Congratulations! Vikram Shivakumar successfully defended his dissertation “Scalable Sequence Analysis Using Compressed Pangenome Indexing” under the guidance of advisor Ben Langmead. Vikram plans to pursue a joint postdoctoral fellowship at the European Bioinformatics Institute, the Wellcome Sanger Institute, and the University of Cambridge. We in the department are extremely proud of our students who have successfully completed their PhD. Congratulations on this achievement and best wishes as you begin an exciting new phase of life!

Congratulations, @vikramshivakumar.bsky.social!

sqz is now available in bioconda!

anaconda.org/channels/bio...

#pangenome #compression #bioinformatics

🚀 SQZ v0.2.0 released!

🔄 Rewritten core algorithm → faster + more robust (fixes graph edge cases)
✨ New commands:
• compress-partial
• compress-additional
• compress-full (now works on compressed graphs)
• check-compressibility
• test

🔗 github.com/codialab/sqz...

#pangenomics #compression

GitHub - mohsenzakeri/Movi: Fast, Cache-Efficient, and Scalable Queries on Pangenomes Fast, Cache-Efficient, and Scalable Queries on Pangenomes - mohsenzakeri/Movi

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...

Wie gesund ist eigentlich Eisbaden?
Patrick Schrauwen vom @ddzdiabetes.bsky.social - Leibniz-Zentrum für Diabetes-Forschung an der @hhu.de in der neuen Folge von #TonspurWissen, dem #Podcast von Rheinischer Post und @leibniz-gemeinschaft.de.
👉 pod.fo/e/33e7e0 ❄️
#Gesundheit #Diabetes #Eisbaden

Staff Scientist About EMBL-EBI EMBL’s European Bioinformatics Institute is a data powerhouse, utilised on a global scale to advance scientific discovery through bioinformatics and solutions to some of the world’s mos...

I am hiring! - looking for a Staff Scientist to co-run my research group with me. Staff Scientist is a senior professional scientist role at EMBL. Please forward to people you might know who could be interested! embl.wd103.myworkdayjobs.com/en-US/EMBL/j...

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 ...

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...

Vikram Shivakumar telling us about "Partitioned Multi-MUM finding for scalable pangenomics" #WABI25! So many kinds of matches!

"Human readable compression of GFA paths using grammar-based code" being presented by Peter Heringer at #WABI25

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.

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

The 25th iteration of the excellent Conference for Algorithms in Bioinformatics (WABI) starts tomorrow at UMD @umdscience.bsky.social at the Brendan Iribe Center. You can find details at the website wabiconf.github.io/2025/. We'll use the tag #WABI25 for the meeting!

We open our second day at #Hitseq @hitseq.bsky.social with our last key note speaker Tobias Marschall and his insightful talk about the human pangenome and the challenges for structural variation analysis. His work has focused on tackling current limitations such as sample size and remaining gaps

Complex genetic variation in nearly complete human genomes - Nature Using sequencing and haplotype-resolved assembly of 65 diverse human genomes, complex regions including the major histocompatibility complex and centromeres are analysed.

Two papers in today's issue of @nature.com ‬: 1) we assemble 65 genomes to near completion, including centromeres and the MHC. tinyurl.com/3huhax6w. 2) we sequence 1,019 genomes from the 1kGP with long reads, revealing SVs down to low allele frequencies tinyurl.com/wbx3we9x.

Sassy solves approximate string matching: finding all matches of a pattern in a text.

Sassy is out now!

Ever need to search for approximate matches of short DNA strings?
Sassy is the tool to use!

Available now wherever you get your code

With @rickbitloo.bsky.social

curiouscoding.nl/papers/sassy...
github.com/ragnarGrootK...

@denbi.bsky.social will offer 3 #workshops at @gcb-bioinformatics.bsky.social 2025, focusing on #cloudcomputing, #pangenomics and #protein structure analysis. For more information see: www.denbi.de/news1/1904-d...

🧬🖥️
📝 To-Do List for #GCB2025:
✅ Check the programme: gcb2025.de
✅ Submit your poster
✅ Buy your conference ticket
✅ Book your hotel room
✅ Take advantage of the DB event offer and travel to Düsseldorf by train at a discounted rate, more info here: gcb2025.de/GCB2025_venu...

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....

🆕 New Features
• Re-rendering of HTML
• Plug in your own reports with !Custom
• Download plots as PNG or SVG
• Select hexagons in NodeDistribution 🔷 and download node ids!

🐞 Fixes & Improvements
• 🐌 Faster similarity calculation
• 🔧 Cleaner YAML syntax
• 🔁 Better handling of dependent analyses

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

🚀 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

Reconstructing rearrangement phylogenies of natural genomes - Algorithms for Molecular Biology Background We study the classical problem of inferring ancestral genomes from a set of extant genomes under a given phylogeny, known as the Small Parsimony Problem (SPP). Genomes are represented as se...

Improved method for inferring ancestral genomes! We introduce a powerful ILP for the Small Parsimony Problem under a complex rearrangement model that handles duplications & indels. Big gains in accuracy & runtime on real and simulated data! #Genomics #Phylogenetics
doi.org/10.1186/s130...

Verkko2 integrates proximity ligation data with long-read De Bruijn graphs for efficient telomere-to-telomere genome assembly, phasing, and scaffolding. #LongReads #HiC #GenomeAssembly #GenomeScaffolding #Bioinformatics @genomeresearch.bsky.social‬
genome.cshlp.org/content/earl...

🧬 & 🖥️
📢Call for Posters #GCB2025 | Join the #bioinformatics and #computationalbiology community at the German Conference on Bioinformatics! Submit your poster now!
Important Deadlines:
📌 Early Bird Registration: 5 July 25
📌 Poster Submission: 7 August 25
🔗 gcb2025.de/GCB2025_call...

Slides from my talk (with @kamilsjaron.bsky.social) on an history of k-mers in bioinformatics: rayan.chikhi.name/pdf/2025-kme...

Human readable compression of GFA paths using grammar-based code Pangenome graphs offer a compact and comprehensive representation of genomic diversity, improving tasks such as variant calling, genotyping, and other downstream analyses. Although the underlying grap...

New in pangenomics: We extend the GFA format to represent haplotype paths in a compressed yet human-readable way. Our tool sqz (/ˈskuzi/) achieves 40× compression on chr19 with 1000 haplotypes, plus 10× faster analysis and 8× lower memory use.
🔗 www.biorxiv.org/content/10.1...
#bioinformatics

Submit your abstracts from all areas of #bioinformatics and #computationalbiology for the German Conference on Bioinformatics - #GCB2025 at University of Dusseldorf from 22 - 24 September 2025!
abstract submission: gcb2025.de
@denbi.bsky.social @openbio.bsky.social @SIB.mstdn.science.ap.brid.gy