Researcher in bioinformatics @institutpasteur and @CNRS. Tweets about methods for DNA sequencing data analysis, and genome assembly.
Joined September 2011
- Tweets2.3K
- Following491
- Followers2.8K
- Likes19.1K
Pinned Tweet
🌎👩🔬 For 15+ years biology has accumulated petabytes (million gigabytes) of🧬DNA sequencing data🧬 from the far reaches of our planet.🦠🍄🌵
Logan now democratizes efficient access to the world’s most comprehensive genetics dataset. Free and open.
doi.org/10.1101/2024.07.30.6…
Rayan Chikhi retweeted
My thought on AI review: lh3.github.io/2026/10/27/let…
TL;DR: journals are banning fully AI-generated review and I think that is the right decision
Rayan Chikhi retweeted
Single-page, interactive overlap assembler for teaching purposes: lh3.github.io/teach-demo/ova… (vibe coded)
Rayan Chikhi retweeted
Minibwa is a hybrid of bwa-mem and minimap2 and the successor of bwa-mem for short-read mapping. ~4X/2.5X as fast as bwa-mem/bwa-mem2 for WGS reads at comparable accuracy. Native support of directional bisulfite-seq. Applicable to long reads. Preprint at arxiv.org/abs/2606.15357
Rayan Chikhi retweeted
Can CPUs outperform top-tier GPUs in protein folding? 🧬
Thrilled to share our new bioRxiv preprint: "Revisiting CPUs for Protein Folding: Xeon-Based Acceleration of AlphaFold2."
We achieve a 1.76x speedup for end-to-end pipeline over an H100 GPU baseline (FastFold)! 🧵👇 (1/n)
Rayan Chikhi retweeted
📢 We are thrilled to announce the keynote speakers for #RECOMB2026:
🧬 Sara Mostafavi
🧬 Manolis Kellis
🧬 Paul Medvedev
🧬 Alexandros Stamatakis
Join us in Thessaloniki for inspiring talks from leaders in computational biology.
Rayan Chikhi retweeted
There are several massive-scale analyses in the preprint, but I'll cut to the chase. We queried #Logan from @RayanChikhi and @RNA_Life for HSV-1 transcripts. Logan indexes the entire SRA and enables queries in a few minutes (in addition to insane sequence discovery) 5/n
Rayan Chikhi retweeted
A beautiful story on the origins of CRISPR -- congrats to @PeterHYoon @kenjmloi and team!
Cool to see the Evo 2 likelihoods being useful for identifying a tricky repeat region.
biorxiv.org/content/10.64898…
Rayan Chikhi retweeted
Blog post on "The AI Rewrite Dilemma": lh3.github.io/2026/04/17/the…
Rayan Chikhi retweeted
Fast and accurate multiple-protein-sequence alignment at scale with FAMSA2 - @sdeorowicz go.nature.com/4muAQsh
Rayan Chikhi retweeted
Excited to share this preprint that describes my latest work on using GPUs to accelerate processing of RNA-seq data.
The title says it all: "RNA-seq analysis in seconds using GPUs" now on biorxiv biorxiv.org/content/10.64898…
Figure 1 shows they key result
Rayan Chikhi retweeted
Evo 2 is out in Nature today, showing that genome language models can predict and design across the full complexity of life, from phages to eukaryotes.
A few surprises from the project, including how ignoring trillions of nucleotides was key to getting a good model. 🧵
Rayan Chikhi retweeted
New preprint alert! 📣
We use Logan, a new database of SRA-wide genome assemblies, to look for an emerging virus in prawns. If you've ever spent too long trying to track down a known sequence in SRA data, this database is a real game changer.
lnkd.in/e9S5GhPc
Rayan Chikhi retweeted
After years of research and continuous refinement, we’re thrilled to share that our paper on the MetaGraph framework — enabling Petabase-scale search across sequencing data — has been published today in Nature (nature.com/articles/s41586-0…).
Rayan Chikhi retweeted
Our trimodal pLM, ProTrek, is now in @NatureBiotech! Search protein by function, not just seq/struc:
BLAST ➡️ 🧬 Seq
Foldseek ➡️ 🏗️ Struc
ProTrek ➡️ 💡 Func (Text）
🔗 Try: search-protrek.com/
🐙 GitHub: github.com/westlake-repl/Pro…
📊 5B embeddings: protrek.westlake.edu.cn/
🚀We just released all embeddings for 6 BILLION proteins!
ProTrek's tri-modal AI (seq + structure + function) is now fully open source. Deploy your own protein search server !
🔬 Try it: search-protrek.com/
📊 Data: protrek.westlake.edu.cn/
💻 Code: github.com/westlake-repl/Pro…
Rayan Chikhi retweeted
#RECOMB2026 is now accepting submissions and we'd love to see your best work!
📌 Abstract registration: Nov 7, 2025
📌 Full paper submission: Nov 14, 2025
📜More info: recomb.org/recomb2026/call_f…
Rayan Chikhi retweeted
#RECOMB2026 will be in Thessaloniki, Greece on May 26-29, 2026. Satellites on May 24-25. Save the date!
Το συνέδριο #RECOMB2026 θα πραγματοποιηθεί στη Θεσσαλονίκη, στις 26-29 Μαΐου 2026. Οι δορυφορικές εκδηλώσεις θα διεξαχθούν στις 24-25 Μαΐου 2026. Σημειώστε την ημερομηνία!
Rayan Chikhi retweeted
Do you know ~60% of human SVs fall in ~1% of GRCh38? See our new preprint: arxiv.org/abs/2509.23057 and the companion blog post on how we started this project and longdust: lh3.github.io/2025/09/29/on-…. Work with @QianAlvinQin1
Rayan Chikhi retweeted
Efficient sequence alignment against millions of prokaryotic genomes with LexicMap go.nature.com/3K09TgJ
Rayan Chikhi retweeted
Our preprint on the challenges of benchmarking Structural Variants (SVs) is out in BioRxiv biorxiv.org/content/10.1101/…
Earth’s genetic diversity is a heritage of humanity. It has been an honour to explore this data with a team of dedicated scientists who shared our vision of making this data free and accessible to all 🌍🧬❤️ Thank you!
Updated preprint: doi.org/10.1101/2024.07.30.6…
