Graham Erwin
Asst. Professor, Baylor College of Medicine. Previously Stanford and UW–Madison. We use molecules and genomes to understand repetitive DNA sequences. #FirstGenAcademic ErwinLab.org
- ASHG25 Poster 4106 Today at 2:30pm! Whole-genome long-read sequencing from 10 NANOGRAMS, not micrograms! ULI-HiFi delivers: ✅ 99.82% F1 for SNVs ✅ 98.9% TR accuracy ✅ Discovered LIMD1 TR expansion progressively increasing from normal→polyp→adenocarcinoma, with evidence of function
- Come check out Cera’s poster (4106) today at 2:30pm! Pre-print: www.medrxiv.org/content/10.1...
- At ASHG25 RIGHT NOW: Deep-coverage PacBio HiFi sequencing reveals hotspots of tandem repeat variation in the male germline. 12 men, paired blood/sperm, 1.7M repeats analyzed. What we found about mutational bias will surprise you! Poster 6044W, 2:30-4:30pm today. Lucas Finot presenting.
- Proud to announce that we received the NIH Director's New Innovator Award to develop a new class of genome editing tools!
- Dr. Graham Erwin @grahamerwin.bsky.social receives NIH New Innovator Award! www.bcm.edu/news/dr-grah... @bcmhouston.bsky.social @bcmgenetics.bsky.social #BCMCancerCenter
- Reposted by Graham ErwinA follow-up to my quote of the day this morning: A short Bluetorial about Vannevar Bush and his legacy
- Interested in modern grant writing in the age of AI? Join us this summer through Stanford Continuing Studies! continuingstudies.stanford.edu/courses/prof...
- Reposted by Graham ErwinBig: The final version of a randomized, controlled World Bank study finds using a GPT-4 tutor with teacher guidance in a six week afterschool program in Nigeria had "more than twice the effect of some of the most effective interventions in education" ("equating to 1.5 to 2 years" of standard school)
- Reposted by Graham ErwinI had such a powerful experience at BCM SKY Retreat this weekend led by @grahamerwin.bsky.social and met so many amazing people! It was a thought-provoking and reflective weekend with lessons that I will carry with me! What a privilege to partake in such a transformative experience! 🥰
- Reposted by Graham ErwinA first in human genomics: a 4-generation pedigree reference, now in Nature. Built with #PacBio HiFi, it maps de novo mutation rates, reveals paternal bias, and captures high mutation rates in tandem repeats—even in Y and repeat-rich regions. Paper here: go.nature.com/4lGMPlP #TheresHiFiForThat
- There are a number of tools (Elicit, Perplexity, Google's Deep Research, Consensus within ChatGPT) to find references. One of the complaints from academics is these tools don't find "the right papers". So far, ChatGPT Deep Research and their o3 model have the best "taste" that I have found. (1/3)
- The two more important papers on polyamide-based transcriptional activators would be Mapp et al PNAS 2000 (the OG on the topic) and our 2017 Science paper (one of the most convincing in a disease model). (2/3)
- The only tool to capture both so far has been ChatGPT Deep Research and o3 (new model from OpenAI released today. It also captures 2 other important papers from Sugiyama and Kodadek. (3/3) bit.ly/LLMtaste
- Here is the output in case there are issues with the link. Prompt: Do research. find peer-reviewed publications of pyrrole-imidazole polyamides used to activate gene expression (transcriptional activators). Expected output: an exhaustive list of references to the original publication.
- The LLM (AMIE in this case) performs higher (59.1% top-10 accuracy) than the clinician with the LLM (51.7%). Another study consistent with what @emollick.bsky.social has been sharing for a while now. www.nature.com/articles/s41...
- Caveat: The authors didn't perform a statistical test comparing these groups, but the trend is the same on bot top-1 and top-10 accuracy.
- Reposted by Graham ErwinUpdated this chart with the newest Gemini. It shows the rapid progress in AI over less than two years: costs for GPT-4 class models has dropped 99.7% and even the most advanced models (beating PhDs at the GPQA) are still 82% cheaper than GPT-4. Probably not worth betting on this trend ending soon.
- Reposted by Graham ErwinA new means of selectively imaging the inner mycolate of mycobacteria using a compound that covalently modifies an enzyme intercepts to create a new intermediate with the Kim lab, @thebrysonlab.bsky.social and the Bernhardt lab. #TB
- First post here! To inaugurate this account, I'd like to share my recent work, now published in JACS. Intercepting a Mycobacterial Biosynthetic Pathway with Covalent Labeling | Journal of the American Chemical Society pubs.acs.org/doi/10.1021/...
- Reposted by Graham ErwinThe strchive.org paper is out!! The paper describes STRchive as a resource to improve the diagnosis of tandem repeat disorders, then goes beyond it to consider what can be learned about childhood onset and population prevalence of these diseases. 🖥️ 🧬 link.springer.com/article/10.1...
