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2. Integrated View of Baseline Protein Expression in Human Tissues

Author

Prakash, Ananth, primary, García-Seisdedos, David, additional, Wang, Shengbo, additional, Kundu, Deepti Jaiswal, additional, Collins, Andrew, additional, George, Nancy, additional, Moreno, Pablo, additional, Papatheodorou, Irene, additional, Jones, Andrew R., additional, and Vizcaíno, Juan Antonio, additional

Published
2022
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4. Rottlerin Stimulates Exosome/Microvesicle Release Via the Increase of Ceramide Levels Mediated by Ampk in an In Vitro Model of Intracellular Lipid Accumulation

Author

Molina, Yessenia L., primary, García-Seisdedos, David, additional, Babiy, Bohdan, additional, Lerma, Milagros, additional, Martínez-Botas, Javier, additional, Casarejos, María J., additional, Vallejo, María T., additional, Gómez-Coronado, Diego, additional, Lasunción, Miguel A., additional, Pastor, Óscar, additional, and Busto, Rebeca, additional

Published
2022
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6. Genetic screening of lysosomal disorders: An account of five years' experience with NGS-based resequencing panels

Author

del Castillo, Francisco J., primary, Muñoz, Gloria, additional, Gandía, Marta, additional, Ciubotariu, Crina, additional, García-Seisdedos, David, additional, Piris-Villaespesa, Miguel, additional, Domínguez-Ruiz, María, additional, Calderón, Enrique, additional, González-Meneses, Antonio, additional, López-Jiménez, Javier, additional, Macher, Hada, additional, Morado, Marta, additional, Gutiérrez-Solana, Luis G., additional, Vitoria, Isidro, additional, Unceta, María, additional, Ceberio, Leticia, additional, Yahyaoui, Raquel, additional, Torralba, Miguel A., additional, Fdil, Naima, additional, Carrillo-Farga, Joaquín, additional, Belanger, Amaya, additional, and Villarrubia, Jesús, additional

Published
2022
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8. Expression Atlas update: gene and protein expression in multiple species

Author

Moreno, Pablo, primary, Fexova, Silvie, additional, George, Nancy, additional, Manning, Jonathan R, additional, Miao, Zhichiao, additional, Mohammed, Suhaib, additional, Muñoz-Pomer, Alfonso, additional, Fullgrabe, Anja, additional, Bi, Yalan, additional, Bush, Natassja, additional, Iqbal, Haider, additional, Kumbham, Upendra, additional, Solovyev, Andrey, additional, Zhao, Lingyun, additional, Prakash, Ananth, additional, García-Seisdedos, David, additional, Kundu, Deepti J, additional, Wang, Shengbo, additional, Walzer, Mathias, additional, Clarke, Laura, additional, Osumi-Sutherland, David, additional, Tello-Ruiz, Marcela Karey, additional, Kumari, Sunita, additional, Ware, Doreen, additional, Eliasova, Jana, additional, Arends, Mark J, additional, Nawijn, Martijn C, additional, Meyer, Kerstin, additional, Burdett, Tony, additional, Marioni, John, additional, Teichmann, Sarah, additional, Vizcaíno, Juan Antonio, additional, Brazma, Alvis, additional, and Papatheodorou, Irene, additional

Published
2021
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9. The PRIDE database resources in 2022: a hub for mass spectrometry-based proteomics evidences

Author

Perez-Riverol, Yasset, primary, Bai, Jingwen, additional, Bandla, Chakradhar, additional, García-Seisdedos, David, additional, Hewapathirana, Suresh, additional, Kamatchinathan, Selvakumar, additional, Kundu, Deepti J, additional, Prakash, Ananth, additional, Frericks-Zipper, Anika, additional, Eisenacher, Martin, additional, Walzer, Mathias, additional, Wang, Shengbo, additional, Brazma, Alvis, additional, and Vizcaíno, Juan Antonio, additional

Published
2021
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10. An integrated view of baseline protein expression in human tissues

