yishay.bsky.social - Profile | ThreadSky | a Reddit-style client for Bluesky

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...

submitted 28 days ago • 0 comments

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

submitted 31 days ago • 0 comments

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

submitted 42 days ago • 11 comments

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

submitted 105 days ago • 50 comments

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

submitted 49 days ago • 27 comments

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

submitted 58 days ago • 1 comment

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

submitted 57 days ago • 0 comments

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 🧵...

submitted 59 days ago • 6 comments

Finally out! Phage therapy for diabetic foot ulcers www.sciencedirect.com/science/arti...

submitted 60 days ago • 4 comments

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.

submitted 60 days ago • 1 comment

Nice study from @annechevallereau.bsky.social's lab! www.biorxiv.org/content/10.1...

submitted 68 days ago • 1 comment

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/...

submitted 74 days ago • 0 comments

nAtUrE iS bEaUtiFuL 🐞 #MedSky

submitted 80 days ago • 11 comments

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...

submitted 86 days ago • 0 comments

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

submitted 86 days ago • 0 comments

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

submitted 87 days ago • 0 comments

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

submitted 87 days ago • 479 comments

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

submitted 88 days ago • 4 comments

Identification and Mitigation of microbial contaminant reads from long-read metagenomic samples https://www.biorxiv.org/content/10.1101/2024.11.26.625374v1

submitted 88 days ago • 0 comments

Very cool to see the SmartPill capsule in action here!🦠🧫 www.nature.com/articles/s41...

submitted 89 days ago • 0 comments

Amazing! Read how MGEs confered resistance to vibriophage, probably contributed to its spread during the 90s cholera epidemic in South America.

submitted 95 days ago • 0 comments

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/...

submitted 96 days ago • 24 comments

Here’s the updated Computational Biology Starter Pack! Let me know if you'd like to be included. go.bsky.app/QVPoZXp

submitted 96 days ago • 82 comments

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

submitted 98 days ago • 4 comments

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

submitted 99 days ago • 0 comments

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...

submitted 99 days ago • 11 comments

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.

submitted 99 days ago • 1 comment

go.bsky.app/ADqj5dt

submitted 100 days ago • 5 comments

(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

submitted 100 days ago • 6 comments

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!

submitted 101 days ago • 1 comment

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

submitted 101 days ago • 1 comment

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

submitted 102 days ago • 15 comments

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.

submitted 101 days ago • 6 comments

Hope I'm the first to post this all time classic on this platform

submitted 101 days ago • 41 comments