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Ben Langmead

@benlangmead.bsky.social
3.6K followers 247 following 147 posts

Professor of Computer Science @ JHU. www.langmead-lab.org www.youtube.com/BenLangmead

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Ben Langmead @benlangmead.bsky.social · 30/09/2026
Have you been thinking of submitting an abstract to Genome Informatics UK this year? You still have time! The deadline is October 5. We'll see you there. coursesandconferences.wellcomeconnectingscience.org/event/genome...
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Jenna Norton @jenna-m-norton.bsky.social · 29/09/2026
A great overview of how the Trump admin cultivated fear inside NIH to force compliance, even with harmful, unethical & unlawful orders. Also covers origins of the Bethesda Declaration community. From my friend & co-organizer Dr. Wen-Ying Sylvia Chou. www.psychologicalscience.org/publications...
psychologicalscience.org
NIH Employees Lived in A Culture of Fear, So They Started Keeping Receipts
Sylvia Chou, former NIH program director, says “nobody’s OK” after massive disruptions to funding policies and infrastructure.
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Stephanie Hicks @stephaniehicks.bsky.social · 29/09/2026
Excited to share that @jhubiostat.bsky.social is hiring for postdoctoral fellows and tenure-track Assistant Professors! Details below and committees will start reviewing for both on Oct 1! 🎉
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Senator Patty Murray @murray.senate.gov · 26/09/2026
This is theft from the American people, plain and simple. These are funds Congress has delivered on a bipartisan basis and should be helping people—not cut off by a president more focused on building a ballroom than investing in families.
politico.com
Trump declares $1B canceled in ‘pocket rescission’ in another affront to Congress’ funding power
Many lawmakers, including some top Republicans, say the tactic is illegal.
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Rob Patro @robp.bsky.social · 24/09/2026
If you are a US citizen or permanent resident looking for a postdoc, the President's Postdoctoral Fellowship Program is a great opportunity faculty.umd.edu/presidentspo...! If you are eligible, working in computational genomics, and interested in my lab, let me know!
faculty.umd.edu
President's Postdoctoral Fellowship Program | Office of Faculty Affairs
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Jenna Norton @jenna-m-norton.bsky.social · 23/09/2026
As you call members of Congress to raise concern about a Vought-led grant review panel, encourage them to sign onto proposed legislation that could help: 1) Follow the Science Act by @degette.house.gov would remove political appointees from the grant-making process: www.congress.gov/bill/119th-c...
congress.gov
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Gamze Gürsoy @gamzeandgursoy.bsky.social · 22/09/2026
We are looking for a creative and highly independent postdoc excited about synthetic biology, genome engineering, molecular programming, and nucleic-acid technologies to work with us on problems related to genome privacy. www.cam.ac.uk/jobs/postdoc...
cam.ac.uk
Postdoctoral Research Associate in Nucleic Acid Computing and Molecular Engineering (Fixed Term)
We invite applications for a 2-year Postdoctoral Research Associate position in Nucleic Acid Computing and Molecular Programming in the laboratory of Dr Gamze Gursoy at the University of Cambridge. Th...
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Abdul El-Sayed @abdulelsayed.bsky.social · 20/09/2026
This is about one thing and one thing alone. Steering our research dollars for cancer, heart disease, and new infectious diseases to Trump’s political allies and friends.
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Sean Carroll @seanmcarroll.bsky.social · 17/09/2026
Hiring philosophers at Johns Hopkins! philjobs.org/job/show/32109?
philjobs.org
Associate Professor (endowed chair), Johns Hopkins University - PhilJobs:JFP Associate Professor (endowed chair), Johns Hopkins University
An international database of jobs for philosophers
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Niema Moshiri @niema.net · 17/09/2026
My department is hiring an Assistant Professor! Come join us at @ucsandiego.bsky.social Computer Science & Engineering! Beautiful city, awesome colleagues, delicious tacos 😄 apol-recruit.ucsd.edu/JPF04649
apol-recruit.ucsd.edu
Assistant Professor - CSE
University of California, San Diego is hiring. Apply now!
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Heng Li @lh3lh3.bsky.social · 17/09/2026
Single-page, interactive overlap assembler for teaching purposes: lh3.github.io/teach-demo/o... (vibe coded)
lh3.github.io
Overlap Graph Assembly Demo
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Barack Obama @barackobama.bsky.social · 15/09/2026
The right to vote is one of the most fundamental parts of our democracy. Check your voter registration at IWillVote.com and make a plan to vote early or on Election Day on November 3.
