Creating medically-driven integrative bioinformatics applications focused on oncology, CNS disorders and their comorbidities (MedBioinformatics)

Resultado final

Promotional material outlining the project's rationale and objectives.

Final report on outreach and dissemination activities

A detailed list of all dissemination activities carried out during the project, with assessment of their impact and degree of compliance with the Communication Plan.

MedBioinformatics website

Website to be updated until the end of the project.

Publicaciones

Patología dual en Depresión: recomendaciones en el tratamiento

Autores: Judit Tirado Muñoz, Adriana Farré, Joan Mestre-Pintó, Nestor Szerman, Marta Torrens
Publicado en: Adicciones, Edición 30/1, 2018, Página(s) 66, ISSN 0214-4840
Editor: Socidrogalcohol
DOI: 10.20882/adicciones.868

Ensembl 2017

Autores: Bronwen L. Aken, Premanand Achuthan, Wasiu Akanni, M. Ridwan Amode, Friederike Bernsdorff, Jyothish Bhai, Konstantinos Billis, Denise Carvalho-Silva, Carla Cummins, Peter Clapham, Laurent Gil, Carlos García Girón, Leo Gordon, Thibaut Hourlier, Sarah E. Hunt, Sophie H. Janacek, Thomas Juettemann, Stephen Keenan, Matthew R. Laird, Ilias Lavidas, Thomas Maurel, William McLaren, Benjamin Moore, Dani
Publicado en: Nucleic Acids Research, Edición 45/D1, 2017, Página(s) D635-D642, ISSN 0305-1048
Editor: Oxford University Press
DOI: 10.1093/nar/gkw1104

Binge ethanol drinking during adolescence modifies cocaine responses in mice

Autores: Anna Esteve-Arenys, Irene Gracia-Rubio, Lídia Cantacorps, Oscar J Pozo, Josep Marcos, Marta Rodríguez-Árias, José Miñarro, Olga Valverde
Publicado en: Journal of Psychopharmacology, Edición 31/1, 2016, Página(s) 86-95, ISSN 0269-8811
Editor: SAGE Publications
DOI: 10.1177/0269881116681457

Exposure of adolescent mice to 3,4-methylenedioxypyrovalerone increases the psychostimulant, rewarding and reinforcing effects of cocaine in adulthood

Autores: R López-Arnau, M A Luján, L Duart-Castells, D Pubill, J Camarasa, O Valverde, E Escubedo
Publicado en: British Journal of Pharmacology, Edición 174/10, 2017, Página(s) 1161-1173, ISSN 0007-1188
Editor: Wiley-Blackwell
DOI: 10.1111/bph.13771

Maternal Separation Impairs Cocaine-Induced Behavioural Sensitization in Adolescent Mice

Autores: Irene Gracia-Rubio, Elena Martinez-Laorden, Maria Moscoso-Castro, M. Victoria Milanés, M. Luisa Laorden, Olga Valverde
Publicado en: PLOS ONE, Edición 11/12, 2016, Página(s) e0167483, ISSN 1932-6203
Editor: Public Library of Science
DOI: 10.1371/journal.pone.0167483

SynergyFinder: a web application for analyzing drug combination dose–response matrix data

Autores: Aleksandr Ianevski, Liye He, Tero Aittokallio, Jing Tang
Publicado en: Bioinformatics, Edición 33/15, 2017, Página(s) 2413-2415, ISSN 1367-4803
Editor: Oxford University Press
DOI: 10.1093/bioinformatics/btx162

Integrating genomic alterations in diffuse large B-cell lymphoma identifies new relevant pathways and potential therapeutic targets

Autores: K Karube, A Enjuanes, I Dlouhy, P Jares, D Martin-Garcia, F Nadeu, G R Ordóñez, J Rovira, G Clot, C Royo, A Navarro, B Gonzalez-Farre, A Vaghefi, G Castellano, C Rubio-Perez, D Tamborero, J Briones, A Salar, J M Sancho, S Mercadal, E Gonzalez-Barca, L Escoda, H Miyoshi, K Ohshima, K Miyawaki, K Kato, K Akashi, A Mozos, L Colomo, M Alcoceba, A Valera, A Carrió, D Costa, N Lopez-Bigas, R Schmitz,
Publicado en: Leukemia, Edición 32/3, 2017, Página(s) 675-684, ISSN 0887-6924
Editor: Nature Publishing Group
DOI: 10.1038/leu.2017.251

