Charles Vaske
@seavaske.com
Genomics, bioinformatics, diagnostics, cancer, housing, and transit. Слава Україні https://orcid.org/0000-0001-8151-6612
Reposted by Charles Vaske
PangyPlot: a new #bioinformatics tools for visualizing pangenomes that supports linear coordinates and large graphs. Applied to @pacbio.bsky.social HiFi genomes to visualize two cystic fibrosis-relevant region not possible to resolve with short read genomes. www.biorxiv.org/content/10.1...
November 10, 2025 at 6:33 PM
PangyPlot: a new #bioinformatics tools for visualizing pangenomes that supports linear coordinates and large graphs. Applied to @pacbio.bsky.social HiFi genomes to visualize two cystic fibrosis-relevant region not possible to resolve with short read genomes. www.biorxiv.org/content/10.1...
Reposted by Charles Vaske
Angelina Jolie used her Instagram platform to shed light on Russia’s so-called ‘human safari’ in Kherson. It is a deeply important and much-appreciated gesture.
November 9, 2025 at 12:51 PM
Angelina Jolie used her Instagram platform to shed light on Russia’s so-called ‘human safari’ in Kherson. It is a deeply important and much-appreciated gesture.
Reposted by Charles Vaske
When people celebrate the individual genius of folks in science, they should also
mourn the collective loss of genius of folks who were actively discouraged or disadvantaged from a career in science because of the same person(s)
mourn the collective loss of genius of folks who were actively discouraged or disadvantaged from a career in science because of the same person(s)
November 7, 2025 at 11:43 PM
When people celebrate the individual genius of folks in science, they should also
mourn the collective loss of genius of folks who were actively discouraged or disadvantaged from a career in science because of the same person(s)
mourn the collective loss of genius of folks who were actively discouraged or disadvantaged from a career in science because of the same person(s)
Reposted by Charles Vaske
@stevenxge, not on Bluesky, on the new feature in iDEP: bioinformatics.sdstate.edu/idep/
New in iDEP: label your k-means clusters with enriched pathways—just a few clicks. Try it on your RNA-seq data today:
New in iDEP: label your k-means clusters with enriched pathways—just a few clicks. Try it on your RNA-seq data today:
November 6, 2025 at 9:09 AM
@stevenxge, not on Bluesky, on the new feature in iDEP: bioinformatics.sdstate.edu/idep/
New in iDEP: label your k-means clusters with enriched pathways—just a few clicks. Try it on your RNA-seq data today:
New in iDEP: label your k-means clusters with enriched pathways—just a few clicks. Try it on your RNA-seq data today:
Reposted by Charles Vaske
@brielin.bsky.social's fantastic work on causal gene network inference from Perturb-seq is published! We estimate total causal effects using guides as instruments, then deconvolve into direct & mediated effects with a directed analog of graphical lasso. Deets: nature.com/articles/s41467-025-64353-7
Large-scale causal discovery using interventional data sheds light on gene network structure in k562 cells - Nature Communications
The authors give a method for learning causal gene networks using Perturb-seq data. In K562 cells, they find a network with small-world and scale-free properties. Analysis shows a relationship between...
nature.com
November 3, 2025 at 7:09 PM
@brielin.bsky.social's fantastic work on causal gene network inference from Perturb-seq is published! We estimate total causal effects using guides as instruments, then deconvolve into direct & mediated effects with a directed analog of graphical lasso. Deets: nature.com/articles/s41467-025-64353-7
Reposted by Charles Vaske
🟣 November means Pancreas Cancer Awareness! 🟣
Via Pancan.org Research Roundtable Webinar: Advancements in Earlier Detection of Pancreatic Cancer.
20 November 11 am PT / 2 pm ET. Register here ⬇️
pancan.org/facing-pancr...
Via Pancan.org Research Roundtable Webinar: Advancements in Earlier Detection of Pancreatic Cancer.
20 November 11 am PT / 2 pm ET. Register here ⬇️
pancan.org/facing-pancr...
