Sign in

david-li.bsky.social

@david-li.bsky.social
114 followers 463 following 2 posts

BioE PhD student at Stanford

PostsRepliesMedia
Reposted by @david-li.bsky.social
Kai Yi @kaiyi94.bsky.social · 29/09/2026
1/7 Excited to share GuideFlip! We use guided discrete flow matching to co-design protein sequences and structures for flexible interactions, with experimental validation across three systems: α-synuclein, RBX1 and active-state GPCR nanobodies.
12518
Reposted by @david-li.bsky.social
Tessa Montague @tessamontague.bsky.social · 29/09/2026
I'm excited to share our new preprint: Generation of a transgenic cephalopod tinyurl.com/pc86jxz8 Cephalopods (cuttlefish, octopus & squid) are crazy critters that dynamically camouflage to their surroundings by changing the color, pattern, & texture of their skin, which they control w their brain.
13332112
Reposted by @david-li.bsky.social
Arc Institute @arcinstitute.org · 23/09/2026
Many important bacterial non-coding RNAs and structural elements remain undiscovered. To help, David Li, Garyk Brixi, Michael Fischbach, @brianhie.bsky.social & team introduce Minerva, which uses a genome language model to predict RNA base pairing, repeats, & other interactions from sequence alone.
12212
Reposted by @david-li.bsky.social
Akos Nyerges @akosnyerges.bsky.social · 19/09/2026
Proud and excited to share our first preprint 🚀 in which we • create a high-fitness firewalled organism, • that stably colonizes the mouse gut for >100 days, • resists all tested phages in the gut, • and blocks horizontal gene transfer. + A new method: Chimera genomes to tailor existing synthetic
33315
Reposted by @david-li.bsky.social
Sjors Scheres @sjorsscheres.bsky.social · 15/09/2026
Michel Goedert and myself are looking for two postdocs to work on #cryoEM and #masspec of #alphasynuclein filaments from neurodegenerative disease. Come join our bubbly and friendly team at the @mrclmb.ac.uk in lovely Cambridge, UK. www.nature.com/naturecareer...
nature.com
Postdoctoral Scientist | Neurobiology | Dr Michel Goedert | LMB 2842 - Cambridgeshire job with MRC Laboratory of Molecular Biology | 12864505
Postdoctoral Scientist Salary £42,694 per annum Fixed term, 3 years MRC Laboratory of Molecular Biology, Cambridge, UK To work in the group of Dr M...
01628
Reposted by @david-li.bsky.social
eartha mae @endoeartha.bsky.social · 28/08/2026
Extremely proud to share @acara333.bsky.social and my new paper, out today in @cp-neuron.bsky.social, where we develop a new fluorescent reporter of neural responses to estrogen! 🔬 paper 📝: www.cell.com/neuron/fullt... addgene page 🧬: www.addgene.org/254753/ #neuroskyence 🧪 1/10
graphical abstract of the manuscript depicting pink estrogen-sensitive neurons with a subset of their nuclei colored in green. These green nuclei represent estrogen receptor dependent neural gene transcription, tracked via the expression of a destabilized GFP with a 2 hour half-life. At top, in green is shown a cartoon of the neural response to estrogen across two estrous cycles, and below there is a cartoon of a mouse implanted with an optic fiber for in vivo imaging.
1319465
Reposted by @david-li.bsky.social
Manx Neurobiologist @garyrlewin.bsky.social · 15/07/2026
For me this paper is a career highlight..truly astonishing biology! www.nature.com/articles/s41...
nature.com
A queen odour mediates reproductive suppression in a eusocial mammal - Nature
Naked mole-rat (Heterocephalus glaber) queens produce isopropyl myristate, a low-volatility ester that high-ranking animals detect and avoid, which alters prolactin and progesterone in other females t...
27532
Reposted by @david-li.bsky.social
Rafael Pinilla-Redondo (Rafa) @rafomics.bsky.social · 16/07/2026
1/10 🚨Preprint! One RING to rule them all (phages)👑💍⚔️ Bacteria build giant DNA-scaffolded RNase rings (larger than the ribosome!) to shut down viral infection🧬🧵👇 biorxiv.org/content/10.6...
