PUBLICATIONS | DELIVERABLES | TOOLS

PUBLICATIONS

• 1. Yadav B, Wennerberg K, Aittokallio T, Tang J. Searching for Drug Synergy in Complex Dose-Response Landscape Using an Interaction Potency Model. Computational and Structural Biotechnology Journal 2015; 13: 504-513. (open access)
  2. Jensen AB, Ajslev TA, Brunak S, Sørensen TI. 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. BMJ Open. 2015 Dec 15;5(12):e008702. doi: 10.1136/bmjopen-2015-008702. (open access)
  3. Ellesøe SG, Jensen AB, Ängquist LH, Hjortdal VE, Larsen LA, Brunak S. How Suitable Are Registry Data for Recurrence Risk Calculations? Validation of Diagnoses on 1,593 Families With Congenital Heart Disease. World J Pediatr Congenit Heart Surg. 2016 Mar;7(2):169-77. doi: 10.1177/2150135115615786. (open access)
  4. Cunningham, F., Moore, B., Ruiz-Schultz, N., Ritchie, G. R., & Eilbeck, K. (2015). Improving the Sequence Ontology terminology for genomic variant annotation. Journal of Biomedical Semantics, 6, 32. http://doi.org/10.1186/s13326-015-0030-4. (open access)
  5. Piñero J., Queralt-Rosinach N., Bravo À., Deu-Pons J., Bauer-Mehren A., Baron M., … Furlong, L. I. (2015). DisGeNET: a discovery platform for the dynamical exploration of human diseases and their genes and variants. Database: The Journal of Biological Databases and Curation, 2015, bav028. http://doi.org/10.1093/database/bav028. (open access)
  6. Ellinghaus D, Jostins L, Spain SL, Cortes A, Bethune J, Han B, Park YR, Raychaudhuri S, Pouget JG, Hübenthal M, Folseraas T, Wang Y, Esko T, Metspalu A, Westra HJ, Franke L, Pers TH, Weersma RK, Collij V, D’Amato M, Halfvarson J, Jensen AB, Lieb W, Degenhardt F, Forstner AJ, Hofmann A; International IBD Genetics Consortium (IIBDGC).; International Genetics of Ankylosing Spondylitis Consortium (IGAS).; International PSC Study Group (IPSCSG).; Genetic Analysis of Psoriasis Consortium (GAPC).; Psoriasis Association Genetics Extension (PAGE)., Schreiber S, Mrowietz U, Juran BD, Lazaridis KN, Brunak S, Dale AM, Trembath RC, Weidinger S, Weichenthal M, Ellinghaus E, Elder JT, Barker JN, Andreassen OA, McGovern DP, Karlsen TH, Barrett JC, Parkes M, Brown MA, Franke A. Analysis of five chronic inflammatory diseases identifies 27 new associations and highlights disease-specific patterns at shared loci. Nat Genet. 2016 May;48(5):510-8. doi:10.1038/ng.3528.
