Publications

Multiomic analysis of malignant pleural mesothelioma identifies molecular axes and specialized tumor profiles driving intertumor heterogeneity
Malignant pleural mesothelioma (MPM) is an aggressive cancer with rising incidence and challenging clinical management. Through a large …
Alex Di Genova, Lise Mangiante, Nicolas Alcala, Alexandra Sexton-Oates, Abel Gonzalez-Perez, Azhar Khandekar, Erik N. Bergstrom, Jaehee Kim, Xiran Liu, Ricardo Blazquez-Encinas, Colin Giacobi, Nolwenn Le Stang, Sandrine Boyault, Cyrille Cuenin, Severine Tabone-Eglinger, Francesca Damiola, Catherine Voegele, Maude Ardin, Marie-Cecile Michallet, Lorraine Soudade, Tiffany M. Delhomme, Arnaud Poret, Marie Brevet, Marie-Christine Copin, Sophie Giusiano-Courcambeck, Diane Damotte, Cecile Girard, Veronique Hofman, Paul Hofman, Jérôme Mouroux, Charlotte Cohen, Stephanie Lacomme, Julien Mazieres, Vincent Thomas de Montpreville, Corinne Perrin, Gaetane Planchard, Nathalie Rousseau, Isabelle Rouquette, Christine Sagan, Arnaud Scherpereel, Francoise Thivolet, Jean-Michel Vignaud, Didier Jean, Anabelle Gilg Soit Ilg, Robert Olaso, Vincent Meyer, Anne Boland-Auge, Jean-Francois Deleuze, Janine Altmuller, Peter Nuernberg, Alejandro Ibáñez-Costa, Justo P. Castaño, Sylvie Lantuejoul, Akram Ghantous, Charles Maussion, Pierre Courtiol, Hector Hernandez-Vargas, Christophe Caux, Nicolas Girard, Nuria Lopez-Bigas, Ludmil B. Alexandrov, Françoise Galateau-Salle, Matthieu Foll, Lynnette Fernandez-Cuesta
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Editorial: Applications of biological networks in biomedicine
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A molecular phenotypic map of malignant pleural mesothelioma
Malignant pleural mesothelioma (MPM) is a rare understudied cancer associated with exposure to asbestos. So far, MPM patients have …
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Genome sequencing and transcriptomic analysis of the Andean killifish Orestias ascotanensis reveals adaptation to high-altitude aquatic life
Orestias ascotanensis (Cyprinodontidae) is a teleost pupfish endemic to springs feeding into the Ascotan saltpan in the Chilean …
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The transposable element-rich genome of the cereal pest Sitophilus oryzae
The rice weevil Sitophilus oryzae is one of the most important agricultural pests, causing extensive damage to cereal in fields and to …
Nicolas Parisot, Carlos Vargas-Chávez, Clément Goubert, Patrice Baa-Puyoulet, Séverine Balmand, Louis Beranger, Caroline Blanc, Aymeric Bonnamour, Matthieu Boulesteix, Nelly Burlet, Federica Calevro, Patrick Callaerts, Théo Chancy, Hubert Charles, Stefano Colella, André Da Silva Barbosa, Elisa Dell’Aglio, Alex Di Genova, Gérard Febvay, Toni Gabaldón, Mariana Galvão Ferrarini, Alexandra Gerber, Benjamin Gillet, Robert Hubley, Sandrine Hughes, Emmanuelle Jacquin-Joly, Justin Maire, Marina Marcet-Houben, Florent Masson, Camille Meslin, Nicolas Montagné, Andrés Moya, Ana Tereza Ribeiro de Vasconcelos, Gautier Richard, Jeb Rosen, Marie-France Sagot, Arian F. A. Smit, Jessica M. Storer, Carole Vincent-Monegat, Agnès Vallier, Aurélien Vigneron, Anna Zaidman-Rémy, Waël Zamoum, Cristina Vieira, Rita Rebollo, Amparo Latorre, Abdelaziz Heddi
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Efficient hybrid de novo assembly of human genomes with WENGAN
Generating accurate genome assemblies of large, repeat-rich human genomes has proved difficult using only long, error-prone reads, and …
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The Chilean socio-ethno-genomic cline
Studies of the current Chilean population performed using classical genetic markers have established that the Chilean population …
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The relevance of enzyme specificity for coenzymes and the presence of 6-phosphogluconate dehydrogenase for polyhydroxyalkanoates production in the metabolism of Pseudomonas sp. LFM046
Reconstruction of genome-based metabolic model is a useful approach for the assessment of metabolic pathways, genes and proteins …
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Mycoplasma hyopneumoniae J elicits an antioxidant response and decreases the expression of ciliary genes in infected swine epithelial cells
Mycoplasma hyopneumoniae is the most costly pathogen for swine production. Although several studies have focused on the host-bacterium …
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Identification of SNPs and InDels associated with berry size in table grapes integrating genetic and transcriptomic approaches
