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rmwaterhouse.bsky.social
Rob Waterhouse
@rmwaterhouse.bsky.social
1.9K followers 1.7K following 1.7K posts
Director, Environmental Bioinformatics Group at SIB Swiss Institute of Bioinformatics @sib.swiss. Chair, European Reference Genome Atlas (ERGA, @ergabiodiv.bsky.social). #biodiversity #genomics www.rmwaterhouse.org
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rmwaterhouse.bsky.social
Rob Waterhouse @rmwaterhouse.bsky.social · Sep 27
Sign up today to receive the monthly newsletter from the ERGA European Reference Genome Atlas to learn about #biodiversy #genomics initiatives in #Europe, courses, jobs, conferences, & more www.youtube.com/watch?v=kYL9...
What is ERGA? - European Reference Genome Atlas
YouTube video by ERGA - European Reference Genome Atlas
www.youtube.com
Reposted by Rob Waterhouse
elixir-europe.org
Large, complex datasets 💾 are fundamental to the life sciences and form the backbone of innovation. 📣 ELIXIR has published a report on the contribution of #OpenSource #software and #workflows to innovation in the #lifesciences 🔬.

Read the news 👉 https://loom.ly/THB_IX4
November 26, 2025 at 9:45 AM
rmwaterhouse.bsky.social
An efficient, accessible solution for #genome annotation in both research and applied settings www.nature.com/articles/s41...
Helixer: ab initio prediction of primary eukaryotic gene models combining deep learning and a hidden Markov model - Nature Methods
By leveraging both deep learning and hidden Markov models, Helixer achieves broad taxonomic coverage for ab initio gene annotation of eukaryotic genomes from fungi, plants, vertebrates and invertebrat...
www.nature.com
November 26, 2025 at 6:56 AM
rmwaterhouse.bsky.social
Findings support the hypothesis that gene duplications, particularly in reproduction and development, contributed to termite eusociality academic.oup.com/mbe/article/...
Genomic Features Underlying the Origin of Sociality and the Diversification of Caste Systems in Termites
Abstract. Termite colonies consist of distinct castes whose developmental pathways fall into 2 types and vary among lineages. Understanding caste evolution
academic.oup.com
November 25, 2025 at 2:18 PM
Reposted by Rob Waterhouse
ergabiodiv.bsky.social
💬 Missed the latest #ERGAPlenary? No problem - catch up now on the #ERGAchannel with the keynote: #biodiversity genomes at @enasequence.bsky.social & the #ERGA Data Portal - talk by Joana Pauperio and Alexey Sokolov from @ebi.embl.org

▶️ youtu.be/gaS61VQzbCk?...

#data #genomes #genomicdata
Biodiversity Reference Genomes at ENA and the ERGA Data Portal - Joana Paupério & Alexey Sokolov
YouTube video by ERGA - European Reference Genome Atlas
youtu.be
November 19, 2025 at 1:46 PM
Reposted by Rob Waterhouse
ergabiodiv.bsky.social
📰🍂 Our November newsletter is here!
www.erga-biodiversity.eu/post/erga-ne...

💻 Join the Taxon Sampling SOP "Hackathon" on December 5: www.erga-biodiversity.eu/post/join-th...
📚 Events, conferences & opportunities
🌍 Updates from committee initiatives
#newsletter #community #science #ERGANews
ERGA News #32 - November 2025
www.erga-biodiversity.eu
November 21, 2025 at 2:47 PM
rmwaterhouse.bsky.social
Analysis of read mapping accuracy and efficiency, missing data, heterozygosity, and inferred phylogenies to evaluate the impact of reference #genome and read-mapping method onlinelibrary.wiley.com/doi/10.1111/...
Variant Calling in the Goldilocks Zone: How Reference Genome Choice and Read Mapping Stringency Impact Heterozygosity Estimates and Phylogenetic Analyses
The increasing numbers of published reference genomes and affordability of whole genome resequencing have enabled multispecies population genomic and phylogenomic studies on non-model organisms, but ....
onlinelibrary.wiley.com
November 25, 2025 at 7:14 AM
Reposted by Rob Waterhouse
ebpgenome.bsky.social
Real conservation action, guided by genomes!
@ergabiodiv.bsky.social @biogeneurope.bsky.social
Why go beyond the reference genome?
Because population genomics reveals hidden risks — low diversity, genetic drift, and declining gene flow. 🌍
Wetlands are disappearing… and so is genetic diversity.
November 24, 2025 at 7:09 PM
Reposted by Rob Waterhouse
ergabiodiv.bsky.social
🗞️ Want to stay up to date with the latest #ERGA updates and the world of #BiodiversityGenomics?
Don’t miss our monthly newsletter ➡️ November: www.erga-biodiversity.eu/post/erga-ne...
Register as an #ERGAmember to stay in the loop: www.erga-biodiversity.eu/join-contact #newsletter #ERGANews
ergabiodiv.bsky.social ERGA - European Reference Genome Atlas @ergabiodiv.bsky.social · 5d
📰🍂 Our November newsletter is here!
www.erga-biodiversity.eu/post/erga-ne...

