Josep F Abril, PhD - Publications

2006- Genetics, Microbiology & Statistics Universitat de Barcelona, Barcelona, Cataluña, Spain 
Computational Biology

44 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2020 Toulis V, García-Monclús S, de la Peña-Ramírez C, Arenas-Galnares R, Abril JF, Todi SV, Khan N, Garanto A, Costa MDC, Marfany G. The Deubiquitinating Enzyme Ataxin-3 Regulates Ciliogenesis and Phagocytosis in the Retina. Cell Reports. 33: 108360. PMID 33176149 DOI: 10.1016/j.celrep.2020.108360  1
2020 Martínez-Puchol S, Rusiñol M, Fernández-Cassi X, Timoneda N, Itarte M, Andrés C, Antón A, Abril JF, Girones R, Bofill-Mas S. Characterisation of the sewage virome: comparison of NGS tools and occurrence of significant pathogens. The Science of the Total Environment. 713: 136604. PMID 31955099 DOI: 10.1016/j.scitotenv.2020.136604  1
2019 Rusiñol M, Martínez-Puchol S, Timoneda N, Fernández-Cassi X, Pérez-Cataluña A, Fernández-Bravo A, Moreno-Mesonero L, Moreno Y, Alonso JL, Figueras MJ, Abril JF, Bofill-Mas S, Girones R. Metagenomic analysis of viruses, bacteria and protozoa in irrigation water. International Journal of Hygiene and Environmental Health. 224: 113440. PMID 31978735 DOI: 10.1016/j.ijheh.2019.113440  1
2019 Arenas-Galnares R, Castillo-Lara S, Toulis V, Boloc D, Gonzàlez-Duarte R, Marfany G, Abril JF. RPGeNet v2.0: expanding the universe of retinal disease gene interactions network. Database : the Journal of Biological Databases and Curation. 2019. PMID 31712826 DOI: 10.1093/database/baz120  1
2019 Castillo-Lara S, Pascual-Carreras E, Abril JF. PlanExp: intuitive integration of complex RNA-seq datasets with planarian omics resources. Bioinformatics (Oxford, England). PMID 31647529 DOI: 10.1093/bioinformatics/btz802  1
2019 Santabárbara-Ruiz P, Esteban-Collado J, Pérez L, Viola G, Abril JF, Milán M, Corominas M, Serras F. Ask1 and Akt act synergistically to promote ROS-dependent regeneration in Drosophila. Plos Genetics. 15: e1007926. PMID 30677014 DOI: 10.1371/journal.pgen.1007926  0.72
2018 Castillo-Lara S, Abril JF. PPaxe: easy extraction of protein occurrence and interactions from the scientific literature. Bioinformatics (Oxford, England). PMID 30500875 DOI: 10.1093/bioinformatics/bty988  1
2018 Roca-Ayats N, Ng PY, Garcia-Giralt N, Falcó-Mascaró M, Cozar M, Abril JF, Quesada Gómez JM, Prieto-Alhambra D, Nogués X, Dunford JE, Russell RG, Baron R, Grinberg D, Balcells S, Díez-Pérez A. Functional characterization of a GGPPS variant identified in atypical femoral fracture patients and delineation of the role of GGPPS in bone-relevant cell types. Journal of Bone and Mineral Research : the Official Journal of the American Society For Bone and Mineral Research. PMID 30184270 DOI: 10.1002/jbmr.3580  1
2018 Rusiñol M, Fernandez-Cassi X, Timoneda N, Carratalà A, Abril JF, Silvera C, Figueras MJ, Gelati E, Rodó X, Kay D, Wyn-Jones P, Bofill-Mas S, Girones R. Corrigendum to "Evidence of viral dissemination and seasonality in a Mediterranean river catchment: implications for water pollution management" [J. Environ. Manag. 159 (2015) 58-67]. Journal of Environmental Management. PMID 29807682 DOI: 10.1016/j.jenvman.2018.05.047  1
