Publications

From Bioinformatics Core Wiki


2018

Pergola: Boosting Visualization and Analysis of Longitudinal Data by Unlocking Genomic Analysis Tools. . 30 November 2018. iScience. 10.1016/j.isci.2018.10.023. [ Link ]
Our team developed a web service for using Pergola via the Internet browser at http://pergola.crg.eu.

2017

Purification of replicating pancreatic β-cells for gene expression studies. Reyes Carballar, Maria de Lluc Canyelles, Claudia Fernández, Yasmina Martí, Sarah Bonnin, Esther Castaño, Eduard Montanya, Noèlia Téllez. 13 December 2017. Scientific Reports. 10.1038/s41598-017-17776-2. [ Link ]
The BioCore performed the microarray data analysis and helped with interpreting the data.
An atlas of alternative splicing profiles and functional associations reveals new regulatory programs and genes that simultaneously express multiple major isoforms. Javier Tapial, Kevin C. H. Ha, Timothy Sterne-Weiler, Ulrich Braunschweig, Antonio Hermoso-Pulido, Mathieu Quesnel-Vallières, Jon Permanyer, Reza Sodaei, Yamile Marquez, Luca Cozzuto, Xinchen Wang, Melisa Gómez-Velázquez, Teresa Rayon, Miguel Manzanares, Julia Ponomarenko, Manuel Irimia, André Gohr, Benjamin J. Blencowe. 1 October 2017. Genome Research. 10.1101/gr.220962.117. [ Link ]
Part of the outcomes of this article can be inspected at VastDB, a database of Alternative Splicing (AS) profiles across multiple tissue and cell types. Event identification and sequence inclusion level quantification in RNA-seq samples were generated from VAST-TOOLS. BioCore was involved in the data management, database design and website development of this online resource.
LncATLAS database for subcellular localization of long noncoding RNAs. David Mas-Ponte, Joana Carlevaro-Fita, Emilio Palumbo, Toni Hermoso Pulido, Roderic Guigo, Rory Johnson. 1 July 2017. RNA. 10.1261/rna.060814.117. [ Link ]
The BioCore contributed in the project by helping to set up a functional containerized environment that could host the underlying Shiny server that was used in this application. Visit the web server.
The microbiome in respiratory medicine: current challenges and future perspectives. Rosa Faner, Oriol Sibila, Alvar Agustí, Eric Bernasconi, James D. Chalmers, Gary B. Huffnagle, Chaysavanh Manichanh, Philip L. Molyneaux, Roger Paredes, Vicente Pérez Brocal, Julia Ponomarenko, Sanjay Sethi, Jordi Dorca, Eduard Monsó. April 2017. The European Respiratory Journal. 10.1183/13993003.02086-2016. [ Link ]
CRG collaborates with the Hospital San Pau, Hospital Clinic, Hospital del Mar and other institutions in Barcelona, which are part of the Barcelona Respiratory Network on studies of the lung microbiomes in patients affected by chronic obstructive pulmonary disease (COPD). The BioCore contribution is the analysis of 16S rRNA sequencing data.
A De Novo Nonsense Mutation in MAGEL2 in a Patient Initially Diagnosed as Opitz-C: Similarities Between Schaaf-Yang and Opitz-C Syndromes. Roser Urreizti, Anna Maria Cueto-Gonzalez, Héctor Franco-Valls, Sílvia Mort-Farre, Neus Roca-Ayats, Julia Ponomarenko, Luca Cozzuto, Carlos Company, Mattia Bosio, Stephan Ossowski, Magda Montfort, Jochen Hecht, Eduardo F. Tizzano, Bru Cormand, Lluïsa Vilageliu, John M. Opitz, Giovanni Neri, Daniel Grinberg, Susana Balcells. 10 March 2017. Scientific Reports. 10.1038/srep44138. [ Link ]
The BioCore collaborated with the geneticists from the University of Barcelona and the Opitz C Association on the analysis of the whole genomes of the Opitz C syndrome patient and her parents. In the result, a de novo nonsense mutation in MAGEL2 was discovered.
Scalable Design of Paired CRISPR Guide RNAs for Genomic Deletion. Carlos Pulido-Quetglas, Estel Aparicio-Prat, Carme Arnan, Taisia Polidori, Toni Hermoso, Emilio Palumbo, Julia Ponomarenko, Roderic Guigo, Rory Johnson. 2 March 2017. PLOS Computational Biology. 10.1371/journal.pcbi.1005341. [ Link ]
This paper presents CRISPETa, a web-tool for designing optimal pairs of sgRNAs for deletion of desired genomic regions; for example, lncRNAs. (Crispeta means popcorn, in Catalan.) The target regions can be supplied in the BED or UCSC format. CRISPETa can be run on any number of targets - from one to thousands. At present, designs can be performed for five species, human, mouse, zebrafish, fruitfly, and worm. The BioCore has designed and developed the website for CRISPETa.
Ten Simple Rules on How to Organize a Scientific Retreat. Julia Ponomarenko, Romina Garrido, Roderic Guigó. 2 February 2017. PLOS Computational Biology. 10.1371/journal.pcbi.1005344. [ Link ]

