Ivan Junier

COCOA-Tree: Phylogenetic visualization and comparative analysis of coevolving residues

COCOA-Tree reanalyzes coevolution datasets to uncover evolutionary properties of coevolving residues and shows different metrics identify distinct groups.

Improved inference of multiscale sequence statistics in generative protein models

This paper introduces a new regularization strategy for generative protein models that improves the inference of multiscale sequence statistics, enabling the generation of functional and diverse protein sequences.

Conserved lifestyle-associated chromosome architectures across mammalian symbionts

This study investigates chromosome organization in obligate mammalian symbionts, revealing conserved architectures linked to their lifestyle and growth conditions.

Unwelcome guests: characterizing the ecological niche of insertion sequences within prokaryotic genomes

The paper analyzes insertion sequences (ISs) in prokaryotic genomes using transposon ecology to uncover general principles and niche specificities shaping their distribution and activity.

Stable chromosome configuration and loop-based polarization in animal symbionts

The paper studies chromosome organization in longitudinally dividing Neisseriaceae bacteria, finding that the origin of replication is at the host-attached pole and that loop-based folding occurs in specific contexts.

circHiC: circular visualization of Hi-C data and integration of genomic data

The paper introduces a Python library for visualizing Hi-C data in circular formats, suitable for bacterial and eukaryotic chromosomes, with tools for overlaying genomic data.

A two-enzyme adaptive unit in bacterial folate metabolism

The paper investigates adaptive dependencies between enzymes in bacterial folate metabolism, showing that DHFR and TYMS form a modular unit that can adapt independently from the rest of the genome.

Conserved units of co-expression in bacterial genomes: an evolutionary insight into gene regulation

The paper identifies conserved co-expression units in bacterial genomes beyond operons, showing that gene regulation can occur through segment-level feedback mechanisms.