Josep F Abril’s Publications


Since 2021 

Target enrichment metaviromics enables comprehensive surveillance of coronaviruses in environmental and animal samples
S. Martínez-Puchol, M. Tarradas-Alemany, C. Mejías-Molina, M. Itarte, M. Rusiñol, J. Baliellas, N. Abasolo, N. Canela, A. Monastiri, M. López-Roig, J. Serra-Cobo, J.F. Abril, S. Bofill-Mas
Heliyon, 10(11) :e31556, 2024.  OPEN ACCESS
Gene regulatory dynamics during the development of a paleopteran insect, the mayfly Cloeon dipterum
J. Pallarès-Albanell, L. Ortega-Flores, T. Senar-Serra, A. Ruiz, J.F. Abril, M. Rosselló , I. Almudi

Corresponding authors
bioRxiv, 2024.  OPEN ACCESS
Wnt/β-catenin signalling is required for pole-specific chromatin remodeling during planarian regeneration.
E. Pascual-Carreras, M. Marín-Barba, S. Castillo-Lara, P. Coronel-Córdoba, M.S. Magri, G.N. Wheeler, J.L. Gómez-Skarmeta, J.F. Abril, E. Saló , T. Adell

Corresponding authors
Nature Communications, 14(298) :1-16, 2023.  OPEN ACCESS
Oxidative Stress Is Associated with Overgrowth in Drosophila l(3)mbt Mutant Imaginal Discs
P. Climent-Cantó , C. Molnar , P. Santabárbara-Ruiz, C. Prieto, J.F. Abril, F. Serras , C. Gonzalez

Contributed equally Corresponding authors Joint senior authors
Cells, 11(16) :2542, 2022.  OPEN ACCESS
Gene Network of Susceptibility to Atypical Femoral Fractures Related to Bisphosphonate Treatment
N. Garcia-Giralt , N. Roca-Ayats, J.F. Abril, N. Martinez-Gil, D Ovejero, S. Castañeda, X. Nogues, D. Grinberg, S. Balcells, R. Rabionet
Genes, 13(1) :146 [1-11], 2022.  OPEN ACCESS
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.  OPEN ACCESS
Host-dependent editing of SARS-CoV-2 in COVID-19 patients
J. Gregori, M.F. Cortese, M. Piñana, C. Campos, D. Garcia-Cehic, C. Andrés, J.F. Abril, M.G. Codina, A. Rando, J. Esperalba, E. Sulleiro, J. Joseph, N Saubí, S. Colomer-Castell, M.C. Martin, C. Castillo, J.I. Esteban, T. Pumarola, F. Rodriguez-Frias, A. Antón, J. Quer
Emerging Microbes and Infections, 10(1) :1777-1789, 2021.  OPEN ACCESS
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

Joint senior authors
Clinical Microbiology and Infection, 27(10) :1542-1544, 2021.


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
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
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
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
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
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
Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project.
ENCODE Project Consortium; E. Birney , J.A. Stamatoyannopoulos , A. Dutta , R. Guigó , T.R. Gingeras , E.H. Margulies , Z. Weng , M. Snyder , E.T. Dermitzakis , R.E. Thurman, et al (including J.F. Abril, 81 of 313)

Corresponding authors
Nature, 447(7146) :799-816, 2007.  FREE FULL TEXT
R. Guigó , P. Flicek , J.F. Abril , A. Reymond, J. Lagarde, F. Denoeud, S. Antonarakis, M. Ashburner, V.B. Bajic, E. Birney, R. Castelo, E. Eyras, C. Ucla, T.R. Gingeras, J. Harrow, T. Hubbard, S.E. Lewis, M.G. Reese

Contributed equally, Corresponding authors
Genome Biology, 7(suppl.1) :s2.1-s2.31, 2006.  OPEN ACCESS


