Simon Heumos
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simonheumos.bsky.social
Simon Heumos
@simonheumos.bsky.social
31 followers 86 following 0 posts
Bioinformatician
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Reposted by Simon Heumos
danydoerr.bsky.social
🚀 Panacus v0.4.0 is out!
Bringing more power, flexibility, and speed to your pangenome reports 🧬📊

👉 Upgrade now & explore: github.com/codialab/pan...

#genomics #bioinformatics #pangenome #panacus
GitHub - codialab/panacus: Panacus is a tool for computing statistics for GFA-formatted pangenome graphs
Panacus is a tool for computing statistics for GFA-formatted pangenome graphs - codialab/panacus
github.com
June 13, 2025 at 12:55 PM
Reposted by Simon Heumos
robp.bsky.social
Vikram Shivakumar telling us about "Partitioned Multi-MUM finding for scalable pangenomics" #WABI25! So many kinds of matches!
August 20, 2025 at 2:33 PM
Reposted by Simon Heumos
sinamajidian.bsky.social
Great talk by Vikram @vikramshivakumar.bsky.social on studying pangenomes and synteny visualization in #WABI25
Github: github.com/vikshiv/mume...
First paper: genomebiology.biomedcentral.com/articles/10....
Second: www.biorxiv.org/content/10.1... #WABI2025
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 computation 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 Common 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 using 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. (A) Phylogeny of geographically diverse A. thaliana accessions (Lian et al. 2024), with broad geographical regions colored. Internal nodes are labeled with the coverage of partial multi-MUMs across the leaves of each node. Internal node partial MUMs are computed by merging subtree-based partitions progressively up the phylogeny. (B) Global multi-MUM synteny across the full dataset shown in blue (with inversions in green). Global MUMs are computed by merging all partitions together (representing the root node). Additionally, three geographically distinct subgroups are highlighted and partition-specific multi-MUMs (in purple, with inversions in pink) reveal local structural variation in centromeric regions.
August 20, 2025 at 3:03 PM
Reposted by Simon Heumos
robp.bsky.social
Ali Ghaffaari introduces "DiVerG: A Scalable Distance Index for Validation of Paires-End Alignments in Sequence Graphs" #WABI25
August 20, 2025 at 3:55 PM
Reposted by Simon Heumos
robp.bsky.social
"Human readable compression of GFA paths using grammar-based code" being presented by Peter Heringer at #WABI25
August 20, 2025 at 5:43 PM
Reposted by Simon Heumos
kazcooke.bsky.social
This what Israel has done to Gaza. Forbidden pics by a Washington Post photographer whose Jordanian air crew didn't pass on Israel's order to only photograph aid being dropped. City, suburbs, schools, people: bombed to rubble. People being starved in makeshift camps on road roundabouts. #Genocide
Aerial shot of Gaza City, burned and bombed into burned and shattered, unliveable wreckage as far as can be seen. Whole area that used to be houses, shops, public transport routes, made into rubble and blackened, unliveable ruins. Aerial shot shows vast area entirely obliterated as habitable, attacked again and again by Israeli forces. Several wrecked Gaza schools, shown from the air, pulverised by Israel's forces: windows all gaping, bombed out and covered in ash and dust. Some people are trying to live in makeshift camps amid the destruction, in former quadrangles and bomb sites. Aerial shots of neighbourhoods with destroyed apartment buildings, houses, offices and shops, all bombed by Israel's government. Starving people are trying to live in tents and makeshift cubbies on the former roundabouts on a main road.
August 3, 2025 at 4:31 AM
Reposted by Simon Heumos
benlangmead.bsky.social
Now published! Note that since Vikram's original post (quoted here), he's made it easy to dynamically update a set of multi-MUMs (e.g. when more genomes are added to a pangenome) and to find multi-MUMs for huge collections like HPRCv2 genomebiology.biomedcentral.com/articles/10....
June 17, 2025 at 2:02 PM
Reposted by Simon Heumos
benedictpaten.bsky.social
Standing up for science in the redwoods :)
March 7, 2025 at 8:26 PM
Reposted by Simon Heumos
espengis.bsky.social
Have done. To avoid Messenger and WhatsApp use signal.org

The best way to beat these Trolls is a) block them and b) Hurt them where it hurts them the most - their wallet and pride!
January 11, 2025 at 5:59 PM
Reposted by Simon Heumos
stephenturner.us
New weekly recap: Pangenome graph construction with nf-core/pangenome, pangenome graphs, single cell multi-omics, RNA foundation models, Nextflow for B-cell receptor sequencing from nontargeted bulk RNA-seq, ... https://blog.stephenturner.us/p/weekly-recap-nov-2024-part-3 🧬🖥️🧪
Weekly Recap (Nov 2024, part 3)
Pangenome graph construction with nf-core/pangenome, pangenome graphs, single cell multi-omics, RNA foundation models, Nextflow for B-cell receptor sequencing from nontargeted bulk RNA-seq, ...
blog.stephenturner.us
November 22, 2024 at 11:10 AM