Julia M. Brown
@viraljules.bsky.social
(mostly) marine microbial and viral ecology via all the 'omics
Mainer from away
check out my lab webpage at juliambrown.github.io
Mainer from away
check out my lab webpage at juliambrown.github.io
Reposted by Julia M. Brown
Please apply if you are interested in marine biogeochemistry and microbial dark oxygen production. Deadline: November 17th.
📣Postdoc opportunity @nordcee.bsky.social , University of Southern Denmark! 📣
Join us and work with Bo Thamdrup and me on microbial dark oxygen production in marine oxygen minimum zones!
Please share widely!
Deadline: 17 November
More information can be found here:
tinyurl.com/2vuur3wh
Join us and work with Bo Thamdrup and me on microbial dark oxygen production in marine oxygen minimum zones!
Please share widely!
Deadline: 17 November
More information can be found here:
tinyurl.com/2vuur3wh
Postdoc on microbial oxygen production in marine oxygen minimum zones
Application deadline: 17 November 2025 at 23:59 hours local Danish time
fa-eosd-saasfaprod1.fa.ocs.oraclecloud.com
November 10, 2025 at 12:06 AM
Please apply if you are interested in marine biogeochemistry and microbial dark oxygen production. Deadline: November 17th.
Reposted by Julia M. Brown
I’m excited to share our effort to obtain one of the first estimates of the net rate, in physical time, of lateral gene transfer (LGT) – nature’s own genetic engineering - across a complex, global microbiome:
doi.org/10.1093/isme...
doi.org/10.1093/isme...
September 7, 2025 at 2:41 PM
I’m excited to share our effort to obtain one of the first estimates of the net rate, in physical time, of lateral gene transfer (LGT) – nature’s own genetic engineering - across a complex, global microbiome:
doi.org/10.1093/isme...
doi.org/10.1093/isme...
Reposted by Julia M. Brown
Phage defence-system abundances vary across environments and increase with viral density
Phil. Trans. R. Soc. B by @seanmeaden.bsky.social, Edze Westra and @peterfineran.bsky.social
royalsocietypublishing.org/doi/10.1098/...
Phil. Trans. R. Soc. B by @seanmeaden.bsky.social, Edze Westra and @peterfineran.bsky.social
royalsocietypublishing.org/doi/10.1098/...
Phage defence-system abundances vary across environments and increase with viral density | Philosophical Transactions of the Royal Society B: Biological Sciences
The defence systems bacteria use to protect themselves from their viruses are mechanistically
and genetically diverse. Yet the ecological conditions that predict when defences
are selected for remain ...
royalsocietypublishing.org
September 5, 2025 at 10:18 AM
Phage defence-system abundances vary across environments and increase with viral density
Phil. Trans. R. Soc. B by @seanmeaden.bsky.social, Edze Westra and @peterfineran.bsky.social
royalsocietypublishing.org/doi/10.1098/...
Phil. Trans. R. Soc. B by @seanmeaden.bsky.social, Edze Westra and @peterfineran.bsky.social
royalsocietypublishing.org/doi/10.1098/...
Reposted by Julia M. Brown
very nice, it's a natural spike-in! I wonder what are the GDPR implications, though, of sharing human reads.
I guess participants now will be asked to consent to their genomic data being shared.
I guess participants now will be asked to consent to their genomic data being shared.
You can get an accurate estimate of total bacterial biomass from stool metagenomes by simply normalizing by host read count, without needing any additional measurements.
Excellent work by UW Master's student Gechlang Tang in @asm.org #mSystems Journal.
journals.asm.org/doi/10.1128/...
🧵
Excellent work by UW Master's student Gechlang Tang in @asm.org #mSystems Journal.
journals.asm.org/doi/10.1128/...
🧵
Metagenomic estimation of absolute bacterial biomass in the mammalian gut through host-derived read normalization | mSystems
In this study, we asked whether normalization by host reads alone was sufficient to
estimate absolute bacterial biomass directly from stool metagenomic data, without
the need for synthetic spike-ins, ...
journals.asm.org
August 22, 2025 at 8:00 AM
very nice, it's a natural spike-in! I wonder what are the GDPR implications, though, of sharing human reads.
I guess participants now will be asked to consent to their genomic data being shared.
I guess participants now will be asked to consent to their genomic data being shared.
Reposted by Julia M. Brown
Happy to team up with @microbe-enjoyer.bsky.social to highlight fantastic work by @gibbological.bsky.social, Alex Carr, and colleagues using community scale metabolic models to predict risk for C. difficile colonization!
See the initial study here: www.cell.com/cell-systems...
See the initial study here: www.cell.com/cell-systems...
