Laurent Farinelli

Laurent Farinelli

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Laurent Farinelli

Laurent Farinelli

Publications by authors named "Laurent Farinelli"

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Small RNA-Omics for Virome Reconstruction and Antiviral Defense Characterization in Mixed Infections of Cultivated Solanum Plants.

Mol Plant Microbe Interact 2018 07 10;31(7):707-723. Epub 2018 May 10.

1 Department of Environmental Sciences, Botany, Zurich-Basel Plant Science Center, University of Basel, Hebelstrasse 1, 4056 Basel, Switzerland.

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http://dx.doi.org/10.1094/MPMI-12-17-0301-RDOI Listing
July 2018

Revisiting the Roles of Tobamovirus Replicase Complex Proteins in Viral Replication and Silencing Suppression.

Mol Plant Microbe Interact 2018 01 15;31(1):125-144. Epub 2017 Nov 15.

1 University of Basel, Department of Environmental Sciences, Basel, Switzerland.

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http://dx.doi.org/10.1094/MPMI-07-17-0164-RDOI Listing
January 2018

Roles of Non-Coding RNA in Sugarcane-Microbe Interaction.

Noncoding RNA 2017 Dec 20;3(4). Epub 2017 Dec 20.

Laboratório de Biologia Molecular de Plantas, Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-901, Brazil.

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http://dx.doi.org/10.3390/ncrna3040025DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5831913PMC
December 2017

Microbial Communities of Conducting and Respiratory Zones of Lung-Transplanted Patients.

Front Microbiol 2016 7;7:1749. Epub 2016 Nov 7.

Transplant Infectious Diseases Unit, Geneva University Hospitals and Department of Microbiology and Molecular Medicine, University of Geneva Geneva, Switzerland.

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http://dx.doi.org/10.3389/fmicb.2016.01749DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5097918PMC
November 2016

MISIS-2: A bioinformatics tool for in-depth analysis of small RNAs and representation of consensus master genome in viral quasispecies.

J Virol Methods 2016 Jul 16;233:37-40. Epub 2016 Mar 16.

University of Basel, Department of Environmental Sciences, Botany, Hebelstrasse 1, 4056 Basel, Switzerland. Electronic address:

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http://dx.doi.org/10.1016/j.jviromet.2016.03.005DOI Listing
July 2016

Unusual RNA plant virus integration in the soybean genome leads to the production of small RNAs.

Plant Sci 2016 May 11;246:62-69. Epub 2016 Feb 11.

Centro de Biotecnologia, Programa de Pós-Graduação em Biologia Celular e Molecular, Universidade Federal do Rio Grande do Sul, RS, Brazil; Departamento de Genética, Programa de Pós-Graduação em Genética e Biologia Molecular, Universidade Federal do Rio Grande do Sul, RS, Brazil. Electronic address:

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http://dx.doi.org/10.1016/j.plantsci.2016.01.011DOI Listing
May 2016

Evidence for the sexual origin of heterokaryosis in arbuscular mycorrhizal fungi.

Nat Microbiol 2016 03 21;1(6):16033. Epub 2016 Mar 21.

Canadian Institute for Advanced Research, Department of Biology, University of Ottawa, Ottawa, Ontario, Canada.

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http://www.nature.com/articles/nmicrobiol201633
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http://dx.doi.org/10.1038/nmicrobiol.2016.33DOI Listing
March 2016

Genome analyses suggest the presence of polyploidy and recent human-driven expansions in eight global populations of the honeybee pathogen Nosema ceranae.

Environ Microbiol 2015 Nov 11;17(11):4443-58. Epub 2015 Jun 11.

Canadian Institute for Advanced Research, Department of Biology; University of Ottawa, Ottawa, ON, Canada.

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http://dx.doi.org/10.1111/1462-2920.12883DOI Listing
November 2015

Embryonic gene expression of Coregonus palaea (whitefish) under pathogen stress as analyzed by high-throughput RNA-sequencing.

