Publications
From Bioinformatics Core Wiki
2024
Nuclear localization of MTHFD2 is required for correct mitosis progression. Natalia Pardo-Lorente, Anestis Gkanogiannis, Luca Cozzuto, Antoni Gañez Zapater, Lorena Espinar, Ritobrata Ghose, Jacqueline Severino, Laura García-López, Rabia Gül Aydin, Laura Martin, Maria Victoria Neguembor, Evangelia Darai, Maria Pia Cosma, Laura Batlle-Morera, Julia Ponomarenko, Sara Sdelci. 12 November 2024. Nature Communications. 10.1038/s41467-024-51847-z. [ Link ]
Elucidation of the Epitranscriptomic RNA Modification Landscape of Chikungunya Virus. Belinda Baquero-Pérez, Enrico Bortoletto, Umberto Rosani, Anna Delgado-Tejedor, Rebeca Medina, Eva Maria Novoa, Paola Venier, Juana Díez. June 2024. Viruses. 10.3390/v16060945. [ Link ]
LATS1 controls CTCF chromatin occupancy and hormonal response of 3D-grown breast cancer cells. Julieta Ramírez-Cuéllar, Roberto Ferrari, Rosario T. Sanz, Marta Valverde-Santiago, Judith García-García, A. Silvina Nacht, David Castillo, Francois Le Dily, Maria Victoria Neguembor, Marco Malatesta, Sarah Bonnin, Marc A. Marti-Renom, Miguel Beato, Guillermo P. Vicent. 2 April 2024. The EMBO journal. 10.1038/s44318-024-00080-x. [ Link ]
2023
SET-PP2A complex as a new therapeutic target in KMT2A (MLL) rearranged AML. Antonella Di Mambro, Yoana Arroyo-Berdugo, Tiziana Fioretti, Michael Randles, Luca Cozzuto, Vinothini Rajeeve, Armando Cevenini, Michael J. Austin, Gabriella Esposito, Julia Ponomarenko, Claire M. Lucas, Pedro Cutillas, John Gribben, Owen Williams, Yolanda Calle, Bela Patel, Maria Teresa Esposito. 27 October 2023. Oncogene. 10.1038/s41388-023-02840-1. [ Link ]
microRNA sequencing for biomarker detection in the diagnosis, classification and prognosis of Diffuse Large B Cell Lymphoma. Ane Larrabeiti-Etxebarria, Nerea Bilbao-Aldaiturriaga, Javier Arzuaga-Mendez, Maialen Martin-Arruti, Luca Cozzuto, Ayman Gaafar, Irune Ruiz-Diaz, Isabel Guerra, Idoia Martin-Guerrero, Elixabet Lopez-Lopez, Angela Gutierrez-Camino. 27 July 2023. Scientific Reports. 10.1038/s41598-023-39271-7. [ Link ]
Nanopore Direct RNA Sequencing Data Processing and Analysis Using MasterOfPores. Luca Cozzuto, Anna Delgado-Tejedor, Toni Hermoso Pulido, Eva Maria Novoa, Julia Ponomarenko. 2023. Springer US. 10.1007/978-1-0716-2962-8_13. [ Link ]
Development of MoP2
2022
Influence of Dietary Inulin on Fecal Microbiota, Cardiometabolic Risk Factors, Eicosanoids, and Oxidative Stress in Rats Fed a High-Fat Diet. Bernat Miralles-Pérez, Maria Rosa Nogués, Vanessa Sánchez-Martos, Àngels Fortuño-Mar, Sara Ramos-Romero, Josep L. Torres, Julia Ponomarenko, Susana Amézqueta, Xiang Zhang, Marta Romeu. 16 December 2022. Foods (Basel, Switzerland). 10.3390/foods11244072. [ Link ]
Fiber-like Action of d-Fagomine on the Gut Microbiota and Body Weight of Healthy Rats. Sara Ramos-Romero, Julia Ponomarenko, Susana Amézqueta, Mercè Hereu, Bernat Miralles-Pérez, Marta Romeu, Lucía Méndez, Isabel Medina, Josep Lluís Torres. 3 November 2022. Nutrients. 10.3390/nu14214656. [ Link ]
Genome‐wide transcriptomic changes reveal the genetic pathways involved in insect migration. Toby Doyle, Eva Jimenez‐Guri, Will L. S. Hawkes, Richard Massy, Federica Mantica, Jon Permanyer, Luca Cozzuto, Toni Hermoso Pulido, Tobias Baril, Alex Hayward, Manuel Irimia, Jason W. Chapman, Chris Bass, Karl R. Wotton. 12 July 2022. Molecular Ecology. 10.1111/mec.16588. [ Link ]
Impact of COVID-19 Lockdown on the Nasopharyngeal Microbiota of Children and Adults Self-Confined at Home. Muntsa Rocafort, Desiree Henares, Pedro Brotons, Cristian Launes, Mariona Fernandez de Sevilla, Victoria Fumado, Irene Barrabeig, Sara Arias, Alba Redin, Julia Ponomarenko, Maria Mele, Pere Millat-Martinez, Joana Claverol, Nuria Balanza, Alex Mira, Juan J. Garcia-Garcia, Quique Bassat, Iolanda Jordan, Carmen Muñoz-Almagro. 12 July 2022. Viruses. 10.3390/v14071521. [ Link ]