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RECOMB Conference Series @recombconf.bsky.social · 15/09/2026
#RECOMB2027 is now accepting submissions and we'd love to see your best work! 📌 Abstract registration: October 28 📌 Full paper submission: November 4 📜More info: recomb.org/recomb2027/c...
recomb.org
Call for Papers
RECOMB 2027
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RECOMB Conference Series @recombconf.bsky.social · 01/09/2026
Save the date! #RECOMB2027 will be in Toronto, Canada 🇨🇦 📅 RECOMB: May 17-20, 2027 📅 Satellite Meetings: May 15-16, 2027
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Aaron Quinlan (he/him) @aaronquinlan.bsky.social · 28/08/2026
I am delighted to announce that The Department of Human Genetics at the University of Utah is continuing a multi-year recruiting initiative for multiple tenure-track faculty positions at the rank of Assistant Professor. Please share and consider applying! utah.peopleadmin.com/postings/208...
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Ben Langmead @benlangmead.bsky.social · 27/08/2026
Sad to see, but good for Canada; those are smart folks making smart investments. Does this sound like a good trend, US industry folks? If not, make noise. The avg person (e.g. me) perceives industry as OK with what's happening to publicly funded science & academics www.nytimes.com/2026/08/27/w...
nytimes.com
Canada Hires U.S. Scholars From Harvard and Other Top Universities (Gift Article)
A crackdown on American academia by the Trump administration has handed Canadian universities a rare opportunity to lure some top researchers north.
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Richard Sever @richardsever.bsky.social · 27/08/2026
$3.7 billion spent on APCs in 2025. That's ~1000X more than it costs to run bioRxiv/medRxiv. Worth thinking about as we consider how to fund infrastructure... arxiv.org/pdf/2608.16322
arxiv.org
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Human Pangenome Reference Consortium @humanpangenome.bsky.social · 26/08/2026
Pangenome coordinates can be complex... Shredtools offers a new approach using exact matches to query pangenome data efficiently. Its tools can extract syntenic regions across hundreds of genomes, making pangenome-scale exploration more accessible. pubmed.ncbi.nlm.nih.gov/42465356/
pubmed.ncbi.nlm.nih.gov
Navigating the pangenome coordinate system with Shredtools - PubMed
Existing notions of pangenome coordinates rely on hard-to-compute multiple sequence alignments. On the other hand, pangenome-wide exact unique matches (multi-MUMs) can be computed efficiently, and represent conserved stretches of columns in the underlying MSA. We introduce Shredtools, which uses mul …
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Claudio Paganini @thehappyproton.bsky.social · 26/08/2026
The real brain drain in the US academic institutions isn't the superstar scientists who leave, it is the students who never come.
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Adam Phillippy @aphillippy.bsky.social · 24/08/2026
On our last day, the lab ran a pop-up coffee shop for our NHGRI colleagues, staffed by our own highly experienced baristas Suhani and Serge. Farewell NIH! Thanks for being a great home for the past 11 years 🥲 Watch for our next pop-up at Hopkins once we get properly equipped 😁
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Mark Copelovitch @mcopelov.bsky.social · 20/08/2026
Requisite Tony Judt quote about the single greatest institutional achievement in 250 years of the Republic:
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Sean Carroll @seanmcarroll.bsky.social · 20/08/2026
Strangling science.
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BF Francis Ouellette @bffo.bsky.social · 19/08/2026
From #NCBI Insight | NCBI Taxonomy Has a New Home | #OpenScience #OpenData #Bioinfornatics #Genomics #Proteomics #Taxonomy #TaxID #Taxon | 🧬🖥️🧪🔓 ⬇️ ncbiinsights.ncbi.nlm.nih.gov/2026/08/19/n...
ncbiinsights.ncbi.nlm.nih.gov
NCBI Taxonomy Has a New Home - NCBI Insights
We are excited to introduce the new NCBI Taxonomy, with updated tools and resources to improve how you browse taxonomic information and access NCBI data, including sequences, genomes, and other resour...
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Needhi Bhalla 💅🏽 @needhibhalla.bsky.social · 18/08/2026
I just completed my standing study section service in June (2022-2026) and want to emphasize Bryan's point: maintaining the integrity of the peer review process is an important act of service for our colleagues, especially right now. If you are asked and can swing it, please consider serving.
