I'm hiring a Bioinformatics Research Associate for the Silent Genomes Project. PhD required, restricted to Canadians, work must be performed in British Columbia. Great for those who love pipelines, whole genome data and work with a social purpose. ubc.wd10.myworkdayjobs.com/ubcfacultyjo...

@saramostafavi.bsky.social (@Genentech) & I (@Stanford) r excited to announce co-advised postdoc positions for candidates with deep expertise in ML for bio (especially sequence to function models, causal perturbational models & single cell models). See details below. Pls RT 1/

Excited to share my first contribution here at Illumina! We developed PromoterAI, a deep neural network that accurately identifies non-coding promoter variants that disrupt gene expression.🧵 (1/)

Two massive glioblastoma papers, datasets, trajectories, insights, and.. a very cool new method for GRN inference - scDORI -from @steglelab.bsky.social @oliverstegle.bsky.social @bayraktarlab.bsky.social & Moritz Mall www.biorxiv.org/content/10.1... www.biorxiv.org/content/10.1...

🧠 Excited to share my main PhD project! We mapped the regulatory rules governing Glioblastoma plasticity using single-cell multi-omics and deep learning. This work is part of a two-paper series with @bayraktarlab.bsky.social @oliverstegle.bsky.social and @moritzmall.bsky.social, Preprint at end🧵👇

Check out our scPrediXcan paper www.cell.com/cell-genomic... Led by the talented @Charles_Zhou12 and supervised by @MengjieChen6 and me, with thanks to many contributors. scPrediXcan integrates deep learning and single cell expression data into a powerful cell type specific TWAS framework.

So excited to see Yawei's manuscript on long-range MPRAs out! Some really great insights into distal enhancer regulation 🙂

Day 1 of #RECOMB2025​-SEQ starts with @rayanchikhi.bsky.social and an introduction to Logan, a planetary-scale effort to assemble everything. Currently cataloguing about 700k virus species! 📄 www.biorxiv.org/content/10.1...

Our latest work now online in Cell: Rewriting regulatory DNA to dissect and reprogram gene expression Our new method (Variant-EFFECTS) uses high-throughput prime editing + flow sorting + sequencing to precisely measure effects of noncoding variants on gene expression Thread 👇

⚡️ Our latest preprint is on bioRxiv! Shift augmentation improves DNA convolutional neural network indel effect predictions www.biorxiv.org/content/10.1...

We released our preprint on the CREsted package. CREsted allows for complete modeling of cell type-specific enhancer codes from scATAC-seq data. We demonstrate CREsted’s robust functionality in various species and tissues, and in vivo validate our findings: www.biorxiv.org/content/10.1...

Bioinformatics Job Opportunity Research Associate / Staff Scientist Vancouver Canada Join the Silent Genomes Project to provide an outstanding genetic variation database for Indigenous peoples of Canada to improve rare disease diagnosis tinyurl.com/bm4ptux3 Priority to Canadians Please repost

Super excited to announce our latest work. On a personal note, it's not an exaggeration to say that blood, sweat, and tears got us to the finish line on this: working w/ an outstanding global team of scientists in Germany, Japan, Russia, and USA responding in >100 pages of complex reviewer comments.

Massively parallel reporter assays (MPRAs) testing >680,000 sequences combined with machine learning to improve regulatory element & variant effect prediction. Amazing work by @vagar.bsky.social, Fumitaka Inoue, @jshendure.bsky.social and many others as part of ENCODE. www.nature.com/articles/s41...

Super excited to announce our latest flagship model Borzoi: major props to Johannes & David Kelley et al for advancing it. It's been a long journey from our prior Enformer model into this one. A few innovations: i) longer DNA context, ii) adaptation to predict RNA-seq abundance and splice isoforms,

Our original biorxiv submission of the ChromBPNet preprint had issues with supp. methods & file links not working (even though we they were uploaded). This updated version has fixed those issues. Everything shud be available now. Thanks for your patience. www.biorxiv.org/content/10.1...

The first preprint of 2025! Together with Matvei, @halfacrocodile.bsky.social, & our amazing team, we are excited to share PARADE: an AI framework for designing mRNA UTRs with enhanced cell-type specificity & stability. www.biorxiv.org/content/10.1...

How to Accurately Time CUDA Kernels in Pytorch In a world of increasingly costly machine learning model deployments, ensuring accurate GPU operation timing is key to resource optimization. In this blog post, we explore best practices to achieve this in PyTorch. www.speechmatics.com/company/arti...

So excited that our work on predicting gene expression from histone modifications using deep learning is out in NAR today. Brilliant to work with lead author @al-murphy.bsky.social and collaborators Aydan Askarova, @borislenhard.bsky.social and Nathan Skene 🧬⭐️🙏 academic.oup.com/nar/advance-...

(1/10) Excited to announce our latest work! @arpita-s.bsky.social, @amanpatel100.bsky.social , and I will be presenting DART-Eval, a rigorous suite of evals for DNA Language Models on transcriptional regulatory DNA at #NeurIPS2024. Check it out! arxiv.org/abs/2412.05430

If you hate statistics like I do, then you'll love my free lectures. Putting science before statistics, 20 lectures from basics of inference & causal modeling to multilevel models & dynamic state space models. It's all free, made with love and sympathy. 🧪 #stats www.youtube.com/playlist?lis...

Transcription and Chromatin Parts 1 and 2 by @jxhoffman.bsky.social Part 1: go.bsky.app/5zgpZfg Part 2: go.bsky.app/Q5sXc6E

Computational Biology go.bsky.app/QVPoZXp

Mapping enhancer-gene regulatory interactions from single-cell data https://www.biorxiv.org/content/10.1101/2024.11.23.624931v1