Data processing workflow for large-scale immune monitoring studies by mass cytometry

Authors: Rybakowska, Paulina, Van Gassen, Sofie, Quintelier, Katrien, Saeys, Yvan, Alarcón-Riquelme, Marta E., Marañón, Concepción

Contributors: Rybakowska,P, Alarcón-Riquelme,ME, Marañón,C GENYO, Centre for Genomics and Oncological Research, Pfizer, University of Granada, Andalusian Regional Government, PTS Granada, Spain. Van Gassen,S, Quintelier,K, Saeys,Y Department of Applied Mathematics, Computer Sciences and Statistics, Ghent University, Gent Belgium. Van Gassen,S, Saeys,Y Data Mining and Modeling for Biomedicine, VIB Center for Inflammation Research, Gent, Belgium. Quintelier,K Department of Pulmonary Diseases, Erasmus MC, Rotterdam, the Netherlands. Alarcón-Riquelme.ME Institute for Environmental Medicine, Karolinska Institute, Stockholm, Sweden., The authors also acknowledge funding from Consejería de la Salud y Familias de la Junta de Andalucía (PIER-0118-2019) and Instituto de Salud Carlos III (PI18/00082), partly supported by European FEDER funds.

Subject Terms: Mass cytometry, Semi-automated data preprocessing, Immune phenotyping, Data normalization, Quality control, Workflow, Artifacts, Flow cytometry, Control de calidad, Flujo de trabajo, Artefactos, Citometría de Flujo, Monitorización inmunológica, Inmunofenotipificación, Medical Subject Headings::Analytical, Diagnostic and Therapeutic Techniques and Equipment::Investigative Techniques::Epidemiologic Methods::Epidemiologic Study Characteristics as Topic::Epidemiologic Studies::Case-Control Studies::Retrospective Studies, Medical Subject Headings::Information Science::Information Science::Systems Analysis::Workflow, Diagnostic and Therapeutic Techniques and Equipment::Diagnosis::Diagnostic Techniques and Procedures::Monitoring, Physiologic::Monitoring, Immunologic, Diagnostic and Therapeutic Techniques and Equipment::Investigative Techniques::Artifacts, Diagnostic and Therapeutic Techniques and Equipment::Investigative Techniques::Methods::Research Design, Medical Subject Headings::Technology and Food and Beverages::Technology, Industry, and Agriculture::Technology::Quality Control, Diagnostic and Therapeutic Techniques and Equipment::Diagnosis::Diagnostic Techniques and Procedures::Clinical Laboratory Techniques::Specimen Handling, Diagnostic and Therapeutic Techniques and Equipment::Investigative Techniques::Epidemiologic Methods::Epidemiologic Study Characteristics as Topic::Clinical Trials as Topic::Multicenter Studies as Topic, Diagnostic and Therapeutic Techniques and Equipment::Investigative Techniques::Immunologic Techniques::Immunologic Tests::Immunophenotyping

File Description: application/pdf; application/vnd.openxmlformats-officedocument.wordprocessingml.document

Relation: https://www.sciencedirect.com/science/article/pii/S2001037021002130; Rybakowska P, Van Gassen S, Quintelier K, Saeys Y, Alarcón-Riquelme ME, Marañón C. Data processing workflow for large-scale immune monitoring studies by mass cytometry. Comput Struct Biotechnol J. 2021 May 21;19:3160-3175; http://hdl.handle.net/10668/4361; PMC8188119

Availability: http://hdl.handle.net/10668/4361
https://doi.org/10.1016/j.csbj.2021.05.032

A versatile workflow to integrate RNA-seq genomic and transcriptomic data into mechanistic models of signaling pathways

Authors: Garrido-Rodriguez, Martín, Lopez-Lopez, Daniel, Ortuno, Francisco M., Peña-Chilet, María, Muñoz, Eduardo, Calzado, Marco A., Dopazo, Joaquin

