Carlos Albors

Can we simulate realistic evolutionary trajectories and “replay the tape of life”? In this work, we propose a flexible, generalizable framework for modeling how the entire protein seq evolves over time while capturing complex interactions across sites. 1/n doi.org/10.64898/2026.…

We are excited to share GPN-Star, a cost-effective, biologically grounded genomic language modeling framework that achieves state-of-the-art performance across a wide range of variant effect prediction tasks relevant to human genetics. biorxiv.org/content/10.110… (1/n)

Happy New Year! Our GPN-MSA paper is finally published, under a slightly different title from the preprint. Please check it out and share it with your colleagues. doi.org/10.1038/s41587… 1/4

It was recently reported that Africans experienced a sharp, severe bottleneck around 900kya and that this signal is absent in non-Africans. Here, we present evidence to show why this is likely a statistical artifact: @ras_nielsen @yun_s_song biorxiv.org/content/10.110… 1/4

We were invited to write a review article on DNA/genomic language models (gLMs). We took this occasion to gather our thoughts on promising applications, and major considerations for developing and evaluating gLMs. Pls share with your colleagues: Preprint: arxiv.org/abs/2407.11435

@brianltrippe @Stanford @StanfordData Congrats Brian!

I am pleased to share that I have accepted a position @Stanford to start as an assistant professor in the department of statistics, with an affiliation in @StanfordData, this fall!

I’ll be presenting GPN-MSA at #ASHG, Reviewers’ Choice Poster PB4125 Fri 3-5PM. Come chat about DNA language models! x.com/yun_s_song/sta…

We recently posted a preprint describing GPN-MSA, a DNA language model that leverages whole-genome alignments across multiple species while taking only a few hours to train. This thread summarizes its performance on the human genome. doi.org/10.1101/2023.1… 1/12

After lengthy anticipation, we finally got to compare PrimateAI-3D with our Cross-Protein Transfer (CPT) model doi.org/10.1186/s13059… Below is a summary of our findings, including a comparison of ESM-1b and ESM-1v protein language models. 1/8

everyone is trying to come up with a copy of twitter when we actually want a copy of 2007-2012 niche hobby blogs with a Google RSS reader that aggregated them into one feed

Very glad to see our CherryML method published online in @naturemethods. The published version has updated and expanded results, so please check it out. doi.org/10.1038/s41592… (1/3)

If you are interested in DNA language models and their potential applications in genome-wide variant effect prediction, please check out our updated GPN paper (with @gsbenegas and @sanjitsbatra): doi.org/10.1101/2022.0… A summary of updates follows. 1/5

@genetisaur @hailgenetics 🙌

Looking for an easily accessible diverse set of genomes? We've got you! The HGDP+1kGP genomes have been jointly called and QC'd as part of gnomAD, complete with SNVs, indels, and SVs: biorxiv.org/content/10.110…. Fully public resource, tutorials included, feedback welcome!

Interested in a fast, accurate method for estimating the parameters of a complex phylogenetic model of molecular evolution (e.g. a general rate matrix describing the co-evolution of protein contact sites in 3D)? If so, please check out our preprint: doi.org/10.1101/2022.1… (1/10)

@GracianoArroyo Five guys

Looking to benchmark a model-guided protein design method? Running into the limitations of existing datasets? Excited to present SLIP (Synthetic Landscape Inference for Proteins), a suite of tuned fitness landscapes. Preprint: biorxiv.org/content/10.110…

Predicting the effects of missense variants is a central problem in human genome interpretation. We are thrilled to share our preprint on using cross-protein transfer (CPT) learning to improve zero-shot prediction of disease variant effects: doi.org/10.1101/2022.1… (1/8)

@GracianoArroyo Money is also a message

@GracianoArroyo No reply is also a reply

@GracianoArroyo 🔛