Discovery of novel drug sensitivities in T-PLL by high-throughput ex vivo drug testing and mutation profiling

Autores: E I Andersson, S Pützer, B Yadav, O Dufva, S Khan, L He, L Sellner, A Schrader, G Crispatzu, M Oleś, H Zhang, S Adnan-Awad, S Lagström, D Bellanger, J P Mpindi, S Eldfors, T Pemovska, P Pietarinen, A Lauhio, K Tomska, C Cuesta-Mateos, E Faber, S Koschmieder, T H Brümmendorf, S Kytölä, E-R Savolainen, T Siitonen, P Ellonen, O Kallioniemi, K Wennerberg, W Ding, M-H Stern, W Huber, S Anders, J
Publicado en: Leukemia, Edición 32/3, 2017, Página(s) 774-787, ISSN 0887-6924
Editor: Nature Publishing Group
DOI: 10.1038/leu.2017.252

Cognitive impairments associated with alterations in synaptic proteins induced by the genetic loss of adenosine A 2A receptors in mice

Autores: Maria Moscoso-Castro, Marc López-Cano, Irene Gracia-Rubio, Francisco Ciruela, Olga Valverde
Publicado en: Neuropharmacology, Edición 126, 2017, Página(s) 48-57, ISSN 0028-3908
Editor: Pergamon Press Ltd.
DOI: 10.1016/j.neuropharm.2017.08.027

Maternal alcohol binge drinking induces persistent neuroinflammation associated with myelin damage and behavioural dysfunctions in offspring mice

Autores: Lídia Cantacorps, Silvia Alfonso-Loeches, Maria Moscoso-Castro, Javier Cuitavi, Irene Gracia-Rubio, Raúl López-Arnau, Elena Escubedo, Consuelo Guerri, Olga Valverde
Publicado en: Neuropharmacology, Edición 123, 2017, Página(s) 368-384, ISSN 0028-3908
Editor: Pergamon Press Ltd.
DOI: 10.1016/j.neuropharm.2017.05.034

Cancer Genome Interpreter annotates the biological and clinical relevance of tumor alterations

Autores: David Tamborero, Carlota Rubio-Perez, Jordi Deu-Pons, Michael P. Schroeder, Ana Vivancos, Ana Rovira, Ignasi Tusquets, Joan Albanell, Jordi Rodon, Josep Tabernero, Carmen de Torres, Rodrigo Dienstmann, Abel Gonzalez-Perez, Nuria Lopez-Bigas
Publicado en: Genome Medicine, Edición 10/1, 2018, ISSN 1756-994X
Editor: BioMed Central
DOI: 10.1186/s13073-018-0531-8

Drug Target Commons: A Community Effort to Build a Consensus Knowledge Base for Drug-Target Interactions

Autores: Jing Tang, Zia-ur-Rehman Tanoli, Balaguru Ravikumar, Zaid Alam, Anni Rebane, Markus Vähä-Koskela, Gopal Peddinti, Arjan J. van Adrichem, Janica Wakkinen, Alok Jaiswal, Ella Karjalainen, Prson Gautam, Liye He, Elina Parri, Suleiman Khan, Abhishekh Gupta, Mehreen Ali, Laxman Yetukuri, Anna-Lena Gustavsson, Brinton Seashore-Ludlow, Anne Hersey, Andrew R. Leach, John P. Overington, Gretchen Repasky,
Publicado en: Cell Chemical Biology, Edición 25/2, 2018, Página(s) 224-229.e2, ISSN 2451-9456
Editor: Elsevier
DOI: 10.1016/j.chembiol.2017.11.009

comoRbidity: an R package for the systematic analysis of disease comorbidities

Autores: Alba Gutiérrez-Sacristán, Àlex Bravo, Alexia Giannoula, Miguel A Mayer, Ferran Sanz, Laura I Furlong
Publicado en: Bioinformatics, 2018, ISSN 1367-4803
Editor: Oxford University Press
DOI: 10.1093/bioinformatics/bty315