  7. Piñero J, Berenstein A, Gonzalez-Perez A, Chernomoretz A, Furlong LI. Uncovering disease mechanisms through network biology in the era of Next Generation Sequencing. Sci Rep. 2016 Apr 15;6:24570. doi: 10.1038/srep24570. (open access)
  8. Yates A, Akanni W, Amode MR, Barrell D, Billis K, Carvalho-Silva D, Cummins C, Clapham P, Fitzgerald S, Gil L, Girón CG, Gordon L, Hourlier T, Hunt SE, Janacek SH, Johnson N, Juettemann T, Keenan S, Lavidas I, Martin FJ, Maurel T, McLaren W, Murphy DN, Nag R, Nuhn M, Parker A, Patricio M, Pignatelli M, Rahtz M, Riat HS, Sheppard D, Taylor K, Thormann A, Vullo A, Wilder SP, Zadissa A, Birney E, Harrow J, Muffato M, Perry E, Ruffier M, Spudich G, Trevanion SJ, Cunningham F, Aken BL, Zerbino DR, Flicek P. Ensembl 2016. Nucleic Acids Res. 2016 Jan 4;44(D1):D710-6. doi: 10.1093/nar/gkv1157. (open access)
  9. Li, T. S., Bravo, À., Furlong, L. I., Good, B. M., & Su, A. I. (2016). A crowdsourcing workflow for extracting chemical-induced disease relations from free text. Database: The Journal of Biological Databases and Curation, 2016, baw051. http://doi.org/10.1093/database/baw051. (open access)
  10. Liye He, Evgeny Kulesskiy, Jani Saarela, Laura Turunen, Krister Wennerberg, Tero Aittokallio, Jing Tang. Methods for High-Throughput Drug Combination Screening and Synergy Scoring. bioRxiv. http://dx.doi.org/10.1101/051698. (open access) This article is a preprint and has not been peer-reviewed
  11. Bravo, À., Li, T. S., Su, A. I., Good, B. M., & Furlong, L. I. (2016). Combining machine learning, crowdsourcing and expert knowledge to detect chemical-induced diseases in text. Database: The Journal of Biological Databases and Curation, 2016, baw094. http://doi.org/10.1093/database/baw094. (open access)
  12. Digles D, Zdrazil B, Neefs JM, Van Vlijmen H, Herhaus C, Caracoti A, Brea J, Roibás B, Loza MI, Queralt-Rosinach N, Furlong LI, Gaulton A, Bartek L, Senger S, Chichester C, Engkvist O, Evelo CT, Franklin NI, Marren D, Ecker GF, Jacoby E. Open PHACTS computational protocols for in silico target validation of cellular phenotypic screens: knowing the knowns. Medchemcomm. 2016 Jun 1;7(6):1237-1244. (open access)
  13. McLaren W, Gil L, Hunt SE, Riat HS, Ritchie GR, Thormann A, Flicek P, Cunningham F. The Ensembl Variant Effect Predictor. Genome Biol. 2016 Jun 6;17(1):122. doi: 10.1186/s13059-016-0974-4. (open access)
  14. Queralt-Rosinach N, Piñero J, Bravo À, Sanz F, Furlong LI. DisGeNET-RDF: harnessing the innovative power of the Semantic Web to explore the genetic basis of diseases. Bioinformatics. 2016 Jul 15;32(14):2236-8. doi:10.1093/bioinformatics/btw214. (open access)
  15. Gutiérrez Sacristán, A., Bravo, A., Portero, M., Valverde, O., Armario, A., Blanco-Gandía, M.C., Farré, A., Fernández-Ibarrondo, L., Fonseca, F., Giraldo, J., Leis, A., Mané, A., Mayer, M.A., Montagud-Romero, S., Nadal, R., Ortiz, J., Pavon, F.J., Perez, E., Rodríguez-Arias, M., Serrano, A., Torrens, M., Warnault, V., Sanz, F., Furlong, Laura I. Text mining and expert curation to develop a database on psychiatric diseases and their genes. Proceedings of the 7th International Symposium on Semantic Mining in Biomedicine. Vol-1650: 48-55. (open access)