A set point in the selection of the αβTCR T cell repertoire imposed by pre-TCR signaling strength. Elena R. Bovolenta, Eva M. García-Cuesta, Lydia Horndler, Julia Ponomarenko, Wolfgang W. Schamel, Mario Mellado, Mario Castro, David Abia, Hisse M. van Santen. 31 May 2022. Proceedings of the National Academy of Sciences of the United States of America. 10.1073/pnas.2201907119. [ Link ]
Controlled X‐chromosome dynamics defines meiotic potential of female mouse in vitro germ cells. Jacqueline Severino, Moritz Bauer, Tom Mattimoe, Niccolò Arecco, Luca Cozzuto, Patricia Lorden, Norio Hamada, Yoshiaki Nosaka, So I Nagaoka, Pauline Audergon, Antonio Tarruell, Holger Heyn, Katsuhiko Hayashi, Mitinori Saitou, Bernhard Payer. 23 May 2022. The EMBO Journal. 10.15252/embj.2021109457. [ Link ]
We made a nextflow pipeline for allele specific RNAseq
Citizen-science reveals changes in the oral microbiome in Spain through age and lifestyle factors. Jesse R. Willis, Ester Saus, Susana Iraola-Guzmán, Ewa Ksiezopolska, Luca Cozzuto, Luis A. Bejarano, Nuria Andreu-Somavilla, Miriam Alloza-Trabado, Andrea Blanco, Anna Puig-Sola, Elisabetta Broglio, Carlo Carolis, Julia Ponomarenko, Jochen Hecht, Toni Gabaldón. 19 May 2022. NPJ biofilms and microbiomes. 10.1038/s41522-022-00279-y. [ Link ]
Selective cleavage of ncRNA and antiviral activity by RNase2/EDN in THP1-induced macrophages. Lu Lu, Jiarui Li, Ranlei Wei, Irene Guidi, Luca Cozzuto, Julia Ponomarenko, Guillem Prats-Ejarque, Ester Boix. 26 March 2022. Cellular and molecular life sciences: CMLS. 10.1007/s00018-022-04229-x. [ Link ]
LCOR mediates interferon-independent tumor immunogenicity and responsiveness to immune-checkpoint blockade in triple-negative breast cancer. Iván Pérez-Núñez, Catalina Rozalén, José Ángel Palomeque, Irene Sangrador, Mariona Dalmau, Laura Comerma, Anna Hernández-Prat, David Casadevall, Silvia Menendez, Daniel Dan Liu, Minhong Shen, Jordi Berenguer, Irene Rius Ruiz, Raul Peña, José Carlos Montañés, M. Mar Albà, Sarah Bonnin, Julia Ponomarenko, Roger R. Gomis, Juan Miguel Cejalvo, Sonia Servitja, Diego M. Marzese, Lluis Morey, Leonie Voorwerk, Joaquín Arribas, Begoña Bermejo, Marleen Kok, Lajos Pusztai, Yibin Kang, Joan Albanell, Toni Celià-Terrassa. March 2022. Nature Cancer. 10.1038/s43018-022-00339-4. [ Link ]
Coordinated post-transcriptional control of oncogene-induced senescence by UNR/CSDE1. Rosario Avolio, Marta Inglés-Ferrándiz, Annagiulia Ciocia, Olga Coll, Sarah Bonnin, Tanit Guitart, Anna Ribó, Fátima Gebauer. 11 January 2022. Cell Reports. 10.1016/j.celrep.2021.110211. [ Link ]
2021
Cross talk between the upstream exon-intron junction and Prp2 facilitates splicing of non-consensus introns. Stefan Hümmer, Sonia Borao, Angel Guerra-Moreno, Luca Cozzuto, Elena Hidalgo, José Ayté. 26 October 2021. Cell Reports. 10.1016/j.celrep.2021.109893. [ Link ]
FA-nf: A Functional Annotation Pipeline for Proteins from Non-Model Organisms Implemented in Nextflow. Anna Vlasova, Toni Hermoso Pulido, Francisco Camara, Julia Ponomarenko, Roderic Guigó. October 2021. Genes. 10.3390/genes12101645. [ Link ]
ExOrthist: a tool to infer exon orthologies at any evolutionary distance. Yamile Márquez, Federica Mantica, Luca Cozzuto, Demian Burguera, Antonio Hermoso-Pulido, Julia Ponomarenko, Scott W. Roy, Manuel Irimia. 20 August 2021. Genome Biology. 10.1186/s13059-021-02441-9. [ Link ]
We collaborated in making the tool reproducible and scalable using github-docker-nextflow.