Patient-Customized Drug Combination Prediction and Testing for T-cell Prolymphocytic Leukemia Patients

Autores: Liye He, Jing Tang, Emma I. Andersson, Sanna Timonen, Steffen Koschmieder, Krister Wennerberg, Satu Mustjoki, Tero Aittokallio
Publicado en: Cancer Research, Edición 78/9, 2018, Página(s) 2407-2418, ISSN 0008-5472
Editor: American Association for Cancer Research
DOI: 10.1158/0008-5472.CAN-17-3644

Identifying temporal patterns in patient disease trajectories using dynamic time warping: A population-based study

Autores: Alexia Giannoula, Alba Gutierrez-Sacristán, Álex Bravo, Ferran Sanz, Laura I. Furlong
Publicado en: Scientific Reports, Edición 8/1, 2018, ISSN 2045-2322
Editor: Nature Publishing Group
DOI: 10.1038/s41598-018-22578-1

Ensembl 2018

Autores: Daniel R Zerbino, Premanand Achuthan, Wasiu Akanni, M Ridwan Amode, Daniel Barrell, Jyothish Bhai, Konstantinos Billis, Carla Cummins, Astrid Gall, Carlos García Girón, Laurent Gil, Leo Gordon, Leanne Haggerty, Erin Haskell, Thibaut Hourlier, Osagie G Izuogu, Sophie H Janacek, Thomas Juettemann, Jimmy Kiang To, Matthew R Laird, Ilias Lavidas, Zhicheng Liu, Jane E Loveland, Thomas Maurel, Willia
Publicado en: Nucleic Acids Research, Edición 46/D1, 2017, Página(s) D754-D761, ISSN 0305-1048
Editor: Oxford University Press
DOI: 10.1093/nar/gkx1098

DisGeNET: a discovery platform for the dynamical exploration of human diseases and their genes

Autores: J. Pinero, N. Queralt-Rosinach, A. Bravo, J. Deu-Pons, A. Bauer-Mehren, M. Baron, F. Sanz, L. I. Furlong
Publicado en: Database, Edición 2015/0, 2015, Página(s) bav028-bav028, ISSN 1758-0463
Editor: Oxford University Press
DOI: 10.1093/database/bav028

A systems approach identifies time-dependent associations of multimorbidities with pancreatic cancer risk

Autores: P. Gomez-Rubio, V. Rosato, M. Márquez, C. Bosetti, E. Molina-Montes, M. Rava, J. Piñero, C. W. Michalski, A. Farré, X. Molero, M. Löhr, L. Ilzarbe, J. Perea, W. Greenhalf, M. O’Rorke, A. Tardón, T. Gress, V. M. Barberá, T. Crnogorac-Jurcevic, L. Muñoz-Bellvís, E. Domínguez-Muñoz, A. Gutiérrez-Sacristán, J. Balsells, E. Costello, C. Guillén-Ponce, J. Huang, M. Iglesias, J. Kleeff, B.
Publicado en: Annals of Oncology, Edición 28/7, 2017, Página(s) 1618-1624, ISSN 0923-7534
Editor: Oxford University Press
DOI: 10.1093/annonc/mdx167

Genetic and functional characterization of disease associations explains comorbidity

Autores: Carlota Rubio-Perez, Emre Guney, Daniel Aguilar, Janet Piñero, Javier Garcia-Garcia, Barbara Iadarola, Ferran Sanz, Narcís Fernandez-Fuentes, Laura I. Furlong, Baldo Oliva
Publicado en: Scientific Reports, Edición 7/1, 2017, ISSN 2045-2322
Editor: Nature Publishing Group
DOI: 10.1038/s41598-017-04939-4

Dual Depression

Autores: Adriana Farré, Judit Tirado-Muñoz, Marta Torrens
Publicado en: Addictive Disorders & Their Treatment, Edición 16/4, 2017, Página(s) 180-186, ISSN 1531-5754
Editor: Lippincott Williams & Wilkins Ltd.
DOI: 10.1097/ADT.0000000000000118

Maternal separation increases alcohol-drinking behaviour and reduces endocannabinoid levels in the mouse striatum and prefrontal cortex