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Shawn Burgess @burgesslab.bsky.social · 13/08/2026
NHGRI is recruiting genomics oriented researchers through the Stadtman mechanism. It is also open to any kind of research, the goal is to match your interests to an institute. The applications are now open until Oct. 1st. Details below:
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Governor Gavin Newsom @governor.ca.gov · 13/08/2026
In just one step, Californians can tell 600+ registered data brokers to delete and no longer sell their online data. Create a profile and make a deletion request through the Delete Request and Opt-Out Platform now ➡️ consumer.drop.privacy.ca.gov
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Ben Langmead @benlangmead.bsky.social · 12/08/2026
Enjoy the eclipse, friends in Iceland, Greenland, Spain and Portugal! I hope for no clouds. Here's a pic from the one we could see in the US in April 2024.
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Randi Weingarten 🖇️📚✊🇺🇸 @rweingarten.bsky.social · 11/08/2026
We're suing to stop the admin. from de-professionalizing nursing, architecture, social work, teaching and other careers. Trump's tax bill for the rich eviscerated education access for poor and working-class students who deserve the opportunity to pursue their dreams, too. www.aft.org/press-releas...
aft.org
‘We Are Professionals’: Coalition of Unions Sue to Block New Student Loan Rule that Will Hurt Patient Care and Worsen Staffing Crises
WASHINGTON—A coalition of unions representing hundreds of thousands of public service and healthcare workers filed a lawsuit this week challenging the Department of Education’s new Reimagining and Imp...
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Robert Aboukhalil @robert.bio · 10/08/2026
You can now turn your GitHub repos into sandbox.bio tutorials! You get a shareable URL, where code blocks are runnable, and files are preloaded in the terminal. For example, @benlangmead.bsky.social used this in a recent kraken2 workshop. You can see it in action here: sandbox.bio/training/git...
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Ran Blekhman @blekhman.bsky.social · 09/08/2026
Huge faculty recruitment effort at the University of Chicago -- a division-wide, open-rank search looking to hire about 20 faculty across 5 research areas in biology. Come be our colleague! Full announcement: uchicago.app.box.com/s/ckih9zv3rj...
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Robert Aboukhalil @robert.bio · 06/08/2026
I can't believe it's already been 5 years since I first released sandbox.bio! 🥳 To celebrate, next week we'll release one new feature every day of the week. Follow along at sandbox.bio/anniversary, or here on BlueSky.
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Adam Phillippy @aphillippy.bsky.social · 06/08/2026
For the past 30 years, “whole-genome sequencing” has been a misnomer. Today the T2T Consortium publishes a dozen papers heralding a future of truly complete genomes for humans and nearly any vertebrate 👨‍🔬🐒🐦🐀🦒🐎🫏🐹🐟 (sorry, no salamanders): www.cell.com/consortium/t... 🧵[1/15]
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Sean Carroll @seanmcarroll.bsky.social · 04/08/2026
Our descent into mean-spirited, selfish barbarism continues.
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Mao-Jan Lin @maojanlin.bsky.social · 03/08/2026
1/ Excited to share our preprint ImpuT2T: a pangenome-based assembly patching tool ImpuT2T scaffolds draft human assemblies with a pangenome (HPRC2) and patches gaps by leveraging linkage disequilibrium and sequence identity between contigs and reference haplotypes Code: github.com/maojanlin/Im...
biorxiv.org
ImpuT2T: Pangenome-Based Patching for Human Genome Assemblies
With improvements in sequencing and assembly have come many high-quality telomere-to-telomere assemblies and reference pangenomes. However, the long-read sequencing recipes needed for high quality ass...
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Sean Carroll @seanmcarroll.bsky.social · 29/07/2026
The Fauci show trial is an amazing illustration of the fundamental immaturity and insecurity of the modern right. What really outrages them is that he dared to suggest that people make sacrifices for the common good. So much of X/techbro/manosphere thought is just insisting that should never happen.
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Mike Rothschild @rothschildmd.bsky.social · 29/07/2026
This Fauci hearing is the biggest explosion of right wing brainworms I've ever seen. Years of debunked and absurd antivax and "gain of function" conspiracy theories expressed as incoherent screaming at an 85 year old man. It's absolutely demented and embarrassing to watch.
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bioRxiv Bioinfo @biorxiv-bioinfo.bsky.social · 29/07/2026
ImpuT2T: Pangenome-Based Patching for Human Genome Assemblies www.biorxiv.org/content/10.64898/20…
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Ben Langmead @benlangmead.bsky.social · 29/07/2026
📢 Genome Informatics 2026 (Hinxton UK + virtual, 2–4 Dec) is coming! Some confirmed speakers now listed: coursesandconferences.wellcomeconnectingscience.org/event/genome... Early-bird registration & bursary deadlines: 7 Sept. Abstract deadline: 5 Oct. Please submit your work & join us!
