Career Profile

I obtained a Computer Science degree in 2011 and a PhD in 2016 working in the field of Artificial Intelligence applied to the analysis of mass spectrometry data at University of Vigo, under Dr. Daniel Glez-Peña and Dr. Miguel Reboiro-Jato supervision. The combination of Artificial Intelligence with Life sciences (especially Bioinformatics) defines my main research line since then. I have being member of the SING research group (Next Generation Computer Systems Group) since 2012 and I am currently working as Junior Researcher (starting May 2021) at Phenotypic Evolution research group at Instituto de Investigação e Inovação (Porto, Portugal). I am also specialized in the development of scientific software applications (mainly in Java) and data analysis (R, Python), with special interest on the creation of automated analysis pipelines.

Experiences

Junior Researcher

2021
i3S - Instituto de Investigação e Inovação da Universidade do Porto (Porto, Portugal)

Postdoctoral Researcher

2018 - 2021
University of Vigo (Ourense, Spain)

Postdoctoral Researcher

2017 - 2018
Instituto de Biologia Molecular e Celular / i3S - Instituto de Investigação e Inovação da Universidade do Porto (Porto, Portugal)

Postdoctoral Researcher

2016 - 2017
Faculdade de Ciências e Tecnologia / Universidade Nova de Lisboa (Caparica, Portugal)

Predoctoral Researcher

2012 - 2016
University of Vigo (Ourense, Spain)

Researcher

2011 - 2012
University of Vigo (Ourense, Spain)

Training Courses

⬇ AI for Medicine Specialization ⬇

AI for Medical Prognosis (2020). deeplearning.ai through Coursera.
AI for Medical Diagnosis (2020). deeplearning.ai through Coursera.

⬇ Deep Learning Specialization ⬇

Sequence Models (2020). deeplearning.ai through Coursera.
Convolutional Neural Networks (2020). deeplearning.ai through Coursera.
Structuring Machine Learning Projects (2020). deeplearning.ai through Coursera.
Improving Deep Neural Networks: Hyperparameter tuning, Regularization and Optimization (2020). deeplearning.ai through Coursera.
Neural Networks and Deep Learning (2019). deeplearning.ai through Coursera.
Understanding Clinical Research: Behind the Statistics (2016). University of Cape Town through Coursera.
Getting and Cleaning Data (2015). Johns Hopkins University through Coursera.
Exploratory Data Analysis (2015). Johns Hopkins University through Coursera.
Machine Learning (2014). Stanford University through Coursera.
Computing for Data Analysis (2012). Johns Hopkins University through Coursera.

Projects

DREIMT (2018 - 2020): a tool for immune modulation drug prioritization.
compi (2018 - Present): an application framework for portable computational pipelines.
Bioinformatics Docker Images Project (2018 - Present): a repository of curated, well-documented Docker imagaes for bioinformatics software and pipelines.
EvoPPI (2017 - Present): an open source web application for easily comparing publicly available data from the main Protein-Protein Interaction (PPI) databases for distinct species.
SEDA (2017 - Present): an open source application for processing FASTA files containing DNA and protein sequences.
DEWE (2016 - 2019): an open source application for performing differential expression analysis in RNA-Seq data.
S2P (2016 - 2018): an open source application for fast and easy processing of 2D-gel and MALDI-based mass spectrometry protein data.
LA-iMageS (2015 - 2016): an open source application to generate 2D/3D images for the elements present in a set of LA-ICP-MS (Laser Ablation Inductively Coupled Plasma Mass Spectrometry) spectra.
GC4S (2014 - Present): a Java library of GUI components for Swing.
RUbioSeq+ (2014 - 2016): a software suite to perform NGS data analysis in a automatic, paralellized and reliable way which is crucial to eliminate manual steps and to speed up result generation.
Mass-Up (2013 - Present): an open-source mass spectrometry software for proteomics designed to support the preprocessing and analysis of MALDI-TOF mass spectrometry data.
BioAnnote (2011 - 2012): an annotator Desktop application able to annotate biomedical texts by using different high-quality online resources, such as Medlineplus and Freebase.
PileLine GUI (2010 - 2011): a Java Swing front-end for the PileLine toolkit along with a genome browser.