2018 Castillo-Lara S, Abril JF. PlanNET: homology-based predicted interactome for multiple planarian transcriptomes. Bioinformatics (Oxford, England). 34: 1016-1023. PMID 29186384 DOI: 10.1093/bioinformatics/btx738  1
2018 Fernandez-Cassi X, Timoneda N, Martínez-Puchol S, Rusiñol M, Rodriguez-Manzano J, Figuerola N, Bofill-Mas S, Abril JF, Girones R. Metagenomics for the study of viruses in urban sewage as a tool for public health surveillance. The Science of the Total Environment. 618: 870-880. PMID 29108696 DOI: 10.1016/j.scitotenv.2017.08.249  1
2017 Gonzales-Gustavson E, Timoneda N, Fernandez-Cassi X, Caballero A, Abril JF, Buti M, Rodriguez-Frias F, Girones R. Identification of sapovirus GV.2, astrovirus VA3 and novel anelloviruses in serum from patients with acute hepatitis of unknown aetiology. Plos One. 12: e0185911. PMID 28982120 DOI: 10.1371/journal.pone.0185911  1
2017 Boloc D, Rodríguez N, Gassó P, Abril JF, Bernardo M, Lafuente A, Mas S. SiNoPsis: Single Nucleotide Polymorphisms selection and promoter profiling. Bioinformatics (Oxford, England). PMID 28968821 DOI: 10.1093/bioinformatics/btx570  1
2017 Fernandez-Cassi X, Timoneda N, Gonzales-Gustavson E, Abril JF, Bofill-Mas S, Girones R. A metagenomic assessment of viral contamination on fresh parsley plants irrigated with fecally tainted river water. International Journal of Food Microbiology. 257: 80-90. PMID 28646670 DOI: 10.1016/j.ijfoodmicro.2017.06.001  1
2017 Roca-Ayats N, Balcells S, Garcia-Giralt N, Falcó-Mascaró M, Martínez-Gil N, Abril JF, Urreizti R, Dopazo J, Quesada-Gómez JM, Nogués X, Mellibovsky L, Prieto-Alhambra D, Dunford JE, Javaid MK, Russell RG, et al. GGPS1 Mutation and Atypical Femoral Fractures with Bisphosphonates. The New England Journal of Medicine. 376: 1794-1795. PMID 28467865 DOI: 10.1056/NEJMc1612804  0.32
2017 Hjelmsø MH, Hellmér M, Fernandez-Cassi X, Timoneda N, Lukjancenko O, Seidel M, Elsässer D, Aarestrup FM, Löfström C, Bofill-Mas S, Abril JF, Girones R, Schultz AC. Evaluation of Methods for the Concentration and Extraction of Viruses from Sewage in the Context of Metagenomic Sequencing. Plos One. 12: e0170199. PMID 28099518 DOI: 10.1371/journal.pone.0170199  0.52
2015 Gabre JL, Martinez P, Nilsson Sköld H, Ortega-Martinez O, Abril JF. The coelomic epithelium transcriptome from a clonal sea star, Coscinasterias muricata. Marine Genomics. PMID 26321383 DOI: 10.1016/J.Margen.2015.07.010  1
2015 Boloc D, Castillo-Lara S, Marfany G, Gonzàlez-Duarte R, Abril JF. Distilling a Visual Network of Retinitis Pigmentosa Gene-Protein Interactions to Uncover New Disease Candidates. Plos One. 10: e0135307. PMID 26267445 DOI: 10.1371/journal.pone.0135307  1
2015 Rusiñol M, Fernandez-Cassi X, Timoneda N, Carratalà A, Abril JF, Silvera C, Figueras MJ, Gelati E, Rodó X, Kay D, Wyn-Jones P, Bofill-Mas S, Girones R. Evidence of viral dissemination and seasonality in a Mediterranean river catchment: Implications for water pollution management. Journal of Environmental Management. 159: 58-67. PMID 26046988 DOI: 10.1016/j.jenvman.2015.05.019  1
2015 Rodríguez-Esteban G, González-Sastre A, Rojo-Laguna JI, Saló E, Abril JF. Digital gene expression approach over multiple RNA-Seq data sets to detect neoblast transcriptional changes in Schmidtea mediterranea. Bmc Genomics. 16: 361. PMID 25952370 DOI: 10.1186/s12864-015-1533-1  1
