Publications
P. Davila-Piñón; A. Nogueira-Rodríguez; A.I. Díez-Martín; L. Codesido; J. Herrero; M. Puga; L. Rivas; E. Sánchez; F. Fdez-Riverola; D. Glez-Peña; M. Reboiro-Jato; H. López-Fernández; J. Cubiella (2024) Optical diagnosis in still images of colorectal polyps: comparison between expert endoscopists and PolyDeep, a Computer-Aided Diagnosis system. Frontiers in Oncology. Accepted manuscript. ISSN: 2234-943X
D. Pérez-Rodríguez; M. Arancha Penedo; T. Rivera-Baltanás; T. Peña-Centeno; S. Burkhardt; A. Fischer; J. M. Prieto-González; J. M. Olivares Díez; H. López-Fernández; R. C. Agís-Balboa (2023)
MiRNA differences related to treatment resistant schizophrenia. International Journal of Molecular Sciences. Volume 24(3), 1891. ISSN: 1422-0067
A. Nogueira-Rodríguez; R. Domínguez-Carbajales; F. Campos-Tato; J. Herrero; M. Puga; D. Remedios; L. Rivas; E. Sánchez; Á. Iglesias; J. Cubiella; F. Fdez-Riverola; H. López-Fernández; M. Reboiro-Jato; D. Glez-Peña (2022)
Real-time polyp detection model using convolutional neural networks. Neural Computing and Applications. Volume 34, pp. 10375-10396. ISSN: (Online) 1433-3058 - (Print) 0941-0643
H. López-Fernández; P. Duque; N. Vázquez; F. Fdez-Riverola; M. Reboiro-Jato; C. P. Vieira; J. Vieira (2022)
SEDA: a Desktop Tool Suite for FASTA Files Processing. IEEE/ACM Transactions on Computational Biology and Bioinformatics. Volume 19(3), pp. 1850-1860. ISSN: 1545-5963
D. Glez-Peña; A. Lourenço; H. López-Fernández; M. Reboiro-Jato; F. Fdez-Riverola (2014)
Web scraping technologies in an API world. Briefings in Bioinformatics. Volume 15, Issue 5, pp. 788-797. ISSN: (Online) 1477-4054 - (Print) 1467-5463
Conferences
P. Davila-Piñón; C. Regueiro; A.I. Díez-Martín; J. Hernández-Camoiras; R. Domínguez-Carbajales; J. Herrero; M. Puga; L. Rivas; E. Sánchez; S. Zarraquiños-Martínez; N. Pin; P. Vega; S. Soto; D. Remedios-Espino; A. Nogueira-Rodríguez; A. González-García; F. Fdez-Riverola; H. López-Fernández; D. Glez-Peña; M. Reboiro-Jato; J. Cubiella (2023)
Clinical validation of polydeep a computer-aided diagnosis system (CADE/X). 31st United European Gastroenterology week. Copenhagen, Dinamarca. 14 - October
M.J. Jiménez-Santos; A. Nogueira-Rodríguez; E. Piñeiro-Yáñez; H. López-Fernández; S. García-Martín; P. Gómez-Plana; M. Reboiro-Jato; G. Gómez-López; D. Glez-Peña; F. Al-Shahrour (2023) PanDrugs2: An Integrated Multi-Omics Methodology for Prioritizing Evidence-Based Drugs in Cancer Treatment. VI CINBIO Annual Meeting 2023. Vigo, Spain. 20 - July
H. López-Fernández; M. Pinto; C.P. Vieira; P. Duque; M. Reboiro-Jato; J. Vieira (2023)
Auto-phylo: A Pipeline Maker for Phylogenetic Studies. 17th International Conference on Practical Applications of Computational Biology & Bioinformatics: PACBB 2023. Guimarães, Portugal. 12 - July
P. Ferreira; R. Soares; H. López-Fernández; C. P. Vieira; J. Vieira (2023) Inferring positively selected amino acid sites (PSS) in Coronavirus species using Auto-PSS-Genome. 3º Encontro Doutoramento em Ciências Biomédicas do ICBAS. Porto, Portugal. 8 - May
