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Reposted by Mike Tisza

Mustafa Karatas @karatasmustafa.bsky.social · 12d

New paper out!

We sampled indoor air for a year in a Belgian daycare and used shotgun metagenomics to track viruses. We recovered many viral genomes of interest.

What would you sample next?

Read at @eurosurveillance.org
@emmanuel-microb.bsky.social, @jellematthijnssens.bsky.social
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Figure 3. (A–N) Sequencing coverage plots of genetic sequences of viruses detected in indoor air samples of a daycare and phylogenetic analyses of sequences of (O) two human bocaviruses and (P) one RSV identified in some samples, Belgium, January–December 2022

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Reposted by Mike Tisza

medRxivpreprint @medrxivpreprint.bsky.social · 20d

Wastewater Sequencing Reveals Persistent Circulation and Rising Prevalence of Several Oncogenic Viruses Across Texas https://www.medrxiv.org/content/10.1101/2025.09.17.25335998v1

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Reposted by Mike Tisza

Falk Hildebrand @bioinf.bsky.social · 29d

How do you long-read sequence metagenomes? I would argue it starts with the right sample storage & DNA extraction, to enable efficient @nanoporetech.com /@pacbio.bsky.social sequencing, which we investigated in our new paper: www.biorxiv.org/content/10.1...

Massive thanks to Klara for driving this

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Reposted by Mike Tisza

Jim Shaw @jimshaw.bsky.social · Sep 7

Preprint out for myloasm, our new nanopore / HiFi metagenome assembler!

Nanopore's getting accurate, but

1. Can this lead to better metagenome assemblies?
2. How, algorithmically, to leverage them?

with co-author Max Marin @mgmarin.bsky.social, supervised by Heng Li @lh3lh3.bsky.social

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bioRxiv Bioinfo @biorxiv-bioinfo.bsky.social · Sep 7

High-resolution metagenome assembly for modern long reads with myloasm https://www.biorxiv.org/content/10.1101/2025.09.05.674543v1

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Antonio Camargo @apcamargo.bsky.social · Sep 6

A BLAST update adding support for compressed files and csv output with headers is a Good Friday night surprise!

blast.ncbi.nlm.nih.gov/doc/blast-ne...

2025 BLAST NEWS — BlastNews 0.1.1 documentation

blast.ncbi.nlm.nih.gov

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Mike Tisza @miketisza.bsky.social · Aug 25

I want to thank my excellent co-authors and collaborators for the fantastic teamwork. If you want to test Cenote-Taker 3 yourself, please see the installation instructions on the GitHub repo: github.com/mtisza1/Ceno...

GitHub - mtisza1/Cenote-Taker3: Discover and annotate the virome

Discover and annotate the virome. Contribute to mtisza1/Cenote-Taker3 development by creating an account on GitHub.

github.com

Mike Tisza @miketisza.bsky.social · Aug 25

I'm very excited to share our manuscript for Cenote-Taker 3. We show that (1) CT3 quickly and accurately annotates previously uncatalogued virus genomes and (2) finds divergent virus genomes in contiguous assemblies. Virome benchmarks are SO hard, but I think we came up with clever and useful ones.

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Mike Tisza @miketisza.bsky.social · Aug 15

Thanks so much, Ludo! Again, these both look great, and i'm hoping to utilize them soon.

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Mike Tisza @miketisza.bsky.social · Aug 14

Can anyone explain how MetaROR and Peer Community In are different? @metaror.bsky.social @peercommunityin.bsky.social
(both seem great)

PLOS Biology @plosbiology.org · Aug 14

We are proud to announce a new agreement with @rorinstitute.bsky.social and @aimosinc.bsky.social to become a partner journal with MetaResearch Open Review (MetaRoR) @metaror.bsky.social

#metaresearch #openscience 🧪

Learn more: plos.io/45wPZB9

PLOS Biology announces agreement to become a MetaROR partner journal - The Official PLOS Blog

Note: PLOS issued the following press release on Thursday, August 14th. SAN FRANCISCO, CA — Today, PLOS Biology announced a new agreement…

plos.io

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Mya Breitbart @viromegirl.bsky.social · Aug 1

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 🦠🌊

Electron micrograph of two phage infecting a host cell side-by-side, with hearts between them

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Caleb Lareau @caleblareau.bsky.social · Jul 22

Excited to share a new preprint from the lab with @ryandhindsa.bsky.social ! www.biorxiv.org/content/10.1...

