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Biostatistics / Bioinformatics

GINYS-IRB-007
Dra. Camille Stephan-Otto Attolini
CORE FACILITY MANAGER
camille.stephan@irbbarcelona.org | 934 020 217 | ORCID | PRC page
FACILITY WEBSITE
The mission of the Biostatistics / Bioinformatics Unit is to carry out collaborative research and offer consultation and quantitative research resources to all IRB Barcelona research groups. We help scientists by offering consulting services both in the short and long term in the following areas:
  • Experimental design: sample size, study design, statistical methodology planning
  • Data analysis: clinical or biomedical databases, genomics data
  • Help with statistical methodology in own or other people's research
  • Software: help in the use of software, software development to meet the special needs of data analysis or study design
  • Methodological research is carried out and resources are developed in all the areas mentioned.

Services

  • Microarrays: quality control, differential expression, GO and KEGG enrichment analysis, GSEA GO and KEGG, signature discovery
  • RNASeq: quality control, differential expression, GO and KEGG enrichment analysis, signature discovery, isoform change, SNP call
  • ChipSeq: processing, quality control, maximum definition + annotation + visualization, differential union + integrative analysis
  • Genome-wide sequencing: processing, quality control, SNP calling, copy number alteration calling
  • Whole exome sequencing: processing, quality control, SNP call, copy number alteration call
  • Proteomics: processing, quality control, differential expression, GO and KEGG enrichment analysis
  • Mining and analysis of public databases: selection, curation of clinical data, expression data processing, association of expression and clinical data, integration of number of copies / genomics
  • TCGA analysis: exploratory analysis in all types of cancer: association between expression and clinical variables, detailed analysis with clinical variables and cured techniques: association with expression, data integration: number of copies, expression, mutations, etc.
  • Microbiome: Quality control + OTU estimation + differential abundance, Phylogenetic analysis
  • Binding prediction: prediction of RNA / DNA binding by proteins / genes
  • Unique cell sequencing: processing, quality control, differential expression, clustering, trajectories, GO and KEGG enrichment analysis
  • Advice: Statistical advice, Data analysis, Personalized services
  • Experimental design

Staff

CORE FACILITY MANAGER
Dra. Camille Stephan-Otto Attolini | camille.stephan@irbbarcelona.org | 934 020 217 | ORCID | PRC Page

