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Ben Langmead

@benlangmead.bsky.social

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

141 Posts3544 Follower246 Folgt
Mao-Jan Lin@maojanlin.bsky.social · 2d ago

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...

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...

biorxiv.org

Sean Carroll@seanmcarroll.bsky.social · last wk.

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.

jamelle@jamellebouie.net · 2w ago

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”

tony romm@tonyromm.bsky.social · 2w ago

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...

tony romm@tonyromm.bsky.social · 2w ago

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...

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.

nytimes.com

Vikram Shivakumar@vikramshivakumar.bsky.social · 3w ago

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

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...

biorxiv.org

Sen. Adam Schiff@schiff.senate.gov · 3w ago

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.

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...

schiff.senate.gov

Mark Peifer (He, him)@peiferlabunc.bsky.social · 4w ago

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

Chris Geidner@chrisgeidner.bsky.social · 4w ago

BREAKING: University professors (AAUP) represented by NAACP LDF and Lambda Legal, with Davis Wright Tremaine, file a federal lawsuit challenging censorship at the Texas Tech University System under the First and Fourteenth Amendments. Complaint: storage.courtlistener.com/recap/gov.us...

IN THE UNITED STATES DISTRICT COURT FOR THE WESTERN DISTRICT OF TEXAS EL PASO DIVISION TEXAS AMERICAN ASSOCIATION OF UNIVERSITY PROFESSORS-AMERICAN FEDERATION OF TEACHERS and the AMERICAN ASSOCIATION OF UNIVERSITY PROFESSORS, Plaintiffs, V. BRANDON CREIGHTON in his official capacity as Chancellor of the Texas Tech University System, and ARCILIA ACOSTA, CODY CAMPBELL, CLAY CASH, TIM CULP, SHELLEY SWEATT, DOUG MCREAKEN, DON SINCLAIR, DUSTIN WOMBLE, and RACHEL MCLELLAND, in their official capacities as members of the Texas Tech University System Board of Regents, Defendants. Case No. 26-1845 COMPLAINT
Sergey Nurk@sergeynurk.bsky.social · 4w ago

Senior Bioinformatics Software Developer opening in my team in ONT's Applications department! Hybrid with a few days a week in our Oxford headquarters. We can sponsor visas! www.linkedin.com/jobs/view/44...

Oxford Nanopore Technologies hiring Senior Bioinformatics Software Engineer, Applications in Oxfordshire, England, United Kingdom | LinkedIn

Posted 3:04:10 PM. Job DescriptionOur goal is to bring the widest benefits to society through enabling the analysis of…See this and similar jobs on LinkedIn.

linkedin.com

Max Kozlov@maxkozlov.bsky.social · last mo.

NIH grants have been under political scrutiny since early 2025. But what does the screening process actually look like? What is being flagged? I spent a month digging into leaked docs and emails. We've published the 235-word list that are being flagged by an internal AI tool. And so much more. 🧵

Inside the new political screening that’s stalling NIH grants

Mandatory reviews by top health officials and checks for 235 disfavoured terms have left hundreds of vetted grant applications in administrative limbo.

nature.com

Ragnar {Groot Koerkamp}@curiouscoding.nl · last mo.

In other news: Great SEA talk by Nathaniel Brown on Orbit, an efficient implementation of the move structure for run-length encoded permutations. Also, congrats on winning a best paper award with this work!

Nathaniel standing in front of his title slide at the start of the presentation.
Ben Langmead@benlangmead.bsky.social · last mo.

Movi 2 has appeared (as an advance article) in Bioinformatics 🧬 Faster, leaner pangenome queries — half the memory of Movi 1, ~30% faster. Paper: academic.oup.com/bioinformati... Code: github.com/mohsenzakeri/Movi (1/6)

Noam Ross@noamross.net · last mo.

Thousands of biomedical studies are stuck in limbo as NIH drags out renewals months after annual budgets expire. Since 2025, the rate of overdue renewals has TRIPLED. This leaves scientists unable to plan, keep staff employed, or maintain long-term research. grant-witness.us/posts/2026-0... #NIH 🧪

Overdue Grant Renewals at NIH and AHRQ – Grant Witness

The government’s delays renewing in-progress research are leaving researchers in limbo.

grant-witness.us

Neil Lewis, Jr.@neillewisjr.bsky.social · last mo.