  16. Auffray C, Balling R, Barroso I, Bencze L, Benson M, Bergeron J, Bernal-Delgado E, Blomberg N, Bock C, Conesa A, Del Signore S, Delogne C, Devilee P, Di Meglio A, Eijkemans M, Flicek P, Graf N, Grimm V, Guchelaar HJ, Guo YK, Gut IG, Hanbury A, Hanif S, Hilgers RD, Honrado Á, Hose DR, Houwing-Duistermaat J, Hubbard T, Janacek SH, Karanikas H, Kievits T, Kohler M, Kremer A, Lanfear J, Lengauer T, Maes E, Meert T, Müller W, Nickel D, Oledzki P, Pedersen B, Petkovic M, Pliakos K, Rattray M, I Màs JR, Schneider R, Sengstag T, Serra-Picamal X, Spek W, Vaas LA, van Batenburg O, Vandelaer M, Varnai P, Villoslada P, Vizcaíno JA, Wubbe JP, Zanetti G. Making sense of big data in health research: Towards an EU action plan. Genome Med. 2016 Jun 23;8(1):71. doi: 10.1186/s13073-016-0323-y. Erratum in: Genome Med. 2016 Nov 7;8(1):118. (open access)
  17. Gracia-Rubio I., Martinez-Laorden E., Moscoso-Castro M., Milanés MV., Laorden ML., Valverde O. Maternal Separation Impairs Cocaine-Induced Behavioural Sensitization in Adolescent Mice. PLoS One. 2016 Dec 9; 11(12):e0167483. doi: 10.1371/journal.pone.0167483. eCollection 2016 (open access)
  18. Esteve-Arenys A., Gracia-Rubio I., Cantacorps L., Pozo OJ., Marcos J., Rodríguez-Árias M., Miñarro J., Valverde O. Binge ethanol drinking during adolescence modifies cocaine responses in mice. J Psychopharmacol. 2017 Jan; 31(1):86-95. doi: 10.1177/0269881116681457.
  19. Aken BL., Achuthan P., Akanni W., Amode MR., Bernsdorff F., Bhai J., Billis K., Carvalho-Silva D., Cummins C., Clapham P., Gil L., Girón CG., Gordon L., Hourlier T., Hunt SE., Janacek SH., Juettemann T., Keenan S., Laird MR., Lavidas I., Maurel T., McLaren W., Moore B., Murphy DN., Nag R., Newman V., Nuhn M., Ong CK,. Parker A., Patricio M., Riat HS., Sheppard D., Sparrow H., Taylor K., Thormann A., Vullo A., Walts B., Wilder SP., Zadissa A., Kostadima M., Martin FJ., Muffato M., Perry E., Ruffier M., Staines DM., Trevanion SJ., Cunningham F., Yates A., Zerbino DR., Flicek P. Ensembl 2017. Nucleic Acids Res. 2017 Jan 4:45(D1):D635-D642. doi: 10.1093/nar/gkw1104. Epub 2016 Nov 28 (open access)
  20. López-Arnau R., Luján MA., Duart-Castells L., Pubill D., Camarasa J., Valverde O., Escubedo E. Exposure of adolescent mice to 3,4-methylenedioxypyrovalerone increases the psychostimulant, rewarding and reinforcing effects of cocaine in adulthood. Br J Pharmacol. 2017 May;174(10):1161-1173. doi: 10.1111/bph.13771.
  21. Tirado Muñoz J., Farré A., Mestre-Pintó J., Szerman N., Torrens M. Dual diagnosis in Depression: treatment recommendations. Adicciones. 2017 Jul 14;0(0):868. doi: 10.20882/adicciones.868. (open access)
  22. Ianevski A., He L., Aittokallio T., Tang J. (2017). SynergyFinder: a web application for analyzing drug combination dose-response matrix data. Bioinformatics. 2017 Aug 1;33(15):2413-2415. doi: 10.1093/bioinformatics/btx162. (open access)
  23. Karube K., Enjuanes A., Dlouhy I., Jares P., Martin-Garcia D., Nadeu F., Ordóñez GR., Rovira J., Clot G., Royo C., Navarro A., Gonzalez-Farre B., Vaghefi A., Castellano G., Rubio-Perez C., Tamborero D., Briones J., Salar A., Sancho JM., Mercadal S., Gonzalez-Barca E., Escoda L., Miyoshi H., Ohshima K., Miyawaki K,, Kato K,, Akashi K., Mozos A., Colomo L., Alcoceba M., Valera A., Carrió A., Costa D., Lopez-Bigas N., Schmitz R., Staudt LM., Salaverria I., López-Guillermo A., Campo E. Integrating genomic alterations in diffuse large B-cell lymphoma identifies new relevant pathways and potential therapeutic targets. Leukemia. 2017 Aug 14. doi: 10.1038/leu.2017.251.
