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Published Papers


Word Cloud of Published Abstracts

Publications by Year

Since 2021 
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Viral populations of SARS-CoV-2 in upper respiratory tract, placenta, amniotic fluid and umbilical cord blood support viral replication in placenta
M. Piñana, J.F. Abril, C. Andrés, A. Silgado, A. Navarro, A. Suy, E. Sulleiro, T. Pumarola, J. Quer , A. Antón
Clinical Microbiology and Infection, 27(10) :1542-1544, 2021.
Exploring the diversity of coronavirus in sewage during COVID-19 pandemic: Don’t miss the forest for the trees.
S. Martínez-Puchol , M. Itarte, M. Rusiñol, E. Forés, C. Mejías-Molina, C. Andrés, A. Antón, J. Quer, J.F. Abril, R. Girones, S. Bofill-Mas
Science of The Total Environment, 800:149562, 2021.


2016-2020 
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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



2010-2015 
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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
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2006-2010 
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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

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