August 20, 2025 at 4:25 PM
Happy to team up with @microbe-enjoyer.bsky.social to highlight fantastic work by @gibbological.bsky.social, Alex Carr, and colleagues using community scale metabolic models to predict risk for C. difficile colonization!
See the initial study here: www.cell.com/cell-systems...
See the initial study here: www.cell.com/cell-systems...
Reposted by Julia M. Brown
Stoked to finally have a preprint out for Phold, our tool that uses protein structural information to enhance phage genome annotation #phagesky 1/n
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Protein Structure Informed Bacteriophage Genome Annotation with Phold
Bacteriophage (phage) genome annotation is essential for understanding their functional potential and suitability for use as therapeutic agents. Here we introduce Phold, an annotation framework utilis...
www.biorxiv.org
August 8, 2025 at 7:11 AM
Stoked to finally have a preprint out for Phold, our tool that uses protein structural information to enhance phage genome annotation #phagesky 1/n
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Reposted by Julia M. Brown
Do you love phage? I have an opening for a postdoc in my lab at the University of South Florida College of Marine Science (@cmarinescience.bsky.social) looking at interactions between marine phage and iron, which is an important limiting trace metal in the oceans (1/5) 🧵#phagesky 🦠🌊
August 1, 2025 at 1:45 PM
Do you love phage? I have an opening for a postdoc in my lab at the University of South Florida College of Marine Science (@cmarinescience.bsky.social) looking at interactions between marine phage and iron, which is an important limiting trace metal in the oceans (1/5) 🧵#phagesky 🦠🌊
Reposted by Julia M. Brown
𝗕𝗿𝗶𝗻𝗴𝗶𝗻𝗴 𝗣𝗵𝗮𝗴𝗲 𝗟𝘆𝘁𝗶𝗰 𝗖𝘆𝗰𝗹𝗲 𝘁𝗼 𝗟𝗶𝗳𝗲 🦠🧬
Dive into the lytic cycle! A bacteriophage injects DNA, hijacks the host, and rapidly replicates until the bacterium lyses, releasing a new swarm of virulent phages!
#blender #3D #cgi #science #research #biology #phage #lyticcycle #bacteria #scicomm #sciart
Dive into the lytic cycle! A bacteriophage injects DNA, hijacks the host, and rapidly replicates until the bacterium lyses, releasing a new swarm of virulent phages!
#blender #3D #cgi #science #research #biology #phage #lyticcycle #bacteria #scicomm #sciart
July 30, 2025 at 3:21 PM
Reposted by Julia M. Brown
New online! Viromics approaches for the study of viral diversity and ecology in microbiomes
Viromics approaches for the study of viral diversity and ecology in microbiomes
Nature Reviews Genetics, Published online: 21 July 2025; doi:10.1038/s41576-025-00871-wIn this Review, Roux and Coclet outline current viromics approaches and discuss how they have contributed to our growing understanding of viral genomic diversity, focusing on uncultivated viruses of microorganisms.
www.nature.com
July 21, 2025 at 6:34 PM
New online! Viromics approaches for the study of viral diversity and ecology in microbiomes
Excited to try this one!
Comprehensive taxonomic identification of microbial species in metagenomic data using SingleM and Sandpiper - @benjwoodcroft.bsky.social go.nature.com/3IwOxHh
Comprehensive taxonomic identification of microbial species in metagenomic data using SingleM and Sandpiper - Nature Biotechnology
Novel microbial species in metagenomes are identified using conserved regions within universal marker genes.
go.nature.com
July 17, 2025 at 5:35 PM
Excited to try this one!
Reposted by Julia M. Brown
"How Little We've Seen"
Imagine measuring an area the size of Houston, then making generalizations about the entire globe.
From analysis of Bell et al., that's just what we're doing with the deep seafloor.
www.science.org/doi/full/10....
Imagine measuring an area the size of Houston, then making generalizations about the entire globe.
From analysis of Bell et al., that's just what we're doing with the deep seafloor.
www.science.org/doi/full/10....
How little we’ve seen: A visual coverage estimate of the deep seafloor
In decades of deep-sea exploration, humans have observed only 0.001% of the deep seafloor, leaving 66% of planet Earth unseen.
www.science.org
June 11, 2025 at 6:17 PM
"How Little We've Seen"
Imagine measuring an area the size of Houston, then making generalizations about the entire globe.
From analysis of Bell et al., that's just what we're doing with the deep seafloor.
www.science.org/doi/full/10....
Imagine measuring an area the size of Houston, then making generalizations about the entire globe.
From analysis of Bell et al., that's just what we're doing with the deep seafloor.
www.science.org/doi/full/10....
Reposted by Julia M. Brown
We have a new 3-year postdoc position in our group at the @hifmb.de to study plasmids and plasmids systems of the marine environment to survey their utility in microbial responses to environmental change.
