Nelle Varoquaux

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.

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.

Global distribution of isoprenoid quinones across Bacteria

This study maps the distribution of isoprenoid quinones in Bacteria using genomic data and phylogenetic analysis, revealing new insights into their evolutionary history and metabolic adaptations.

Multi-season analysis reveals hundreds of drought-responsive genes in sorghum

This study identifies hundreds of drought-responsive genes in sorghum using multi-season transcriptomic data from field experiments.

HDMAX2-surv: high-dimensional mediation analysis of survival data with application to pancreatic cancer

HDMAX2-surv identifies epigenetic mediators of survival outcomes in pancreatic cancer using a two-step framework with latent factor modeling and survival models.

Penalized likelihood optimization for censored missing value imputation in proteomics

The paper introduces Pirat, a method for imputing missing values in proteomics data by modeling instrument limits and peptide correlations, showing improved performance over existing methods.

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.

Inference of genome 3D architecture by modeling overdispersion of Hi-C data

The paper introduces a new model, Pastis-NB, for inferring 3D genome architecture from Hi-C data by addressing overdispersion in contact counts, showing improved accuracy and robustness compared to existing methods.

Unveiling the links between peptide identification and differential analysis FDR controls by means of a practical introduction to knockoff filters

This paper introduces knockoff filters for FDR control in proteomic differential analysis, comparing them to traditional methods on real and simulated data.

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.

Inferring diploid 3D chromatin structures from Hi-C data

This paper introduces a method to infer 3D diploid chromatin structures from Hi-C data and validates it on simulated and mouse chromosome X data.

Effective normalization for copy number variation in Hi-C data

This paper introduces a normalization method for Hi-C data that accounts for copy number variations, improving downstream analysis of genome organization.

Changes in genome organization of parasite-specific gene families during the Plasmodium transmission stages

This study examines changes in genome organization during the transmission stages of Plasmodium parasites and finds that three-dimensional genome structure is linked to transcriptional activity of gene families involved in pathogenesis and immune evasion.