Julien Mozziconacci

Learning from Hi-C reveals nuclear dynamical reorganization in budding yeast across the cell cycle

This paper uses Hi-C data to infer 3D genome structure and chromatin dynamics in budding yeast without prior assumptions about nuclear organization.

Metabolic reorganization shapes the dynamics of a water kefir microbial community

This study investigates how microbial interactions shape metabolic dynamics in water kefir fermentation, revealing a shift in collective metabolism around 20 h of fermentation.

The mammalian genome is punctuated by regularly spaced nucleosome islands

The paper trains a deep-learning model to predict nucleosome occupancy from DNA sequence in mouse embryonic stem cells and identifies short DNA motifs that organize nucleosome arrays.

Unique territorial and compartmental organization of chromosomes in the holocentric silkworm

The paper discovers a novel chromatin folding structure, compartment S, in the silkworm Bombyx mori using Hi-C, showing unique loop extrusion and contact patterns.

Near-critical chromatin fluctuations facilitate long-range contacts in Drosophila chromosomes

This study shows that near-critical chromatin dynamics in Drosophila embryos best explain experimental data on long-range contacts and structural organization.

In silico design of DNA sequences for in vivo nucleosome positioning

The paper designs synthetic DNA sequences for in vivo nucleosome positioning in yeast using a kinetic Monte Carlo framework combined with deep learning predictions.

Design, Construction, and Functional Characterization of a tRNA Neochromosome in Yeast

A de novo yeast neochromosome carrying all 275 tRNA genes was built and characterized; it imposes a growth burden, with genome doubling and deletions in haploids possibly reflecting compensation.

Synthetic chromosome fusion: effects on genome structure and function

The paper synthesizes a shorter yeast chromosome and studies its fusion with other chromosomes, revealing new 3D structural interactions and Red1 binding patterns.

Application of fuzzy measures to move towards the cyber-taxonomy

The paper applies fuzzy measures to automatically connect and match identical specimens across multiple databases in the context of cyber-taxonomy.

A layer cake model for plant and metazoan chromatin

The paper compares 3D chromatin organization across species to propose a layer cake model that refines the two compartments model by identifying distinct chromatin layers.

Exogenous chromosomes reveal how sequence composition drives chromatin assembly, activity, folding and compartmentalization

This study shows that bacterial chromosomes can undergo chromatin assembly, activity, looping, and compartmentalization in yeast, driven by their sequence composition.

Condensin I folds the C. elegans genome

This study shows that condensin I/IDC, not cohesin, is the major genome loop extruder in C. elegans, leading to genome decompaction and loss of TAD structures.

Nucleosome positioning on large tandem DNA repeats of the '601' sequence engineered in Saccharomyces cerevisiae

The paper tests if the 601 DNA sequence can position nucleosomes in vivo in yeast, finding that it does not reliably do so in a tandem repeat array context.

Epigenetic rewriting at centromeric DNA repeats leads to increased chromatin accessibility and chromosomal instability

The paper shows that reducing H3K9me3 at centromeric repeats using TALE-JMJD2B increases chromatin accessibility and causes chromosomal instability.

Contribution of 3D genome topological domains to genetic risk of cancers

This paper investigates the distribution of disease-associated SNPs relative to 3D genome topological domains and finds that cancer risk loci are preferentially located at TAD borders.

Genome Functional Annotation using Deep Convolutional Neural Networks

This paper trains convolutional neural networks to annotate genomes using sequence data, showing cross-species applicability for transcription start site prediction.

Boost-HiC : Computational enhancement of long-range contacts in chromosomal contact maps

Boost-HiC enhances long-range chromosomal contact maps by improving resolution using sparse data, enabling detection of Hi-C patterns with reduced sequencing depth.

Redesigning chromosomes for optimized Hi-C assay provides insights on loop formation and homologs pairing during meiosis

The paper redesigns a genomic region for improved Hi-C analysis, revealing insights into homolog pairing and loop formation during meiosis.

Choreography of budding yeast chromosomes during the cell cycle

The paper uses Hi-C to analyze chromosome structure dynamics in budding yeast during the cell cycle, revealing SMC-dependent structural transitions and mitotic reorganization.