Author

Prakash, Ananth, primary, García-Seisdedos, David, additional, Wang, Shengbo, additional, Kundu, Deepti Jaiswal, additional, Collins, Andrew, additional, George, Nancy, additional, Moreno, Pablo, additional, Papatheodorou, Irene, additional, Jones, Andrew R., additional, and Vizcaíno, Juan Antonio, additional

Published
2021
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11. Implementing the reuse of public DIA proteomics datasets: from the PRIDE database to Expression Atlas

Author

Walzer, Mathias, primary, García-Seisdedos, David, additional, Prakash, Ananth, additional, Brack, Paul, additional, Crowther, Peter, additional, Graham, Robert L., additional, George, Nancy, additional, Mohammed, Suhaib, additional, Moreno, Pablo, additional, Papathedourou, Irene, additional, Hubbard, Simon J., additional, and Vizcaíno, Juan Antonio, additional

Published
2021
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12. Somatic Mutation Profiling in the Liquid Biopsy and Clinical Analysis of Hereditary and Familial Pancreatic Cancer Cases Reveals KRAS Negativity and a Longer Overall Survival

Author

Instituto de Salud Carlos III, European Commission, Asociación Española Contra el Cáncer, Fundación Mutua Madrileña, Asociación Cáncer de Páncreas (España), Asociación Española de Pancreatología, Earl, Julie, Barreto, Emma, Castillo, María E., Fuentes, Raquel, Rodríguez-Garrote, Mercedes, Ferreiro, Reyes, Reguera, Pablo, Muñoz, Gloria, García-Seisdedos, David, Sainz, Bruno Jr., Malats, Núria, Carrato, Alfredo, Instituto de Salud Carlos III, European Commission, Asociación Española Contra el Cáncer, Fundación Mutua Madrileña, Asociación Cáncer de Páncreas (España), Asociación Española de Pancreatología, Earl, Julie, Barreto, Emma, Castillo, María E., Fuentes, Raquel, Rodríguez-Garrote, Mercedes, Ferreiro, Reyes, Reguera, Pablo, Muñoz, Gloria, García-Seisdedos, David, Sainz, Bruno Jr., Malats, Núria, and Carrato, Alfredo

Abstract

Pancreatic ductal adenocarcinoma (PDAC) presents many challenges in the clinic and there are many areas for improvement in diagnostics and patient management. The five-year survival rate is around 7.2% as the majority of patients present with advanced disease at diagnosis that is treatment resistant. Approximately 10–15% of PDAC cases have a hereditary basis or Familial Pancreatic Cancer (FPC). Here we demonstrate the use of circulating free DNA (cfDNA) in plasma as a prognostic biomarker in PDAC. The levels of cfDNA correlated with disease status, disease stage, and overall survival. Furthermore, we show for the first time via BEAMing that the majority of hereditary or familial PDAC cases (around 84%) are negative for a KRAS somatic mutation. In addition, KRAS mutation negative cases harbor somatic mutations in potentially druggable genes such as KIT, PDGFR, MET, BRAF, and PIK3CA that could be exploited in the clinic. Finally, familial or hereditary cases have a longer overall survival compared to sporadic cases (10.2 vs. 21.7 months, respectively). Currently, all patients are treated the same in the clinic with cytotoxic agents, although here we demonstrate that there are different subtypes of tumors at the genetic level that could pave the way to personalized treatment.

Published
2021

13. The Antipsychotic Risperidone Alters Dihydroceramide and Ceramide Composition and Plasma Membrane Function in Leukocytes In Vitro and In Vivo

Author

Canfrán-Duque, Alberto, primary, Pastor, Óscar, additional, García-Seisdedos, David, additional, Molina, Yessenia L., additional, Babiy, Bohdan, additional, Lerma, Milagros, additional, Sánchez-Castellano, Carmen, additional, Martínez-Botas, Javier, additional, Gómez-Coronado, Diego, additional, Lasunción, Miguel A., additional, Cruz-Jentoft, Alfonso J., additional, and Busto, Rebeca, additional

Published
2021
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15. A comprehensive analysis of candidate genes in familial pancreatic cancer families reveals a high frequency of potentially pathogenic germline variants