Publications

The efficacy of chemotherapy is limited by intratumoral senescent cells expressing PD-L2.
Chaib, S., López-Domínguez, J. A., Lalinde-Gutiérrez, M., Prats, N., Marin, I., Boix, O., García-Garijo, A., Meyer, K., Muñoz, M. I., Aguilera, M., Mateo, L., Stephan-Otto Attolini, C., Llanos, S., Pérez-Ramos, S., Escorihuela, M., Al-Shahrour, F., Cash, T. P., Tchkonia, T., Kirkland, J. L., … Serrano, M.
Nature Cancer, 5(3), 448–462. (2024a)
DOI: 10.1038/s43018-023-00712-x
Roastgsa: a comparison of rotation-based scores for gene set enrichment analysis.
Caballé-Mestres, A., Berenguer-Llergo, A., & Stephan-Otto Attolini, C.
BMC Bioinformatics, 24(1), 408. (2023a)
DOI: 10.1186/s12859-023-05510-x
Vitamin B12 is a limiting factor for induced cellular plasticity and tissue repair.
Kovatcheva, M., Melendez, E., Chondronasiou, D., Pietrocola, F., Bernad, R., Caballe, A., Junza, A., Capellades, J., Holguín-Horcajo, A., Prats, N., Durand, S., Rovira, M., Yanes, O., Stephan-Otto Attolini, C., Kroemer, G., & Serrano, M.
Nature Metabolism, 5(11), 1911–1930 (2023b)
DOI: 10.1038/s42255-023-00916-6
Cellular Senescence Is Immunogenic and Promotes Antitumor Immunity.
Marin, I., Boix, O., Garcia-Garijo, A., Sirois, I., Caballe, A., Zarzuela, E., Ruano, I., Attolini, C. S.-O., Prats, N., López-Domínguez, J. A., Kovatcheva, M., Garralda, E., Muñoz, J., Caron, E., Abad, M., Gros, A., Pietrocola, F., & Serrano, M.
Cancer Discovery, 13(2), 410–431 (2023a)
DOI: 10.1158/2159-8290.CD-22-0523
MAF amplification licenses ERα through epigenetic remodelling to drive breast cancer metastasis.
Llorente, A., Blasco, M. T., Espuny, I., Guiu, M., Ballaré, C., Blanco, E., Caballé, A., Bellmunt, A., Salvador, F., Morales, A., Nuñez, M., Loren, G., Imbastari, F., Fidalgo, M., Figueras-Puig, C., Gibler, P., Graupera, M., Monteiro, F., Riera, A., … Gomis, R. R.
Nature Cell Biology, 25(12), 1833–1847 (2023a)
DOI: 10.1038/s41556-023-01281-y
Mex3a marks drug-tolerant persister colorectal cancer cells that mediate relapse after chemotherapy.
Álvarez-Varela, A., Novellasdemunt, L., Barriga, F. M., Hernando-Momblona, X., Cañellas-Socias, A., Cano-Crespo, S., Sevillano, M., Cortina, C., Stork, D., Morral, C., Turon, G., Slebe, F., Jiménez-Gracia, L., Caratù, G., Jung, P., Stassi, G., Heyn, H., Tauriello, D. V. F., Mateo, L., … Batlle, E.
Nature Cancer, 3(9), 1052–1070 (2022a)
DOI: 10.1038/s43018-022-00402-0
Lysine 27 dimethylation of Drosophila linker histone dH1 contributes to heterochromatin organization independently of H3K9 methylation.
Bernués, J., Izquierdo-Boulstridge, A., Reina, O., Castejón, L., Fernández-Castañer, E., Leal, N., Guerrero-Pepinosa, N., Bonet-Costa, C., Vujatovic, O., Climent-Cantó, P., & Azorín, F.
Nucleic Acids Research, 50(16), 9212–9225 (2022a)
DOI: 10.1093/nar/gkac716
Metastatic recurrence in colorectal cancer arises from residual EMP1+ cells.
Cañellas-Socias, A., Cortina, C., Hernando-Momblona, X., Palomo-Ponce, S., Mulholland, E. J., Turon, G., Mateo, L., Conti, S., Roman, O., Sevillano, M., Slebe, F., Stork, D., Caballé-Mestres, A., Berenguer-Llergo, A., Álvarez-Varela, A., Fenderico, N., Novellasdemunt, L., Jiménez-Gracia, L., Sipka, T., … Batlle, E.
Nature, 611(7936), 603–613 (2022a)
DOI: 10.1038/s41586-022-05402-9
Functional patient-derived organoid screenings identify MCLA-158 as a therapeutic EGFR × LGR5 bispecific antibody with efficacy in epithelial tumors.
Herpers, B., Eppink, B., James, M. I., Cortina, C., Cañellas-Socias, A., Boj, S. F., Hernando-Momblona, X., Glodzik, D., Roovers, R. C., van de Wetering, M., Bartelink-Clements, C., Zondag-van der Zande, V., Mateos, J. G., Yan, K., Salinaro, L., Basmeleh, A., Fatrai, S., Maussang, D., Lammerts van Bueren, J. J., … Throsby, M.
Nature Cancer, 3(4), 418–436 (2022a)
DOI: 10.1038/s43018-022-00359-0

INSTITUTE

IRB Barcelona - Institut de Recerca Biomèdica

Parc Científic de Barcelona
Baldiri Reixac, 10

08028 Barcelona http://www.irbbarcelona.org/ca

DOMAINS RIS3CAT

  • Education and knowledge generation system
  • Industrial system
  • Socio-sanitary system

CATEGORIES

  • INFORMATION TECNOLOGIES
    • Bioinformatics
    • Biostatistics

RATES AND ACCESS

Availability Level: Low
Access Procedures:

Open

FACILITIES NETWORKS

INB – Bioinformatics Platform
Provide world-class basic bioinformatics resources to the national and international life sciences research community in key fields such as functional genomics, RNA-Seq transcriptomics, genotyping, genomic medicine, and molecular dynamics simulations. Provide a platform for integrated basic bioinformatics services to the research community. Facilitate the coordinated participation of bioinformatics groups in large-scale national and international projects that require and benefit from closely collaborating teams that are known and accustomed to working together.
Network link
Reach: Spain
Status: Active
PRC page
BiB – Bioinformatics Network of Catalonia

Bioinformatics Barcelona (BIB) is an association for the provision of education and training, the promotion of advanced research, the transfer of knowledge and technology, the stimulation of competitiveness and innovation in the industrial sector, and the provision of 'greater visibility as an international entity. BIB was born to cover the need to generate synergies between biology and computer science, for a stronger union between these areas and for the development of high quality education and training programs in the creation of bioinformatics talent.

Network link
Reach: Catalonia
Status: Active
PRC page
CERCA - Ginys