Ben Langmead
@benlangmead.bsky.social
Professor of Computer Science @ JHU. https://www.langmead-lab.org/ https://www.youtube.com/BenLangmead
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!!
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/....
More youtube videos coming soon to www.youtube.com/BenLangmead! New recording setup. I've got a couple videos in the editing phase and hope to keep up a rhythm of 1 new video per week.
September 9, 2025 at 3:25 PM
More youtube videos coming soon to www.youtube.com/BenLangmead! New recording setup. I've got a couple videos in the editing phase and hope to keep up a rhythm of 1 new video per week.
Farewell to friend & labmate Dr. @oahmed.bsky.social whom I hooded today! He's moving on to exciting new things in his postdoc at @nygenome.org with @nevillesanjana.bsky.social & @tuuliel.bsky.social. You are already much missed, Omar! 🫡 ❤️ 🎓
May 19, 2025 at 8:29 PM
Farewell to friend & labmate Dr. @oahmed.bsky.social whom I hooded today! He's moving on to exciting new things in his postdoc at @nygenome.org with @nevillesanjana.bsky.social & @tuuliel.bsky.social. You are already much missed, Omar! 🫡 ❤️ 🎓
It’s that time again
May 19, 2025 at 12:51 PM
It’s that time again
If I understand right, sounds like what the CountMin people call "conservative update." Possibly relevant excerpt from "Probability and Computing" by Mitzenmacher & Upfal:
March 18, 2025 at 5:07 PM
If I understand right, sounds like what the CountMin people call "conservative update." Possibly relevant excerpt from "Probability and Computing" by Mitzenmacher & Upfal:
Scenes from #StandUpForScience2025 in DC today. Huge contingent from Johns Hopkins, and also from UMD & DC/Virginia Unis.
March 8, 2025 at 3:34 AM
Scenes from #StandUpForScience2025 in DC today. Huge contingent from Johns Hopkins, and also from UMD & DC/Virginia Unis.
As a result, Movi is blazingly fast; its streamlined inner loop is simple, with only a few memory accesses. The cost of the memory access that is most likely to incur a cache miss is "hidden" with memory prefetching ("latency hiding").
December 11, 2024 at 4:48 PM
As a result, Movi is blazingly fast; its streamlined inner loop is simple, with only a few memory accesses. The cost of the memory access that is most likely to incur a cache miss is "hidden" with memory prefetching ("latency hiding").
This is the status of a key paper 6 months post submission. If I withdrew at this point, would it be (a) inappropriate, since I'm wasting reviewers' time? (b) appropriate, since the reviewers/editors are wasting our time and it is blocking a student from publishing their flagship project?
November 20, 2024 at 1:38 PM
This is the status of a key paper 6 months post submission. If I withdrew at this point, would it be (a) inappropriate, since I'm wasting reviewers' time? (b) appropriate, since the reviewers/editors are wasting our time and it is blocking a student from publishing their flagship project?
This allows for sequence classification that is aware of the match co-linearity with respect to both read and reference, at basically no additional time cost and a mild space increase compared to an index that only reports matches and is unaware of co-linearity w/r/t the reference. (2/3)
November 12, 2024 at 1:31 PM
This allows for sequence classification that is aware of the match co-linearity with respect to both read and reference, at basically no additional time cost and a mild space increase compared to an index that only reports matches and is unaware of co-linearity w/r/t the reference. (2/3)
My remote office while at the IGGSy 2024 conference in Ascona, Switzerland is, you know, not bad
July 2, 2024 at 5:59 AM
My remote office while at the IGGSy 2024 conference in Ascona, Switzerland is, you know, not bad
@mohsenzakeri.bsky.social presented his excellent work on the Movi pangenome indexing software, based on Nishimoto & Tabei's move structure, at RECOMB-seq at MIT today. Preprint www.biorxiv.org/content/10.1.... Software: github.com/mohsenzakeri....
April 27, 2024 at 3:36 PM
@mohsenzakeri.bsky.social presented his excellent work on the Movi pangenome indexing software, based on Nishimoto & Tabei's move structure, at RECOMB-seq at MIT today. Preprint www.biorxiv.org/content/10.1.... Software: github.com/mohsenzakeri....
Hackerman Hall, Moon, Malone Hall
February 28, 2024 at 10:24 PM
Hackerman Hall, Moon, Malone Hall
Updating this slide for a lecture tomorrow. SRA doubling times are getting longer, even if you ignore the leftmost doubling shown, which includes an unusually big TOPMed upload. R code: bit.ly/sra-growth which in turn uses trace.ncbi.nlm.nih.gov/Traces/sra/s...
January 22, 2024 at 8:29 PM
Updating this slide for a lecture tomorrow. SRA doubling times are getting longer, even if you ignore the leftmost doubling shown, which includes an unusually big TOPMed upload. R code: bit.ly/sra-growth which in turn uses trace.ncbi.nlm.nih.gov/Traces/sra/s...
Just dropping this here. Some folks know what I'm talking about...
December 15, 2023 at 10:48 PM
Just dropping this here. Some folks know what I'm talking about...
October 2023 batch of Kraken 2 indexes now available. New this round: the archives and website include `library_report.tsv` files listing all FASTA headers & URLs for sequences in the database, making it easy to check if specific sequences are there. Thanks to AWS Public Data program for the space!
October 13, 2023 at 12:17 PM
October 2023 batch of Kraken 2 indexes now available. New this round: the archives and website include `library_report.tsv` files listing all FASTA headers & URLs for sequences in the database, making it easy to check if specific sequences are there. Thanks to AWS Public Data program for the space!
To celebrate the O's division clinch and new 30-year lease in Baltimore, behold, my signed Ben McDonald rookie cards
September 29, 2023 at 1:33 AM
To celebrate the O's division clinch and new 30-year lease in Baltimore, behold, my signed Ben McDonald rookie cards