M. Reboiro-Jato; J. Vieira; S. Rocha; A.D. Sousa; H. López-Fernández; C.P. Vieira (2022) EvoPPI 2: an updated version of a powerful Protein-Protein Interaction database aggregator and analysis platform. V CINBIO Annual Meeting 2022. Vigo, Spain. 28 - July
D. Pérez-Rodríguez; H. López-Fernández; R.C. Agís-Balboa (2021) On the reproducibility of miRNA-Seq differential expression analyses in neuropsychiatric diseases. XIII Spanish Drug Discovery Network (SDDN) Meeting. Madrid, Spain. 29 - November
H. López-Fernández; P. Ferreira; M. Reboiro-Jato; C.P. Vieira; J. Vieira (2021)
The pegi3s Bioinformatics Docker Images Project. 15th International Conference on Practical Applications of Computational Biology & Bioinformatics: PACBB 2021. Salamanca, Spain. 6 - October
P. Ferreira; H. López-Fernández; C. P. Vieira; J. Vieira (2021) Positively selected sites (PSS) found in Coronaviridae species using Auto-PSS-Genome. II International Meeting of the Portuguese Society of Genetics. Vila Real, Portugal. 1 - July
D. Pérez-Rodríguez; H. López-Fernández; R.C. Agís-Balboa (2021) Re-analysis of miRNA-Seq differential expression analyses in neuropsychiatric diseases. IV CINBIO Annual Meeting 2021. Vigo, Spain. 01 - July
A. Nogueira-Rodríguez; R. Domínguez-Carbajales; F. Campos-Tato; J. Herrero; M. Puga; D. Remedios; L. Rivas; E. Sánchez; Á. Iglesias; L. Codesido; J. Cubiella; F. Fdez-Riverola; H. López-Fernández; M. Reboiro-Jato; D. Glez-Peña (2021) Development of a Computer-Aided Diagnosis system based on deep learning for colorectal polyp detection and classification. IV CINBIO Annual Meeting 2021. Vigo, Spain. 01 - July
S. Rocha; J. Vieira; N. Vázquez; H. López-Fernández; F. Fdez-Riverola; M. Reboiro-Jato; A. D. Sousa; C. P. Vieira (2019) Binding differences of wild-type and expanded ATXN1 are mainly explained by the N-terminal region. 8th i3S Annual Meeting. Póvoa de Varzim, Portugal. 28 - November
P. Duque; H. López-Fernández; P. Ferreira; N. Vázquez; F. Fdez-Riverola; M. Reboiro-Jato; C. P. Vieira; J. Vieira (2019) Inferring Positive Selection in Large Viral Datasets. 8th i3S Annual Meeting. Póvoa de Varzim, Portugal. 28 - November
P. Ferreira; H. López-Fernández; P. Duque; C.P. Vieira; F. Fdez-Riverola; M. Reboiro-Jato; J. Vieira (2019) Bioinformatics Docker Images. 8th i3S Annual Meeting. Póvoa de Varzim, Portugal. 28 - November
H. López-Fernández; F. Fdez-Riverola; D. Glez-Peña; M. Reboiro-Jato (2019) Free and Open-Source Software for Mass Spectrometry Data Analysis. 6th International Congress on Analytical Proteomics: ICAP 2019. Costa de Caparica, Portugal. 8 - July
O. Estévez; L. Anibarro; E. Garet; A. Pallares; L. Barcia; A. Pena; C. Maueia; T. Mussá; F. Fdez-Riverola; D. Glez-Peña; M. Reboiro-Jato; H. López-Fernández; N. Fonseca; R. Reljic; A. González (2019) Differential gene expression analysis for the identification of different TB infection profiles. III CINBIO Annual Meeting 2019. Vigo, Spain. 1 - July
P. Ferreira; H. López-Fernández; P. Duque; C.P. Vieira; F. Fdez-Riverola; M. Reboiro-Jato; J. Vieira (2019) Bioinformatics Docker Images. III CINBIO Annual Meeting 2019. Vigo, Spain. 1 - July