411857
Reposted by @david-li.bsky.social
Aaron and the Hoskins Lab at UW Madison @uwmadisonrna.bsky.social · 15/07/2026
This would seem to throw some cold water on the @cellpress.bsky.social paper claiming to have made "the first eukaryote functionally independent of the spliceosome"
1106
Reposted by @david-li.bsky.social
Arturo Carabias @arturocdr.bsky.social · 16/07/2026
🧬 Thrilled to share our latest @biorxiv-microbiol.bsky.social preprint! Here we find that Retron-IX build crazy supramolecular rings scaffolded by DNA molecules that sense phage infection! www.biorxiv.org/content/10.6... Read more below🧵! (1/X)
37128
Reposted by @david-li.bsky.social
Ján Bíňovský @jbinovsky.bsky.social · 02/07/2026
🔥My first (co)first-author paper is out🔥 The surfaces of Gram+ and Gram- bacteria are markedly different from each other. How are phages equipped to breach the Gram+ envelope❓ 💡We report a baseplate structure uniquely adapted to infect Gram+ S. aureus. A 🧵⬇️ 1/8 #phagesky #cryoEM 🧪
412135
Reposted by @david-li.bsky.social
Kevin Forsberg @kvnforsberg.bsky.social · 02/07/2026
Humans and bacteria share strategies to defend against viruses. We wondered: could they use each other's genes? Yes, both can! Bacteria can use human immune genes to defend against phages AND Human cells can use bacterial genes for viral defense. www.biorxiv.org/content/10.6...
biorxiv.org
Bacterial and human exonucleases mediate interkingdom antiviral immunity
All kingdoms of life have developed strategies to limit viral infection. In humans, interferons induce a suite of antiviral factors that collectively provide immunity. Some human immune genes are homo...
511950
Reposted by @david-li.bsky.social
Silvia Ramundo @sramundo.bsky.social · 24/06/2026
1/7 New preprint: we found that Chlamydomonas carries a giant and unexpectedly elaborate chloroplast RNA polymerase with 12 previously unknown subunits, overturning the idea that the complexity of this organellar enzyme emerged during plant terrestrialization! www.biorxiv.org/content/10.6...
biorxiv.org
The structure of a 2-MDa chloroplast RNA polymerase reveals unexpected evolutionary complexity
Transcription in chloroplasts depends on the Plastid-Encoded RNA polymerase (PEP), a bacterial-derived enzyme whose catalytic core remains encoded by the highly reduced genome inherited from the cyano...
510843
Reposted by @david-li.bsky.social
Kristian G. Andersen @kgandersen.bsky.social · 23/05/2026
The Proximal Origin of the MV Hondius Andes virus outbreak. virological.org/t/potential-...
virological.org
Potential geographical and ecological origin of the MV Hondius Andes virus outbreak
The recent outbreak aboard the MV Hondius caused by Andes virus raises two key questions [1]: (i) where do the outbreak genomes cluster geographically, and (ii) how can the phylogenetic signal be reco...
49746
Reposted by @david-li.bsky.social
Victoria Deneke @vdeneke.bsky.social · 22/05/2026
How do sperm and egg fuse? Surprisingly, we still don’t fully know… Our field has uncovered many pieces of the fertilization puzzle, but not how they fit together. We identify ✨ SPARK ✨ - a conserved sperm complex that couples sperm-egg binding to fusion. tinyurl.com/34cm4xat Read on! 🧵👇
2033891
Reposted by @david-li.bsky.social
Alex Gao @algao.bsky.social · 16/04/2026
Excited to share our new findings in @science.org on how the DRT3 bacterial defense system uses a reverse transcriptase that builds DNA repeats without a nucleic acid template. Microbes never cease to amaze! www.science.org/doi/10.1126/...
science.org
Science | AAAS
412460
Reposted by @david-li.bsky.social
Ali Seleit @aliseleit.bsky.social · 05/05/2026
(1/15) Thrilled to share new Evo-Devo work where we address the molecular, cellular & morphometric basis of an extreme axis segmentation program in the Japanese eel — an animal that forms 120 vertebrae.
biorxiv.org
1412446
Reposted by @david-li.bsky.social
Simone Alma Evans @simone-alma.bsky.social · 15/11/2025
I am so excited to share our project with you! We find prokaryotic proteases activate toxic enzymes and pores as a modular strategy in phage defense. We studied four fascinating protease-toxin pairs that are abundant across bacterial genomes: www.biorxiv.org/content/10.1...
biorxiv.org
Proteolytic activation of diverse antiviral defense modules in prokaryotes
Linked protease–effector modules are widespread in prokaryotic antiviral defense, yet the mechanisms of most remain poorly understood. Here we show that four of the most prevalent modules—metallo-β-la...