Berry size is considered as one of the main selection criteria in table grapes breeding programs, due to the consumer preferences. …
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Development of a small panel of SNPs to infer ancestry in Chileans that distinguishes Aymara and Mapuche components
Current South American populations trace their origins mainly to three continental ancestries, i.e. European, Amerindian and African. …
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RNA-Seq analysis and transcriptome assembly of raspberry fruit (Rubus idaeus ¨Heritage¨) revealed several candidate genes involved in fruit development and ripening
Using Illumina HiSeq ™ 2000 sequencing platform (100 bp double-end reads), we performed transcriptome analysis of flower (F), green (G) …
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Whole Genome Sequence, Variant Discovery and Annotation in Mapuche-Huilliche Native South Americans
Whole human genome sequencing initiatives help us understand population history and the basis of genetic diseases. Current data mostly …
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Comparing genomic signatures of domestication in two Atlantic salmon (Salmo salar L.) populations with different geographical origins
Selective breeding and genetic improvement have left detectable signatures on the genomes of domestic species. The elucidation of such …
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Genomic variation underlying complex life-history traits revealed by genome sequencing in Chinook salmon
A broad portfolio of phenotypic diversity in natural organisms can buffer against exploitation and increase species persistence in …
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Fast-SG: an alignment-free algorithm for hybrid assembly
Long-read sequencing technologies are the ultimate solution for genome repeats, allowing near reference-level reconstructions of large …
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The genome sequence of the soft-rot fungus Penicillium purpurogenum reveals a high gene dosage for lignocellulolytic enzymes
The high lignocellulolytic activity displayed by the soft-rot fungus Penicillium purpurogenum has made it a target for the study of …
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Reconstruction of the microalga Nannochloropsis salina genome-scale metabolic model with applications to lipid production
Nannochloropsis salina (= Eustigmatophyceae) is a marine microalga which has become a biotechnological target because of its high …
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Global gene expression analysis provides insight into local adaptation to geothermal streams in tadpoles of the Andean toad Rhinella spinulosa
The anuran Rhinella spinulosa is distributed along the Andes Range at altitudes that undergo wide daily and seasonal variation in …
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Genome wide association study for resistance to Caligus rogercresseyi in Atlantic salmon (Salmo salar L.) using a 50K SNP genotyping array
The sea louse (Caligus rogercresseyi) is an external parasite and considered one of the most important health problems in the salmon …
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The bioleaching potential of a bacterial consortium
This work presents the molecular foundation of a consortium of five efficient bacteria strains isolated from copper mines currently …
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The Atlantic salmon genome provides insights into rediploidization
The whole-genome duplication 80 million years ago of the common ancestor of salmonids (salmonid-specific fourth vertebrate whole-genome …
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Transcriptome profiling of grapevine seedless segregants during berry development reveals candidate genes associated with berry weight
Berry size is considered as one of the main selection criteria in table grape breeding programs. However, this is a quantitative and …
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Genomewide single nucleotide polymorphism discovery in Atlantic salmon (Salmo salar): validation in wild and farmed American and European populations
A considerable number of single nucleotide polymorphisms (SNPs) are required to elucidate genotype–phenotype associations and determine …
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Genome-wide association analysis reveals loci associated with resistance against Piscirickettsia salmonis in two Atlantic salmon (Salmo salar L.) chromosomes