Contributors: Garrido-Rodriguez,M, Lopez-Lopez,D, Ortuno,FM, Peña-Chilet,M, Dopazo,J Clinical Bioinformatics Area, Fundación Progreso y Salud (FPS), Hospital Virgen del Rocío, Sevilla, Spain. Garrido-Rodriguez,M, Calzado,MA Departamento de Biología Celular, Fisiología e Inmunología, Universidad de Córdoba, Córdoba, Spain. Garrido-Rodriguez,M, Muñoz,E, Calzado,MA Instituto Maimónides de Investigación Biomédica de Córdoba (IMIBIC), Córdoba, Spain. Garrido-Rodriguez,M, Calzado.MA Hospital Universitario Reina Sofía, Córdoba, Spain. Lopez-Lopez.D: Ortuno,FM, Dopazo,J Computational Systems Medicine, Institute of Biomedicine of Seville (IBIS), Sevilla, Spain. Peña-Chilet,M, Dopazo,J Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), FPS, Hospital Virgen del Rocío, Sevilla, Spain. Dopazo,J FPS/ELIXIR-es, Hospital Virgen del Rocío, Sevilla, Spain, JD has received these grants: SAF2017- 88908-R from the Ministerio de Economı´a y Competitividad and PT17/0009/0006 from the Instituto de Salud Carlos III, as well as an FP7 People Marie-Curie Actions 813533 and and Horizon 2020 Framework Programme 676559. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.

Subject Terms: Transcriptome, RNA massive sequencing, RNA-seq, Workflow, Signaling pathways, Transcriptoma, Flujo de trabajo, Secuenciación de escopeta completa del transcriptoma, Medical Subject Headings::Phenomena and Processes::Mathematical Concepts::Algorithms, Medical Subject Headings::Anatomy::Cells::Cells, Cultured::Cell Line::Cell Line, Tumor, Medical Subject Headings::Disciplines and Occupations::Natural Science Disciplines::Biological Science Disciplines::Biology::Computational Biology, Medical Subject Headings::Information Science::Information Science::Information Storage and Retrieval::Databases as Topic::Databases, Factual, Medical Subject Headings::Analytical, Diagnostic and Therapeutic Techniques and Equipment::Investigative Techniques::Genetic Techniques::Gene Expression Profiling, Diagnostic and Therapeutic Techniques and Equipment::Investigative Techniques::Genetic Techniques::Sequence Analysis::High-Throughput Nucleotide Sequencing, Medical Subject Headings::Organisms::Eukaryota::Animals::Chordata::Vertebrates::Mammals::Primates::Haplorhini::Catarrhini::Hominidae::Humans, Diagnostic and Therapeutic Techniques and Equipment::Investigative Techniques::Models, Theoretical, Medical Subject Headings::Phenomena and Processes::Genetic Phenomena::Genetic Variation::Mutation, Medical Subject Headings::Information Science::Information Science::Computing Methodologies::Software, Medical Subject Headings::Phenomena and Processes::Chemical Phenomena::Biochemical Phenomena::Biochemical Processes::Transcription, Genetic::Transcriptome, Medical Subject Headings::Information Science::Information Science::Systems Analysis::Workflow, Medical Subject Headings::Disciplines and Occupations::Natural Science Disciplines::Biological Science Disciplines::Biology::Genetics::Genomics, Medical Subject Headings::Phenomena and Processes::Chemical Phenomena::Biochemical Phenomena::Biochemical Processes::Signal Transduction

File Description: application/pdf; application/vnd.openxmlformats-officedocument.spreadsheetml.sheet

Relation: https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1008748; Garrido-Rodriguez M, Lopez-Lopez D, Ortuno FM, Peña-Chilet M, Muñoz E, Calzado MA, et al. A versatile workflow to integrate RNA-seq genomic and transcriptomic data into mechanistic models of signaling pathways. PLoS Comput Biol. 2021 Feb 11;17(2):e1008748; http://hdl.handle.net/10668/4220; PMC7904194