2016

Extreme genomic erosion after recurrent demographic bottlenecks in the highly endangered Iberian lynx. Federico Abascal, André Corvelo, Fernando Cruz, José L. Villanueva-Cañas, Anna Vlasova, Marina Marcet-Houben, Begoña Martínez-Cruz, Jade Yu Cheng, Pablo Prieto, Víctor Quesada, Javier Quilez, Gang Li, Francisca García, Miriam Rubio-Camarillo, Leonor Frias, Paolo Ribeca, Salvador Capella-Gutiérrez, José M. Rodríguez, Francisco Câmara, Ernesto Lowy, Luca Cozzuto, Ionas Erb, Michael L. Tress, Jose L. Rodriguez-Ales, Jorge Ruiz-Orera, Ferran Reverter, Mireia Casas-Marce, Laura Soriano, Javier R. Arango, Sophia Derdak, Beatriz Galán, Julie Blanc, Marta Gut, Belen Lorente-Galdos, Marta Andrés-Nieto, Carlos López-Otín, Alfonso Valencia, Ivo Gut, José L. García, Roderic Guigó, William J. Murphy, Aurora Ruiz-Herrera, Tomas Marques-Bonet, Guglielmo Roma, Cedric Notredame, Thomas Mailund, M. Mar Albà, Toni Gabaldón, Tyler Alioto, José A. Godoy. December 2016. Genome Biology. 10.1186/s13059-016-1090-1. [ Link ]
The Iberian lynx genome is a collaborative effort of six research centers in Spain. It is part of the Project Zero program FGCSIC 2010 in Endangered Species and was funded by Banco Santander and Fundación General CSIC. The BioCore was involved in generation of a first annotated draft of the genome.
Whole genome sequencing of turbot (Scophthalmus maximus; Pleuronectiformes): a fish adapted to demersal life. Antonio Figueras, Diego Robledo, André Corvelo, Miguel Hermida, Patricia Pereiro, Juan A. Rubiolo, Jèssica Gómez-Garrido, Laia Carreté, Xabier Bello, Marta Gut, Ivo Glynne Gut, Marina Marcet-Houben, Gabriel Forn-Cuní, Beatriz Galán, José Luis García, José Luis Abal-Fabeiro, Belen G. Pardo, Xoana Taboada, Carlos Fernández, Anna Vlasova, Antonio Hermoso-Pulido, Roderic Guigó, José Antonio Álvarez-Dios, Antonio Gómez-Tato, Ana Viñas, Xulio Maside, Toni Gabaldón, Beatriz Novoa, Carmen Bouza, Tyler Alioto, Paulino Martínez. June 2016. DNA research: an international journal for rapid publication of reports on genes and genomes. 10.1093/dnares/dsw007. [ Link ]
PHF13 is a molecular reader and transcriptional co-regulator of H3K4me2/3. Ho-Ryun Chung, Chao Xu, Alisa Fuchs, Andreas Mund, Martin Lange, Hannah Staege, Tobias Schubert, Chuanbing Bian, Ilona Dunkel, Anton Eberharter, Catherine Regnard, Henrike Klinker, David Meierhofer, Luca Cozzuto, Andreas Winterpacht, Luciano Di Croce, Jinrong Min, Hans Will, Sarah Kinkley. 25 May 2016. eLife. 10.7554/eLife.10607. [ Link ]
Genome and transcriptome analysis of the Mesoamerican common bean and the role of gene duplications in establishing tissue and temporal specialization of genes. Anna Vlasova, Salvador Capella-Gutiérrez, Martha Rendón-Anaya, Miguel Hernández-Oñate, André E. Minoche, Ionas Erb, Francisco Câmara, Pablo Prieto-Barja, André Corvelo, Walter Sanseverino, Gastón Westergaard, Juliane C. Dohm, Georgios J. Pappas, Soledad Saburido-Alvarez, Darek Kedra, Irene Gonzalez, Luca Cozzuto, Jessica Gómez-Garrido, María A. Aguilar-Morón, Nuria Andreu, O. Mario Aguilar, Jordi Garcia-Mas, Maik Zehnsdorf, Martín P. Vázquez, Alfonso Delgado-Salinas, Luis Delaye, Ernesto Lowy, Alejandro Mentaberry, Rosana P. Vianello-Brondani, José Luís García, Tyler Alioto, Federico Sánchez, Heinz Himmelbauer, Marta Santalla, Cedric Notredame, Toni Gabaldón, Alfredo Herrera-Estrella, Roderic Guigó. 25 February 2016. Genome Biology. 10.1186/s13059-016-0883-6. [ Link ]
The BioCore collaborated with an international consortium to decode the genome of the Mesoamerican common bean Phaseolus vulgarism. The core contributed to the project by identifying small ncRNAs and annotating genes predicted from the genome sequences.
Integration of multi-omics data of a genome-reduced bacterium: Prevalence of post-transcriptional regulation and its correlation with protein abundances. Wei-Hua Chen, Vera van Noort, Maria Lluch-Senar, Marco L. Hennrich, Judith A. H. Wodke, Eva Yus, Andreu Alibés, Guglielmo Roma, Daniel R. Mende, Christina Pesavento, Athanasios Typas, Anne-Claude Gavin, Luis Serrano, Peer Bork. 18 February 2016. Nucleic Acids Research. 10.1093/nar/gkw004. [ Link ]
GREENC: a Wiki-based database of plant lncRNAs. Andreu Paytuví Gallart, Antonio Hermoso Pulido, Irantzu Anzar Martínez de Lagrán, Walter Sanseverino, Riccardo Aiese Cigliano. 4 January 2016. Nucleic Acids Research. 10.1093/nar/gkv1215. [ Link ]
Prp4 Kinase Grants the License to Splice: Control of Weak Splice Sites during Spliceosome Activation. Daniela Eckert, Nicole Andrée, Aleh Razanau, Susanne Zock-Emmenthal, Martin Lützelberger, Susann Plath, Henning Schmidt, Angel Guerra-Moreno, Luca Cozzuto, José Ayté, Norbert F. Käufer. January 2016. PLoS genetics. 10.1371/journal.pgen.1005768. [ Link ]

