machine learning and functional/statistical genetics. Associate Prof @Columbia and Core Faculty @nygenome. he/him/his. https://daklab.github.io/https://bsky.app/profile/davidaknowles.bsky.socialhttps://bsky.app/profile/davidaknowles.bsky.social/post/3mphudr2fjk2jWe're still looking for reviewers for #MLCB2026. If you're interested please sign-up at https://forms.gle/UdbdPfPCte2jZLXN8. We've also extended the abstract/paper deadline to July 3rd, see mlcb.org for more deets! Please RP.30 Jun 2026 01:34 +0000at://did:plc:whucaade2z7mpi3caeku243m/app.bsky.feed.post/3mphudr2fjk2jhttps://bsky.app/profile/davidaknowles.bsky.social/post/3moxj5nnydc2cReminder that the #MLCB2026 paper/abstract deadline is July 1st! Conf is Nov 16-17 @nygenome.org. Fantastic lineup of keynote speakers @drannecarpenter.bsky.social (Broad/Purdue), Ellen Zhong (Princeton), Christina Leslie (MSKCC) & Michael Brenner (Harvard). More deets at mlcb.org. Please RP!23 Jun 2026 13:31 +0000at://did:plc:whucaade2z7mpi3caeku243m/app.bsky.feed.post/3moxj5nnydc2chttps://bsky.app/profile/davidaknowles.bsky.social/post/3ml7m7yr5fc2y#MLCB2026 will be November 16-17 at (once again) @nygenome.org, NYC! Paper/abstract deadline is July 1st, more deets at mlcb.org. We'll be opening in-person registration alongside paper decisions. Mailing list to stay in the loop: groups.google.com/g/mlcb. Keynotes TBA! Please RP!06 May 2026 21:07 +0000at://did:plc:whucaade2z7mpi3caeku243m/app.bsky.feed.post/3ml7m7yr5fc2yhttps://bsky.app/profile/davidaknowles.bsky.social/post/3mijcmyadl22o@nygenome.org is hiring Genomic AI Fellows! (fancy postdoc positions) If you're interested in working at the interface of AI and genomics in a great environment please apply at: https://jobs.silkroad.com/NYGenome/Careers/Jobs/77902 Apr 2026 13:26 +0000at://did:plc:whucaade2z7mpi3caeku243m/app.bsky.feed.post/3mijcmyadl22ohttps://bsky.app/profile/davidaknowles.bsky.social/post/3mhvoo66pfs2q@fertiglab.bsky.social and I are co-chairing the MLCSB track at ISMB July 12-16 in DC. We have a fantastic line-up of keynotes: Rita Singh, Young Hwan Chang, Katie Pollard, and Yun Song. Abstract submissions are due April 9th! https://www.iscb.org/ismb2026/call-for-submissions/abstracts25 Mar 2026 18:08 +0000at://did:plc:whucaade2z7mpi3caeku243m/app.bsky.feed.post/3mhvoo66pfs2qhttps://bsky.app/profile/davidaknowles.bsky.social/post/3mbugdci67c23Alan's elegant work on evolutionary contrastive learning for understanding promoter regulatory logic out in @GeneticsGSA! https://academic.oup.com/genetics/article/232/1/iyaf209/8268197 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!07 Jan 2026 21:35 +0000at://did:plc:whucaade2z7mpi3caeku243m/app.bsky.feed.post/3mbugdci67c23https://bsky.app/profile/davidaknowles.bsky.social/post/3mbrntwjk2k2cExcited to see this out https://www.nature.com/articles/s41587-025-02965-6! 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!06 Jan 2026 19:12 +0000at://did:plc:whucaade2z7mpi3caeku243m/app.bsky.feed.post/3mbrntwjk2k2chttps://bsky.app/profile/davidaknowles.bsky.social/post/3mbcwjiemdc2k#MLCB2025 proceedings are up at proceedings.mlr.press/v311/ ! https://proceedings.mlr.press/v311/31 Dec 2025 22:37 +0000at://did:plc:whucaade2z7mpi3caeku243m/app.bsky.feed.post/3mbcwjiemdc2khttps://bsky.app/profile/davidaknowles.bsky.social/post/3m5wvcxjqds22I'm a longtime fan of Affinity Designer as an affordable Illustrator-killer for figures, and... it's now free?! https://www.canva.com/newsroom/news/affinity-free/ Highly recommended if you're sick of paying Adobe $. Maybe Canva can buy NPG too and get rid of the OA fees.18 Nov 2025 23:28 +0000at://did:plc:whucaade2z7mpi3caeku243m/app.bsky.feed.post/3m5wvcxjqds22https://bsky.app/profile/davidaknowles.bsky.social/post/3m4vcc4mqfc2eLittle