Compi pipelines

Auto-PSS-Genome (Automatic Positively Selected Sites Genome) (2020): Automatic detection of positively selected sites in complete genomes.
IPSSA (Integrated Positively Selected Sites Analyses) (2020): Automatic detection of positively selected amino acid sites.
GenomeFastScreen (2020): Fast identification of genes with positively selected amino acid sites for detailed analyses in complete genomes.
FastScreen (2019 - 2020): Fast identification of genes with positively selected amino acid sites for detailed analyses.

Publications

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 (2021) Real-time polyp detection model using convolutional neural networks. Neural Computing and Applications. Accepted for publication. ISSN: (Online) 1433-3058 - (Print) 0941-0643
D. Pérez-Rodríguez; H. López-Fernández; R.C. Agís-Balboa (2021) Application of miRNA-seq in neuropsychiatry: a methodological perspective. Computers in Biology and Medicine. Volume 135, Article ID 104603. ISSN: 0010-4825
H. López-Fernández; O. Graña-Castro; A. Nogueira-Rodríguez; M. Reboiro-Jato; D. Glez-Peña (2021) Compi: a Framework for Portable and Reproducible Pipelines. PeerJ Computer Science. Volume 7: e593. ISSN: 2376-5992
S. Vimal; D. Pelusi; J.H. Park; F. Fdez-Riverola; M. Rocha; H. López-Fernández, guest editors (2021) Special Issue: Enabling Technologies for Genomic and sequence analysis Using Artificial Intelligence in Smart medical applications. Interdisciplinary Sciences: Computational Life Sciences. Volume 13/2. ISSN: (Online) 1867-1462 - (Print) 1913-2751
H. López-Fernández; C. P. Vieira; P. Ferreira; P. Gouveia; F. Fdez-Riverola; M. Reboiro-Jato; J. Vieira (2021) On the identification of clinically relevant bacterial amino acid changes at the whole genome level using Auto-PSS-Genome. Interdisciplinary Sciences: Computational Life Sciences. Volume 13/2, pp. 334–343. ISSN: (Online) 1867-1462 - (Print) 1913-2751
A. Nogueira-Rodríguez; R. Domínguez-Carbajales; H. López-Fernández; Á. Iglesias; J. Cubiella; F. Fdez-Riverola; M. Reboiro-Jato; D. Glez-Peña (2021) Deep Neural Networks approaches for detecting and classifying colorectal polyps. Neurocomputing. Volume 423, pp. 721-734. ISSN: 0925-2312
H. López-Fernández; P. Duque; N. Vázquez; F. Fdez-Riverola; M. Reboiro-Jato; C. P. Vieira; J. Vieira (2021) SEDA: a Desktop Tool Suite for FASTA Files Processing. IEEE/ACM Transactions on Computational Biology and Bioinformatics. Accepted for publication. ISSN: 1545-5963
K. Troulé; H. López-Fernández; S. García-Martín; M. Reboiro-Jato; C. Carretero-Puche; J. Martorell-Marugán; G. Martín-Serrano; P. Carmona-Sáez; D. González-Peña; F. Al-Shahrour; G. Gómez-López (2021) DREIMT: a drug repositioning database and prioritization tool for immunomodulation. Bioinformatics. Volume 37, Issue 4, pp. 578-579. ISSN: (Online) 1460-2059 - (Print) 1367-480
O. Estévez; L. Anibarro; E. Garet; Á. Pallares; L. Barcia; L. Calviño; C. Maueia; T. Mussá; F. Fdez-Riverola; D. Glez-Peña; M. Reboiro-Jato; H. López-Fernández; N. Fonseca; R. Reljic; Á. González-Fernández (2020) An RNA-seq based machine learning approach identifies latent tuberculosis patients with an active tuberculosis profile. Frontiers in Immunology. Volume 11, article ID 1470. ISSN: 1664-3224
