Sijae Woo

We used #GPT4 to greatly simplify medical consent forms for patients in new @NEJM_AI paper ai.nejm.org/stoken/default… Our #LLM simplified forms are now used in the largest health system in Rhode Island. Medical documents like consent forms are often hard to understand--great use case for LLM. We had medical + legal experts review the simplified forms to ensure accuracy. Great job led by @RohaidAliMD Fatima Mirza @oliverytang @IDavidConnolly and wonderful collaborators! 🚀

🧬 Our #ENCODE4 paper is out now @GenomeBiology! Dissecting uncharted regions in our DNA and their influence on our health. 🧬 Dive into the world of disease genetics and genomic "dark matter" with us as we explore our trailblazing new method. Ready? Let’s go! 🚀 🧵 #Genomics #GenomeFunction #ScienceTwitter doi.org/10.1186/s13059… 1/

Awesome. Google's Gemini Pro and Gemini Pro Vision are now available on @kaggle at no cost. There is also a notebook to help you get started: kaggle.com/code/prathames…

Gemini has launched! We are starting a series of notebooks demonstrating Gemini in Colab, starting with using Sheets and Colab to facilitate creation of a personalized holiday note. Once you have a Gemini API key from Google AI Studio, try it out here: colab.research.google.com/github/googlec…

Exclusive: Buried in the online autumn statement is a bit of news with potentially huge implications for biopharma. The UK is going to try to create a pathway for individually customised medicines! economist.com/britain/2023/1… @mhra @stopbatten @GenomicsEngland @OHRareDisease

Can we find new more effective ways to use standard-of-care cancer drugs? We address this in our new paper, performing massive-scale targeted CRISPR screens in cells treated with common chemotherapeutics… (1/n) nature.com/articles/s4146…

1/n: We are excited to share that our paper on Chroma, a general purpose diffusion model for proteins, is out today in @Nature! nature.com/articles/s4158… A couple of my favorite highlights in the 🧵below 👇

1/ Excited to share our latest work on mapping the transcribed cis-regulatory elements (tCREs) in single-cells across 23 human tissues for dissecting trait heritability with cellular contexts. doi.org/10.1101/2023.1…

Interested in LLMs for genomic research but don't know where to start? looking for a review/survey to get started in this field? 👇👇😀 I am very excited to share that our review paper titled "To Transformers and Beyond: Large Language Models for the Genome" is now available as a preprint (arxiv.org/abs/2311.07621)! Our review unveils a revolution in genomics analysis with Genome LLMs. 🧬 🔍 What's Inside: ✅ The power & challenges of transformers in genomics. ✅ Cutting-edge models like HeynaDNA and scGPT & their impact. ✅ Deep dives into Enformer, DNABERT, and other Genome LLMs. 🌍 Why it Matters: 1. GPT-4's influence reshapes AI in genomics. Unmatched insights into transformers' role in genomics. 2. Critical analysis of new models, addressing interpretability, privacy, & computational needs. 3. Essential for computational biologists & computer scientists to navigate the future of genomic data analysis. This is a work led by the amazing PhD student, Mica Consens, in the lab! Also, a huge collaborative work with lots of field leaders @fabian_theis @genophoria @MKarimzade @michaelwainberg and Alan Moses! @UofT @VectorInst @UofTCompSci @UofT_LMP @UHN @pmcc_ai @UHNAIHUB

Excited to share our latest work on bioRxiv! biorxiv.org/content/10.110… A highly collaborative effort with @ksmualim @karbalayghareh, @mayayayas, @kanishkadey, @evelynjagoda,@WangXijhu, @LarsMSteinmetz, @anshulkundaje, @jengreitz and many others from @ENCODE_NIH! Thread👇

Not enough people know about bioicons.com Open source vector graphics. Free alternatives to BioRender.

As part of #AMPath23, @ClinGenResource and @illumina will be hosting a workshop on November 15 at 4:00pm MST "ACMG/AMP/CAP/ClinGen DRAFT Standards for Sequence Variant Classification v4.0" featuring @HeidiRehm and Steven Harrison. Learn more clinicalgenome.org/about/events/c… (1/2)

We’re excited to share that the RGC-ME Browser is live! The RGC-ME Browser offers allele frequencies, ancestry estimates, constraint metrics, and transcript annotations based upon a catalog of human protein-coding variations from the exome data of ~1M individuals.

The #gnomAD team is proud to announce the release of gnomAD v4! The v4 dataset includes 730,947 exomes & 76,215 genomes, which is ~5x larger than the v2 & v3 releases combined, & includes nearly 120K indivs of non-European genetic ancestry broad.io/gnomad_v4 #ASHG23 (1/11)

Excited to show a glimpse of the next generation of AlphaFold from our teams at @IsomorphicLabs and @GoogleDeepMind. This model expands beyond proteins to include other molecules like small molecules and nucleic acids, and improves accuracy on proteins 1/n bit.ly/45Qt4yT

New! We’ve just put up a note evaluating the latest, in-development version of AlphaFold (“AlphaFold-latest”). This is a preview - development is still in progress - but performance across a wide range of tasks is striking. deepmind.google/discover/blog/… Highlights in the thread. 1/7

Previous viral evolution can shed light on future immune evasion. EVEscape, now out in @Nature, is our first step in applying pre-pandemic data to forecast antibody escape through the course of a pandemic. nature.com/articles/s4158… 🧵1/6

Published online at AJHG! 🎉 Our work on the "Contribution and therapeutic implications of retroelement insertions in ataxia telangiectasia". Thanks for the support and guidance from my wonderful co-mentors Drs. E. Alice Lee @EAliceLee2 and Timothy W. Yu @timyu !

RNAseq counting tools are not perfect. I simulated 240 GTEx samples to test multiple tools. Below I show the difference between actual and estimated counts for each simulated sample. But, what is causing this? And will it affect differential expression? (1/7) #Bioinformatics

Programmable concatenation of cDNA molecules increases the throughput of PacBio sequencing about 15-fold go.nature.com/3J5xk4Z