsevier.com
August 20, 2025 at 10:06 PM
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...
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
July 29, 2025 at 4:35 PM
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...
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
July 2, 2025 at 11:46 PM
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.
May 31, 2025 at 10:30 PM
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.
Machine Learning in Computational Biology
Youtube channel for the Machine Learning in Computational Biology conference.
youtube.com
May 26, 2025 at 4:16 PM
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.
Machine Learning in Computational Biology
Youtube channel for the Machine Learning in Computational Biology conference: https://mlcb.github.io/
youtube.com
May 15, 2025 at 12:24 AM
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.
Reposted by David A Knowles
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
April 21, 2025 at 1:48 PM
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...
Reposted by David A Knowles
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
March 15, 2025 at 11:05 PM
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.
March 11, 2025 at 12:41 PM
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.
Reposted by David A Knowles
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
February 8, 2025 at 6:28 PM
This is dangerously irresponsible on every level. Indiscriminately slashing this funding will cripple lifesaving research on everything from cancer to opioid addiction.
Reposted by David A Knowles
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.
February 8, 2025 at 9:41 PM
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.
Reposted by David A Knowles
@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
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
January 31, 2025 at 12:22 AM
@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
www.amazon.com/Intuitive-Pr...
I just bought a copy for the lab.
Reposted by David A Knowles
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.
We're seeing traffic move quicker into and within Manhattan, which benefits all New Yorkers—drivers, bus riders, emergency vehicle operators, pedestrians, and more.
January 30, 2025 at 10:00 PM
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.
We're seeing traffic move quicker into and within Manhattan, which benefits all New Yorkers—drivers, bus riders, emergency vehicle operators, pedestrians, and more.