Sistemas Informáticos de Nueva Generación (SING)

Blanco G, Yanez Martinez R, Lourenco A. Leveraging deep learning to detectstance in Spanish tweets on COVID-19 vaccination. JAMIA Open. 2025 Jan31;8(1):ooaf007. doi: 10.1093/jamiaopen/ooaf007. eCollection 2025 Feb. PubMedPMID: 40008184; PubMed Central PMCID: PMC11854073.
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Celard P, Iglesias EL, Sorribes-Fernández JM, Borrajo L, Vieira AS. New Metrics and Dataset for Biological Development Video Generation. ACM Trans Multimedia Comput Commun Appl. 2024;21(1):article ID 12, pp. 1–23. ISSN: (Online) 1551-6865 – (Print) 1551-6857
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Davila-Pinon P, Diez Martin AI, Nogueira-Rodriguez A, Dominguez-Carbajales R,Fdez-Riverola F, Zarraquinos S, de Castro L, Herrero J, Fernandez N, Vega P,Remedios D, Martinez A, Puga M, Alonso S, Pin N, Garcia-Morales N, Rivas L, LedoA, Macenlle R, Cid L, Rodriguez A, Soto S, Baiocchi F, Perez-Medrano I, SanchezE, Glez-Pena D, Reboiro-Jato M, Lopez-Fernandez H, Cubiella J. ClinicalEvaluation of PolyDeep, A Computer-Aided Detection System: A MulticenterRandomized Tandem Colonoscopy Trial. Diagnostics (Basel). 2025 Oct30;15(21):2751. doi: 10.3390/diagnostics15212751. PubMed PMID: 41226043; PubMedCentral PMCID: PMC12607807.
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Davila-Pinon P, Pedrido T, Diez-Martin AI, Herrero J, Puga M, Rivas L, SanchezE, Zarraquinos S, Pin N, Vega P, Soto S, Remedios D, Dominguez-Carbajales R,Fdez-Riverola F, Nogueira-Rodriguez A, Glez-Pena D, Reboiro-Jato M,Lopez-Fernandez H, Cubiella J. PolyDeep Advance 1: Clinical Validation of aComputer-Aided Detection System for Colorectal Polyp Detection with a SecondObserver Design. Diagnostics (Basel). 2025 Feb 13;15(4):458. doi:10.3390/diagnostics15040458. PubMed PMID: 40002609; PubMed Central PMCID:PMC11854325.
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Nogueira-Rodriguez A, Glez-Pena D, Vieira CP, Vieira J, Lopez-Fernandez H.Towards a more accurate and reliable evaluation of machine learningprotein-protein interaction prediction model performance in the presence ofunavoidable dataset biases. J Integr Bioinform. 2025 Apr 2. doi:10.1515/jib-2024-0054. Online ahead of print. PubMed PMID: 40165676.
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Pedro Celard, Eva Lorenzo Iglesias, José Manuel Sorribes-Fdez, Rubén Romero, Adrián Seara Vieira, Lourdes Borrajo, Modified LDA vector and feedback analysis for short query Information Retrieval systems, Logic Journal of the IGPL, 2024; jzae044, https://doi.org/10.1093/jigpal/jzae044
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Perez-Rodriguez D, Agis-Balboa RC, Lopez-Fernandez H. Fcodes update: a kinshipencoding framework with F-Tree GUI & LLM inference. J Integr Bioinform. 2025Mar 31. doi: 10.1515/jib-2024-0046. Online ahead of print. PubMed PMID: 40155191.
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Vieira J, Barros M, Lopez-Fernandez H, Glez-Pena D, Nogueira-Rodriguez A,Vieira CP. Predicting Which Mitophagy Proteins Are Dysregulated inSpinocerebellar Ataxia Type 3 (SCA3) Using the Auto-p2docking Pipeline. Int J MolSci. 2025 Feb 4;26(3):1325. doi: 10.3390/ijms26031325. PubMed PMID: 39941093;PubMed Central PMCID: PMC11818632.
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M. Pérez-Pérez; M. Fernández-González; R. Pavón; R. Laza; M. Novo-Lourés. Sistema de detección mediante intelixencia artificial para o reconto e a análise de mostras biolóxicas en imaxes xeradas por microscopio. Pags. 135-156. INOU 2024: Investigación aplicada na provincia de Ourense. Vicerrectoría del Campus de Ourense-Campus Auga, Universidad de Vigo. ISBN: 978-84-1188-035-0, 2025, España
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Celard P, Iglesias EL, Sorribes-Fernández JM, Borrajo L, Vieira AS. New Metrics and Dataset for Biological Development Video Generation. ACM Transactions on Multimedia Computing, Communications and Applications. 2024;21(1):12, pp. 1–23.
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Celard P, Seara Vieira A, Sorribes-Fdez JM, Iglesias EL, Borrajo L. Improving Generation and Evaluation of Long Image Sequences for Embryo Development Prediction. Electronics (Switzerland). 2024;13(3);476.

Celard P, Seara Vieira A, Sorribes-Fdez JM, Iglesias EL, Borrajo L. Temporal Development GAN (TD-GAN): Crafting More Accurate Image Sequences of Biological Development. Information (Switzerland). 2024;15(1), Article Number 12.

Davila-Pinon P, Nogueira-Rodriguez A, Diez-Martin AI, Codesido L, Herrero J,Puga M, Rivas L, Sanchez E, Fdez-Riverola F, Glez-Pena D, Reboiro-Jato M,Lopez-Fernandez H, Cubiella J. Optical diagnosis in still images of colorectalpolyps: comparison between expert endoscopists and PolyDeep, a Computer-AidedDiagnosis system. Front Oncol. 2024 May 23;14:1393815. doi:10.3389/fonc.2024.1393815. eCollection 2024. PubMed PMID: 38846970; PubMedCentral PMCID: PMC11153726.

Ferreira P, Soares R, Lopez-Fernandez H, Vazquez N, Reboiro-Jato M, Vieira CP,Vieira J. Multiple Lines of Evidence Support 199 SARS-CoV-2 Positively SelectedAmino Acid Sites. Int J Mol Sci. 2024 Feb 19;25(4):2428. doi:10.3390/ijms25042428. PubMed PMID: 38397104; PubMed Central PMCID: PMC10889775.

