Pangenomes, really?
Most early “pangenomes” = oligogenomes (oligo, Gr., few).
More recent “pangenomes” generally = poligenomes (polis, Gr., many).
True pangenomes (pas, Gr., every/all) would be rare indeed.
🙏🏼 @zbao.bsky.social for pointing out his review.
www.nature.com/articles/s41...
Most early “pangenomes” = oligogenomes (oligo, Gr., few).
More recent “pangenomes” generally = poligenomes (polis, Gr., many).
True pangenomes (pas, Gr., every/all) would be rare indeed.
🙏🏼 @zbao.bsky.social for pointing out his review.
www.nature.com/articles/s41...
March 2, 2026 at 6:19 PM
Pangenomes, really?
Most early “pangenomes” = oligogenomes (oligo, Gr., few).
More recent “pangenomes” generally = poligenomes (polis, Gr., many).
True pangenomes (pas, Gr., every/all) would be rare indeed.
🙏🏼 @zbao.bsky.social for pointing out his review.
www.nature.com/articles/s41...
Most early “pangenomes” = oligogenomes (oligo, Gr., few).
More recent “pangenomes” generally = poligenomes (polis, Gr., many).
True pangenomes (pas, Gr., every/all) would be rare indeed.
🙏🏼 @zbao.bsky.social for pointing out his review.
www.nature.com/articles/s41...
1/2 Want to become up to date with pangenomes and genome graphs and their history? Check out this fantastic review by @zbao.bsky.social!
Complexity welcome: Pangenome graphs for comprehensive population genomics
#pangenomes #plantscience #genomegraphs
www.cambridge.org/core/journal...
Complexity welcome: Pangenome graphs for comprehensive population genomics
#pangenomes #plantscience #genomegraphs
www.cambridge.org/core/journal...
October 27, 2025 at 5:53 PM
1/2 Want to become up to date with pangenomes and genome graphs and their history? Check out this fantastic review by @zbao.bsky.social!
Complexity welcome: Pangenome graphs for comprehensive population genomics
#pangenomes #plantscience #genomegraphs
www.cambridge.org/core/journal...
Complexity welcome: Pangenome graphs for comprehensive population genomics
#pangenomes #plantscience #genomegraphs
www.cambridge.org/core/journal...
I'm super bummed to be missing #ESEB2025 @eseb2025.bsky.social due to a cancelled flight! Here's a quick overview of my talk "Gene- and genome-focused perspectives on microbial pangenomes" slated to be part of The Evolution of Microbial Pangenomes -- which I recommend you attend tomorrow (Fri) !
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August 21, 2025 at 4:57 PM
I'm super bummed to be missing #ESEB2025 @eseb2025.bsky.social due to a cancelled flight! Here's a quick overview of my talk "Gene- and genome-focused perspectives on microbial pangenomes" slated to be part of The Evolution of Microbial Pangenomes -- which I recommend you attend tomorrow (Fri) !
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Structural polymorphism and population-variable coding capacity of HERV-K(HML-2) in human pangenomes https://www.biorxiv.org/content/10.64898/2026.09.22.753638v1
September 28, 2026 at 11:31 PM
Structural polymorphism and population-variable coding capacity of HERV-K(HML-2) in human pangenomes https://www.biorxiv.org/content/10.64898/2026.09.22.753638v1
Mumemto: efficient maximal matching across pangenomes https://www.biorxiv.org/content/10.1101/2025.01.05.631388v1
January 6, 2025 at 3:46 AM
Mumemto: efficient maximal matching across pangenomes https://www.biorxiv.org/content/10.1101/2025.01.05.631388v1
This week in @science.org, a celebration of plant pangenomes. A pangenome analysis for massively polyploid sugarcane species, and one for Brassica rapa giving insight into subspeciation.
What's all the fuss about pangenomes? Pamela and Douglas Soltis explore this in an insightful Perspective(1/4)
What's all the fuss about pangenomes? Pamela and Douglas Soltis explore this in an insightful Perspective(1/4)
February 6, 2026 at 9:57 AM
This week in @science.org, a celebration of plant pangenomes. A pangenome analysis for massively polyploid sugarcane species, and one for Brassica rapa giving insight into subspeciation.
