David Stern
@dbstern.bsky.social
Evolution, bioinformatics, bioforensics | PI at NBACC | Postdoc at Univ. Wisc | PhD at GWU https://thedbstern.github.io/
Hybridization capture sequencing for Vibrio spp. and associated virulence factors | mBio journals.asm.org/doi/10.1128/...
Hybridization capture sequencing for Vibrio spp. and associated virulence factors | mBio
The increasing prevalence of pathogenic Vibrio spp. in aquatic ecosystems, driven by climate change, is closely linked to a rise
in cholera and vibriosis cases, emphasizing the need for improved envir...
journals.asm.org
July 2, 2025 at 10:25 AM
Hybridization capture sequencing for Vibrio spp. and associated virulence factors | mBio journals.asm.org/doi/10.1128/...
Reposted by David Stern
Promising toolkit for binning and visualizing assembly graphs. The assembly graph is an underutilized source of binning information IMO
gbintk.readthedocs.io/en/latest/
gbintk.readthedocs.io/en/latest/
May 30, 2025 at 2:51 AM
Promising toolkit for binning and visualizing assembly graphs. The assembly graph is an underutilized source of binning information IMO
gbintk.readthedocs.io/en/latest/
gbintk.readthedocs.io/en/latest/
Nice review of dynamic field theory in linguistics by the other Stern @secretly-stern.bsky.social
Dynamic Field Theory unifies discrete and continuous aspects of linguistic representations
| Proceedings of the Linguistic Society of America
journals.linguisticsociety.org
May 24, 2025 at 2:04 PM
Nice review of dynamic field theory in linguistics by the other Stern @secretly-stern.bsky.social
Happy to see this one out. Lots of fun work identifying bacteriophages in gut metagenomes www.tandfonline.com/doi/full/10....
Delivery Mode Impacts Gut Bacteriophage Colonization During Infancy
Cesarean section delivery is associated with altered early-life bacterial colonization and later adverse inflammatory outcomes. Although gut bacteriophages can alter the gut microbiome and host res...
www.tandfonline.com
March 18, 2025 at 5:47 PM
Happy to see this one out. Lots of fun work identifying bacteriophages in gut metagenomes www.tandfonline.com/doi/full/10....
Reposted by David Stern
“I think it’s going to destroy research universities in the short term, and I don’t know after that.” Story by @by-cjewett.bsky.social on the new NIH policy that will shrivel support for research. www.nytimes.com/2025/02/07/u...
Deep Cuts to Medical Research Funds Could Hobble University Budgets (Gift Article)
Grants from the National Institutes of Health come with additional money for overhead. Proposed funding cuts would leave colleges with large budget gaps.
www.nytimes.com
February 8, 2025 at 3:52 PM
“I think it’s going to destroy research universities in the short term, and I don’t know after that.” Story by @by-cjewett.bsky.social on the new NIH policy that will shrivel support for research. www.nytimes.com/2025/02/07/u...
Reposted by David Stern
Here we provide evidence of henipaviruses in North America with the discovery of Camp hill virus in the Northern Short-Tailed Shrew, Alabama. Early release article available from EID
wwwnc.cdc.gov/eid/article/... #virology
wwwnc.cdc.gov/eid/article/... #virology
January 18, 2025 at 11:39 PM
Here we provide evidence of henipaviruses in North America with the discovery of Camp hill virus in the Northern Short-Tailed Shrew, Alabama. Early release article available from EID
wwwnc.cdc.gov/eid/article/... #virology
wwwnc.cdc.gov/eid/article/... #virology
Reposted by David Stern
Genomes assembled from #metagenomes (a.k.a. MAGs) are awesome and have revolutionized our ability to study uncultivated microbes
...BUT: they still don't capture a lot of the 🦠 species that are out there
New @jgi.doe.gov paper led by Dongying Wu and Natalia Ivanova: www.science.org/doi/10.1126/...
...BUT: they still don't capture a lot of the 🦠 species that are out there
New @jgi.doe.gov paper led by Dongying Wu and Natalia Ivanova: www.science.org/doi/10.1126/...
January 17, 2025 at 9:53 PM
Genomes assembled from #metagenomes (a.k.a. MAGs) are awesome and have revolutionized our ability to study uncultivated microbes
...BUT: they still don't capture a lot of the 🦠 species that are out there
New @jgi.doe.gov paper led by Dongying Wu and Natalia Ivanova: www.science.org/doi/10.1126/...
...BUT: they still don't capture a lot of the 🦠 species that are out there
New @jgi.doe.gov paper led by Dongying Wu and Natalia Ivanova: www.science.org/doi/10.1126/...