Gallego-Garcia P, Estevez-Gomez N, De Chiara L, Alvarino P, Juiz-Gonzalez PM,Torres-Beceiro I, Poza M, Vallejo JA, Rumbo-Feal S, Conde-Perez K, Aja-Macaya P,Ladra S, Moreno-Flores A, Gude-Gonzalez MJ, Coira A, Aguilera A, Costa-AlcaldeJJ, Trastoy R, Barbeito-Castineiras G, Garcia-Souto D, Tubio JMC, Trigo-DaportaM, Camacho-Zamora P, Costa JG, Gonzalez-Dominguez M, Canoura-Fernandez L,Glez-Pena D, Perez-Castro S, Cabrera JJ, Davina-Nunez C, Godoy-Diz M,Treinta-Alvarez AB, Veiga MI, Sousa JC, Osorio NS, Comas I, Gonzalez-Candelas F,Hong SL, Bollen N, Dellicour S, Baele G, Suchard MA, Lemey P, Agulla A, Bou G,Alonso-Garcia P, Perez-Del-Molino ML, Garcia-Campello M, Paz-Vidal I, Regueiro B,Posada D. Dispersal history of SARS-CoV-2 in Galicia, Spain. J Med Virol. 2024Jul;96(7):e29773. doi: 10.1002/jmv.29773. PubMed PMID: 38940448; PubMed CentralPMCID: PMC11742125.

Glez-Pena D, Lopez-Fernandez H, Duque P, Vieira CP, Vieira J. Inferences onthe evolution of the ascorbic acid synthesis pathway in insects usingPhylogenetic Tree Collapser (PTC), a tool for the automated collapsing ofphylogenetic trees using taxonomic information. J Integr Bioinform. 2024 Jul24;21(2):20230051. doi: 10.1515/jib-2023-0051. eCollection 2024 Jun 1. PubMedPMID: 39054685; PubMed Central PMCID: PMC11377030.
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Lopez-Fernandez H, Pinto M, Vieira CP, Duque P, Reboiro-Jato M, Vieira J.Auto-phylo v2 and auto-phylo-pipeliner: building advanced, flexible, and reusablepipelines for phylogenetic inferences, estimation of variability levels andidentification of positively selected amino acid sites. J Integr Bioinform. 2024Mar 27;21(2):20230046. doi: 10.1515/jib-2023-0046. eCollection 2024 Jun 1. PubMedPMID: 38529929; PubMed Central PMCID: PMC11378518.

Perez-Perez M, Fernandez Gonzalez M, Rodriguez-Rajo FJ, Fdez-Riverola F.Tracking the Spread of Pollen on Social Media Using Pollen-Related Messages FromTwitter: Retrospective Analysis. J Med Internet Res. 2024 Oct 21;26:e58309. doi:10.2196/58309. PubMed PMID: 39432897; PubMed Central PMCID: PMC11535798.
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Pérez-Pérez M, Ribeiro M, Fdez-Riverola F, Igrejas G. Insights into wheat science: A bibliometric review using unsupervised machine learning techniques. Journal of Cereal Science. 2024 Jul 1;118:103960–0.

Reboiro-Jato M, Perez-Rodriguez D, Da Silva MJ, Vila-Fernandez D, Vieira CP,Vieira J, Lopez-Fernandez H. SEDA 2024 update: enhancing the SEquence DAtasetbuilder for seamless integration into automated data analysis pipelines. BMCBioinformatics. 2024 May 27;25(1):200. doi: 10.1186/s12859-024-05818-2. PubMedPMID: 38802733; PubMed Central PMCID: PMC11131258.

Blanco-Miguez A, Marcos-Fernandez R, Guadamuro-Garcia L, Fdez-Riverola F,Cubiella J, Lourenco A, Margolles A, Sanchez B. Targeted depletion ofpks+ bacteria from a fecal microbiota using specific antibodies.mSystems. 2023 Jun 29;8(3):e0007923. doi: 10.1128/msystems.00079-23. Epub 2023May 23. PubMed PMID: 37219498; PubMed Central PMCID: PMC10308883.

Carvalho LB, Capelo JL, Lodeiro C, Dhir R, Pinheiro LC, Lopez-Fernandez H,Martins G, Medeiros M, Diaz F, Santos HM. Pathway-guided monitoring of thedisease course in bladder cancer with longitudinal urine proteomics. Commun Med(Lond). 2023 Jan 16;3(1):8. doi: 10.1038/s43856-023-00238-4. PubMed PMID:36646893; PubMed Central PMCID: PMC9842762.

Carvalho LB, Jorge S, Lopez-Fernandez H, Lodeiro C, Dhir R, Campos Pinheiro L,Medeiros M, Santos HM, Capelo JL. Proteomic analysis of chromophobe renal cellcarcinoma and benign renal oncocytoma biopsies reveals shared metabolicdysregulation. Clin Proteomics. 2023 Nov 28;20(1):54. doi:10.1186/s12014-023-09443-8. PubMed PMID: 38017382; PubMed Central PMCID:PMC10683195.

Celard P, Iglesias EL, Sorribes-Fdez JM, Romero R, Vieira AS, Borrajo L. Asurvey on deep learning applied to medical images: from simple artificial neuralnetworks to generative models. Neural Comput Appl. 2023;35(3):2291-2323. doi:10.1007/s00521-022-07953-4. Epub 2022 Nov 4. PubMed PMID: 36373133; PubMedCentral PMCID: PMC9638354.

Concu R, Cordeiro MNDS, Perez-Perez M, Fdez-Riverola F. MOZART, a QSARMulti-Target Web-Based Tool to Predict Multiple Drug-Enzyme Interactions.Molecules. 2023 Jan 25;28(3):1182. doi: 10.3390/molecules28031182. PubMed PMID:36770857; PubMed Central PMCID: PMC9921108.

Jimenez-Santos MJ, Nogueira-Rodriguez A, Pineiro-Yanez E, Lopez-Fernandez H,Garcia-Martin S, Gomez-Plana P, Reboiro-Jato M, Gomez-Lopez G, Glez-Pena D,Al-Shahrour F. PanDrugs2: prioritizing cancer therapies using integratedindividual multi-omics data. Nucleic Acids Res. 2023 Jul 5;51(W1):W411-W418. doi:10.1093/nar/gkad412. PubMed PMID: 37207338; PubMed Central PMCID: PMC10320188.

