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benlangmead.bsky.social
Ben Langmead
@benlangmead.bsky.social
3.4K followers 240 following 98 posts
Professor of Computer Science @ JHU. https://www.langmead-lab.org/ https://www.youtube.com/BenLangmead
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Reposted by Ben Langmead
stephaniehicks.bsky.social
Very excited to share that Department of Biomedical Engineering @hopkinsengineer.bsky.social is hiring for open rank tenure-track faculty in #Biomedical #DataScience!

🔗 apply.interfolio.com/177042
Apps starting to be reviewed Dec 5 and ongoing after!

🧪🧬🖥️🧠 #StatsSky #WomenInSTEM
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November 6, 2025 at 6:20 AM
Reposted by Ben Langmead
ence.bsky.social
We spent a year investigating billionaires for @washingtonpost.com.

We found: the wealthiest 100 Americans gave $1.1 billion to influence the 2024 elections — 140x more than they did in 2000. And almost all of that giving boosted Republicans.

washingtonpost.com/politics/int...
November 21, 2025 at 2:56 PM
Reposted by Ben Langmead
sinamajidian.bsky.social
Our trilogy of orthology publications is online!
Review on Hierarchical Orthologous Groups doi.org/10.1007/s00239-025-10277-1

OrthoXML-Tools doi.org/10.1007/s00239-025-10271-7

A great community effort on Quest for Orthologs in the era of Data Deluge and AI doi.org/10.1007/s00239-025-10272-6
https://link.springer.com/article/10.1007/s00239-025-10277-1 Conceptual overview of hierarchical orthologous groups. An example of one HOG, or gene family. A Species tree with four taxa: plant (green), fish (blue), human (orange), and mouse (yellow), each with one or more genes. B The implied gene tree, dubbed “HOG tree,” and inferred nested HOG composition. Duplication nodes (red) can be deduced based on the species tree topology and clusters of homologous genes at each level. Ancestral genes from which the HOGs descended are shown in gray. C HOGs returned at different taxonomic levels. Consider a gene family that was present in the last eukaryotic common ancestor (LECA). At this level, a single HOG encompasses all genes descending from that ancestral gene. At the Vertebrata level, this gene underwent duplication, leading to two distinct copies, i.e., HOGs. At the Mammalia level, a second duplication further subdivides one of these HOGs, showing how deeper HOGs split into nested subHOGs at more recent levels. The HOG composition implies that a loss event occurred after the mammalian speciation https://link.springer.com/article/10.1007/s00239-025-10272-6 Summary of the QfO8 meeting. a Hot topics and future directions in method development and applications within the QfO community, namely artificial intelligence, protein domains, protein structure, RNA and splicing isoforms. b Definition of orthology and paralogy, including various paralogous subtypes (e.g. in-paralogs and out-paralogs). c Duplications and functional divergence. d Applications of orthology https://link.springer.com/article/10.1007/s00239-025-10271-7 Overview of the OrthoXML File Format (simplified). A schematic representation of an OrthoXML file, a standardized XML-based format for representing orthology data. OrthoXML follows a hierarchical structure where elements are enclosed within opening < tag > and closing </tag > tags. < orthoXML > is the root element enclosing other elements. The < species > element contains information about genes. An OrthoXML file can include a < taxonomy > element, which specifies the species tree used to generate the file. Additionally, the < groups > element encapsulates the orthology and paralogy relationships among genes
November 21, 2025 at 4:26 PM
Reposted by Ben Langmead
iscb.bsky.social
Connect with the UK’s #bioinformatics and #computationalbiology community at #ISCBUK 2026. Share your latest research, build new collaborations, and be part of this inaugural meeting.

Submissions are open until February 5, 2026.

📥 Submit: https://www.iscb.org/uk2026/call-for-submissions/abstracts
November 19, 2025 at 11:16 AM
Reposted by Ben Langmead
davidaknowles.bsky.social
I'm a longtime fan of Affinity Designer as an affordable Illustrator-killer for figures, and... it's now free?! www.canva.com/newsroom/new...
Highly recommended if you're sick of paying Adobe $. Maybe Canva can buy NPG too and get rid of the OA fees.
Why we made Affinity free, and how we’ll keep it that way
We’ve made Affinity completely free, empowering professional designers with studio-grade creative software, supported by Canva’s sustainable ecosystem.
www.canva.com
November 18, 2025 at 11:28 PM
Reposted by Ben Langmead
jxtxfoundation.bsky.social
The James P. Taylor Foundation for Open Science is pleased to announce the recipients of the 2025 JXTX+CSHL Genome Informatics Scholarships. JXTX provides support for students to attend conferences in CompBio and data science, where they can present their work [1/8]
November 6, 2025 at 3:27 PM
Reposted by Ben Langmead
joefore.bsky.social
Former UVA president Jim Ryan, who resigned over the summer due to pressure from the Trump Administration, just shared this 12-page letter with the Faculty Senate, detailing his experience with the Board of Visitors and DOJ.