2015 Perea-Atienza E, Gavilán B, Chiodin M, Abril JF, Hoff KJ, Poustka AJ, Martinez P. The nervous system of Xenacoelomorpha: a genomic perspective. The Journal of Experimental Biology. 218: 618-28. PMID 25696825 DOI: 10.1242/Jeb.110379  1
2013 Steijger T, Abril JF, Engström PG, Kokocinski F, Hubbard TJ, Guigó R, Harrow J, Bertone P. Assessment of transcript reconstruction methods for RNA-seq. Nature Methods. 10: 1177-84. PMID 24185837 DOI: 10.1038/Nmeth.2714  1
2013 Isolani ME, Abril JF, Saló E, Deri P, Bianucci AM, Batistoni R. Planarians as a model to assess in vivo the role of matrix metalloproteinase genes during homeostasis and regeneration. Plos One. 8: e55649. PMID 23405188 DOI: 10.1371/journal.pone.0055649  1
2011 Garanto A, Riera M, Pomares E, Permanyer J, de Castro-Miró M, Sava F, Abril JF, Marfany G, Gonzàlez-Duarte R. High transcriptional complexity of the retinitis pigmentosa CERKL gene in human and mouse. Investigative Ophthalmology & Visual Science. 52: 5202-14. PMID 21508105 DOI: 10.1167/iovs.10-7101  1
2011 Fernández-Taboada E, Rodríguez-Esteban G, Saló E, Abril JF. A proteomics approach to decipher the molecular nature of planarian stem cells. Bmc Genomics. 12: 133. PMID 21356107 DOI: 10.1186/1471-2164-12-133  1
2010 Abril JF, Cebrià F, Rodríguez-Esteban G, Horn T, Fraguas S, Calvo B, Bartscherer K, Saló E. Smed454 dataset: unravelling the transcriptome of Schmidtea mediterranea. Bmc Genomics. 11: 731. PMID 21194483 DOI: 10.1186/1471-2164-11-731  1
2009 Irimia M, Roy SW, Neafsey DE, Abril JF, Garcia-Fernandez J, Koonin EV. Complex selection on 5' splice sites in intron-rich organisms. Genome Research. 19: 2021-7. PMID 19745111 DOI: 10.1101/Gr.089276.108  1
2009 Blanco E, Abril JF. Computational gene annotation in new genome assemblies using GeneID Methods in Molecular Biology. 537: 243-261. PMID 19378148 DOI: 10.1007/978-1-59745-251-9_12  1
2009 Saló E, Abril JF, Adell T, Cebrià F, Eckelt K, Fernandez-Taboada E, Handberg-Thorsager M, Iglesias M, Molina MD, Rodríguez-Esteban G. Planarian regeneration: achievements and future directions after 20 years of research. The International Journal of Developmental Biology. 53: 1317-27. PMID 19247944 DOI: 10.1387/ijdb.072414es  1
2007 Levy S, Sutton G, Ng PC, Feuk L, Halpern AL, Walenz BP, Axelrod N, Huang J, Kirkness EF, Denisov G, Lin Y, MacDonald JR, Pang AW, Shago M, Stockwell TB, ... ... Abril JF, et al. The diploid genome sequence of an individual human. Plos Biology. 5: e254. PMID 17803354 DOI: 10.1371/Journal.Pbio.0050254  1
2007 Birney E, Stamatoyannopoulos JA, Dutta A, Guigó R, Gingeras TR, Margulies EH, Weng Z, Snyder M, Dermitzakis ET, Thurman RE, Kuehn MS, Taylor CM, Neph S, Koch CM, ... ... Abril JF, et al. Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature. 447: 799-816. PMID 17571346 DOI: 10.1038/Nature05874  1
2006 Guigó R, Flicek P, Abril JF, Reymond A, Lagarde J, Denoeud F, Antonarakis S, Ashburner M, Bajic VB, Birney E, Castelo R, Eyras E, Ucla C, Gingeras TR, Harrow J, et al. EGASP: the human ENCODE Genome Annotation Assessment Project. Genome Biology. 7: S2.1-31. PMID 16925836 DOI: 10.1186/Gb-2006-7-S1-S2  1