O. Graña-Castro; H. López-Fernández; A. Nogueira-Rodríguez; F. Fdez-Riverola; F. Al-Shahrour; D. Glez-Peña (2020) Metatax: Metataxonomics with a Compi-based pipeline for Precision Medicine. Interdisciplinary Sciences: Computational Life Sciences. Volume 12/1, pp. 252–257. ISSN: (Online) 1867-1462 - (Print) 1913-2751
S. Jorge; K. Pereira; H. López-Fernández; W. LaFramboise; R. Dhir; J. Fernández-Lodeiro; C. Lodeiro; H. M. Santos; J. L. Capelo-Martínez (2020) Ultrasonic-assisted extraction and digestion of proteins from solid biopsies followed by peptide sequential extraction hyphenated to MALDI-based profiling holds the promise of distinguishing renal oncocytoma from chromophobe renal cell carcinoma. Talanta. Volume 206, Article 120180. ISSN: 0039-9140
S. Rocha; J. Vieira; N. Vázquez; H. López-Fernández; F. Fdez-Riverola; M. Reboiro-Jato; A. D. Sousa; C. P. Vieira (2019) ATXN1 N-terminal region explains the binding differences of wild-type and expanded forms. BMC Medical Genomics. Volume 12: 145. ISSN: 1755-8794
J. Vieira; S. Rocha; N. Vázquez; H. López-Fernández; F. Fdez-Riverola; M. Reboiro-Jato; C.P. Vieira (2019) Predicting specificities under the non-self gametophytic self-incompatibility recognition model. Frontiers in Plant Science. Volume 10, Article 879. ISSN: 1664-462X
S. Henriques; P. Duque; H. López-Fernández; N. Vázquez; F. Fdez-Riverola; M. Reboiro-Jato; C.P. Vieira; J. Vieira (2019) Multiple independent L-gulonolactone oxidase (GULO) gene losses and Vitamin C synthesis reacquisition events in non-Deuterostomian animal species. BMC Evolutionary Biology. Volume 19: 126. ISSN: 1471-2148
H. López-Fernández; A. Blanco-Míguez; F. Fdez-Riverola; B. Sánchez; A. Lourenço (2019) DEWE: a novel tool for executing differential expression RNA-Seq workflows in biomedical research. Computers in Biology and Medicine. Volume 107, pp. 197-205. ISSN: 0010-4825
N. Vázquez; H. López-Fernández; C.P. Vieira; F. Fdez-Riverola; J. Vieira; M. Reboiro-Jato (2019) BDBM 1.0: A Desktop Application for Efficient Retrieval and Processing of High Quality Sequence Data and Application to the Identification of the Putative Coffea S-locus. Interdisciplinary Sciences: Computational Life Sciences. Volume 11(1), pp. 57-67. ISSN: 1913-2751
N. Vázquez; S. Rocha; H. López-Fernández; A. Torres; R. Camacho; F. Fdez-Riverola; J. Vieira; C.P. Vieira; M. Reboiro-Jato (2019) EvoPPI 1.0: a Web Platform for Within and Between Species Multiple Interactome Comparisons and Application to Nine polyQ Proteins Determining Neurodegenerative Diseases. Interdisciplinary Sciences: Computational Life Sciences. Volume 11(1), pp. 45-56. ISSN: 1913-2751
H. López-Fernández; P. Duque; S. Henriques; N. Vázquez; F. Fdez-Riverola; C.P. Vieira; M. Reboiro-Jato; J. Vieira (2019) Bioinformatics Protocols for Quickly Obtaining Large-Scale Data Sets for Phylogenetic Inferences. Interdisciplinary Sciences: Computational Life Sciences. Volume 11(1), pp. 1-9. ISSN: 1913-2751
H. López-Fernández; M. Reboiro-Jato; D. Glez-Peña; R. Laza; R. Pavón; F. Fdez-Riverola (2018) GC4S: a bioinformatics-oriented Java software library of reusable graphical user interface components. PLOS ONE. Volume 13(9): e0204474. ISSN: 1932-6203
