Ben Langmead
@benlangmead.bsky.social
Professor of Computer Science @ JHU. https://www.langmead-lab.org/ https://www.youtube.com/BenLangmead
Reposted by Ben Langmead
Reminder that the abstract deadline for the Biology of Genomes meeting at CSHL is on Feb 13! We have a fantastic lineup of keynote speakers (Janet Kelso and Jonathan Pritchard) and session chairs. Submit your best science to this exciting and engaged meeting!
meetings.cshl.edu/meetings.asp...
meetings.cshl.edu/meetings.asp...
The Biology of Genomes
Cold Spring Harbor Laboratory Meetings & Courses -- a private, non-profit institution with research programs in cancer, neuroscience, plant biology, genomics, bioinformatics.
meetings.cshl.edu
February 5, 2026 at 2:24 PM
Reminder that the abstract deadline for the Biology of Genomes meeting at CSHL is on Feb 13! We have a fantastic lineup of keynote speakers (Janet Kelso and Jonathan Pritchard) and session chairs. Submit your best science to this exciting and engaged meeting!
meetings.cshl.edu/meetings.asp...
meetings.cshl.edu/meetings.asp...
Reposted by Ben Langmead
Time for a thread on our Christmas preprint “Origin and evolution of acrocentric chromosomes in human and great apes”. I had so much fun with this project and paper. It will be hard to summarize in a thread, but I’ll try www.biorxiv.org/content/10.6... [1/21]
February 2, 2026 at 2:58 PM
Time for a thread on our Christmas preprint “Origin and evolution of acrocentric chromosomes in human and great apes”. I had so much fun with this project and paper. It will be hard to summarize in a thread, but I’ll try www.biorxiv.org/content/10.6... [1/21]
Reposted by Ben Langmead
New tool from @alexsweeten.bsky.social to find and classify all your satellites: "AniAnn's: alignment-free annotation of tandem repeat arrays using fast average nucleotide identity estimates"
📄 www.biorxiv.org/content/10.6...
📦 github.com/marbl/anianns
📄 www.biorxiv.org/content/10.6...
📦 github.com/marbl/anianns
January 29, 2026 at 1:05 PM
New tool from @alexsweeten.bsky.social to find and classify all your satellites: "AniAnn's: alignment-free annotation of tandem repeat arrays using fast average nucleotide identity estimates"
📄 www.biorxiv.org/content/10.6...
📦 github.com/marbl/anianns
📄 www.biorxiv.org/content/10.6...
📦 github.com/marbl/anianns
Reposted by Ben Langmead
Announcing a new tool for "denoising" long-read amplicon sequences: savont.
Savont enables amplicon sequence variants (ASVs) directly from nanopore (or HiFi) long reads. Tested on 16S nanopore amplicons -- seems to work okay.
1/4
github.com/bluenote-157...
Savont enables amplicon sequence variants (ASVs) directly from nanopore (or HiFi) long reads. Tested on 16S nanopore amplicons -- seems to work okay.
1/4
github.com/bluenote-157...
GitHub - bluenote-1577/savont: Amplicon sequencing variants from 16s ONT R10.4 / HiFi long reads
Amplicon sequencing variants from 16s ONT R10.4 / HiFi long reads - bluenote-1577/savont
github.com
January 28, 2026 at 6:46 PM
Announcing a new tool for "denoising" long-read amplicon sequences: savont.
Savont enables amplicon sequence variants (ASVs) directly from nanopore (or HiFi) long reads. Tested on 16S nanopore amplicons -- seems to work okay.
1/4
github.com/bluenote-157...
Savont enables amplicon sequence variants (ASVs) directly from nanopore (or HiFi) long reads. Tested on 16S nanopore amplicons -- seems to work okay.
1/4
github.com/bluenote-157...
Reposted by Ben Langmead
RFKJr's principal accomplishment as the nation's health guardian.
January 28, 2026 at 4:08 PM
RFKJr's principal accomplishment as the nation's health guardian.
Reposted by Ben Langmead
Congratulations to @hopkinsengineer.bsky.social undergrads Arda Uzunoğlu, Steven Tan, Suyu Ye, and Alvin Zhang on their Honorable Mentions for the Computing Research Association’s 2026 Outstanding Undergraduate Researcher Awards!
2025-26 CRA Outstanding Undergraduate Researcher Award Recipients Announced
By Sheila Khan, Program Associate, CRA-E The Computing Research Association (CRA) congratulates the recipients of the 2025-26 CRA Outstanding Undergraduate Researcher Award. Faculty from institutio…
cra.org
January 27, 2026 at 7:55 PM
Congratulations to @hopkinsengineer.bsky.social undergrads Arda Uzunoğlu, Steven Tan, Suyu Ye, and Alvin Zhang on their Honorable Mentions for the Computing Research Association’s 2026 Outstanding Undergraduate Researcher Awards!
Reposted by Ben Langmead
Reposted by Ben Langmead
A video of Alex Pretti reading out the final salute of an unnamed veteran he cared for until the end of his life in the ICU, posted to Facebook by his son.
January 25, 2026 at 1:18 AM
A video of Alex Pretti reading out the final salute of an unnamed veteran he cared for until the end of his life in the ICU, posted to Facebook by his son.
Reposted by Ben Langmead
We have to see the logic of the killings as well as the killings themselves. The horror is a truth in itself. But it is also a sign of a political logic, one known from the totalitarian regimes of the twentieth century.
snyder.substack.com/p/lies-and-l...
snyder.substack.com/p/lies-and-l...
Lies and Lawlessness
The Camps, the Executions, and the Future
snyder.substack.com
January 25, 2026 at 7:26 PM
We have to see the logic of the killings as well as the killings themselves. The horror is a truth in itself. But it is also a sign of a political logic, one known from the totalitarian regimes of the twentieth century.
snyder.substack.com/p/lies-and-l...
snyder.substack.com/p/lies-and-l...
Reposted by Ben Langmead
RLBWT-Based LCP Computation in Compressed Space for Terabase-Scale Pangenome Analysis https://www.biorxiv.org/content/10.64898/2026.01.23.701410v1
January 25, 2026 at 6:46 PM
RLBWT-Based LCP Computation in Compressed Space for Terabase-Scale Pangenome Analysis https://www.biorxiv.org/content/10.64898/2026.01.23.701410v1
Reposted by Ben Langmead
The killing of Alex Pretti is a heartbreaking tragedy. It should also be a wake-up call to every American, regardless of party, that many of our core values as a nation are increasingly under assault.
January 25, 2026 at 5:39 PM
The killing of Alex Pretti is a heartbreaking tragedy. It should also be a wake-up call to every American, regardless of party, that many of our core values as a nation are increasingly under assault.
Reposted by Ben Langmead
A powerful piece by M. Gessen
I can't do it justice by excerpt
go read it (gift link)
www.nytimes.com/2026/01/24/o...
I can't do it justice by excerpt
go read it (gift link)
www.nytimes.com/2026/01/24/o...
Opinion | State Terror Has Arrived
www.nytimes.com
January 25, 2026 at 8:17 AM
A powerful piece by M. Gessen
I can't do it justice by excerpt
go read it (gift link)
www.nytimes.com/2026/01/24/o...
I can't do it justice by excerpt
go read it (gift link)
www.nytimes.com/2026/01/24/o...
Reposted by Ben Langmead
Reposted by Ben Langmead
“Students and scholars shouldn’t have to live in fear that ICE agents could seize them from their homes merely for engaging in political expression. Today’s judgment makes emphatically clear that the administration’s campaign of intimidation must end.”