Wellcome Genome Campus aerial shot
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jamelle @jamellebouie.net · 24/07/2026
interesting to me that as the administration treats democratic-voting states like conquered or occupied territories, you don’t have pundits demanding the president respect “half the country”
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tony romm @tonyromm.bsky.social · 24/07/2026
NEW: In a stunning admission, the Trump administration admitted in court documents that it canceled billions in energy grants to states "based solely" on politics -- and whether that state was represented by Democrats and backed Harris in 2024. www.nytimes.com/2026/07/24/b...
nytimes.com
Trump Administration Admits Canceling Grants to States That Did Not Vote for Him
Federal officials said in court documents that they halted billions of dollars in funding for energy projects to states “based solely” on whether they backed President Trump in the 2024 election.
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Mike Schatz @mikeschatz.bsky.social · 22/07/2026
Application portal is open for travel and registration scholarships from the @jxtxfoundation.bsky.social to the CSHL Biological Data Science conference. Applications are due by Aug 5 #cshldata26 #methodsmatter Apply here: jxtxfoundation.org/news/2026-06... Learn more: bit.ly/cshl-biodata26
jxtxfoundation.org
JXTX + CSHL 2026 Biological Data Science Scholarship
JXTX + CSHL 2026 Biological Data Science Scholarship
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bioRxiv Genomics @biorxiv-genomic.bsky.social · 22/07/2026
HPRC2: A human pangenome reference with near-complete coverage of common genetic variation www.biorxiv.org/content/10.64898/20…
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Bioinformatics Open Source Conference (BOSC) @bosc.bsky.social · 15/07/2026
Eric Green's #BOSC2026 keynote was a fascinating tour of the past, present and future of #Genomics and #GenomicMedicine. #ISMB
Eric Green
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Vikram Shivakumar @vikramshivakumar.bsky.social · 15/07/2026
1/ Excited to share the newest tool in the pangenome MUMiverse: Shredtools! Shredtools enables a user to navigate the pangenome coordinate system with multi-MUMs. More in the thread🧵 Code: github.com/vikshiv/shredtools Interactive tool for querying HPRC assemblies: vikshiv.github.io/shredtools
biorxiv.org
Navigating the pangenome coordinate system with Shredtools
Existing notions of pangenome coordinates rely on hard-to-compute multiple sequence alignments. On the other hand, pangenome-wide exact unique matches (multi-MUMs) can be computed efficiently, and rep...
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Martin Steinegger 🇺🇦 @martinsteinegger.bsky.social · 13/07/2026
Richard Durbin starts the #ISMB2026 with his keynote about BWT for genomic search. A walk-through from BWA to his most recent work on pan-genomes GBWT. www.biorxiv.org/content/10.6.... Congratulations on the accomplishments by a Senior Scientist Award.
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Sen. Adam Schiff @schiff.senate.gov · 12/07/2026
CA leads the nation in scientific advancements & cutting-edge research. White House Office of Management and Budget new proposed rule puts all this in jeopardy & makes way for politically motivated decisions that serve the President over science.   They must rescind this rule immediately.
schiff.senate.gov
NEWS: As California Leads Nation in Scientific Advancements, Schiff, Lofgren, 42 Colleagues Urge OMB to Rescind Politicized Rule on Federal Grants
Washington, D.C. — U.S. Senators Adam Schiff (D-Calif.), U.S. Representative Zoe Lofgren (D-Calif.-18), and 42 members of the California congressional delegation are demanding the Office of Management...
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Ben Langmead @benlangmead.bsky.social · 12/07/2026
Very happy to be presenting "Taxonomic classification using Kraken 2" in today's #ISMB2026 tutorial "Metagenomic sequence analysis using k-mer based methods": www.iscb.org/ismb2026/wha... In about 15 minutes!
iscb.org
Tutorials - ISMB 2026
ISCB - International Society for Computational Biology
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bioRxiv Bioinfo @biorxiv-bioinfo.bsky.social · 09/07/2026
Navigating the pangenome coordinate system with Shredtools www.biorxiv.org/content/10.64898/20…
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Sina Majidian @sinamajidian.bsky.social · 09/07/2026
JOB ALERT! I'm hiring two postdocs in Computational Genomics to join our lab in beautiful Gothenburg, Sweden. Please share and repost! CGRLab.github.io/research/
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Mark Peifer (He, him) @peiferlabunc.bsky.social · 08/07/2026
If you are a faculty member and worried about the fact no one seems to be fighting back against the attacks on academic freedom, it might be time to join @aaup.org
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