@env_biochem

Post-doc with @waterargome, lover of nature, biochemist of water microbes, and an okay dancer. First gen.

mobileogdb.flsi.cloud.vt.edu/
Joined July 2013
  • Tweets832
  • Following598
  • Followers285
28Media
now live: how should we relate AR indicators in sewage to community resistance? one look at this issue using deep longitudinal metagenomics, modeling, and lots of bioinformatics @waterARGome @petervikesland @AyellaMM
medRxiv@medrxivpreprint12 Dec 2024
Metagenomics disentangles epidemiological and microbial ecological associations between community antibiotic use and antibiotic resistance indicators measured in sewage medrxiv.org/cgi/content/shor… #medRxiv
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This is a really good paper (frontiersin.org/journals/mic…) and I'm proud to have contributed to its conception. Moumi took ownership of this project and taught herself much about one of the most challenging and complex topics (1/2)

Frontiers | ARGContextProfiler: extracting and scoring the genomic contexts of antibiotic resista...

Antibiotic resistance (AR) presents a global health challenge, necessitating an improved understanding of the ecology, evolution, and dissemination of antibi...

frontiersin.org
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in metagenomics - the assembly graph. The resulting tool will help address a major bottleneck facing metagenomics for biological surveillance - particularly in how we address antibiotic resistance. Cheers to all involved. 2/2
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Connor Brown retweeted
Uli Klümper@UliKluemper5 Apr 2025
Our new @biorxivpreprint together with the German Environmental Agency (@Umweltbundesamt): Suppressing selection for antibiotic resistance in the environment: A transparent, ecology-based approach to predicted no-effect concentrations biorxiv.org/content/10.1101/…

Suppressing selection for antibiotic resistance in the environment: A transparent, ecology-based...

Selection for antibiotic resistance has been demonstrated at low, environmentally-relevant antibiotic concentrations. Over the past decade, the concept of minimum selective concentrations (MSC) has...

biorxiv.org
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Replication coordination marks the domestication of large extrachromosomal replicons in bacteria | bioRxiv biorxiv.org/content/10.1101/…
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Connor Brown retweeted
Petr Kohout@Kohout_mycor6 Mar 2025
You can now download the entire community matrix for ~83,000 samples (with metadata) and ~75,000 fungal taxa with just one click! Explore the GlobalFungi database.
GlobalFungi@globalfungi6 Mar 2025
The GlobalFungi team is happy to announce that data downloads are now available from GlobalFungi (globalfungi.com). No matter if you are interested in fungal genera, species or species hypotheses, you can now get their sequence counts in all samples at once.
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Telomeric transposons are pervasive in linear bacterial genomes | Science science.org/doi/10.1126/scie…

Telomeric transposons are pervasive in linear bacterial genomes

Eukaryotes have linear DNA, and their telomeres are hotspots for transposons, which in some cases took over telomere maintenance. We identified several families of independently evolved telomeric...

science.org
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Roche SBX preprint out biorxiv.org/content/10.1101/…

Sequencing by Expansion (SBX) – a novel, high-throughput single-molecule sequencing technology

Remarkable advances in high-throughput sequencing have enabled major biological discoveries and clinical applications, but achieving wider distribution and use depends critically on further improve...

biorxiv.org
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RNA-guided nucleases enable a gene drive of insertion sequences in plasmids | bioRxiv biorxiv.org/content/10.1101/…

RNA-guided nucleases enable a gene drive of insertion sequences in plasmids

Mobile genetic elements (MGEs) and the interactions between them are a major source of evolutionary innovation. Insertion sequences, the simplest MGEs usually encoding only the necessary genes for...

biorxiv.org
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Our preprint describing a family of Tn7-like transposons that evolved to target CRISPR repeats is now published at Mobile DNA #Tn7 #transposons #mobileDNA 1/10 mobilednajournal.biomedcentr…

A family of Tn7-like transposons evolved to target CRISPR repeats

Mobile DNA - Tn7 family transposons are mobile genetic elements known for precise target site selection, with some co-opting CRISPR-Cas systems for RNA-guided transposition. We identified a novel...