N. Vázquez; C. P. Vieira; B. S. R. Amorim; A. Torres; H. López-Fernández; F. Fdez-Riverola; J. L. R. Sousa; M. Reboiro-Jato; J. Vieira (2018) Large scale analyses and visualization of adaptive amino acid changes projects. Interdisciplinary Sciences: Computational Life Sciences. Volume 10, pp. 24-32. ISSN: (Online) 1867-1462 - (Print) 1913-2751
O. Graña; H. López-Fernández; F. Fdez-Riverola; D. Pisano; D. Glez-Peña (2018) bicycle: a bioinformatics pipeline to analyze bisulfite sequencing data. Bioinformatics. Volume 34, Issue 8, pp. 1414-1415. ISSN: (Online) 1460-2059 - (Print) 1367-4803
J. Prates; G. Martins; H. López-Fernández; C. Lodeiro; J. L. Capelo; H. M. Santos (2018) Modulating the protein content of complex proteomes using acetonitrile. Talanta. Volume 182, pp. 333-339. ISSN: 0039-9140
F. Aparicio; M.L. Morales-Botello; M. Rubio; A. Hernando; R. Muñoz; H. López-Fernández; D. Glez-Peña; F. Fdez-Riverola; M. de la Villa; M. Maña; D. Gachet; M. de Buenaga (2018) Perceptions of the use of intelligent information access systems in university level active learning activities among teachers of biomedical subjects. International Journal of Medical Informatics. Volume 112, pp. 21-33. ISSN: 1386-5056
J.E. Araújo; H. López-Fernández; P.M. Baltazar; L. Campos-Pinheiro; F. Calais-Da-Silva; M. Carrascal; P. Videira; H.M. Santos; J.L. Capelo-Martínez (2018) Dithiothreitol-based protein equalization technology to unravel biomarkers for bladder cancer. Talanta. Volume 180, pp. 36-46. ISSN: 0039-9140
H. López-Fernández; J.E. Araújo; S. Jorge; D. Glez-Peña; M. Reboiro-Jato; F. Fdez-Riverola; H.M. Santos; J.L. Capelo-Martínez (2018) S2P: A Software Tool to Quickly Carry Out Reproducible Biomedical Research Projects Involving 2D-Gel and MALDI-TOF MS Protein Data. Computer Methods and Programs in Biomedicine. Volume 155, pp. 1-9. ISSN: 0169-2607
J. Romário de Jesus; H.M. Santos; H. López-Fernández; C. Lodeiro; M.A.Z. Arruda; J.L. Capelo-Martínez (2018) Ultrasonic-Based Membrane Aided Sample Preparation of Urine Proteomes. Talanta. Volume 178, pp. 864-869. ISSN: 0039-9140
M. Rubio-Camarillo; H. López-Fernández; G. Gómez-López; Á. Carro; J.M. Fernández; C. Fustero-Torre; F. Fdez-Riverola; D. Glez-Peña (2017) RUbioSeq+: a multiplatform application that executes parallelized pipelines to analyse next-generation sequencing data. Computer Methods and Programs in Biomedicine. Volume 138, pp. 73-81. ISSN: 0169-2607
H. López-Fernández; G. de S. Pessôa; M.A.Z. Arruda; J.L. Capelo-Martínez; F. Fdez-Riverola; D. Glez-Peña; M. Reboiro-Jato (2016) LA-iMageS: a software for elemental distribution bioimaging using LA-ICP-MS data. Journal of Cheminformatics. Volume 8:65. ISSN: 1758-2946
H. López-Fernández; M. Reboiro-Jato; J.A. Pérez-Rodríguez; F. Fdez-Riverola; D. Glez-Peña (2016) The Artificial Intelligence Workbench: a retrospective review. Advances in Distributed Computing and Artificial Intelligence Journal. Volume 5/1, pp. 73-85. ISSN: 2255-2863
H. López-Fernández; M. Reboiro-Jato; J.A. Pérez Rodríguez; F. Fdez-Riverola; D. Glez-Peña (2016) Implementing effective machine learning-based workflows for the analysis of mass spectrometry data. Journal of Integrated OMICS, a methodological journal. Volume 6/1, pp. 1-5.ISSN: 2182-0287
H. López-Fernández (2016) Application of data mining and artificial intelligence techniques to mass spectrometry data for knowledge discovery. Revista Iberoamericana de Inteligencia Artificial. Volume 19(57), pp. 22-25. ISSN: 1988-3064
