Quaid Morris @quaidmorris.bsky.social · 01/10/2026Why would you be paying the shipping costs in the first place? 110
Reposted by Quaid MorrisCaroline Bartman @cbartman.bsky.social · 26/09/2026Are there key discoveries made with spatial RNA seq? Or what are your favorite spatial rna seq papers? Pls reski! 31716
Reposted by Quaid MorrisAsher Cutter @asherdcutter.bsky.social · 17/09/2026Come to @romtoronto.bsky.social and EEB in Toronto! ROM is seeking entomologist/arachnologist curator who would also be faculty in EEB at UofT royalontariomuseum.applytojob.com/apply/mdMTpA...royalontariomuseum.applytojob.comCurator of Insects & Arachnids - Royal Ontario Museum - Career PageApply to Curator of Insects & Arachnids at Royal Ontario Museum in Toronto, ON, Canada. 02431
Reposted by Quaid MorrisTanja Stadler @tanjastadler.bsky.social · 15/09/2026🚀 Interested in joining our Computational Evolution group at ETH Zürich in Basel @bsse.ethz.ch as a Postdoc? We will be hosting ETH AI Center's Postdoc Fellows on AI x evolution, AI x single cell biology as well as AI x public health. Apply now 👉 ai.ethz.ch/apply Deadline: Oct 27, 2026ai.ethz.chFellowship ProgramsThe application portal for the ETH AI Center Fellowship Programs is now closed. The deadline for submitting reference letters is 23:59 CET on November 14, 2025. 01210
Reposted by Quaid MorrisGeorge O'Toole (he/him/his) @geiselbiofilm.bsky.social · 15/09/2026Pls share: Princeton has an open rank faculty search in the areas of cancer biology, cancer prevention, and cancer-relevant computational science, including connections between cancer and immunology or metabolism. apply.interfolio.com/191852 11514
Quaid Morris @quaidmorris.bsky.social · 04/09/2026Probably what Toronto accent mapped to the USA should look like: SW Ontario, a bit of Vancouver and some snowbirds in South Florida 010
Reposted by Quaid MorrisJudith Kribelbauer @jk-swietek.bsky.social · 10/08/2026Huge undertaking of many labs for many years, highlighting the power of multi-platform comparisons and open collaborations! So many Zoom meetings, bridging an 11h+ time zone difference to make it all happen! 0144
Quaid Morris @quaidmorris.bsky.social · 07/08/2026.. @IvanDKoz, @nikitagryzunov, @VorontsovIE, @halfacrocodile, @legoushque, @AntoniGralak, @ZinkevichA, @JKribelbauer, @ArttuJolma and see also ibis.autosome.org/docs/about_usibis.autosome.orgIBIS Challenge 010
Quaid Morris @quaidmorris.bsky.social · 07/08/2026Kudos to the Codebook and GRECO-BIT consortium members including @BartDeplancke, @MakeevSeva, @EPD_SIB, @OFornes, @ImYellan, .. 100
Quaid Morris @quaidmorris.bsky.social · 07/08/20261,421 human TFs now have a characterized DNA-binding specificity, and nearly all 1,638 have been assayed. Analyses in www.nature.com/articles/s41... indicate, however, that many previously characterized TF binding specificities may be inaccurate. 100
Quaid Morris @quaidmorris.bsky.social · 07/08/2026Collectively the uncharacterized TFs bind directly to tens of thousands of conserved sequences, providing biochemical functions for these sites. Intriguingly, many of these sites are in genomic “dark matter”. Details in www.nature.com/articles/s41... 100
Quaid Morris @quaidmorris.bsky.social · 07/08/2026Methods for PWM discovery and benchmarking are explored in detail in an accompanying manuscript: www.nature.com/articles/s42... 100
Quaid Morris @quaidmorris.bsky.social · 07/08/2026Of the 332 uncharacterized TFs, PWMs were identified for 177, the vast majority of which have unique and previously unseen motifs. 100
Quaid Morris @quaidmorris.bsky.social · 07/08/2026We applied five different assays to 332 uncharacterized TFs (i.e., Codebook TFs) and 61 control TFs, including a new assay, GHT-SELEX, described in: www.nature.com/articles/s41... 100
Quaid Morris @quaidmorris.bsky.social · 07/08/2026Excited to share the results of the Codebook Project, an international effort to identify accurate DNA-binding motifs and genomic binding loci for >300 uncharacterized human transcription factors (TFs) www.nature.com/articles/s41...nature.comAn expanded codebook of human transcription factor DNA-binding specificity - NatureResults from a panel of assays that analyse different aspects of DNA sequence specificity reveal more than 100 new motifs to aid the characterization of putative human transcription factors. 14710
Reposted by Quaid MorrisMartin Steinegger 🇺🇦 @martinsteinegger.bsky.social · 01/08/2026Riboseek 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 218075
Reposted by Quaid MorrisStirling Churchman @stirlingchurchman.bsky.social · 28/07/2026RNA-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...biorxiv.orgAnalog intrinsic recoding measures RNA dynamics without chemical conversionSteady-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... 215361
Reposted by Quaid MorrisAlejandro Montenegro @aemonten.bsky.social · 25/07/2026"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... 1157
Reposted by Quaid MorrisBenjamin D. Greenbaum @bengrbm.bsky.social · 21/07/2026Matching 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 0137
Quaid Morris @quaidmorris.bsky.social · 21/07/2026Led by Olga Lyudovyk, Jonathan Levine (@levinejon.bsky.social) & Melissa Pathil, with S. Martis, A, Streltsov, Z. Sethna, Y. Elhanati, Vinod Balachandran, Quaid Morris & Benjamin Greenbaum. Code + tutorials: github.com/jonlevi/enFoldX 020
Quaid Morris @quaidmorris.bsky.social · 21/07/2026Takeaway: structural ensembles—not single predicted structures—contain the biophysical signal needed for robust generalization in TCR:pMHC prediction. The same framework should extend beyond AF3 to Boltz, RoseTTAFold, OpenFold, and related models. 111