M. Novo-Lourés; M. Fernández-González; R. Pavón; K.C. Sánchez; R. Laza; G. Guada; J.R. Méndez; F. Fdez-Riverola; F.J. Rodríguez-Rajo (2023) Alnus airborne pollen trends during the last 26 years for improving machine learning-based forecasting methods. Forests. Volume 14(8), Article ID 1586. ISSN: 1999-4907

Nogueira-Rodriguez A, Glez-Pena D, Reboiro-Jato M, Lopez-Fernandez H. NegativeSamples for Improving Object Detection-A Case Study in AI-Assisted Colonoscopyfor Polyp Detection. Diagnostics (Basel). 2023 Mar 3;13(5):966. doi:10.3390/diagnostics13050966. PubMed PMID: 36900110; PubMed Central PMCID:PMC10001273.

Perez-Perez M, Ferreira T, Igrejas G, Fdez-Riverola F. A novel glutenknowledge base of potential biomedical and health-related interactions extractedfrom the literature: Using machine learning and graph analysis methodologies toreconstruct the bibliome. J Biomed Inform. 2023 Jul;143:104398. doi:10.1016/j.jbi.2023.104398. Epub 2023 May 23. PubMed PMID: 37230405.

Perez-Rodriguez D, Agis-Balboa RC, Lopez-Fernandez H. MyBrain-Seq: A Pipelinefor MiRNA-Seq Data Analysis in Neuropsychiatric Disorders. Biomedicines. 2023 Apr21;11(4):1230. doi: 10.3390/biomedicines11041230. PubMed PMID: 37189848; PubMedCentral PMCID: PMC10135678.

Perez-Rodriguez D, Penedo MA, Rivera-Baltanas T, Pena-Centeno T, Burkhardt S,Fischer A, Prieto-Gonzalez JM, Olivares JM, Lopez-Fernandez H, Agis-Balboa RC.MiRNA Differences Related to Treatment-Resistant Schizophrenia. Int J Mol Sci.2023 Jan 18;24(3):1891. doi: 10.3390/ijms24031891. PubMed PMID: 36768211; PubMedCentral PMCID: PMC9916039.

Rodriguez-Conde I, Campos C, Fdez-Riverola F. Horizontally DistributedInference of Deep Neural Networks for AI-Enabled IoT. Sensors (Basel). 2023 Feb8;23(4):1911. doi: 10.3390/s23041911. PubMed PMID: 36850508; PubMed CentralPMCID: PMC9958567.

Sousa A, Rocha S, Vieira J, Reboiro-Jato M, Lopez-Fernandez H, Vieira CP. Onthe identification of potential novel therapeutic targets for spinocerebellarataxia type 1 (SCA1) neurodegenerative disease using EvoPPI3. J Integr Bioinform.2023 Feb 28;20(2):20220056. doi: 10.1515/jib-2022-0056. eCollection 2023 Jun 1.PubMed PMID: 36848492; PubMed Central PMCID: PMC10561075.

Yáñez Martínez R, Blanco G, Lourenço A. Spanish Corpora of tweets about COVID-19 vaccination for automatic stance detection. Information Processing & Management. 2023; 60(3):103294. DOI: 10.1016/j.ipm.2023.103294.

A. Seara-Vieira; N. García-Hervella; A.I. González-Fernández. Aplicabilidad de técnicas de inteligencia artificial en sistemas de resolución de conflictos en línea. Pages 251-283. Mediación medioambiental. Tirant lo Blanch. ISBN: 978-84-1147-883-0, 2023, Spain

Blanco G, Lourenço, A. Optimism and pessimism analysis using deep learning on COVID-19 related twitter conversations. Information Processing & Management. 2022; 59(3):102918. DOI: 10.1016/j.ipm.2022.102918.

Gonçalves CA, Vieira AS, Gonçalves CT, Camacho R, Iglesias EL, Diz LB. A Novel Multi-View Ensemble Learning Architecture to Improve the Structured Text Classification. Information. 2022; 13(6):283. DOI: 10.3390/info13060283

Lopez-Fernandez H, Duque P, Vazquez N, Fdez-Riverola F, Reboiro-Jato M, Vieira CP, Vieira J. SEDA: A Desktop Tool Suite for FASTA Files Processing. IEEE/ACM Trans Comput Biol Bioinforma. 2022 Nov;19(3):1850–60. PMID: 33237866. DOI: 10.1109/TCBB.2020.3040383. http://www.ncbi.nlm.nih.gov/pubmed/33237866
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Nogueira-Rodríguez A, Domínguez-Carbajales R, Campos-Tato F, Herrero J, Puga M, Remedios D, Rivas L, Sánchez E, Iglesias Á, Cubiella J, Fdez-Riverola F, López-Fernández H, Reboiro-Jato M, Glez-Peña D. Real-time polyp detection model using convolutional neural networks. Neural Comput Appl. 2022 Jul;34(13):10375–96. DOI: 10.1007/s00521-021-06496-4. http://doi.org/10.1007/s00521-021-06496-4%0A
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Nogueira-Rodriguez A, Reboiro-Jato M, Glez-Pena D, Lopez-Fernandez H.Performance of Convolutional Neural Networks for Polyp Localization on PublicColonoscopy Image Datasets. Diagnostics (Basel). 2022 Apr 4;12(4):898. doi:10.3390/diagnostics12040898. PubMed PMID: 35453946; PubMed Central PMCID:PMC9027927.

Novo Lourés M, Lage Y, Pavón Rial MR, Laza Fidalgo R, Ruano Ordás D, Méndez JR. Improving Pipelining Tools for Pre-processing Data. IJIMAI. 2022;7(4):214-24. https://doi.org/10.9781/ijimai.2021.10.004%0A
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Ocampo-Quintero N, Vidal-Cortes P, Del Rio Carbajo L, Fdez-Riverola F,Reboiro-Jato M, Glez-Pena D. Enhancing sepsis management through machine learningtechniques: A review. Med Intensiva (Engl Ed). 2022 Mar;46(3):140-156. doi:10.1016/j.medine.2020.04.015. PubMed PMID: 35221003.
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Pérez-Pérez M, Ferreira T, Igrejas G, Fdez-Riverola F.A deep learning relation extraction approach to support a biomedical semi-automatic curation task: The case of the gluten bibliome. Expert Systems with Applications. 2022; 195:116616. DOI: 10.1016/j.eswa.2022.116616.

