John Prensner
@johnprensner.bsky.social
Pediatric neuro-oncologist, Asst Prof U-Michigan | Cancer researcher | RNA & ribosome enthusiast | Broad Institute, DFCI alum | book & music & tea lover | Dad | Views are mine (he/him). https://prensnerlab.org
Reposted by John Prensner
The room is
almost all
elephant.
Almost none
of it isn’t.
Pretty much
solid elephant.
So there’s no
room to talk
about it.
-Kay Ryan, “The Elephant in the Room”
#everynightapoem
almost all
elephant.
Almost none
of it isn’t.
Pretty much
solid elephant.
So there’s no
room to talk
about it.
-Kay Ryan, “The Elephant in the Room”
#everynightapoem
November 13, 2025 at 12:13 AM
The room is
almost all
elephant.
Almost none
of it isn’t.
Pretty much
solid elephant.
So there’s no
room to talk
about it.
-Kay Ryan, “The Elephant in the Room”
#everynightapoem
almost all
elephant.
Almost none
of it isn’t.
Pretty much
solid elephant.
So there’s no
room to talk
about it.
-Kay Ryan, “The Elephant in the Room”
#everynightapoem
So honored to take this position with @wearecbtn.bsky.social and it will be delightful to work on behalf of the pediatric brain tumor community!
CBTN welcomes new Scientific Co-Chair, John Prensner of University of Michigan. His work in data-driven discovery is shaping the next era of pediatric brain tumor research.
🔗 https://monkeylink.co/c0c2ec
🔗 https://monkeylink.co/c0c2ec
November 11, 2025 at 12:31 PM
So honored to take this position with @wearecbtn.bsky.social and it will be delightful to work on behalf of the pediatric brain tumor community!
Reposted by John Prensner
Very well done story on 60 Minutes about the harms of grant terminations and freezes at Harvard with Joan Brugge, Don Engbar, David Liu, and a very compelling young cancer patient, now cured with Liu's technology.
Transcript and video here
www.cbsnews.com/news/researc...
Transcript and video here
www.cbsnews.com/news/researc...
Battle between Trump and universities hurting scientific research in need of federal funding
Federal research funding to universities has fueled breakthroughs for years. The White House is pressuring universities to align with the president's political agenda, or risk losing their funding.
www.cbsnews.com
November 10, 2025 at 1:03 AM
Very well done story on 60 Minutes about the harms of grant terminations and freezes at Harvard with Joan Brugge, Don Engbar, David Liu, and a very compelling young cancer patient, now cured with Liu's technology.
Transcript and video here
www.cbsnews.com/news/researc...
Transcript and video here
www.cbsnews.com/news/researc...
Reposted by John Prensner
The R2 platform : Democratizing bioinformatics through an easily accessible public online software platform for non-experts in the field of Genomics
r2platform.com
#genomics #datascience #expertise #fair #public #science #bioinformatics #nocode #tcga #gtex #depmap
r2platform.com
#genomics #datascience #expertise #fair #public #science #bioinformatics #nocode #tcga #gtex #depmap
November 2, 2025 at 9:10 PM
The R2 platform : Democratizing bioinformatics through an easily accessible public online software platform for non-experts in the field of Genomics
r2platform.com
#genomics #datascience #expertise #fair #public #science #bioinformatics #nocode #tcga #gtex #depmap
r2platform.com
#genomics #datascience #expertise #fair #public #science #bioinformatics #nocode #tcga #gtex #depmap
Reposted by John Prensner
💬 Viewpoint: The evolving health care landscape necessitates a new clinician-scholar paradigm incorporating humanities and social sciences to address complex challenges and enhance scientific inquiry and health outcomes.
ja.ma/4qtBLL0
ja.ma/4qtBLL0
November 2, 2025 at 11:00 AM
💬 Viewpoint: The evolving health care landscape necessitates a new clinician-scholar paradigm incorporating humanities and social sciences to address complex challenges and enhance scientific inquiry and health outcomes.
ja.ma/4qtBLL0
ja.ma/4qtBLL0
Reposted by John Prensner
I feel like I’m going to reference this all the time. A+ meme.