Led by @sherrynyeo.bsky.social, @erinmayc.bsky.social, and friends, we continue our journey to find viral DNA in our favorite place-- the overlooked and discarded reads in existing data! 1/

the treasure trove of all sequencing datasets

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Simon Roux @simrouxvirus.bsky.social · Jun 13

New pre-print out \o/ All about CRISPR, metagenomes, and what you learn when you collect (a lot of) spacers from natural communities, with @apcamargo.bsky.social @urineri.bsky.social @lhug.bsky.social but also Uri Gophna, Nikhil George (not on Bsky I think) & others at JGI doi.org/10.1101/2025...

doi.org

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Evelien Adriaenssens @evelienadri.bsky.social · May 29

Join my lab as a postdoctoral research scientist to investigate the diversity of drug-resistant #Salmonella and how #bacteriophages can help future food safety.

Apply by 2 July, details below!

Quadram Institute @quadraminstitute.bsky.social · May 29

🆕 Vacancy! We’re looking for a Research Scientist to join Dr @evelienadri.bsky.social‬ 's group to study bacteriophages, drug resistance and genetic evolution of Salmonella 🦠

💷 £36,720 to £39,750
🗓️ Apply by 2 July 2025
➡️ buff.ly/7M2mDaa

A social card with an illustration of a bacteriophage and bacteria and the text "Research Scientist to join Dr Evelien Adrianssen's group to study bacteriophage, drug resistance and genetic evolution of Salmonella, Salary: 36,720 to 39,750, Contract length: 1.5 years, Apply by 2 July 2025

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Reposted by Mike Tisza

Daan Speth @daanspeth.bsky.social · Jun 10

I'm happy to announce the latest release of the GlobDB, available at globdb.org.

The GlobDB is a database of "species dereplicated" microbial genomes, and as of release 226 contains twice the number of species-representative genomes (306,260) than the latest GTDB release.

home | GlobDB

globdb.org

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Jim Shaw @jimshaw.bsky.social · May 28

Announcing myloasm, a new long-read (ONT R10/PacBio) metagenome assembler that I've been working on during my postdoc in the Heng Li lab (@lh3lh3.bsky.social).

myloasm-docs.github.io

myloasm - metagenomic assembly with (noisy) long reads

myloasm-docs.github.io

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From the Labs at Baylor College of Medicine @bcmfromthelabs.bsky.social · May 13

An innovative outbreak detection program that tracks viruses in #wastewater identified the #measles virus in #Houston in early January 2025, before cases were reported. #TailorLabs #saracregeen @miketisza.bsky.social @bcmhouston.bsky.social #TEPHITexas #RiceU @apha.org www.bcm.edu/news/measles...

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Anthony William Maresso Ph.D. @tailor-labs.bsky.social · May 9

Another example of how wastewater sequencing is going to positively impact Public Health. TEPHI's Outbreak Detection program shows once more the sensitivity and specificity of agnostic sequencing .... ajph.aphapublications.org/doi/abs/10.2...

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Cameron Thrash @jcamthrash.bsky.social · May 8

Recombination and the Species Structure of the Genus Bacteroides www.biorxiv.org/content/10.1... #jcampubs

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Mustafa Karatas @karatasmustafa.bsky.social · Apr 29

🎉🎉 Happy to share our new paper! 🎉🎉

Have you ever wondered about the animal viruses living right alongside us in our cities?