Autores: Marta Portero-Tresserra, Irene Gracia-Rubio, Lídia Cantacorps, Oscar J. Pozo, Alejandro Gómez-Gómez, Antoni Pastor, Raúl López-Arnau, Rafael de la Torre, Olga Valverde
Publicado en: European Neuropsychopharmacology, Edición 28/4, 2018, Página(s) 499-512, ISSN 0924-977X
Editor: Elsevier BV
DOI: 10.1016/j.euroneuro.2018.02.003

Altered brain functional connectivity and behaviour in a mouse model of maternal alcohol binge-drinking

Autores: Lídia Cantacorps, Héctor González-Pardo, Jorge L. Arias, Olga Valverde, Nélida M. Conejo
Publicado en: Progress in Neuro-Psychopharmacology and Biological Psychiatry, Edición 84, 2018, Página(s) 237-249, ISSN 0278-5846
Editor: Elsevier BV
DOI: 10.1016/j.pnpbp.2018.03.006

Psychiatric comorbidity and intimate partner violence among women who inject drugs in Europe: a cross-sectional study

Autores: Judit Tirado-Muñoz, Gail Gilchrist, Gabriele Fischer, Avril Taylor, Jacek Moskalewicz, Cinzia Giammarchi, Birgit Köchl, Alison Munro, Katarzyna Dąbrowska, April Shaw, Lucia Di Furia, Isabella Leeb, Caroline Hopf, Marta Torrens
Publicado en: Archives of Women's Mental Health, Edición 21/3, 2018, Página(s) 259-269, ISSN 1434-1816
Editor: Springer Verlag
DOI: 10.1007/s00737-017-0800-3

Replicability and Prediction: Lessons and Challenges from GWAS

Autores: Urko M. Marigorta, Juan Antonio Rodríguez, Greg Gibson, Arcadi Navarro
Publicado en: Trends in Genetics, Edición 34/7, 2018, Página(s) 504-517, ISSN 0168-9525
Editor: Elsevier BV
DOI: 10.1016/j.tig.2018.03.005

Long-term risk of cardiovascular and cerebrovascular disease after removal of the colonic microbiota by colectomy: a cohort study based on the Danish National Patient Register from 1996 to 2014

Autores: Anders Boeck Jensen, Teresa Adeltoft Ajslev, Søren Brunak, Thorkild I A Sørensen
Publicado en: BMJ Open, Edición 5/12, 2015, Página(s) e008702, ISSN 2044-6055
Editor: BMJ Publishing Group
DOI: 10.1136/bmjopen-2015-008702

Searching for Drug Synergy in Complex Dose–Response Landscapes Using an Interaction Potency Model

Autores: Bhagwan Yadav, Krister Wennerberg, Tero Aittokallio, Jing Tang
Publicado en: Computational and Structural Biotechnology Journal, Edición 13, 2015, Página(s) 504-513, ISSN 2001-0370
Editor: Elsevier
DOI: 10.1016/j.csbj.2015.09.001

How Suitable Are Registry Data for Recurrence Risk Calculations? Validation of Diagnoses on 1,593 Families With Congenital Heart Disease

Autores: S. G. Ellesoe, A. B. Jensen, L. H. A ngquist, V. E. Hjortdal, L. A. Larsen, S. Brunak
Publicado en: World Journal for Pediatric and Congenital Heart Surgery, Edición 7/2, 2016, Página(s) 169-177, ISSN 2150-1351
Editor: Sage Periodicals Press
DOI: 10.1177/2150135115615786

Analysis of five chronic inflammatory diseases identifies 27 new associations and highlights disease-specific patterns at shared loci

Autores: David Ellinghaus, Luke Jostins, Sarah L Spain, Adrian Cortes, Jörn Bethune, Buhm Han, Yu Rang Park, Soumya Raychaudhuri, Jennie G Pouget, Matthias Hübenthal, Trine Folseraas, Yunpeng Wang, Tonu Esko, Andres Metspalu, Harm-Jan Westra, Lude Franke, Tune H Pers, Rinse K Weersma, Valerie Collij, Mauro D'Amato, Jonas Halfvarson, Anders Boeck Jensen, Wolfgang Lieb, Franziska Degenhardt, Andreas J Fors
Publicado en: Nature Genetics, Edición 48/5, 2016, Página(s) 510-518, ISSN 1061-4036
Editor: Nature Publishing Group
DOI: 10.1038/ng.3528