2015

Molecular signatures of plastic phenotypes in two eusocial insect species with simple societies. Solenn Patalano, Anna Vlasova, Chris Wyatt, Philip Ewels, Francisco Camara, Pedro G. Ferreira, Claire L. Asher, Tomasz P. Jurkowski, Anne Segonds-Pichon, Martin Bachman, Irene González-Navarrete, André E. Minoche, Felix Krueger, Ernesto Lowy, Marina Marcet-Houben, Jose Luis Rodriguez-Ales, Fabio S. Nascimento, Shankar Balasubramanian, Toni Gabaldon, James E. Tarver, Simon Andrews, Heinz Himmelbauer, William O. H. Hughes, Roderic Guigó, Wolf Reik, Seirian Sumner. 10 November 2015. Proceedings of the National Academy of Sciences of the United States of America. 10.1073/pnas.1515937112. [ Link ]
Comparative "-omics" in Mycoplasma pneumoniae Clinical Isolates Reveals Key Virulence Factors. Maria Lluch-Senar, Luca Cozzuto, Jaime Cano, Javier Delgado, Verónica Llórens-Rico, Sabine Pereyre, Cécile Bebear, Luis Serrano. 2015. PloS One. 10.1371/journal.pone.0137354. [ Link ]
MyMpn: a database for the systems biology model organism Mycoplasma pneumoniae. Judith A. H. Wodke, Andreu Alibés, Luca Cozzuto, Antonio Hermoso, Eva Yus, Maria Lluch-Senar, Luis Serrano, Guglielmo Roma. January 2015. Nucleic Acids Research. 10.1093/nar/gku1105. [ Link ]
The BioCore developed MyMpn database to host and analyze omics-data generated by the Design of Biological Systems Group (CRG) and collaborators at the EMBL and other institutions.
SuperFly: a comparative database for quantified spatio-temporal gene expression patterns in early dipteran embryos. Damjan Cicin-Sain, Antonio Hermoso Pulido, Anton Crombach, Karl R. Wotton, Eva Jiménez-Guri, Jean-François Taly, Guglielmo Roma, Johannes Jaeger. January 2015. Nucleic Acids Research. 10.1093/nar/gku1142. [ Link ]
SuperFly is a database for the comparative analysis of spatio-temporal gene expression patterns and regulation in dipteran species (flies, midges, and mosquitoes). It currently hosts data on the vinegar fly Drosophila melanogaster, the scuttle fly Megaselia abdita, and the moth midge Clogmia albipunctata. The BioCore designed and developed the database and the website to collect and visualize data.

