Publications 2017

Lanaud C. et al.
Deciphering the Theobroma cacao self-incompatibility system: from genomics to diagnostic markers for self-compatibility.
J Exp Bot. (2017) Oct. 68(17):4775-4790.
doi: 10.1093/jxb/erx293

Recanati A. et al.
A spectral algorithm for fast de novo layout of uncorrected long nanopore reads.
Bioinformatics (2017) Oct. 33(20):3188-3194.
doi: 10.1093/bioinformatics/btx370

Schmidt MHW. et al.
De novo assembly of a new Solanum pennellii accession using nanopore sequencing.
Plant Cell (2017) Oct. 29(10):2336-2348.
doi: 10.1105/tpc.17.00521

Terrat S. et al.
Mapping and predictive variations of soil bacterial richness across France.
PLoS One (2017) Oct. 12(10):e0186766.
doi: 10.1371/journal.pone.0186766

Plouhinec JL. et al.
A molecular atlas of the developing ectoderm defines neural, neural crest, placode, and nonneural progenitor identity in vertebrates.
PLoS Biol. (2017) Oct. 15(10):e2004045.
doi: 10.1371/journal.pbio.2004045

Ceolin L. et al.
Cell Type-Specific mRNA Dysregulation in Hippocampal CA1 Pyramidal Neurons of the Fragile X Syndrome Mouse Model.
Front Mol Neurosci. (2017) Oct. 10:340.
doi: 10.3389/fnmol.2017.00340

Varrault A. et al.
Identification of Plagl1/Zac1 binding sites and target genes establishes its role in the regulation of extracellular matrix genes and the imprinted gene network.
Nucleic Acids Res. (2017) Oct 13.45(18):10466-10480.
doi: 10.1093/nar/gkx672

Loire E. et al.
Do changes in gene expression contribute to sexual isolation and reinforcement in the house mouse?
Mol Ecol. (2017) Oct. 26(19):5189-5202.
doi: 10.1111/mec.14212

Saudemont B. et al.
The fitness cost of mis-splicing is the main determinant of alternative splicing patterns.
Genome Biology (2017) Oct. 18(1):208.
doi: 10.1186/s13059-017-1344-6

Frachon L. et al.
Intermediate degrees of synergistic pleiotropy drive adaptive evolution in ecological time.
Nature Ecology Evolution (2017) Oct. 1:1551–1561
doi: 10.1038/s41559-017-0297-1

Cohen-Boulakia S. et al.
Scientific workflows for computational reproducibility in the life sciences: Status, challenges and opportunities.
Future Generation Computer Systems (2017) Oct. 75:284-298.
doi: 10.1016/j.future.2017.01.012

Ivanova C. et al.
Genome sequencing and transcriptome analysis of Trichoderma reesei QM9978 strain reveals a distal chromosome translocation to be responsible for loss of vib1 expression and loss of cellulase induction.
Biotechnology for Biofuels (2017) Sep. 10:209.
doi: 10.1186/s13068-017-0897-7

Argout X. et al.
The cacao Criollo genome v2.0: an improved version of the genome for genetic and functional genomic studies.
BMC Genomics (2017), Sep. 18(1):730.
doi: 10.1186/s12864-017-4120-9

Arrigoni R. et al.
A new sequence data set of SSU rRNA gene for Scleractinia and its phylogenetic and ecological applications.
Mol Ecol Resour. (2017) Sep. 17(5):1054-1071.
doi: 10.1111/1755-0998.12640

Madoui MA. et al.
New insights into global biogeography, population structure and natural selection from the genome of the epipelagic copepod Oithona.
Mol Ecol. (2017) Sep. 26(17):4467-4482.
doi: 10.1111/mec.14214

Martin G. et al.
Evolution of the Banana genome (Musa acuminata) is Impacted by large chromosomal translocations.
Mol Biol Evol. (2017) Sep. 34(9):2140-2152.
doi: 10.1093/molbev/msx164

Ivanova ELet al.
Homozygous truncating variants in TBC1D23 cause Pontocerebellar Hypoplasia and alter cortical development.
Am J Hum Genet. (2017) Sep. 101(3):428-440.
doi: 10.1016/j.ajhg.2017.07.010

Su XP. et al.
NSD1 inactivation and SETD2 mutation drive a convergence toward loss of function of H3K36 writers in Clear Cell Renal Cell Carcinomas.
Cancer Res. (2017) Sept. 77 (18): 4835-4845
doi: 10.1158/0008-5472.CAN-17-0143

Chaignaud P. et al.
Genomic and transcriptomic analysis of growth-supporting dehalogenation of chlorinated methanes in Methylobacterium.
Front Microbiol. (2017) Se. 8:1600.
doi: 10.3389/fmicb.2017.01600

Rochat T. et al.
Genomic characterization of Flavobacterium psychrophilum serotypes and development of a multiplex PCR-based serotyping scheme.
Front in Microbiol.(2017) Sep. 8:1752.
doi: 10.3389/fmicb.2017.01752

Payelleville A. et al.
DNA adenine methyltransferase (Dam) overexpression impairs Photorhabdus luminescens Motility and Virulence.
Front Microbiol. (2017) Sep. 8: 1671
doi: 10.3389/fmicb.2017.01671

Medigue C. et al.
MicroScope-an integrated resource for community expertise of gene functions and comparative analysis of microbial genomic and metabolic data. In
Brief Bioinformatics (2017) Sep.
doi: 10.1093/bib/bbx11

Belda E. et al.
Accurate microbial genome annotation using an integrated and user-friendly environment for community expertise of gene functions: The MicroScope Platform. In
Hydrocarbon and Lipid Microbiology Protocols: Genetic, Genomic and System Analyses of Pure Cultures (2017) pp 141-169. Berlin, Heidelberg
doi:

Gouin A. et al.
Two genomes of highly polyphagous lepidopteran pests (Spodoptera frugiperda, Noctuidae) with different host-plant ranges.
Scie. Rep. (2017) Sep. 7(1):11816.
doi: 10.1038/s41598-017-10461-4

Eoche-Bosy D. et al.
Genome scans on experimentally evolved populations reveal candidate regions for adaptation to plant resistance in the potato cyst nematode Globodera pallida.
Mol Ecol. (2017) Sep. 26(18):4700-4711.
doi: 10.1111/mec.14240

Sims R. et al.
Rare coding variants in PLCG2, ABI3, and TREM2 implicate microglial-mediated innate immunity in Alzheimer's disease.
Nat. Genetics (2017) Sept. 49(9):1373-1384.
doi: 10.1038/ng.3916

Goudot C. et al.
Aryl Hydrocarbon receptor controls monocyte differentiation into dendritic cells versus macrophages.
Immunity (2017) Sep. 47(3):582-596.e6.
doi: 10.1016/j.immuni.2017.08.016

Bonnet A. et al.
Quaking RNA-binding proteins control early myofibril formation by modulating Tropomyosin.
Dev Cell. (2017) Sep. 42(5):527-541.e4.
doi: 10.1016/j.devcel.2017.08.004

Ghoumid J. et al.
Blepharocheilodontic syndrome is a CDH1 pathway-related disorder due to mutations in CDH1 and CTNND1.
Genet Med. (2017) Sep.19(9):1013-1021.
doi: 10.1038/gim.2017.11

Garcia-Seco D. et al.
Transcriptome and proteome analysis reveal new insight into proximal and distal responses of wheat to foliar infection by Xanthomonas translucens.
Sci Rep. (2017) Aug.7(1):10157.
doi: 10.1038/s41598-017-10568-8