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Yishay Pinto

@yishay.bsky.social
2.5K followers 1.6K following 45 posts

Computational biologist. Studying genomes of phages and microbes. sites.biu.ac.il/en/pinto-lab

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Reposted by Yishay Pinto
Rafal Mostowy @rafalmostowy.bsky.social · 15/07/2026
PhD opening in my lab @jagiellonskiuni.bsky.social: using AI to predict how phage enzymes break down bacterial capsules — joint work with ML group GMUM and Zuzanna Drulis-Kawa's phage lab (Wrocław), spanning genomics, AI & evolution. mostowylab.com/job-phd-ai-d... Deadline: 15 August 2026
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Yuval Mulla @yuvalmulla.bsky.social · 06/07/2026
Interested in a PhD on bacteriophages? Check out www.academictransfer.com/nl/jobs/3623... #phagesky if you are interested and also happen to be at #VOM2026, send me a dm
academictransfer.com
How do phages kill dormant bacteria
Are you excited about exploring the biology behind phages infecting dormant bacteria? Join forces to uncover fundamental biology with great potential for clinical impact. We offer a fully funded PhD p...
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Ákos T Kovács @evolvedbiofilm.bsky.social · 24/05/2026
Revisiting the life cycle of temperate phages @natrevmicro.nature.com by @jakob-tr.bsky.social, Cora Chmielowska, @albertomarina.bsky.social, and @jrpenades.bsky.social www.nature.com/articles/s41... #PhageSky
nature.com
Revisiting the life cycle of temperate phages - Nature Reviews Microbiology
The life cycle of temperate bacteriophages involves lytic or lysogenic cycles and has historically served as a model for studying genetic regulation. This Review provides an updated overview of these ...
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Yishay Pinto @yishay.bsky.social · 17/05/2026
Are gut phages friends or foes? A nice "forum" in Cell Host&Microbe by @naamagz.bsky.social discussing it's all about context. Depending on host inflammation and ecology, phages can shift between stabilizing and destabilizing our microbiome. www.cell.com/cell-host-mi... #phagesky
cell.com
The gut phageome: Friend or foe?
Gut bacteriophages defy simple classification as beneficial or harmful, instead shifting between roles that stabilize or destabilize microbial communities depending on phage lifestyle dynamics, host i...
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Yishay Pinto @yishay.bsky.social · 28/04/2026
Excited to share this interview on our lab's research!We're diving deep into the gut virome using AI and computational tools to read (and write?) viral genomes for the future of personalized medicine. Check it out: dangoor-medicine.biu.ac.il/node/416 #phagesky #Microbiome #Genomics #Virome
dangoor-medicine.biu.ac.il
Genetic Matryoshka: Exploring the Viruses Hidden Within the Bacteria Inside Us | The Dangoor Center For Personalized Medicine
Billions of viruses inhabit our gut. Dr. Yishay Pinto, a principal investigator in the Faculty of Life Sciences at Bar-Ilan University and the Dangoor Center for Personalized Medicine, is developing c...
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Tami Lieberman @contaminatedsci.bsky.social · 18/03/2026
If you're a senior PhD student or recent graduate interested in doing work at the intersection of AI and microbial genomics and/or microbiomes, please feel free to reach out to discuss the possibility of applying together for an MIT Novo Nordisk Fellowship engineering.mit.edu/novo-nordisk
engineering.mit.edu
Novo Nordisk Fellowship
Potential areas of focus for postdoctoral fellows participating in the MIT-Novo Nordisk Postdoc Program include, but are not limited to, the following: Your complete application should include: In the...
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Nandita Garud @nanditagarud.bsky.social · 12/02/2026
I am seeking a postdoc to join my group at UCLA -- ideally the candidate would have some experience in either population genetics or microbes/microbiome (computational background needed). We have a range of projects and are happy to tailer to your interests. Please dm/email me if interested.
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Rob Edwards @linsalrob.bsky.social · 26/11/2025
Long read Metagenomics, #phage and #prophage in the gut by Ami Bhatt's group. Beautiful data showing changes in phages over two years #phagesky www.nature.com/articles/s41...
nature.com
Long-read metagenomics reveals phage dynamics in the human gut microbiome - Nature
Complex prophage integration dynamics, including low-level induction, cross-family host range and transposase-mediated mobilization, challenge existing paradigms and deepen our understanding of phage–...
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Emmanuele Severi @emmseveri.bsky.social · 27/11/2025
#microsky #phagesky #phage in the gut www.nature.com/articles/s41...
nature.com
Long-read metagenomics reveals phage dynamics in the human gut microbiome - Nature
Complex prophage integration dynamics, including low-level induction, cross-family host range and transposase-mediated mobilization, challenge existing paradigms and deepen our understanding of phage–...