2014

Zrf1 is required to establish and maintain neural progenitor identity. Luigi Aloia, Bruno Di Stefano, Alessandro Sessa, Lluis Morey, Alexandra Santanach, Arantxa Gutierrez, Luca Cozzuto, Salvador Aznar Benitah, Thomas Graf, Vania Broccoli, Luciano Di Croce. 15 January 2014. Genes & Development. 10.1101/gad.228510.113. [ Link ]

2013

DPY30 regulates pathways in cellular senescence through ID protein expression. Elisabeth Simboeck, Arantxa Gutierrez, Luca Cozzuto, Malte Beringer, Livia Caizzi, William M. Keyes, Luciano Di Croce. 14 August 2013. The EMBO journal. 10.1038/emboj.2013.159. [ Link ]
Comparative transcriptomics of early dipteran development. Eva Jiménez-Guri, Jaime Huerta-Cepas, Luca Cozzuto, Karl R. Wotton, Hui Kang, Heinz Himmelbauer, Guglielmo Roma, Toni Gabaldón, Johannes Jaeger. 24 February 2013. BMC genomics. 10.1186/1471-2164-14-123. [ Link ]
The BioCore collaborated with the group of Dr. Yogi Jaeger (CRG) to publish the de novo transcriptomes of three non-drosophilid diptera, Clogmia albipunctata, Megaselia abdita, and Episyrphus balteatus.
RYBP and Cbx7 define specific biological functions of polycomb complexes in mouse embryonic stem cells. Lluis Morey, Luigi Aloia, Luca Cozzuto, Salvador Aznar Benitah, Luciano Di Croce. 31 January 2013. Cell Reports. 10.1016/j.celrep.2012.11.026. [ Link ]
PRGdb 2.0: towards a community-based database model for the analysis of R-genes in plants. Walter Sanseverino, Antonio Hermoso, Raffaella D'Alessandro, Anna Vlasova, Giuseppe Andolfo, Luigi Frusciante, Ernesto Lowy, Guglielmo Roma, Maria Raffaella Ercolano. January 2013. Nucleic Acids Research. 10.1093/nar/gks1183. [ Link ]
The Plant Resistance Genes database, PRGdb, is a comprehensive resource on pathogen resistance genes (R-genes) in plants. Initiated in 2009, it currently provides data on 112 known and 104,310 putative R-genes in 233 plant species and conferring resistance to 122 pathogens. The BioCore re-designed the database website using the Semantic MediaWiki technologies.

