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Yishay Pinto

@yishay.bsky.social

2.4K followers 1.5K following 41 posts

Computational biologist. Studying genomes of phages and microbes. https://scholar.google.com/citations?user=nYRQiRMAAAAJ&hl=en

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Yishay Pinto @yishay.bsky.social · Nov 19

1/ Our review on sequencing-based #microbiome analysis is in the Dec 24 issue of Nature Reviews Genetics. We explore DNA/RNA-sequencing approaches for studying microbiome structure and function, highlighting the biological insights sequencing-based microbiome research offers.
go.nature.com/3XFqonu

Sequencing-based analysis of microbiomes - Nature Reviews Genetics

In this Review, Pinto and Bhatt provide an overview of DNA-sequencing and RNA-sequencing approaches that can be used to study the composition, structure, and function of microbiomes and discuss the bi...

go.nature.com

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Yishay Pinto @yishay.bsky.social · Aug 15

Big congratulations to danica, Gavin, Ami, and the entire team on this publication!

Yishay Pinto @yishay.bsky.social · Aug 15

Fantastic piece of research that discovered the atypical lifestyle of the prototypic crAssphage. This project showcased so much determination, brilliance, and open-mindedness, proving that great discoveries are made by following the evidence wherever it leads.

Cell Host & Microbe @cp-cellhostmicrobe.bsky.social · Jul 28

The prototypic crAssphage is a linear phage-plasmid

New work demonstrates that C. communis, a ubiquitous human gut phage that evades conventional plaque-based isolation, predominately replicates as a low-copy linear phage-plasmid w/ broad host range
www.cell.com/cell-host-mi...

The prototypic crAssphage is a linear phage-plasmid

Schmidtke et al. demonstrate that C. communis, a ubiquitous human gut phage that evades conventional plaque-based isolation, predominately replicates as a low-copy linear phage-plasmid with a broad ho...

www.cell.com

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Reposted by Yishay Pinto

Dor Salomon @drdorsalomon.bsky.social · Apr 18

Phage people - does anyone have a lambda phage with a deletion/mutation in the integrase gene (unable to lysogenize)? If so, can you please share it with us to help us test a cool hypothesis?
Thanks!
Please RT. 🦠🙏

a cartoon character from south park says " i m gonna need your help "

ALT: a cartoon character from south park says " i m gonna need your help "

media.tenor.com

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Reposted by Yishay Pinto

bioRxiv Microbiology @biorxiv-microbiol.bsky.social · Mar 17

Replicative selfish genetic elements are driving rapid pathogenic adaptation of Enterococcus faecium https://www.biorxiv.org/content/10.1101/2025.03.16.643550v1

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Yishay Pinto @yishay.bsky.social · Jan 31

Talking about read-based methods to profile phages in metagenomes, check out Marker-MAGu by @miketisza.bsky.social —a marker gene-based method for identifying phages.
bsky.app/profile/natu...

Yishay Pinto @yishay.bsky.social · Jan 28

Check out my "tools of the trade" piece on Phanta! I cover the need it addresses (phage inclusion in microbiome studies), the features we prioritized (sensitivity & ease of use), our vision (phage profiling as the norm), and the future we envision.
Check it out and try Phanta!
tinyurl.com/ToTPhanta

Beyond bacteria: Phanta adds flavour to microbiome profiling with a focus on phages - Nature Reviews Immunology

In this Tools of the Trade article, Yishay Pinto describes a tool, called Phanta, that profiles phages alongside their bacterial hosts in microbiome analysis.

www.nature.com

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Yishay Pinto @yishay.bsky.social · Jan 28

Beyond bacteria: Phanta adds flavour to microbiome profiling with a focus on phages - Nature Reviews Immunology

In this Tools of the Trade article, Yishay Pinto describes a tool, called Phanta, that profiles phages alongside their bacterial hosts in microbiome analysis.

www.nature.com

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Reposted by Yishay Pinto

Michael Baym @baym.lol · Jan 17

This paper has been a long time coming: We looked at the genomes of historical bacterial samples over a century to look for trends of antibiotic resistance genes, finding multiple instances of them in infections before the age of antibiotics, but an increase in both frequency and mobility after

bioRxiv Microbiology @biorxiv-microbiol.bsky.social · Jan 17

Genomic resistance in historical clinical isolates increased in frequency and mobility after the age of antibiotics https://www.biorxiv.org/content/10.1101/2025.01.16.633422v1

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Yishay Pinto @yishay.bsky.social · Nov 15

Starter pack for metagenomics and microbial genomics lovers.
go.bsky.app/MFipoLH

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Yishay Pinto @yishay.bsky.social · Jan 10

💙

Reposted by Yishay Pinto

Andrew Page @andrewjpage.bsky.social · Jan 10

I'm putting together a Microbial Bioinformatics starter pack to help get everyone connected in our community. Let me know if there are any bluesky users to be added and share so that twitter refugees can tune back in to the fantastic world microbes go.bsky.app/3ezLo7e

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Igor Ulitsky @igorulitsky.bsky.social · Dec 31

In the spirit of summaries, simple rules that, if everyone followed, would make academic publishing less painful in 2025.
As a reviewer:
*Separate major and minor comments
*Write your explicit recommendation in the "for authors" section
*If co-reviewing with trainees, read the paper yourself
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Igor Ulitsky @igorulitsky.bsky.social · Dec 31

Time for the annual peer-review summary! I did 46 peer reviews in 2024. A busier year than 2022-23, but still sub-2021 levels. This year I attempted to review revisions same-day, which worked ~75% of the time (the other 25% took way longer...).

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AI x Bio Discovery @aixbiobot.bsky.social · Jan 1

Empathi: Embedding-based Phage Protein Annotation Tool by Hierarchical Assignment [new]
Empathi: Classifies phage proteins using embeddings, IDs multi-func.