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Antonio Camargo @apcamargo.bsky.social · 06/11/2025
🚨New preprint out! We present a foundational genomic resource of human gut microbiome viruses. It delivers high-quality, deeply curated data spanning taxonomy, predicted hosts, structures, and functions, providing a reference for gut virome research. (1/8) www.biorxiv.org/content/10.1...
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Philipp Engel @pengellab.bsky.social · 04/11/2025
🐝🦠 New paper: rdcu.be/eOf7A Phages may drive microbial diversity, yet we often don’t even know how phages & bacteria correlate in nature. Our new study tackles this in the honeybee gut, thanks to the great work of PhD student @malickndiaye.bsky.social at @dmf-unil.bsky.social @fbm-unil.bsky.social
nature.com
Phage diversity mirrors bacterial strain diversity in the honey bee gut microbiota - Nature Communications
Authors analyse paired viral and bacterial shotgun metagenomics data from individual honeybee guts, revealing modular, nested phage–bacteria networks, with viral diversity mirroring bacterial strain c...
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Luis Orellana (Coto) @cotoorellana.bsky.social · 30/10/2025
The average nucleotide identity (ANI) underpins how we map microbial diversity, compare species, and connect genomes to ecology. I wrote a short piece reflecting on the discovery and significance of this metric (and really enjoyed digging into the context and story behind it!) #microsky 🧬
nature.com
Average nucleotide identity — the backbone of modern ecological genomics - Nature Reviews Genetics
In this Journal Club, Luis Orellana recalls a 2005 publication by Konstantinidis and Tiedje that introduced average nucleotide identity as a sequence-based metric to determine the relatedness between ...
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Yishay Pinto @yishay.bsky.social · 15/08/2025
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.
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Dor Salomon @drdorsalomon.bsky.social · 18/04/2025
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. 🦠🙏
media.tenor.com
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 "
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bioRxiv Microbiology @biorxiv-microbiol.bsky.social · 17/03/2025
Replicative selfish genetic elements are driving rapid pathogenic adaptation of Enterococcus faecium www.biorxiv.org/content/10.1101/202…
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Yishay Pinto @yishay.bsky.social · 31/01/2025
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...
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Yishay Pinto @yishay.bsky.social · 28/01/2025
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
nature.com
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.
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Michael Baym @baym.lol · 17/01/2025
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
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Yishay Pinto @yishay.bsky.social · 15/11/2024
Starter pack for metagenomics and microbial genomics lovers. go.bsky.app/MFipoLH
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Andrew Page @andrewjpage.bsky.social · 10/01/2025
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 · 31/12/2024
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 1/2
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AI x Bio Discovery @aixbiobot.bsky.social · 01/01/2025
Empathi: Embedding-based Phage Protein Annotation Tool by Hierarchical Assignment [new] Empathi: Classifies phage proteins using embeddings, IDs multi-func.
Empathi: Embedding-based Phage Protein Annotation Tool by Hierarchical AssignmentFigure 1Figure 2Figure 3
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Luuk Loeff @lloeff.bsky.social · 31/12/2024
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 · 30/12/2024
Finally out! Phage therapy for diabetic foot ulcers www.sciencedirect.com/science/arti...
sciencedirect.com
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…
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Asaf Levy @asaflevylab.bsky.social · 30/12/2024
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.
sciencedirect.com
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 …
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João Botelho @joaoftsbotelho.bsky.social · 22/12/2024
Nice study from @annechevallereau.bsky.social's lab! www.biorxiv.org/content/10.1...
biorxiv.org
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...
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Lars Barquist @lbarquist.bsky.social · 16/12/2024
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/...
journals.plos.org
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...
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ᐯIᑕTOᖇ ᑎIᘔET, ᗰᗪ @nizet.bsky.social · 10/12/2024
nAtUrE iS bEaUtiFuL 🐞 #MedSky
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colinhillucc.bsky.social @colinhillucc.bsky.social · 04/12/2024
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...
sciencedirect.com
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…
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bioRxivpreprint @biorxivpreprint.bsky.social · 04/12/2024
Prophage induction contributes to alterations in the gut phageome during intestinal inflammation www.biorxiv.org/content/10.1101/202…
biorxiv.org
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
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European Virus Bioinformatics Center @evbc.bsky.social · 03/12/2024
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
doi.org
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...
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Bluesky @bsky.app · 03/12/2024
Scientists, academics, researchers: We’re excited to share that @altmetric.com is now tracking mentions of your research on Bluesky! 🧪
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Paul Bollyky @pbollyky.bsky.social · 02/12/2024
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
nature.com
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...
