Christophe Dessimoz

On the state of protein function prediction: a report on the fourth CAFA challenge

This paper reports on the fourth CAFA challenge, showing improvements in Gene Ontology term prediction but highlighting challenges in new evaluation settings.

PhytClust: Efficient and Optimal Monophyletic Partitioning of Rooted Phylogenetic Trees

PhytClust partitions rooted phylogenetic trees into monophyletic clusters without user-defined thresholds, achieving optimal and reproducible results across diverse biological datasets.

OMAnnotator: a novel approach to building an annotated consensus genome sequence

OMAnnotator improves genome annotation by integrating multiple evidence sources using evolutionary information, outperforming existing pipelines in re-annotating Drosophila and other genomes.

AmpliPhy improves gene trees by adding homologous sequences without affecting alignments

Structural phylogenetics unravels the evolutionary diversification of communication systems in gram-positive bacteria and their viruses

The paper introduces a structure-informed phylogenetic framework to study the evolutionary diversification of RRNPPA quorum sensing receptors in gram-positive bacteria and their viruses.

EdgeHOG: fine-grained ancestral gene order inference at tree-of-life scale

EdgeHOG infers ancestral gene order across the tree of life, producing 1,133 ancestral genomes and revealing conserved and rapidly evolving gene adjacencies.

CDK4 Restricts Triple-Negative Breast Cancer Cell Migration via Phosphorylation-Driven Activation of Myo9b RhoGAP Function

This study shows CDK4 inhibits TNBC cell migration by phosphorylating Myo9b, which suppresses RhoA signaling, and suggests targeting Myo9b-RhoA could improve CDK4/6 inhibitor therapy.

Orthology inference at scale with FastOMA

FastOMA scales orthology inference to handle large genome datasets efficiently while maintaining accuracy.

Unveiling the Functional Fate of Duplicated Genes Through Expression Profiling and Structural Analysis

This study tests the least diverged orthologue conjecture by analyzing sequence and expression data across multiple species, finding that the least diverged orthologue tends to retain ancestral functions.

Exploring Disease Model Mouse Using Knowledge Graphs: Combining Gene Expression, Orthology, and Disease Datasets

The paper integrates multiple biological datasets to explore disease-related genes and bioresources using SPARQL queries, identifying relevant genes and anatomical parts for Alzheimer's and melanoma research.

Multifaceted quality assessment of gene repertoire annotation with OMArk

OMArk evaluates gene repertoire quality by assessing completeness, consistency, and contamination across species, identifying issues in reference proteomes.

Reconstructing protein interactions across time using phylogeny-aware graph neural networks

The paper introduces a phylogenetic profiling method using graph neural networks to reconstruct protein interactions across time, showing improved performance over traditional methods.

Read2Tree: scalable and accurate phylogenetic trees from raw reads

Read2Tree processes raw sequencing reads to build phylogenetic trees, outperforming conventional methods in speed and accuracy across diverse datasets.

A Linear-Time Solution to the Labeled Robinson-Foulds Distance Problem

The paper introduces a linear-time algorithm for computing the Labeled Robinson-Foulds edit distance between trees with labeled internal nodes, showing it improves upon previous methods.

OMAMO: orthology-based model organism selection

OMAMO selects the best simple model organism for studying a biological process based on orthologous relationships between humans and species.

OMAmer: tree-driven and alignment-free protein assignment to subfamilies outperforms closest sequence approaches

OMAmer improves protein subfamily assignment by using alignment-free methods and phylogenetic information, reducing misassignments compared to closest sequence approaches.

Scalable Phylogenetic Profiling using MinHash Uncovers Likely Eukaryotic Sexual Reproduction Genes

HogProf is a scalable phylogenetic profiling method that identifies genes involved in sexual reproduction by comparing gene presence/absence across eukaryotic genomes.

Genomic encryption of digital data stored in synthetic DNA

The paper demonstrates storing encrypted digital data in synthetic DNA using keys derived from human DNA's short tandem repeats, with successful decryption via sequencing.

The CAFA challenge reports improved protein function prediction and new functional annotations for hundreds of genes through experimental screens

The paper reports results from the CAFA3 challenge, showing improved computational protein function prediction and new annotations for over 1000 genes through experimental screens in C. albicans, P. aureginosa, and Drosophila.

Parallel and Scalable Precise Clustering for Homologous Protein Discovery

This paper introduces ClusterMerge, a precise clustering algorithm that efficiently identifies homologous proteins by reducing computational complexity and enabling parallel processing.

OMA standalone: orthology inference among public and custom genomes and transcriptomes

OMA standalone is a tool for orthology inference across public and custom genomes, enabling analysis of both existing and user-provided data.

Enabling Semantic Queries Across Federated Bioinformatics Databases

The paper introduces a semantic model and federated approach to integrate heterogeneous biological databases, enabling joint queries across gene expression, orthology, and protein data sources.

Phylogenetic approaches to identifying fragments of the same gene, with application to the wheat genome

The paper introduces two phylogenetic tests to identify gene fragments in the wheat genome and finds 1221 likely gene fragment pairs in a draft assembly.

Taxon sampling unequally affects individual nodes in a phylogenetic tree: consequences for model gene tree construction in SwissTree

The paper shows taxon sampling unevenly impacts gene tree nodes and introduces a two-step method to construct more reliable model gene trees using SwissTree.

Lessons Learned: Recommendations for Establishing Critical Periodic Scientific Benchmarking

This paper describes OpenEBench, a continuous automated benchmarking system for bioinformatics methods, tools, and web services to improve reproducibility and interoperability.

Transient structural variations alter gene expression and quantitative traits in Schizosaccharomyces pombe.

The paper investigates how structural variations in yeast genomes affect gene expression and quantitative traits, finding that copy number variants significantly influence phenotypes and reproductive isolation.