L
Lucas Paoli
Researcher at Swiss Institute of Bioinformatics
Publications - 19
Citations - 923
Lucas Paoli is an academic researcher from Swiss Institute of Bioinformatics. The author has contributed to research in topics: Biology & Genome. The author has an hindex of 8, co-authored 16 publications receiving 401 citations. Previous affiliations of Lucas Paoli include University of Alberta & École Normale Supérieure.
Papers
More filters
Journal ArticleDOI
Microbial abundance, activity and population genomic profiling with mOTUs2
Alessio Milanese,Daniel R. Mende,Lucas Paoli,Guillem Salazar,Hans-Joachim Ruscheweyh,Miguelangel Cuenca,Pascal Hingamp,Renato J. Alves,Paul I. Costea,Luis Pedro Coelho,Thomas Schmidt,Alexandre Almeida,Alex L. Mitchell,Robert D. Finn,Jaime Huerta-Cepas,Peer Bork,Georg Zeller,Shinichi Sunagawa +17 more
TL;DR: mOTUs2, an updated and functionally extended profiling tool for microbial abundance, activity and population profiling, shows that mOTUs, which are based on essential housekeeping genes, are demonstrably well-suited for quantification of basal transcriptional activity of community members.
Journal ArticleDOI
Gene Expression Changes and Community Turnover Differentially Shape the Global Ocean Metatranscriptome
Guillem Salazar,Lucas Paoli,Adriana Alberti,Jaime Huerta-Cepas,Hans-Joachim Ruscheweyh,Miguelangel Cuenca,Christopher M. Field,Luis Pedro Coelho,Corinne Cruaud,Stefan Engelen,Ann C. Gregory,Karine Labadie,Claudie Marec,Claudie Marec,Eric Pelletier,Marta Royo-Llonch,Simon Roux,Pablo Sánchez,Hideya Uehara,Ahmed A. Zayed,Georg Zeller,Margaux Carmichael,Céline Dimier,Céline Dimier,Joannie Ferland,Stefanie Kandels,Marc Picheral,Sergey Pisarev,Julie Poulain,Silvia G. Acinas,Marcel Babin,Peer Bork,Emmanuel Boss,Chris Bowler,Guy Cochrane,Colomban de Vargas,Michael J. Follows,Gabriel Gorsky,Nigel Grimsley,Lionel Guidi,Pascal Hingamp,Daniele Iudicone,Olivier Jaillon,Stefanie Kandels-Lewis,Lee Karp-Boss,Eric Karsenti,Fabrice Not,Hiroyuki Ogata,Stephane Pesant,Nicole J. Poulton,Jeroen Raes,Christian Sardet,Sabrina Speich,Lars Stemmann,Matthew B. Sullivan,Shinichi Sunagawa,Patrick Wincker +56 more
TL;DR: The relative contribution of gene expression changes to be significantly lower in polar than in non-polar waters and it is hypothesized that in polar regions, alterations in community activity in response to ocean warming will be driven more strongly by changes in organismal composition than by gene regulatory mechanisms.
Journal ArticleDOI
metaSNV: A tool for metagenomic strain level analysis.
TL;DR: MetaSNV as mentioned in this paper is a tool for single nucleotide variant (SNV) analysis in metagenomic samples, capable of comparing populations of thousands of bacterial and archaeal species.
Journal ArticleDOI
Biosynthetic potential of the global ocean microbiome
Lucas Paoli,Hans-Joachim Ruscheweyh,Clarissa C. Forneris,Florian Hubrich,Satria A. Kautsar,Agneya Bhushan,Alessandro Lotti,Quentin Clayssen,Guillem Salazar,Alessio Milanese,Charlotte I. Carlström,Chrysa Papadopoulou,Dan Gehrig,Mikhail Karasikov,Harun Mustafa,Martin Larralde,Laura M. Carroll,Pablo Sánchez,Ahmed A. Zayed,Dylan R. Cronin,Silvia G. Acinas,Peer Bork,Chris Bowler,Tom O. Delmont,Josep M. Gasol,Alvar D. Gossert,André Kahles,Matthew B. Sullivan,Patrick Wincker,Georg Zeller,Serina L. Robinson,Jörn Piel,Shinichi Sunagawa +32 more
TL;DR: This paper investigated the diversity and novelty of biosynthetic gene clusters in the ocean by integrating around 10,000 microbial genomes from cultivated and single cells with more than 25,000 newly reconstructed draft genomes from more than 1,000 seawater samples.
Journal ArticleDOI
Deep ocean metagenomes provide insight into the metabolic architecture of bathypelagic microbial communities.
Silvia G. Acinas,Pablo Sánchez,Guillem Salazar,Guillem Salazar,Francisco M. Cornejo-Castillo,Francisco M. Cornejo-Castillo,Marta Sebastián,Marta Sebastián,Ramiro Logares,Marta Royo-Llonch,Lucas Paoli,Shinichi Sunagawa,Pascal Hingamp,Hiroyuki Ogata,Gipsi Lima-Mendez,Simon Roux,Simon Roux,José M. González,Jesús M. Arrieta,Intikhab Alam,Allan Anthony Kamau,Chris Bowler,Jeroen Raes,Stephane Pesant,Stephane Pesant,Peer Bork,Susana Agustí,Takashi Gojobori,Dolors Vaqué,Matthew B. Sullivan,Carlos Pedrós-Alió,Ramon Massana,Carlos M. Duarte,Josep M. Gasol,Josep M. Gasol +34 more
TL;DR: The Malaspina Gene Database as mentioned in this paper was used to analyze 58 metagenomes from tropical and subtropical deep oceans to generate a deep metagenome-assembled Genomes.