Distinct roles for PARP-1 and PARP-2 in c-Myc-driven B-cell lymphoma in mice. Miguel A Galindo-Campos, Nura Lutfi, Sarah Bonnin, Carlos Martínez, Talia Velasco-Hernandez, Violeta García-Hernández, Juan Martin-Caballero, Coral Ampurdanés, Ramón Gimeno, Lluis Colomo, Gael Roue, Guillaume Guilbaud, Françoise Dantzer, Pilar Navarro, Matilde Murga, Oscar Fernandez-Capetillo, Anna Bigas, Pablo Menendez, Julian Sale, José Yélamos. 6 August 2021. Blood. 10.1182/blood.2021012805. [ Link ]
NFAT5 Amplifies Antipathogen Responses by Enhancing Chromatin Accessibility, H3K27 Demethylation, and Transcription Factor Recruitment. Giulia Lunazzi, Maria Buxadé, Marta Riera-Borrull, Laura Higuera, Sarah Bonnin, Hector Huerga Encabo, Silvia Gaggero, Diana Reyes-Garau, Carlos Company, Luca Cozzuto, Julia Ponomarenko, José Aramburu, Cristina López-Rodríguez. 24 May 2021. The Journal of Immunology. 10.4049/jimmunol.2000624. [ Link ]
QCloud2: An Improved Cloud-based Quality-Control System for Mass-Spectrometry-based Proteomics Laboratories. Roger Olivella, Cristina Chiva, Marc Serret, Daniel Mancera, Luca Cozzuto, Antoni Hermoso, Eva Borràs, Guadalupe Espadas, Julia Morales, Olga Pastor, Amanda Solé, Julia Ponomarenko, Eduard Sabidó. 16 March 2021. Journal of Proteome Research. 10.1021/acs.jproteome.0c00853. [ Link ]
Environmental Enrichment Induces Epigenomic and Genome Organization Changes Relevant for Cognition. Sergio Espeso-Gil, Aliaksei Z. Holik, Sarah Bonnin, Shalu Jhanwar, Sandhya Chandrasekaran, Roger Pique-Regi, Júlia Albaigès-Ràfols, Michael Maher, Jon Permanyer, Manuel Irimia, Marc R. Friedländer, Meritxell Pons-Espinal, Schahram Akbarian, Mara Dierssen, Philipp G. Maass, Charlotte N. Hor, Stephan Ossowski. 2021. Frontiers in Molecular Neuroscience. 10.3389/fnmol.2021.664912. [ Link ]
Citizen-science based study of the oral microbiome in Cystic fibrosis and matched controls reveals major differences in diversity and abundance of bacterial and fungal species. Jesse R. Willis, Ester Saus, Susana Iraola-Guzmán, Elena Cabello-Yeves, Ewa Ksiezopolska, Luca Cozzuto, Luis A. Bejarano, Nuria Andreu-Somavilla, Miriam Alloza-Trabado, Andrea Blanco, Anna Puig-Sola, Elisabetta Broglio, Carlo Carolis, Julia Ponomarenko, Jochen Hecht, Toni Gabaldón. 1 January 2021. Journal of Oral Microbiology. 10.1080/20002297.2021.1897328. [ Link ]
2020
Oral microbiome in down syndrome and its implications on oral health. Jesse R. Willis, Susana Iraola-Guzmán, Ester Saus, Ewa Ksiezopolska, Luca Cozzuto, Luis A. Bejarano, Nuria Andreu-Somavilla, Miriam Alloza-Trabado, Anna Puig-Sola, Andrea Blanco, Elisabetta Broglio, Carlo Carolis, Jochen Hecht, Julia Ponomarenko, Toni Gabaldón. 30 December 2020. Journal of Oral Microbiology. 10.1080/20002297.2020.1865690. [ Link ]