💻 Join the Taxon Sampling SOP "Hackathon" on December 5: www.erga-biodiversity.eu/post/join-th...
📚 Events, conferences & opportunities
🌍 Updates from committee initiatives
#newsletter #community #science #ERGANews
ERGA News #32 - November 2025
www.erga-biodiversity.eu
November 24, 2025 at 10:30 AM
Reposted by Rob Waterhouse
petermulhair.bsky.social
Latest work out today in @currentbiology.bsky.social

We find the fly development gene bicoid is much older than previously thought (~20 million yrs older!) 🪰🧬

To pinpoint its origins we tackled the Diptera phylogeny, providing some resolution (many open questions remain).

🔗 tinyurl.com/2vyuevpy
Revised evolutionary relationships within Brachycera and the early origin of bicoid in flies
Mulhair et al. uncover a functional bicoid in non-cyclorrhaphan flies, pushing the gene's origin back by ∼20 million years. Reassessing the Diptera phylogeny using the largest dataset to date permits ...
www.cell.com
October 17, 2025 at 3:14 PM
rmwaterhouse.bsky.social
Google introduces Scholar Labs, an AI powered Scholar search that is designed to help you answer detailed research questions scholar.googleblog.com/2025/11/scho...
Scholar Labs: An AI Powered Scholar Search
Research questions are often detailed. Answering them can require looking at a topic from multiple angles. Today, we are introducing Scholar...
scholar.googleblog.com
November 23, 2025 at 2:16 PM
Reposted by Rob Waterhouse
genomejournal.bsky.social
Saving the bellicose #bumblebee! 🐝 Brazil’s endemic Bombus bellicosus faces habitat loss & #ClimateChange. Sequencing its #genome shows it’s genetically diverse enough to survive, thanks in part to #CitizenScientists who helped locate populations.
🔗 doi.org/10.1139/gen-...
The nuclear and mitochondrial genomes of the bellicose bumblebee (Bombus bellicosus, Hymenoptera: Apidae), a threatened pollinator in a changing South American landscape
We present the first genome of a Brazilian bumblebee species, the bellicose bumblebee (Bombus bellicosus). This is an endemic species in southern South America facing local extinction due to habitat…
doi.org
November 21, 2025 at 2:22 PM
Reposted by Rob Waterhouse
transposableman.bsky.social
#TEsky Draft Genome Assembly of Parnassius epaphus Provides New Insights into Transposable Elements That Drive Genome Expansion in Alpine Parnassius butterflies doi.org/10.3390/d171...
doi.org
November 21, 2025 at 6:13 PM
rmwaterhouse.bsky.social
Modern octopod #genomes were extensively shaped by chromosomal fusion-with-mixing followed by inter-chromosomal translocations www.cell.com/iscience/ful... #biodiversity #genomics
Giant genome of the vampire squid reveals the derived state of modern octopod karyotypes
Marine organism; Genetics; Evolutionary mechanisms; Phylogenetics; Genomic analysis
www.cell.com
November 22, 2025 at 1:23 PM
rmwaterhouse.bsky.social
High-quality #genomes for northern bluefin tunas provide genomic tools for improving phylogenomic & evolutionary physiology analyses of this lineage & are important for potential functional assays for population biology of these commercially important species www.biorxiv.org/content/10.1...
Whole Genome Assembly of the Atlantic Bluefin Tuna Thunnus thynnus, with Phased Haplotypes
Atlantic bluefin tuna ( Thunnus thynnus ) are highly migratory fish, the largest tuna in the genus Thunnus . These fish possess a unique suite of traits, including regional endothermy, in their swimmi...
www.biorxiv.org
November 22, 2025 at 1:19 PM
rmwaterhouse.bsky.social
Neo-sex chromosome systems in frogs 🐸 www.nature.com/articles/s42...
Investigating the evolution of large meiotic rings of multiple X and Y sex chromosomes in two Leptodactylus frog species (Anura, Leptodactylidae) - Communications Biology
Comparative analysis of repetitive DNA in two Amazonian frogs reveals multiple sex chromosome systems and ring multivalents, clarifying chromosomal composition and evolution in Leptodactylus pentadact...
www.nature.com
November 22, 2025 at 1:15 PM
rmwaterhouse.bsky.social
Snail score value corresponds closely to a qualitative assessment of overall #genome assembly quality from visual interpretation of a snail plot www.biorxiv.org/content/10.1... #bidiversity #genomics
Snail plots are badges of genome assembly quality
Assembly quality is frequently assessed using independent measures of assembly span, contiguity, sequence composition and completeness. Among contiguity metrics, contig and scaffold N50 have perhaps g...
www.biorxiv.org
November 22, 2025 at 1:11 PM
rmwaterhouse.bsky.social
The @elixir-europe.org research infrastructure organises scientific- & technological-themed communities as one of its key mechanisms to ensure that services are user-focused, facilitating collaboration & impact through life science data generated across #Europe f1000research.com/articles/14-...
F1000Research Article: Fostering and sustaining collaborative innovation: Insights from ELIXIR Europe's life science Communities.
Read the latest article version by Clare Garrard, Katharina F Heil, Maria Cristina Aspromonte, Bérénice Batut, Magda Chegkazi, John M Hancock, Elaine Harrison, Naveed Ishaque, Giselle Ke...
f1000research.com
November 21, 2025 at 4:39 PM
Reposted by Rob Waterhouse
sinamajidian.bsky.social
Our trilogy of orthology publications is online!
Review on Hierarchical Orthologous Groups doi.org/10.1007/s00239-025-10277-1