A. Nogueira-Rodríguez; H. López-Fernández; Á. Iglesias; J.M. Herrero; L. Rivas; M.P. Giménez de Azcarate; E. Sánchez; D. Remedios; F. Fdez-Riverola; J. Cubiella; M. Reboiro-Jato; D. Glez-Peña (2019) Real Time Computer-Aided Diagnosis in Colorectal Cancer using Deep Learning Techniques. III CINBIO Annual Meeting 2019. Vigo, Spain. 1 - July
H. López-Fernández; P. Duque; N. Vázquez; F. Fdez-Riverola; M. Reboiro-Jato; C.P. Vieira; J. Vieira (2019)
Inferring Positive Selection in Large Viral Datasets. 13th International Conference on Practical Applications of Computational Biology & Bioinformatics: PACBB 2019. Ávila, Spain. 26 - June
C.P. Vieira; S. Rocha; N. Vázquez; H. López-Fernández; A. Torres; R. Camacho; F. Fdez-Riverola; M. Reboiro-Jato; J. Vieira (2019) EvoPPI 1.0: a Web Platform for Within and Between Species Multiple Interactome Comparisons and Application to Nine polyQ Proteins Determining Neurodegenerative Diseases. Bioinformatics Open Days: BOD 2019. Braga, Portugal. 21 - February
P. Ferreira; H. López-Fernández; P. Duque; Cristina P. Vieira; F. Fdez-Riverola; Miguel Reboiro-Jato; J. Vieira (2019)
Bioinformatics Docker Images. Bioinformatics Open Days: BOD 2019. Braga, Portugal. 21 - February
S. Henriques; P. Duque; H. López-Fernández; N. Vázquez; F. Fdez-Riverola; M. Reboiro-Jato; C.P. Vieira; J. Vieira (2018) L-ascorbate synthesis in non-Bilateria and Protostomian species. 7th i3S Annual Meeting. Póvoa de Varzim, Portugal. 29 - November
S. Rocha; N. Vázquez; H. López-Fernández; A. Torres; R. Camacho; F. Fdez-Riverola; M. Reboiro-Jato; J. Vieira; C.P. Vieira (2017) Comparisons of to Nine polyQ Proteins Determining Neurodegenerative Diseases Interactomes, using EvoPPI 1.0- a Web Platform for Within and Between Species comparisons. 7th i3S Annual Meeting. Póvoa de Varzim, Portugal. 29 - November
K. Troulé; M. Reboiro-Jato; H. Tejero; H. López-Fernández; J. Perales-Patón; D. Glez-Peña; F. Al-Shahrour; G. Gómez-López (2018) The druggable immune system: drug repositioning in immune transcriptome. XIV Symposium on Bioinformatics, JBI 2018. Granada, Spain. 14 - November
H. López-Fernández; M. Reboiro-Jato; N. Vázquez; P. Duque; F. Fdez-Riverola; C.P. Vieira; J. Vieira (2018) A toolbox for facilitating the manipulation of FASTA sequences. II CINBIO Annual Meeting 2018. Vigo, Spain. 25 - June
H. López-Fernández; M. Reboiro-Jato; E. Araújo; H. M. Santos; D. Glez-Peña; F. Fdez-Riverola; J.L. Capelo-Martínez (2018) Facilitating MALDI-TOF mass spectrometry data analysis with S2P and Mass-Up. XII EuPA (European Proteomics Association) Congress. Santiago de Compostela, Spain. 18 - June
J. Vieira; S. Rocha; N. Vázquez; H. López-Fernández; M. Reboiro-Jato; F. Fdez-Riverola; C. P. Vieira (2018) Bioinformatic tools to study Solanaceae S-pollen gametophytic self-incompatibility evolution: BDBM, ADOPS and B+ database. Portuguese Society of Genetics Annual Meeting 2018. Porto, Portugal. 14 - June
S. F. Henriques; P. Duque; H. López-Fernández; C. P. Vieira; J. Vieira (2018) Vitamin C biosynthesis in D. melanogaster: alternatives to GULO and influence of microbiome. Portuguese Society of Genetics Annual Meeting 2018. Porto, Portugal. 14 - June