Please see the official job ad here, and spread the word:
jobs.awi.de/Vacancies/20...
Please see the official job ad here, and spread the word:
jobs.awi.de/Vacancies/20...
PostDoc in ecology and evolution of plasmids in polar waters at HIFMB (f/d/m)
Layout AWI HIPP extern, englisch
jobs.awi.de
June 5, 2025 at 8:09 AM
We have a new 3-year postdoc position in our group at the @hifmb.de to study plasmids and plasmids systems of the marine environment to survey their utility in microbial responses to environmental change.
Please see the official job ad here, and spread the word:
jobs.awi.de/Vacancies/20...
Please see the official job ad here, and spread the word:
jobs.awi.de/Vacancies/20...
Reposted by Julia M. Brown
Simons Graduate Fellowships in Ecology and Evolution www.simonsfoundation.org/grant/simons...
Application Deadline July 31, 2025
Application Deadline July 31, 2025
Simons Graduate Fellowships in Ecology and Evolution
The purpose of these awards is to provide support for students entering U.S.-based Ph.D. programs with a plan to perform research in ecology and evolution. While we will consider all projects in ecolo...
www.simonsfoundation.org
June 2, 2025 at 4:35 PM
Simons Graduate Fellowships in Ecology and Evolution www.simonsfoundation.org/grant/simons...
Application Deadline July 31, 2025
Application Deadline July 31, 2025
Reposted by Julia M. Brown
NIH funding supporting the HMMER and Infernal software projects has been terminated. NIH states that our work, as well as all other federally funded research at Harvard, is of no benefit to the US.
May 22, 2025 at 12:42 PM
NIH funding supporting the HMMER and Infernal software projects has been terminated. NIH states that our work, as well as all other federally funded research at Harvard, is of no benefit to the US.
Reposted by Julia M. Brown
#phagesky
Some partnerships are always fun!! Excited to share one such 🎉 product w Simon Roux, perspectives on our favorite “atypical” phages, for special issue to celebrate my former mentor Carol Gross @ UCSF
Tapping the treasure trove of atypical phages
www.sciencedirect.com/science/arti...
Some partnerships are always fun!! Excited to share one such 🎉 product w Simon Roux, perspectives on our favorite “atypical” phages, for special issue to celebrate my former mentor Carol Gross @ UCSF
Tapping the treasure trove of atypical phages
www.sciencedirect.com/science/arti...
Tapping the treasure trove of atypical phages
With advancements in genomics technologies, a vast diversity of ‘atypical’ phages, that is, with single-stranded DNA or RNA genomes, are being uncover…
www.sciencedirect.com
November 21, 2024 at 2:01 PM
#phagesky
Some partnerships are always fun!! Excited to share one such 🎉 product w Simon Roux, perspectives on our favorite “atypical” phages, for special issue to celebrate my former mentor Carol Gross @ UCSF
Tapping the treasure trove of atypical phages
www.sciencedirect.com/science/arti...
Some partnerships are always fun!! Excited to share one such 🎉 product w Simon Roux, perspectives on our favorite “atypical” phages, for special issue to celebrate my former mentor Carol Gross @ UCSF
Tapping the treasure trove of atypical phages
www.sciencedirect.com/science/arti...
Reposted by Julia M. Brown
Time to catch up on the past week’s news about science and medicine in the US. Whew. 1/10
May 1, 2025 at 11:50 PM
Time to catch up on the past week’s news about science and medicine in the US. Whew. 1/10
Reposted by Julia M. Brown
Not really my announcement to make--I am but a lesser co-author--but IQ-TREE 3 has just been released!
(Most credit to Minh Bui and @roblanfear.bsky.social and their labs)
ecoevorxiv.org/repository/v...
(Most credit to Minh Bui and @roblanfear.bsky.social and their labs)
ecoevorxiv.org/repository/v...
IQ-TREE 3: Phylogenomic Inference Software using Complex Evolutionary Models
ecoevorxiv.org
April 10, 2025 at 2:13 PM
Not really my announcement to make--I am but a lesser co-author--but IQ-TREE 3 has just been released!
(Most credit to Minh Bui and @roblanfear.bsky.social and their labs)
ecoevorxiv.org/repository/v...
(Most credit to Minh Bui and @roblanfear.bsky.social and their labs)
ecoevorxiv.org/repository/v...
Reposted by Julia M. Brown
CoverM is published!
CoverM: Read alignment statistics for metagenomics academic.oup.com/bioinformati... #jcampubs
CoverM: Read alignment statistics for metagenomics academic.oup.com/bioinformati... #jcampubs
CoverM: Read alignment statistics for metagenomics
AbstractSummary. Genome-centric analysis of metagenomic samples is a powerful method for understanding the function of microbial communities. Calculating r
academic.oup.com
April 9, 2025 at 1:24 PM
CoverM is published!
