Gaurav Diwan
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gddiwan.bsky.social
Gaurav Diwan
@gddiwan.bsky.social
62 followers 62 following 13 posts
Postdoc Bioquant | Uni Heidelberg
Molecular Evolution 🧬
Phylogenomics 🪾
Bioinformatics 🖥️
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gddiwan.bsky.social
Gaurav Diwan @gddiwan.bsky.social · Sep 23
Pleased to announce that our #preprint on the evolutionary history of gene functions is now online at #bioRxiv! We overlayed functional annotations on the evolutionary history of ~4.5M genes from 508 species across the tree of life and found some very cool stuff!

tinyurl.com/FuncEvol

🧵 1/10
Number of genes, domains and pathways gained at every node of a cladogram of 508 species
Reposted by Gaurav Diwan
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
gddiwan.bsky.social
Pleased to announce that our #preprint on the evolutionary history of gene functions is now online at #bioRxiv! We overlayed functional annotations on the evolutionary history of ~4.5M genes from 508 species across the tree of life and found some very cool stuff!

tinyurl.com/FuncEvol

🧵 1/10
Number of genes, domains and pathways gained at every node of a cladogram of 508 species
September 23, 2025 at 9:53 AM
gddiwan.bsky.social
Good morning people at #ESEB2025

Come check out my poster P03.068 today to know about

- The evolutionary history of genes and gene functions from >500 species across the tree of life 🪾

- How that helps us reveal widespread parallelisms in the move from water to land and multicellularity 🧬
August 21, 2025 at 6:00 AM
gddiwan.bsky.social
Fantastic day 1 @eseb2025.bsky.social ! Talks showing how incorrect orthology and hidden paralogy could affect phylogenetic tree structures; species tree inference from WGA; and how pre-LUCA protein sequences tell you the order in which amino acids emerged!
Super cool stuff #ESEB2025
August 18, 2025 at 6:55 PM
gddiwan.bsky.social
Checked in @eseb2025.bsky.social in Barcelona. Come check out my poster on Thursday if you want to know the evolutionary history of any gene or its function! #ESEB2025
August 17, 2025 at 6:36 PM