Availability: http://hdl.handle.net/10668/4220
https://doi.org/10.1371/journal.pcbi.1008748

Evaluating, Filtering and Clustering Genetic Disease Cohorts Based on Human Phenotype Ontology Data with Cohort Analyzer

Authors: Rojano, Elena, Córdoba-Caballero, José, Jabato, Fernando M., Gallego, Diana, Serrano, Mercedes, Pérez, Belén, Parés-Aguilar, Álvaro, Perkins, James R., Ranea, Juan A G., Seoane-Zonjic, Pedro

Contributors: Rojano,E, Córdoba-Caballero,J, Parés-Aguilar,Á, Perkins,JR, Ranea,JAG, Seoane-Zonjic,P Department of Molecular Biology and Biochemistry, University of Málaga, Málaga, Spain. Rojano,E, Jabato,FM, Seoane-Zonjic,P Institute of Biomedical Research in Málaga (IBIMA), Málaga, Spain. Jabato,FM Supercomputation and Bioinformatics (SCBI), University of Malaga, Malaga, Spain. Jabato,FM LifeWatch-ERIC, Seville, Spain. Gallego,D, Serrano,M, Pérez,B, Seoane-Zonjic,P Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Madrid, Málaga, Barcelona , Instituto de Salud Carlos III, Madrid, Spain. Gallego,D, Pérez,B Centro de Diagnóstico de Enfermedades Moleculares, Centro de Biología Molecular-SO UAM-CSIC, Universidad Autónoma de Madrid, Madrid, Spain. Gallego,D, Pérez,B Instituto de Investigación Sanitaria idiPAZ, Madrid, Spain. Serrano,M Neuropediatric Department, Institut de Recerca Hospital Sant Joan de Déu, Barcelona, Spain., This work was supported by The Spanish Ministry of Economy and Competitiveness with European Regional Development Fund PID2019-108096RB-C21, the Andalusian Government with European Regional Development Fund UMA18-FEDERJA-102 and PAIDI 2020:PY20-00372, biomedicine research project PI-0075-2017 (Fundación Progreso y Salud), the Carlos III Health Institute PI19/01155, the Madrid Government B2017/BMD-3721, the Ramón Areces foundation for rare disease investigation (National call for research on life and material sciences, XIX edition). We thank the patients and patients’ families for their collaboration and consent. PMM2-CDG research is supported by national grants from the National Plan on I+D+I, cofinanced by ISCIII (Subdirección General de Evaluación y Fomento de la Investigación Sanitaria) and FEDER (Fondo Europeo de Desarrollo Regional) PI14/00021, PI17/00101 . Dr. Serrano’s research work is supported by a grant from the Generalitat de Catalunya PERIS SLT008/18/00194 . The CIBERER is an initiative from the Carlos III Health Institute (Instituto de Salud Carlos III).

Subject Terms: Genetic diseases, Cohort analyzer, Human phenotype ontology, Cluster analysis, Phenotype quality assessment, Enfermedades genéticas congénitas, Ontología de genes, Análisis por grupos, Fenotipo, Garantía de la calidad de atención de salud, Medical Subject Headings::Organisms::Eukaryota::Animals::Chordata::Vertebrates::Mammals::Primates::Haplorhini::Catarrhini::Hominidae::Humans, Medical Subject Headings::Information Science::Information Science::Systems Analysis::Workflow, Medical Subject Headings::Phenomena and Processes::Genetic Phenomena::Phenotype, Medical Subject Headings::Disciplines and Occupations::Natural Science Disciplines::Biological Science Disciplines::Biology::Genetics::Genomics, Medical Subject Headings::Analytical, Diagnostic and Therapeutic Techniques and Equipment::Investigative Techniques::Epidemiologic Methods::Statistics as Topic::Cluster Analysis

