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1.
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23 p, 7.8 MB |
Deep learning applications in single-cell genomics and transcriptomics data analysis
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Erfanian, Nafiseh (Birjand University of Medical Sciences, Birjand, Iran) ;
Heydari, A.Ali (University of California, USA) ;
Feriz, Adib Miraki (Birjand University of Medical Sciences, Birjand, Iran) ;
Iañez, Pablo (Institut Germans Trias i Pujol. Institut de Recerca contra la Leucèmia Josep Carreras) ;
Derakhshani, Afshin (University of Calgary, Canada) ;
Ghasemigol, Mohammad (University of North Dakota, USA) ;
Farahpour, Mohsen (University of Birjand, Iran) ;
Razavi, Seyyed Mohammad (University of Birjand, Iran) ;
Nasseri, Saeed (Birjand University of Medical Sciences, Iran) ;
Safarpour, Hossein (Birjand University of Medical Sciences, Iran) ;
Sahebkar, Amirhossein (Mashhad University of Medical Sciences, Mashhad, Iran)
Traditional bulk sequencing methods are limited to measuring the average signal in a group of cells, potentially masking heterogeneity, and rare populations. The single-cell resolution, however, enhances our understanding of complex biological systems and diseases, such as cancer, the immune system, and chronic diseases. [...]
2023 -  10.1016/j.biopha.2023.115077
Biomedicine & pharmacotherapy, Vol. 165 (september 2023)
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2.
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15 p, 9.2 MB |
Morphologically different hydroxyapatite nanoparticles exert differential genotoxic effects in Drosophila
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Güneş, Merve (Akdeniz University. Department of Biology) ;
Yalçın, Burçin (Akdeniz University. Department of Biology) ;
Burgazlı, Ayşen Yağmur (Akdeniz University. Department of Biology) ;
Tagorti, Ghada (Akdeniz University. Department of Biology) ;
Yavuz, Emre (Akdeniz University. Department of Chemistry) ;
Akarsu, Esin (Akdeniz University. Department of Chemistry) ;
Kaya, Nuray (Akdeniz University. Department of Biology) ;
Marcos Dauder, Ricardo (Universitat Autònoma de Barcelona. Departament de Genètica i de Microbiologia) ;
Kaya, Bülent (Akdeniz University. Department of Biology)
Hydroxyapatite (HAP) occurs naturally in sedimentary and metamorphic rocks and constitutes the hard structures in many organisms. Since synthetic nano-sized HAP (HAP-NPs) are used in orthopedic applications and for heavy metal remediation in aquatic and terrestrial media, both environment and humans are exposed to them. [...]
2023 - 10.1016/j.scitotenv.2023.166556
Science of the total environment, Vol. 904 (December 2023) , art. 166556
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3.
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14 p, 1.2 MB |
Progress in cardiac research : From rebooting cardiac regeneration to a complete cell atlas of the heart
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Davidson, Sean M (Hatter Cardiovascular Institute. University College London) ;
Padró, Teresa (Institut d'Investigació Biomèdica Sant Pau) ;
Bollini, S. (Department of Experimental Medicine (DIMES). University of Genova) ;
Vilahur, Gemma (Institut d'Investigació Biomèdica Sant Pau) ;
Duncker, D.J. (Division of Experimental Cardiology. Department of Cardiology. Erasmus University Medical Center) ;
Evans, P.C. (Department of Infection. Immunity and Cardiovascular Disease and Insigneo Institute. University of Sheffield) ;
Guzik, T. (Department of Medicine. Jagiellonian University. Collegium Medicum) ;
Hoefer, I.E. (Central Diagnostic Laboratory. University Medical Center Utrecht) ;
Waltenberger, J. (Department of Cardiovascular Medicine. Medical Faculty. University of Muenster) ;
Wojta, J. (Department of Internal Medicine Ii. Medical University of Vienna) ;
Weber, C. (Cardiovascular Research Institute Maastricht (CARIM). Department of Biochemistry. Maastricht University)
We review some of the important discoveries and advances made in basic and translational cardiac research in 2020. For example, in the field of myocardial infarction (MI), new aspects of autophagy and the importance of eosinophils were described. [...]
2021 - 10.1093/cvr/cvab200
Cardiovascular research, Vol. 117 Núm. 10 (january 2021) , p. 2161-2174
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4.