Pérez-Pérez M, Ferreira T, Lourenço A, Igrejas G, Fdez-Riverola F. Boosting biomedical document classification through the use of domain entity recognizers and semantic ontologies for document representation: The case of gluten bibliome. Neurocomputing. 2022 May;484(E-PUB):223–37. DOI: 10.1016/j.neucom.2021.10.100. https://doi.org/10.1016/j.neucom.2021.10.100%0A
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R. Romero, P. Celard, J.M. Sorribes-Fdez, A. Seara Vieira, E.L. Iglesias, L. Borrajo. MobyDeep: A lightweight CNN architecture to configure models for text classification. Knowledge-Based Systems. 2022; 257:109914. DOI: 10.1016/j.knosys.2022.109914.

Rodriguez-Conde I, Campos C, Fdez-Riverola F. Optimized convolutional neural network architectures for efficient on-device vision-based object detection. Neural Comput Appl. 2022 Jul;34(13):10469–501. https://doi.org/10.1007/s00521-021-06830-w%0A
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M. Novo; S. Álvarez-López; L. Borrajo; E. Lorenzo; M. Míguez; R. Pavón; J. R. Méndez; P. Araújo-Nespereira; F. Fdez-Riverola; R. Laza; F. J. Rodríguez-Rajo; M. Fernández-González. Detección automática de momentos de risco alérxico da poboación ourensá. Pags. 75-97. INOU 2021: Investigación aplicada na provincia de Ourense. Vicerrectoría del Campus de Ourense, Universidad de Vigo. ISBN: 978-84-8158-949-8, 2022, España

Blanco G, Sanchez B, Ruiz L, Fdez-Riverola F, Margolles A, Lourenco A. Computational Approach to the Systematic Prediction of Glycolytic Abilities: Looking Into Human Microbiota. IEEE/ACM Trans Comput Biol Bioinforma. 2021;18(6):2302–13. PMID: 32149650. DOI: 10.1109/TCBB.2020.2978461. http://www.ncbi.nlm.nih.gov/pubmed/32149650
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Ferreiro-Díaz M, Cotos-Yáñez, Tomás R, Méndez, José R, Ruano-Ordás D. The bdpar Package: Big Data Pipelining Architecture for R. R J. 2021;13(1):130. DOI: 10.32614/RJ-2021-065. https://doi.org/10.32614/RJ-2021-065%0A
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López-Fernández H, Graña-Castro O, Nogueira-Rodríguez A, Reboiro-Jato M, Glez-Peña D. Compi: a framework for portable and reproducible pipelines. PeerJ Comput Sci. 2021;7:e593. PMID: 34239974. DOI: 10.7717/peerj-cs.593. http://www.ncbi.nlm.nih.gov/pubmed/34239974
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López-Fernández H, Vieira CP, Ferreira P, Gouveia P, Fdez-Riverola F, Reboiro-Jato M, Vieira J. On the Identification of Clinically Relevant Bacterial Amino Acid Changes at the Whole Genome Level Using Auto-PSS-Genome. Interdiscip Sci. 2021 Jun;13(2):334–43. PMID: 34009546. DOI: 10.1007/s12539-021-00439-2. http://www.ncbi.nlm.nih.gov/pubmed/34009546
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Nogueira-Rodríguez A, Domínguez-Carbajales R, López-Fernández H, Iglesias Á, Cubiella J, Fdez-Riverola F, Reboiro-Jato M, Glez-Peña D. Deep Neural Networks approaches for detecting and classifying colorectal polyps. Neurocomputing. 2021 Jan;423:721–34. DOI: 10.1016/j.neucom.2020.02.123. https://doi.org/10.1016/j.neucom.2020.02.123%0A
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Oliveira Gonçalves CA, Camacho R, Gonçalves CT, Seara Vieira A, Borrajo Diz L, Lorenzo Iglesias E. Classification of Full Text Biomedical Documents: Sections Importance Assessment. Appl Sci. 2021 Mar;11(6):2674. DOI: 10.3390/app11062674. https://doi.org/10.3390/app11062674%0A
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Pascoal-Ferreira P, Glez-Peña D, Miranda C, Poeta P, Coutinho J, Fdez-Riverola F, Torrado-Agrasar A, Rúa ML, Igrejas G. Are There Benefits from Thermal Bacteria for Health? The Hydrogenome Role. Water. 2021 May;13(11):1439. DOI: 10.3390/w13111439. https://doi.org/10.3390/w13111439%0A
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Pérez-Pérez M, Igrejas G, Fdez-Riverola F, Lourenço A. A framework to extract biomedical knowledge from gluten-related tweets: The case of dietary concerns in digital era. Artif Intell Med. 2021;118:102131. PMID: 34412847. DOI: 10.1016/j.artmed.2021.102131. http://www.ncbi.nlm.nih.gov/pubmed/34412847
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Pérez-Rodríguez D, López-Fernández H, Agís-Balboa RC. Application of miRNA-seq in neuropsychiatry: A methodological perspective. Comput Biol Med. 2021 Jun;135:104603. PMID: 34216893. DOI: 10.1016/j.compbiomed.2021.104603. http://www.ncbi.nlm.nih.gov/pubmed/34216893
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Ramoa A, Condeço J, Fdez-Riverola F, Lourenço A. HaemoKBS: A knowledge-based system for real-time, continuous categorisation of adverse reactions in blood recipients. Neurocomputing. 2021 Jan;423:756–67. DOI: 10.1016/j.neucom.2020.04.101. https://doi.org/10.1016/j.neucom.2020.04.101%0A
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Rodriguez-Conde I, Campos C, Fdez-Riverola F. On-Device Object Detection for More Efficient and Privacy-Compliant Visual Perception in Context-Aware Systems. Appl Sci. 2021 Oct;11(19):9173. DOI: 10.3390/app11199173. https://doi.org/10.3390/app11199173%0A
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Roldán-Molina GR, Ruano-Ordás D, Basto-Fernandes V, Méndez JR. An ontology knowledge inspection methodology for quality assessment and continuous improvement. Data Knowl Eng. 2021 May;133:101889. DOI: 10.1016/j.datak.2021.101889. https://doi.org/10.1016/j.datak.2021.101889%0A
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Ruano-Ordás D, Méndez JR, Basto Fernandes V, Suárez-Tangil G. Novel Tools for the Management, Representation, and Exploitation of Textual Information. Sci Program. 2021 Aug;2021:1–3. DOI: 10.1155/2021/9781923. https://doi.org/10.1155/2021/9781923%0A
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Silva S, Seara Vieira A, Celard P, Iglesias EL, Borrajo L. A Query Expansion Method Using Multinomial Naive Bayes. Appl Sci. 2021 Nov;11(21):10284. DOI: 10.3390/app112110284. http://doi.org/10.3390/app112110284%0A
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T Magalhães B, Lourenço A, Azevedo NF. Computational resources and strategies to assess single-molecule dynamics of the translation process in S. cerevisiae. Brief Bioinform. 2021;22(1):219–31. PMID: 31879749. DOI: 10.1093/bib/bbz149. http://www.ncbi.nlm.nih.gov/pubmed/31879749
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Troulé K, López-Fernández H, García-Martín S, Reboiro-Jato M, Carretero-Puche C, Martorell-Marugán J, Martín-Serrano G, Carmona-Sáez P, Glez-Peña D, Al-Shahrour F, Gómez-López G. DREIMT: a drug repositioning database and prioritization tool for immunomodulation. Bioinformatics. 2021;37(4):578–9. PMID: 32818254. DOI: 10.1093/bioinformatics/btaa727. http://www.ncbi.nlm.nih.gov/pubmed/32818254
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M. Ferreiro; R. Laza; L. Borrajo; E. Lorenzo; R. Pavón. Extracción e preprocesamento de opinións sobre o sector enoturístico na provincia de Ourense. Pags. 183-204. Proxectos INOU 2020: Investigación aplicada na provincia de Ourense. Vicerrectoría del Campus de Ourense, Universidad de Vigo. ISBN: 978-84-8158-916-0, 2021, España