Editorial: ECCB/JBI 2005.
R. Guigó, F. Morán, A. Valencia, J.F. Abril
Bioinformatics, 21(suppl.2) :ii1–ii2, 2005.  FREE FULL TEXT
Comparison of splice sites in mammals and chicken.
J.F. Abril, R. Castelo, R. Guigó
Genome Research, 15(1) :111-119, 2005.  FREE FULL TEXT
Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution.
International Chicken Genome Sequencing Consortium; L.W. Hillier, W. Miller, E. Birney, W. Warren, R.C. Hardison, C.P. Ponting, P. Bork, D.W. Burt, M.A. Groenen, M.E. Delany, J.B. Dodgson, A.T. Chinwalla, P.F. Cliften, S.W. Clifton, et al (including J.F. Abril, 173 of 184).
Nature, 432(7018) :695–716, 2004.  FREE FULL TEXT
Genome sequence of the Brown Norway rat yields insights into mammalian evolution.
Rat Genome Sequencing Project Consortium; R.A. Gibbs , G.M. Weinstock, M.L. Metzker, D.M. Muzny, E.J. Sodergren, S. Scherer, G. Scott, D. Steffen, K.C. Worley, P.E. Burch, G. Okwuonu, S. Hines, L. Lewis, C. DeRamo, O. Delgado, et al (including J.F. Abril, 125 of 230).
Nature, 428(6982) :493–521, 2004.  FREE FULL TEXT
gff2aplot: plotting sequence comparisons.
J.F. Abril , R. Guigó, T. Wiehe
Bioinformatics, 19(18) :2477–2479, 2003.  FREE FULL TEXT
Comparative gene prediction in human and mouse.
G. Parra, P. Agarwal, J.F. Abril, T. Wiehe, J.W. Fickett, R. Guigó
Genome Research, 13(1) :108-117, 2003.  FREE FULL TEXT
Initial sequencing and comparative analysis of the mouse genome.
Mouse Genome Sequencing Consortium; R.H. Waterston , K. Lindblad-Toh , E. Birney, J. Rogers, J.F. Abril, P. Agarwal, R. Agarwala, R. Ainscough, M. Alexandersson, P. An, S.E. Antonarakis, J. Attwood, R. Baertsch, J. Bailey, K. Barlow, S. Beck, E. Berry, B. Birren, T. Bloom, P. Bork, M. Botcherby, N. Bray, M.R. Brent, et al

Corresponding authors (including E.S. Lander)
Nature, 420(6915) :520–562, 2002.  FREE FULL TEXT
The genome sequence of the malaria mosquito Anopheles gambiae.
R.A. Holt , G.M. Subramanian, A. Halpern, G.G. Sutton, R. Charlab, D.R. Nusskern, P. Wincker, A.G. Clark, J.M.C. Ribeiro, R. Wides, S.L. Salzberg, B. Loftus, M. Yandell, W.H. Majoros, D.B. Rusch, Z. Lai, C.L. Kraft, J.F. Abril, et al
Science, 298(5591) :129-149, 2002.  FREE FULL TEXT
Sequence and analysis of chromosome 2 of Dictyostelium discoideum.
G. Glöckner , L. Eichinger , K. Szafranski, J.A. Pachebat, A.T. Bankier, P.H. Dear, R. Lehmann, C. Baumgart, G. Parra, J.F. Abril, R. Guigó, K. Kumpf, B. Tunggal, E. Cox, M.A. Quail, M. Platzer, A. Rosenthal, A.A. Noegel , et al; Dictyostelium Genome Sequencing Consortium

Corresponding authors
Nature, 418(6893) :79-85, 2002.
Comparison of mouse and human genomes followed by experimental verification yields an estimated 1,019 additional genes.
R. Guigo , E.T. Dermitzakis , P. Agarwal, C.P. Ponting, G. Parra, A. Reymond, J.F. Abril, E. Keibler, R. Lyle, C. Ucla, S.E. Antonarakis, M.R. Brent

