Scott Adamson
@sadamson.bsky.social
Post-doc studying genetics and post-transcriptional gene regulation. Outdoor hobbyist, sports fan, and amateur critter photographer.
One of the things I love about living in New York is that closing down the street for wrestling is something that happened today.
The best laid plans of Mets and men...
New York Mets@mets.com · 3w agoCheck out our 2027 schedule! 🗓️
With my postdocs Nathan Andrews and @josiegleeson.bsky.social , we demonstrate the importance and analyze methods for isoform-level resolution in single cell-CRISPR perturbations. TL;DR: Long reads are the way. 3/3 www.biorxiv.org/content/10.6...
Isoform-level resolution in single-cell CRISPR screens reveals hidden functional consequences of gene perturbation
Single-cell CRISPR screens have enabled systematic investigation of gene function, but studies have largely focused on gene-level effects, overlooking transcriptional complexity and isoform usage. Met...
biorxiv.org
We're recruiting! An open functional genomics postdoc position at @scilifelab-ngi.bsky.social / my lab / Robert Månsson lab. Top notch environment for technology and applications development in lovely Stockholm. Please spread the word or apply if interested: www.kth.se/lediga-jobb/...
KTH | Postdoc in genomics
KTH jobs is where you search for jobs at www.kth.se.
kth.se
How can a splicing factor bind to thousands of exons but regulate only a few of them? In our new preprint, we show that SRSF6 resolves this paradox through two distinct binding modes. @lab-nmr.bsky.social & @julianvonehr.bsky.social. Check it out: www.researchsquare.com/article/rs-9...
New paper! How do RNAs "know" where to go inside a cell? We dug into the sequence elements that route RNAs to the right place. It turns out that, in mammals, they're surprisingly massive (>200 nt), multipartite, and wonderfully complicated. 🧵
www.sciencedirect.com/science/arti...
Comprehensive RNA-binding protein analyses and deep learning uncover genetic constraints and disease associations in protein-RNA interfaces
RNA-binding proteins (RBPs) orchestrate post-transcriptional processes, including splicing, cleavage and polyadenylation, and translation. Our updated…
sciencedirect.com
link.springer.com/article/10.1...
Alu-mediated RNA duplexes are associated with widespread exon skipping across primate transcriptomes - Genome Biology
Alternative splicing patterns have diverged rapidly during vertebrate evolution. By integrating genome-wide predictions of stable RNA duplexes, alternative splicing profiles, and proximity ligation-de...
link.springer.com
I'd say be there or be square, but if you're there, you're in the square! Puns aside -- there will be a @standupforscience.bsky.social rally in NYC! Plz repost!
Our most recent work on the “function and evolution” of #nuclear-speckles is now online at Cell @cp-cell.bsky.social doi.org/10.1016/j.ce... Read the thread👇 for the highlights of our findings.
Redirecting
doi.org
SAVE THE DATE: the yearly NY Population Genetics meeting will be back on March 9 2026, generously hosted by the @simonsfoundation.org. Details to follow. Please RT.
KATMAP infers splicing factor activity and regulatory targets from knockdown data - @daspliceisright.bsky.social go.nature.com/47ycrMJ
KATMAP infers splicing factor activity and regulatory targets from knockdown data - Nature Biotechnology
A biophysical model uses knockdown or overexpression data to infer splicing factor activity.
go.nature.com
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...
nature.com
A resource of RNA-binding protein motifs across eukaryotes reveals evolutionary dynamics and gene-regulatory function go.nature.com/4mc1SmQ
A resource of RNA-binding protein motifs across eukaryotes reveals evolutionary dynamics and gene-regulatory function - Nature Biotechnology
RNA-binding motifs in eukaryotic proteins are presented in a comprehensive resource.
go.nature.com
Very excited that our most significant work, a collaboration w/ Dr. Can Cenik at UT Austin on translational gene regulation, was finally published in Nature Biotechnology in a dual set of studies: Paper 1 -- an AI model trained to predict translation rates from mRNA sequences: rdcu.be/exN1l
Predicting the translation efficiency of messenger RNA in mammalian cells
Nature Biotechnology - A deep convolutional neural network model predicts the influence of the full-length mRNA sequence on translation efficiency.
url.de.m.mimecastprotect.com
Love RNA biology and care about reproducibility? I’m co-editing a @bio-protocol.bsky.social special issue with @marionhogg.bsky.social & Renate Weizbauer —focusing open access and transparent RNA detection protocols. Submit yours today - en.bio-protocol.org/content17 #OpenScience #ReproRNAbiology
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...
biorxiv.org
Our new contribution to the quest to find causal GWAS genes! Sam Ghatan from my lab at @nygenome.org led a systematic comparison of eQTLs and CRISPRi+scRNA-seq screens. TL;DR: they provide highly complementary insights, with ortogonal pros and cons. 🧵👇 www.biorxiv.org/content/10.1...
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...
Leveraging functional annotations to map rare variants associated with Alzheimer's disease with gruyere
The increasing availability of whole-genome sequencing (WGS) has begun to elucidate the contribution of rare variants (RVs), both coding and non-coding, to complex disease. Multiple RV association tes...
medrxiv.org
If we post enough complementary Heng Li memes, he'll surely join.
Timothy Stiles@stiles.io · 2y agowhen you implement a couple of basic alignment algorithms in an afternoon
New preprint alert! EuPRI has everything: * New binding data (174 RBPs) * New motifs (34,000 RBPs) * New ML for inferring motifs from protein sequence (JPLE) * Evolution of RBP motifs across eukaryotes * 12 Plant RBPs assigned PTR function. Stay tuned for more www.biorxiv.org/content/10.1...
Reconstructing the sequence specificities of RNA-binding proteins across eukaryotes
RNA-binding proteins (RBPs) are key regulators of gene expression. Here, we introduce EuPRI (Eukaryotic Protein-RNA Interactions) — a freely available resource of RNA motifs for 34,736 RBPs from 690 e...
biorxiv.org
We're recruiting postdocs! Join our lab at @scilifelab.bsky.social and KTH in Stockholm to work on functional genomics at the experimental and/or computational intersection of CRISPR/scRNA-seq/genetics approaches. Close links to our team at NY Genome Center. 1/