File Description: application/pdf

Relation: https://www.mdpi.com/2075-4426/11/8/730/htm; Rojano E, Córdoba-Caballero J, Jabato FM, Gallego D, Serrano M, Pérez B, et al. Evaluating, Filtering and Clustering Genetic Disease Cohorts Based on Human Phenotype Ontology Data with Cohort Analyzer. J Pers Med. 2021 Jul 27;11(8):730; http://hdl.handle.net/10668/3924; PMC8398478

Availability: http://hdl.handle.net/10668/3924
https://doi.org/10.3390/jpm11080730

Clinical Audits in Outpatient Clinics for Chronic Obstructive Pulmonary Disease: Methodological Considerations and Workflow.

Authors: López-Campos, Jose Luis, Abad Arranz, María, Calero Acuña, Carmen, Romero Valero, Fernando, Ayerbe García, Ruth, Hidalgo Molina, Antonio, Aguilar Pérez-Grovas, Ricardo Ismael, García Gil, Francisco, Casas Maldonado, Francisco, Caballero Ballesteros, Laura, Sánchez Palop, María, Pérez-Tejero, Dolores, Segado, Alejandro, Calvo Bonachera, Jose, Hernández Sierra, Bárbara, Doménech, Adolfo, Arroyo Varela, Macarena, González Vargas, Francisco, Cruz Rueda, Juan Jose

Contributors: López-Campos,JL, Abad Arranz,M, Calero Acuña,C Unidad Médico-Quirúrgica de Enfermedades Respiratorias, Instituto de Biomedicina de Sevilla (IBiS), Hospital Universitario Virgen del Rocío/Universidad de Sevilla, Seville, Spain. López-Campos,JL, Calero Acuña,C CIBER de Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III, Madrid, Spain. Romero Valero,F, Hidalgo Molina,A Hospital Puerta del Mar, Cádiz, Spain. Ayerbe García,R, Aguilar Pérez-Grovas,RI Hospital Juan Ramón Jiménez, Huelva, Spain. García Gil,F, Caballero Ballesteros,L Hospital Universitario Reina Sofía, Córdoba, Spain. Casas Maldonado,F, Sánchez Palop,M Hospital Universitario San Cecilio, Granada, Spain. Pérez-Tejero,D, Segado,A Hospital Infanta Margarita, Cabra, Córdoba, Spain. Calvo Bonachera,J, Hernández Sierra,B Hospital Torrecárdenas, Almería, Spain. Doménech,A, Arroyo Varela,M 9 Hospital Regional Universitario de Málaga, Spain. González Vargas,F, Cruz Rueda,JJ Hospital Universitario Virgen de las Nieves, Granada, Spain., This study was financially supported by an unrestricted grant from Laboratorios Menarini, SA (Barcelona, Spain).

Subject Terms: Andalucía, Instituciones de atención ambulatoria, Auditoría clínica, Recolección de datos, Humanos, Enfermedad pulmonar obstructiva crónica, Flujo de trabajo, Medical Subject Headings::Health Care::Health Services Administration::Organization and Administration::Management Audit::Benchmarking, Medical Subject Headings::Health Care::Health Services Administration::Quality of Health Care::Quality Assurance, Health Care::Clinical Audit, Medical Subject Headings::Analytical, Diagnostic and Therapeutic Techniques and Equipment::Investigative Techniques::Epidemiologic Methods::Data Collection, Medical Subject Headings::Organisms::Eukaryota::Animals::Chordata::Vertebrates::Mammals::Primates::Haplorhini::Catarrhini::Hominidae::Humans, Medical Subject Headings::Information Science::Information Science::Computing Methodologies::Computer Systems::Computer Communication Networks::Internet, Medical Subject Headings::Check Tags::Male, Medical Subject Headings::Diseases::Respiratory Tract Diseases::Lung Diseases::Lung Diseases, Obstructive::Pulmonary Disease, Chronic Obstructive, Medical Subject Headings::Information Science::Information Science::Systems Analysis::Workflow, Medical Subject Headings::Health Care::Health Care Facilities, Manpower, and Services::Health Facilities::Ambulatory Care Facilities, Medical Subject Headings::Geographicals::Geographic Locations::Europe::Spain, Medical Subject Headings::Check Tags::Female