G. de S. Pessôa; J.L. Capelo-Martínez; F. Fdez-Riverola; H. López-Fernández; D. Glez-Peña; M. Reboiro-Jato; M.A.Z. Arruda (2016) Laser ablation and inductively coupled plasma mass spectrometry focusing on bioimaging from elemental distribution using MatLab software: a practical guide. Journal of Analytical Atomic Spectrometry. Volume 31, Issue 4, pp. 832-840. ISSN: 0267-9477
H. López-Fernández; H.M. Santos; J.L. Capelo; F. Fdez-Riverola; D. Glez-Peña; M. Reboiro-Jato (2015) Mass-Up: an all-in-one open software application for MALDI-TOF mass spectrometry knowledge discovery. BMC Bioinformatics. 16:318. ISSN: 1471-2105
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
H. López-Fernández; M. Reboiro-Jato; D. Glez-Peña; F. Fdez-Riverola (2014) A comprehensive analysis about the influence of low-level preprocessing techniques on mass spectrometry data for sample classification. International Journal of Data Mining and Bioinformatics. Volume 10/4, pp. 455-473. ISSN: (Online) 1748-5681 - (Print) 1748-5673
M. Galesio; H. López-Fdez; M. Reboiro-Jato; S. Gómez-Meire; D. Glez-Peña; F. Fdez-Riverola; C. Lodeiro; M. Diniz; J.L. Capelo (2013) Speeding up the screening of steroids in urine: development of a user-friendly library. Steroids. Volume 78/12-13, pp. 1226-1232. ISSN: 0039-128X
H. López-Fernández; D. Glez-Peña; M. Reboiro-Jato; F. Aparicio; D. Gachet; M. Buenaga; F. Fdez-Riverola (2013) BioAnnote: A software platform for annotating biomedical documents with application in medical learning environments. Computer Methods and Programs in Biomedicine. 111/1, pp. 139-147. ISSN: 0169-2607
M. Reboiro-Jato; R. Laza; H. López-Fernández; D. Glez-Peña; F. Díaz; F. Fdez-Riverola (2013) genEnsemble: a new model for the combination of classifiers and integration of biological knowledge applied to genomic data. Expert Systems With Applications. Volume 40/1, pp. 52-63. ISSN: 0957-4174 ScienceDirect Top 25 Hottest Articles::Decision Sciences [12/25] - July to September 2013 | ScienceDirect Top 25 Hottest Articles::Decision Sciences & Expert Systems with Applications [8/25] - July to September 2013
R. López-Cortés; E. Oliveira; C. Núñez; C. Lodeiro; M. Páez de la Cadena; F. Fdez-Riverola; H. López-Fernández; M. Reboiro-Jato; D. Glez-Peña; J.L. Capelo; H.M. Santos (2012) Fast human serum profiling through chemical depletion coupled to gold-nanoparticle-assisted protein separation. Talanta. Volume 100, pp. 239-245. ISSN: 0039-9140
F. Fdez-Riverola; D. Glez-Peña; H. López-Fernández; M. Reboiro-Jato; J.R. Méndez (2012) A Java application framework for scientific software development. Software: Practice & Experience. Volume 42/8, pp. 1015-1036. ISSN: 0038-0644
H. López-Fernández; M. Reboiro-Jato; D. Glez-Peña; J.R. Méndez-Reboredo; H.M. Santos; R.J. Carreira; J.L. Capelo; F. Fdez-Riverola (2011) Rapid development of proteomic applications with the AIBench framework. Journal of Integrative Bioinformatics. 8/3:171. ISSN: 1613-4516
H. López-Fernández; D. Glez-Peña; M. Reboiro-Jato; G. Gómez-López; D.G. Pisano; F. Fdez-Riverola (2011) PileLineGUI: a desktop environment for handling genome position files in next-generation sequencing studies. Nucleic Acids Research. Volume 39 (suppl 2), pp. W562-W566. ISSN: 0305-1048