Quaid Morris @quaidmorris.bsky.social · 21/07/2026SHAP identifies the key features: iPAEs dominate, iPTMs contribute, top global feature is pLDDT. Interestingly the peptide:MHC interface also matters, suggesting successful presentation contributes alongside TCR recognition. Both ensemble means and SDs contribute independently. 111
Quaid Morris @quaidmorris.bsky.social · 21/07/2026And the neoantigen task: cognate vs non-cognate when the peptide differs by ONE residue. Across 8 mutational-scan datasets enFoldX leads the field (median AUC 0.71) — ahead of sequence models, TCRen, and a single-structure version of our own features. 111
Quaid Morris @quaidmorris.bsky.social · 21/07/2026On IMMREP25's unseen-peptide challenge — epitopes ≥4 substitutions from anything published — enFoldX beat every sequence- and structure-based method. 110
Quaid Morris @quaidmorris.bsky.social · 21/07/2026Ten-fold CV on VDJdb: AUC 0.82 (TCR-split) human, 0.98 mouse. And a model trained only on human data also classifies mouse TCR:pMHCs at AUC 0.76 — cross-species transfer learning, a first for this task. 100
Quaid Morris @quaidmorris.bsky.social · 21/07/2026How it works: fold an ensemble (10 seeds × 5 samples), extract 106 structural, confidence, and biophysical features per prediction—focused primarily on the TCR:pMHC interface and peptide–CDR3 contacts—then summarize each as a mean and SD across the ensemble. 100
Quaid Morris @quaidmorris.bsky.social · 21/07/2026Rather than trusting one prediction, enFoldX summarizes an AF3 ensemble. Non-cognate pairs show greater structural disagreement (higher RMSD, higher iPAE), and performance keeps improving as more ensemble members are included, unlike single-structure models. 100
Quaid Morris @quaidmorris.bsky.social · 21/07/2026AF3 hallucinates for both binders and non-binders—but how often it hallucinates is informative. For CMV epitope NLVPMVATV and its M5K mutant, misdocked structures appear in 7/10 seeds for the non-cognate complex, but only rarely for the cognate. 100
Quaid Morris @quaidmorris.bsky.social · 21/07/2026Predicting which TCR recognizes which peptide-MHC is a longstanding AI challenge. Sequence-based models struggle to generalize to new peptides or TCRs, while AF3 often predicts plausible-looking structures even for non-cognate pairs. 100
Quaid Morris @quaidmorris.bsky.social · 21/07/2026Can 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/enFoldXbiorxiv.orgEnsembles of in silico structures enable T cell peptide-MHC binding predictionAdaptive 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... 13114
Reposted by Quaid MorrisAndrew Gordon Wilson @andrewgwils.bsky.social · 14/07/2026How 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/🧵 27512
Quaid Morris @quaidmorris.bsky.social · 02/07/2026It is not unusual for tenure to be granted at the Full Professor level, or separately from promotion to Associate Professor. More common among medical schools and institutes, less common at places where your salary comes from teaching. 000
Reposted by Quaid MorrisDr. Samantha Montano @samlmontano.bsky.social · 02/07/2026Sorry 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? 9121
Quaid Morris @quaidmorris.bsky.social · 11/06/2026I had to quickly check bioRvix to see whether that was one of my papers 020
Quaid Morris @quaidmorris.bsky.social · 11/06/2026Not bioRxiv's fault -- some authors are just very forceable and bioRxiv doesn't judge 130
Reposted by Quaid MorrisKate Cook @eskay8.bsky.social · 10/06/2026Getting 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 221
Reposted by Quaid MorrisMolly Knight @mollyknight.bsky.social · 31/05/2026Are we rooting for the Thunder or the Spurs 46311
Reposted by Quaid MorrisMann Lab @mannlab.bsky.social · 28/05/20261/5 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 310030
Reposted by Quaid MorrisDoug Gordon @brooklynspoke.bsky.social · 28/05/2026Pedestrianizing 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.nyc.streetsblog.orgData Show Why Mamdani Must Pedestrianize the Financial District - Streetsblog New York CityPeople walk in the Financial District, but the neighborhood's business group prioritizes the car. 1011516
Quaid Morris @quaidmorris.bsky.social · 28/05/2026Great point! What do you think of pedestrianizing Soho? 000
Reposted by Quaid MorrisLarry Hunter @proflhunter.bsky.social · 20/05/2026New 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...huggingface.coCarbon - a Hugging Face Space by HuggingFaceBioEnter 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... 0173
Reposted by Quaid MorrisDr. Julie Claycomb @farmgirlphd.bsky.social · 13/05/2026Attention 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. 1125
Reposted by Quaid MorrisDavid A Knowles @davidaknowles.bsky.social · 06/05/2026#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! 074
Reposted by Quaid MorrisNature Methods @natmethods.nature.com · 29/04/2026Orthus: 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...nature.comOrthrus: toward evolutionary and functional RNA foundation models - Nature MethodsOrthrus 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... 1143
Reposted by Quaid MorrisHarvard_MCB @harvardmcb.bsky.social · 16/04/2026Small 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.edumcb.harvard.eduSmall Model, Big Insight: RNA Structure Rules Emerge from Minimal Data - Harvard University - Department of Molecular & Cellular BiologyMCB 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... 0175