File Description: application/pdf

Relation: http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0141856#abstract0; López-Campos JL, Abad Arranz M, Calero Acuña C, Romero Valero F, Ayerbe García R, Hidalgo Molina A, et al. Clinical Audits in Outpatient Clinics for Chronic Obstructive Pulmonary Disease: Methodological Considerations and Workflow. PLoS ONE. 2015; 10(11):e0141856; http://hdl.handle.net/10668/2315; PMC4636163

Availability: http://hdl.handle.net/10668/2315
https://doi.org/10.1371/journal.pone.0141856

MAPI: towards the integrated exploitation of bioinformatics Web Services.

Authors: Ramirez, Sergio, Karlsson, Johan, Trelles, Oswaldo

Contributors: Ramirez,S, Karlsson,J, Trelles,O Computer Architecture Department,University of Malaga, Malaga, Spain. Karlsson,J Fundación IMABIS, Hospital Carlos Haya, Malaga, Spain. Trelles,O Instituto Nacional de Bioinformatica, Madrid, Spain., This work has been partially supported by the National Institute of Bioinformatics (INB), Spain (a platform of the ISCIII) and the RIRAAF network (RD07/0064/0017).

Subject Terms: Biología Computacional, Internet, Bibliotecas, Diseño de Programas Informáticos, Flujo de Trabajo, Medical Subject Headings::Information Science::Information Science::Computing Methodologies::Computer Systems::Computer Communication Networks::Internet, Medical Subject Headings::Information Science::Information Science::Information Centers::Libraries, Medical Subject Headings::Information Science::Information Science::Computing Methodologies::Software, Medical Subject Headings::Information Science::Information Science::Systems Analysis::Workflow, Medical Subject Headings::Disciplines and Occupations::Natural Science Disciplines::Biological Science Disciplines::Biology::Computational Biology

File Description: application/pdf

Relation: http://www.biomedcentral.com/1471-2105/12/419; Ramirez S, Karlsson J, Trelles O. MAPI: towards the integrated exploitation of bioinformatics Web Services. BMC Bioinformatics;2011 Oct;12:419.; WOS000297110700001; http://hdl.handle.net/10668/504; PMC3219744

Availability: http://hdl.handle.net/10668/504
https://doi.org/10.1186/1471-2105-12-419

Visualization of coronary arteries in paediatric patients using whole-heart coronary magnetic resonance angiography: comparison of image-navigation and the standard approach for respiratory motion compensation

Authors: Velasco Forte, Mari Nieves, Valverde, Israel, Prabhu, Nanda, Correia, Teresa, Narayan, Srinivas Ananth, Bell, Aaron, Mathur, Sujeev, Razavi, Reza, Hussain, Tarique, Pushparajah, Kuberan, Henningsson, Markus

Contributors: Velasco Forte,MN, Valverde,I, Correia,T, Narayan,SA, Razavi,R, Hussain,T, Pushparajah,K, Henningsson,M Division of Biomedical Engineering and Imaging Sciences, King's College London, London, UK. Velasco Forte,MN, Prabhu,N, Bell,A, Mathur,S, Pushparajah,K Department of Congenital Heart Disease, Evelina London Children's Hospital, Guy's and St Thomas NHS Foundation Trust, London, UK. Velasco Forte,MN, Valverde,I Cardiovascular Pathology Unit, Institute of Biomedicine of Seville, IBIS, Virgen del Rocio University Hospital/CSIC/University of Seville, Seville, Spain. Hussain,T Department of Pediatrics, University of Texas Southwestern Medical Center, 1935 Medical District Drive, Dallas, USA. Henningsson,M Division of Cardiovascular Medicine, Department of Medical and Health Sciences, Linköping University, Linköping, Sweden., This work was supported by the National Institute for Health Research (NIHR) Cardiovascular Healthcare Technology Cooperative (HTC) and Biomedical Research Centre (BRC) awarded to Guy’s & St Thomas’ NHS Foundation Trust in partnership with King’s College London. This work was additionally supported by the Wellcome/EPSRC Centre for Medical Engineering at King’s College London WT 088641/Z/09/Z) as well as the BHF Centre of Excellence (British Heart Foundation award RE/08/03).