S. Rocha; J. Vieira; N. Vázquez; H. López-Fernández; S. Macedo-Ribeiro; A. Torres; R. Camacho; F. Fdez-Riverola; M. Reboiro-Jato; C. P. Vieira (2018) New in-silico approach to infer binding surfaces in wild-type and mutant Ataxin-1. Portuguese Society of Genetics Annual Meeting 2018. Porto, Portugal. 14 - June
H. López-Fernández; M. Reboiro-Jato; D. Glez-Peña; R. Laza; R. Pavón; F. Fdez-Riverola (2018) Lessons learned developing GUI in bioinformatics software: from end-user applications to resources for programmers. Bioinformatics Open Days: BOD 2018. Braga, Portugal. 15 - March
C.P. Vieira; N. Vázquez; M. Reboiro-Jato; H. López-Fernández; F. Fdez-Riverola; J. Vieira (2018) Inferring positive selection: ADOPS and B+ database. Bioinformatics Open Days: BOD 2018. Braga, Portugal. 15 - March
I. M. Costa; S. Rocha; H. López-Fernández; I. Guterres de Carvalho; S. Macedo-Ribeiro; R. Camacho; J. Vieira; C.P. Vieira (2018) Comparative evolutionary analyses of the protein-protein interactions of the wild-type polyQ proteins ataxin-2 and androgen receptor, associated with neurodegenerative disorders in Homo sapiens. Encontro de Investigação Jovem da Universidade do Porto: IJUP 2018. Porto, Portugal. 7 - February.
H. López-Fernández; N. Vázquez; C.P. Vieira; B.S.R. Amorim; A. Torres; F. Fdez-Riverola; José L. R. Sousa; M. Reboiro-Jato; J. Vieira (2017) The B+ repository: a public database of adaptive amino acid changes data. 6th i3S Annual Meeting. Póvoa de Varzim, Portugal. 9 - November
S. Rocha; H. López-Fernández; I. Guterres de Carvalho; I. Costa; S. Macedo-Ribeiro; R. Camacho; J. Vieira; C. P. Vieira (2017) Evolution of the polyglutamine wild-type protein networks, associated to human neurodegenerative diseases. 6th i3S Annual Meeting. Póvoa de Varzim, Portugal. 9 - November
S. F. Henriques; H. López-Fernández; P. Duque; C. P. Vieira; J. Vieira (2017) Evolution of the Vitamin C biosynthetic pathway: role of D. melanogaster Regucalcin and GULO genes in Vit C synthesis and cold acclimatization. 6th i3S Annual Meeting. Póvoa de Varzim, Portugal. 9 - November
F. Teixeira-Costa; J. E. Araújo; H. López-Fernández; S. Jorge; A. Ramos; H. M. Santos; J.L. Capelo-Martínez (2017) Proteomic analysis of the peritoneal dialysis effluent. 3rd International Caparica Conference on Urine OMICS. Caparica, Portugal. 18 - September.
J. Romário de Jesus; H.M. Santos; H. López-Fernández; M.A.Z. Arruda; J.L. Capelo-Martínez (2017) Ultrasonic-Based Membrane Aided Sample Preparation of Urine Proteomes. 3rd International Caparica Conference on Urine OMICS. Caparica, Portugal. 18 - September.
S. Jorge; E. Araújo; H. López-Fernández; H. M. Santos; C. Lodeiro; A. Chiechi; J. Y. Ljubimova; J. L Capelo (2017) The size of the particulate matter addresses the pathways to the brain. Sao Paulo School of Advanced Science on Mass Spectrometry-based Proteomics (SPSAS-MS). Sao Paulo, Brazil. 28 - August.
J. E. Araújo; H. López-Fernández; S. Jorge; F. Teixeira-Costa; A. Ramos; A. Rodrigues; G. Mayer; H. M. Santos; J. L Capelo (2017) Unraveling peritoneal dialysis effluent proteome evolution. Sao Paulo School of Advanced Science on Mass Spectrometry-based Proteomics (SPSAS-MS). Sao Paulo, Brazil. 28 - August.