October 28, 2025 at 9:46 AM
I feel like I’m going to reference this all the time. A+ meme.
Reposted by John Prensner
Fred Hutch's Human Biology Division is recruiting an Assistant or Associate Professor to lead a laboratory-based research program focused on the biological mechanisms of solid tumor cancers and their clinical translation. Learn more and apply: https://apply.interfolio.com/174007
October 25, 2025 at 5:16 PM
Fred Hutch's Human Biology Division is recruiting an Assistant or Associate Professor to lead a laboratory-based research program focused on the biological mechanisms of solid tumor cancers and their clinical translation. Learn more and apply: https://apply.interfolio.com/174007
Reposted by John Prensner
In 1983, the MacNeil/Lehrer NewsHour became the nation’s first hour-long nightly broadcast of national news, says Deema Zein.
October 23, 2025 at 11:59 AM
In 1983, the MacNeil/Lehrer NewsHour became the nation’s first hour-long nightly broadcast of national news, says Deema Zein.
Reposted by John Prensner
Check out our new paper @jci.org
High 4E-BP-1 expression associates with chromosome 8 gain and CDK4/6 sensitivity in Ewing Sarcoma
www.jci.org/articles/vie...
We show that chr8 gains drive poor outcome in EwS via 4E-BP-1
@dkfz.bsky.social
@nct-heidelberg.bsky.social
@uniheidelberg.bsky.social
High 4E-BP-1 expression associates with chromosome 8 gain and CDK4/6 sensitivity in Ewing Sarcoma
www.jci.org/articles/vie...
We show that chr8 gains drive poor outcome in EwS via 4E-BP-1
@dkfz.bsky.social
@nct-heidelberg.bsky.social
@uniheidelberg.bsky.social
JCI -
High 4E-BP-1 expression associates with chromosome 8 gain and CDK4/6 sensitivity in Ewing Sarcoma
www.jci.org
October 17, 2025 at 6:31 PM
Check out our new paper @jci.org
High 4E-BP-1 expression associates with chromosome 8 gain and CDK4/6 sensitivity in Ewing Sarcoma
www.jci.org/articles/vie...
We show that chr8 gains drive poor outcome in EwS via 4E-BP-1
@dkfz.bsky.social
@nct-heidelberg.bsky.social
@uniheidelberg.bsky.social
High 4E-BP-1 expression associates with chromosome 8 gain and CDK4/6 sensitivity in Ewing Sarcoma
www.jci.org/articles/vie...
We show that chr8 gains drive poor outcome in EwS via 4E-BP-1
@dkfz.bsky.social
@nct-heidelberg.bsky.social
@uniheidelberg.bsky.social
Reposted by John Prensner
The pangenome resources and genome assembly/inference approaches we are building will eventually enable complete, personalized “T2T” genomes for everyone. This is the thesis of the Q100 project (www.biorxiv.org/content/10.1...) and what my group is currently working towards. Stay tuned... [10/10]
A complete diploid human genome benchmark for personalized genomics
Human genome resequencing typically involves mapping reads to a reference genome to call variants; however, this approach suffers from both technical and reference biases, leaving many duplicated and ...
www.biorxiv.org
October 13, 2025 at 8:17 PM
The pangenome resources and genome assembly/inference approaches we are building will eventually enable complete, personalized “T2T” genomes for everyone. This is the thesis of the Q100 project (www.biorxiv.org/content/10.1...) and what my group is currently working towards. Stay tuned... [10/10]
Wow!
Thrilled to share our work on transcription initiation and termination being spatially coordinated out today in Science! www.science.org/doi/10.1126/...
mRNA initiation and termination are spatially coordinated
Transcriptional initiation and termination decisions drive messenger RNA (mRNA) isoform diversity but the relationship between them remains poorly understood. By systematically profiling joint usage o...
www.science.org
October 12, 2025 at 6:07 PM
Wow!