Between our pets at home, rats in the sewers, pigeons on the streets, insects everywhere, and even farm animals nearby, it’s no surprise +++

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Florian Trigodet @floriantrigodet.bsky.social · Apr 28

I am very happy (and anxious) to share with you our most recent work in which we evaluated four of the most popular long-read assemblers,

www.biorxiv.org/content/10.1...

and tell you just a little bit about it in the following 🧵

Assemblies of long-read metagenomes suffer from diverse errors

Genomes from metagenomes have revolutionised our understanding of microbial diversity, ecology, and evolution, propelling advances in basic science, biomedicine, and biotechnology. Assembly algorithms...

www.biorxiv.org

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Ben Adler @benadler.bsky.social · Mar 31

🧪🧪🧪10 incredible findings about Cas10-relative, mCpol:
result number 10 will surprise you!🧪🧪🧪

@erinedoherty.bsky.social and I teamed up to understand the role and function of Cas10-relative, mCpol, and its role in antiphage immunity. For more, check out Erin's thread 👇

Erin Doherty @erinedoherty.bsky.social · Mar 31

Preprint alert! ✨ In this project that I co-led with @benadler.bsky.social, we show that a miniature CRISPR-Cas10-like enzyme, mCpol, uses a novel inverse signaling mechanism to prevent the spread of viruses that attempt immune evasion by depleting host cyclic nucleotides.

Check it out:

A miniature CRISPR-Cas10 enzyme confers immunity by an inverse signaling pathway

Microbial and viral co-evolution has created immunity mechanisms involving oligonucleotide signaling that share mechanistic features with human anti-viral systems. In these pathways, including CBASS a...

www.biorxiv.org

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Reposted by Mike Tisza

bioRxiv Microbiology @biorxiv-microbiol.bsky.social · Mar 26

Comparative wastewater virome analysis with different enrichment methods https://www.biorxiv.org/content/10.1101/2025.03.25.645222v1

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Reposted by Mike Tisza

Mustafa Karatas @karatasmustafa.bsky.social · Mar 27

📢 Excited to share the first paper of my PhD: 14 years of rotavirus epidemiology in Belgium!

Read the full story on Eurosurveillance: @eurosurveillance.org

👉 www.eurosurveillance.org/content/10.2...

#Rotavirus #Virology #PublicHealth #Epidemiology #EpiSky #IDsky

Key messages -->

Eurosurveillance journal @eurosurveillance.org · Mar 27

To answer their study question on the influence of the COVID-19 pandemic on rotavirus infections in Belgium, @karatasmustafa.bsky.social et al. used data collected 10 years before, 2 years during, and 2 years after the pandemic

#IDsky #EpiSky 🦠

👇🏽

Jelle Matthijnssens @jellematthijnssens.bsky.social · Mar 27

🚨 New paper alert! 🚨 How did the #COVID_19 pandemic impact #rotavirus epidemiology in Belgium? Read all about it in our latest paper in @Eurosurveillanc:
eurosurveillance.org/content/10.2...
@karatasmustafa.bsky.social @vanranstmarc.bsky.social @wollants.bsky.social

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Evelien Adriaenssens @evelienadri.bsky.social · Mar 19

🎓 #PhDPosition available in my group!

🫁 Understanding the microbiome and phageome in chronic lung infections for the development of phage therapy with me & Prof Eleanor Mishra

📅 Apply by Monday 14 April

➡️ buff.ly/7v9JVDU

Happy to answer questions, but don't send your CV through email.

Illustrations of the microbiome including bacteriophages with the text "Funded PhD, understanding the microbiome and phageome in chronic lung infections for the development of phage therapy with Dr Evelien Adriaenssens and Professor Eleanor Mishra. Apply by 14 April 2025" Logos of the Quadram Institute and Microbes Microbiomes Bioinformatics Doctoral Training Partnership

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Reposted by Mike Tisza

Richard Sever @richardsever.bsky.social · Mar 11

Big news: we are setting up a new non-profit organization to run bioRxiv and medRxiv. It's called openRxiv [no it's not a new preprint server; it's dedicated organization to oversee the servers] openrxiv.org 1/n

Homepage - openRxiv

openRxiv is an independent non-profit, the new organizational home for bioRxiv and medRxiv, enabling researchers to instantly share groundbreaking findings with the global scientific community.

openrxiv.org

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