Computational Genomics Lab Publications

NOW-2016

• PlanNET: homology-based predicted interactome for multiple planarian transcriptomes
  S. Castillo-Lara, J.F. Abril
  Bioinformatics, epub ahead of print, 2017. OPEN Access
  

  PubMed

  Full Text

  PDF

  PlanNET

• Metagenomics for the study of viruses in urban sewage as a tool for public health surveillance.
  X. Fernandez-Cassi*, N. Timoneda*, S. Martínez-Puchol, M. Rusiñol, J. Rodriguez-Manzano, N. Figuerola, S. Bofill-Mas, JF Abril, R. Girones
  The Science of the Total Environment, epub ahead of print, 2017.
  *Contributed equally
  

  PubMed

  Abstract

• Identification of sapovirus GV.2, astrovirus VA3 and novel anelloviruses in serum from patients with acute hepatitis of unknown aetiology
  E. Gonzales-Gustavson*, N. Timoneda*, X. Fernandez-Cassi, A. Caballero, J.F. Abril, M. Buti, F. Rodriguez-Frias, R. Girones
  PLoS One, 12(10):e0185911, 2017. OPEN Access
  *Contributed equally
  

  PubMed

  Full Text

  PDF

• SiNoPsis: Single Nucleotide Polymorphisms selection and promoter profiling
  D. Boloc, N. Rodríguez, P. Gassó, J.F. Abril, M. Bernardo, A. Lafuente, S. Mas
  Bioinformatics, epub ahead of print, 2017.
  

  PubMed

  Abstract

  SiNoPsis

• A metagenomic assessment of viral contamination on fresh parsley plants irrigated with fecally tainted river water
  X. Fernandez-Cassi*, N. Timoneda*, E. Gonzales-Gustavson, J.F. Abril, S. Bofill-Mas, R. Girones
  International Journal of Food Microbiology, 257: 80–90, 2017.
  *Contributed equally
  

  PubMed

  Full Text

• GGPS1 Mutation and Atypical Femoral Fractures with Bisphosphonates.
  N. Roca-Ayats, S. Balcells, N. Garcia-Giralt, M. Falcó-Mascaró, N. Martínez-Gil, J.F. Abril, R. Urreizti, J. Dopazo, J.M. Quesada-Gómez, X. Nogués, L. Mellibovsky, D. Prieto-Alhambra, J.E. Dunford, M.K. Javaid, R.G. Russell, D. Grinberg, A. Díez-Pérez
  The New England Journal of Medicine, 376(18): 1794-1795, 2017.
  

  PubMed

  Full Text

  PDF

• Evaluation of Methods for the Concentration and Extraction of Viruses from Sewage in the Context of Metagenomic Sequencing.
  M.H. Hjelmsø, M. Hellmér, X. Fernandez-Cassi, N. Timoneda, O. Lukjancenko, M. Seidel, D. Elsässer, F.M. Aarestrup, C. Löfström, S. Bofill-Mas, J.F. Abril, R. Girones, A.C. Schultz
  PLoS ONE, 12(1): e0170199, 2017. OPEN Access
  

  PubMed

  Full Text

  PDF

2015-2010

• The coelomic epithelium transcriptome from a clonal sea star, Coscinasterias muricata.
  J.L. Gabre, P. Martinez, H. Nilsson Sköld, O. Ortega-Martinez, J.F. Abril
  Marine Genomics, 24(Part3):245–248, 2015 (AOP August 28th, 2015)
  

  Abstract

  DATA

  GBrowse

• Distilling a Visual Network of Retinitis Pigmentosa Gene-Protein Interactions to Uncover New Disease Candidates.
  D. Boloc, S. Castillo-Lara, G. Marfany, R. Gonzàlez-Duarte, J.F. Abril
  PLoS ONE, 10(8):e0135307, 2015 OPEN Access
  

  PubMed

  Full Text

  PDF

  RPGeNet

• Evidence of viral dissemination and seasonality in a Mediterranean river catchment: Implications for water pollution management
  M. Rusiñol, X. Fernandez-Cassi, N. Timoneda, A. Carratalà, J.F. Abril, C. Silvera, M.J. Figueras, E. Gelati, X. Rodó, D. Kay, P. Wyn-Jones, S. Bofill-Mas, R. Girones
  Journal of Environmental Management, 159:58–67, 2015 (Epub June 2nd, 2015)
  

  PubMed

  Abstract

• Digital Gene Expression approach over multiple RNA-Seq data sets to detect neoblast transcriptional changes in Schmidtea mediterranea
  G. Rodríguez-Esteban, A. González-Sastre, J.I. Rojo-Laguna, E. Saló, J.F. Abril
  BMC genomics, 8;16(1):361, 2015 (Epub May 8th, 2015) HIGHLY ACCESSED OPEN Access
  