Author

Earl, Julie, primary, Galindo-Pumariño, Cristina, additional, Encinas, Jessica, additional, Barreto, Emma, additional, Castillo, Maria E., additional, Pachón, Vanessa, additional, Ferreiro, Reyes, additional, Rodríguez-Garrote, Mercedes, additional, González-Martínez, Silvia, additional, Ramon y Cajal, Teresa, additional, Diaz, Luis Robles, additional, Chirivella-Gonzalez, Isabel, additional, Rodriguez, Montse, additional, de Castro, Eva Martínez, additional, García-Seisdedos, David, additional, Muñoz, Gloria, additional, Rosa, Juan Manuel Rosa, additional, Marquez, Mirari, additional, Malats, Nuría, additional, and Carrato, Alfredo, additional

Published
2020
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16. Early detection of lysosomal diseases by screening of cases of idiopathic splenomegaly and/or thrombocytopenia with a next‐generation sequencing gene panel

Author

Muñoz, Gloria, primary, García‐Seisdedos, David, additional, Ciubotariu, Crina, additional, Piris‐Villaespesa, Miguel, additional, Gandía, Marta, additional, Martín‐Moro, Fernando, additional, Gutiérrez‐Solana, Luis G., additional, Morado, Marta, additional, López‐Jiménez, Javier, additional, Sánchez‐Herranz, Antonio, additional, Villarrubia, Jesús, additional, and Castillo, Francisco J., additional

Published
2019
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18. Expression Atlas update: gene and protein expression in multiple species.

Author

Moreno, Pablo, Fexova, Silvie, George, Nancy, Manning, Jonathan R, Miao, Zhichiao, Mohammed, Suhaib, Muñoz-Pomer, Alfonso, Fullgrabe, Anja, Bi, Yalan, Bush, Natassja, Iqbal, Haider, Kumbham, Upendra, Solovyev, Andrey, Zhao, Lingyun, Prakash, Ananth, García-Seisdedos, David, Kundu, Deepti J, Wang, Shengbo, Walzer, Mathias, and Clarke, Laura

Published
2022
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19. The ProteomeXchange consortium in 2020: enabling 'big data' approaches in proteomics

Author

30439244, Deutsch, Eric W, Bandeira, Nuno, Sharma, Vagisha, Perez-Riverol, Yasset, Carver, Jeremy J, Kundu, Deepti J, García-Seisdedos, David, Jarnuczak, Andrew F, Hewapathirana, Suresh, Pullman, Benjamin S, Wertz, Julie, Sun, Zhi, Kawano, Shin, Okuda, Shujiro, Watanabe, Yu, Hermjakob, Henning, MacLean, Brendan, MacCoss, Michael J, Zhu, Yunping, Ishihama, Yasushi, Vizcaíno, Juan A, 30439244, Deutsch, Eric W, Bandeira, Nuno, Sharma, Vagisha, Perez-Riverol, Yasset, Carver, Jeremy J, Kundu, Deepti J, García-Seisdedos, David, Jarnuczak, Andrew F, Hewapathirana, Suresh, Pullman, Benjamin S, Wertz, Julie, Sun, Zhi, Kawano, Shin, Okuda, Shujiro, Watanabe, Yu, Hermjakob, Henning, MacLean, Brendan, MacCoss, Michael J, Zhu, Yunping, Ishihama, Yasushi, and Vizcaíno, Juan A

Abstract

The ProteomeXchange (PX) consortium of proteomics resources (http://www.proteomexchange.org) has standardized data submission and dissemination of mass spectrometry proteomics data worldwide since 2012. In this paper, we describe the main developments since the previous update manuscript was published in Nucleic Acids Research in 2017. Since then, in addition to the four PX existing members at the time (PRIDE, PeptideAtlas including the PASSEL resource, MassIVE and jPOST), two new resources have joined PX: iProX (China) and Panorama Public (USA). We first describe the updated submission guidelines, now expanded to include six members. Next, with current data submission statistics, we demonstrate that the proteomics field is now actively embracing public open data policies. At the end of June 2019, more than 14 100 datasets had been submitted to PX resources since 2012, and from those, more than 9 500 in just the last three years. In parallel, an unprecedented increase of data re-use activities in the field, including ‘big data’ approaches, is enabling novel research and new data resources. At last, we also outline some of our future plans for the coming years.