Conferences

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 Presentation file
D. Pérez-Rodríguez; H. López-Fernández; R.C. Agís-Balboa (2021) On the reproducibility of miRNA-Seq differential expression analyses in neuropsychiatric diseases. 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
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 (2021) Desarrollo de un sistema de Inteligencia Artificial para la detección de pólipos en tiempo real. 24ª Reunión Anual de la Asociación Española de Gastroenterología. 2 - June
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 (2021) Desarrollo inicial de un Sistema de Diagnóstico Asistido por Computadora (CAD) que facilite el diagnóstico óptico de pólipos colorrectales. 24ª Reunión Anual de la Asociación Española de Gastroenterología. 2 - June
H. López-Fernández; C.P. Vieira; F. Fdez-Riverola; M. Reboiro-Jato; J. Vieira (2020) Inferences on Mycobacterium leprae host immune response escape and antibiotic resistance using genomic data and GenomeFastScreen. 14th International Conference on Practical Applications of Computational Biology & Bioinformatics: PACBB 2020. L'Aquila, Italy. 7 - October
A. Nogueira-Rodríguez; H. López-Fernández; O. Graña; M. Reboiro-Jato; D. Glez-Peña (2020) Compi Hub: a Public Repository for Sharing and Discovering Compi Pipelines. 14th International Conference on Practical Applications of Computational Biology & Bioinformatics: PACBB 2020. L'Aquila, Italy. 7 - October
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
A. Nogueira-Rodríguez; H. López-Fernández; D. Glez-Peña (2019) Deep Learning Techniques for Real Time Computer-Aided Diagnosis in Colorectal Cancer. 16th International Conference on Distributed Computing and Artificial Intelligence (Special Sessions - Doctoral Consortium): DCAI 2019. Ávila, Spain. 26 - June
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 Presentation file
O. Graña-Castro; H. López-Fernández; F. Fdez-Riverola; F. Al-Shahrour; D. Glez-Peña (2019) Proposal of a New Bioinformatics Pipeline for Metataxonomics in Precision Medicine. 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; P. Duque; S. Henriques; N. Vázquez; F. Fdez-Riverola; C.P. Vieira; M. Reboiro-Jato; J. Vieira (2018) A bioinformatics protocol for quickly creating large-scale phylogenetic trees. 12th International Conference on Practical Applications of Computational Biology & Bioinformatics: PACBB 2018. Toledo, Spain. 20 - June
N. Vázquez; S. Rocha; H. López-Fernández; A. Torres; R. Camacho; F. Fdez-Riverola; J. Vieira; C.P. Vieira; M. Reboiro-Jato (2018) EvoPPI: a web application to compare protein-protein interactions (PPIs) from different databases and species. 12th International Conference on Practical Applications of Computational Biology & Bioinformatics: PACBB 2018. Toledo, Spain. 20 - June Presentation file
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; N. Vázquez; P. Duque; F. Fdez-Riverola; C.P. Vieira; J. Vieira (2018) Developing a standalone toolbox for processing FASTA files. Portuguese Society of Genetics Annual Meeting 2018. Porto, Portugal. 14 - June
H. López-Fernández; M. Reboiro-Jato; N. Vázquez; P. Duque; F. Fdez-Riverola; C.P. Vieira; J. Vieira (2018) Developing a standalone toolbox for processing FASTA files. Bioinformatics Open Days: BOD 2018. Braga, Portugal. 15 - March
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.
P.M. Baltazar; J.E. Araújo; H. López-Fernández; L. Campos-Pinheiro; F. Calais-Da-Silva; M. Carrascal; P. Videira; H.M. Santos; J.L. Capelo-Martínez (2017) Dithiothreitol-based protein equalization method: A powerful tool in bladder cancer biomarker discovery. 9th European Multidisciplinary Meeting on Urological Cancers. Barcelona, Spain. 16 - November
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; M. Reboiro-Jato; G. de S. Pessôa; M. A. Z. Arruda; J.E. Araújo; H.M. Santos; F. Fdez-Riverola; D. Glez-Peña; J. L. Capelo-Martínez (2017) Bioinformatics software for effective analysis of mass spectrometry data: S2P, Mass-Up and LA-iMageS. V International Conference on Analytical Proteomics. Caparica, Portugal. 3 - July.
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.
J. E. Araújo; S. Jorge; H. M. Santos; C. Lodeiro; J.Y. Ljubimova; H. López-Fernández; J. L. Capelo (2017) Proteomic Dynamic Evolution of Rat Brain Response to Particulate Matter Size. 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.