What's all the fuss about pangenomes? Pamela and Douglas Soltis explore this in an insightful Perspective(1/4)
What's all the fuss about pangenomes? Pamela and Douglas Soltis explore this in an insightful Perspective(1/4)
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.
Mumemto: efficient maximal matching across pangenomes
Aligning genomes into common coordinates is central to pangenome analysis and construction, but it is also computationally expensive. Multi-sequence maximal unique matches (multi-MUMs) are guideposts ...
www.biorxiv.org
January 6, 2025 at 3:27 PM
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.
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
October 21, 2025 at 8:00 PM
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...
Population-scale long-read datasets, involving sequencing and de novo assembly of multiple individuals within a species, are better at capturing the full spectrum of structural variants, but such datasets are rare outside of humans www.science.org/doi/10.1126/... #biodiversity #genomics
Multispecies pangenomes reveal a pervasive influence of population size on structural variation
Structural variants (SVs) are widespread in vertebrate genomes, yet their evolutionary dynamics remain poorly understood. Using 45 long-read de novo genome assemblies and pangenome tools, we analyze S...
www.science.org
December 15, 2025 at 5:27 PM
Population-scale long-read datasets, involving sequencing and de novo assembly of multiple individuals within a species, are better at capturing the full spectrum of structural variants, but such datasets are rare outside of humans www.science.org/doi/10.1126/... #biodiversity #genomics
Pangenomes, but scalable.
Panmap: phylogeny-guided framework for read alignment, genotyping, sample placement on pangenomes. 600x smaller indexes, faster builds, and placement from 20K to 8M genomes. @amkram.bsky.social @alanbyzhang.bsky.social @russcd.bsky.social
www.biorxiv.org/content/10.6...
Panmap: phylogeny-guided framework for read alignment, genotyping, sample placement on pangenomes. 600x smaller indexes, faster builds, and placement from 20K to 8M genomes. @amkram.bsky.social @alanbyzhang.bsky.social @russcd.bsky.social
www.biorxiv.org/content/10.6...
www.biorxiv.org
April 7, 2026 at 6:14 PM
Pangenomes, but scalable.
Panmap: phylogeny-guided framework for read alignment, genotyping, sample placement on pangenomes. 600x smaller indexes, faster builds, and placement from 20K to 8M genomes. @amkram.bsky.social @alanbyzhang.bsky.social @russcd.bsky.social
www.biorxiv.org/content/10.6...
Panmap: phylogeny-guided framework for read alignment, genotyping, sample placement on pangenomes. 600x smaller indexes, faster builds, and placement from 20K to 8M genomes. @amkram.bsky.social @alanbyzhang.bsky.social @russcd.bsky.social
www.biorxiv.org/content/10.6...
Mumemto: efficient maximal matching across pangenomes https://www.biorxiv.org/content/10.1101/2025.01.05.631388v1 🧬🖥️🧪 https://github.com/vikshiv/mumemto
January 6, 2025 at 7:30 PM
Mumemto: efficient maximal matching across pangenomes https://www.biorxiv.org/content/10.1101/2025.01.05.631388v1 🧬🖥️🧪 https://github.com/vikshiv/mumemto
The great @johannconfais.bsky.social on a reference-free approach (panREPET) to annotate #Transposons in #pangenomes 🧬
January 14, 2025 at 7:24 PM
The great @johannconfais.bsky.social on a reference-free approach (panREPET) to annotate #Transposons in #pangenomes 🧬
Postdoc position opening in my group! Research projects: pangenomes for diverse organisms, genome evolution, biocomputing, language models. Please reach out if interested!
July 17, 2025 at 7:53 AM
Postdoc position opening in my group! Research projects: pangenomes for diverse organisms, genome evolution, biocomputing, language models. Please reach out if interested!
Out after peer review, collaborative study from Nordborg & Weigel labs with help from many others. Not the largest collection of new Arabidopsis thaliana genomes, but we hopefully put forward some good ideas for how to think about pangenomes and their analysis!
www.nature.com/articles/s41...
www.nature.com/articles/s41...
August 20, 2025 at 6:23 AM
Out after peer review, collaborative study from Nordborg & Weigel labs with help from many others. Not the largest collection of new Arabidopsis thaliana genomes, but we hopefully put forward some good ideas for how to think about pangenomes and their analysis!
