Quaid Morris
@quaidmorris.bsky.social
Computational biology, machine learning, AI, RNA, cancer genomics. My views are my own. https://www.morrislab.ai He/him/his
Riboseek is a fast RNA/DNA search. More sensitive than nhmmer at 250x speed. Structure-aware realignment produces MSAs approaching rMSA quality. Plus 1.7M precomputed RNA MSAs, and an API to search your own 📄 www.biorxiv.org/content/10.6... 💾 github.com/steineggerla... 🌐 search.foldseek.com/riboseek
RNA-seq tells us how much RNA is present in the cell. But to understand gene regulation, we need to easily measure the synthesis and decay rates driving this abundance. We introduce AIR-seq: analog intrinsic recoding sequencing. (1/6) www.biorxiv.org/content/10.6...
Analog intrinsic recoding measures RNA dynamics without chemical conversion
Steady-state RNA abundance measurements mask the synthesis and decay rates that shape gene expression. Analog intrinsic recoding sequencing (AIR-seq) repurposes the base-pairing properties of N4-hydro...
biorxiv.org
"We show here that the protein sequence is insufficient for the biogenesis of fully active IDR-containing transcriptional regulators in cells, suggesting that mRNA 3′ UTRs control their activity by preventing co-translational misfolding" doi.org/10.1016/j.ce...
🖥️🧬🧪
Quaid Morris@quaidmorris.bsky.social · 2w agoCan we predict which T cells recognize which peptides? A lot of the signal is hiding in AlphaFold3's (AF3's) hallucinations. enFoldX: instead of one predicted structure, we use the whole noisy ensemble to predict TCR:pMHC binding. www.biorxiv.org/content/10.6... 💻 🧬 github.com/jonlevi/enFoldX
Matching T cells to their cognate peptides presented on MHC molecules from sequence data is a key unsolved problem in computational immunology. A transformative collaboration with @quaidmorris.bsky.social. Led by Olga Lyudovyk, @levinejon.bsky.social & Melissa Pathil! 👇 @mskcancercenter.bsky.social
Quaid Morris@quaidmorris.bsky.social · 2w agoCan we predict which T cells recognize which peptides? A lot of the signal is hiding in AlphaFold3's (AF3's) hallucinations. enFoldX: instead of one predicted structure, we use the whole noisy ensemble to predict TCR:pMHC binding. www.biorxiv.org/content/10.6... 💻 🧬 github.com/jonlevi/enFoldX
Can we predict which T cells recognize which peptides? A lot of the signal is hiding in AlphaFold3's (AF3's) hallucinations. enFoldX: instead of one predicted structure, we use the whole noisy ensemble to predict TCR:pMHC binding. www.biorxiv.org/content/10.6... 💻 🧬 github.com/jonlevi/enFoldX
Ensembles of in silico structures enable T cell peptide-MHC binding prediction
Adaptive immunity relies on T-cell receptor (TCR) recognition of peptides presented by the major histocompatibility complex (pMHC). Accurate prediction of TCR:pMHC binding pairs from sequence data rem...
biorxiv.org
How far can we compress billion-parameter LLMs? We introduce requential coding, which achieves < 1-bit per param compression, and explains why scaling doesn't hit a generalization wall! arxiv.org/pdf/2607.11883 w/ Shikai Qiu, Marc Finzi, Yujia Zheng, Kun Zhang 1/🧵
Sorry if this is a silly question but do you not put tenure on your CV? I googled it and it seems like you don’t? Surely that is worthy of note?
Getting there. I signed up for a sale at the end of the month (my first!) and am trying to get a bunch of stuff finished
1/5 Cell identity is written in the proteome, not in the DNA, and not always in the RNA. Out on bioRxiv today: The first cell type-resolved, MS-based proteomic atlas of the human body. www.biorxiv.org/content/10.6...
biorxiv.org
Pedestrianizing the Financial District would be another one of those projects where as soon as it went into effect people would wonder why New York didn't do it earlier and, before too long, even more people would forget it was ever any different.
Data Show Why Mamdani Must Pedestrianize the Financial District - Streetsblog New York City
People walk in the Financial District, but the neighborhood's business group prioritizes the car.
nyc.streetsblog.org
New family of generative DNA language models trained on 1T 6-mer DNA tokens in long genomic contexts. Open weights, open source, open training data... h/t @mmitchell.bsky.social huggingface.co/spaces/Huggi...
Carbon - a Hugging Face Space by HuggingFaceBio
Enter a DNA string and the Carbon model can continue the sequence, score genetic variants, or predict the protein’s 3‑D structure. You can also explore gene‑embedding visualisations and see the ful...
huggingface.co
Attention all #RNA26 Montreal @rnasociety.bsky.social attendees! Get your special edition @rnacanada.ca RNEh? tshirt to celebrate your Canadian RNA pride. Order here: gametime.gearware.com/stores/rna thru Friday, May 29th. Delivery ONLY to RNA2026 in MTL/no shipping. Image design by Jasmine Tsang.
RNA Canada@rnacanada.ca · 3mo agoRNA Canada ARN is having a flash sale for T-Shirts! The sale ends Friday to pick up your shirt at the RNA Society Meeting. Shirt pickup will be at the exhibition hall at the RNA Society meeting. Order our shirts now to show your Candian RNA pride: gametime.gearware.com/Shop/Store.a...
#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!