Fish Shellfish Immunol 2015 Nov 2;47(1):130-40. Epub 2015 Sep 2.

Department of Ecology and Evolution, Biophore, University of Lausanne, 1015 Lausanne, Switzerland.

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http://dx.doi.org/10.1016/j.fsi.2015.08.035DOI Listing
November 2015

bacterial infection drives the expression dynamics of microRNAs and their isomiRs.

PLoS Genet 2015 Mar 20;11(3):e1005064. Epub 2015 Mar 20.

Institut Pasteur, Unit of Human Evolutionary Genetics, Paris, France; Centre National de la Recherche Scientifique, Paris, France.

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http://dx.doi.org/10.1371/journal.pgen.1005064DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4368565PMC
March 2015

Genome-wide identification of microRNA and siRNA responsive to endophytic beneficial diazotrophic bacteria in maize.

BMC Genomics 2014 Sep 6;15:766. Epub 2014 Sep 6.

Laboratório de Biologia Molecular de Plantas, Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Cidade Universitária, Avenida Carlos Chagas Filho, 373, CCS, Bl,L-29ss, Rio de Janeiro RJ 21941-599, Brazil.

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http://dx.doi.org/10.1186/1471-2164-15-766DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4168055PMC
September 2014

Sugarcane genome sequencing by methylation filtration provides tools for genomic research in the genus Saccharum.

Plant J 2014 Jul 17;79(1):162-72. Epub 2014 Jun 17.

Laboratório de Biologia Molecular de Plantas, Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Av. Carlos Chagas Filho 373, CCS, Bl.L-29, Cidade Universitária, Rio de Janeiro, 21941-599, RJ, Brazil.

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http://dx.doi.org/10.1111/tpj.12539DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4458261PMC
July 2014

Implication of sperm RNAs in transgenerational inheritance of the effects of early trauma in mice.

Nat Neurosci 2014 May 13;17(5):667-9. Epub 2014 Apr 13.

Brain Research Institute, Neuroscience Center Zürich, University of Zürich and Swiss Federal Institute of Technology, Zürich, Switzerland.

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http://dx.doi.org/10.1038/nn.3695DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4333222PMC
May 2014

A genomic perspective on a new bacterial genus and species from the Alcaligenaceae family, Basilea psittacipulmonis.

BMC Genomics 2014 Mar 1;15:169. Epub 2014 Mar 1.

Genomic Research Laboratory, Department of Internal Medicine, Service of Infectious Diseases, Geneva University Hospitals, Gabrielle-Perret-Gentil 4, CH-1211 Geneva 14, Switzerland.

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http://dx.doi.org/10.1186/1471-2164-15-169DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4028982PMC
March 2014

Duality of the murine CD8 compartment.

Proc Natl Acad Sci U S A 2014 Mar 4;111(11):E1007-15. Epub 2014 Mar 4.

Ludwig Centre for Cancer Research, University of Lausanne, 1066 Epalinges, Switzerland.

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http://dx.doi.org/10.1073/pnas.1317847111DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3964049PMC
March 2014

Extreme diversification of the mating type-high-mobility group (MATA-HMG) gene family in a plant-associated arbuscular mycorrhizal fungus.

New Phytol 2014 Jan 27;201(1):254-68. Epub 2013 Aug 27.

Canadian Institute for Advanced Research, Department of Biology, University of Ottawa, Ottawa, ON, K1N 6N5, Canada.

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http://dx.doi.org/10.1111/nph.12462DOI Listing
January 2014

De novo finished 2.8 Mbp Staphylococcus aureus genome assembly from 100 bp short and long range paired-end reads.

Bioinformatics 2014 Jan 15;30(1):40-9. Epub 2013 Oct 15.

Genomic Research Laboratory, Infectious Diseases Service, Geneva University Hospitals, 1211 Geneva 4, Switzerland, Scripps Translational Science Institute, The Scripps Research Institute, La Jolla, CA 92037, USA, BioMérieux, Data and Knowledge Laboratory, 69280 Marcy l'Etoile, France and Fasteris SA, PO Box 28, 1228 Plan-les-Ouates, Switzerland.