H. López-Fernández; J.E. Araújo; D. Glez-Peña; M. Reboiro-Jato; F. Fdez-Riverola; J.L. Capelo-Martínez (2017) S2P: a desktop application for fast and easy processing of 2D-gel and MALDI-based mass spectrometry protein data. 11th International Conference on Practical Applications of Computational Biology & Bioinformatics: PACBB 2017. Porto, Portugal. 21 - June Presentation file
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
J.E. Araújo; H. López-Fernández; D. Glez-Peña; M. Reboiro-Jato; F. Fdez-Riverola; J.L. Capelo-Martínez (2017) An open-source software for fast and automatic processing of 2D-gel and MALDI-based mass spectrometry protein data. EUBIC Winter School 2017. Semmering, Austria. 10 - January
H. López-Fernández; D. Glez-Peña; M. Reboiro-Jato; F. Fdez-Riverola; J.L. Capelo-Martínez; H.M. Santos (2017) Mass-Up and Decision Peptide-Driven: two open-source applications for MALDI-TOF MS data analysis and protein quantification. EUBIC Winter School 2017. Semmering, Austria. 10 - January
H. López-Fernández; M. Reboiro-Jato; G. Pessôa; M.A.Z. Arruda; H.M. Santos; J.L. Capelo-Martínez; F. Fdez-Riverola; D. Glez-Peña (2016) Biomarker discovery and bioimaging bioinformatics tools for mass spectrometry-based applications: Mass-Up and LA-iMageS. II Caparica Christmas Conference on Sample Treatment. Caparica, Portugal. 5 - December.
H. López-Fernández; J. E. Araújo; D. Glez-Peña; M. Reboiro-Jato; F. Fdez-Riverola; J.L. Capelo-Martínez (2016) Fast processing of 2D-gel and MALDI-based mass spectrometry protein data. II Caparica Christmas Conference on Sample Treatment. Caparica, Portugal. 5 - December.
M. Rubio-Camarillo; H. López-Fernández; G. Gómez-López; Á. Carro; J.M. Fernández; F. Fdez-Riverola; D. Glez-Peña; D.G. Pisano (2016) RUbioSeq+: an application that executes parallelized pipelines to analyse next-generation sequencing data. 10th International Conference on Practical Applications of Computational Biology & Bioinformatics: PACBB 2016. Sevilla, Spain. 01 - 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
D. Glez-Peña (2014) Bioinformatics Applications in the SING research Group. Case study: Mass‑Up, a proteomics workbench. Bioinformatics Open Days: BOD 2014. Braga, Portugal. 27 - February Imagen relacionada con la noticia
T. Santos; J.L. Capelo; H.M. Santos; H. López-Fernández; C. Marinho; P. Poeta; G. Igrejas (2013) Bacterial characterization by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry and bioinformatic tools. XXXVIII Jornadas Portuguesas de Genetica. Porto, Portugal. 4 - June
H. López-Fernández; M. Reboiro-Jato; S.C. Madeira; R. López-Cortés; J.D. Nunes-Miranda; H.M. Santos; F. Fdez-Riverola; D. Glez-Peña (2013) A workflow for the application of biclustering to mass spectrometry data. 7th International Conference on Practical Applications of Computational Biology & Bioinformatics: PACBB 2013. Salamanca, Spain. 22 - May
H. López-Fernández; D. Glez-Peña; M. Reboiro-Jato; G. Gómez-López; D.G.Pisano; F. Fdez-Riverola (2012) Applying AIBench framework to develop rich user interfaces in NGS studies. 6th International Conference on Practical Applications of Computational Biology & Bioinformatics: PACBB 2012. Salamanca, Spain. 28 - March
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
H. López-Fernández; F. Fdez-Riverola; M. Reboiro-Jato; D. Glez-Peña; J.R. Méndez. Using CBR as design methodology for developing adaptable decision support systems. Pags. 123-144. Efficient Decision Support Systems - Practice and Challenges From Current to Future. Chiang Jao (editor). Intech. ISBN: 978-953-307-326-2, 2011, Croatia

PhD Students

Alba Nogueira Rodríquez (2018 - Present). Técnicas de aprendizaje profundo para diagnóstico asistido por computador en cáncer colorrectal.
Rubén Domínguez Carbajales (2018 - Present). Desarrollo de un sistema para la mejora de la calidad de diagnóstico asistido por computador en procedimientos de endoscopia digestiva.
Daniel Pérez Rodríguez (2020 - Present). Protocolo bioinformático para la búsqueda de miARNs como biomarcadores en enfermedades neuropsiquiátricas.
Pedro Miguel da Silva Ferreira (2021 - Present). Predicting the behavior of COVID-19 pandemics.