—Ramya Krishnan, @knightcolumbia.org
—Ramya Krishnan, @knightcolumbia.org
Judge warns Trump administration from changing plaintiffs immigration status in First Amendment case
A federal judge ruled that the academics, who are party to a lawsuit alleging U.S. policy singles out noncitizens for detention or deportation over their pro-Palestinian activism on college campuses, ...
apnews.com
January 23, 2026 at 5:51 PM
“Students and scholars shouldn’t have to live in fear that ICE agents could seize them from their homes merely for engaging in political expression. Today’s judgment makes emphatically clear that the administration’s campaign of intimidation must end.”
—Ramya Krishnan, @knightcolumbia.org
—Ramya Krishnan, @knightcolumbia.org
Reposted by Ben Langmead
Optimizing sparse and skew hashing: faster k-mer dictionaries https://www.biorxiv.org/content/10.64898/2026.01.21.700884v1
January 22, 2026 at 9:46 PM
Optimizing sparse and skew hashing: faster k-mer dictionaries https://www.biorxiv.org/content/10.64898/2026.01.21.700884v1
Reposted by Ben Langmead
If you / your lab / your institution rely on NIH funding, you need to read this and understand how this is one of many changes affecting you. www.nature.com/articles/d41...
Exclusive: key NIH review panels due to lose all members by the end of 2026
Thirteen of the agency’s advisory councils, which must review grant applications before funding is awarded, are on track to have no voting members.
www.nature.com
January 23, 2026 at 1:44 PM
If you / your lab / your institution rely on NIH funding, you need to read this and understand how this is one of many changes affecting you. www.nature.com/articles/d41...
Reposted by Ben Langmead
Not only was DOGE illegally accessing your Social Security information, but it was also illegally offering to share it with third-party political groups working to overturn elections.
This is a deep betrayal of the public trust and must be fully investigated. www.nytimes.com/2026/01/20/u...
This is a deep betrayal of the public trust and must be fully investigated. www.nytimes.com/2026/01/20/u...
DOGE Employees Shared Social Security Data, Court Filing Shows
www.nytimes.com
January 22, 2026 at 3:11 PM
Not only was DOGE illegally accessing your Social Security information, but it was also illegally offering to share it with third-party political groups working to overturn elections.
This is a deep betrayal of the public trust and must be fully investigated. www.nytimes.com/2026/01/20/u...
This is a deep betrayal of the public trust and must be fully investigated. www.nytimes.com/2026/01/20/u...
Reposted by Ben Langmead
Pregnancy loss is common in humans, and chromosomal abnormalities are the leading cause. Using genetic data from ~140,000 IVF embryos, we show that maternal variation in meiosis genes influences recombination and aneuploidy risk.
First authors: @saracarioscia.bsky.social & @aabiddanda.github.io
First authors: @saracarioscia.bsky.social & @aabiddanda.github.io
Common variation in meiosis genes shapes human recombination and aneuploidy - Nature
Analysis of data from pre-implantation genetic testing sheds light on the genetic basis of meiotic-origin aneuploidy, the leading cause of human pregnancy loss, identifying common genetic variants ass...
www.nature.com
January 21, 2026 at 9:14 PM
Pregnancy loss is common in humans, and chromosomal abnormalities are the leading cause. Using genetic data from ~140,000 IVF embryos, we show that maternal variation in meiosis genes influences recombination and aneuploidy risk.
First authors: @saracarioscia.bsky.social & @aabiddanda.github.io
First authors: @saracarioscia.bsky.social & @aabiddanda.github.io
Reposted by Ben Langmead
What is the contribution made by universities to their research output?
It's complicated to compute, but an estimate by MIT suggests that for every dollar they obtain from the federal government, they co-invest one dollar.
More here: issues.org/federal-rese...
It's complicated to compute, but an estimate by MIT suggests that for every dollar they obtain from the federal government, they co-invest one dollar.
More here: issues.org/federal-rese...
January 21, 2026 at 5:40 PM
What is the contribution made by universities to their research output?
It's complicated to compute, but an estimate by MIT suggests that for every dollar they obtain from the federal government, they co-invest one dollar.
