An AI system to help scientists write expert-level empirical software
The cycle of scientific discovery is frequently bottlenecked by the slow, manual creation of software to support computational experiments. To address this, we present an AI system that creates expert...
Just spotted this paper saying their tree search/genetic algorithm writes better bioinformatics software than SOTA. Does batch correction of scRNAseq, and covid hospitalisation estim.
Noth outside my wheelhouse. Does anyone have expertise and energy to look at it?
arxiv.org/abs/2509.06503
09.09.2025 20:54 — 👍 12 🔁 4 💬 3 📌 1
Efficient sequence alignment against millions of prokaryotic genomes with LexicMap - Nature Biotechnology
LexicMap uses a fixed set of probes to efficiently query gene sequences for fast and low-memory alignment.
Sometimes you meet absolutely incredible bioinfo-magicians.
It was a huge privilege when @shenwei356.bsky.social
joined our group for a year on an @embl.org sabbatical.
While here, he developed a new way of aligning to
millions of bacteria, called LexicMap 1/n
www.nature.com/articles/s41...
10.09.2025 09:12 — 👍 189 🔁 98 💬 5 📌 4
💥 Excited to introduce Bacformer 🦠 - the first foundation model for bacterial genomics. Bacformer represents genomes as sequences of ordered proteins, learning the “grammar” of how genes are arranged, interact and evolve.
Preprint 📝: biorxiv.org/content/10.1...
🧵 1/n
21.07.2025 09:55 — 👍 91 🔁 59 💬 3 📌 2
This campaign needs you now
Protect the CDC's National STD Reference Laboratory
The CDC's Sexually Transmitted Diseases Reference Laboratory is the only one of its kind in the US. It is a key resource for keeping Americans healthy. Sign the petition to rescind its unjustified closure. chng.it/pxjfWmRm2w
10.04.2025 14:58 — 👍 2 🔁 1 💬 0 📌 0
Professor, UW Biology / Santa Fe Institute
I study how information flows in biology, science, and society.
Book: *Calling Bullshit*, http://tinyurl.com/fdcuvd7b
LLM course: https://thebullshitmachines.com
Corvids: https://tinyurl.com/mr2n5ymk
he/him
Professor of Biology, Temple University's Institute for Genomics and Evolutionary Medicine, Department of Biology, Sunny Philadelphia, USA
Professor at Stanford. Probabilistic optimist.
#healthpolicy | #publichealth | infectious disease | decision science | simulation modeling | economic evaluation
Director http://ppml.stanford.edu
science journalist. author. molecular biologist. curious.
interested in #microbes, #misinformation and all things #blue
contributing correspondent at @science.org
co-host of @pandemia.bsky.social
2024 KSJ fellow at MIT
Signal: kakape.93
The Huttenhower Lab at the Harvard T.H. Chan School of Public Health: microbial community function and human microbiome population health;
Moderators: @jtnearing.bsky.social, @chahat.bsky.social
Microbiology, evolution, and bacteriophages. University of Pittsburgh School of Medicine.
Faculty in Epidemiology at the UNC Gillings School of Global Public Health. Helps coordinate the COVID-19 Scenario Modeling Hub https://covid19scenariomodelinghub.org/
Semi-informed molecular biologist & recovering football coach / Research Professor / Microbial Genomics / Evolution / AMR /
/ https://www.fhi.no / www.haploid.no
Viral evolution and infection biology. Assoc. professor at University of Illinois at Urbana-Champaign. brookelab.org
Writing a book about horizontal gene transfer and non treelike evolution. Bioinformatics, Evolutionary Biology. Pangenomes. Chair in Evolutionary Biology. 🇮🇪 http://github.com/mol-evol/panGPT
Computational Epidemiologist and Associate Prof at WSU. Maker of artisinal, small-batch simulation models for the discerning infectious disease consumer. WoW and zombie epidemiology. Adopter of dogs. Not taking this terribly seriously. He/him.
Professor of Immunology at University of Arizona studying immune responses to infections and vaccines. Views my own.
Work in progress | Evolution | Ecology | Systems Biology | Experiments | Theory | Running a lab @ucsdbiosciences | http://sklab.science | https://thoughtsforbreakfast.wordpress.com/
Professor of Antimicrobial Resistance. Institute of Microbiology and Infection, University of Birmingham. Director University of Birmingham Doctoral School. Editor in Chief of npj Antimicrobials and Resistance.
Fighting infections with math. Reformed physicist. Wannabe epidemiologist. Asst Prof at Johns Hopkins Biomedical Engineering. Member of Infectious Disease Dynamics group and Institute for Computational Medicine.
https://www.hsph.harvard.edu/profile/ankur-pandya/
Interested in microbial ecology & evolution. Views are only my own. (he/him)
🎓: https://scholar.google.com/citations?hl=en&user=OBPpZq4AAAAJ&view_op=list_works&sortby=pubdate
👨💻: https://github.com/raufs
Professor, evolution of drug resistance, modeling, population genetics, coding, SF State University, mom, Dutch
ID doc (MGH), PI (Broad Institute), antibiotic resistance resister, sepsis immune profiler, COVID doc, husband, dad. Coffee, tennis, kindness, science, & sleep enthusiast. Here to learn, as that other place devolves. Views mine. | bhattacharyyalab.org
Senior Program Officer in the Genomic Epidemiology and Modelling team at The Bill & Melinda Gates Foundation. Pathogen genomics and bioinformatics.