2012

Age-associated inflammation inhibits epidermal stem cell function. Jason Doles, Mekayla Storer, Luca Cozzuto, Guglielmo Roma, William M. Keyes. 1 October 2012. Genes & Development. 10.1101/gad.192294.112. [ Link ]
The genome of melon (Cucumis melo L.). Jordi Garcia-Mas, Andrej Benjak, Walter Sanseverino, Michael Bourgeois, Gisela Mir, Víctor M. González, Elizabeth Hénaff, Francisco Câmara, Luca Cozzuto, Ernesto Lowy, Tyler Alioto, Salvador Capella-Gutiérrez, Jose Blanca, Joaquín Cañizares, Pello Ziarsolo, Daniel Gonzalez-Ibeas, Luis Rodríguez-Moreno, Marcus Droege, Lei Du, Miguel Alvarez-Tejado, Belen Lorente-Galdos, Marta Melé, Luming Yang, Yiqun Weng, Arcadi Navarro, Tomas Marques-Bonet, Miguel A. Aranda, Fernando Nuez, Belén Picó, Toni Gabaldón, Guglielmo Roma, Roderic Guigó, Josep M. Casacuberta, Pere Arús, Pere Puigdomènech. 17 July 2012. Proceedings of the National Academy of Sciences of the United States of America. 10.1073/pnas.1205415109. [ Link ]
To decipher the melon genome, the governmental foundation Genoma España funded the project MELONOMICS, to which the BioCore contributed by predicting small non-coding RNAs and pathogen resistant genes.
Nonoverlapping functions of the Polycomb group Cbx family of proteins in embryonic stem cells. Lluis Morey, Gloria Pascual, Luca Cozzuto, Guglielmo Roma, Anton Wutz, Salvador Aznar Benitah, Luciano Di Croce. 6 January 2012. Cell Stem Cell. 10.1016/j.stem.2011.12.006. [ Link ]
Widespread generation of alternative UTRs contributes to sex-specific RNA binding by UNR. Marija Mihailovic, Marija Mihailovich, Laurence Wurth, Federico Zambelli, Irina Abaza, Cristina Militti, Francesco M. Mancuso, Guglielmo Roma, Giulio Pavesi, Fátima Gebauer. January 2012. RNA (New York, N.Y.). 10.1261/rna.029603.111. [ Link ]

2011

HumMeth27QCReport: an R package for quality control and primary analysis of Illumina Infinium methylation data. Francesco M. Mancuso, Magda Montfort, Anna Carreras, Andreu Alibés, Guglielmo Roma. 19 December 2011. BMC research notes. 10.1186/1756-0500-4-546. [ Link ]
E-box-independent regulation of transcription and differentiation by MYC. Iris Uribesalgo, Marcus Buschbeck, Arantxa Gutiérrez, Sophia Teichmann, Santiago Demajo, Bernd Kuebler, Josep F. Nomdedéu, Juan Martín-Caballero, Guglielmo Roma, Salvador Aznar Benitah, Luciano Di Croce. 23 October 2011. Nature Cell Biology. 10.1038/ncb2355. [ Link ]
Regulation of human epidermal stem cell proliferation and senescence requires polycomb- dependent and -independent functions of Cbx4. Nuno Miguel Luis, Lluis Morey, Stefania Mejetta, Gloria Pascual, Peggy Janich, Bernd Kuebler, Luca Cozutto, Guglielmo Roma, Elisabete Nascimento, Michaela Frye, Luciano Di Croce, Salvador Aznar Benitah. 2 September 2011. Cell Stem Cell. 10.1016/j.stem.2011.07.013. [ Link ]
TEQC: an R package for quality control in target capture experiments. Manuela Hummel, Sarah Bonnin, Ernesto Lowy, Guglielmo Roma. 1 May 2011. Bioinformatics (Oxford, England). 10.1093/bioinformatics/btr122. [ Link ]

2010

Lack of sik1 in mouse embryonic stem cells impairs cardiomyogenesis by down-regulating the cyclin-dependent kinase inhibitor p57kip2. Antonio Romito, Enza Lonardo, Guglielmo Roma, Gabriella Minchiotti, Andrea Ballabio, Gilda Cobellis. 3 February 2010. PloS One. 10.1371/journal.pone.0009029. [ Link ]
PRGdb: a bioinformatics platform for plant resistance gene analysis. Walter Sanseverino, Guglielmo Roma, Marco De Simone, Luigi Faino, Sara Melito, Elia Stupka, Luigi Frusciante, Maria Raffaella Ercolano. January 2010. Nucleic Acids Research. 10.1093/nar/gkp978. [ Link ]


Bioinformatics Core Facility @ CRG — 2011-2018