Chris Shaffer 🧬🔬🧪

Integrated host phage RNA seq analysis of Mycobacteriophage D29 infection reveals dual arm balanced phage genome expression and inhibited expression of host transporter and VapC target genes. The Mycobacteriophage D29 infects Mycobacterium species. Many of these are deadly human pathogens. In earlier studies, we performed proteomic analyses using a temperature-sensitive variant of D29, cal...

good old D29 for the win;
www.biorxiv.org/content/10.1...

Phages with fully-synthetic DNA can be edited gene by gene A team led by University of Pittsburgh's Graham Hatfull has developed a method to construct bacteriophages with entirely synthetic genetic material, allowing researchers to add and subtract genes at w...

phys.org/news/2025-11...

Rational design of a hospital-specific phage cocktail to treat Enterobacter cloacae complex infections - Nature Microbiology The Entelli-02 phage product containing five phages has frontline potential to address infections caused by the multidrug-resistant Enterobacter cloacae complex.

OUT NOW: Rational design of a hospital-specific phage cocktail to treat Enterobacter cloacae complex infections

By Dinesh Subedi, Jeremy Barr & colleagues @jeremyjbarr.bsky.social

www.nature.com/articles/s41...

Synteny and linkage decay in bacteriophage pangenomes Bacteriophages are rich in genetic diversity, due to frequent horizontal transfer and recombination. This makes traditional microbial phylogenetic analyses, often based on the assumption of vertical i...

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

Map of 200+ GEP institutions in the continental United States and Puerto Rico (U.S.).

What does a national research network look like?
📍 This map shows 209 active GEP institutions across the U.S. and its territories.

That’s 209 campuses where students are learning genomics by doing real research.

#GenomicsEducation #GEPteach #GEPtools

Graphic of the UCSC Genome Browser with accompanying text. Image text: "The Pathways Project: Free, open-access genomics curriculum for undergraduates. Learn more at thegep.org."

Undergrads learning real genomics?
Yes—through the Pathways Project.

The GEP provides:
• A gene annotation walkthrough
• A full YouTube video series
• All prerequisite curriculum materials
—all free and open-access.

Explore here: thegep.org/projects/pat...

#Genomics #STEMed #GEPtools

In 2005, a small team of researchers asked:
What if undergrads didn’t just learn genomics, but contributed to real discoveries?

That question launched the Genomics Education Partnership (GEP).
#GenomicsEducation #UndergradResearch #GEPCUREs

The winning #LaskerEssay, "Are You Listening?” by Amanda Pinski makes the case for the power of podcasts in #SciComm and science education. 🧪 Read it here: laskerfoundation.org/wp-content/u... @washumedicine.bsky.social @jclinical-invest.bsky.social

My colleague Pilar Domingo-Calap @pilardomingoc.bsky.social successfully treated a patient with prosthetic joint infection by her phage therapy 👏👏🏆🦠🧪🧫 #microsky #viruses #phages @uv.es @csic.es @ucciuv.bsky.social

’We couldn’t live without it’: the UCSC Genome Browser turns 25 After a quarter of a century, the website remains an essential tool for navigating the genome and understanding its structure, function and clinical impact.

It’s been 25 years since the UCSC Genome Browser launched. Nature profiles how the website remains an essential tool for navigating the genome and understanding its structure, function, and clinical impact. #Academicsky 🧬 🧪

We’ve wrapped up the 2025 GEP National Faculty Workshop—and we want to say a big THANK YOU to everyone who joined us! 🧬
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In challenging times for science research and education, consider donating to an organization devoted to training the next generation of scientists. secure.givelively.org/donate/genom...

Summary of emerging technologies to study chromatin-protein interactions on native chromatin / in vivo.

🧬NEW review article from Henikoff and Ahmad about emerging epigenomic mapping technologies to study chromatin regulation. Very comprehensive - great for beginners and experts alike!

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

GEP | Pathways Project - YouTube This series of videos is intended to help GEP students annotate a Pathways Project gene from start to finish.

NEW GEP VIDEO SERIES: We are happy to announce that our Pathways Project video walk-through series is now available! You can watch the full series - detailing our gene annotation protocol - on the GEP’s official YouTube channel. www.youtube.com/playlist?lis...

We would love feedback on a new NCBI-BLAST service we are launching today: sky-blast.com

Under the hood it's the same BLAST executable and databases provided by NCBI, with a replica of the NIH's interface - providing an alternative to the US gov service that's less congested, faster & more reliable