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22 p, 5.6 MB |
Epigenetic and transcriptomic reprogramming in monocytes of severe COVID-19 patients reflects alterations in myeloid differentiation and the influence of inflammatory cytokines
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Godoy-Tena, Gerard (Institut Germans Trias i Pujol. Institut de Recerca contra la Leucèmia Josep Carreras) ;
Barmada, Anis (University of Cambridge. Department of Medical Genetics) ;
Morante-Palacios, Octavio (Institut Germans Trias i Pujol. Institut de Recerca contra la Leucèmia Josep Carreras) ;
de la Calle-Fabregat, Carlos (Institut Germans Trias i Pujol. Institut de Recerca contra la Leucèmia Josep Carreras) ;
Martins-Ferreira, Ricardo (Institut Germans Trias i Pujol. Institut de Recerca contra la Leucèmia Josep Carreras) ;
Ferreté-Bonastre, Anna G. (Institut Germans Trias i Pujol. Institut de Recerca contra la Leucèmia Josep Carreras) ;
Ciudad, Laura (Institut Germans Trias i Pujol. Institut de Recerca contra la Leucèmia Josep Carreras) ;
Ruiz-Sanmartín, Adolfo (Universitat Autònoma de Barcelona. Departament de Medicina) ;
Martínez Gallo, Mónica (Hospital Universitari Vall d'Hebron) ;
Ferrer, Ricard (Universitat Autònoma de Barcelona. Departament de Medicina) ;
Ruiz-Rodriguez, Juan Carlos (Universitat Autònoma de Barcelona. Departament de Medicina) ;
Rodríguez-Ubreva, Javier (Institut Germans Trias i Pujol. Institut de Recerca contra la Leucèmia Josep Carreras) ;
Vento-Tormo, Roser (Wellcome Sanger Institute. Wellcome Genome Campus, Hinxton, UK) ;
Ballestar, Esteban (Institut Germans Trias i Pujol. Institut de Recerca contra la Leucèmia Josep Carreras)
COVID-19 manifests with a wide spectrum of clinical phenotypes, ranging from asymptomatic and mild to severe and critical. Severe and critical COVID-19 patients are characterized by marked changes in the myeloid compartment, especially monocytes. [...]
2022 - 10.1186/s13073-022-01137-4
Genome Medicine, Vol. 14 (november 2022)
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5.
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6.
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6 p, 4.8 MB |
Bacteria Detection at a Single-Cell Level through a Cyanotype-Based Photochemical Reaction
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Dietvorst, Jiri (Institut de Microelectrònica de Barcelona) ;
Ferrer-Vilanova, Amparo (Universitat Autònoma de Barcelona. Departament de Química) ;
Iyengar, S. N. (Kungl. Tekniska högskolan (Estocolm (Suècia)) ;
Russom, Aman (Kungl. Tekniska högskolan (Estocolm (Suècia)) ;
Vigués, Núria (Universitat Autònoma de Barcelona. Departament de Genètica i de Microbiologia) ;
Mas Gordi, Jordi (Universitat Autònoma de Barcelona. Departament de Genètica i de Microbiologia) ;
Vilaplana, Lluïsa (Centro de Investigación Biomédica en Red de Bioingeniería, Biomateriales y Nanomedicina) ;
Marco, María Pilar (Centro de Investigación Biomédica en Red de Bioingeniería, Biomateriales y Nanomedicina) ;
Guirado López, Gonzalo (Universitat Autònoma de Barcelona. Departament de Química) ;
Muñoz Berbel, Xavier (Institut de Microelectrònica de Barcelona)
The detection of living organisms at very low concentrations is necessary for the early diagnosis of bacterial infections, but it is still challenging as there is a need for signal amplification. Cell culture, nucleic acid amplification, or nanostructure-based signal enhancement are the most common amplification methods, relying on long, tedious, complex, or expensive procedures. [...]
2021 - 10.1021/acs.analchem.1c03326
Analytical chemistry, Vol. 94, Issue 2 (January 2021) , p. 787-792
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7.
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16 p, 1.4 MB |
Sampling time-dependent artifacts in single-cell genomics studies
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Massoni-Badosa, R. (Centre de Regulació Genòmica) ;
Iacono, G. (Centre de Regulació Genòmica) ;
Moutinho, Catia (Centre de Regulació Genòmica) ;
Kulis, M. (Institut d'Investigacions Biomèdiques August Pi i Sunyer) ;
Palau, Núria (Hospital Universitari Vall d'Hebron. Institut de Recerca) ;
Marchese, Domenica (Centre de Regulació Genòmica) ;
Rodríguez-Ubreva, Javier (Institut Germans Trias i Pujol. Institut de Recerca contra la Leucèmia Josep Carreras) ;
Ballestar, Esteban (Hospital Clínic i Provincial de Barcelona) ;
Rodriguez-Esteban, G. (Centre de Regulació Genòmica) ;
Marsal, S. (Hospital Universitari Vall d'Hebron. Institut de Recerca) ;
Aymerich, Marta (Hospital Clínic i Provincial de Barcelona) ;
Colomer, Dolors (Centro de Investigación Biomédica en Red de Cáncer) ;
Campo, Elias (Centro de Investigación Biomédica en Red de Cáncer) ;
Julià Cano, Antonio (Hospital Universitari Vall d'Hebron. Institut de Recerca) ;
Martín-Subero, Jose Ignacio (Institució Catalana de Recerca i Estudis Avançats) ;
Heyn, Holger (Universitat Pompeu Fabra) ;
Universitat Autònoma de Barcelona
Robust protocols and automation now enable large-scale single-cell RNA and ATAC sequencing experiments and their application on biobank and clinical cohorts. However, technical biases introduced during sample acquisition can hinder solid, reproducible results, and a systematic benchmarking is required before entering large-scale data production. [...]
