Ben Langmead
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benlangmead.bsky.social
Ben Langmead
@benlangmead.bsky.social
3.4K followers 240 following 97 posts
Professor of Computer Science @ JHU. https://www.langmead-lab.org/ https://www.youtube.com/BenLangmead
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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
benlangmead.bsky.social
Oooo, that's very nice
October 15, 2025 at 11:29 AM
benlangmead.bsky.social
The generated illustrations are SVGs -- you can load them into Illustrator, Inkscape, Designer, etc, and edit away. I tried to put the components of the image into SVG groups so you can treat them as "layers" in those editors (e.g. you can hide bits you don't need).
October 14, 2025 at 8:51 PM
benlangmead.bsky.social
Wow! Very helpful
October 13, 2025 at 2:16 PM
benlangmead.bsky.social
Huge congrats, Andre!
October 10, 2025 at 2:18 AM