Published Papers

Word Cloud of Published Abstracts

Publications by Year


Genomic analyses reveal FoxG as an upstream regulator of wnt1 required for posterior identity specification in planarians
E. Pascual-Carreras, M. Marin-Barba, S. Castillo-Lara, P. Coronel-Cordoba, M. Silva Magri, G.N. Wheeler, J.F. Abril, J.L. Gomez-Skarmeta, E. Saló , T. Adell

Joint senior authors
bioRxiv, 2020.  OPEN ACCESS
The Deubiquitinating Enzyme Ataxin-3 Regulates Ciliogenesis and Phagocytosis in the Retina.
V. Toulis, S. García-Monclús, C. de la Peña-Ramírez, R. Arenas-Galnares, J.F. Abril, S. Todi, N. Khan, A. Garanto, M. do Carmo Costa, G. Marfany
Cell Reports, 33(6) :108360, 2020.  OPEN ACCESS
Implementation and integration of microbial source tracking in a river watershed monitoring plan.
E. Ballesté, K. Demeter, B. Masterson, N. Timoneda, L. Sala-Comorera, W.G. Meijer
Science of The Total Environment, 736:139573, 2020.  OPEN ACCESS
Characterisation of the sewage virome: comparison of NGS tools and occurrence of significant pathogens
S. Martínez-Puchol , M. Rusiñol, X. Fernández-Cassi, N. Timoneda, M. Itarte, C. Andrés, A. Antón, J.F. Abril, R. Girones, S. Bofill-Mas
Science of The Total Environment, 713:136604, 2020.
Metagenomic analysis of viruses, bacteria and protozoa in irrigation water
M. Rusiñol , S. Martínez-Puchol, N. Timoneda, X. Fernández-Cassi, A. Pérez-Cataluña, A. Fernández-Bravo, L. Moreno-Mesonero, Y. Moreno, J.L. Alonso, M.J. Figueras, J.F. Abril, S. Bofill-Mas, R. Girones
International Journal of Hygiene and Environmental Health, 224:113440, 2020.
PlanExp: intuitive integration of complex RNA-seq datasets with planarian omics resources
S. Castillo-Lara, E. Pascual-Carreras, J.F. Abril
Bioinformatics, 36(6) :1889-1895, 2020.
RPGeNet v2.0: expanding the universe of retinal disease gene interactions network
R. Arenas-Galnares , S. Castillo-Lara , V. Toulis, D. Boloc, R. Gonzàlez-Duarte, G. Marfany , J. F. Abril

Contributed equally Joint senior authors
Database, vol2019:baz120, 2019.  OPEN ACCESS
PPaxe: easy extraction of protein occurrence and interactions from the scientific literature
S. Castillo-Lara, J.F. Abril
Bioinformatics, 35(14) :2523–2524, 2019.
Ask1 and Akt act synergistically to promote ROS-dependent regeneration in Drosophila
P. Santabárbara-Ruiz , J. Esteban-Collado , L. Pérez, G. Viola, J.F. Abril, M. Milán, M. Corominas, F. Serras

Contributed equally
PLoS Genetics, 15(1) :1—27, 2019.  OPEN ACCESS
Genome Annotation
J.F. Abril, S. Castellano

Book chapter, pages 195–209.
In: Ranganathan S., Nakai K., Schönbach C., and Gribskov M. (eds)
Encyclopedia of Bioinformatics and Computational Biology, vol 2, 2019.
Elsevier Inc. ISBN: 978-0-12-811432-2