Methods for High-Throughput Drug Combination Screening and Synergy Scoring

Autores: Liye He, Evgeny Kulesskiy, Jani Saarela, Laura Turunen, Krister Wennerberg, Tero Aittokallio, Jing Tang
Publicado en: bioRxiv, 2016, ISSN 0028-0836
Editor: Nature Publishing Group
DOI: 10.1101/051698

Improving the Sequence Ontology terminology for genomic variant annotation

Autores: Fiona Cunningham, Barry Moore, Nicole Ruiz-Schultz, Graham RS Ritchie, Karen Eilbeck
Publicado en: Journal of Biomedical Semantics, Edición 6/1, 2015, ISSN 2041-1480
Editor: BioMed Central
DOI: 10.1186/s13326-015-0030-4

DisGeNET-RDF: harnessing the innovative power of the Semantic Web to explore the genetic basis of diseases

Autores: Núria Queralt-Rosinach, Janet Piñero, Àlex Bravo, Ferran Sanz, Laura I. Furlong
Publicado en: Bioinformatics, Edición 32/14, 2016, Página(s) 2236-2238, ISSN 1367-4803
Editor: Oxford University Press
DOI: 10.1093/bioinformatics/btw214

A crowdsourcing workflow for extracting chemical-induced disease relations from free text

Autores: Tong Shu Li, Àlex Bravo, Laura I. Furlong, Benjamin M. Good, Andrew I. Su
Publicado en: Database, Edición 2016, 2016, Página(s) baw051, ISSN 1758-0463
Editor: Oxford University Press
DOI: 10.1093/database/baw051

Ensembl 2016

Autores: Andrew Yates, Wasiu Akanni, M. Ridwan Amode, Daniel Barrell, Konstantinos Billis, Denise Carvalho-Silva, Carla Cummins, Peter Clapham, Stephen Fitzgerald, Laurent Gil, Carlos García Girón, Leo Gordon, Thibaut Hourlier, Sarah E. Hunt, Sophie H. Janacek, Nathan Johnson, Thomas Juettemann, Stephen Keenan, Ilias Lavidas, Fergal J. Martin, Thomas Maurel, William McLaren, Daniel N. Murphy, Rishi Nag,
Publicado en: Nucleic Acids Research, Edición 44/D1, 2016, Página(s) D710-D716, ISSN 0305-1048
Editor: Oxford University Press
DOI: 10.1093/nar/gkv1157

Open PHACTS computational protocols for in silico target validation of cellular phenotypic screens: knowing the knowns

Autores: D. Digles, B. Zdrazil, J.-M. Neefs, H. Van Vlijmen, C. Herhaus, A. Caracoti, J. Brea, B. Roibás, M. I. Loza, N. Queralt-Rosinach, L. I. Furlong, A. Gaulton, L. Bartek, S. Senger, C. Chichester, O. Engkvist, C. T. Evelo, N. I. Franklin, D. Marren, G. F. Ecker, E. Jacoby
Publicado en: Med. Chem. Commun., Edición 7/6, 2016, Página(s) 1237-1244, ISSN 2040-2503
Editor: Royal Society of Chemistry
DOI: 10.1039/C6MD00065G

The Ensembl Variant Effect Predictor

Autores: Hunt, Sarah E; Cunningham, Fiona; Riat, Harpreet Singh; Gil, Laurent; Flicek, Paul; McLaren, William; Thormann, Anja; Ritchie, Graham R. S.
Publicado en: Genome Biology 17(1) 122 (2016), Edición 1, 2016, ISSN 1474-760X
Editor: BioMed Central
DOI: 10.1186/s13059-016-0974-4

Uncovering disease mechanisms through network biology in the era of Next Generation Sequencing

Autores: Janet Piñero, Ariel Berenstein, Abel Gonzalez-Perez, Ariel Chernomoretz, Laura I. Furlong
Publicado en: Scientific Reports, Edición 6, 2016, Página(s) 24570, ISSN 2045-2322
Editor: Nature Publishing Group
DOI: 10.1038/srep24570

