Cale Seymour
@caleoseymour.bsky.social
Bioinformatics analyst at UCSD Health. Current member of the Pannaraj Lab. Incoming UCSD BISB PhD student.
Previously: Hedlund lab at University of Nevada, Las Vegas; CDC Foundation
I write code to mine microbial datasets.
Previously: Hedlund lab at University of Nevada, Las Vegas; CDC Foundation
I write code to mine microbial datasets.
Reposted by Cale Seymour
The landscape of microbial associations in human cancer www.science.org/doi/10.1126/...
TLDR -- most cancers do not have microbiomes...but a few do have consistent microbe associations (i.e., colorectal and oral cancers). Make sense!
TLDR -- most cancers do not have microbiomes...but a few do have consistent microbe associations (i.e., colorectal and oral cancers). Make sense!
The landscape of microbial associations in human cancer
Differences between cancer types, infectious disease, and potential prognostic markers are uncovered by studying microbes within cancer DNA.
www.science.org
September 12, 2025 at 7:40 PM
The landscape of microbial associations in human cancer www.science.org/doi/10.1126/...
TLDR -- most cancers do not have microbiomes...but a few do have consistent microbe associations (i.e., colorectal and oral cancers). Make sense!
TLDR -- most cancers do not have microbiomes...but a few do have consistent microbe associations (i.e., colorectal and oral cancers). Make sense!
Reposted by Cale Seymour
Read the associated news and views:
Microbial chocolatiers of fine flavour 🍫
by Pablo Cruz-Morales
www.nature.com/articles/s41...
Microbial chocolatiers of fine flavour 🍫
by Pablo Cruz-Morales
www.nature.com/articles/s41...
August 18, 2025 at 3:37 PM
Read the associated news and views:
Microbial chocolatiers of fine flavour 🍫
by Pablo Cruz-Morales
www.nature.com/articles/s41...
Microbial chocolatiers of fine flavour 🍫
by Pablo Cruz-Morales
www.nature.com/articles/s41...
Reposted by Cale Seymour
Out in @natbiotech.nature.com: Metagenome taxonomy profilers usually ignore unknown species. SingleM is an accurate profiler which doesn't, even detecting phyla with no MAGs. Profiles of 700,000 metagenomes at sandpiper.qut.edu.au. A 🧵
July 16, 2025 at 9:59 PM
Out in @natbiotech.nature.com: Metagenome taxonomy profilers usually ignore unknown species. SingleM is an accurate profiler which doesn't, even detecting phyla with no MAGs. Profiles of 700,000 metagenomes at sandpiper.qut.edu.au. A 🧵
Reposted by Cale Seymour
Isolation and characterization of a bacterium affiliated with the hitherto uncultured candidate phylum WOR-3 from a deep-sea hydrothermal fluid | Applied and Environmental Microbiology https://journals.asm.org/doi/full/10.1128/aem.00188-25?af=R
Isolation and characterization of a bacterium affiliated with the hitherto uncultured candidate phylum WOR-3 from a deep-sea hydrothermal fluid | Applied and Environmental Microbiology
Genome analysis from various environments has revealed the overall diversity of microorganisms. However, there are many lineages for which culture representatives do not yet exist, and the characteristics and ecological significance of many of these ...
journals.asm.org
June 10, 2025 at 11:57 PM
Isolation and characterization of a bacterium affiliated with the hitherto uncultured candidate phylum WOR-3 from a deep-sea hydrothermal fluid | Applied and Environmental Microbiology https://journals.asm.org/doi/full/10.1128/aem.00188-25?af=R
Reposted by Cale Seymour
New Journal Club:
Predicting child health with gut microbiome development trajectories
by Douglas Johnson & Roshonda Jones @blackinmicro.bsky.social
www.nature.com/articles/s41...
Predicting child health with gut microbiome development trajectories
by Douglas Johnson & Roshonda Jones @blackinmicro.bsky.social
www.nature.com/articles/s41...
Predicting child health with gut microbiome development trajectories - Nature Microbiology
Nature Microbiology - Predicting child health with gut microbiome development trajectories
www.nature.com
January 30, 2025 at 9:14 AM
New Journal Club:
Predicting child health with gut microbiome development trajectories
by Douglas Johnson & Roshonda Jones @blackinmicro.bsky.social
www.nature.com/articles/s41...
Predicting child health with gut microbiome development trajectories
by Douglas Johnson & Roshonda Jones @blackinmicro.bsky.social
www.nature.com/articles/s41...
Reposted by Cale Seymour
🅲🅾🅾🅻 🆃🅴🅲🅷🅽🅾🅻🅾🅶🆈
“Bacterial-MERFISH” provides ~1000-fold volumetric expansion of individual cells, charts gene expression in hundreds of thousands of cells, deciphering bacterial single-cell heterogeneity, intracellular transcriptome organization, and bacterial adaptation to µm-scale niches in vivo
“Bacterial-MERFISH” provides ~1000-fold volumetric expansion of individual cells, charts gene expression in hundreds of thousands of cells, deciphering bacterial single-cell heterogeneity, intracellular transcriptome organization, and bacterial adaptation to µm-scale niches in vivo
Highly multiplexed spatial transcriptomics in bacteria
Single-cell decisions made in complex environments underlie many bacterial phenomena. Image-based transcriptomics approaches offer an avenue to study such behaviors, yet these approaches have been hin...
www.science.org
January 25, 2025 at 5:33 PM
🅲🅾🅾🅻 🆃🅴🅲🅷🅽🅾🅻🅾🅶🆈
“Bacterial-MERFISH” provides ~1000-fold volumetric expansion of individual cells, charts gene expression in hundreds of thousands of cells, deciphering bacterial single-cell heterogeneity, intracellular transcriptome organization, and bacterial adaptation to µm-scale niches in vivo
“Bacterial-MERFISH” provides ~1000-fold volumetric expansion of individual cells, charts gene expression in hundreds of thousands of cells, deciphering bacterial single-cell heterogeneity, intracellular transcriptome organization, and bacterial adaptation to µm-scale niches in vivo
Reposted by Cale Seymour
This is worth a read for anybody interested in microbial diversity www.science.org/doi/10.1126/...
A metagenomic perspective on the microbial prokaryotic genome census
Microbial sequencing reveals vast diversity, emphasizing metagenome contributions and urgent need for targeted cultivation.
www.science.org
January 22, 2025 at 4:44 PM
This is worth a read for anybody interested in microbial diversity www.science.org/doi/10.1126/...