OrthoXML-Tools doi.org/10.1007/s00239-025-10271-7

A great community effort on Quest for Orthologs in the era of Data Deluge and AI doi.org/10.1007/s00239-025-10272-6
https://link.springer.com/article/10.1007/s00239-025-10277-1 Conceptual overview of hierarchical orthologous groups. An example of one HOG, or gene family. A Species tree with four taxa: plant (green), fish (blue), human (orange), and mouse (yellow), each with one or more genes. B The implied gene tree, dubbed “HOG tree,” and inferred nested HOG composition. Duplication nodes (red) can be deduced based on the species tree topology and clusters of homologous genes at each level. Ancestral genes from which the HOGs descended are shown in gray. C HOGs returned at different taxonomic levels. Consider a gene family that was present in the last eukaryotic common ancestor (LECA). At this level, a single HOG encompasses all genes descending from that ancestral gene. At the Vertebrata level, this gene underwent duplication, leading to two distinct copies, i.e., HOGs. At the Mammalia level, a second duplication further subdivides one of these HOGs, showing how deeper HOGs split into nested subHOGs at more recent levels. The HOG composition implies that a loss event occurred after the mammalian speciation https://link.springer.com/article/10.1007/s00239-025-10272-6 Summary of the QfO8 meeting. a Hot topics and future directions in method development and applications within the QfO community, namely artificial intelligence, protein domains, protein structure, RNA and splicing isoforms. b Definition of orthology and paralogy, including various paralogous subtypes (e.g. in-paralogs and out-paralogs). c Duplications and functional divergence. d Applications of orthology https://link.springer.com/article/10.1007/s00239-025-10271-7 Overview of the OrthoXML File Format (simplified). A schematic representation of an OrthoXML file, a standardized XML-based format for representing orthology data. OrthoXML follows a hierarchical structure where elements are enclosed within opening < tag > and closing </tag > tags. < orthoXML > is the root element enclosing other elements. The < species > element contains information about genes. An OrthoXML file can include a < taxonomy > element, which specifies the species tree used to generate the file. Additionally, the < groups > element encapsulates the orthology and paralogy relationships among genes
November 21, 2025 at 4:26 PM
rmwaterhouse.bsky.social
Investigating #genome-wide signatures of selection in response to a broad climatic gradient and a geographic mosaic of coevolution between a social parasite and its host academic.oup.com/mbe/advance-...
Genomic Signatures of Selection Across Climate Gradients and a Geographic Mosaic of Coevolution in an Ant Social Parasite-Host System
Abstract. Coevolutionary dynamics in host-parasite systems are shaped by reciprocal selection and environmental context. When hosts and parasites share anc
academic.oup.com
November 21, 2025 at 10:11 AM
Reposted by Rob Waterhouse
phil-donoghue.bsky.social
Come and do a PhD on 'Genome duplication, extinction and diversification in the evolution of flowering plants' with myself @jameswclark.bsky.social and Ilia Leitch @bristolpalaeo.bsky.social and join the @wgdip.bsky.social studying rediploidisation. Apply: tinyurl.com/26pmfvvc by Jan 8
November 20, 2025 at 9:26 AM
Reposted by Rob Waterhouse
heredityjournal.bsky.social
Genome sequence analysis provides evidence that a boreal crustacean colonised Svalbard well before the ongoing Atlantification of the Arctic
www.nature.com/articles/s41...