Magalhães BT, Santos RS, Azevedo NF, Lourenço A. Computational Resources and Strategies to Construct Single-Molecule Models of FISH. Methods in Molecular Biology book series (MIMB, volume 2246). New York, NY: Humana; 2021. p. 317–30. ISBN: 978-1-0716-1115-9. https://doi.org/10.1007/978-1-0716-1115-9_21
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Blanco G, Pérez-López R, Fdez-Riverola F, Lourenço AMG. Understanding the social evolution of the Java community in Stack Overflow: A 10-year study of developer interactions. Futur Gener Comput Syst. 2020 Apr;105:446–54. DOI: 10.1016/j.future.2019.12.021. http://doi.org/10.1016/j.future.2019.12.021
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Blanco G, Ruiz L, Tamés H, Ruas-Madiedo P, Fdez-Riverola F, Sánchez B, Lourenço A, Margolles A. Revisiting the Metabolic Capabilities of Bifidobacterium longum susbp. longum and Bifidobacterium longum subsp. infantis from a Glycoside Hydrolase Perspective. Microorganisms. 2020 May;8(5) PMID: 32413974. DOI: 10.3390/microorganisms8050723. http://www.ncbi.nlm.nih.gov/pubmed/32413974
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Borrajo L, Vieira AS, Iglesias EL. An HMM-based synthetic view generator to improve the efficiency of ensemble systems. Log J IGPL. 2020 Jan;28(1):4–18. DOI: 10.1093/jigpal/jzz067. https://doi.org/10.1093/jigpal/jzz067
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Cambeiro-Pérez N, Hidalgo-Cantabrana C, Moro-García MA, Blanco-Míguez A, Fdez-Riverola F, Riestra S, Lourenço A, Alonso-Arias R, Margolles A, Martínez-Carballo E, Sánchez B. In silico and functional analyses of immunomodulatory peptides encrypted in the human gut metaproteome. J Funct Foods. 2020 Jul;70:103969. DOI: 10.1016/j.jff.2020.103969. https://doi.org/10.1016/j.jff.2020.103969
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Celard P, Vieira AS, Iglesias EL, Borrajo L. LDA filter: A Latent Dirichlet Allocation preprocess method for Weka. PLoS One. 2020;15(11):e0241701. PMID: 33166342. DOI: 10.1371/journal.pone.0241701. http://www.ncbi.nlm.nih.gov/pubmed/33166342
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Estévez O, Anibarro L, Garet E, Pallares Á, Barcia L, Calviño L, Maueia C, Mussá T, Fdez-Riverola F, Glez-Peña D, Reboiro-Jato M, López-Fernández H, Fonseca NA, Reljic R, González-Fernández Á. An RNA-seq Based Machine Learning Approach Identifies Latent Tuberculosis Patients With an Active Tuberculosis Profile. Front Immunol. 2020;11:1470. PMID: 32760401. DOI: 10.3389/fimmu.2020.01470. http://www.ncbi.nlm.nih.gov/pubmed/32760401
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Graña-Castro O, López-Fernández H, Nogueira-Rodríguez A, Fdez-Riverola F, Al-Shahrour F, Glez-Peña D. Metatax: Metataxonomics with a Compi-Based Pipeline for Precision Medicine. Interdiscip Sci. 2020 Sep;12(3):252–7. PMID: 32350726. DOI: 10.1007/s12539-020-00368-6. http://www.ncbi.nlm.nih.gov/pubmed/32350726
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Hidalgo-Cantabrana C, Moro-García MA, Blanco-Míguez A, Fdez-Riverola F, Oliván M, Royo LJ, Riestra S, Margolles A, Lourenço A, Alonso-Arias R, Sánchez B. The extracellular proteins of Lactobacillus acidophilus DSM 20079T display anti-inflammatory effect in both in piglets, healthy human donors and Crohn’s Disease patients. J Funct Foods. 2020 Jan;64:103660. DOI: 10.1016/j.jff.2019.103660. https://doi.org/10.1016/j.jff.2019.103660%0A
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Jorge S, Pereira K, López-Fernández H, LaFramboise W, Dhir R, Fernández-Lodeiro J, Lodeiro C, Santos HM, Capelo-Martínez JL. 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. 2020 Jan;206:120180. PMID: 31514886. DOI: 10.1016/j.talanta.2019.120180. http://www.ncbi.nlm.nih.gov/pubmed/31514886
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Pérez-Rodríguez G, Pérez-Pérez M, Fdez-Riverola F, Lourenço A. Mining the sociome for Health Informatics: Analysis of therapeutic lifestyle adherence of diabetic patients in Twitter. Futur Gener Comput Syst. 2020 Sep;110:214–32. DOI: 10.1016/j.future.2020.04.025. https://doi.org/10.1016/j.future.2020.04.025
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Roldan-Molina GR, Mendez JR, Yevseyeva I, Basto-Fernandes V. Ontology Fixing by Using Software Engineering Technology. Appl Sci. 2020 Sep;10(18):6328. DOI: 10.3390/app10186328. http://doi.org/10.3390/app10186328
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Reboiro-Jato M, Glez-Peña D, López-Fernández H. Statistics, Data Mining and Modeling. In: Winkler R (ed.). PROCESSING METABOLOMICS AND PROTEOMICS DATA WITH OPEN SOFTWARE: A PRACTICAL GUIDE New Developments in Mass Spectrometry. Cambridge: ROYAL SOC CHEMISTRY; 2020. p. 120–200. ISBN: 978-1-78801-721-3. https://doi.org/10.1039/9781788019880