H. López-Fernández; J.E. Araújo; H.M. Santos; A. Fernández-Lodeiro; C. Fernández-Lodeiro; J. Djafari; J. Coelho; G. Pinto; N. Morais; G. Marcelo; J. Machado; S. Jorge; J. Prates; E. Oliveira; J. Fernández-Lodeiro; C. Lodeiro-Espiño; J. L. Capelo-Martínez (2017)
Using S2P to process emPAI quantitation results obtained from MS/MS Mascot searches. V International Conference on Analytical Proteomics. Caparica, Portugal. 3 - July.
S. Jorge; J. E. Araújo; H. López-Fernández; H. M. Santos; C. Lodeiro; Antonella Chiechi; J.Y. Ljubimova; J. L. Capelo (2017) Tracking down the brain-related pathways triggered by particulate matter. V International Conference on Analytical Proteomics. Caparica, Portugal. 3 - July.
H. M. Santos; R. Magriço; G. Martins; J. Prates; S. Jorge; E. Araújo; A. Fernández-Lodeiro; J. Djafari; E. Oliveira; J. Fernández-Lodeiro; H. López-Fernández; A. Ramos; C. Lodeiro; J. L. Capelo (2017) Time-resolved proteome profiling of urine and serum of a cysteamine-treated cystinosis patient. V International Conference on Analytical Proteomics. Caparica, Portugal. 3 - July.
J. Prates; G. Martins; S. Jorge; E. Araújo; A. Fernández-Lodeiro; J. Djafari; E. Oliveira; J. Fernández-Lodeiro; H. López-Fernández; C. Lodeiro; J. L. Capelo; H. M. Santos (2017) Diagnostics and prognostics utilizing permanent digital maps of non-invasive biopsies of multiple myeloma and lymphoma. V International Conference on Analytical Proteomics. Caparica, Portugal. 3 - July.
N. Vázquez; C.P. Vieira; B.S.R. Amorim; A. Torres; H. López-Fernández; F. Fdez-Riverola; José L. R. Sousa; M. Reboiro-Jato; J. Vieira (2017)
Automated collection and sharing of adaptive amino acid changes data. 11th International Conference on Practical Applications of Computational Biology & Bioinformatics: PACBB 2017. Porto, Portugal. 21 - June
H. López-Fernández; J.L. Capelo-Martínez; F. Fdez-Riverola; D. Glez-Peña; M. Reboiro-Jato (2014) Understanding data from MALDI-TOF mass spectrometry experiments with Mass-Up. II Jornadas de Investigación Biomédica. Ourense, España. 29 - May
R. Carreira; J.D. Nunes-Miranda; H.M. Santos; C. Lodeiro; F. Fdez-Riverola; H. López-Fernández; M. Reboiro-Jato; D. Glez-Peña; L. Barbeito; J.L. Capelo (2012) Fast sample treatment for bacterial identification. Jornadas de Investigación Biomédica. Ourense, España. 14 - March
H. López-Fernández; F. Aparicio; D. Glez-Peña; M.J. Maña López; M. Buenaga; F. Fdez-Riverola; M. Reboiro-Jato (2012) BioAnote: sistema de anotación de textos médicos mediante ontologías orientado a la formación en medicina. Jornadas de Investigación Biomédica. Ourense, España. 14 - March
M.P. de la Cadena; F. Fdez-Riverola; H. López-Fernández; M. Reboiro-Jato; D. Glez-Peña; J.L. Capelo (2012) Gold-Nanoparticle-Based human plasma profiling helps medical diagnostics. Jornadas de Investigación Biomédica. Ourense, España. 14 - March
H. López-Fernández; F. Aparicio; D. Glez-Peña; M. Buenaga; F. Fdez-Riverola (2011) Herramienta biomédica de anotación y acceso inteligente a información . III Jornada Gallega de Bioinformática. Vigo, España. 16 - September