Reposted by John Prensner
Happy to share work spearheaded by former grad student Colin Shew testing shared duplicated cis regulatory elements (CREs) using an MPRA. While we find some high effect CREs, collectively paralog differences represent modest effects accounting for observed gene expression divergence.
Influence of cis-regulatory elements on regulatory divergence in human segmental duplications https://www.biorxiv.org/content/10.1101/2025.10.03.680410v1
October 7, 2025 at 2:31 AM
Happy to share work spearheaded by former grad student Colin Shew testing shared duplicated cis regulatory elements (CREs) using an MPRA. While we find some high effect CREs, collectively paralog differences represent modest effects accounting for observed gene expression divergence.
Reposted by John Prensner
⚠️ Paper alert: Using a novel CRISPR screening approach, we mapped the entire regulatory network controlling Xist—key for X-chromosome inactivation.
👉 We discover how sex and development signals are decoded at a single gene locus.
www.nature.com/articles/s41...
👇 Bluetorial
👉 We discover how sex and development signals are decoded at a single gene locus.
www.nature.com/articles/s41...
👇 Bluetorial
Reporter CRISPR screens decipher cis-regulatory and trans-regulatory principles at the Xist locus - Nature Structural & Molecular Biology
Here Schwämmle et al. develop CRISPR reporter screens to map transcription-factor-regulatory element interactions at the Xist locus, revealing a two-step mechanism integrating developmental and X-dosage signals to initiate X-chromosome inactivation.
www.nature.com
October 6, 2025 at 1:02 PM
⚠️ Paper alert: Using a novel CRISPR screening approach, we mapped the entire regulatory network controlling Xist—key for X-chromosome inactivation.
👉 We discover how sex and development signals are decoded at a single gene locus.
www.nature.com/articles/s41...
👇 Bluetorial
👉 We discover how sex and development signals are decoded at a single gene locus.
www.nature.com/articles/s41...
👇 Bluetorial
Reposted by John Prensner
Stress granules have a limited impact on global translation regulation but serve to protect small ribosomal subunits and preinitiation complexes from degradation
October 4, 2025 at 6:37 PM
Stress granules have a limited impact on global translation regulation but serve to protect small ribosomal subunits and preinitiation complexes from degradation
Reposted by John Prensner
Beautiful reconstitution of amino acid stress-dependent ISR activation by my @harvardcellbio.bsky.social colleagues presenting a unifying mechanism for GCN2 activation, which requires ribosome collisions and is enhanced by cognate uncharged tRNA in the A site! www.science.org/doi/10.1126/...
GCN1 couples GCN2 to ribosomal state to initiate amino acid response pathway signaling
During nutrient deprivation, activation of the protein kinase GCN2 regulates cell survival and metabolic homeostasis. In addition to amino acid stress, GCN2 is activated by a variety of cellular stres...
www.science.org
October 3, 2025 at 11:02 AM
Beautiful reconstitution of amino acid stress-dependent ISR activation by my @harvardcellbio.bsky.social colleagues presenting a unifying mechanism for GCN2 activation, which requires ribosome collisions and is enhanced by cognate uncharged tRNA in the A site! www.science.org/doi/10.1126/...
Reposted by John Prensner
After testing virtually all reasonable permutations of sample prep, spectra acquisition, database selection, data processing...
This team (convincingly, I think) demonstrates that ~85% of the small, *annotated* bacterial proteins are undetectable by mass spec—much less non-annotated ones. (1/4) 🧵
This team (convincingly, I think) demonstrates that ~85% of the small, *annotated* bacterial proteins are undetectable by mass spec—much less non-annotated ones. (1/4) 🧵
September 26, 2025 at 6:41 PM
After testing virtually all reasonable permutations of sample prep, spectra acquisition, database selection, data processing...
This team (convincingly, I think) demonstrates that ~85% of the small, *annotated* bacterial proteins are undetectable by mass spec—much less non-annotated ones. (1/4) 🧵
This team (convincingly, I think) demonstrates that ~85% of the small, *annotated* bacterial proteins are undetectable by mass spec—much less non-annotated ones. (1/4) 🧵
Supporting the #chadtough run to support #DMG/DIPG research for children with #childhoodcancer. What a great run!