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Blanco G, Sánchez B, Fdez-Riverola F, Margolles A, Lourenço A. In silico Approach for Unveiling the Glycoside Hydrolase Activities in Faecalibacterium prausnitzii Through a Systematic and Integrative Large-Scale Analysis. Front Microbiol. 2019;10(APR):517. PMID: 31024464. DOI: 10.3389/fmicb.2019.00517. http://www.ncbi.nlm.nih.gov/pubmed/31024464
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Blanco-Míguez A, Blanco G, Gutierrez-Jácome A, Fdez-Riverola F, Sánchez B, Lourenço A. Computational prediction of the bioactivity potential of proteomes based on expert knowledge. J Biomed Inform. 2019;91:103121. PMID: 30738947. DOI: 10.1016/j.jbi.2019.103121. http://www.ncbi.nlm.nih.gov/pubmed/30738947
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Blanco-Míguez A, Fdez-Riverola F, Lourenço A, Sánchez B. In silico prediction reveals the existence of potential bioactive neuropeptides produced by the human gut microbiota. Food Res Int. 2019;119:221–6. PMID: 30884651. DOI: 10.1016/j.foodres.2019.01.069. http://www.ncbi.nlm.nih.gov/pubmed/30884651
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Blanco-Míguez A, Fdez-Riverola F, Sánchez B, Lourenço A. Resources and tools for the high-throughput, multi-omic study of intestinal microbiota. Brief Bioinform. 2019 May;20(3):1032–56. PMID: 29186315. DOI: 10.1093/bib/bbx156. http://www.ncbi.nlm.nih.gov/pubmed/29186315
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Fdez-Riverola F, Rocha M. Selected Extended Papers of the 12th International Conference on Practical Applications of Computational Biology and Bioinformatics (PACBB). J Integr Bioinform. 2019 Feb;16(1) DOI: 10.1515/jib-2019-0004. https://doi.org/10.1515/jib-2019-0004
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Henriques SF, Duque P, López-Fernández H, Vázquez N, Fdez-Riverola F, Reboiro-Jato M, Vieira CP, Vieira J. Multiple independent L-gulonolactone oxidase (GULO) gene losses and vitamin C synthesis reacquisition events in non-Deuterostomian animal species. BMC Evol Biol. BMC Evolutionary Biology; 2019;19(1):126. PMID: 31215418. DOI: 10.1186/s12862-019-1454-8. http://www.ncbi.nlm.nih.gov/pubmed/31215418
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López-Fernández H, Blanco-Míguez A, Fdez-Riverola F, Sánchez B, Lourenço A. DEWE: A novel tool for executing differential expression RNA-Seq workflows in biomedical research. Comput Biol Med. 2019;107:197–205. PMID: 30849608. DOI: 10.1016/j.compbiomed.2019.02.021. http://www.ncbi.nlm.nih.gov/pubmed/30849608
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López-Fernández H, Duque P, Henriques S, Vázquez N, Fdez-Riverola F, Vieira CP, Reboiro-Jato M, Vieira J. Bioinformatics Protocols for Quickly Obtaining Large-Scale Data Sets for Phylogenetic Inferences. Interdiscip Sci. 2019 Mar;11(1):1–9. PMID: 30511150. DOI: 10.1007/s12539-018-0312-5. http://www.ncbi.nlm.nih.gov/pubmed/30511150
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Maia P, Pérez-Rodríguez G, Pérez-Pérez M, Fdez-Riverola F, Lourenço A, Azevedo NF. Application of agent-based modelling to assess single-molecule transport across the cell envelope of E. coli. Comput Biol Med. 2019;107:218–26. PMID: 30852248. DOI: 10.1016/j.compbiomed.2019.02.020. http://www.ncbi.nlm.nih.gov/pubmed/30852248
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Pérez-Pérez M, Pérez-Rodríguez G, Blanco-Míguez A, Fdez-Riverola F, Valencia A, Krallinger M, Lourenço A. Next generation community assessment of biomedical entity recognition web servers: metrics, performance, interoperability aspects of BeCalm. J Cheminform. Springer International Publishing; 2019 Jun;11(1):42. PMID: 31236786. DOI: 10.1186/s13321-019-0363-6. http://www.ncbi.nlm.nih.gov/pubmed/31236786
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Pérez-Pérez M, Pérez-Rodríguez G, Fdez-Riverola F, Lourenço A. Using Twitter to Understand the Human Bowel Disease Community: Exploratory Analysis of Key Topics. J Med Internet Res. 2019;21(8):e12610. PMID: 31411142. DOI: 10.2196/12610. https://www.jmir.org/2019/8/e12610/pdf
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Pérez-Rodríguez G, Pérez-Pérez M, Fdez-Riverola F, Lourenço A. Online visibility of software-related web sites: The case of biomedical text mining tools. Inf Process Manag. Elsevier; 2019 May;56(3):565–83. DOI: 10.1016/j.ipm.2018.11.011. https://doi.org/10.1016/j.ipm.2018.11.011