  24. Andersson EI., Pützer S., Yadav B., Dufva O., Khan S., He L., Sellner L., Schrader A., Crispatzu G., Oleś M., Zhang H., Adnan-Awad S., Lagström S., Bellanger D., Mpindi JP., Eldfors S., Pemovska T., Pietarinen P., Lauhio A., Tomska K., Cuesta-Mateos C., Faber E., Koschmieder S., Brümmendorf TH., Kytölä S., Savolainen ER., Siitonen T., Ellonen P., Kallioniemi O., Wennerberg K., Ding W., Stern MH., Huber W., Anders S., Tang J., Aittokallio T., Zenz T., Herling M., Mustjoki S. Discovery of novel drug sensitivities in T-PLL by high-throughput ex vivo drug testing and mutation profiling. Leukemia. 2017 Aug 14. doi: 10.1038/leu.2017.252. [Epub ahead of print]
  25. Moscoso-Castro M., López-Cano M., Gracia-Rubio I., Ciruela F., Valverde O. Cognitive impairments associated with alterations in synaptic proteins induced by the genetic loss of adenosine A2A receptors in mice. Neuropharmacology. 2017 Aug 26; 126: 48-57. doi: 10.1016/j.neuropharm.2017.08.027.
  26. Cantacorps L., Alfonso-Loeches S., Moscoso-Castro M., Cuitavi J., Gracia-Rubio I., López-Arnau R., Escubedo E., Guerri C., Valverde O. Maternal alcohol binge drinking induces persistent neuroinflammation associated with myelin damage and behavioural dysfunctions in offspring mice. Neuropharmacology. 2017 Sep 1; 123: 368-384. doi: 10.1016/j.neuropharm.2017.05.034.
  27. Silva LB., Jimenez RC., Blomberg N., Oliveira JL. General guidelines for biomedical software development [version 2; referees: 2 approved]. F1000Research 2017, 6:273 doi: 10.12688/f1000research.10750.2. (open access)
  28. Tamborero D., Rubio-Perez C., Deu-Pons J., Schroeder MP., Vivancos A., Rovira A., Tusquets I., Albanell J., Rodon J., Tabernero J., de Torres C., Dienstmann R., Gonzalez-Perez A., Lopez-Bigas N. Cancer Genome Interpreter Annotates The Biological And Clinical Relevance Of Tumor Alterations. Genome Medicine 2018 10:25. doi:10.1186/s13073-018-0531-8. (open access)
  29. Tang J., Tanoli Z., Ravikumar B., Alam Z., Rebane A., Vähä-Koskela M., Peddinti G., van Adrichem A., Wakkinen J., Jaiswal A., Karjalainen E., Gautam P., He L., Parri E., Khan S., Gupta A., Ali M., Yetukuri L., Gustavsson A., Seashore-Ludlow B., Hersey A., Leach A., Overington J., Repasky G., Wennerberg K. and Aittokallio T. Drug Target Commons: a community-effort to build a consensus knowledgebase for drug-target interactions. Cell Chemical Biology 2017 Dec 15. pii: S2451-9456(17)30426-9. (open access)
  30. He L., Tang J., Andersson EI., Timonen S., Koschmieder S., Wennerberg K., Mustjoki S., Aittokallio T. Patient-customized Drug Combination Prediction and Testing for T-cell Prolymphocytic Leukemia Patients. Cancer Res. 2018 Feb 26. pii: canres.3644.2017. doi: 10.1158/0008-5472.CAN-17-3644. (open access)
  31. Gutiérrez-Sacristán A., Bravo A., Giannoula A., Mayer MA., Sanz F., Furlong L.I. comoRbidity: An R package for the systematic analysis of disease comorbidities. Bioinformatics, , bty315. doi: 10.1093/bioinformatics/bty315. (open access)