It's a surreal--and troubling--read.

drive.google.com/file/d/1Is6x...
November 14, 2025 at 2:15 PM
Reposted by Ben Langmead
markhisted.org
A bad thing is unfolding at NIH this week: It looks like the Trump administration is trying to replace key civil servant scientific leaders, the Institute Directors, with political hires. These directors control the NIH budget, tens of billions.

A bit of a video explainer here: 1/ 🧪
November 13, 2025 at 10:31 PM
Reposted by Ben Langmead
aphillippy.bsky.social
‼️ There are an unprecedented number of Institute Director vacancies at the NIH and many of the application windows close this week or next, including ones that are essential to genomics research in the US including NHGRI, NLM/NCBI, and NIGMS. Please spread the word: hr.nih.gov/careers/open...
hr.nih.gov
November 10, 2025 at 4:08 PM
Reposted by Ben Langmead
vikramshivakumar.bsky.social
Really excited to see our new work in scaling Mumemto to any size pangenome published in Genome Research this morning. And right on cue with the great opportunity to present this work at #GI2025 this week.
genomeresearch.bsky.social Genome Research @genomeresearch.bsky.social · 15d
#GI2025 Vikram Shivakumar from Ben Langmead's lab (@benlangmead.bsky.social) presents "MumemtoM - partitioned Multi-MUM finding for scalable pangenomics ". Now published in Genome Research @genomeresearch.bsky.social. Read full text here ➡️ tinyurl.com/Genome-Res-2...
November 7, 2025 at 9:29 PM
Reposted by Ben Langmead
genomeresearch.bsky.social
#GI2025 Vikram Shivakumar from Ben Langmead's lab (@benlangmead.bsky.social) presents "MumemtoM - partitioned Multi-MUM finding for scalable pangenomics ". Now published in Genome Research @genomeresearch.bsky.social. Read full text here ➡️ tinyurl.com/Genome-Res-2...
November 7, 2025 at 3:08 PM
Reposted by Ben Langmead
sinamajidian.bsky.social
Fantastic talk by @vikramshivakumar.bsky.social Mumemto—Scalable multi-MUM finding for pangenomes
Papers biorxiv.org/content/10.1101/2025.05.20.654611 & doi.org/10.1186/s13059-025-03644-0
Code: github.com/vikshiv/mume...
Very efficient pangenome visualization tool, revealing synteny and variations!
Figure 1: (A) Anchor-based merging requires a common sequence (red) present in each partition. Multi-MUMs are merged by identifying overlaps between partition-specific matches in the anchor coordinate space, and a uniqueness threshold determines if a MUM is still unique in each partition after truncation. (B) String-based merging enables compu- tation of multi-MUMs between partitions without a common sequence. An example tree (left) is shown, highlighting the use case where partial multi-MUMs specific to internal nodes (starred) can be computed by merging subclade-based partitions up a tree. (right) MUM overlaps are computed by running Mumemto on the MUM sequences, and the uniqueness threshold array ensures overlaps remain unique across the merged dataset. (C) An example Burrows-Wheeler Transform (BWT), matrix (BWM), and Longest Com- mon Prefix (LCP) array, with sequence IDs for each suffix shown (ID). A non-maximal unique match (UM) is shown, and the uniqueness threshold for this match is found us- ing the flanking LCP values. (D) A partial multi-MUM (in blue) is found in all-but-one sequence (excluded in red). Using two anchor sequences (red and orange), all-but-one partial MUMs can be computed using an augmented anchor-based merging method (sec- tion 2.6).
November 6, 2025 at 1:13 AM
Reposted by Ben Langmead
lahuuki.bsky.social
Proud to announce our paper ‘Transcriptomic Analysis of the Human Habenula in Schizophrenia’ from @lieberinstitute.bsky.social is the cover article for the November issue of the American Journal of Psychiatry! 🧠 #HabenulaLIBD #snRNAseq #Habenula doi.org/10.1176/appi...
Transcriptomic Analysis of the Human Habenula in Schizophrenia | American Journal of Psychiatry
Objective: The objective of this study was to define the molecular neuroanatomy of the human habenula (Hb) and identify transcriptomic differences between brains of individuals with schizophrenia and ...
doi.org
November 4, 2025 at 9:31 PM
Reposted by Ben Langmead
jhucompsci.bsky.social
Check out the cool work being presented by our students at Genome Informatics! This year’s event was co-organized by @benlangmead.bsky.social, & features talks from @vikramshivakumar.bsky.social & more, plus posters from @alexsweeten.bsky.social, @maojanlin.bsky.social, & @sinamajidian.bsky.social:
Johns Hopkins researchers to present at Genome Informatics 2025
Students from the Department of Computer Science will give talks and present posters on their research in genome informatics.
www.cs.jhu.edu
November 4, 2025 at 5:14 PM
benlangmead.bsky.social
As our beloved Genome Informatics 2025 (#gi2025) approaches, I'm moved to share some photos from past years at CSHL. A couple more photos coming in a reply below...
Driveway at Cold Spring Harbor Lab, with conference attendees walking to a meal Dolan Hall Pic from a nighttime stroll
November 3, 2025 at 8:47 PM
benlangmead.bsky.social
Huge congratulations to Steven Tan, a superb undergraduate junior at JHU CS whose first-author paper "Movi Color: fast and accurate taxonomic classification with the move structure" won best paper at ACM-BCB. Please check it out: www.biorxiv.org/content/10.1.... Congrats, Steven!!
Steven Tan accepting ACM-BCB 2025 best paper award
October 31, 2025 at 5:54 PM
Reposted by Ben Langmead
curiouscoding.nl
I'm very happy with `sassy grep` now!
If you ever need to inspect what's in your data, please try and let me know how it goes :)