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Rocha S, Vieira J, Vázquez N, López-Fernández H, Fdez-Riverola F, Reboiro-Jato M, Sousa AD, Vieira CP. ATXN1 N-terminal region explains the binding differences of wild-type and expanded forms. BMC Med Genomics. BMC Medical Genomics; 2019;12(1):145. PMID: 31655597. DOI: 10.1186/s12920-019-0594-4. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6814966/pdf/12920_2019_Article_594.pdf
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Ruano-Ordás D, Burggraaff L, Liu R, van der Horst C, Heitman LH, Emmerich MTM, Mendez JR, Yevseyeva I, van Westen GJP. A multiple classifier system identifies novel cannabinoid CB2 receptor ligands. J Cheminform. Springer International Publishing; 2019 Dec;11(1):66. DOI: 10.1186/s13321-019-0389-9. http://doi.org/10.1186/s13321-019-0389-9
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Ruano-Ordás D, Yevseyeva I, Fernandes VB, Méndez JR, Emmerich MTM. Improving the drug discovery process by using multiple classifier systems. Expert Syst Appl. 2019 May;121(351):292–303. DOI: 10.1016/j.eswa.2018.12.032. https://repositorio.iscte-iul.pt/bitstream/10071/17465/1/Manuscript_REV2.pdf
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Vázquez N, López-Fernández H, Vieira CP, Fdez-Riverola F, Vieira J, Reboiro-Jato M. 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. Interdiscip Sci. 2019 Mar;11(1):57–67. PMID: 30712176. DOI: 10.1007/s12539-019-00320-3. http://www.ncbi.nlm.nih.gov/pubmed/30712176
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Vázquez N, Rocha S, López-Fernández H, Torres A, Camacho R, Fdez-Riverola F, Vieira J, Vieira CP, Reboiro-Jato M. EvoPPI 1.0: a Web Platform for Within- and Between-Species Multiple Interactome Comparisons and Application to Nine PolyQ Proteins Determining Neurodegenerative Diseases. Interdiscip Sci. 2019 Mar;11(1):45–56. PMID: 30707359. DOI: 10.1007/s12539-019-00317-y. http://www.ncbi.nlm.nih.gov/pubmed/30707359
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Vieira J, Rocha S, Vázquez N, López-Fernández H, Fdez-Riverola F, Reboiro-Jato M, Vieira CP. Predicting Specificities Under the Non-self Gametophytic Self-Incompatibility Recognition Model. Front Plant Sci. 2019;10(July):879. PMID: 31379893. DOI: 10.3389/fpls.2019.00879. http://www.ncbi.nlm.nih.gov/pubmed/31379893
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Villamarín-Bello B, Uriel-Latorre B, Fdez-Riverola F, Sande-Meijide M, Glez-Peña D. Gold Standard Evaluation of an Automatic HAIs Surveillance System. Biomed Res Int. 2019;2019(iii):1049575. PMID: 31662963. DOI: 10.1155/2019/1049575. http://www.ncbi.nlm.nih.gov/pubmed/31662963
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Aparicio F, Morales-Botello ML, Rubio M, Hernando A, Muñoz R, López-Fernández H, Glez-Peña D, Fdez-Riverola F, de la Villa M, Maña M, Gachet D, Buenaga M de. Perceptions of the use of intelligent information access systems in university level active learning activities among teachers of biomedical subjects. Int J Med Inform. 2018 Apr;112:21–33. PMID: 29500018. DOI: 10.1016/j.ijmedinf.2017.12.016. http://www.ncbi.nlm.nih.gov/pubmed/29500018
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Araújo JE, López-Fernández H, Diniz MS, Baltazar PM, Pinheiro LC, da Silva FC, Carrascal M, Videira P, Santos HM, Capelo JL. Dithiothreitol-based protein equalization technology to unravel biomarkers for bladder cancer. Talanta. 2018 Apr;180:36–46. PMID: 29332824. DOI: 10.1016/j.talanta.2017.11.063. http://www.ncbi.nlm.nih.gov/pubmed/29332824
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Blanco-Míguez A, Fdez-Riverola F, Sánchez B, Lourenço A. BlasterJS: A novel interactive JavaScript visualisation component for BLAST alignment results. PLoS One. 2018;13(10):e0205286. PMID: 30300406. DOI: 10.1371/journal.pone.0205286. http://www.ncbi.nlm.nih.gov/pubmed/30300406
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Fdez-Glez J, Ruano-Ordás D, Méndez JR, Fdez-Riverola F, Laza R, Pavón R. Determining the Influence of Class Imbalance for the Triage of Biomedical Documents. Curr Bioinform. 2018 Nov;13(6):592–605. DOI: 10.2174/1574893612666170718151238. http://www.eurekaselect.com/154289/article
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Grainha TRR, Jorge PA da S, Perez-Perez M, Perez Rodriguez G, Pereira MOBO, Lourenco AMG. Exploring anti-quorum sensing and anti-virulence based strategies to fight Candida albicans infections: an in silico approach. FEMS Yeast Res. 2018 May;18(3) PMID: 29518242. DOI: 10.1093/femsyr/foy022.