CoverM: Read alignment statistics for metagenomics academic.oup.com/bioinformati... #jcampubs
CoverM: Read alignment statistics for metagenomics academic.oup.com/bioinformati... #jcampubs
Reposted by Julia M. Brown
Check out this list of awesome #virome tools and be sure to add yours!
github.com/shandley/awe...
#phagesky #microsky
github.com/shandley/awe...
#phagesky #microsky
GitHub - shandley/awesome-virome: A listing of software, tools and databases useful for virome analysis
A listing of software, tools and databases useful for virome analysis - shandley/awesome-virome
github.com
March 12, 2025 at 8:46 PM
Check out this list of awesome #virome tools and be sure to add yours!
github.com/shandley/awe...
#phagesky #microsky
github.com/shandley/awe...
#phagesky #microsky
Reposted by Julia M. Brown
We're looking for suggestions on how to update and adapt the Minimum Information about an Uncultured Viral Genome (MIUVIG) reporting standard. What works? What needs updating? Check out the survey forms.gle/DPHvMFe8Gsdj... 🧵
MIUViG Update Survey
Since the development of the Minimum Information about an Uncultured Viral Genome (MIUViG) standard (Roux et al. 2019), there has been an explosion in the number of genomic data generated on unculture...
forms.gle
February 11, 2025 at 5:47 AM
We're looking for suggestions on how to update and adapt the Minimum Information about an Uncultured Viral Genome (MIUVIG) reporting standard. What works? What needs updating? Check out the survey forms.gle/DPHvMFe8Gsdj... 🧵
Reposted by Julia M. Brown
Out now, a comprehensive guide to metagenomics -- from sample collection to data analysis. This primer covers best practices, challenges, and applications in health, agriculture & environment. A roadmap for studying microbial communities 👇
www.nature.com/articles/s43...
www.nature.com/articles/s43...
January 27, 2025 at 9:53 PM
Out now, a comprehensive guide to metagenomics -- from sample collection to data analysis. This primer covers best practices, challenges, and applications in health, agriculture & environment. A roadmap for studying microbial communities 👇
www.nature.com/articles/s43...
www.nature.com/articles/s43...
Reposted by Julia M. Brown
Characteristics of Phages and Their Interactions With Hosts in Anaerobic Reactors enviromicro-journals.onlinelibrary.wiley.com/doi/10.1111/... #jcampubs
Characteristics of Phages and Their Interactions With Hosts in Anaerobic Reactors
Diverse and novel phages were recovered from anaerobic fatty acid–fed reactors. Phages linked to hosts in all three functional groups primarily consisted of generalists and temperate species, especia...
enviromicro-journals.onlinelibrary.wiley.com
January 28, 2025 at 3:03 PM
Characteristics of Phages and Their Interactions With Hosts in Anaerobic Reactors enviromicro-journals.onlinelibrary.wiley.com/doi/10.1111/... #jcampubs
Reposted by Julia M. Brown
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 Julia M. Brown
Phage-induced disturbance of a marine sponge microbiome.
DOI: 10.1186/s40793-024-00637-7
https://pubmed.ncbi.nlm.nih.gov/39593141/
DOI: 10.1186/s40793-024-00637-7
https://pubmed.ncbi.nlm.nih.gov/39593141/
Phage-induced disturbance of a marine sponge microbiome - PubMed
Our findings suggest that sponge microbiome diversity and, by extension, its resilience depend on the maintenance of resident bacterial community members, irrespective of their abundance. Phage-induced disturbances can significantly alter community structure by promoting the growth of opportunistic …
pubmed.ncbi.nlm.nih.gov
December 1, 2024 at 3:37 AM
Phage-induced disturbance of a marine sponge microbiome.
DOI: 10.1186/s40793-024-00637-7
https://pubmed.ncbi.nlm.nih.gov/39593141/
DOI: 10.1186/s40793-024-00637-7
https://pubmed.ncbi.nlm.nih.gov/39593141/
Reposted by Julia M. Brown
If you had a really nice looking alignment of about thirty 100kb virus genomes and you wanted to find recombination breakpoints, what software/methods would you use?
All suggestions, snark, links to papers etc. welcome. Trying to navigate a new field...
Please repost!
🧪
All suggestions, snark, links to papers etc. welcome. Trying to navigate a new field...
Please repost!
🧪
November 26, 2024 at 3:11 AM
If you had a really nice looking alignment of about thirty 100kb virus genomes and you wanted to find recombination breakpoints, what software/methods would you use?
All suggestions, snark, links to papers etc. welcome. Trying to navigate a new field...
Please repost!
🧪
All suggestions, snark, links to papers etc. welcome. Trying to navigate a new field...
Please repost!
🧪