Research Roundtable: Advancements in Earlier Detection of Pancreatic Cancer - Thursday, 11/20
Join PanCAN on World Pancreatic Cancer Day, November 20, at 11 a.m. PT / 2 p.m. ET, for a free webinar featuring top scientists and leaders in the field talking about the latest advances in testing an...
pancan.org
November 3, 2025 at 4:18 PM
🟣 November means Pancreas Cancer Awareness! 🟣
Via Pancan.org Research Roundtable Webinar: Advancements in Earlier Detection of Pancreatic Cancer.
20 November 11 am PT / 2 pm ET. Register here ⬇️
pancan.org/facing-pancr...
Via Pancan.org Research Roundtable Webinar: Advancements in Earlier Detection of Pancreatic Cancer.
20 November 11 am PT / 2 pm ET. Register here ⬇️
pancan.org/facing-pancr...
Reposted by Charles Vaske
What's happening in the United States right now is like how Germany's universities began to empty out as the Nazis were consolidating power. Except this time, there is no United States for those scholars to flee to.
A poll from the journal Nature found that 75% of researchers in the U.S. are considering leaving the country. That includes a man who’s been dubbed the "Mozart of Math." (This PBS story on the scientific brain drain is heartbreaking & ominous for medicine, imo.) www.youtube.com/watch?v=yLvO...
Top researchers consider leaving U.S. amid funding cuts: 'The science world is ending'
YouTube video by PBS NewsHour
www.youtube.com
October 31, 2025 at 4:09 AM
What's happening in the United States right now is like how Germany's universities began to empty out as the Nazis were consolidating power. Except this time, there is no United States for those scholars to flee to.
Reposted by Charles Vaske
End qualified immunity.
"According to his running club, the man, who is a U.S. citizen, was returning from a team run when agents pulled him out of his vehicle, tackled him to the ground and kneeled on top of him, allegedly breaking six ribs and causing internal bleeding"
US citizen, 67, ‘has six ribs broken’ by Border Patrol agents, his running club says
The incident unfolded Saturday in Chicago’s Old Irving Park neighborhood, where residents say federal agents disrupted a children’s Halloween parade
www.independent.co.uk
October 29, 2025 at 1:54 AM
End qualified immunity.
Reposted by Charles Vaske
Two back-to-back stories on mitosis led by my incredible postdoc @krunovuk.bsky.social at @institutrb.bsky.social, in which we challenge the gliding model of CENP-E-driven chromosome congression! Today in @natcomms.nature.com
doi.org/10.1038/s414...
doi.org/10.1038/s414...
doi.org/10.1038/s414...
doi.org/10.1038/s414...
October 21, 2025 at 11:14 AM
Two back-to-back stories on mitosis led by my incredible postdoc @krunovuk.bsky.social at @institutrb.bsky.social, in which we challenge the gliding model of CENP-E-driven chromosome congression! Today in @natcomms.nature.com
doi.org/10.1038/s414...
doi.org/10.1038/s414...
doi.org/10.1038/s414...
doi.org/10.1038/s414...
Reposted by Charles Vaske
So many gene clusters and operons chock full of hypothetical proteins. So much of our world is deeply unknown. Any feature in this window that starts with an "HFM" is likely unknown. This is just a glimpse into one fragment of a random microbe that grew in my soap. #TritonTrue
October 23, 2025 at 6:35 PM
So many gene clusters and operons chock full of hypothetical proteins. So much of our world is deeply unknown. Any feature in this window that starts with an "HFM" is likely unknown. This is just a glimpse into one fragment of a random microbe that grew in my soap. #TritonTrue
Reposted by Charles Vaske
More than 420 anti-science bills attacking longstanding public health protections – vaccines, milk safety and fluoride – have been introduced in statehouses across the U.S. this year, part of an organized, politically savvy campaign to enshrine a conspiracy theory-driven agenda into law.