Orthus: an RNA foundation model pretrained via contrastive learning based on splicing isoforms and orthologous transcripts. @phil-fradkin.bsky.social @heyitsmeianshi.bsky.social @taykhoomdalal.bsky.social @bowang87.bsky.social @quaidmorris.bsky.social www.nature.com/articles/s41...
Orthrus: toward evolutionary and functional RNA foundation models - Nature Methods
Orthrus is an RNA foundation model pretrained via contrastive learning based on splicing isoforms and orthologous transcripts. This pretraining strategy leads to its strong performances in various tas...
nature.com
Small Model, Big Insight: RNA Structure Rules Emerge from Minimal Data 🧬 #AcademicSky #higherEd #RNA www.mcb.harvard.edu/department/n... @rachellegaudet.bsky.social @naoshigeuchida.bsky.social @nature.com @harvard.edu
Small Model, Big Insight: RNA Structure Rules Emerge from Minimal Data - Harvard University - Department of Molecular & Cellular Biology
MCB Senior Research Fellow Elena Rivas and colleagues have demonstrated that the fundamental rules governing RNA structure can be learned using a remarkably simple computational model—challenging assu...
mcb.harvard.edu
New research from MSK, led by Dr. Scott Lowe, Dr. Dana Pe'er, & colleagues, shows how pancreatic cells can shift from a benign state to cancer — revealing a key “switch” in this process. The study, published in @cellpress.bsky.social, identifies a critical window for early detection and prevention.
From Benign Growth to Pancreatic Cancer: New Study Shows How the Switch Gets Flipped | Memorial Sloan Kettering Cancer Center
An MSK study reveals new details about how pancreatic cells carrying oncogenic mutations transition from benign to malignant — shining new light on the ecosystems that supports emerging tumors.
mskcc.org
Ever wondered how a eukaryotic transcription factor finds its specific DNA motif in the vast genome? In this preprint, we directly measured the dynamics of this search process in living cells, revealing a cooperative mechanism mediated by disordered regions. 1/10 doi.org/10.64898/202...
doi.org
The Donnelly Centre is hiring a new Research and Communications Officer! As a vital part of our administration team, this role covers the external and internal communications of our community. Learn more about the role and apply at the link below: jobs.utoronto.ca/job/Toronto-...
Research & Communications Officer
Research & Communications Officer
jobs.utoronto.ca
We’re hiring: Research Group Leader in computational biology. Are you generating more research ideas than you can explore? Lead cutting-edge AI & biology research at EMBL-EBI. Apply by 11 April 2026: embl.wd103.myworkdayjobs.com/en-US/EMBL/j... #ScienceCareers @ewaldlab.org @embl.org
In a new paper, we introduce Metient, a new method to reconstruct the migration history of metastatic clones, and learn cancer-type specific patterns of metastatic spread, from bulk or single-cell sequencing data. www.nature.com/articles/s41...
Inferring cancer type-specific patterns of metastatic spread using Metient - Nature Methods
Metient is a statistical framework that infers patterns of metastatic spread and reconstructs cancer migration histories.
nature.com
AlphaGenome is out in @nature.com today along with model weights! 🧬 📄 Paper: www.nature.com/articles/s41... 💻 Weights: github.com/google-deepm... Getting here wasn’t a straight path. We discussed the story behind the model, paper & API in the following roundtable: youtu.be/V8lhUqKqzUc
Now with a bioinformatics/genomics label 🖥️🧬
Quaid Morris@quaidmorris.bsky.social · 6mo agoIn a new paper, we introduce Metient, a new method to reconstruct the migration history of metastatic clones, and learn cancer-type specific patterns of metastatic spread, from bulk or single-cell sequencing data. www.nature.com/articles/s41...
In a new paper, we introduce Metient, a new method to reconstruct the migration history of metastatic clones, and learn cancer-type specific patterns of metastatic spread, from bulk or single-cell sequencing data. www.nature.com/articles/s41...
Inferring cancer type-specific patterns of metastatic spread using Metient - Nature Methods
Metient is a statistical framework that infers patterns of metastatic spread and reconstructs cancer migration histories.
nature.com
Join @stirlingchurchman.bsky.social, @moffittlab.bsky.social, @saramostafavi.bsky.social, me and all speakers for the 2026 CSHL meeting Systems Biology: Global Regulation of Gene Expression, March 11-14. Abstract deadline January 9! More infos and registration at meetings.cshl.edu/meetings.asp...
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.
We are very excited to share the first preprint of a new direction for our group. Led by the fearless duo of @arthurwchow.bsky.social and @hoyinchu.bsky.social, our foray into computational protein design—
bioRxiv Bioengineering@biorxiv-bioeng.bsky.social · 8mo agoSequence and structural determinants of efficacious de novo chimeric antigen receptors https://www.biorxiv.org/content/10.64898/2025.12.12.694033v1
New Reactome paper in NAR 2026 Databases Issue: doi.org/10.1093/nar/... Redesigned Angular interface ReacFoam & entity-level visualizations Multi-omics analysis tools React-to-Me chatbot FAIR-compliant, CoreTrustSeal certified, and ELIXIR-recognized 🖥️🧬
The Reactome Knowledgebase 2026
Abstract. The Reactome Knowledgebase (https://reactome.org) is a freely accessible, expert-curated, open-source, and open-data resource that describes huma
doi.org
