Tony Cox
@coxtonyj.bsky.social
Bioinformatics, string algorithms, DNA sequence analysis. Formerly Solexa/Illumina, now bioinformatics consulting at genomerics.com https://www.linkedin.com/in/coxtonyj/
Reposted by Tony Cox
The last five months with Claude Code have completely changed how we work.
matsen.group/agentic.html details:
• How agents work (& why it matters)
• Git Flow with agents
• Using agents for science
• The human-agent interface
Questions? What has your experience been?
matsen.group/agentic.html details:
• How agents work (& why it matters)
• Git Flow with agents
• Using agents for science
• The human-agent interface
Questions? What has your experience been?
Agentic Coding For Scientists
A four-part series on using coding agents like Claude Code for scientific programming, covering fundamentals, workflows, best practices, and the human side of AI-assisted development.
matsen.group
November 13, 2025 at 5:08 PM
The last five months with Claude Code have completely changed how we work.
matsen.group/agentic.html details:
• How agents work (& why it matters)
• Git Flow with agents
• Using agents for science
• The human-agent interface
Questions? What has your experience been?
matsen.group/agentic.html details:
• How agents work (& why it matters)
• Git Flow with agents
• Using agents for science
• The human-agent interface
Questions? What has your experience been?
Reposted by Tony Cox
So glad this is finally out. The method has been instrumental in allowing us to compress the AllTheBacteria data - ~2 million bacterial genomes shrink from 3Terabytes (gzipped) to 100Gb using phylogenetic compression. Great work by @brinda.eu
Our latest paper, in which @brinda.eu (along with @zaminiqbal.bsky.social and others) introduces phylogenetic compression for storage and search of enormous microbial genome libraries, was published today in @naturemethods.bsky.social:
rdcu.be/eg4OA
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rdcu.be/eg4OA
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Efficient and robust search of microbial genomes via phylogenetic compression
Nature Methods - Phylogenetic compression achieves performant and lossless compression of massive collections of microbial genomes, facilitating fast BLAST-like search and versatile alignment tasks.
rdcu.be
April 9, 2025 at 10:27 PM
So glad this is finally out. The method has been instrumental in allowing us to compress the AllTheBacteria data - ~2 million bacterial genomes shrink from 3Terabytes (gzipped) to 100Gb using phylogenetic compression. Great work by @brinda.eu
Now we just need an LLM to win the the literature prize #nobelprize
October 9, 2024 at 12:32 PM
Now we just need an LLM to win the the literature prize #nobelprize
Pleased to announce I'm joining Cohort 7 of the Carbon13 venture builder, aiming to develop climate tech solutions with the potential to significantly reduce and prevent carbon emissions. www.linkedin.com/posts/coxton...
Anthony Cox on LinkedIn: I am delighted to be joining the next cohort of Carbon13's Venture Builder…
I am delighted to be joining the next cohort of Carbon13's Venture Builder Programme for the climate emergency. Carbon13 builds and backs teams addressing…
www.linkedin.com
September 19, 2024 at 1:02 PM
Pleased to announce I'm joining Cohort 7 of the Carbon13 venture builder, aiming to develop climate tech solutions with the potential to significantly reduce and prevent carbon emissions. www.linkedin.com/posts/coxton...
Reposted by Tony Cox
BWT construction and search at the terabase scale https://arxiv.org/abs/2409.00613 🧬🖥️ https://github.com/lh3/ropebwt3
September 4, 2024 at 8:00 PM
BWT construction and search at the terabase scale https://arxiv.org/abs/2409.00613 🧬🖥️ https://github.com/lh3/ropebwt3
Great to see the study I worked on at Illumina's AI lab make it into Nature! www.nature.com/articles/s41... A lot of hard work by the lead authors, really pleased this has paid off. 🧬 🖥️
November 30, 2023 at 10:44 AM
Great to see the study I worked on at Illumina's AI lab make it into Nature! www.nature.com/articles/s41... A lot of hard work by the lead authors, really pleased this has paid off. 🧬 🖥️
Reposted by Tony Cox
.@jnalanko.bsky.social and co. led groundbreaking work recently in terms of defining the SBWT & subset rank & select, and developing data structures for these. This new preprint provides reductions to standard rank & select, claiming similar space and 5-7x faster query arxiv.org/abs/2310.19702 🤯🧬🖥️
arxiv.org
November 1, 2023 at 3:28 AM
.@jnalanko.bsky.social and co. led groundbreaking work recently in terms of defining the SBWT & subset rank & select, and developing data structures for these. This new preprint provides reductions to standard rank & select, claiming similar space and 5-7x faster query arxiv.org/abs/2310.19702 🤯🧬🖥️