Anti-science bills hit statehouses, attacking longstanding public health protections
More than 420 anti-science bills attacking longstanding public health protections – vaccines, milk safety and fluoride – have been introduced in statehouses across the U.S. this year.
www.pbs.org
October 22, 2025 at 6:10 PM
More than 420 anti-science bills attacking longstanding public health protections – vaccines, milk safety and fluoride – have been introduced in statehouses across the U.S. this year, part of an organized, politically savvy campaign to enshrine a conspiracy theory-driven agenda into law.
Reposted by Charles Vaske
1/6 Movi 2 is here: faster and more space-efficient for pangenome queries. Its fastest mode uses half the memory of Movi 1 while running ~30% faster. github.com/mohsenzakeri...
GitHub - mohsenzakeri/Movi: Fast, Cache-Efficient, and Scalable Queries on Pangenomes
Fast, Cache-Efficient, and Scalable Queries on Pangenomes - mohsenzakeri/Movi
github.com
October 21, 2025 at 8:00 PM
1/6 Movi 2 is here: faster and more space-efficient for pangenome queries. Its fastest mode uses half the memory of Movi 1 while running ~30% faster. github.com/mohsenzakeri...
Jenny Chase is a legendary analyst of solar power, not least for pointing out how projections are always too low. So these projections are very funny for falling into the same trap, a sharp shoulder that is completely unjustified, and has no evidence. Much more solar than this will be installed.
42. Annual build volumes of solar are rising, but they are not guaranteed to rise forever. This is a symptom of solar starting to actually make a dent in power demand, with negative feedback effects such as power price cannibalization.
October 21, 2025 at 4:19 PM
Jenny Chase is a legendary analyst of solar power, not least for pointing out how projections are always too low. So these projections are very funny for falling into the same trap, a sharp shoulder that is completely unjustified, and has no evidence. Much more solar than this will be installed.
Reposted by Charles Vaske
She acknowledged Filipp was Ukrainian, loved his country, and didn’t want to go to Russia. She broke him, re-educated him, and made him Russian.
While Moscow denies forcibly removing children, one of Putin’s own officials has publicly confirmed that’s exactly what Russia is doing.
While Moscow denies forcibly removing children, one of Putin’s own officials has publicly confirmed that’s exactly what Russia is doing.
October 21, 2025 at 2:18 PM
She acknowledged Filipp was Ukrainian, loved his country, and didn’t want to go to Russia. She broke him, re-educated him, and made him Russian.
While Moscow denies forcibly removing children, one of Putin’s own officials has publicly confirmed that’s exactly what Russia is doing.
While Moscow denies forcibly removing children, one of Putin’s own officials has publicly confirmed that’s exactly what Russia is doing.
Reposted by Charles Vaske
It's just unbelievable how easy it is for propaganda to manipulate people. Take a capitulation demand, call it a "peace deal" and watch idiots around the world pressure victim of the aggression to "take the deal." 😐
October 20, 2025 at 2:12 PM
It's just unbelievable how easy it is for propaganda to manipulate people. Take a capitulation demand, call it a "peace deal" and watch idiots around the world pressure victim of the aggression to "take the deal." 😐
Reposted by Charles Vaske
2. Our new analysis suggests that protest events in 2025 have occurred across a wider range of US counties than we observed during Trump's first term. And the current protest movement has already reached deeper into Trump country than at almost any point during the first Trump administration.
October 16, 2025 at 8:11 PM
2. Our new analysis suggests that protest events in 2025 have occurred across a wider range of US counties than we observed during Trump's first term. And the current protest movement has already reached deeper into Trump country than at almost any point during the first Trump administration.