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Yishay Pinto @yishay.bsky.social · Dec 31

Amazing. Congrats!

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Luuk Loeff @lloeff.bsky.social · Dec 31

What a great way to end the year! ✨

Today in @cellpress.bsky.social we report the structure and function of the Shedu anti-phage defense system.

tinyurl.com/4crj6dnx

A long 🧵...

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Ran Nir-Paz @nirpaz.bsky.social · Dec 30

Finally out!
Phage therapy for diabetic foot ulcers

www.sciencedirect.com/science/arti...

Randomized double-blind study on safety and tolerability of TP-102 phage cocktail in patients with infected and non-infected diabetic foot ulcers

Phage therapy offers a promising alternative for treating serious infections, including diabetic foot ulcers (DFUs), through the lytic action of phage…

www.sciencedirect.com

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Reposted by Yishay Pinto

Asaf Levy @asaflevylab.bsky.social · Dec 30

We wrote a new review paper in @cp-trendsmicrobiol.bsky.social on recently developed bioinformatic tools that facilitate elucidating protein functions in the era of big genomics data.
www.sciencedirect.com/science/arti...
This is the 1st paper of 2 talented students Shani Cheskis and Avital Akerman.

Deciphering bacterial protein functions with innovative computational methods

Bacteria colonize every niche on Earth and play key roles in many environmental and host-associated processes. The sequencing revolution revealed the …

www.sciencedirect.com

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Reposted by Yishay Pinto

João Botelho @joaoftsbotelho.bsky.social · Dec 22

Nice study from @annechevallereau.bsky.social's lab!

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

Systematic functional assessment of antiphage systems in their native host

Bacterial resistance to bacteriophages (phages) relies on two primary strategies: preventing phage attachment and blocking post-attachment steps. These latter mechanisms are mediated by defence system...

www.biorxiv.org

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Reposted by Yishay Pinto

Lars Barquist @lbarquist.bsky.social · Dec 16

New paper from the Faber lab in @plosbiology.org characterizing the C. difficle ncRNA ModT, with effects on sporulation and the transition into stationary phase, evidence for RBP association -- and similar abundance to some ribosomal RNAs! 🧫🦠 journals.plos.org/plosbiology/...

The conserved noncoding RNA ModT coordinates growth and virulence in Clostridioides difficile

Bacterial non-coding RNAs influence various cellular functions and often have complex tertiary structures. This study characterizes ModT, a conserved ncRNA found in 2,500 bacterial species, found to r...

journals.plos.org

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Yishay Pinto @yishay.bsky.social · Dec 10

🙋‍♂️🙏

Reposted by Yishay Pinto

ᐯIᑕTOᖇ ᑎIᘔET, ᗰᗪ @nizet.bsky.social · Dec 10

nAtUrE iS bEaUtiFuL 🐞
#MedSky

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colinhillucc.bsky.social @colinhillucc.bsky.social · Dec 4

Feel like this paper slipped under the radar on ‘the other platform’ so giving it another airing here. Phage can significantly remodel the bacteriome in faecal samples - yet another confounder 🙄 www.sciencedirect.com/science/arti...

Dynamic nature of viral and bacterial communities in human faeces

Bacteriophages are a major component of the gut microbiome and are believed to play a role in establishment and stabilization of microbial communities…

www.sciencedirect.com

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bioRxivpreprint @biorxivpreprint.bsky.social · Dec 4

Prophage induction contributes to alterations in the gut phageome during intestinal inflammation https://www.biorxiv.org/content/10.1101/2024.12.03.626644v1

Bacteriophages (phages) are abundant members of the gut microbiota and regulators of bacterial commu

www.biorxiv.org

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Reposted by Yishay Pinto

European Virus Bioinformatics Center @evbc.bsky.social · Dec 3

Exploring the diverse RNA #virome in urban freshwater ecosystems, this study uncovers novel viruses with recombinant genomes, expanding our knowledge of virus diversity. #Metagenomics #FreshwaterEcology #ViralDiversity

📄 doi.org/10.3390/micr...
EVBC👤: R. Zell

Metagenomic Analyses of Water Samples of Two Urban Freshwaters in Berlin, Germany, Reveal New Highly Diverse Invertebrate Viruses

In an attempt to explore the RNA viromes of two German rivers, we searched the virus particle contents of one 50 L water sample each from the Teltow Canal and the Havel River for viruses assumed to in...

doi.org

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Bluesky @bsky.app · Dec 3

Scientists, academics, researchers: We’re excited to share that @altmetric.com is now tracking mentions of your research on Bluesky! 🧪

Altmetric @altmetric.com · Dec 3

There are already many articles for which there is more attention on Bluesky than on other comparable micro-blogging sites, meaning the academic community and the general public have clearly adopted Bluesky as one of its core places to disseminate and discuss new research.

A Place of Joy.

‘A place of joy’: why scientists are joining the rush to Bluesky
Researchers say the social-media platform — an alternative to X — offers more control over the content they see and the people they engage with.: https://www.nature.com/articles/d41586-024-03784-6

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Paul Bollyky @pbollyky.bsky.social · Dec 2

Excited to share our work on broadly effective phage-antibiotic cocktails. We report 4 cocktails that each work against 96% of 153 antibiotic resistant Pseudomonas isolates. Check it out here: www.nature.com/articles/s41... Congrats to Kevin Kim @KevinMinyo6651

A blueprint for broadly effective bacteriophage-antibiotic cocktails against bacterial infections - Nature Communications

The application of phage therapy for multidrug-resistant infections is mainly limited to personalized therapy due to the narrow host range of individual phages. Here, Kim et al. identify groups of pha...

www.nature.com

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