- Reposted by Graham ErwinA new article from Laurel Hiatt and @hdashnow.bsky.social describing STRchive is now available at Genome Medicine. genomemedicine.biomedcentral.com/articles/10.... Check out the database resource, as STRchive "streamlines TR variant interpretation at disease-associated loci." strchive.org
- Reposted by Graham ErwinEvidence that a well prompted LLM can help learning from a (small, single-subject) randomized controlled trial at Harvard: “here we show that students learn more than twice as much in less time with an AI tutor compared to an active learning classroom, while also being more engaged and motivated.”
- Reposted by Graham ErwinWe don't spend a penny on marketing. It's all word of mouth for @costplusdrugs.com That's how we keep prices so low. Please spread the word !
- Reposted by Graham ErwinThe first bifunctional protein degrader to deliver Phase III data! It seems to work, but people were definitely expecting more:
- Reposted by Graham Erwin5 yr anniversary of the day I started my COVID ICU visit
- Reposted by Graham ErwinSpectacular news this morning for CRISPR gene editing to treat genetic disease from Beam Therapeutics. This method was developed by David Liu's lab at the Broad. = "academic" science produces innovations that enables the biotech sector to build medicines investors.beamtx.com/news-release...
- Reposted by Graham ErwinExcited to share the peer-reviewed version of our paper, which is out today!! Bispecific antibodies targeting the N-terminal and receptor binding domains potently neutralize SARS-CoV-2 variants of concern | Science Translational Medicine www.science.org/doi/10.1126/...
- Reposted by Graham ErwinResearchers from @pollyfordyce.bsky.social lab explore what makes some transcription factors more or less selective for their DNA ligands. This work could guide the design of more selective DNA-binding proteins for many bioengineering applications:
- Reposted by Graham ErwinChatGPT Code Interpreter is still my favorite implementation of the pattern where an LLM can write code, run it, see any errors and iterate to fix them It's been stuck on GPT-4o for ages - today it got a huge upgrade and now work with GPT4.5 and o3-mini! simonwillison.net/2025/Mar/5/c...
- Reposted by Graham ErwinAs #AGBT approaches, discover how #PacBio SPRQ chemistry for Revio is advancing #HiFisequencing efficiency, reducing costs, and unlocking new research possibilities. bit.ly/4g89HXK #AGBT25
- Reposted by Graham ErwinWe are starting to see what "AI will accelerate science" actually looks like. This Google paper describes novel discoveries being made by AI working with human co-scientists (something I think we have all been waiting to see), along with an early version of an AI scientist for wider use.
- Reposted by Graham ErwinAt #BPS2025? Check out the posters by @sovannytaylor.bsky.social and @gtleung.bsky.social on Monday. Venom peptides as tools to study cell penetrance and designer condensates to probe cytoplasmic rheology across length scales.
- Highly recommend the Unpaywall extension to access manuscripts — it's easier than Sci-Hub, and legal! unpaywall.org/products/ext...
- Reposted by Graham ErwinHere’s my post on the NIH indirect costs slash-and-burn. God, these people are exhausting:
- Reposted by Graham ErwinYou will never guess the report that took Deep Research the longest to generate of any I made before. 30 pages, 10,600 words, and actually super interesting to read based off a single prompt. Full report (and prompt): chatgpt.com/share/67a152...
- Reposted by Graham ErwinA long post about what’s happening to the science funding agencies in the US and why. As mentioned, this one just kept getting longer even as I kept stripping curse words from it. www.science.org/content/blog...
- Reposted by Graham ErwinFriends and colleagues, I’ve written a book on effective functional genomics study design, which will be available on Amazon in a couple of weeks. Sharing the TOC to spark interest. I hope students and those planning genomics experiments will find it useful! I’ll share updates soon
- Reposted by Graham ErwinFirst real post on @bsky.app! Check out our latest work identifying covalent fragments as inhibitors of the Fph serine hydrolases in S. aureus. Great work from Tulsi Upadhyay and our many collaborators. www.researchsquare.com/article/rs-5...
- Reposted by Graham ErwinI think you're describing science, IMO. Everything is atop a foundation of basic research. An example: at a previous company, I worked on a series of small-molecule inhibitors of Hormone-Sensitive Lipase, a possible target for Type II diabetes and related conditions. (1/10)
- Reposted by Graham ErwinDeeply saddened by the news of Fraser Stoddart’s passing. Here is a piece I wrote on the occasion of his 2016 @nobelprize.bsky.social at ACSCentSci. pubs.acs.org/doi/10.1021/...
- Reposted by Graham Erwin'But that’s not the only reason Science has named lenacapavir its 2024 Breakthrough of the Year. The off-the-charts success of the drug as PrEP sprang from a basic research advance: a new understanding of the structure and function of HIV’s capsid protein, which lenacapavir targets'
- Reposted by Graham Erwin🎶 Hark! The folded proteins sing, Stable chains and everything. Joyful folds in ribboned form, Structures bright, precise, and warm.* 🎶 Life depends on such designs, Aligned through microscopic lines. Peace on Earth and molecules bring, Hark! The folded proteins sing. 🎶
- Reposted by Graham ErwinTurn a GitHub repo into a single text file for LLM-friendly input: app takes a GitHub repo URL, displays the directory structure, lets you choose which files to include, and provides a single plain text file you can feed into any LLM. blog.stephenturner.us/p/github-rep... w/ #rstats example
- Reposted by Graham ErwinApparently, Biorender now does graphing. Do not use. Terms of service likely include them owning your first-born child.
