Jordan Hoff @jn_hoff
PhD student at MIT Micro. Metagenomics, genomic language models, phage enthusiast, Dead Head. Cambridge, MA Joined January 2022-
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Excited to share work with @ZhidianZ, Milot Mirdita, Martin Steinegger, and @sokrypton biorxiv.org/content/10.110… TLDR: We introduce MSA Pairformer, a 111M parameter protein language model that challenges the scaling paradigm in self-supervised protein language modeling 🧵
Thanks Abhi @owl_posting for a wonderful conversation! It was a an honor to be the 3rd guest on the show. 😎
Thanks Abhi @owl_posting for a wonderful conversation! It was a an honor to be the 3rd guest on the show. 😎
Engineering bacteriophages through deep mining of metagenomic motifs science.org/doi/full/10.11…
31 University of California faculty were **fired** for refusing to sign loyalty oaths during McCarthy Era…rising from the ashes: modern tenure, a UC President, and a Chair of MIT Corp (latter two were UCLA Prof David Saxton, who refused to sign). I wrote: pmc.ncbi.nlm.nih.gov/articles/PMC99…
“It is hard to put into words the extent of the damage being done to the US research enterprise, which is of almost incalculable value to both the nation itself and the wider world… An assault on science and scientists anywhere is an assault on science and scientists…
So happy that I can finally share the results of my first postdoc paper with @baym!! Turns out plasmids are an amazing system to study multi-scale evolution and we can track within-cell and between-cell dynamics! Here’s a photo of plasmids competing inside cells in a colony (1/n)
DefensePredictor: A Machine Learning Model to Discover Novel Prokaryotic Immune Systems biorxiv.org/cgi/content/sh… #biorxiv_micrbio
Last month the De La Cour ranch in the Southern Sierras burned down in a wildfire. This place means a lot to me and so many others. If you have the financial freedom this holiday season, a donation of any size to help rebuild would go a long way. gofundme.com/f/de-la-cour-r…
Search your favorite protein sequences with Gaia🌎! We are excited to release a context-aware protein search tool, extending search and discovery capabilities beyond sequence and structure, to include *genomic context* gaia.tatta.bio 1/🧵
Search your favorite protein sequences with Gaia🌎! We are excited to release a context-aware protein search tool, extending search and discovery capabilities beyond sequence and structure, to include *genomic context* gaia.tatta.bio 1/🧵
Pseudo-perplexity in One Fell Swoop for Protein Fitness Estimation - Use ESM-2-650M embeddings from an unmasked sequence to predict masked one-at-a-time probability vectors (by MLP), reducing the need for multiple forward passes - Combine OFS pseudo-perplexity technique within an…
Today we're open-sourcing DGEB, the first large-scale functional evaluation benchmark for biological language models 🧬 DGEB fills a key gap in BioML by providing diverse functional benchmarks for assessing pLM and gLM representations. #BioML 🧵 x.com/tatta_bio/stat…
Today we're open-sourcing DGEB, the first large-scale functional evaluation benchmark for biological language models 🧬 DGEB fills a key gap in BioML by providing diverse functional benchmarks for assessing pLM and gLM representations. #BioML 🧵 x.com/tatta_bio/stat… https://t.co/11Uv7FA7QV
Weekend project: Comparing ESM3 from @EvoscaleAI to ESM2 and inv_cov. The ultimate test of a protein language models is how well the pairwise dependencies it learns correlate to structure. (1/8)
Extremely excited to see our Methanoperedens ECE paper online in @NatureMicrobiol !! In one sentence, we discover a lot of new ECEs associated with Methanoperedens and elucidate their interactions! Please check here 👇 nature.com/articles/s4156… rdcu.be/dLP3t (free)
We have trained ESM3 and we're excited to introduce EvolutionaryScale. ESM3 is a generative language model for programming biology. In experiments, we found ESM3 can simulate 500M years of evolution to generate new fluorescent proteins. Read more: evolutionaryscale.ai/blog/esm3-rele…
The #microbiome of the cow rumen produces ~30 % of anthropogenic #methane, but how does this microbiome change when methane production is suppressed. Wonderful work by @alvinpf1 explores this as part of our amazing collaboration with @TheHessLab. #genomics #rumen #microbiology
The #microbiome of the cow rumen produces ~30 % of anthropogenic #methane, but how does this microbiome change when methane production is suppressed. Wonderful work by @alvinpf1 explores this as part of our amazing collaboration with @TheHessLab. #genomics #rumen #microbiology
The benefits of biotech are too great to risk misuse. Let’s help firms compete on security with monthly audits of gene synth providers, in which experts try to obtain hazards. Adequate screening = audit scores close to leaders. Time to support the IGSC. statnews.com/2024/05/08/sho…
What limits rubisco function? Is it the chemical mechanism? Evolution? In an updated pre-print @prywes et. al explore this question by assaying >99% of single amino acid mutants in Form II rubisco (1/7)
Excited to share the final version of our genomic language model (gLM) paper out in @NatureComms! gLM learns hidden evolutionary patterns from metagenomes to expand functional inference beyond sequence and structure to include genomic context. nature.com/articles/s4146…
New tool from @CultivariumFRO: models to predict oxygen tolerance, temperature, salinity, and pH optima from a genome - without using pesky gene annotations. Very excited to share this resource. Quick explainer: 1/10
New tool from @CultivariumFRO: models to predict oxygen tolerance, temperature, salinity, and pH optima from a genome - without using pesky gene annotations. Very excited to share this resource. Quick explainer: 1/10
In an unprecedented new move, Congress has slashed this year’s National Science Foundation budget by 8%. scim.ag/6ht
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