@gensocuk.bsky.social
Genome sequence analysis provides evidence that a boreal crustacean colonised Svalbard well before the ongoing Atlantification of the Arctic - Heredity
Heredity - Genome sequence analysis provides evidence that a boreal crustacean colonised Svalbard well before the ongoing Atlantification of the Arctic
www.nature.com
November 20, 2025 at 10:33 AM
Reposted by Rob Waterhouse
heredityjournal.bsky.social
Lineage-specific targets of positive selection in three leaf beetles correspond with defence capacity against their shared parasitoid wasp
www.nature.com/articles/s41...

@gensocuk.bsky.social
Lineage-specific targets of positive selection in three leaf beetles correspond with defence capacity against their shared parasitoid wasp - Heredity
Heredity - Lineage-specific targets of positive selection in three leaf beetles correspond with defence capacity against their shared parasitoid wasp
www.nature.com
November 20, 2025 at 10:34 AM
Reposted by Rob Waterhouse
ipbes.net
📣SAVE THE DATE📣

Next week, 🏡 IPBES #2ndGlobalAssessment authors will meet for the first time in Paris, France at the UNESCO Headquarters.

The #GA2 will assess relevant knowledge that has become available since the publication of #GlobalAssessment.🌍

🧪 https://www.ipbes.net/second-global-assessment
Flags of various countries flying outside UNESCO Headquarters in Paris with a globe structure in the background. Overlay text reads: SAVE THE DATE. First Author Meeting of the Second Global Assessment. 24-28 November 2025. UNESCO Headquarters, Paris, France.
November 20, 2025 at 11:25 AM
Reposted by Rob Waterhouse
hoehna.bsky.social
PhD position available in evolutionary genomics/bioinformatics (hoehnalab.github.io/job_adverts/...). Topic: analyzing gene expression evolution across several firefly species and linking expression changes to genomic architecture. The position is jointly supervised with @anaevolcatalan.bsky.social
hoehnalab.github.io
November 11, 2025 at 9:00 AM
Reposted by Rob Waterhouse
posnienlab.bsky.social
🧬 PhD Position: Evolutionary & Comparative Genomics 🕷️
Join us at @uni-goettingen.de for a 3-year PhD (65% TV-L E13).
We will investigate the genomic & phenotypic impact of gene duplication across 233 arthropod genomes!
More infos 👇 and s.gwdg.de/eDrAAY
#Evolution #Genomics #Bioinformatics
Posnien - Georg-August-Universität Göttingen
Webseiten der Georg-August-Universität Göttingen
s.gwdg.de
November 18, 2025 at 7:04 AM