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http://dx.doi.org/10.1093/bioinformatics/btt590DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6280916PMC
January 2014

MISIS: a bioinformatics tool to view and analyze maps of small RNAs derived from viruses and genomic loci generating multiple small RNAs.

J Virol Methods 2014 Jan 14;195:120-2. Epub 2013 Oct 14.

Zürich-Basel Plant Science Center, University of Basel, Department of Environmental Sciences, Botany, Hebelstrasse 1, 4056 Basel, Switzerland; Fasteris SA, Ch. du Pont-du-Centenaire 109, 1228 Plan-les-Ouates, Switzerland.

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http://dx.doi.org/10.1016/j.jviromet.2013.10.013DOI Listing
January 2014

Analysis of the Elodea nuttallii transcriptome in response to mercury and cadmium pollution: development of sensitive tools for rapid ecotoxicological testing.

Environ Sci Technol 2013 Aug 25;47(15):8825-34. Epub 2013 Jul 25.

Institut F.-A. Forel, University of Geneva , 10 route de Suisse, CP416, 1290 Versoix, Switzerland.

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http://dx.doi.org/10.1021/es401082hDOI Listing
August 2013

Extremely reduced levels of heterozygosity in the vertebrate pathogen Encephalitozoon cuniculi.

Eukaryot Cell 2013 Apr 2;12(4):496-502. Epub 2013 Feb 2.

Canadian Institute for Advanced Research, Department of Biology, University of Ottawa, Ottawa, Ontario, Canada.

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http://ec.asm.org/lookup/doi/10.1128/EC.00307-12
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http://dx.doi.org/10.1128/EC.00307-12DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3623448PMC
April 2013

Whole-Genome Shotgun Sequence of Pseudomonas viridiflava, a Bacterium Species Pathogenic to Ararabidopsis thaliana.

Genome Announc 2013 Jan 24;1(1). Epub 2013 Jan 24.

Plants and Pathogens Group, Research Institute Earth Nature and Environment, hepia, University of Applied Sciences of Western Switzerland, Jussy, Switzerland.

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http://dx.doi.org/10.1128/genomeA.00116-12DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3569360PMC
January 2013

Global alteration of microRNAs and transposon-derived small RNAs in cotton (Gossypium hirsutum) during Cotton leafroll dwarf polerovirus (CLRDV) infection.

Plant Mol Biol 2012 Nov 18;80(4-5):443-60. Epub 2012 Sep 18.

Departamento de Genética, Instituto de Biologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil.

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http://dx.doi.org/10.1007/s11103-012-9959-1DOI Listing
November 2012

Computational identification and analysis of novel sugarcane microRNAs.

BMC Genomics 2012 Jul 2;13:290. Epub 2012 Jul 2.

Laboratorio de Biologia Molecular de Plantas, Instituto de Bioquímica Médica, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil.

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http://dx.doi.org/10.1186/1471-2164-13-290DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3464620PMC
July 2012

Gain and loss of multiple functionally related, horizontally transferred genes in the reduced genomes of two microsporidian parasites.

Proc Natl Acad Sci U S A 2012 Jul 16;109(31):12638-43. Epub 2012 Jul 16.

Department of Botany, Canadian Institute for Advanced Research, University of British Columbia, Vancouver, BC V6T 1Z4, Canada.

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http://dx.doi.org/10.1073/pnas.1205020109DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3412028PMC
July 2012

Highly diverse TCRα chain repertoire of pre-immune CD8⁺ T cells reveals new insights in gene recombination.

EMBO J 2012 Apr 28;31(7):1666-78. Epub 2012 Feb 28.

Ludwig Centre for Cancer Research, University of Lausanne, Epalinges, Switzerland.

