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Computational
Genomics Lab Comp Gen Lab C.G.L.
Published Papers


Word Cloud of Published Abstracts

Publications by Year

Since 2021 
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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
Development, 151(20) :dev203017, 2024.  OPEN ACCESS
PubMed Abstract Full Text PDF Suppl.Mat SRA CODE
CAPTVRED: An automated pipeline for viral tracking and discovery from capture-based metagenomics samples.
M. Tarradas-Alemany, S. Martı́nez-Puchol, C. Mejı́as-Molina, M. Itarte, M. Rusiñol, S. Bofill-Mas, J.F. Abril
Bioinformatics Advances, 4(1) :vbae150, 2024.  OPEN ACCESS
Abstract Full Text PDF GitHub DATA
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
Abstract Full Text PDF RAW_DATA
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
Abstract Full Text PDF
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
Abstract Full Text PDF SRA GitHub CSM JBrowse
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
Abstract Full Text PDF Suppl.Mat
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
PubMed Abstract Full Text PDF Suppl.Mat
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
PubMed Abstract Full Text PDF
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
PubMed Abstract Full Text PDF
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.
PubMed Full Text PDF


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.S. Magri, G.N. Wheeler, J.F. Abril, J.L. Gomez-Skarmeta, E. Saló , T. Adell

Joint senior authors
bioRxiv, 2020.  OPEN ACCESS
Abstract PDF PlanEXP
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
PubMed Abstract Full Text PDF
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
PubMed Abstract Full Text PDF
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.
PubMed Abstract PDF
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.
PubMed Full Text PDF
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.
PubMed Abstract PlanExp
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
PubMed Full Text PDF Suppl.Material RPGeNet
PPaxe: easy extraction of protein occurrence and interactions from the scientific literature
S. Castillo-Lara, J.F. Abril
Bioinformatics, 35(14) :2523–2524, 2019.
PubMed Abstract PPaxe
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
PubMed Full Text PDF
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

Abstract
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.
PDF
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.
PubMed Abstract
PlanNET: homology-based predicted interactome for multiple planarian transcriptomes
S. Castillo-Lara, J.F. Abril
Bioinformatics, 34(6) :1016—1023, 2018.  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

Contributed equally
The Science of the Total Environment, 618:870—880, 2018.
PubMed Abstract
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.
PubMed Abstract Full Text PDF SiNoPsis
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
PubMed Full Text PDF
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.
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

Contributed equally
PLoS ONE, 12(1) :e0170199, 2017.  OPEN ACCESS
PubMed Full Text PDF MetaWater



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.
PubMed Abstract DATA GBrowse
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.
PubMed Abstract PDF
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
PubMed Full Text PDF RPGeNet
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
PubMed Full Text PDF DATA
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
PubMed Abstract Full Text PDF
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
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
PubMed 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.  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

Contributed equally
Invest Ophthalmol Vis Sci (IOVS), 52(8) :5202—14, 2011.  FREE FULL TEXT
PubMed Full Text PDF Suppl Material
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
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

Contributed equally
BMC Genomics, 11:731, 2010.  OPEN ACCESS
PubMed Abstract Full Text PDF DATA



Pre-Computational Genomics Lab Papers
Image

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
PubMed Abstract Full Text PDF
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

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

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

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