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Comparative population pangenomes reveal unexpected complexity and fitness effects of structural variants https://www.biorxiv.org/content/10.1101/2025.02.11.637762v1
February 14, 2025 at 7:32 AM
Comparative population pangenomes reveal unexpected complexity and fitness effects of structural variants https://www.biorxiv.org/content/10.1101/2025.02.11.637762v1
A really great #pangenomes session at #SMBE2026 with a wide variety of organisms and methods, and a packed room too! Thanks to all the amazing speakers! Consider joining the ERGA @ergabiodiv.bsky.social pangenomes working group to continue the discussions!
July 1, 2026 at 12:10 PM
A really great #pangenomes session at #SMBE2026 with a wide variety of organisms and methods, and a packed room too! Thanks to all the amazing speakers! Consider joining the ERGA @ergabiodiv.bsky.social pangenomes working group to continue the discussions!
Join our pangenomes course in April. Details here: t.co/GnUnjmLEN8
Analysis of Prokaryotic Pangenomes
ONLINE, 15-17 April 2024 To foster international participation, this course will be held online
t.co
March 24, 2024 at 2:18 PM
Join our pangenomes course in April. Details here: t.co/GnUnjmLEN8
Thank you coral microbe friends for coming to my talk on Symbiodinaceae microbiome pangenomes at ASM in D.C. If you are here, let’s hang out!!
June 5, 2026 at 5:19 PM
Thank you coral microbe friends for coming to my talk on Symbiodinaceae microbiome pangenomes at ASM in D.C. If you are here, let’s hang out!!
Excited to be awarded a BBSRC grant with @henrylnorth.bsky.social to study pangenomes of hybridising Lepidoptera species
May 14, 2026 at 6:20 PM
Excited to be awarded a BBSRC grant with @henrylnorth.bsky.social to study pangenomes of hybridising Lepidoptera species
@annadewar.bsky.social now giving the fourth @asn-amnat.bsky.social Early Career Scientist Award lectures at #Evol2025 about bacterial pangenomes, cooperation, and gene transfer
June 21, 2025 at 8:36 PM
@annadewar.bsky.social now giving the fourth @asn-amnat.bsky.social Early Career Scientist Award lectures at #Evol2025 about bacterial pangenomes, cooperation, and gene transfer
Pangenome analysis of transposable element insertion polymorphisms reveals features underlying cold tolerance in rice. #TransposableElements #TE #Pangenomes #RiceGenomes @natcomms.nature.com
www.nature.com/articles/s41...
www.nature.com/articles/s41...
August 17, 2025 at 7:05 PM
Pangenome analysis of transposable element insertion polymorphisms reveals features underlying cold tolerance in rice. #TransposableElements #TE #Pangenomes #RiceGenomes @natcomms.nature.com
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Alex Kramer, Alan Zhang and friends posted our preprint today. In it, we introduce Panmap, a tool for phylogenetic placement, assembly, lineage abundance estimation, and eDNA assignment using phylogenetic pangenomes.
www.biorxiv.org/content/10.6...
www.biorxiv.org/content/10.6...
www.biorxiv.org
March 31, 2026 at 8:21 PM
Alex Kramer, Alan Zhang and friends posted our preprint today. In it, we introduce Panmap, a tool for phylogenetic placement, assembly, lineage abundance estimation, and eDNA assignment using phylogenetic pangenomes.
www.biorxiv.org/content/10.6...
www.biorxiv.org/content/10.6...
Excited for this - visualizing pangenomes!! #bog25
Excited to share our latest work on comparing and visualizing multiple genome assemblies to identify conservation and structural variation in pangenomes with Mumemto! Check out poster 250 at #bog25 if you are here. New preprint coming very soon 👀
May 9, 2025 at 4:27 PM
Excited for this - visualizing pangenomes!! #bog25
A pangenome can reveal the spectrum of genome variation within a species. A technology feature in Nature #Methods describes the new tools for working with pangenomes. 🧬 🧪
It’s a colorful pangenome world - Nature Methods
A pangenome can reveal the spectrum of genome variation within a species. The toolbox for working with pangenomes is filling up.
go.nature.com
March 15, 2026 at 10:16 PM
A pangenome can reveal the spectrum of genome variation within a species. A technology feature in Nature #Methods describes the new tools for working with pangenomes. 🧬 🧪