2020 - 10.1186/s13059-020-02032-0
Genome biology, Vol. 21 Núm. 1 (november 2020) , p. 112
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8.
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14 p, 5.0 MB |
Single-cell telomere-length quantification couples telomere length to meristem activity and stem cell development in Arabidopsis
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González-García, Mary Paz (Centre de Recerca en Agrigenòmica) ;
Pavelescu, Irina (Centre de Recerca en Agrigenòmica) ;
Canela, Andrés (Centro Nacional de Investigaciones Oncológicas) ;
Sevillano, Xavier (Universitat Ramon Llull. Grup de Recerca en Tecnologies Mèdia) ;
Leehy, Katherine A. (Texas A&M University. Department of Biochemistry and Biophysics) ;
Nelson, Andrew D. L. (Texas A&M University. Department of Biochemistry and Biophysics) ;
Ibañes, Marta (Universitat de Barcelona. Departament d'Estructura i Constituents de la Matèria) ;
Shippen, Dorothy E. (Texas A&M University. Department of Biochemistry and Biophysics) ;
Blasco, María A. (Centro Nacional de Investigaciones Oncológicas) ;
Caño Delgado, Ana I. (Centre de Recerca en Agrigenòmica)
Telomeres are specialized nucleoprotein caps that protect chromosome ends assuring cell division. Single-cell telomere quantification in animals established a critical role for telomerase in stem cells, yet, in plants, telomere-length quantification has been reported only at the organ level. [...]
2015 - 10.1016/j.celrep.2015.04.013
Cell reports, Vol. 11, issue 6 (May 2015) , p. 977-989
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9.
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15 p, 3.0 MB |
Single-cell transcriptome conservation in cryopreserved cells and tissues
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Guillaumet-Adkins, Amy (Centre de Regulació Genòmica) ;
Rodríguez-Esteban, Gustavo (Centre de Regulació Genòmica) ;
Mereu, Elisabetta (Centre de Regulació Genòmica) ;
Mendez-Lago, Maria (Centre de Regulació Genòmica) ;
Jaitin, Diego A. (Weizmann Institute of Science (Israel). Department of Immunology) ;
Villanueva, Alberto (Hospital Universitari de Bellvitge) ;
Vidal, August (Institut d'Investigació Biomèdica de Bellvitge) ;
Martinez-Marti, Alex (Universitat Autònoma de Barcelona. Departament de Medicina) ;
Felip, Enriqueta (Universitat Autònoma de Barcelona. Departament de Medicina) ;
Vivancos, Ana (Vall d'Hebron Institut d'Oncologia) ;
Keren-Shaul, Hadas (Weizmann Institute of Science (Israel). Department of Immunology) ;
Heath, Simon (Centre de Regulació Genòmica) ;
Gut, Marta (Centre de Regulació Genòmica) ;
Amit, Ido (Weizmann Institute of Science (Israel). Department of Immunology) ;
Gut, Ivo (Centre de Regulació Genòmica) ;
Heyn, Holger (Centre de Regulació Genòmica)
A variety of single-cell RNA preparation procedures have been described. So far, protocols require fresh material, which hinders complex study designs. We describe a sample preservation method that maintains transcripts in viable single cells, allowing one to disconnect time and place of sampling from subsequent processing steps. [...]
2017 - 10.1186/s13059-017-1171-9
Genome biology, Vol. 18 (march 2017)
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10.
