Congrats to Xiaoqian(Annie) Yu Xiaoqian(Annie) Yu and coauthors for a powerful study that elucidates mechanisms of coexistence of functionally redundant bacteria: academic.oup.com/ismej/article/…

👋DefenseFinder news ! Thinking of how we can better help the community, we provide a new website that includes a wiki on defense systems, a structure database and precomputed DefenseFinder results on >22k genomes. defensefinder.mdmlab.fr Preprint: biorxiv.org/content/10.110…

A ten year journey from Boston to Vienna! Thanks to everyone who inspired and helped me along the way and never gave up on me🥹 🍺 to my coauthors craig mclean Christopher Corzett Liz Kujawinski Eric Alm Martin Polz

ChatGPT, but make it help me annotate viruses! Our work "Large language models improve annotation of prokaryotic viral proteins" by Einstein MSTP Albert Einstein College of Medicine - Official grad student extraordinaire Zachary Flamholz, and Steve Biller Wellesley College in Nature Microbiology rdcu.be/dxcnE (1/11)

Check out some of my thesis work, using protein language models to improve prokaryotic viral protein function prediction, now out in Nature Microbiology under the guidance of my amazing advisor Libusha Kelly and in collaboration with Steve Biller. doi.org/10.1038/s41564… 1/9

New research from Susan Bullman /CJohnstonLab, with superstar 1st author @mzepedar, out now in nature pinpoints “high-risk” subtype of Fusobacterium nucleatum that dominates the colorectal cancer (CRC) niche in human patient's Link : rdcu.be/dBUjH Tweet🧵below:

NSURP CALLS FOR AID! Sign up as a mentor at NSURP.org. Please share (but also sign up 😀) #nsurp2024 #nolabnoproblem

Congrats to Allie Stanton sabeti_lab @harvard Virology PhD graduate successfully defending a tour de force thesis “Massively Parallel Approaches to Functional Characterization of Natural and Engineered VIruses” 🎓🧪 🦠 1/10 🧵

Excited to share our work: Episymbiotic Saccharibacteria TM7x modulates the susceptibility of its host bacteria to phage infection and promotes their coexistence Jeffrey McLean Batbileg Bor Pu-Ting Dong The ADA Forsyth Institute Jun Liu Lab | PNAS pnas.org/doi/10.1073/pn…

Woohoo, our paper on the discovery of 65 new phages dependent on conjugative plasmids is published in it's final form today in Nature Communications ! Here follows a thread (1/ ) link.springer.com/article/10.103…

Three’s a crowd: Saccharibacteria episymbiosis modulates phage predation of host bacteria | PNAS pnas.org/doi/10.1073/pn… commentary by Richard Lamont on our recent collabarative work Batbileg Bor Jeffrey McLean Pu-Ting Dong Lulucen The ADA Forsyth Institute

🚨🚨 Conference announcement: VEGA 2024 is officially *on* \o/ Will be Nov. 12 - 13, 2024, in Berkeley, in collaboration with NIST. More info to come soon re: speakers, etc, but in the meantime you can already check the provisional agenda and register at jgi.doe.gov/events/vega/

Check out the new preprint by Annie Yu Xiaoqian(Annie) Yu and colleagues on how genome wide selective sweeps structure the human microbiome: biorxiv.org/content/10.110…

Current MD/PhD with research in metagenomics and phage genomics looking to do basic and translational work in the space. All leads welcome for research residency or post-doc opportunities

New preprint alert!🚀 Excited to share our latest preprint, where we discover a vast arsenal of phage anti-defense proteins using an interpretable machine-learning approach. Big thanks to Martin Polz, @ShaulPollak, Mariusz Ferenc, and all collaborators! biorxiv.org/content/10.110…

It's true, cleaned up my bench today after a memorable 6.5 years in the Michael Baym lab! Very excited to start my own lab next month at the NYSDOH Wadsworth Center doing public health adjacent basic research exploring "exotic" bacteriophages!! #newpi

🎉 Exciting news! We've just published MVP: a Modular Viromics Pipeline 🦠✨ journals.asm.org/doi/epub/10.11…

If you work with metagenomes (or metatranscriptomes), would like to explore what viruses/phages are in your datasets, but don't know where to start, we have (an) MVP for you now \o/ Really happy to see this one published, and also welcoming feedback/suggestion of improvement!

Spacedust: de novo discovery of conserved gene clusters. Combining sensitive Foldseek structure search and conserved neighborhood detection to discover functionally-associated gene clusters in prokaryotic & viral genomes. 🚀github.com/soedinglab/spa… 📄biorxiv.org/content/10.110… 1/6🧵

My lab is up and running and just needs enthusiastic phage biologists to populate it! Contact me or apply in the link if you are interested in a postdoc exploring plasmid-dependent phage biology in beautiful (and super affordable!) upstate New York🍎healthresearch.wd1.myworkdayjobs.com/en-US/HRI_Care… 1/3