Pisciricketssia salmonis is the causal agent of Salmon Rickettsial Syndrome (SRS), which affects salmon species and causes severe …
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The BioMart community portal: an innovative alternative to large, centralized data repositories
The BioMart Community Portal (www.biomart.org) is a community-driven effort to provide a unified interface to biomedical databases that …
Damian Smedley, Syed Haider, Steffen Durinck, Luca Pandini, Paolo Provero, James Allen, Olivier Arnaiz, Mohammad Hamza Awedh, Richard Baldock, Giulia Barbiera, Philippe Bardou, Tim Beck, Andrew Blake, Merideth Bonierbale, Anthony J. Brookes, Gabriele Bucci, Iwan Buetti, Sarah Burge, Cédric Cabau, Joseph W. Carlson, Claude Chelala, Charalambos Chrysostomou, Davide Cittaro, Olivier Collin, Raul Cordova, Rosalind J. Cutts, Erik Dassi, Alex Di Genova, Anis Djari, Anthony Esposito, Heather Estrella, Eduardo Eyras, Julio Fernandez-Banet, Simon Forbes, Robert C. Free, Takatomo Fujisawa, Emanuela Gadaleta, Jose M. Garcia-Manteiga, David Goodstein, Kristian Gray, José Afonso Guerra-Assunção, Bernard Haggarty, Dong-Jin Han, Byung Woo Han, Todd Harris, Jayson Harshbarger, Robert K. Hastings, Richard D. Hayes, Claire Hoede, Shen Hu, Zhi-Liang Hu, Lucie Hutchins, Zhengyan Kan, Hideya Kawaji, Aminah Keliet, Arnaud Kerhornou, Sunghoon Kim, Rhoda Kinsella, Christophe Klopp, Lei Kong, Daniel Lawson, Dejan Lazarevic, Ji-Hyun Lee, Thomas Letellier, Chuan-Yun Li, Pietro Lio, Chu-Jun Liu, Jie Luo, Alejandro Maass, Jerome Mariette, Thomas Maurel, Stefania Merella, Azza Mostafa Mohamed, Francois Moreews, Ibounyamine Nabihoudine, Nelson Ndegwa, Céline Noirot, Cristian Perez-Llamas, Michael Primig, Alessandro Quattrone, Hadi Quesneville, Davide Rambaldi, James Reecy, Michela Riba, Steven Rosanoff, Amna Ali Saddiq, Elisa Salas, Olivier Sallou, Rebecca Shepherd, Reinhard Simon, Linda Sperling, William Spooner, Daniel M. Staines, Delphine Steinbach, Kevin Stone, Elia Stupka, Jon W. Teague, Abu Z. Dayem Ullah, Jun Wang, Doreen Ware, Marie Wong-Erasmus, Ken Youens-Clark, Amonida Zadissa, Shi-Jian Zhang, Arek Kasprzyk
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Transcriptome sequencing of Prunus sp. rootstocks roots to identify candidate genes involved in the response to root hypoxia
Root hypoxia in fruit trees affects growth, vegetative development, and reproductive development, which is reflected in low …
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A new genome of Acidithiobacillus thiooxidans provides insights into adaptation to a bioleaching environment
Acidithiobacillus thiooxidans is a sulfur oxidizing acidophilic bacterium found in many sulfur-rich environments. It is particularly …
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Whole genome comparison between table and wine grapes reveals a comprehensive catalog of structural variants
Grapevine (Vitis vinifera L.) is the most important Mediterranean fruit crop, used to produce both wine and spirits as well as table …
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Identification of two putative reference genes from grapevine suitable for gene expression analysis in berry and related tissues derived from RNA-Seq data
Data normalization is a key step in gene expression analysis by qPCR. Endogenous control genes are used to estimate variations and …
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Construction of Reference Chromosome-Scale Pseudomolecules for Potato: Integrating the Potato Genome with Genetic and Physical Maps
The genome of potato, a major global food crop, was recently sequenced. The work presented here details the integration of the potato …
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Cdk5 regulates Rap1 activity
Rap1 signaling is important for migration, differentiation, axonal growth, and during neuronal polarity. Rap1 can be activated by …
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Bioinformatic survey for new physiological substrates of Cyclin-dependent kinase 5
Cyclin-dependent kinase 5 (Cdk5) is a proline-directed serine/threonine kinase predominantly active in the nervous system where it …
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Draft Genome Sequence of the Sulfobacillus thermosulfidooxidans Cutipay Strain, an Indigenous Bacterium Isolated from a Naturally Extreme Mining Environment in Northern Chile
Sulfobacillus thermosulfidooxidans strain Cutipay is a mixotrophic, acidophilic, moderately thermophilic bacterium isolated from mining …
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Genome wide identification of Acidithiobacillus ferrooxidans (ATCC 23270) transcription factors and comparative analysis of ArsR and MerR metal regulators