More here: issues.org/federal-rese...
It's complicated to compute, but an estimate by MIT suggests that for every dollar they obtain from the federal government, they co-invest one dollar.
More here: issues.org/federal-rese...
Reposted by Ben Langmead
This is the most astonishing graph of what the Trump regime has done to US science. They have destroyed the federal science workforce across the board. The negative impacts on Americans will be felt for generations, and the US might never be the same again.
www.nature.com/immersive/d4...
www.nature.com/immersive/d4...
January 20, 2026 at 10:53 PM
This is the most astonishing graph of what the Trump regime has done to US science. They have destroyed the federal science workforce across the board. The negative impacts on Americans will be felt for generations, and the US might never be the same again.
www.nature.com/immersive/d4...
www.nature.com/immersive/d4...
Reposted by Ben Langmead
The Carney speech is worth reading in full: globalnews.ca/news/1162087...
Read the full transcript of Carney’s speech to World Economic Forum - National | Globalnews.ca
Prime Minister Mark Carney gave a forceful speech in Davos, Switzerland, on the 'new world order' and how middle powers like Canada can benefit by working together.
globalnews.ca
January 20, 2026 at 8:42 PM
The Carney speech is worth reading in full: globalnews.ca/news/1162087...
Reposted by Ben Langmead
Trump administration concedes DOGE team may have misused Social Security data
Trump administration concedes DOGE team may have misused Social Security data
Some DOGE personnel had more access to data than previously acknowledged, according to a court filing.
dlvr.it
January 20, 2026 at 6:45 PM
Trump administration concedes DOGE team may have misused Social Security data
Reposted by Ben Langmead
Change has never been easy. It takes persistence and determination, and requires all of us to speak out and stand up for what we believe in. As we honor Dr. King today, let’s draw strength from his example, and do our part to build on his legacy.
January 19, 2026 at 2:01 PM
Change has never been easy. It takes persistence and determination, and requires all of us to speak out and stand up for what we believe in. As we honor Dr. King today, let’s draw strength from his example, and do our part to build on his legacy.
Reposted by Ben Langmead
"Darkness cannot drive out darkness; only light can do that. Hate cannot drive out hate, only love can do that." -MLK
As always, Dr. King's message is right on time. Today calls on all of us to hear his wisdom and put it into action.
As always, Dr. King's message is right on time. Today calls on all of us to hear his wisdom and put it into action.
January 19, 2026 at 2:33 PM
"Darkness cannot drive out darkness; only light can do that. Hate cannot drive out hate, only love can do that." -MLK
As always, Dr. King's message is right on time. Today calls on all of us to hear his wisdom and put it into action.
As always, Dr. King's message is right on time. Today calls on all of us to hear his wisdom and put it into action.
Reposted by Ben Langmead
My specific experience is with NIH, but I’ll stand up and say it:
The people who work at NIH are together one of the great wonders of the world. US biomedical science, cancer cures, dementia research all are built on their talent and dedication.
The people who work at NIH are together one of the great wonders of the world. US biomedical science, cancer cures, dementia research all are built on their talent and dedication.
For some reason, very few people these days will stand up and say it, but: the US federal bureaucracy is one of the great wonders of the world, staffed with incredibly diligent people who do their jobs well and care deeply.
Trump's destruction of the federal apparaus was a historic crime.
Trump's destruction of the federal apparaus was a historic crime.
The Purged
Donald Trump’s destruction of the civil service is a tragedy not just for the roughly 300,000 workers who have been discarded, but for an entire nation.
www.theatlantic.com
January 18, 2026 at 7:29 PM
My specific experience is with NIH, but I’ll stand up and say it:
The people who work at NIH are together one of the great wonders of the world. US biomedical science, cancer cures, dementia research all are built on their talent and dedication.
The people who work at NIH are together one of the great wonders of the world. US biomedical science, cancer cures, dementia research all are built on their talent and dedication.