- Reposted by Graham ErwinModels like o1 suggest that people won’t generally notice AGI-ish systems that are better than humans at most intellectual tasks, but which are not autonomous or self-directed Most folks don’t regularly have a lot of tasks that bump up against the limits of human intelligence, so won’t see it
- Reposted by Graham ErwinHello, #MedSky community! We’re excited to begin our Bluesky journey. Here is a sampling of the trusted, influential, and essential information you can expect when you follow us:
- Reposted by Graham ErwinScared to share this after 10 freaking years of waiting, but here we go: We found that temperature *perception* can change the biology of the next generations, even when “it’s just in the parents' head”. Read how C. elegans neurons control epigenetic inheritance! www.biorxiv.org/content/10.1...
- Reposted by Graham ErwinBiology of Genomes 2025 is coming up: - meeting dates: May 6 - 10, 2025 - abstract deadline: Feb 14, 2025 We hope to see you there for another great meeting with a fantastic speaker lineup! meetings.cshl.edu/meetings.asp...
- Reposted by Graham ErwinScientists, academics, researchers: We’re excited to share that @altmetric.com is now tracking mentions of your research on Bluesky! 🧪
- Reposted by Graham ErwinFluorescently labeled proteins are essential to research. But we should never forget how messed-up their behavior can be. An example from condensates:
- Reposted by Graham ErwinYou probably aren’t being ambitious enough in your AI experiments. Start with completely out there applications, assess them, and then reign in your ambitions from there. You might be inspired or surprised about how good AI is, or you might discover useful limitations earlier.
- Reposted by Graham ErwinStriking similarity of some of the genetic signals in mismatch repair genes (MSH3, FAN1 and PMS2) between GWAS of somatic expansion of CAG repeats in TCF4 gene (estimated from UKB WGS data) & GWAS of age at onset of cognitive changes in Huntington's. www.biorxiv.org/content/10.1...
- Reposted by Graham ErwinGene 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...
- Reposted by Graham ErwinSometimes you just have to persevere through negative reviews. Reviewers, please be kind :) #methodsmatter bit.ly/gs2-scholar
- Reposted by Graham Erwin🎨 In case anyone need… The NIH BioArt Source is an awesome library of *free* professionally drawn illustrations for scientific presentations or figures. Downloadable in HD. Thank you NIH for this invaluable tool 🙏! Check it out 👇 bioart.niaid.nih.gov
- Reposted by Graham Erwin
[This post could not be retrieved] - Reposted by Graham ErwinOrganizations (including university labs) should stockpile problems they could use help on from the new set of agentic & o1-like systems that are coming soon. I suspect that they will be less useful to non-experts at first, but open up some new opportunities for complex work that AIs can do.
- What a fantastic day at Tufts University! Sergei Mirkin, Catherine Freudenreich, and @sarahhengel.bsky.social. What a special place.
- Reposted by Graham ErwinMass spec meme to get things started here 😆
- Reposted by Graham ErwinThe Long-read sequencing Special Issue is now LIVE! Guest-edited by @ahoischen.bsky.social , @sedlazeck.bsky.social, and @anaconesa.bsky.social.
- SPECIAL ISSUE! This month Genome Research publishes a diverse collection of research and review articles in a special issue highlighting advances in long-read sequencing applications in biology and medicine. Full issue links here: tinyurl.com/Genome-Res-3....
- Reposted by Graham ErwinThanks @dereklowe.bsky.social for amplifying this fun piece in ACS Cent Sci. I shall think through my own eureka moments and make a contribution!
- Reposted by Graham ErwinSingle-molecule states link transcription factor binding to gene expression www.nature.com/articles/s41...
- Reposted by Graham ErwinLong-read special issue of GR is out, including our paper on T2T assembly using only Nanopore. Just in time for ONT to discontinue duplex cells on Nov 27 😅😂 Good thing Verkko also works great with HERRO-corrected simplex data! 📄 genome.cshlp.org/content/34/1... 📖 genome.cshlp.org/content/34/1...
- Reposted by Graham ErwinYay!! @amerchemsociety.bsky.social is in the house clap👏
- Hi #ChemSky! 👋 We see you! Please give us a moment to get settled here.
- Reposted by Graham ErwinOur special issue @genomeresearch.bsky.social is out on long-read sequencing (@pacbio.bsky.social & ONT): genome.cshlp.org/content/34/1... Super excited about all the new work and special thanks to all the authors! Big thanks to Hillary @ahoischen.bsky.social @anaconesa.bsky.social
