Sandeep J. Joseph
@sandeep-j-joseph.bsky.social
Public health Scientist at
@CDCSTD
. #Microbialgenomics #genomicepidemiology #STDgenomics #husband #dad. All thoughts are my own. https://scholar.google.com/citations?user=yZCT5TwAAAAJ&hl=en https://github.com/CDCgov/neissflow
@CDCSTD
. #Microbialgenomics #genomicepidemiology #STDgenomics #husband #dad. All thoughts are my own. https://scholar.google.com/citations?user=yZCT5TwAAAAJ&hl=en https://github.com/CDCgov/neissflow
journals.asm.org/doi/full/10.... glad to be part of the discovery of a possible new commensal Neisseria species that could potentially disrupt the Roche cobas diagnostics
A novel commensal Neisseria species harboring the gonococcal diagnostic marker DR-9 causes false-positive Roche cobas NAAT results | Journal of Clinical Microbiology
Accurate diagnosis of gonorrhea is critical for effective treatment and antimicrobial
stewardship. Nucleic acid amplification tests, the mainstay of gonococcal diagnostic
testing, can yield false-posi...
journals.asm.org
November 23, 2025 at 12:58 PM
journals.asm.org/doi/full/10.... glad to be part of the discovery of a possible new commensal Neisseria species that could potentially disrupt the Roche cobas diagnostics
Reposted by Sandeep J. Joseph
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
Noth outside my wheelhouse. Does anyone have expertise and energy to look at it?
arxiv.org/abs/2509.06503
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...
arxiv.org
September 9, 2025 at 8:54 PM
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
Noth outside my wheelhouse. Does anyone have expertise and energy to look at it?
arxiv.org/abs/2509.06503
Reposted by Sandeep J. Joseph
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...
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...
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.
www.nature.com
September 10, 2025 at 9:12 AM
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...
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...
Reposted by Sandeep J. Joseph
“I think of antibiotics as infrastructure” @yhgrad.bsky.social interviewed for the Harvard Gazette, 'Racing against antibiotic resistance'. Read it here at bit.ly/47PdOqv
Racing against antibiotic resistance — Harvard Gazette
Scientists fear funding cuts will slow momentum in their war with evolving bacteria— one of America’s most urgent healthcare problems.
bit.ly
August 28, 2025 at 4:12 PM
“I think of antibiotics as infrastructure” @yhgrad.bsky.social interviewed for the Harvard Gazette, 'Racing against antibiotic resistance'. Read it here at bit.ly/47PdOqv
Reposted by Sandeep J. Joseph
Wow, more than 2.4M of assembled bacteria in the new release of ABT! We plan to index these using our efficient colored De Bruijn graph index, Fulgor. We recently conducted experiments with nearly 1M genomes…getting there :)
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
AllTheBacteria - all bacterial genomes assembled, available and searchable
The bacterial sequence data publicly available via the global DNA archives is a vast potential source of information on the evolution of bacteria. However, most of this sequence data is unassembled, o...
www.biorxiv.org
August 28, 2025 at 12:16 PM
Wow, more than 2.4M of assembled bacteria in the new release of ABT! We plan to index these using our efficient colored De Bruijn graph index, Fulgor. We recently conducted experiments with nearly 1M genomes…getting there :)
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Reposted by Sandeep J. Joseph
💥 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
Preprint 📝: biorxiv.org/content/10.1...
🧵 1/n
July 21, 2025 at 9:56 AM
💥 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
Preprint 📝: biorxiv.org/content/10.1...
🧵 1/n
It's STI Awareness Month—So Why Did They Just Shut Down This CDC STI Lab?
open.substack.com/pub/emilydep...
open.substack.com/pub/emilydep...
It's STI Awareness Month—So Why Did They Just Shut Down This CDC STI Lab?
The Quiet Closure of a Crucial CDC Lab Reveals a Dangerous Shift: From Public Health Priority to Moral Judgment
open.substack.com
April 11, 2025 at 10:01 PM
It's STI Awareness Month—So Why Did They Just Shut Down This CDC STI Lab?
open.substack.com/pub/emilydep...
open.substack.com/pub/emilydep...
Reposted by Sandeep J. Joseph
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
This campaign needs you now
Protect the CDC's National STD Reference Laboratory
chng.it
April 10, 2025 at 2:59 PM
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