Of course, it's fast: >1GB/s when using multiple threads.
curiouscoding.nl Ragnar {Groot Koerkamp} @curiouscoding.nl · 22d
Following ish's `filter` and bqtools' `grep`, Sassy now also has initial support for grep and filter!

Grep mode shows all matches, grouped per record, and is meant for human consumption.
Filter mode prints full matching (or non-matching) records to stdout or output files.
Output of `sassy grep -p ACTGGCATGAGAACTGAG -k1 human-genome.fa`. Should fuzzy matches with up to one error, grouped by file, then by record. The matching part is highlighted with colours (green=match, orange=mismatch, red=delete, blue=insert), and the strandedness of each match, the location, and the cost are shown.
October 31, 2025 at 3:58 PM
Reposted by Ben Langmead
stephaniehicks.bsky.social
Come work with me! @jhubiostat.bsky.social is hiring for a tenure-track Assistant Professor position 🥳 Apps due Nov 15

🔗 apply.interfolio.com/176686

🧪🧬💻🧠 #StatsSky #WomenInSTEM
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October 31, 2025 at 6:58 AM
benlangmead.bsky.social
October 2025 batch of Kraken 2 indexes, including core_nt and many others, available: benlangmead.github.io/aws-indexes/k2

Coming soon to K2: a feature for querying many K2 indexes as though they're a single index. Highly useful if the index you want to query is too big to build and/or fit in RAM.
Index zone by BenLangmead
benlangmead.github.io
October 30, 2025 at 6:11 PM
Reposted by Ben Langmead
jhucompsci.bsky.social
The Department of Computer Science is pleased to welcome nine new tenure-track faculty to its ranks this academic year! Featuring @anandbhattad.bsky.social, @uthsav.bsky.social, @gligoric.bsky.social, @murat-kocaoglu.bsky.social, @tiziano.bsky.social, and more:
Nine new tenure-track faculty join Johns Hopkins Computer Science
Their research spans social computing and human-computer interaction to the theoretical foundations and real-world applications of machine learning models.
www.cs.jhu.edu
October 29, 2025 at 1:43 PM
benlangmead.bsky.social
Very excited about Movi 2! Excellent work by Mohsen here. FYI, I have a series of 5 videos on the move structure starting with this one: youtu.be/REniD2dKf6A?...
October 21, 2025 at 9:39 PM
Reposted by Ben Langmead
mohsenzakeri.bsky.social
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
Reposted by Ben Langmead
robp.bsky.social
We're looking for an instructor for the algorithms course in our Bioinformatics MS program. The course assets have already been made (by me) and used in several previous offerings, but we need an instructor! If you're in the DMV area, check it out: www.linkedin.com/posts/robert...
October 17, 2025 at 2:56 PM
benlangmead.bsky.social
New tool "bwt-svg" for making illustrations of the BWT and the many auxiliary arrays and other structures related to it. Pyodide-based no-installation-necessary interface here: benlangmead.github.io/bwt-svg/. (H/t to @robert.bio for pointing me to pyodide!) Full repo: github.com/benlangmead/....
Illustration of Burrows-Wheeler Transform and many auxiliary structures from the input string how$now$brown$cow$#
October 14, 2025 at 8:48 PM
Reposted by Ben Langmead
robp.bsky.social
Have you recently completed (or finishing soon) a PhD in CS or a related discipline? Do you want to do research advancing the theory & practice of algorithmic genomics & build tools that people love to use? I'll be looking to hire a postdoc! Official ad coming soon:
docs.google.com/document/d/1...
Postdoc Description.docx
Title: Postdoctoral Associate Summary statement: The postdoctoral research associate is responsible for developing novel computational methodology for high-throughput sequence genomics tasks, as well ...
docs.google.com
October 8, 2025 at 4:03 PM