Ben Langmead
LightNews LightNews
banner
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
Posts Replies Media Videos
benlangmead.bsky.social
Huge congrats, Zam!! Amazing!
November 14, 2025 at 3:06 PM
benlangmead.bsky.social
Many thanks. I really enjoy making them. It was great to meet in person at CSHL!
November 10, 2025 at 6:21 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
benlangmead.bsky.social
Another lit up house from nighttime stroll Several lab buildings from nighttime stroll
November 3, 2025 at 8:49 PM
benlangmead.bsky.social
As far as I know, it's been done for Centrifuge only: benlangmead.github.io/aws-indexes/...
Index zone by BenLangmead
benlangmead.github.io
October 31, 2025 at 1:27 PM