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http://dx.doi.org/10.1038/emboj.2012.48DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3321212PMC
April 2012

Analysis of the salivary microbiome using culture-independent techniques.

J Clin Bioinforma 2012 Feb 2;2. Epub 2012 Feb 2.

Genomic Research Laboratory, Division of Infectious Diseases, Geneva University Hospitals, Rue Gabrielle-Perret-Gentil 4, CH-1211 Geneva 14, Switzerland.

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http://dx.doi.org/10.1186/2043-9113-2-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3296672PMC
February 2012

Rhinovirus genome variation during chronic upper and lower respiratory tract infections.

PLoS One 2011 21;6(6):e21163. Epub 2011 Jun 21.

Laboratory of Virology, Division of Infectious Diseases and Division of Laboratory Medicine, University of Geneva Hospitals, Geneva, Switzerland.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0021163PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3119694PMC
November 2011

Profile of small interfering RNAs from cotton plants infected with the polerovirus Cotton leafroll dwarf virus.

BMC Mol Biol 2011 Aug 24;12:40. Epub 2011 Aug 24.

Laboratório de Virologia Molecular Vegetal, Depto, Virologia, IMPPG, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brasil.

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http://dx.doi.org/10.1186/1471-2199-12-40DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3189115PMC
August 2011

Efficient mutation identification in zebrafish by microarray capturing and next generation sequencing.

Biochem Biophys Res Commun 2011 Feb 8;405(3):373-6. Epub 2011 Jan 8.

Department of Zoology and Animal Biology, University of Geneva, Switzerland.

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http://dx.doi.org/10.1016/j.bbrc.2011.01.024DOI Listing
February 2011

The complete sequence of the smallest known nuclear genome from the microsporidian Encephalitozoon intestinalis.

Nat Commun 2010 Sep 21;1:77. Epub 2010 Sep 21.

Department of Botany, Canadian Institute for Advanced Research, University of British Columbia, 3529-6270 University Boulevard, Vancouver, British Columbia, Canada V6T 1Z4.

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http://dx.doi.org/10.1038/ncomms1082DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4355639PMC
September 2010

Rhinovirus genome evolution during experimental human infection.

PLoS One 2010 May 11;5(5):e10588. Epub 2010 May 11.

Laboratory of Virology, Division of Infectious Diseases and Division of Laboratory Medicine, University of Geneva Hospitals, Geneva, Switzerland.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0010588PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2868056PMC
May 2010

Chromatin immunoprecipitation (ChIP) of plant transcription factors followed by sequencing (ChIP-SEQ) or hybridization to whole genome arrays (ChIP-CHIP).

Nat Protoc 2010 Mar 18;5(3):457-72. Epub 2010 Feb 18.

Laboratory of Molecular Biology, Wageningen University, Wageningen, The Netherlands.

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http://dx.doi.org/10.1038/nprot.2009.244DOI Listing
March 2010

Metagenomic study of the oral microbiota by Illumina high-throughput sequencing.

J Microbiol Methods 2009 Dec 29;79(3):266-71. Epub 2009 Sep 29.

Genomic Research Laboratory, Geneva University Hospitals, Rue Gabrielle-Perret-Gentil 4, CH-1211 Geneva 14, Switzerland.

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http://dx.doi.org/10.1016/j.mimet.2009.09.012DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3568755PMC
December 2009

Probabilistic base calling of Solexa sequencing data.

BMC Bioinformatics 2008 Oct 13;9:431. Epub 2008 Oct 13.

School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland.

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http://dx.doi.org/10.1186/1471-2105-9-431DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2575221PMC
October 2008

De novo bacterial genome sequencing: millions of very short reads assembled on a desktop computer.

Genome Res 2008 May 10;18(5):802-9. Epub 2008 Mar 10.

Genomic Research Laboratory, Infectious Diseases Service, Geneva University Hospitals and the University of Geneva, CH-1211 Geneva 4, Switzerland.

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http://dx.doi.org/10.1101/gr.072033.107DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2336802PMC
May 2008