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bioRxiv Bioinfo @biorxiv-bioinfo.bsky.social · 02/12/2024
Identification and Mitigation of microbial contaminant reads from long-read metagenomic samples www.biorxiv.org/content/10.1101/202…
biorxiv.org
Identification and Mitigation of microbial contaminant reads from long-read metagenomic samples https://www.biorxiv.org/content/10.1101/2024.11.26.625374v1
Metagenomic sequencing has revolutionized our understanding of microbial communities, but the presen
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Prof. Ruth Ley FRS @microbiome.bsky.social · 01/12/2024
Very cool to see the SmartPill capsule in action here!🦠🧫 www.nature.com/articles/s41...
nature.com
Gut physiology and environment explain variations in human gut microbiome composition and metabolism - Nature Microbiology
An observational longitudinal clinical trial, incorporating a SmartPill and metabolomics, reveals the role of host factors in shaping the gut microbiome in healthy human adults.
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Yishay Pinto @yishay.bsky.social · 25/11/2024
Amazing! Read how MGEs confered resistance to vibriophage, probably contributed to its spread during the 90s cholera epidemic in South America.
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Madhu Pai, MD, PhD @madhupai.bsky.social · 24/11/2024
Non-native English speakers need 50% more time to write a paper When they do, they face a 2.5 times higher chance of being rejected because of language journals.plos.org/plosbiology/...
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Su-In Lee @suinlee.bsky.social · 24/11/2024
Here’s the updated Computational Biology Starter Pack! Let me know if you'd like to be included. go.bsky.app/QVPoZXp
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Scott Saunders @saunderslab.bsky.social · 22/11/2024
Wow - bluesky! 📈 🦠 Please help me amplify a special faculty search. We're looking for someone in "Microbial Systems Biology" to join me and @kreynoldslab.bsky.social at UTSW Sys Bio / Bioinformatics. There is an empty lab space right next to us waiting for you! apply.interfolio.com/154339 1/4
chalk + chalkboard with diagramslab group silly picture
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bioRxiv Microbiology @biorxiv-microbiol.bsky.social · 21/11/2024
The impact of transplant location on the gut microbiome and resistome in patients undergoing hematopoietic stem cell transplantation at home versus in the hospital www.biorxiv.org/content/10.1101/202…
biorxiv.org
The impact of transplant location on the gut microbiome and resistome in patients undergoing hematopoietic stem cell transplantation at home versus in the hospital https://www.biorxiv.org/content/10.1101/2024.11.19.624359v1
Objectives: Home-based hematopoietic stem cell transplantation (HCT) is a novel approach that has th
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Michael Baym @baym.lol · 21/11/2024
The first review article from my lab, helmed by @celiasouque.bsky.social, "From Petri Dishes to Patients to Populations: Scales and Evolutionary Mechanisms Driving Antibiotic Resistance" is now online and open access at Annual Reviews Microbiology: www.annualreviews.org/content/jour...
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Yishay Pinto @yishay.bsky.social · 21/11/2024
1/ A new preprint from the @gangfang.bsky.social group highlights challenges in detecting low-abundance modifications with ONT sequencing and proposes a framework to improve reliability.
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Chris Damman, MD 🍓 @gutbitesmd.bsky.social · 20/11/2024
go.bsky.app/ADqj5dt
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Gang Fang @gangfang.bsky.social · 20/11/2024
(1st post @BlueSky) Preprint alert🚨a long thread. Cautions in the use of @nanopore sequencing to map DNA modifications: officially reported “accuracy” ≠ reliable mapping in real applications. We performed a critical assessment of nanopore sequencing (across different versions of models) for the 1/n
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Jay 🦋 @jay.bsky.team · 17/11/2024
You think I’m kidding, but all our servers are actually named after mushrooms. 🍄‍🟫 🍄 🍄‍🟫 🍄 🍄‍🟫 🍄
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Yishay Pinto @yishay.bsky.social · 19/11/2024
I'm giving a guest lecture in computational genomics and have 90 minutes to inspire students to fall in love with the #microbiome and #metagenomics. I'll cover studies, approaches, algorithms, and their impact. Any findings/technologies/methods that blew your mind? Would love to brainstorm!
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Asaf Levy @asaflevylab.bsky.social · 19/11/2024
We found something interesting in the evolution of plant microbiota. It is under review and we published the preprint today. Avi Bograd from my lab analyzed the genomes of 38,912 bacteria and identified a clear depletion of all MGE types in plant-associated bacteria vs. non-plant associated bacteria
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Cyril Anjou @cyril-anjou.bsky.social · 18/11/2024
I didn't see one so I just created the Gut Microbiota starter pack! Please feel free to share, ask for joining or recommend must-added! go.bsky.app/UkXi7to
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Laura White @laurakwhite.bsky.social · 19/11/2024
New preprint on our method aa-tRNA-seq: chemically capturing aminoacylated tRNA molecules & pulling them through nanopores. It’s been a blast working with my collaborator Aleks Radakovic to take this from idea to promising pilot data to some looking exciting biology to chase down in future work.
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Oded Rechavi @odedrechavi.bsky.social · 19/11/2024
Hope I'm the first to post this all time classic on this platform
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