Combining machine learning, crowdsourcing and expert knowledge to detect chemical-induced diseases in text

Autores: Àlex Bravo, Tong Shu Li, Andrew I. Su, Benjamin M. Good, Laura I. Furlong
Publicado en: Database, Edición 2016, 2016, Página(s) baw094, ISSN 1758-0463
Editor: Oxford University Press
DOI: 10.1093/database/baw094

Making sense of big data in health research: Towards an EU action plan

Autores: Charles Auffray, Rudi Balling, Inês Barroso, László Bencze, Mikael Benson, Jay Bergeron, Enrique Bernal-Delgado, Niklas Blomberg, Christoph Bock, Ana Conesa, Susanna Del Signore, Christophe Delogne, Peter Devilee, Alberto Di Meglio, Marinus Eijkemans, Paul Flicek, Norbert Graf, Vera Grimm, Henk-Jan Guchelaar, Yi-Ke Guo, Ivo Glynne Gut, Allan Hanbury, Shahid Hanif, Ralf-Dieter Hilgers, Ángel Ho
Publicado en: Genome Medicine, Edición 8/1, 2016, ISSN 1756-994X
Editor: BioMed Central
DOI: 10.1186/s13073-016-0323-y

BioCreative V BioC track overview: collaborative biocurator assistant task for BioGRID

Autores: Sun Kim, Rezarta Islamaj Doğan, Andrew Chatr-Aryamontri, Christie S. Chang, Rose Oughtred, Jennifer Rust, Riza Batista-Navarro, Jacob Carter, Sophia Ananiadou, Sérgio Matos, André Santos, David Campos, José Luís Oliveira, Onkar Singh, Jitendra Jonnagaddala, Hong-Jie Dai, Emily Chia-Yu Su, Yung-Chun Chang, Yu-Chen Su, Chun-Han Chu, Chien Chin Chen, Wen-Lian Hsu, Yifan Peng, Cecilia Arighi, Cat
Publicado en: Database, Edición 2016, 2016, Página(s) baw121, ISSN 1758-0463
Editor: Oxford University Press
DOI: 10.1093/database/baw121

DisGeNET: a comprehensive platform integrating information on human disease-associated genes and variants

Autores: Janet Piñero, Àlex Bravo, Núria Queralt-Rosinach, Alba Gutiérrez-Sacristán, Jordi Deu-Pons, Emilio Centeno, Javier García-García, Ferran Sanz, Laura I. Furlong
Publicado en: Nucleic Acids Research, 2016, Página(s) gkw943, ISSN 0305-1048
Editor: Oxford University Press
DOI: 10.1093/nar/gkw943

General guidelines for biomedical software development

Autores: Silva LB, Jimenez RC, Blomberg N and Luis Oliveira J.
Publicado en: F1000Research, Edición 6:273, 2017, ISSN 2046-1402
Editor: F1000 Research Ltd.
DOI: 10.12688/f1000research.10750.1

Using Electronic Health Records to Assess Depression and Cancer Comorbidities

Autores: Miguel A. Mayer, Alba Gutierrez-Sacristan, Angela Leis, Santiago De La Peña, Ferran Sanz, Laura I. Furlong
Publicado en: Stud Health Technol Inform., 2017, Página(s) 236-240
Editor: IOS Press
DOI: 10.3233/978-1-61499-753-5-236

Text mining and expert curation to develop a database on psychiatric diseases and their genes

Autores: Alba Gutiérrez Sacristán, Álex Bravo, Marta Portero, Olga Valverde, Antonio Armario, M.C. Blanco-Gandía, Adriana Farré, Lierni Fernández-Ibarrondo, Francina Fonseca, Jesús Giraldo, Angela Leis, Anna Mané, M.A. Mayer, Sandra Montagud-Romero, Roser Nadal, Jordi Ortiz, Francisco Javier Pavon, Ezequiel Perez, Marta Rodríguez-Arias, Antonia Serrano, Marta Torrens, Vincent Warnault, Ferran Sanz
Publicado en: Proceedings of the 7th International Symposium on Semantic Mining in Biomedicine, Edición Vol-1650, 2016, Página(s) 48-55, ISSN 1613-0073
Editor: CEUR Workshop Proceedings

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