Contributed equally
Proc Natl Acad Sci U S A (PNAS), 100(3) :1140-1145, 2002.  FREE FULL TEXT
The sequence of the human genome.
J.C. Venter , M.D. Adams, E.W. Myers, P.W. Li, R.J. Mural, G.G. Sutton, H.O. Smith, M. Yandell, C.A. Evans, R.A. Holt, J.D. Gocayne, P. Amanatides, R.M. Ballew, D.H. Huson, J.R. Wortman, et al (including J.F. Abril, 191 of 274)
Science, 291(5507) :1304-1351, 2001.  FREE FULL TEXT

Until 2000 

Fusion of the human gene for the polyubiquitination coeffector UEV1 with Kua, a newly identified gene.
T.M. Thomson , J.J. Lozano , N. Loukili , R. Carrió, F. Serras, B. Cormand, M. Valeri, V.M. Díaz, J.F. Abril, M. Burset, J. Merino, A. Macaya, M. Corominas, R. Guigó

Contributed equally
Genome Research, 10(11) :1743-1756, 2000.  FREE FULL TEXT
An assessment of gene prediction accuracy in large DNA sequences.
R. Guigó , P. Agarwal, J.F. Abril, M. Burset, J.W. Fickett
Genome Research, 10(10) :1631-1642, 2000.  FREE FULL TEXT
gff2ps: visualizing genomic annotations.
J.F. Abril , R. Guigó
Bioinformatics, 16(8) :743–744, 2000.  FREE FULL TEXT
Genome annotation assessment in Drosophila melanogaster.
M.G. Reese , G. Hartzell, N.L. Harris, U. Ohler, J.F. Abril, S.E. Lewis
Genome Research, 10(4) :483-501, 2000.  FREE FULL TEXT
The genome sequence of Drosophila melanogaster.
M.D. Adams , S.E. Celniker, R.A. Holt, C.A. Evans, J.D. Gocayne, P.G. Amanatides, S.E. Scherer, P.W. Li, R.A. Hoskins, R.F. Galle, R.A. George, S.E. Lewis, S. Richards, M. Ashburner, S.N. Henderson, et al (including Abril J.F., 32 of 195).
Science, 287(5461) :2185-2195, 2000.  FREE FULL TEXT

Other Publications

Book Chapters

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

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
La regeneració i l’homeòstasi en les planàries, un model clàssic de biologia del desenvolupament.
‘’Regeneration and homeostasis in the planarians, a classic model of developmental biology’.’
F. Cebrià, T. Adell, J.F. Abril, E. Saló
Book chapter, pages 93-106.
In: Corominas M. and Valls M. (eds)
Organismes model en Biologia, vol 62, 2011.
Treballs de la Societat Catalana de Biologia. ISSN: 0212-3037
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

Sequence Similarity Based Gene Prediction.
R. Guigó, M. Burset, P. Agarwal, J.F. Abril, R.F. Smith, J.W. Fickett
Book chapter 8, pages 95-105.
In: Suhai S. (ed).
Genomics and Proteomics: Functional and Computational Aspects, 31 July 2000.
Kluwer Academic/Plenum Publishing Press, New York. ISBN: 0-306-46312-1

PhD Theses

Computational methods for the identification of emergent viruses analyzed by high-throughput sequencing in water and food.
Mètodes computacionals per a la identificació de virus emergents analitzats per seqüenciació en massa en aigua i aliments.
Natàlia Timoneda
PhD Thesis, Universitat de Barcelona, July 27th, 2017.
Codirected by J.F. Abril and R. Girones.
Characterizing Neoblasts as Stem Cell Model
Caracterización del Neoblasto como Modelo de Célula Madre
Gustavo Rodriguez-Esteban
PhD Thesis, Universitat de Barcelona, February 4th, 2016.
Codirected by J.F. Abril and E. Saló.
Comparative Analysis of Eukaryotic Gene Sequence Features
Josep F. Abril
PhD Thesis, Universitat Pompeu Fabra, May 17th, 2005.
Directed by R. Guigó

Page last modified on Monday 25 of October, 2021 19:35:50 CEST