link.springer.com
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mobileOG-db 2.0 pre-release available if anyone is still on twitter github.com/clb21565/mobileOG… let us know your thoughts #microbiome #mobilegeneticelements #phages #plasmids #etc

GitHub - clb21565/mobileOG-db: code repo for mobileOG-db

code repo for mobileOG-db. Contribute to clb21565/mobileOG-db development by creating an account on GitHub.

github.com
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In Science Advances: a microbial genome census from publicly available databases using publicly available genome sequence data generated over the past three decades. @kyrpides @IMG_DATA @doescience biosciences.lbl.gov/2025/01/…

Taking Stock of the Known and Unknown Microbial Space - Biosciences Area

Using publicly available genome sequence data generated over the past three decades, JGI researchers assess the known fraction of microbial diversity. 

biosciences.lbl.gov
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David Coil@davidacoil8 Jan 2025
Currently reading the very interesting "Ebolavirus evolution and emergence are associated with land use change"... a nice mix of phylogenetic analysis combined with broader ecological factors. esajournals.onlinelibrary.wi…

Ebolavirus evolution and emergence are associated with land use change

Anthropogenic land use change facilitates disease emergence by altering the interface between humans and pathogen reservoirs and is hypothesized to drive pathogen evolution. Here, we show a positive...

esajournals.onlinelibrary.wiley.com
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» Homologous recombination shapes the architecture and evolution of bacterial genomes | Nucleic Acids Research | Oxford Academic academic.oup.com/nar/advance…

Homologous recombination shapes the architecture and evolution of bacterial genomes

Abstract. Homologous recombination is a key evolutionary force that varies considerably across bacterial species. However, how the landscape of homologous

academic.oup.com
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Connor Brown retweeted
ASM
@ASMicrobiology13 Dec 2024
Exciting news! ASM is partnering with @IDSAInfo to launch an annual conference on #AMR. This landmark event will unite experts from academia & industry to collaborate and respond to the urgent need for novel antimicrobial solutions. Read the announcement: asm.social/2e4
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Antibiotic resistance mediated by gene amplifications🧬 This review is available open-access to read @npjAMR! @kptsilva @AnuKhareLab (1/5) nature.com/articles/s44259-0…
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Thrilled to share that the FIRST paper from our group is live in @NatureComms ! Kudos to my amazing students @yingxian_g , Balu, and Anthony and all the collaborators. And thanks @VTCeZAP for the support!
Ying-Xian Goh@yingxian_g20 Nov 2024
Happy to share our recent study (nature.com/articles/s41467-0……) led by myself with @JingqiuLiao published in @NatureComms! A short thread 🧵 ...

Evidence of horizontal gene transfer and environmental selection impacting antibiotic resistance...

Nature Communications - It remains elusive how environmental antibiotic resistance evolves and spreads. Goh et al. analyzed a nationwide genomic dataset of soil-dwelling Listeria and find evidence...

nature.com
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Connor Brown retweeted
Elana Simon@ElanaPearl18 Nov 2024
🧬What are protein language models (PLMs) actually learning about biology? Our paper introduces InterPLM - a framework that reveals interpretable features in PLMs using sparse autoencoders, giving us a window into how these models represent protein structure and function. 🧵(1/9)
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New preprint up! We sequenced hundreds of samples from across one of Earth's oldest living organisms - the Pando aspen clone - to understand how mutations accumulate and spread in long-lived clonal organisms. Our results were…surprising. 1/30
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Gamma-Mobile-Trio systems are mobile elements rich in bacterial defensive and offensive tools | Nature Microbiology nature.com/articles/s41564-0…

Gamma-Mobile-Trio systems are mobile elements rich in bacterial defensive and offensive tools

Nature Microbiology - GMT-containing genomic islands in Vibrio parahaemolyticus and other diverse bacteria serve as a stockpile of immune and anti-phage defence systems, antibiotic-resistance genes...

nature.com
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