Stephen Turner
@stephenturner.us
Associate Professor of Data Science & asst. Dean of Research at UVA School of Data Science, #Rstats enthusiast, dad, runner, guitar noise-maker. Views my own.
Web: https://stephenturner.us/
Newsletter: https://blog.stephenturner.us
Web: https://stephenturner.us/
Newsletter: https://blog.stephenturner.us
Pinned
Stephen Turner
@stephenturner.us
· Aug 29
All models are wrong; some are useful.
All LLM outputs are hallucinations. Some are useful.
All LLM outputs are hallucinations. Some are useful.
Pandagma: A tool for identifying pan-gene sets and gene families at desired evolutionary depths and accommodating whole genome duplications academic.oup.com/bioinformati... 🧬🖥️ github.com/legumeinfo/p...
December 26, 2025 at 7:03 PM
Pandagma: A tool for identifying pan-gene sets and gene families at desired evolutionary depths and accommodating whole genome duplications academic.oup.com/bioinformati... 🧬🖥️ github.com/legumeinfo/p...
R2G2: A Python-R Framework for Seamless Integration of R/Bioconductor Tools into Galaxy www.biorxiv.org/content/10.6... #rstats 🧬🖥️🧪 github.com/BlankenbergL...
December 26, 2025 at 5:01 PM
R2G2: A Python-R Framework for Seamless Integration of R/Bioconductor Tools into Galaxy www.biorxiv.org/content/10.6... #rstats 🧬🖥️🧪 github.com/BlankenbergL...
TIL Avocados change functional sex from male to female at different times during the same day (heterodichogamy).
Balanced polymorphism in a floral transcription factor underlies an ancient rhythm of daily sex alternation in avocado www.biorxiv.org/content/10.6...
Balanced polymorphism in a floral transcription factor underlies an ancient rhythm of daily sex alternation in avocado www.biorxiv.org/content/10.6...
December 26, 2025 at 3:00 PM
TIL Avocados change functional sex from male to female at different times during the same day (heterodichogamy).
Balanced polymorphism in a floral transcription factor underlies an ancient rhythm of daily sex alternation in avocado www.biorxiv.org/content/10.6...
Balanced polymorphism in a floral transcription factor underlies an ancient rhythm of daily sex alternation in avocado www.biorxiv.org/content/10.6...
(Nucleotide Transformer v3) A foundational model for joint sequence-function multi-species modeling at scale for long-range genomic prediction instadeep.com/wp-content/u... 🧬🖥️🧪 github.com/instadeepai/... (noncommercial)
December 26, 2025 at 11:03 AM
(Nucleotide Transformer v3) A foundational model for joint sequence-function multi-species modeling at scale for long-range genomic prediction instadeep.com/wp-content/u... 🧬🖥️🧪 github.com/instadeepai/... (noncommercial)
The love of my life bought me a pillow with the other love of my life printed on it 🎁
December 25, 2025 at 6:01 PM
The love of my life bought me a pillow with the other love of my life printed on it 🎁
Benchmarking text-integrated protein language model embeddings and embedding fusion on diverse downstream tasks www.biorxiv.org/content/10.1... 🧬🖥️ github.com/Wang-lab-UCS...
December 24, 2025 at 7:02 PM
Benchmarking text-integrated protein language model embeddings and embedding fusion on diverse downstream tasks www.biorxiv.org/content/10.1... 🧬🖥️ github.com/Wang-lab-UCS...
WheresWalker: a pipeline for rapid mutation mapping using WGS www.biorxiv.org/content/10.1... 🧬🖥️ github.com/alekseyzimin...
December 24, 2025 at 5:02 PM
WheresWalker: a pipeline for rapid mutation mapping using WGS www.biorxiv.org/content/10.1... 🧬🖥️ github.com/alekseyzimin...
A SNP panel for co-analysis of capture and shotgun ancient DNA data www.biorxiv.org/content/10.1...
