Nelle Varoquaux
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Explore the profile of Nelle Varoquaux including associated specialties, affiliations and a list of published articles.
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1793
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Recent Articles
1.
Chobert S, Roger-Margueritat M, Flandrin L, Berraies S, Lefevre C, Pelosi L, et al.
ISME J
. 2024 Dec;
19(1.
PMID: 39693360
It is currently unclear how Pseudomonadota, a phylum that originated around the time of the Great Oxidation Event, became one of the most abundant and diverse bacterial phyla on Earth,...
2.
Kazemzadeh K, Pelosi L, Chenal C, Chobert S, Chehade M, Jullien M, et al.
Mol Biol Evol
. 2023 Oct;
40(10).
PMID: 37788637
The availability of an ever-increasing diversity of prokaryotic genomes and metagenomes represents a major opportunity to understand and decipher the mechanisms behind the functional diversification of microbial biosynthetic pathways. However,...
3.
Varoquaux N, Noble W, Vert J
Bioinformatics
. 2023 Jan;
39(1).
PMID: 36594573
Motivation: We address the challenge of inferring a consensus 3D model of genome architecture from Hi-C data. Existing approaches most often rely on a two-step algorithm: first, convert the contact...
4.
Etourneau L, Varoquaux N, Burger T
Methods Mol Biol
. 2022 Oct;
2426:1-24.
PMID: 36308682
In proteomic differential analysis, FDR control is often performed through a multiple test correction (i.e., the adjustment of the original p-values). In this protocol, we apply a recent and alternative...
5.
Paxton A, Varoquaux N, Holdgraf C, Geiger R
Cogn Sci
. 2022 May;
46(5):e13134.
PMID: 35579857
Free and open-source software projects have become essential digital infrastructure over the past decade. These projects are largely created and maintained by unpaid volunteers, presenting a potential vulnerability if the...
6.
Gao C, Courty P, Varoquaux N, Cole B, Montoya L, Xu L, et al.
Mol Ecol
. 2022 Jan;
32(10):2674-2687.
PMID: 35000239
The shifts in adaptive strategies revealed by ecological succession and the mechanisms that facilitate these shifts are fundamental to ecology. These adaptive strategies could be particularly important in communities of...
7.
Scavuzzo-Duggan T, Varoquaux N, Madera M, Vogel J, Dahlberg J, Hutmacher R, et al.
Front Plant Sci
. 2021 Dec;
12:747225.
PMID: 34868130
Renewable fuels are needed to replace fossil fuels in the immediate future. Lignocellulosic bioenergy crops provide a renewable alternative that sequesters atmospheric carbon. To prevent displacement of food crops, it...
8.
Lioy V, Lorenzi J, Najah S, Poinsignon T, Leh H, Saulnier C, et al.
Nat Commun
. 2021 Sep;
12(1):5221.
PMID: 34471117
Bacteria of the genus Streptomyces are prolific producers of specialized metabolites, including antibiotics. The linear chromosome includes a central region harboring core genes, as well as extremities enriched in specialized...
9.
Varoquaux N, Lioy V, Boccard F, Junier I
Methods Mol Biol
. 2021 Aug;
2301:197-207.
PMID: 34415537
Just as in eukaryotes, high-throughput chromosome conformation capture (Hi-C) data have revealed nested organizations of bacterial chromosomes into overlapping interaction domains. In this chapter, we present a multiscale analysis framework...
10.
Xu L, Dong Z, Chiniquy D, Pierroz G, Deng S, Gao C, et al.
Nat Commun
. 2021 May;
12(1):3209.
PMID: 34050180
Recent studies have demonstrated that drought leads to dramatic, highly conserved shifts in the root microbiome. At present, the molecular mechanisms underlying these responses remain largely uncharacterized. Here we employ...