From research to rapid response: mass COVID-19 testing by volunteers at the Centre for Genomic Regulation. Ritobrata Ghose, Álvaro Aranguren-Ibáñez, Niccolò Arecco, Diego Balboa, Marc Bataller, Sergi Beltran, Hannah Benisty, Angèle Bénard, Edgar Bernardo, Sílvia Carbonell Sala, Eloi Casals, Ludovica Ciampi, Livia Condemi, Alberto Corvó, Marta Cosín-Tomás, Mirabai Cuenca-Ardura, Juan Manuel Duran Serrano, María Isabel Espejo Díaz, Marcos Fernandez Callejo, Antoni Gañez-Zapater, Raquel Garcia-Castellanos, Romina Garrido, Gil Henkin, Toni Hermoso Pulido, Xavier Hernandez-Alias, Jorge Herrero Vicente, Matthew Ingham, Wei Ming Lim, Sílvia Llonch, Elena Marmesat Bertoli, Irene Miguel-Escalada, Ariadna Montero-Blay, Cristina Navarrete Hernández, Maria Victoria Neguembor, Róisín-Ana Ní Chárthaigh, Natalia Pardo-Lorente, Laura Pascual-Reguant, Sílvia Pérez-Lluch, Reyes Perza, Martina Pesaresi, Daniel Picó Amador, Paula Pifarré, Davide Piscia, Marcos Plana-Carmona, Julia Ponomarenko, Leandro Radusky, Ezequiel Rivero, Malgorzata Rogalska, Guillem Torcal Garcia, José Wojnacki. 16 November 2020. . . [ Link ]
The altered transcriptome of pediatric myelodysplastic syndrome revealed by RNA sequencing. Zubovic L, Piazza S, Tebaldi T, Cozzuto L, Palazzo G, Sidarovich V, De Sanctis V, Bertorelli R, Lammens T, Hofmans M, De Moerloose B, Ponomarenko J, Pigazzi M, Masetti R, Mecucci C, Basso G, Macchi P. 12 October 2020. . . [ Link ]
External validation of putative biomarkers in eutopic endometrium of women with endometriosis using NanoString technology. Vallvé-Juanico J, López-Gil C, Ponomarenko J, Melnychuk T, Castellví J, Ballesteros A, Colás E, Gil-Moreno A, Santamaria Costa X. 9 October 2020. . . [ Link ]
Determination of primary microRNA processing in clinical samples by targeted pri-miR-sequencing. Thomas Conrad, Evgenia Ntini, Benjamin Lang, Luca Cozzuto, Jesper B. Andersen, Jens U. Marquardt, Julia Ponomarenko, Gian Gaetano Tartaglia, Ulf A. Vang Orom. 15 July 2020. RNA (New York, N.Y.). 10.1261/rna.076240.120. [ Link ]
Transcriptomic microRNA Profiling of Dendritic Cells in Response to Gut Microbiota-Secreted Vesicles. Natalia Díaz-Garrido, Sarah Bonnin, Marta Riera, Rosa Gíménez, Josefa Badia, Laura Baldomà. June 2020. Cells. 10.3390/cells9061534. [ Link ]
The penile microbiota of Black South African men: relationship with human papillomavirus and HIV infection. Harris Onywera, Anna-Lise Williamson, Luca Cozzuto, Sarah Bonnin, Zizipho Z. A. Mbulawa, David Coetzee, Julia Ponomarenko, Tracy L. Meiring. 6 April 2020. BMC Microbiology. 10.1186/s12866-020-01759-x. [ Link ]
This paper is the result of the six-months internship with us of Harris Onywera from the University Cape Town, South Africa, on the CRG-Novartis-Africa Mobility Programme. The findings indicate that there is a strong link between the penile microbiota and viral STIs, specifically HIV and HPV.