Reposted by David Stern
Reposted by David Stern
🚨😷🧪 NEW: A growing body of evidence shows that pandemics, biodiversity loss, and climate change are part of a broader polycrisis - but there are no simple solutions. A sweeping overview of "Pathogens and planetary change" for the first issue of @natrevbiodiv.bsky.social, out now 🔓 rdcu.be/d6lHl
January 15, 2025 at 2:16 PM
🚨😷🧪 NEW: A growing body of evidence shows that pandemics, biodiversity loss, and climate change are part of a broader polycrisis - but there are no simple solutions. A sweeping overview of "Pathogens and planetary change" for the first issue of @natrevbiodiv.bsky.social, out now 🔓 rdcu.be/d6lHl
Reposted by David Stern
Interesting work and dataset to investigate the genetic population structure and colonization history of Plasmodium vivax in Latin America, inferring multiple waves of pre/post colonial migration & evolutionary contributions from European and African populations.
🔗 journals.plos.org/plospathogen...
🔗 journals.plos.org/plospathogen...
January 15, 2025 at 3:12 AM
Interesting work and dataset to investigate the genetic population structure and colonization history of Plasmodium vivax in Latin America, inferring multiple waves of pre/post colonial migration & evolutionary contributions from European and African populations.
🔗 journals.plos.org/plospathogen...
🔗 journals.plos.org/plospathogen...
Out now in @genomebiolevol.bsky.social! With colleagues at NBACC and PNNL, we helped answer a long-standing question about how widely-divergent cyanobacteria produce saxitoxin, a major cause of paralytic shellfish poisoning. We assembled a new genome for a producer of saxitoxin and ...
Novel Toxin Biosynthetic Gene Cluster in Harmful Algal Bloom-Causing Heteroscytonema crispum: Insights into the Origins of Paralytic Shellfish Toxins
Abstract. Caused by both eukaryotic dinoflagellates and prokaryotic cyanobacteria, harmful algal blooms are events of severe ecological, economic, and publ
academic.oup.com
January 14, 2025 at 3:07 AM
Out now in @genomebiolevol.bsky.social! With colleagues at NBACC and PNNL, we helped answer a long-standing question about how widely-divergent cyanobacteria produce saxitoxin, a major cause of paralytic shellfish poisoning. We assembled a new genome for a producer of saxitoxin and ...
Reposted by David Stern
And it’s been a while since I dipped my toe into the questions of what ‘species’ might mean for bacteria, and how they relate to ecology. But still interests me! genomebiology.biomedcentral.com/articles/10....
Relating ecological diversity to genetic discontinuity across bacterial species - Genome Biology
Background Genetic discontinuity represents abrupt breaks in genomic identity among species. Advances in genome sequencing have enhanced our ability to track and characterize genetic discontinuity in ...
genomebiology.biomedcentral.com
January 13, 2025 at 3:43 PM
And it’s been a while since I dipped my toe into the questions of what ‘species’ might mean for bacteria, and how they relate to ecology. But still interests me! genomebiology.biomedcentral.com/articles/10....
Reposted by David Stern
Interesting new paper -- evolutionary adaptations in Bifidobacterium across a huge range of host species
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
January 13, 2025 at 10:17 PM
Interesting new paper -- evolutionary adaptations in Bifidobacterium across a huge range of host species
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Reposted by David Stern
Check out our just-published AI-based (temporal convolutional network) system, PSAURON, for predicting eukaryotic proteins, from @markusjsommer.bsky.social. We used a similar method in BALROG, our bacterial gene finder. Note: the "P" is silent in PSAURON 🤣 academic.oup.com/nargab/artic...
PSAURON: a tool for assessing protein annotation across a broad range of species
Abstract. Evaluating the accuracy of protein-coding sequences in genome annotations is a challenging problem for which there is no broadly applicable solut
academic.oup.com
January 11, 2025 at 6:22 PM
Check out our just-published AI-based (temporal convolutional network) system, PSAURON, for predicting eukaryotic proteins, from @markusjsommer.bsky.social. We used a similar method in BALROG, our bacterial gene finder. Note: the "P" is silent in PSAURON 🤣 academic.oup.com/nargab/artic...
Reposted by David Stern
Unicore identifies single-copy protein structures across genomes using Foldseek, bypassing slow structure predictions by utilizing 3Di predictions from ProstT5, enabling rapid phylogenetic inference at the tree-of-life scale. 1/n
📄 www.biorxiv.org/content/10.1...
💾 github.com/steineggerla...
📄 www.biorxiv.org/content/10.1...
💾 github.com/steineggerla...
December 23, 2024 at 4:39 PM
Unicore identifies single-copy protein structures across genomes using Foldseek, bypassing slow structure predictions by utilizing 3Di predictions from ProstT5, enabling rapid phylogenetic inference at the tree-of-life scale. 1/n
📄 www.biorxiv.org/content/10.1...
💾 github.com/steineggerla...
📄 www.biorxiv.org/content/10.1...
💾 github.com/steineggerla...