Published
2019

20. Segmentación de núcleos celulares en imágenes de microscopía ayudados por redes neuronales convolucionales

Author

García Seisdedos, David, Universitat Oberta de Catalunya, and Alférez Baquero, Edwin Santiago

Subjects
Bioinformática -- TFM, machine learning, aprendizaje automático, microscopy, convolutional neural network, microscopía, redes neuronales convolucionales, xarxes neuronals convolucionals, Bioinformàtica -- TFM, aprenentatge automàtic, Bioinformatics -- TFM
Abstract

El objetivo de este proyecto fue desarrollar una herramienta bioinformática para detectar y aislar núcleos celulares. El método desarrollado realiza la detección y segmentación en tres pasos. Primero, se lleva a cabo una segmentación inicial de la imagen en bruto. Segundo, los fragmentos obtenidos se clasifican mediante una red neuronal convolucional (CNN) en tres grupos: mono-núcleos, poli-núcleos o artefactos no-nucleares. Tercero, los mono-núcleos se almacenan, los artefactos se eliminan y los fragmentos polinucleares son segmentados y re-analizados desde el segundo paso. Así es posible subdividir por recursividad el elemento problema -acumulo de núcleos- en sub-problemas más sencillos. The aim of this project is to develop a bioinformatics tool to detect and isolate cell nuclei. The developed model performs detection and segmentation in three steps. First, an initial segmentation of the raw image is carried out. Second, the fragments obtained are classified by means of a convolutional neural network (CNN) into three groups: mono-nuclei, poly-nuclei or non-nuclear artifacts. Third, the artifacts will be removed and the polynuclear fragments will be segmented and will be analyzed from the second step again. Thus, the main problem - accumulation of nuclei - is subdivided by recursiveness into simpler sub-problems. L'objectiu d'aquest projecte va ser desenvolupar una eina bioinformática per detectar i aïllar nuclis cel·lulars. El mètode desenvolupat realitza la detecció i segmentació en tres passos. Primer, es duu a terme una segmentació inicial de la imatge en brut. Segon, els fragments obtinguts es classifiquen mitjançant una xarxa neuronal convolucional (CNN) en tres grups: mico-nuclis, poli-nuclis o artefactes no-nuclears. Tercer, els mico-nuclis s'emmagatzemen, els artefactes s'eliminen i els fragments polinucleares són segmentats i re-analitzats des del segon pas. Així és possible subdividir per recursividad l'element problema -acumulo de nuclis- en sub-problemes més senzills.

Published
2018

21. The ProteomeXchange consortium in 2020: enabling ‘big data’ approaches in proteomics

Author

Deutsch, Eric W, primary, Bandeira, Nuno, additional, Sharma, Vagisha, additional, Perez-Riverol, Yasset, additional, Carver, Jeremy J, additional, Kundu, Deepti J, additional, García-Seisdedos, David, additional, Jarnuczak, Andrew F, additional, Hewapathirana, Suresh, additional, Pullman, Benjamin S, additional, Wertz, Julie, additional, Sun, Zhi, additional, Kawano, Shin, additional, Okuda, Shujiro, additional, Watanabe, Yu, additional, Hermjakob, Henning, additional, MacLean, Brendan, additional, MacCoss, Michael J, additional, Zhu, Yunping, additional, Ishihama, Yasushi, additional, and Vizcaíno, Juan A, additional

Published
2019
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23. A comprehensive evaluation of omega-3 fatty acid supplementation in cystic fibrosis patients using lipidomics

Author

Pastor, Óscar, primary, Guzmán-Lafuente, Paula, additional, Serna, Jorge, additional, Muñoz-Hernández, Marta, additional, López Neyra, Alejandro, additional, García-Rozas, Patricia, additional, García-Seisdedos, David, additional, Alcázar, Alberto, additional, Lasunción, Miguel A., additional, Busto, Rebeca, additional, and Lamas Ferreiro, Adelaida, additional

Published
2019
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24. The ProteomeXchange consortium in 2020: enabling 'big data' approaches in proteomics.