  PubMed

  Abstract

  Full Text

  PDF

  DATA

• Health risks derived from consumption of lettuces irrigated with tertiary effluent containing norovirus
  H. Sales-Ortells, X. Fernandez-Cassi, N. Timoneda, W. Dürig, R. Girones, G. Medema
  Food Research International, 68(Special Issue):70-77, 2015
  

  Abstract

• The nervous system of Xenacoelomorpha: a genomic perspective.
  E. Perea-Atienza, B. Gavilán, M. Chiodin, J.F. Abril, K.J. Hoff, A.J. Poustka, P. Martinez
  J Exp Biol., 218(Pt4):618-28, 2015 OPEN Access
  

  PubMed

  Abstract

  Full Text

  PDF

• Assessment of transcript reconstruction methods for RNA-seq.
  T. Steijger*, J.F. Abril*, P.G. Engström*, F. Kokocinski*, T.J. Hubbard, R. Guigó, J. Harrow, P. Bertone, RGASP Consortium
  Nat Methods, 10(12):1177-84, 2013 (Epub Nov 3rd, 2013) FREE Full Text
  *Contributed equally
  

  PubMed

  Abstract

  Full Text

  PDF

  Suppl Material

  DATA

• Planarians as a Model to Assess In Vivo the Role of Matrix Metalloproteinase Genes during Homeostasis and Regeneration
  M.E. Isolani, J.F. Abril, E. Saló, P. Deri, A.M. Bianucci, R. Batistoni
  PLoS ONE, 8(2):e55649, 2013 (Epub Feb 6th, 2013) OPEN Access
  

  PubMed

  Full Text

  PDF

• High transcriptional complexity of the retinitis pigmentosa CERKL gene in human and mouse
  A. Garanto, M. Riera, E. Pomares, J. Permanyer, M. de Castro-Miró, F Sava, J.F. Abril, G. Marfany, R. Gonzàlez-Duarte
  Invest Ophthalmol Vis Sci (IOVS), 52(8):5202-14, 2011 FREE Full Text
  

  PubMed

  Full Text

  PDF

• A proteomics approach to decipher the molecular nature of planarian stem cells
  E. Fernández-Taboada*, G. Rodríguez-Esteban*, E. Saló, J.F. Abril
  BMC genomics, 12:133, 2011 HIGHLY ACCESSED OPEN Access
  *Contributed equally
  

  PubMed

  Abstract

  Full Text

  PDF

  DATA

• Smed454 dataset: unravelling the transcriptome of Schmidtea mediterranea
  J.F. Abril*, F. Cebrià*, G. Rodríguez-Esteban, S. Fraguas, T. Horn, B. Calvo, K. Bartscherer, E. Saló
  BMC genomics, 11:731, 2010 HIGHLY ACCESSED OPEN Access
  *Contributed equally
  

  PubMed

  Abstract

  Full Text

  PDF

  DATA

Pre-Computational Genomics Lab Papers

2010-2006

• Complex selection on 5' splice sites in intron-rich organisms
  M. Irimia, S.W. Roy, D.E. Neafsey, J.F. Abril, J. Garcia-Fernandez, E.V. Koonin
  Genome Research, 19(11):2021-7, 2009. (Epub Sep 10th, 2009) OPEN Access
  

  PubMed

  Abstract

  Full Text

  PDF

• Computational gene annotation in new genome assemblies using GeneID
  E. Blanco, J.F. Abril
  Methods Mol Biol., 537:243-61, 2009.
  

  PubMed

  Abstract

• Planarian regeneration: achievements and future directions after 20 years of research
  E. Saló, J.F. Abril, T. Adell, F. Cebrià, K. Eckelt, E. Fernández-Taboada, M. Handberg-Thorsager, M. Iglesias, M. D. Molina, G. Rodríguez-Esteban
  International Journal of Developmental Biology, 53(8-10):1317-27, 2009 FREE Full Text
  

  PubMed

  Abstract

  PDF

• The diploid genome sequence of an individual human
  S. Levy, G. Sutton, P.C. Ng, L. Feuk, A.L. Halpern, B.P. Walenz, N. Axelrod, J. Huang, E.F. Kirkness, G. Denisov, Y. Lin, J.R. MacDonald, A.W. Pang, M. Shago, T.B. Stockwell, A. Tsiamouri, V. Bafna, V. Bansal, S.A. Kravitz, D.A. Busam, K.Y. Beeson, T.C. McIntosh, K.A. Remington, J.F. Abril, J. Gill, J. Borman, Y.H. Rogers, M.E. Frazier, S.W. Scherer, R.L. Strausberg, J.C. Venter
  PLoS Biology, 5(10):e254, 2007 OPEN Access
  

  PubMed

  Full Text

  PDF

  POSTER_WEB

  POSTER_PDF