Genetic study of atypical femoral fractures using exome sequencing in three affected sisters and three unrelated patients.
N. Roca-Ayats , M. Falcó-Mascaró, N. García-Giralt, M. Cozar, J.F. Abril, J.M. Quesada-Gómez, D. Prieto-Alhambra, X. Nogués, L. Mellibovsky, A. Díez-Pérez, D. Grinberg, S. Balcells
Rev Osteoporos Metab Miner. , 10(4) :108—118, 2018.
Functional Characterization of a GGPPS Variant Identified in Atypical Femoral Fracture Patients and Delineation of the Role of GGPPS in Bone‐Relevant Cell Types
N. Roca‐Ayats, P. Ying Ng, N. Garcia‐Giralt , M. Falcó‐Mascaró, M. Cozar, J.F. Abril, J.M. Quesada Gómez, D. Prieto‐Alhambra, X. Nogués, J. E. Dunford, R.G. Russell, R. Baron, D. Grinberg, S. Balcells, A. Díez‐Pérez
Journal of Bone and Mineral Research, 33(12) :2091—2098, 2018.
PlanNET: homology-based predicted interactome for multiple planarian transcriptomes
S. Castillo-Lara, J.F. Abril
Bioinformatics, 34(6) :1016—1023, 2018.  OPEN ACCESS
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

Contributed equally
The Science of the Total Environment, 618:870—880, 2018.
SiNoPsis: Single Nucleotide Polymorphisms selection and promoter profiling
D. Boloc, N. Rodríguez, P. Gassó, J.F. Abril, M. Bernardo, A. Lafuente, S. Mas
Bioinformatics, 34(2) :303—305, 2018.
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

Contributed equally
PLoS One, 12(10) :e0185911, 2017.  OPEN ACCESS
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

Contributed equally
International Journal of Food Microbiology, 257:80—90, 2017.
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.
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

Contributed equally
PLoS ONE, 12(1) :e0170199, 2017.  OPEN ACCESS


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.
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.
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

Joint senior authors Corresponding authors
PLoS ONE, 10(8) :e0135307, 2015.  OPEN ACCESS
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

Contributed equally Corresponding authors
BMC Genomics, 16:361, 2015.  OPEN ACCESS
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
Journal of Experimental Biology, 218(pt4) :618—28, 2015.  OPEN ACCESS
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.
Gene-finding related terms and definitions.
E. Blanco, J.F. Abril, R. Guigó
Contributed articles for computational gene-finding terms.
In: Zvelebil M.J. and Hancock J.M. (eds)
Concise Encyclopaedia of Bioinformatics and Computational Biology, 2nd ed., 2014.
Wiley-Blackwell. ISBN: 978-0-470-97871-9
Assessment of transcript reconstruction methods for RNA-seq
T. Steijger , J.F. Abril , P.G. Engström , F. Kokocinski , RGASP Consortium, T.J. Hubbard, R. Guigó, J. Harrow, P. Bertone

Contributed equally
Nature Methods, 10(12) :1177-84, 2013.  FREE FULL TEXT
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.  OPEN ACCESS
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

Contributed equally
Invest Ophthalmol Vis Sci (IOVS), 52(8) :5202—14, 2011.  FREE FULL TEXT
A proteomics approach to decipher the molecular nature of planarian stem cells
E. Fernández-Taboada , G. Rodríguez-Esteban , E. Saló, J.F. Abril

Contributed equally
BMC Genomics, 12:133, 2011.  OPEN ACCESS
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

Contributed equally
BMC Genomics, 11:731, 2010.  OPEN ACCESS

Pre-Computational Genomics Lab Papers


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

Contributed equally
Genome Research, 19(11) :2021—7, 2009.  OPEN ACCESS
Computational gene annotation in new genome assemblies using GeneID
E. Blanco, J.F. Abril

Book chapter, pages 243—261.
In: Posada D. (ed)
Bioinformatics for DNA Sequence Analysis.
Methods in Molecular Biology (Methods and Protocols), vol 537, 2009.
Humana Press. ISBN: 978-1-58829-910-9

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

Corresponding author
International Journal of Developmental Biology, 53(8-10) :1317—27, 2009.  FREE FULL TEXT
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

Page last modified on Friday 06 of March, 2020 17:18:55 CET