MasterOfPores: A Workflow for the Analysis of Oxford Nanopore Direct RNA Sequencing Datasets. Luca Cozzuto, Huanle Liu, Leszek P. Pryszcz, Toni Hermoso Pulido, Anna Delgado-Tejedor, Julia Ponomarenko, Eva Maria Novoa. 2020. Frontiers in Genetics. 10.3389/fgene.2020.00211. [ Link ]
The Penile Microbiota in Uncircumcised and Circumcised Men: Relationships With HIV and Human Papillomavirus Infections and Cervicovaginal Microbiota. Harris Onywera, Anna-Lise Williamson, Julia Ponomarenko, Tracy L. Meiring. 2020. Frontiers in Medicine. 10.3389/fmed.2020.00383. [ Link ]
2019
Genome Sequence of the Yeast Saprochaete ingens CBS 517.90. Viktória Hodorová, Hana Lichancová, Stanislav Zubenko, Karolina Sienkiewicz, Sarah Mae U. Penir, Philipp Afanasyev, Dominic Boceck, Sarah Bonnin, Siras Hakobyan, Urszula Smyczynska, Erik Zhivkoplias, Maryna Zlatohurska, Eugeniusz Tralle, Alina Frolova, Leszek P. Pryszcz, Broňa Brejová, Tomáš Vinař, Jozef Nosek. 12 December 2019. Microbiology Resource Announcements. 10.1128/MRA.01366-19. [ Link ]
EV-associated miRNAs from pleural lavage as potential diagnostic biomarkers in lung cancer. Berta Roman-Canal, Cristian Pablo Moiola, Sònia Gatius, Sarah Bonnin, Maria Ruiz-Miró, Esperanza González, Amaia Ojanguren, José Luis Recuero, Antonio Gil-Moreno, Juan M. Falcón-Pérez, Julia Ponomarenko, José M. Porcel, Xavier Matias-Guiu, Eva Colas. 21 October 2019. Scientific Reports. 10.1038/s41598-019-51578-y. [ Link ]
RRAS2 shapes the TCR repertoire by setting the threshold for negative selection. Ana Martínez-Riaño, Elena R. Bovolenta, Viola L. Boccasavia, Julia Ponomarenko, David Abia, Clara L. Oeste, Manuel Fresno, Hisse M. van Santen, Balbino Alarcon. 7 October 2019. The Journal of Experimental Medicine. 10.1084/jem.20181959. [ Link ]
This publication in a high-impact medical journal is the result of collaboration between the Biocore and researcher of the Centro Biología Molecular Severo Ochoa, Consejo Superior de Investigaciones Científicas, Universidad Autónoma de Madrid. Topics: autoimmunity, immune tolerance, T-cell repertoire. Impact Factor 11.
Pergola-web: a web server for the visualization and analysis of longitudinal behavioral data using repurposed genomics tools and standards. Jose Espinosa-Carrasco, Toni Hermoso Pulido, Ionas Erb, Mara Dierssen, Julia Ponomarenko, Cedric Notredame. 2 July 2019. Nucleic Acids Research. 10.1093/nar/gkz414. [ Link ]
This paper (and another one published by the same authors in 2018 in iScience) presents a novel approach at visualizing and analyzing longitudinal biological data that can range from monitoring mouse physiological signs to human behavioral data collected from wearable devices. The presented tool Pergola can be accessed at http://pergola.crg.eu. Topics: animal behavior, longitudinal biological data, web server. Impact Factor 11,2.
EV-associated miRNAs from peritoneal lavage as potential diagnostic biomarkers in colorectal cancer. Berta Roman-Canal, Jordi Tarragona, Cristian Pablo Moiola, Sònia Gatius, Sarah Bonnin, Maria Ruiz-Miró, José Enrique Sierra, Maria Rufas, Esperanza González, José M. Porcel, Antonio Gil-Moreno, Juan M. Falcón-Pérez, Julia Ponomarenko, Xavier Matias-Guiu, Eva Colas. 20 June 2019. Journal of Translational Medicine. 10.1186/s12967-019-1954-8. [ Link ]
EV-Associated miRNAs from Peritoneal Lavage are a Source of Biomarkers in Endometrial Cancer. Eva Colas, Xavier Matias-Guiu, Julia Ponomarenko, Juan M. Falcón-Pérez, Antonio Gil-Moreno, José M. Porcel, Isabel Hernández, Ivanna Llordella, Xavier González-Tallada, Esperanza González, Maria Ruiz-Miró, Sarah Bonnin, Sònia Gatius, Cristian Pablo Moiola, Berta Roman-Canal. June 2019. Cancers. 10.3390/cancers11060839. [ Link ]
This publication in a high-impact cancer research journal is the result of a collaboration of the Biocore with the cancer researchers from the Vall D'hebron Hospital. This paper demonstrates that miRNAs isolated from extracellular vesicles from the peritoneal lavage can serve as biomarkers in endometrial cancer. Topics: cancer, biomarker discovery, translational medicine. Impact Factor 6,2.