Books
M. Reboiro-Jato; D. Glez-Peña; H. López-Fernández.
Statistics, Data Mining and Modeling. Chapter 5. Pags. 120-200. Processing Metabolomics and Proteomics Data with Open Software, A practical guide. Royal Society of Chemistry. ISBN: 978-1-78801-721-3, PDF eISBN: 978-1-78801-988-0, 2020, England
M. Reboiro-Jato; H. López-Fernández; R. Laza; R. Pavón; F. Rojas Rodríguez; A. Vieira Vázquez; T. Rivera Baltanás; C. Spuch; A. Varela Pomar; F. Otero Lamas; A. Piñón Blanco. MultiTasking Cubes - Unha ferramenta para a rehabilitación cognitiva. Pags. 63-77. Proxectos INOU 2017: Investigación aplicada na provincia de Ourense. Vicerrectoría del Campus de Ourense, Universidad de Vigo. ISBN: 978-84-8158-800-2, 2018, España
H. López-Fernández; G. de S. Pessôa; M. A. Z. Arruda; J. L. Capelo-Martínez; A. Seara Vieira; M. Pérez-Pérez; G. Pérez-Rodríguez; F. Fdez-Riverola; D. Glez-Peña; M. Reboiro-Jato. LA-iMageS: unha ferramenta para a análise e a xeración de bioimaxes mediante ablación láser con fonte de acoplamento indutivo. Pags. 111-128. Proxectos INOU 2016: Investigación aplicada na provincia de Ourense. Vicerectoría del Campus de Ourense, Universidad de Vigo. ISBN: 978-84-8158-760-9, 2017, España
M.R. Pavón; H. López-Fernández; A. Seara; R. Laza. Sistema de clasificación automática de contidos web para o sector do termalismo ourensán. Pags. 107-128. Proxectos INOU 2015: Investigación aplicada na provincia de Ourense. Vicerrectoría del Campus de Ourense, Universidad de Vigo. ISBN: 978-84-8158-717-3, 2016, España
M. Reboiro-Jato; E. Lorenzo Iglesias; J.R. Méndez Reboredo; R. Pavón Rial; H. López-Fernández; F. Fdez-Riverola; D. Glez-Peña, J.L. Capelo; H.M. Santos. Mass-Up: aplicación de software libre para a análise de datos de espectrometría de masas MALDI-TOF. Pags. 101-123. Proxectos INOU 2014: Investigación aplicada na provincia de Ourense. Vicerrectoría del Campus de Ourense, Universidade de Vigo. ISBN: 978-84-8158-698-5, 2015, España
M. Reboiro-Jato; H. López-Fernández. Entorno Tecnológico (Alternativas). Pags. 119-151. Comercio y Negocio Electrónico. Universidad de Salamanca. ISBN: 978-84-692-7976-2, 2012, España
M. Reboiro-Jato; H. López-Fernández. Entorno Tecnológico (Servidores). Pags. 153-158. Comercio y Negocio Electrónico. Universidad de Salamanca. ISBN: 978-84-692-7976-2, 2012, España
M. Reboiro-Jato; H. López-Fernández. Entorno Tecnológico (Lenguajes). Pags. 1-45. Comercio y Negocio Electrónico. Universidad de Salamanca. ISBN: 978-84-692-7978-6, 2012, España
M. Reboiro-Jato; H. López-Fernández. Entorno Tecnológico (Alternativas). Pags. 255-286. Comercio y Negocio Electrónico. Universidad de Salamanca. ISBN: 978-84-692-7976-2, 2011, España
M. Reboiro-Jato; H. López-Fernández. Entorno Tecnológico (Servidores). Pags. 287-292. Comercio y Negocio Electrónico. Universidad de Salamanca. ISBN: 978-84-692-7976-2, 2011, España
M. Reboiro-Jato; H. López-Fernández. Entorno Tecnológico (Lenguajes). Pags. 1-44. Comercio y Negocio Electrónico. Universidad de Salamanca. ISBN: 978-84-692-7978-6, 2011, España