A SNP panel for co-analysis of capture and shotgun ancient DNA data
Advances in technology have decreased the cost of generating genetic variation data from ancient people, resulting in exponentially increasing numbers of individuals with whole genome data. However,…
www.biorxiv.org
December 24, 2025 at 3:00 PM
A SNP panel for co-analysis of capture and shotgun ancient DNA data www.biorxiv.org/content/10.1...
Super interesting new program from DARPA BTO on developing gene drive technologies to eradicate invasive species. Proposer's day Jan 27. sam.gov/workspace/co...
December 24, 2025 at 10:17 AM
Super interesting new program from DARPA BTO on developing gene drive technologies to eradicate invasive species. Proposer's day Jan 27. sam.gov/workspace/co...
Weekly Recap a few days early this week: #Rstats updates (R Data Scientist, R Weekly), AI accelerating wet lab bio research, Docker hardened images, LLMs in review, machinal bypass, science funding, new papers. blog.stephenturner.us/p/weekly-rec...
Weekly Recap (December 24, 2025)
R updates (R Data Scientist, R Weekly), AI accelerating wet lab bio research, Docker hardened images, LLMs in review, machinal bypass, science funding, new papers.
blog.stephenturner.us
December 24, 2025 at 10:09 AM
Weekly Recap a few days early this week: #Rstats updates (R Data Scientist, R Weekly), AI accelerating wet lab bio research, Docker hardened images, LLMs in review, machinal bypass, science funding, new papers. blog.stephenturner.us/p/weekly-rec...
Designing synthetic regulatory elements using the generative AI framework DNA-Diffusion www.nature.com/articles/s41... 🧬🖥️🧪 github.com/pinellolab/D... (noncommercial)
December 23, 2025 at 7:00 PM
Designing synthetic regulatory elements using the generative AI framework DNA-Diffusion www.nature.com/articles/s41... 🧬🖥️🧪 github.com/pinellolab/D... (noncommercial)
What sets the mutation rate of a cell type in an animal species? www.biorxiv.org/content/10.6... 🧬🖥️🧪
December 23, 2025 at 5:01 PM
What sets the mutation rate of a cell type in an animal species? www.biorxiv.org/content/10.6... 🧬🖥️🧪
Understanding the LLM-based gene embeddings www.biorxiv.org/content/10.6... 🧬🖥️🧪
December 23, 2025 at 3:00 PM
Understanding the LLM-based gene embeddings www.biorxiv.org/content/10.6... 🧬🖥️🧪
Inbox on January 5
December 23, 2025 at 12:23 PM
Inbox on January 5
It’s official. I’ve gone full on Hoo for Christmas
December 23, 2025 at 11:50 AM
It’s official. I’ve gone full on Hoo for Christmas
Another casualty of tariffs. And these teetotaling GenZ kids.
Jim Beam, America’s largest bourbon distiller, is closing its flagship facility for 2026 after more than two decades of rapid growth. The move underlines the immense challenges facing the country's whiskey industry.
Jim Beam Halts Production at Flagship Distillery as Whiskey and Bourbon Markets Struggle
The bourbon giant is closing its flagship distilling operation for all of 2026.
nyti.ms
December 23, 2025 at 10:15 AM
Another casualty of tariffs. And these teetotaling GenZ kids.
The nature of the last universal common ancestor and its impact on the early Earth system www.nature.com/articles/s41... (read free: rdcu.be/dRPdk)
December 22, 2025 at 7:02 PM
The nature of the last universal common ancestor and its impact on the early Earth system www.nature.com/articles/s41... (read free: rdcu.be/dRPdk)
RAND Corporation report:
The Operational Risks of AI in Large-Scale Biological Attacks: Results of a Red-Team Study
doi.org/10.7249/RRA2...
The Operational Risks of AI in Large-Scale Biological Attacks: Results of a Red-Team Study
doi.org/10.7249/RRA2...