September 28, 2025 at 5:52 PM
Supporting the #chadtough run to support #DMG/DIPG research for children with #childhoodcancer. What a great run!
Reposted by John Prensner
EWS::WT1 Isoform-Dependent Regulation of Neogenes in Desmoplastic Small Round Cell Tumors https://www.biorxiv.org/content/10.1101/2025.09.22.676906v1
September 24, 2025 at 12:35 AM
EWS::WT1 Isoform-Dependent Regulation of Neogenes in Desmoplastic Small Round Cell Tumors https://www.biorxiv.org/content/10.1101/2025.09.22.676906v1
Reposted by John Prensner
Delighted to finally announce a preprint describing the Q100 project! “A complete diploid human genome benchmark for personalized genomics” For which we finished HG002 to near-perfect accuracy: www.biorxiv.org/content/10.1... 🧵[1/14]
A complete diploid human genome benchmark for personalized genomics
Human genome resequencing typically involves mapping reads to a reference genome to call variants; however, this approach suffers from both technical and reference biases, leaving many duplicated and ...
www.biorxiv.org
September 22, 2025 at 5:01 PM
Delighted to finally announce a preprint describing the Q100 project! “A complete diploid human genome benchmark for personalized genomics” For which we finished HG002 to near-perfect accuracy: www.biorxiv.org/content/10.1... 🧵[1/14]
Reposted by John Prensner
We are excited to share GPN-Star, a cost-effective, biologically grounded genomic language modeling framework that achieves state-of-the-art performance across a wide range of variant effect prediction tasks relevant to human genetics.
www.biorxiv.org/content/10.1...
(1/n)
www.biorxiv.org/content/10.1...
(1/n)
September 22, 2025 at 5:29 AM
We are excited to share GPN-Star, a cost-effective, biologically grounded genomic language modeling framework that achieves state-of-the-art performance across a wide range of variant effect prediction tasks relevant to human genetics.
www.biorxiv.org/content/10.1...
(1/n)
www.biorxiv.org/content/10.1...
(1/n)
Reposted by John Prensner
The reference genome of the human diploid cell line RPE-1. #HumanReferenceGenome #HumanDiploidCellLine @natcomms.nature.com 🧬 🖥️
www.nature.com/articles/s41...
www.nature.com/articles/s41...
September 14, 2025 at 3:00 PM
The reference genome of the human diploid cell line RPE-1. #HumanReferenceGenome #HumanDiploidCellLine @natcomms.nature.com 🧬 🖥️
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Reposted by John Prensner
Excited to share our discovery of potent TRIM21 molecular glues with anticancer activity, online today @CD_AACR: "Defining the antitumor mechanism of action of a clinical-stage compound as a selective degrader of the nuclear pore complex". 1/18
September 2, 2025 at 6:39 PM
Excited to share our discovery of potent TRIM21 molecular glues with anticancer activity, online today @CD_AACR: "Defining the antitumor mechanism of action of a clinical-stage compound as a selective degrader of the nuclear pore complex". 1/18
Reposted by John Prensner
"Honey, wake up. New CUT protocol just dropped" www.biorxiv.org/content/10.1...
CUT&TIME captures the history of open chromatin in developing neurons
Chromatin structure plays a central role in defining cell identity by regulating gene expression. During development, shifts in chromatin structure facilitate changes in gene expression needed to spec...
www.biorxiv.org
September 1, 2025 at 9:19 AM
"Honey, wake up. New CUT protocol just dropped" www.biorxiv.org/content/10.1...
Back to school shopping with kids, and seeing the 90s baggy sign, and remembering that my 90s baggy pants are actually from the 90s, and reflecting on how time passes….
August 30, 2025 at 7:26 PM
Back to school shopping with kids, and seeing the 90s baggy sign, and remembering that my 90s baggy pants are actually from the 90s, and reflecting on how time passes….