Author

Deutsch, Eric W, Bandeira, Nuno, Sharma, Vagisha, Perez-Riverol, Yasset, Carver, Jeremy J, Kundu, Deepti J, García-Seisdedos, David, Jarnuczak, Andrew F, Hewapathirana, Suresh, Pullman, Benjamin S, Wertz, Julie, Sun, Zhi, Kawano, Shin, Okuda, Shujiro, Watanabe, Yu, Hermjakob, Henning, MacLean, Brendan, MacCoss, Michael J, Zhu, Yunping, and Ishihama, Yasushi

Published
2020
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26. Ellagic acid protects from myelin-associated sphingolipid loss in experimental autoimmune encephalomyelitis

Author

Busto, Rebeca, primary, Serna, Jorge, additional, Perianes-Cachero, Aránzazu, additional, Quintana-Portillo, Rocío, additional, García-Seisdedos, David, additional, Canfrán-Duque, Alberto, additional, Paino, Carlos L., additional, Lerma, Milagros, additional, Casado, María E., additional, Martín-Hidalgo, Antonia, additional, Arilla-Ferreiro, Eduardo, additional, Lasunción, Miguel A., additional, and Pastor, Óscar, additional

Published
2018
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27. Fast genetic diagnosis of lysosomal disorders by means of a novel NGS-based resequencing gene panel

Author

del Castillo, Francisco J., primary, Muñoz, Gloria, additional, García-Seisdedos, David, additional, Sánchez-Herranz, Antonio, additional, Morado, Marta, additional, Valles, Ana, additional, Piris, Miguel, additional, Martín-Moro, Fernando, additional, Sanz-Rupérez, Alejandro, additional, López-Jiménez, Javier, additional, and Villarrubia, Jesús, additional

Published
2018
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30. The PRIDE database resources in 2022: a hub for mass spectrometry-based proteomics evidences.

Author

Perez-Riverol Y, Bai J, Bandla C, García-Seisdedos D, Hewapathirana S, Kamatchinathan S, Kundu DJ, Prakash A, Frericks-Zipper A, Eisenacher M, Walzer M, Wang S, Brazma A, and Vizcaíno JA

Subjects
Amino Acid Sequence, Bibliometrics, Datasets as Topic, Humans, Information Storage and Retrieval, Internet, Mass Spectrometry, Peptides genetics, Peptides metabolism, Proteins genetics, Proteins metabolism, Proteomics instrumentation, Proteomics methods, Sequence Alignment, Databases, Protein, Metadata statistics & numerical data, Molecular Sequence Annotation statistics & numerical data, Peptides chemistry, Proteins chemistry, Software
Abstract

The PRoteomics IDEntifications (PRIDE) database (https://www.ebi.ac.uk/pride/) is the world's largest data repository of mass spectrometry-based proteomics data. PRIDE is one of the founding members of the global ProteomeXchange (PX) consortium and an ELIXIR core data resource. In this manuscript, we summarize the developments in PRIDE resources and related tools since the previous update manuscript was published in Nucleic Acids Research in 2019. The number of submitted datasets to PRIDE Archive (the archival component of PRIDE) has reached on average around 500 datasets per month during 2021. In addition to continuous improvements in PRIDE Archive data pipelines and infrastructure, the PRIDE Spectra Archive has been developed to provide direct access to the submitted mass spectra using Universal Spectrum Identifiers. As a key point, the file format MAGE-TAB for proteomics has been developed to enable the improvement of sample metadata annotation. Additionally, the resource PRIDE Peptidome provides access to aggregated peptide/protein evidences across PRIDE Archive. Furthermore, we will describe how PRIDE has increased its efforts to reuse and disseminate high-quality proteomics data into other added-value resources such as UniProt, Ensembl and Expression Atlas., (© The Author(s) 2021. Published by Oxford University Press on behalf of Nucleic Acids Research.)

Published
2022
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