22719
Reposted by @david-li.bsky.social
Max Wilkinson @maxewilkinson.bsky.social · 31/10/2025
The Wilkinson Lab is open for science! @mskcancercenter.bsky.social 🧬We'll be finding funky new RNA biology, mainly by looking at reverse transcriptases (i.e. the Best Enzymes In The World)🧬 annnd: I'm hiring - come join! Especially postdocs and PhD students - please get in touch (NYC is great)
wilkinsonlab.bio
Wilkinson Lab
We discover and study reverse transcriptases
59946
Reposted by @david-li.bsky.social
Sjors Scheres @sjorsscheres.bsky.social · 09/12/2025
Star student & postdoc Kiarash Jamali is setting up his own group at the Ellison institute in Oxford. Join him for the most exciting machine learning research in structural biology and beyond!! 🤩 #ProudPI
0187
david-li.bsky.social @david-li.bsky.social · 09/12/2025
Kiarash is awesome, go work with him!
120
Reposted by @david-li.bsky.social
Samuel King @samuelhking.bsky.social · 17/09/2025
Many of the most complex and useful functions in biology emerge at the scale of whole genomes. Today, we share our preprint “Generative design of novel bacteriophages with genome language models”, where we validate the first, functional AI-generated genomes 🧵
35020
Reposted by @david-li.bsky.social
Misha Ahrens @mishaahrens.bsky.social · 08/09/2025
Preprint - Excited to present WHOLISTIC, which extends the concept of whole-brain functional imaging to the entire body. Pioneering work by incredibly talented Virginia Ruetten @vmsruetten.bsky.social, this platform reveals whole-organism cellular dynamics in vivo. www.biorxiv.org/content/10.1...
319370
Reposted by @david-li.bsky.social
Christel Depienne @christeldepienne.bsky.social · 05/09/2025
After our study on RNU4-2 and RNU5B-1 published in May (Nava et al, Nature Genetics 2025), I am excited to share our new preprint reporting dominant and recessive variants in RNU2-2 as a frequent cause of developmental and epileptic encephalopathy (DEE). 📄 www.medrxiv.org/content/10.1...
medrxiv.org
Systematic analysis of snRNA genes reveals frequent RNU2-2 variants in dominant and recessive developmental and epileptic encephalopathies
Variants in spliceosomal small nuclear RNA (snRNA) genes RNU4-2 (ReNU syndrome), RNU5B-1 , and RNU2-2 have recently been linked to dominant neurodevelopmental disorders (NDDs), revealing a major, prev...
12116
Reposted by @david-li.bsky.social
Kerstin Ludwig @kuludwig.bsky.social · 22/07/2025
🔔Paper alert! Extremely excited to share a preprint from our lab! Spearheaded by @axel-schmidt.bsky.social, a super talented medical & computational geneticist, we studied latent Epstein-Barr virus (EBV) infection at population-scale. Interested in how this works & what we found? Read along! 👇
12212
Reposted by @david-li.bsky.social
Caleb Lareau @caleblareau.bsky.social · 22/07/2025
Excited to share a new preprint from the lab with @ryandhindsa.bsky.social ! www.biorxiv.org/content/10.1... Led by @sherrynyeo.bsky.social, @erinmayc.bsky.social, and friends, we continue our journey to find viral DNA in our favorite place-- the overlooked and discarded reads in existing data! 1/
the treasure trove of all sequencing datasets
17237
Reposted by @david-li.bsky.social
Max Wilkinson @maxewilkinson.bsky.social · 03/07/2025
If you like transposons... If you you love genome editing... Or if you just like random bird animations, we have the paper for you! We (@kedmonds.bsky.social et al) are happy to share our work turning a songbird retrotransposon into a genome editing tool. 🐣 (1/n)
44516
Reposted by @david-li.bsky.social
Sjors Scheres @sjorsscheres.bsky.social · 25/06/2025
We have a 3-year funded postdoc position to work on structures of #amyloid filaments. If you are an expert in protein biochemistry, structural biology or #cryoEM / #cryoET, this could be for you! Feel free to email me with any questions. Come join us! 🤩 www.nature.com/naturecareer...
nature.com
Postdoctoral Scientist - Structural Studies - Dr Sjors Scheres - LMB 2640 - Cambridgeshire job with MRC Laboratory of Molecular Biology (LMB) | 12840844
Postdoctoral Scientist Starting Salary: £41,344 Fixed term: 3 years MRC Laboratory of Molecular Biology, Cambridge, UK We are looking for a postdoc...
05542
Reposted by @david-li.bsky.social
Sternberg Lab @sternberglab.bsky.social · 11/06/2025
1/10 New pre-print(s) from the Sternberg Lab in collaboration with Leifu Chang's Lab! We uncover the unprecedented molecular mechanism of CRISPR-Cas12f-like proteins, which drive RNA-guided transcription independently of canonical promoter motifs. Full story here: www.biorxiv.org/content/10.1...
