Ben Langmead
@benlangmead.bsky.social
Professor of Computer Science @ JHU. https://www.langmead-lab.org/ https://www.youtube.com/BenLangmead
Reposted by Ben Langmead
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
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]
Reposted by Ben Langmead
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...
It's a surreal--and troubling--read.
drive.google.com/file/d/1Is6x...
November 14, 2025 at 2:15 PM
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...
It's a surreal--and troubling--read.
drive.google.com/file/d/1Is6x...
Reposted by Ben Langmead
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/ 🧪
A bit of a video explainer here: 1/ 🧪
November 13, 2025 at 10:31 PM
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/ 🧪
A bit of a video explainer here: 1/ 🧪
Reposted by Ben Langmead
‼️ 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
‼️ 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...
Reposted by Ben Langmead
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.
#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
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.
Reposted by Ben Langmead
#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
#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...
Reposted by Ben Langmead
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!
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!
November 6, 2025 at 1:13 AM
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!
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!
Reposted by Ben Langmead
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
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...
Reposted by Ben Langmead
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
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:
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...
November 3, 2025 at 8:47 PM
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...
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!!
October 31, 2025 at 5:54 PM
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!!
Reposted by Ben Langmead
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.
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.
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.
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.
October 31, 2025 at 3:58 PM
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.
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.
Reposted by Ben Langmead
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
🔗 apply.interfolio.com/176686
🧪🧬💻🧠 #StatsSky #WomenInSTEM
Apply - Interfolio
{{$ctrl.$state.data.pageTitle}} - Apply - Interfolio
apply.interfolio.com
October 31, 2025 at 6:58 AM
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
🔗 apply.interfolio.com/176686
🧪🧬💻🧠 #StatsSky #WomenInSTEM
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.
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
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.
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.
Reposted by Ben Langmead
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
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:
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
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?...
Reposted by Ben Langmead
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...
Reposted by Ben Langmead
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
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...
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/....
October 14, 2025 at 8:48 PM
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/....
Reposted by Ben Langmead
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...
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
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...
docs.google.com/document/d/1...
Reposted by Ben Langmead
Just published an interactive article about a magical algorithm known as the Burrows-Wheeler Transform, which powers sequence alignment tools like bowtie and bwa: sandbox.bio/concepts/bwt
It's also notoriously unintuitive so I'm hoping this article helps you build that intuition.
It's also notoriously unintuitive so I'm hoping this article helps you build that intuition.
October 9, 2025 at 5:05 PM
Just published an interactive article about a magical algorithm known as the Burrows-Wheeler Transform, which powers sequence alignment tools like bowtie and bwa: sandbox.bio/concepts/bwt
It's also notoriously unintuitive so I'm hoping this article helps you build that intuition.
It's also notoriously unintuitive so I'm hoping this article helps you build that intuition.
Reposted by Ben Langmead
10 new CS professors! 🥳
@anandbhattad.bsky.social @uthsav.bsky.social @gligoric.bsky.social @murat-kocaoglu.bsky.social @tiziano.bsky.social
@anandbhattad.bsky.social @uthsav.bsky.social @gligoric.bsky.social @murat-kocaoglu.bsky.social @tiziano.bsky.social
#HopkinsDSAI welcomes 22 new faculty members, who join more than 150 DSAI faculty members across @jhu.edu in advancing the study of data science, machine learning, and #AI and translation to a range of critical and emerging fields.
ai.jhu.edu/news/data-sc...
ai.jhu.edu/news/data-sc...
October 8, 2025 at 5:43 PM
Reposted by Ben Langmead
And it's posted! If you're interested and eligible, please consider applying through the UMD portal: umd.wd1.myworkdayjobs.com/en-US/UMCP/j....
If you're a PI working in algorithmic genomics (& you can recommend my lab to your top graduating students ;P), please let them know!
If you're a PI working in algorithmic genomics (& you can recommend my lab to your top graduating students ;P), please let them know!
October 8, 2025 at 4:53 PM
And it's posted! If you're interested and eligible, please consider applying through the UMD portal: umd.wd1.myworkdayjobs.com/en-US/UMCP/j....
If you're a PI working in algorithmic genomics (& you can recommend my lab to your top graduating students ;P), please let them know!
If you're a PI working in algorithmic genomics (& you can recommend my lab to your top graduating students ;P), please let them know!
I've added 7 videos to my Burrows-Wheeler indexing playlist (www.youtube.com/playlist?lis...), rounding out the r-index series and adding a 5-part series on the move structure. Now 27 videos in that playlist. I aim to add videos on prefix-free parsing, PBWT, Wheeler languages/automata in the future.
Burrows-Wheeler Indexing - YouTube
Videos on : (a) the Burrows-Wheeler Transform (BWT), (b) the FM Index, which uses the BWT to construct a full-text index, (c) Wheeler graphs, (d) r-index, an...
www.youtube.com
October 7, 2025 at 2:17 PM
I've added 7 videos to my Burrows-Wheeler indexing playlist (www.youtube.com/playlist?lis...), rounding out the r-index series and adding a 5-part series on the move structure. Now 27 videos in that playlist. I aim to add videos on prefix-free parsing, PBWT, Wheeler languages/automata in the future.
Reposted by Ben Langmead
BREAKING: WE WON!!!
💥 💥 💥
Federal Judge William G. Young ruled today in our lawsuit against the Trump administration that the policy of arresting, detaining, & deporting noncitizen students & faculty members for their pro-Palestinian advocacy violates the 1st Amendment.
Full ruling here:
💥 💥 💥
Federal Judge William G. Young ruled today in our lawsuit against the Trump administration that the policy of arresting, detaining, & deporting noncitizen students & faculty members for their pro-Palestinian advocacy violates the 1st Amendment.
Full ruling here:
Findings of Fact & Conclusions of Law – #261 in American Association of University Professors v. Rubio (D. Mass., 1:25-cv-10685) – CourtListener.com
Judge William G. Young: ORDER entered. FINDINGS OF FACT AND RULINGS OF LAW, PURSUANT TO FED. R. CIV. P. 52(A)(Sonnenberg, Elizabeth) (Additional attachment(s) added on 9/30/2025: # 1 Main Document) (J...
www.courtlistener.com
September 30, 2025 at 5:43 PM
BREAKING: WE WON!!!
💥 💥 💥
Federal Judge William G. Young ruled today in our lawsuit against the Trump administration that the policy of arresting, detaining, & deporting noncitizen students & faculty members for their pro-Palestinian advocacy violates the 1st Amendment.
Full ruling here:
💥 💥 💥
Federal Judge William G. Young ruled today in our lawsuit against the Trump administration that the policy of arresting, detaining, & deporting noncitizen students & faculty members for their pro-Palestinian advocacy violates the 1st Amendment.
Full ruling here: