Chris Shaffer 🧬🔬🧪
@cdshaffer.bsky.social
Scientist, teacher, computer enthusiast 🧬
Reposted by Chris Shaffer 🧬🔬🧪
Our team highlighted this #cryoET work from Pitt looking at how bacteriophages fight TB. New #cryoEM work shows how phage Bxb1 attaches to the bacterial surface and delivers its DNA—promising insight for tackling antibiotic-resistant infections. #TeamTomo ter.li/fp1kwi
December 10, 2025 at 4:46 PM
Our team highlighted this #cryoET work from Pitt looking at how bacteriophages fight TB. New #cryoEM work shows how phage Bxb1 attaches to the bacterial surface and delivers its DNA—promising insight for tackling antibiotic-resistant infections. #TeamTomo ter.li/fp1kwi
good old D29 for the win;
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
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...
www.biorxiv.org
November 23, 2025 at 2:35 AM
good old D29 for the win;
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Reposted by Chris Shaffer 🧬🔬🧪
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...
By Dinesh Subedi, Jeremy Barr & colleagues @jeremyjbarr.bsky.social
www.nature.com/articles/s41...
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.
www.nature.com
September 25, 2025 at 10:47 AM
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...
By Dinesh Subedi, Jeremy Barr & colleagues @jeremyjbarr.bsky.social
www.nature.com/articles/s41...
Reposted by Chris Shaffer 🧬🔬🧪
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
📍 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
August 12, 2025 at 3:37 PM
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
📍 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
Reposted by Chris Shaffer 🧬🔬🧪
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
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
August 7, 2025 at 12:03 AM
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
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
Reposted by Chris Shaffer 🧬🔬🧪
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
What if undergrads didn’t just learn genomics, but contributed to real discoveries?
That question launched the Genomics Education Partnership (GEP).
#GenomicsEducation #UndergradResearch #GEPCUREs
August 8, 2025 at 1:22 AM
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
What if undergrads didn’t just learn genomics, but contributed to real discoveries?
That question launched the Genomics Education Partnership (GEP).
#GenomicsEducation #UndergradResearch #GEPCUREs
Reposted by Chris Shaffer 🧬🔬🧪
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
July 17, 2025 at 2:32 PM
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
Reposted by Chris Shaffer 🧬🔬🧪
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
Phage therapy in a patient with prosthetic join infection in Spain! Another sucessful treatment from the #EnBiVir #VLCphagehunters @i2sysbio.es and #EvolvingTherapeutics in collaboration with Dr. de la Villa #GregorioMarañon
@uv.es
@csic.es
www.sciencedirect.com/science/arti...
@uv.es
@csic.es
www.sciencedirect.com/science/arti...
Successful phage therapy in a patient with prosthetic joint infection
www.sciencedirect.com
July 12, 2025 at 9:52 PM
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
Reposted by Chris Shaffer 🧬🔬🧪
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 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.
go.nature.com
July 9, 2025 at 1:26 AM
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 🧬 🧪
Reposted by Chris Shaffer 🧬🔬🧪
We’ve wrapped up the 2025 GEP National Faculty Workshop—and we want to say a big THANK YOU to everyone who joined us! 🧬
[thread ⬇️] 1/5
[thread ⬇️] 1/5
July 1, 2025 at 9:36 PM
We’ve wrapped up the 2025 GEP National Faculty Workshop—and we want to say a big THANK YOU to everyone who joined us! 🧬
[thread ⬇️] 1/5
[thread ⬇️] 1/5
Reposted by Chris Shaffer 🧬🔬🧪
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...
Explore the GEP’s free genomics curriculum—perfect for undergrads and easy to bring into your course.
#GenomicsEd #FreeSTEMResources #TeachSTEM #BioEd #GEPCUREs
#GenomicsEd #FreeSTEMResources #TeachSTEM #BioEd #GEPCUREs
June 9, 2025 at 8:45 PM
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...
Reposted by Chris Shaffer 🧬🔬🧪
🧬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...
www.sciencedirect.com/science/arti...
May 21, 2025 at 12:39 PM
🧬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...
www.sciencedirect.com/science/arti...
Reposted by Chris Shaffer 🧬🔬🧪
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...
GEP | Pathways Project - YouTube
This series of videos is intended to help GEP students annotate a Pathways Project gene from start to finish.
www.youtube.com
March 23, 2025 at 12:43 AM
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...
Reposted by Chris Shaffer 🧬🔬🧪
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
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
March 11, 2025 at 11:50 PM
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
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