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11 p, 779.0 KB |
Antitubercular drugs for an old target : GSK693 as a promising InhA direct inhibitor
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Martínez-Hoyos, María (Diseases of the Developing World, GlaxoSmithKline, Severo Ochoa 2, 28760 Tres Cantos, Madrid, Spain) ;
Perez-Herran, Esther (Diseases of the Developing World, GlaxoSmithKline, Severo Ochoa 2, 28760 Tres Cantos, Madrid, Spain) ;
Gulten, Gulcin (Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843, USA) ;
Encinas, Lourdes (Diseases of the Developing World, GlaxoSmithKline, Severo Ochoa 2, 28760 Tres Cantos, Madrid, Spain) ;
Álvarez-Gómez, Daniel (Diseases of the Developing World, GlaxoSmithKline, Severo Ochoa 2, 28760 Tres Cantos, Madrid, Spain) ;
Alvarez, Emilio (Diseases of the Developing World, GlaxoSmithKline, Severo Ochoa 2, 28760 Tres Cantos, Madrid, Spain) ;
Ferrer-Bazaga, Santiago (Diseases of the Developing World, GlaxoSmithKline, Severo Ochoa 2, 28760 Tres Cantos, Madrid, Spain) ;
García-Pérez, Adolfo (Diseases of the Developing World, GlaxoSmithKline, Severo Ochoa 2, 28760 Tres Cantos, Madrid, Spain) ;
Ortega, Fátima (Diseases of the Developing World, GlaxoSmithKline, Severo Ochoa 2, 28760 Tres Cantos, Madrid, Spain) ;
Angulo-Barturen, Iñigo (Diseases of the Developing World, GlaxoSmithKline, Severo Ochoa 2, 28760 Tres Cantos, Madrid, Spain) ;
Rullas-Trincado, Joaquin (Diseases of the Developing World, GlaxoSmithKline, Severo Ochoa 2, 28760 Tres Cantos, Madrid, Spain) ;
Blanco Ruano, Delia (Diseases of the Developing World, GlaxoSmithKline, Severo Ochoa 2, 28760 Tres Cantos, Madrid, Spain) ;
Torres, Pedro (Diseases of the Developing World, GlaxoSmithKline, Severo Ochoa 2, 28760 Tres Cantos, Madrid, Spain) ;
Castañeda, Pablo (Diseases of the Developing World, GlaxoSmithKline, Severo Ochoa 2, 28760 Tres Cantos, Madrid, Spain) ;
Huss, Sophie (Diseases of the Developing World, GlaxoSmithKline, Severo Ochoa 2, 28760 Tres Cantos, Madrid, Spain) ;
Fernández Menéndez, Raquel (Diseases of the Developing World, GlaxoSmithKline, Severo Ochoa 2, 28760 Tres Cantos, Madrid, Spain) ;
González del Valle, Silvia (Diseases of the Developing World, GlaxoSmithKline, Severo Ochoa 2, 28760 Tres Cantos, Madrid, Spain) ;
Ballell, Lluis (Diseases of the Developing World, GlaxoSmithKline, Severo Ochoa 2, 28760 Tres Cantos, Madrid, Spain) ;
Barros, David (Diseases of the Developing World, GlaxoSmithKline, Severo Ochoa 2, 28760 Tres Cantos, Madrid, Spain) ;
Modha, Sundip (Target and Pathway Validation, Molecular Discovery Research, GlaxoSmithKline, Stevenage, Herts, UK) ;
Dhar, Neeraj (School of Life Sciences, Swiss Federal Institute of Technology in Lausanne (EPFL), Lausanne 1015, Switzerland) ;
Signorino-Gelo, François (Target and Pathway Validation, Molecular Discovery Research, GlaxoSmithKline, Stevenage, Herts, UK) ;
McKinney, John D. (Target and Pathway Validation, Molecular Discovery Research, GlaxoSmithKline, Stevenage, Herts, UK) ;
García-Bustos, Jose Francisco (Diseases of the Developing World, GlaxoSmithKline, Severo Ochoa 2, 28760 Tres Cantos, Madrid, Spain) ;
Lavandera, Jose Luis (Diseases of the Developing World, GlaxoSmithKline, Severo Ochoa 2, 28760 Tres Cantos, Madrid, Spain) ;
Sacchettini, James C. (Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843, USA) ;
Jimenez, M. Soledad (Instituto de Salud Carlos III) ;
Martín-Casabona, Nuria (Hospital Universitari Vall d'Hebron) ;
Castro-Pichel, Julia (Diseases of the Developing World, GlaxoSmithKline, Severo Ochoa 2, 28760 Tres Cantos, Madrid, Spain) ;
Mendoza-Losana, Alfonso (Diseases of the Developing World, GlaxoSmithKline, Severo Ochoa 2, 28760 Tres Cantos, Madrid, Spain) ;
Universitat Autònoma de Barcelona
Despite being one of the first antitubercular agents identified, isoniazid (INH) is still the most prescribed drug for prophylaxis and tuberculosis (TB) treatment and, together with rifampicin, the pillars of current chemotherapy. [...]
2016 - 10.1016/j.ebiom.2016.05.006
EBioMedicine, Vol. 8 (may 2016) , p. 291-301
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