gist for getting coauthor list from PubMed for NSF COA list. Thanks to coauthors gpt5 and claude. https://gist.github.com/davidaknowles/b315ec42602de9b8230b2171054b270905 Nov 2025 14:50 +0000at://did:plc:whucaade2z7mpi3caeku243m/app.bsky.feed.post/3m4vcc4mqfc2ehttps://bsky.app/profile/davidaknowles.bsky.social/post/3m4qpuul27s26@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 https://nature.com/articles/s41467-025-64353-703 Nov 2025 19:09 +0000at://did:plc:whucaade2z7mpi3caeku243m/app.bsky.feed.post/3m4qpuul27s26https://bsky.app/profile/davidaknowles.bsky.social/post/3m4bbey6qdk22Anyone else not able to log into dbGaP? Can't tell if it's shutdown-related or just the usual struggles. eRA commons seems fine.28 Oct 2025 15:40 +0000at://did:plc:whucaade2z7mpi3caeku243m/app.bsky.feed.post/3m4bbey6qdk22https://bsky.app/profile/davidaknowles.bsky.social/post/3lykuze4qhc23MLCB2025 day 2 kicking off with Jacob Schreiber on DL for interpreting and designing regulatory DNA sequence. youtube.com/@mlcbconf11 Sep 2025 13:45 +0000at://did:plc:whucaade2z7mpi3caeku243m/app.bsky.feed.post/3lykuze4qhc23https://bsky.app/profile/davidaknowles.bsky.social/post/3lyic4r3lws2jYouTube link for MLCB2025 is up! Starting in 30 min. https://www.youtube.com/live/19I7xTh5Qb4?si=dS5G9fZ4oOxTpbz110 Sep 2025 13:01 +0000at://did:plc:whucaade2z7mpi3caeku243m/app.bsky.feed.post/3lyic4r3lws2jhttps://bsky.app/profile/davidaknowles.bsky.social/post/3lygxemwzq22u#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! https://www.mlcb.org/schedule10 Sep 2025 00:16 +0000at://did:plc:whucaade2z7mpi3caeku243m/app.bsky.feed.post/3lygxemwzq22uhttps://bsky.app/profile/davidaknowles.bsky.social/post/3lwugqslxyc2aShiny 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 https://authors.elsevier.com/a/1ldzwgeXDzHj20 Aug 2025 22:05 +0000at://did:plc:whucaade2z7mpi3caeku243m/app.bsky.feed.post/3lwugqslxyc2ahttps://bsky.app/profile/davidaknowles.bsky.social/post/3lv4jynrq4s2mExcited for this to be out officially! It was a great team effort and has a lot of useful tidbits for studying isoform function. https://www.nature.com/articles/s41467-025-62066-529 Jul 2025 16:34 +0000at://did:plc:whucaade2z7mpi3caeku243m/app.bsky.feed.post/3lv4jynrq4s2mhttps://bsky.app/profile/davidaknowles.bsky.social/post/3lszfiq2dac24New 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. https://www.biorxiv.org/content/10.1101/2025.07.02.662769v102 Jul 2025 23:46 +0000at://did:plc:whucaade2z7mpi3caeku243m/app.bsky.feed.post/3lszfiq2dac24https://bsky.app/profile/davidaknowles.bsky.social/post/3lqisdsw3z22cWe 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.31 May 2025 22:30 +0000at://did:plc:whucaade2z7mpi3caeku243m/app.bsky.feed.post/3lqisdsw3z22chttps://bsky.app/profile/davidaknowles.bsky.social/post/3lq3l5gbdys2dJust under a week until the #MLCB2025 paper/abstract deadline on June 1st! In-person registration is full but you can join the wait list https://forms.gle/gnj6AAV7oWj6Hjgk6 or watch online at youtube.com/@mlcbconf. Sept 10-11 at @nygenome.org. Full deets at mlcb.org! Please RP. https://youtube.com/@mlcbconf26 May 2025 16:16 +0000at://did:plc:whucaade2z7mpi3caeku243m/app.bsky.feed.post/3lq3l5gbdys2dhttps://bsky.app/profile/davidaknowles.bsky.social/post/3lp6asi4n522fFree 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. https://youtube.com/@mlcbconf15 May 2025 00:24 +0000at://did:plc:whucaade2z7mpi3caeku243m/app.bsky.feed.post/3lp6asi4n522fhttps://bsky.app/profile/davidaknowles.bsky.social/post/3lk43oxsaek2cWow. "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.11 Mar 2025 12:41 +0000at://did:plc:whucaade2z7mpi3caeku243m/app.bsky.feed.post/3lk43oxsaek2c