Reposted by Charles Vaske
Forensic genetics in the omics era. #ForensicGenetics @natrevgenet.nature.com
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Forensic genetics in the omics era - Nature Reviews Genetics
Recent advances in forensic genetics have improved the range, precision and reliability of forensic information obtainable from biological trace material. The author reviews how non-targeted and…
www.nature.com
October 17, 2025 at 4:32 PM
Forensic genetics in the omics era. #ForensicGenetics @natrevgenet.nature.com
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Reposted by Charles Vaske
Now: Erica Vaccari: Reimbursement of germline genetic testing for cancer is impacted by socioeconomic characteristics and insurer type #ASHG25 🧪🧬🖥️
October 16, 2025 at 9:37 PM
Now: Erica Vaccari: Reimbursement of germline genetic testing for cancer is impacted by socioeconomic characteristics and insurer type #ASHG25 🧪🧬🖥️
Reposted by Charles Vaske
Anyways, this passed! In a purple city in a county that Trump won in 2024, they will enforce laws requiring ICE agents to unmask.
October 16, 2025 at 1:27 AM
Anyways, this passed! In a purple city in a county that Trump won in 2024, they will enforce laws requiring ICE agents to unmask.
Reposted by Charles Vaske
"In cancer many of the underlying modifications are large structural variants (SVs), (translocations, inversion, duplications, and deletions) that standard short-read sequencing often misses or cannot mechanistically interpret".
www.the-scientist.com/emerging-3d-...
www.the-scientist.com/emerging-3d-...
Emerging 3D DNA Structure Technology Powers Genomic Discovery
Mathew Easterday from Dovetail Genomics highlights how combined sequence and structure analysis reveals genome architecture’s role in disease.
www.the-scientist.com
October 14, 2025 at 12:39 PM
"In cancer many of the underlying modifications are large structural variants (SVs), (translocations, inversion, duplications, and deletions) that standard short-read sequencing often misses or cannot mechanistically interpret".
www.the-scientist.com/emerging-3d-...
www.the-scientist.com/emerging-3d-...
Fantastic short video explaining RNA velocity
What is RNA velocity in situ? ChatGPT kept getting it wrong...
So I made this video explaining how RNA velocity in situ infers gene expression dynamics by distinguishing nuclear vs. cytoplasmic expression in spatial transcriptomics data: youtu.be/z9Oxf1hvum0
#AcademicSky
So I made this video explaining how RNA velocity in situ infers gene expression dynamics by distinguishing nuclear vs. cytoplasmic expression in spatial transcriptomics data: youtu.be/z9Oxf1hvum0
#AcademicSky
RNA velocity in situ infers gene expression dynamics using spatial transcriptomics data
YouTube video by Prof. Jean Fan
youtu.be
October 13, 2025 at 7:18 PM
Fantastic short video explaining RNA velocity
Reposted by Charles Vaske
The novel Three Body Problem (spoiler alert) is about an alien civilization that tries to destroy scientific advancement on Earth so they could take over. Just saying.
BREAKING: Friday night massacre underway at CDC. Doznes of "disease detectives," high-level scientists, entire Washington staff and editors of the MMWR (Morbidity and Mortality Weekly Report) have all been RIFed and received the following notice:
October 11, 2025 at 4:22 PM
The novel Three Body Problem (spoiler alert) is about an alien civilization that tries to destroy scientific advancement on Earth so they could take over. Just saying.
Reposted by Charles Vaske
Reposted by Charles Vaske
So much of doing science is just “We couldn’t get X to work. We don’t know if we did something wrong or if there is something in the methods that we don’t know about.”
September 26, 2025 at 8:08 PM
So much of doing science is just “We couldn’t get X to work. We don’t know if we did something wrong or if there is something in the methods that we don’t know about.”
Reposted by Charles Vaske
‘Completely shattered.’ Changes to NSF’s graduate student fellowship spur outcry | Science | AAAS www.science.org/content/arti...
‘Completely shattered.’ Changes to NSF’s graduate student fellowship spur outcry
The announcement comes months later than usual, leaving many would-be applicants stranded
www.science.org
September 26, 2025 at 11:16 PM
‘Completely shattered.’ Changes to NSF’s graduate student fellowship spur outcry | Science | AAAS www.science.org/content/arti...