"Program managers would normally rush to inform potential and current grantees about such dramatic changes. But the memo tells program managers to keep their mouths shut. 'This information is highly confidential...Please do not communicate anything to PIs.'” www.science.org/content/arti...

Exclusive: NSF slashes research programs to support new tech initiative, insiders say

Unexpected shift in funds has meant sharp drop in grants this fiscal year

science.org

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Heng Li@lh3lh3.bsky.social · 2mo ago

Minibwa is a hybrid of bwa-mem and minimap2 and the successor of bwa-mem for short-read mapping. ~4X/2.5X as fast as bwa-mem/bwa-mem2 for WGS reads at comparable accuracy. Native support of directional bisulfite-seq. Applicable to long reads. Preprint at arxiv.org/abs/2606.15357

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Matt Seybold@mattseybold.bsky.social · 2mo ago

The AAUP chapters at Vanderbilt & Wash U have issued a joint statement denouncing the “State of Scholarship” report commissioned by their chancellors. Please, let’s make this as widely read as the gaslighting to which it responds.

Joint Statement on the "State of Scholarship" Report The Vanderbilt University and Washington University chapters of the American Association of University Professors express our profound disagreement with the "State of Scholarship" report commissioned by our universities' chancellors. The report distorts the state of humanistic and social scientific scholarship at our universities and in the academy overall. Worse, it proposes a shocking intrusion of university administration into faculty governance and portends greater threats to academic freedom that should concern all faculty. The report currently appears on Vanderbilt's website under the insignia of both Vanderbilt and Washington Universities. It is already receiving public condemnation. As the American Council of Learned Societies makes clear, the report is founded on false premises and anecdotal evidence and thus does nothing to "ensure deeper and more meaningful relations among scholars and members of the public." No doubt more rebuttals from scholars, departments, and professional societies will follow. It suffices for us to say that the report falls far short of the standards of political neutrality and disinterested inquiry it claims to champion. Historians, literary scholars, and anthropologists are singled out for caricature while the authors fail to acknowledge their own public biases against scholarship performed in the name of social justice. Nor does the report divulge its source of funding or conflicts of interest that may entail - standard practice for any work of humanistic or social scientific scholarship. In sum, the report is itself a clear example of "politicized" research that its authors attempt to decry. What is most alarming is the guidance the report offers to its intended audience of university chancellors and presidents. By falsely arguing that humanities and social science departments are in the throes of an epistemological crisis, the authors lay the groundwork for university adminis…Weakening faculty governance does nothing to solve the real challenges facing our universities, and undermines our ability to effectively address society's most profound problems and challenges, from the inequalities of wealth and white supremacy to the political consequences of climate change. Indeed, the direst threats to public trust in higher education are not philosophical debates about the nature of truth. Currently, the federal government is dramatically cutting funding for the humanities and social sciences as well as for the natural sciences, engineering, medicine, public health, and the arts. In response, university administrations have instituted austerity measures, even as administrative salaries and administrative positions have taken up an increasing share of decreasing budgets. The best way for scholars to cultivate diverse opinions and advance knowledge is by strengthening academic freedom. Political threats to higher education have degraded, and will continue to degrade, the quality of all fields of our universities' research, to the detriment of America's global standing. We note that the organizations now working most actively and successfully to defend academic free inquiry from politicized federal interference are not university leaders but the American Council of Learned Societies, the Modern Language Association, and the American Historical Association - professional societies of the very disciplines chastised by the report. We call on our chancellors to rescind the report and affirm their commitment to the intellectual autonomy of faculty, academic departments, and governing faculty bodies. Administrative interference into academic departments, as licensed by this report, is a violation of the standards of academic freedom that have made American universities the envy of the world. Rather than undermining these bedrock principles, administrators should vigorously and publicly defend them. Vanderbilt University AAUP vanderbiltaaup@gmail.com Wa…