39240
Reposted by @david-li.bsky.social
Daan Speth @daanspeth.bsky.social · 10/06/2025
I'm happy to announce the latest release of the GlobDB, available at globdb.org. The GlobDB is a database of "species dereplicated" microbial genomes, and as of release 226 contains twice the number of species-representative genomes (306,260) than the latest GTDB release.
globdb.org
home | GlobDB
311563
Reposted by @david-li.bsky.social
Eli Weinstein @eliweinstein.bsky.social · 29/05/2025
Thrilled to announce that I am joining DTU in Copenhagen in the fall, as an assistant professor of chemistry. My research group will focus on fundamental methodology in machine learning for molecules.
85811
Reposted by @david-li.bsky.social
Sjors Scheres @sjorsscheres.bsky.social · 28/05/2025
The amazing Sofia Lövestam initiated the below project, when she became interested in the vault particles that we sometimes observe in #cryoEM images of brain-derived #amyloid filaments. www.biorxiv.org/content/10.1...
biorxiv.org
Cryo-EM structure of the vault from human brain reveals symmetry mismatch at its caps
The vault protein is expressed in most eukaryotic cells, where it is assembled on polyribosomes into large hollow barrel-shaped complexes. Despite its widespread and abundant presence in cells, the bi...
26023
Reposted by @david-li.bsky.social
Svetlana Dodonova @dodonova-sveta.bsky.social · 26/05/2025
We’ve uncovered Asgard chromatin structures formed by a Hodarchaeal histone : closed hypernucleosome conserved in archaea and an open form resembling the H3-H4 eukaryotic octasome. Fantastic work by @harshranawat.bsky.social! www.biorxiv.org/content/10.1... #Chromatin #Asgard #Archaea #cryoEM
13237101
Reposted by @david-li.bsky.social
Kristian G. Andersen @kgandersen.bsky.social · 07/04/2025
We were just notified that our contract to UCSD and Scripps Research to support wastewater surveillance in San Diego (searchcovid.info) was terminated immediately for the same reasons 👇. That means no more genomic wastewater surveillance, and our proposed extensions to measles, Hep A, others, gone.
searchcovid.info
Home - SEARCH
17575389
Reposted by @david-li.bsky.social
Maya Voichek @mayavoichek.bsky.social · 17/03/2025
1/ Transposable elements are often called "jumping genes" because they mobilize within genomes. 🧬 But did you know they can also jump 𝘣𝘦𝘵𝘸𝘦𝘦𝘯 cells? 🤯 Our new study reveals how retrotransposons invade the germline directly from somatic cells. www.biorxiv.org/content/10.1... A short thread 🧵👇
Drosophila follicle showing retrotransposons (pink & yellow) expressed in somatic cells infecting the oocyte
12547259
david-li.bsky.social @david-li.bsky.social · 02/03/2025
Check out this amazing work by the superstar team of @guilhemfaure.bsky.social, Makoto Saito, and @maxewilkinson.bsky.social !!! Very curious what the natural function of TIGR-Tas is
000
Reposted by @david-li.bsky.social
Max Wilkinson @maxewilkinson.bsky.social · 01/03/2025
we recently found some really neat RNA-guided DNA-cutting systems in phages. Despite remarkable similarities to CRISPR systems, including encoding guide RNAs in arrays, they appear entirely evolutionarily distinct (but definitely related to snoRNAs 🤓) We decided to call them TIGR-Tas systems 🐯
220978
Reposted by @david-li.bsky.social
Scott_Boyd_Lab_Stanford @scottboydlab.bsky.social · 21/02/2025
Attempting to read the language of B cell and T cell receptor sequences to diagnose immunological diseases: Our new paper, led by the outstanding Maxim Zaslavsky @maximzaslavsky.bsky.social sky.bsky.social with help from me and Anshul Kundaje @anshulkundaje.bsky.social. Link: buff.ly/3QvxSVf
A figure showing a model for using BCR and TCR sequences to classify immunological disorders.
14815
Reposted by @david-li.bsky.social
Sjors Scheres @sjorsscheres.bsky.social · 21/02/2025
BIG news: Jason Chin is leaving the Division of Protein & Nucleic Acid Chemistry of @mrclmb.bsky.social to spend yet another billionaire's ££ in Oxford. This will create a gap that will need filling! So, if you're thinking of making a move, now is the time to reach out! www.eit.org/news/profess...
eit.org
Professor Jason Chin joins EIT to lead its new Generative Biology Institute | Ellison Institute of Technology Oxford
GBI will tackle the key challenges in making biology engineerable, and thereby unlock the unrivalled power of biology for the benefit of humanity.
