Tessera

@danydoerr.bsky.social

🚀 Open PhD position in bioinformatics (100% TV-L E13, 3 years)! Develop GEMs integrating multi-omics and metabolic imaging to study cardio-diabetes. Seeking candidates with backgrounds in bioinformatics, computer science, or data science. Apply: www.linkedin.com/jobs/view/44...

University of Düsseldorf hiring PhD position in bioinformatics / metabolic modeling in Düsseldorf, North Rhine-Westphalia, Germany | LinkedIn

Posted 7:10:42 AM. As part of the recently funded CRC1774, a PhD position (100% TV-L E13, 3 years) in bioinformatics…See this and similar jobs on LinkedIn.

linkedin.com

Heinrich-Heine-Universität Düsseldorf @hhu.de · 6d ago

Diabetes ist weit mehr als ein erhöhter Blutzucker. Forschende aus Düsseldorf arbeiten daran, die Erkrankung früher zu erkennen und Therapien individueller zu gestalten. Das Ziel: Folgeerkrankungen verhindern, bevor sie entstehen. ^lm

James Ferguson @psy-fer.bsky.social · last wk.

The case study covers rustar-aligner (a re-write of STAR into rust), svb (a streamvbyte+VBZ/EX-ZD codec for signal compression), and kuva (scientific plotting library in rust github.com/scverse/rust... github.com/Psy-Fer/svb github.com/Psy-Fer/kuva

GitHub - scverse/rustar-aligner: A rust implementation of STAR

A rust implementation of STAR. Contribute to scverse/rustar-aligner development by creating an account on GitHub.

github.com

bioRxiv Genomics @biorxiv-genomic.bsky.social · 2w ago

HPRC2: A human pangenome reference with near-complete coverage of common genetic variation https://www.biorxiv.org/content/10.64898/2026.07.21.739710v1

@danydoerr.bsky.social · 3w ago

New Nature Reviews Genetics paper out! How are graph-based pangenomes removing reference bias and opening up new possibilities in GWAS and rare- and common disease genetics? 🔗 nature.com/articles/s41576-026-00987-7 #pangenome #geneticdiversity #referencebias

Building and applying pangenome references to capture genetic diversity - Nature Reviews Genetics

Pangenomes are genome references that integrate sequences from multiple individuals into graph-based or multi-haplotype representations, capturing genetic variation beyond a single linear reference. H...

nature.com

@danydoerr.bsky.social · 2mo ago

🧬 panacus v0.5.0 is out—a major upgrade for pangenome graph statistics! What's new: ✅ VCF file support ✅ sqz-ified GFA support ✅ RegionalVariation (Hill numbers) analysis ✅ RegionalGrowth & SectionGrowth analyses ✅ YAML parameter replacement 👉 github.com/codialab/pan... #Bioinformatics #Pangenomics

Release v0.5.0 · codialab/panacus

Major upgrade for panacus, introducing new formats and new analyses. Add: Support for VCF files Support for sqz-ified GFA files (see SQZ) RegionalVariation (Hill numbers) analysis RegionalGrowth a...

github.com

Floris Barthel @florisbarthel.bsky.social · 3mo ago

The human genome's most variable and clinically important regions (centromeres, telomeres, and acrocentric short arms) have been hardest to study at scale. Thrilled to share KaryoScope, our new preprint that brings them within reach. 🧵 www.biorxiv.org/content/10.6...

KaryoScope karyotype of the HG002 diploid assembly. All 22 autosomes plus X and Y, each shown as paired haplotypes (h1, h2). Each chromosome has a full-length track colored by chromosome of origin, a centromere zoom panel showing satellite composition, and a subtelomere zoom panel. Legends map chromosomes, satellite families, and subtelomeric features to colors.

Laurel Oldach @laureloldach.bsky.social · 3mo ago

For our obit of Craig Venter, @maxhenrybarnhart.bsky.social dug up pre-HGP drama that I had never even heard of (spoiler: it's to do with patenting genes.) And @phylogenomics.bsky.social graciously shared remembrances of a complex, but really influential scientist. cen.acs.org/people/obitu...

J. Craig Venter, foil of the Human Genome Project, dies at 79

He helped develop the technique of whole-genome shotgun sequencing, still widely used today

cen.acs.org

JHU Computer Science @jhucompsci.bsky.social · 5mo ago

Congratulations, @vikramshivakumar.bsky.social!

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!

@danydoerr.bsky.social · 5mo ago

sqz is now available in bioconda! anaconda.org/channels/bio... #pangenome #compression #bioinformatics

sqz - bioconda | Anaconda.org

Install sqz with Anaconda.org. sqz is a tool for compressing and decompressing path annotations in GFA files.

anaconda.org

@danydoerr.bsky.social · 5mo ago

🚀 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

Release Updated algorithm · codialab/sqz

What's changed Rewrite of the main algorithm, this version should be both faster and fixes a couple of issues were the old version ran into problems with certain graphs. Additionally, it adds funct...

github.com

Mohsen Zakeri @mohsenzakeri.bsky.social · 10mo ago

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...

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

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

github.com

Leibniz-Gemeinschaft @leibniz-gemeinschaft.de · 10mo ago

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

Ewan Birney @ewanbirney.bsky.social · 10mo ago

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...

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...

embl.wd103.myworkdayjobs.com

Rob Patro @robp.bsky.social · 10mo ago

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...

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 ...

docs.google.com

Rob Patro @robp.bsky.social · 12mo ago

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

Rob Patro @robp.bsky.social · 12mo ago

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

Sina Majidian @sinamajidian.bsky.social · 12mo ago

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.

Rob Patro @robp.bsky.social · 12mo ago

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!

WABI 2025

WABI Conference on Algorithms in Bioinformatics

wabiconf.github.io

HiTSeq 2026 Conference @hitseq.bsky.social · last yr.

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

Tobias Marschall @tobiasmar.bsky.social · last yr.

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.

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.

tinyurl.com

Ragnar {Groot Koerkamp}@curiouscoding.nl · last yr.

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...

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

de.NBI & ELIXIR Germany @denbi.bsky.social · last yr.

@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...

German Conference on Bioinformatics #GCB2026 @gcb-bioinformatics.bsky.social · last yr.

🧬🖥️ 📝 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...

Ben Langmead @benlangmead.bsky.social · last yr.

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....

Mumemto: efficient maximal matching across pangenomes - Genome Biology

Aligning genomes into common coordinates is central to pangenome construction, though computationally expensive. Multi-sequence maximal unique matches (multi-MUMs) help to frame and solve the multiple...

genomebiology.biomedcentral.com

Vikram Shivakumar@vikramshivakumar.bsky.social · 2y ago

Excited to share a preprint for (w/ @benlangmead.bsky.social) our new tool, Mumemto, on biorxiv! Mumemto finds multi-MUMs across pangenomes (i.e. mummer but for pangenomes). It can rapidly visualize synteny, identify misassemblies, and accelerate core genome and multiple alignment, highlighting SVs.

@danydoerr.bsky.social · last yr.

🚀 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

@danydoerr.bsky.social · last yr.

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...

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...

doi.org

Javier Santoyo @jsantoyo.bsky.social · last yr.

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...

German Conference on Bioinformatics #GCB2026 @gcb-bioinformatics.bsky.social · last yr.

🧬 & 🖥️ 📢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...

Rayan Chikhi @rayanchikhi.bsky.social · last yr.

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