Phages invented sgRNAs before humans!! 🧬 Obviously, for mischief… 😈 Loved seeing this story unfold!

Dr. Indra Gonzalez Ojeda gave a great thesis defense this morning, including some wisdom for starting PhD students, or frankly, anyone.

(1/8) Very excited to share my first PhD preprint on phages from Hawaiian volcanic fumaroles from the East Rift Zone (ERZ) of Kīlauea! www.biorxiv.org/content/10.6...

Excited to share our discovery of a new programmable RNA-guided DNA-targeting system hiding inside bacteriophages that predates CRISPR. We call it VIPR (Viral Interference Programmable Repeat), and it uses an entirely new logic to find its targets. Thread + link below.

Excited to see our work out in Science today! Using machine learning to identify prokaryotic immune systems www.science.org/doi/10.1126/...

Great new story from Sophie Helaine and Molly Sargen! www.helainelab.com

This was a really fun and interesting Molecule of the Month to do! Check out the article to see even more elaborate RNA-only structures.

🎉 New year, NEW PREPRINT! Bacteria exhibit astonishing genetic diversity, but where do new genes come from? My best friend Arya Kaul (/labmate in the @baym lab) investigates how advantageous deletions can spawn new genes - "deletion-born fusions." 🧵:

🚀New preprint from our lab! I am very excited to finally share what has been the main focus of my PhD for the past almost 3 years! It is about viral dark matter and a powerful tool we built to shed light on it. 🧬💡 Continue reading (🧵)

This is it!!! This is the work I never want to stop hearing about. Kepler’s creativity and curiosity really shine through in this paper. Give it a read and enjoy 😎

Super excited that the bulk of my PhD work is now preprinted! Here we used whole-community competition, or coalescence, experiments to quantify selection acting on genetically diverged strains within larger communities. (1/n) www.biorxiv.org/content/10.1...

Been working on a really strange retron bacterial immune system, here's the preprint: www.biorxiv.org/content/10.1... Type VI retrons are unlike any other. Phage infection triggers reverse transcription of a DNA fragment that activates translation of a toxin to kill the infected cell.

1/10 Genome maintenance by telomerase is a fundamental process in nearly all eukaryotes. But where does it come from? Today, we report the discovery of telomerase homologs in a family of antiviral RTs, revealing an unexpected evolutionary origin in bacteria. www.biorxiv.org/content/10.1...

RNA Structure beyond Canonical Base Pairs Guided by Evolution 🧪🧬 #AcademicSky #higherEd www.mcb.harvard.edu/department/n... @rivaselenarivas.bsky.social @rachellegaudet.bsky.social @cryptogenomicon.bsky.social @dulaclab.bsky.social @neurovenki.bsky.social @naoshigeuchida.bsky.social

You’ve heard of ubiquitination, meet deazaguanylation: Doug Wassarman in our lab discovered phage defense pathways have co-opted Q nucleobase biosynthetic enzymes to catalyze a new form of protein conjugation chemistry @science.org www.science.org/doi/10.1126/...

What was antibiotic resistance like before we ever used antibiotics? How did we change what antibiotic resistance genes looked like over 100 years? Our paper looking at resistance genes from a century of NCTC historical isolates now out in mGen: www.microbiologyresearch.org/content/jour...

Phage DisCo! Our targeted phage discovery method in press today: journals.asm.org/doi/10.1128/... Perfectly timed with our four summer undergrad's first successful phage hunt... disco lights in the lab to mark the occasion 🕺

My father worked in a tire factory in Appalachia. Friends and family in the military. Used to vote Republican. Got into college on a diversity program for the underprivileged. Ended up a Harvard professor. And now my funding is terminated because we're trying to stick it to the elites.

The war on science in the US is already having an effect on private sector research like AlphaFold. Bears repeating but the private sector builds on top of things created by academic research for the public good. This hurts everyone.

(1/7) Very excited to share my first PhD preprint on the interactions of two of my favorite mobile genetic elements: phages and group II introns! www.biorxiv.org/content/10.1...

Final grad paper is officially out! Grateful for the incredible team and all the support along the way! www.nature.com/articles/s41...

Super excited to share a new preprint from our lab on design of small-molecule binding proteins using neural networks! The paper has a bit of everything. A new graph neural network, new design algorithms, and experimental validation. www.biorxiv.org/content/10.1... 🧵🧪

Llamas, dolphins and measles? Oh my! So thankful this story is finally breaking containment from my time in the Manguso Lab at the Broad. Using pieces from viruses and llamas we engineered selective cell specific viral like particles with reduced immunogenicity for in vivo gene delivery

rnahub.og A webserver to generate RNA alignments with secondary structure assessment www.biorxiv.org/content/10.1...

I'm so happy that I can finally share the results of my first postdoc paper with @baym.lol!!! Turns out plasmids are an amazing system to study multi-scale evolution and we can track within-cell and between-cell dynamics! (1/n) www.biorxiv.org/content/earl...