Acidithiobacillus ferrooxidans is a chemolithoautotrophic acidophilic bacterium that obtains its energy from the oxidation of ferrous …
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Genome sequence and analysis of the tuber crop potato
Potato (Solanum tuberosum L.) is the world’s most important non-grain food crop and is central to global food security. It is clonally …
Xun Xu, Shengkai Pan, Shifeng Cheng, Bo Zhang, Desheng Mu, Peixiang Ni, Gengyun Zhang, Shuang Yang, Ruiqiang Li, Jun Wang, Gisella Orjeda, Frank Guzman, Michael Torres, Roberto Lozano, Olga Ponce, Diana Martinez, German de la Cruz, S. K. Chakrabarti, Virupaksh U. Patil, Konstantin G. Skryabin, Boris B. Kuznetsov, Nikolai V. Ravin, Tatjana V. Kolganova, Alexey V. Beletsky, Andrei V. Mardanov, Alex Di Genova, Daniel M. Bolser, David M. A. Martin, Guangcun Li, Yu Yang, Hanhui Kuang, Qun Hu, Xingyao Xiong, Gerard J. Bishop, Boris Sagredo, Nilo Mejía, Wlodzimierz Zagorski, Robert Gromadka, Jan Gawor, Pawel Szczesny, Sanwen Huang, Zhonghua Zhang, Chunbo Liang, Jun He, Ying Li, Ying He, Jianfei Xu, Youjun Zhang, Binyan Xie, Yongchen Du, Dongyu Qu, Merideth Bonierbale, Marc Ghislain, Maria del Rosario Herrera, Giovanni Giuliano, Marco Pietrella, Gaetano Perrotta, Paolo Facella, Kimberly O’Brien, Sergio E. Feingold, Leandro E. Barreiro, Gabriela A. Massa, Luis Diambra, Brett R. Whitty, Brieanne Vaillancourt, Haining Lin, Alicia N. Massa, Michael Geoffroy, Steven Lundback, Dean DellaPenna, C. Robin Buell, Sanjeev Kumar Sharma, David F. Marshall, Robbie Waugh, Glenn J. Bryan, Marialaura Destefanis, Istvan Nagy, Dan Milbourne, Susan J. Thomson, Mark Fiers, Jeanne M. E. Jacobs, Kåre L. Nielsen, Mads Sønderkær, Marina Iovene, Giovana A. Torres, Jiming Jiang, Richard E. Veilleux, Christian W. B. Bachem, Jan de Boer, Theo Borm, Bjorn Kloosterman, Herman van Eck, Erwin Datema, Bas te Lintel Hekkert, Aska Goverse, Roeland C. H. J. van Ham, Richard G. F. Visser, The Potato Genome Sequencing Consortium, BGI-Shenzhen, Cayetano Heredia University, Central Potato Research Institute, Centre Bioengineering RAS, Universidad de Chile CGR-CMM, University of Dundee College of Life Sciences, Shandong Academy of Agricultural Sciences High Technology Research Center, Huazhong Agriculture University, Hunan Agricultural University, Imperial College London, Instituto de Investigaciones Agropecuarias, Institute of Biochemistry & Biophysics, Chinese Academy of Agricultural Sciences Institute of Vegetables & Flowers, International Potato Center, Energy & Sustainable Development Italian National Agency for New Technologies, J Craig Venter Institute, Instituto Nacional de Tecnología Agropecuaria Laboratorio de Agrobiotecnología, Universidad Nacional de LaPlata Laboratorio de Biología de Sistemas, Michigan State University, Scottish Crop Research Institute, Teagasc Crops Research Centre, The New Zealand Institute for Plant & Food Research Ltd, University of Aalborg, University of Wisconsin, Virginia Polytechnic Institute & State University, Wageningen University & Research Centre
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SalmonDB: a bioinformatics resource for Salmo salar and Oncorhynchus mykiss
SalmonDB is a new multiorganism database containing EST sequences from Salmo salar, Oncorhynchus mykiss and the whole genome sequence …
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BioMart Central Portal: an open database network for the biological community
BioMart Central Portal is a first of its kind, community-driven effort to provide unified access to dozens of biological databases …
Jonathan M. Guberman, J. Ai, O. Arnaiz, Joachim Baran, Andrew Blake, Richard Baldock, Claude Chelala, David Croft, Anthony Cros, Rosalind J. Cutts, A. Di Genova, Simon Forbes, T. Fujisawa, E. Gadaleta, D. M. Goodstein, Gunes Gundem, Bernard Haggarty, Syed Haider, Matthew Hall, Todd Harris, Robin Haw, S. Hu, Simon Hubbard, Jack Hsu, Vivek Iyer, Philip Jones, Toshiaki Katayama, R. Kinsella, Lei Kong, Daniel Lawson, Yong Liang, Nuria Lopez-Bigas, J. Luo, Michael Lush, Jeremy Mason, Francois Moreews, Nelson Ndegwa, Darren Oakley, Christian Perez-Llamas, Michael Primig, Elena Rivkin, S. Rosanoff, Rebecca Shepherd, Reinhard Simon, B. Skarnes, Damian Smedley, Linda Sperling, William Spooner, Peter Stevenson, Kevin Stone, J. Teague, Jun Wang, Jianxin Wang, Brett Whitty, D. T. Wong, Marie Wong-Erasmus, L. Yao, Ken Youens-Clark, Christina Yung, Junjun Zhang, Arek Kasprzyk
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