Subject Terms: Coronary magnetic resonance angiography, Respiratory motion compensation, Coronary artery disease, Image-based navigation, Magnetic resonance angiography, Angiografía por resonancia magnética, Enfermedad de la arteria coronaria, Medical Subject Headings::Persons::Persons::Age Groups::Adolescent, Medical Subject Headings::Analytical, Diagnostic and Therapeutic Techniques and Equipment::Investigative Techniques::Artifacts, Medical Subject Headings::Persons::Persons::Age Groups::Child, Medical Subject Headings::Persons::Persons::Age Groups::Child::Child, Preschool, Medical Subject Headings::Chemicals and Drugs::Chemical Actions and Uses::Pharmacologic Actions::Diagnostic Uses of Chemicals::Contrast Media, Medical Subject Headings::Anatomy::Cardiovascular System::Blood Vessels::Arteries::Coronary Vessels, Medical Subject Headings::Check Tags::Female, Medical Subject Headings::Diseases::Cardiovascular Diseases::Cardiovascular Abnormalities::Heart Defects, Congenital, Medical Subject Headings::Organisms::Eukaryota::Animals::Chordata::Vertebrates::Mammals::Primates::Haplorhini::Catarrhini::Hominidae::Humans, Medical Subject Headings::Persons::Persons::Age Groups::Infant, Medical Subject Headings::Check Tags::Male, Medical Subject Headings::Chemicals and Drugs::Organic Chemicals::Alcohols::Sugar Alcohols::Sorbitol::Meglumine, Medical Subject Headings::Chemicals and Drugs::Organic Chemicals::Organometallic Compounds, Diagnostic and Therapeutic Techniques and Equipment::Investigative Techniques::Epidemiologic Methods::Epidemiologic Research Design::Sensitivity and Specificity::Predictive Value of Tests, Diagnostic and Therapeutic Techniques and Equipment::Investigative Techniques::Evaluation Studies as Topic::Reproducibility of Results, Medical Subject Headings::Phenomena and Processes::Physical Phenomena::Time::Time Factors, Medical Subject Headings::Information Science::Information Science::Systems Analysis::Workflow, Diagnostic and Therapeutic Techniques and Equipment::Diagnosis::Diagnostic Techniques and Procedures::Diagnostic Techniques, Cardiovascular::Angiography::Magnetic Resonance Angiography, Diagnostic and Therapeutic Techniques and Equipment::Diagnosis::Diagnostic Techniques and Procedures::Diagnostic Imaging::Magnetic Resonance Imaging::Magnetic Resonance Imaging

File Description: application/pdf

Relation: https://jcmr-online.biomedcentral.com/articles/10.1186/s12968-019-0525-8; Velasco Forte MN, Valverde I, Prabhu N, Correia T, Narayan SA, Bell A, et al. Visualization of coronary arteries in paediatric patients using whole-heart coronary magnetic resonance angiography: comparison of image-navigation and the standard approach for respiratory motion compensation. J Cardiovasc Magn Reson. 2019 Feb 25;21(1):13.; http://hdl.handle.net/10668/3175; PMC6388473

Availability: http://hdl.handle.net/10668/3175
https://doi.org/10.1186/s12968-019-0525-8