42921
Reposted by @david-li.bsky.social
Nick Burton @nickburton.bsky.social · 18/02/2025
One of the coolest and most novel findings I’ve seen in years. This is why I work in worms. To find things no one even really knew to look for. Like a conserved system that splices transposons out of mRNAs to prevent otherwise lethal insertions in essential genes! - www.biorxiv.org/content/10.1...
biorxiv.org
An RNA Splicing System that Excises Transposons from Animal mRNAs
All genomes harbor mobile genetic parasites called transposable elements (TEs). Here we describe a system, which we term SOS splicing, that protects C. elegans and human genes from DNA transposon-medi...
07022
Reposted by @david-li.bsky.social
Sorek Lab @soreklab.bsky.social · 30/01/2025
Our paper out @Nature: CARD domains mediate anti-phage defense in bacterial gasdermin systems CARDs are essential for caspase recruitment during human inflammasome activation. We now find them in bacterial immune systems Congrats Tana Wein! Thank you Kranzusch lab! www.nature.com/articles/s41...
419366
Reposted by @david-li.bsky.social
George Ghanim @automnenine.bsky.social · 28/01/2025
After many years at @mrclmb.bsky.social, I've moved back home to start my own lab at @princetonmolbio.bsky.social. I'm so thankful to my mentors, especially Kelly Nguyen and Don Rio! We have some exciting results on LINE-1 in the works and are recruiting. Find out more: ghanim.lab.princeton.edu
8575
Reposted by @david-li.bsky.social
Rui Zhang @ruizhangmt.bsky.social · 01/01/2025
Best way to start 2025! Thrilled to share our Nature paper about the structures of axonemal components from sperm flagella and from epithelial cilia of the oviduct and brain ventricles. Great collaboration with Tzviya Zeev-Ben-Mordehai and @alanbrownhms.bsky.social www.nature.com/articles/s41...
410934
Reposted by @david-li.bsky.social
Possu Huang Lab @possuhuanglab.bsky.social · 17/12/2024
1/ In two back-to-back papers, we present our de novo TRACeR platform for targeting MHC-I and MHC-II antigens TRACeR for MHC-I: go.nature.com/4gcLzn5 TRACeR for MHC-II: go.nature.com/4gj5OQk
29129
Reposted by @david-li.bsky.social
Laurence Ettwiller @ettwiller.bsky.social · 09/12/2024
www.biorxiv.org/content/10.1... Our study published today on #bioRxiv describe the identification of a deaminase that converts 5mC to T, enabling direct sequencing of the human methylome and genome. This achievement was made possible through a collaborative effort across all departments at #NEB.
511357
Reposted by @david-li.bsky.social
estella newcombe @estellaan.bsky.social · 27/11/2024
We did this crazy project where we tried to see if proteins could interact with their mirror image ligand. Seems impossible when proteins need to form 3D structures to interact. But what about if the interaction remains disordered??? www.nature.com/articles/s41...
nature.com
Stereochemistry in the disorder–order continuum of protein interactions - Nature
Studies on protein–protein interactions using proteins containing d- or l-amino acids show that stereoselectivity of binding varies with the degree of disorder within the complex.
717863
Reposted by @david-li.bsky.social
Mitch Guttman @mitchguttman.bsky.social · 27/11/2024
Gene regulation involves thousands of proteins that bind DNA, yet comprehensively mapping these is challenging. Our paper in Nature Genetics describes ChIP-DIP, a method for genome-wide mapping of hundreds of DNA-protein interactions in a single experiment. www.nature.com/articles/s41...
nature.com
ChIP-DIP maps binding of hundreds of proteins to DNA simultaneously and identifies diverse gene regulatory elements - Nature Genetics
ChIP-DIP (ChIP done in parallel) is a highly multiplex assay for protein–DNA binding, scalable to hundreds of proteins including modified histones, chromatin regulators and transcription factors, offe...
9382150
Reposted by @david-li.bsky.social
Martin Steinegger 🇺🇦 @martinsteinegger.bsky.social · 23/11/2024
Our Big Fantastic Virus Database (BFVD) is now published NAR! It contains protein structure predictions of major viral clades, enhanced by petabase-scale homology search and it's explorable on the web. 🌐 bfvd.foldseek.com 💾 bfvd.steineggerlab.workers.dev 📄 academic.oup.com/nar/advance-...
6339126