2005 Abril JF, Castelo R, Guigó R. Comparison of splice sites in mammals and chicken. Genome Research. 15: 111-9. PMID 15590946 DOI: 10.1101/gr.3108805  1
2004 Gibbs RA, Weinstock GM, Metzker ML, Muzny DM, Sodergren EJ, Scherer S, Scott G, Steffen D, Worley KC, Burch PE, Okwuonu G, Hines S, Lewis L, DeRamo C, Delgado O, ... ... Abril JF, et al. Genome sequence of the Brown Norway rat yields insights into mammalian evolution. Nature. 428: 493-521. PMID 15057822 DOI: 10.1038/Nature02426  0.01
2003 Abril JF, Guigó R, Wiehe T. gff2aplot: Plotting sequence comparisons. Bioinformatics (Oxford, England). 19: 2477-9. PMID 14668236 DOI: 10.1093/bioinformatics/btg334  1
2003 Guigo R, Dermitzakis ET, Agarwal P, Ponting CP, Parra G, Reymond A, Abril JF, Keibler E, Lyle R, Ucla C, Antonarakis SE, Brent MR. Comparison of mouse and human genomes followed by experimental verification yields an estimated 1,019 additional genes. Proceedings of the National Academy of Sciences of the United States of America. 100: 1140-5. PMID 12552088 DOI: 10.1073/Pnas.0337561100  1
2003 Parra G, Agarwal P, Abril JF, Wiehe T, Fickett JW, Guigó R. Comparative gene prediction in human and mouse. Genome Research. 13: 108-17. PMID 12529313 DOI: 10.1101/gr.871403  1
2002 Waterston RH, Lindblad-Toh K, Birney E, Rogers J, Abril JF, Agarwal P, Agarwala R, Ainscough R, Alexandersson M, An P, Antonarakis SE, Attwood J, Baertsch R, Bailey J, et al. Initial sequencing and comparative analysis of the mouse genome. Nature. 420: 520-62. PMID 12466850 DOI: 10.1038/Nature01262  1
2002 Holt RA, Subramanian GM, Halpern A, Sutton GG, Charlab R, Nusskern DR, Wincker P, Clark AG, Ribeiro JM, Wides R, Salzberg SL, Loftus B, Yandell M, Majoros WH, Rusch DB, ... ... Abril JF, et al. The genome sequence of the malaria mosquito Anopheles gambiae. Science (New York, N.Y.). 298: 129-49. PMID 12364791 DOI: 10.1126/Science.1076181  1
2002 Glöckner G, Eichinger L, Szafranski K, Pachebat JA, Bankier AT, Dear PH, Lehmann R, Baumgart C, Parra G, Abril JF, Guigó R, Kumpf K, Tunggal B, Cox E, Quail MA, et al. Sequence and analysis of chromosome 2 of Dictyostelium discoideum. Nature. 418: 79-85. PMID 12097910 DOI: 10.1038/Nature00847  1
2000 Abril JF, Guigó R. gff2ps: visualizing genomic annotations. Bioinformatics (Oxford, England). 16: 743-4. PMID 11099262 DOI: 10.1093/bioinformatics/16.8.743  1
2000 Guigó R, Agarwal P, Abril JF, Burset M, Fickett JW. An assessment of gene prediction accuracy in large DNA sequences. Genome Research. 10: 1631-42. PMID 11042160 DOI: 10.1101/gr.122800  1
2000 Reese MG, Hartzell G, Harris NL, Ohler U, Abril JF, Lewis SE. Genome annotation assessment in Drosophila melanogaster Genome Research. 10: 483-501. PMID 10779488 DOI: 10.1101/Gr.10.4.483  1
2000 Adams MD, Celniker SE, Holt RA, Evans CA, Gocayne JD, Amanatides PG, Scherer SE, Li PW, Hoskins RA, Galle RF, George RA, Lewis SE, Richards S, Ashburner M, Henderson SN, ... ... Abril JF, et al. The genome sequence of Drosophila melanogaster. Science (New York, N.Y.). 287: 2185-95. PMID 10731132 DOI: 10.1126/Science.287.5461.2185  1
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