Fine tuning the extracellular environment accelerates the derivation of kidney organoids from human pluripotent stem cells. Nuria Montserrat, Carmen Hurtado del Pozo, Juan Carlos Izpisúa Belmonte, Josep M. Campistol, Luca Cozzuto, Aleix Gavaldà-Navarro, Pere Roca-Cusachs, Xavier Trepat, Dobryna Zalvidea, Elisa Martí, Lucia Fanlo, Roger Oria, Carolina Tarantino, Patricia Prado, Elena Garreta. April 2019. Nature Materials. 10.1038/s41563-019-0287-6. [ Link ]
This paper is the result of the Biocore's collaboration with the Institute for Bioengineering of Catalonia (IBEC), in the frame of the Barcelona Institute of Technology (BIST), Barcelona, Spain. Topics: human organoids, cell differentiation. Impact Factor 47.
Genome Sequence of Flavor-Producing Yeast Saprochaete suaveolens NRRL Y-17571. Jozef Nosek, Tomáš Vinař, Broňa Brejová, Leszek P. Pryszcz, Alina Frolova, Eugeniusz Tralle, Adrian Odrzywolski, Maryna Zlatohurska, Erik Zhivkoplias, Urszula Smyczynska, Pawel S. Krawczyk, Siras Hakobyan, Sarah Bonnin, Dominic Boceck, Philipp Afanasyev, Sarah Mae U. Penir, Karolina Sienkiewicz, Viktória Hodorová, Hana Lichancová. 28 February 2019. Microbiology Resource Announcements. 10.1128/MRA.00094-19. [ Link ]
Wnt/β-catenin signaling pathway safeguards epigenetic stability and homeostasis of mouse embryonic stem cells. Ilda Theka, Francesco Sottile, Marco Cammisa, Sarah Bonnin, Marta Sanchez-Delgado, Umberto Di Vicino, Maria Victoria Neguembor, Karthik Arumugam, Francesco Aulicino, David Monk, Andrea Riccio, Maria Pia Cosma. 30 January 2019. Scientific Reports. 10.1038/s41598-018-37442-5. [ Link ]
Identification of a Novel Transcription Factor Required For Osteogenic Differentiation Of Mesenchymal Stem Cells. Francesca Querques, Anna D'Agostino, Carmine Cozzolino, Luca Cozzuto, Barbara Lombardo, Eleonora Leggiero, Carlo Ruosi, Lucio Pastore. 18 January 2019. Stem Cells and Development. 10.1089/scd.2018.0152. [ Link ]
2018
Citizen science charts two major "stomatotypes" in the oral microbiome of adolescents and reveals links with habits and drinking water composition. Jesse R. Willis, Pedro González-Torres, Alexandros A. Pittis, Luis A. Bejarano, Luca Cozzuto, Nuria Andreu-Somavilla, Miriam Alloza-Trabado, Antonia Valentín, Ewa Ksiezopolska, Carlos Company, Harris Onywera, Magda Montfort, Antonio Hermoso, Susana Iraola-Guzmán, Ester Saus, Annick Labeeuw, Carlo Carolis, Jochen Hecht, Julia Ponomarenko, Toni Gabaldón. 6 December 2018. Microbiome. 10.1186/s40168-018-0592-3. [ Link ]
This paper is the output of an unprecendentally large Spanish-wide citizen-science project ran by CRG to study the mouth microbiome of healthy adolescents. It was a truly collaborative project, involving the CRG group, communication department and three facilities. This project was important for CRG to establish itself as a reference site for microbiome studies. Also, in the result of this project, the CRG Core Facilities programme has established a pipeline for providing the integrative service for microbiome studies - from DNA extraction to final analysis of sequencing data. Topics: metagenomics, human microbiome, citizen science. Impact Factor 10,5.
Pergola: Boosting Visualization and Analysis of Longitudinal Data by Unlocking Genomic Analysis Tools. Jose Espinosa-Carrasco, Ionas Erb, Toni Hermoso Pulido, Julia Ponomarenko, Mara Dierssen, Cedric Notredame. 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 ]
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 ]
This paper is an example of an ongoing successful collaboration between the Biocore and one of the CRG group. Biocore was involved in the design and development ofVastDB, the online database of Alternative Splicing (AS) profiles across multiple tissue and cell types. Topics: alternative splicing, databases, web server, Genome Browser. Impact Factor 10,1.
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 ]
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. Topics: WGS, rare disease. Impact Factor 4,1.
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. Impact factor 4,4.
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 ]
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.
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 ]
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 ]