December 22, 2025 at 5:04 PM
RAND Corporation report:
The Operational Risks of AI in Large-Scale Biological Attacks: Results of a Red-Team Study
doi.org/10.7249/RRA2...
The Operational Risks of AI in Large-Scale Biological Attacks: Results of a Red-Team Study
doi.org/10.7249/RRA2...
Real-time Plasmid Transmission Detection Pipeline www.biorxiv.org/content/10.1... 🧬🖥️
December 22, 2025 at 3:03 PM
Real-time Plasmid Transmission Detection Pipeline www.biorxiv.org/content/10.1... 🧬🖥️
Reposted by Stephen Turner
When we say "no, everything hasn't been digitized," I need you to understand that we really mean is that virtually nothing has been digitized. This is because the realm of primary sources that historians use is incomprehensibly large.
Seems like it's worth posting this one again.
Why Do Historians Still Have To Go To Archives?
Why do historians go to archives? Hasn’t everything already been digitized?
contingentmagazine.org
December 22, 2025 at 1:40 AM
When we say "no, everything hasn't been digitized," I need you to understand that we really mean is that virtually nothing has been digitized. This is because the realm of primary sources that historians use is incomprehensibly large.
Reposted by Stephen Turner
Not for the first time, I wonder where the bright line of virtue is between using a literature search engine vs asking a chatbot for recs
December 21, 2025 at 10:32 PM
Not for the first time, I wonder where the bright line of virtue is between using a literature search engine vs asking a chatbot for recs
Searching for tablature for an old song I haven't heard or played in years, landed on one I published 15 years ago and forgot about 😎
December 21, 2025 at 9:07 PM
Searching for tablature for an old song I haven't heard or played in years, landed on one I published 15 years ago and forgot about 😎
Reposted by Stephen Turner
In a similar vein as the “don’t cite a paper you didn’t read” article earlier, I quite like Stephen’s take here on AI for writing.
I *could* ask AI to read papers for me, I *could* ask it to draft my text, but I choose not to, because the process IS the point. Even - especially! - when it’s hard.
I *could* ask AI to read papers for me, I *could* ask it to draft my text, but I choose not to, because the process IS the point. Even - especially! - when it’s hard.
New blog post: Spiritual Bypass, but with GPUs. The "Machinal Bypass," when AI becomes a shortcut around the work that makes us human, and why some tasks should feel a little hard. blog.stephenturner.us/p/machinal-b...
Spiritual Bypass, but with GPUs
The "Machinal Bypass," when AI becomes a shortcut around the work that makes us human, and why some tasks should feel a little hard.
blog.stephenturner.us
December 21, 2025 at 5:38 PM
In a similar vein as the “don’t cite a paper you didn’t read” article earlier, I quite like Stephen’s take here on AI for writing.
I *could* ask AI to read papers for me, I *could* ask it to draft my text, but I choose not to, because the process IS the point. Even - especially! - when it’s hard.
I *could* ask AI to read papers for me, I *could* ask it to draft my text, but I choose not to, because the process IS the point. Even - especially! - when it’s hard.
Position-dependent function of human sequence-specific transcription factors www.nature.com/articles/s41... (read free: rdcu.be/dRxBL)
December 21, 2025 at 5:03 PM
Position-dependent function of human sequence-specific transcription factors www.nature.com/articles/s41... (read free: rdcu.be/dRxBL)
New blog post: Spiritual Bypass, but with GPUs. The "Machinal Bypass," when AI becomes a shortcut around the work that makes us human, and why some tasks should feel a little hard. blog.stephenturner.us/p/machinal-b...
Spiritual Bypass, but with GPUs
The "Machinal Bypass," when AI becomes a shortcut around the work that makes us human, and why some tasks should feel a little hard.
blog.stephenturner.us
December 21, 2025 at 11:46 AM
New blog post: Spiritual Bypass, but with GPUs. The "Machinal Bypass," when AI becomes a shortcut around the work that makes us human, and why some tasks should feel a little hard. blog.stephenturner.us/p/machinal-b...