Grana O, Lopez-Fernandez H, Fdez-Riverola F, Gonzalez Pisano D, Glez-Pena D, Graña O, López-Fernández H, Fdez-Riverola F, González Pisano D, Glez-Peña D. Bicycle: a bioinformatics pipeline to analyze bisulfite sequencing data. Bioinformatics. 2018 Apr;34(8):1414–5. PMID: 29211825. DOI: 10.1093/bioinformatics/btx778. http://www.ncbi.nlm.nih.gov/pubmed/29211825
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Graña O, Rubio-Camarillo M, Fdez-Riverola F, Pisano DG, Glez-Peña D. Nextpresso: Next Generation Sequencing Expression Analysis Pipeline. Curr Bioinform. 2018 Nov;13(6):583–91. DOI: 10.2174/1574893612666170810153850. www.doi.org/10.2174/1574893612666170810153850
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Jesus JR, Santos HM, López-Fernández H, Lodeiro C, Arruda MAZ, Capelo JL. Ultrasonic-based membrane aided sample preparation of urine proteomes. Talanta. 2018 Feb;178:864–9. PMID: 29136907. DOI: 10.1016/j.talanta.2017.09.078. http://www.ncbi.nlm.nih.gov/pubmed/29136907
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López-Fernández H, Araújo JE, Jorge S, Glez-Peña D, Reboiro-Jato M, Santos HM, Fdez-Riverola F, Capelo JL. S2P: A software tool to quickly carry out reproducible biomedical research projects involving 2D-gel and MALDI-TOF MS protein data. Comput Methods Programs Biomed. 2018 Mar;155:1–9. PMID: 29512488. DOI: 10.1016/j.cmpb.2017.11.024. http://www.ncbi.nlm.nih.gov/pubmed/29512488
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López-Fernández H, Reboiro-Jato M, Glez-Peña D, Laza R, Pavón R, Fdez-Riverola F. GC4S: A bioinformatics-oriented Java software library of reusable graphical user interface components. PLoS One. 2018;13(9):e0204474. PMID: 30235322. DOI: 10.1371/journal.pone.0204474. http://www.ncbi.nlm.nih.gov/pubmed/30235322
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Marcelino I, Laza R, Domingues P, Gómez-Meire S, Fdez-Riverola F, Pereira A. Active and Assisted Living Ecosystem for the Elderly. Sensors (Basel). 2018 Apr;18(4):1–18. PMID: 29673234. DOI: 10.3390/s18041246. http://www.ncbi.nlm.nih.gov/pubmed/29673234
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Pérez-Rodríguez G, Dias S, Pérez-Pérez M, Fdez-Riverola F, Azevedo NF, Lourenço A. Agent-based model of diffusion of N-acyl homoserine lactones in a multicellular environment of Pseudomonas aeruginosa and Candida albicans. Biofouling. 2018 Mar;34(3):335–45. PMID: 29516751. DOI: 10.1080/08927014.2018.1440392. http://www.ncbi.nlm.nih.gov/pubmed/29516751
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Piñeiro-Yáñez E, Reboiro-Jato M, Gómez-López G, Perales-Patón J, Troulé K, Rodríguez JM, Tejero H, Shimamura T, López-Casas PP, Carretero J, Valencia A, Hidalgo M, Glez-Peña D, Al-Shahrour F. PanDrugs: a novel method to prioritize anticancer drug treatments according to individual genomic data. Genome Med. Genome Medicine; 2018;10(1):41. PMID: 29848362. DOI: 10.1186/s13073-018-0546-1. http://www.ncbi.nlm.nih.gov/pubmed/29848362
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Prates J, Martins G, López-Fernández H, Lodeiro C, Capelo JL, Santos HM. Modulating the protein content of complex proteomes using acetonitrile. Talanta. 2018 May;182:333–9. PMID: 29501161. DOI: 10.1016/j.talanta.2018.01.057. http://www.ncbi.nlm.nih.gov/pubmed/29501161
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Ramoa A, Condeço J, Escoval MA, Faber J-C, Fdez-Riverola F, Lourenço A. The Evolving Role of Information Technology in Haemovigilance Systems. J Healthc Eng. 2018;2018:6183468. PMID: 29707185. DOI: 10.1155/2018/6183468. http://www.ncbi.nlm.nih.gov/pubmed/29707185
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Rocha M, Fdez-Riverola F. Advanced Practical Applications of Computational Biology & Bioinformatics: PACBB’15. Curr Bioinform. 2018 Nov;13(6):565–565. DOI: 10.2174/157489361306181107184700. http://www.eurekaselect.com/167161/article
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Vazquez N, Vieira CP, Amorim BSRBSR, Torres AA, Lopez-Fernandez H, Fdez-Riverola F, Sousa JLRJLR, Reboiro-Jato M, Vieira J, Vázquez N, Vieira CP, Amorim BSRBSR, Torres AA, López-Fernández H, Fdez-Riverola F, Sousa JLRJLR, Reboiro-Jato M, Vieira J. Large Scale Analyses and Visualization of Adaptive Amino Acid Changes Projects. Interdiscip Sci Comput Life Sci. 2018 Mar;10(1):24–32. PMID: 29383564. DOI: 10.1007/s12539-018-0282-7. http://www.ncbi.nlm.nih.gov/pubmed/29383564
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Reboiro-Jato M, López-Fernández H, Laza-Fidalgo R, Pavón-Rial MR, Rojas-Rodríguez F, Vieira-Vázquez A, Rivera-Baltanás T, Spuch-Calvar C, Varela-Pomar A, Otero-Lamas F, Piñón-Blanco A. MultiTasking Cubes: unha ferramenta para a rehabilitacion cognitiva. In: De-Blas-Varela E, Rodríguez-Vázquez V, Vila-Sobrino XA, Álvarez-González S (eds.). Proxectos INOU 2017 Investigación aplicada na provincia de Ourense. Universidade de Vigo; 2018. p. 63–77. DL: VG 665-2018. ISBN: 978-84-8158-800-2. https://dialnet.unirioja.es/servlet/articulo?codigo=6691641
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Azeredo J, Azevedo NF, Briandet R, Cerca N, Coenye T, Costa AR, Desvaux M, Di Bonaventura G, Hébraud M, Jaglic Z, Ka?ániová M, Knøchel S, Lourenço A, Mergulhão F, Meyer RL, Nychas G, Simões M, Tresse O, Sternberg C. Critical review on biofilm methods. Crit Rev Microbiol. 2017 May;43(3):313–51. DOI: 10.1080/1040841X.2016.1208146. https://www.tandfonline.com/doi/full/10.1080/1040841X.2016.1208146
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Blanco-Míguez A, Fdez-Riverola F, Lourenço A, Sánchez B. P4P: A peptidome-based strain-level genome comparison web tool. Nucleic Acids Res. 2017 Jul;45(W1):W265–9. PMID: 28482090. DOI: 10.1093/nar/gkx389. IF2017: 11.561; D1. http://www.ncbi.nlm.nih.gov/pubmed/28482090
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Blanco-Míguez A, Gutiérrez-Jácome A, Fdez-Riverola F, Lourenço A, Sánchez B. MAHMI database: a comprehensive MetaHit-based resource for the study of the mechanism of action of the human microbiota. Database (Oxford). 2017 Jan;2017(1):baw157. PMID: 28077565. DOI: 10.1093/database/baw157. IF2017: 3.978; D1. http://www.ncbi.nlm.nih.gov/pubmed/28077565
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Fdez-Riverola F, de Paz JF, Domínguez-Mayo FJ, Rocha MP, Saberi Mohamad M. Special Issue: Practical Applications of Computational Biology & Bioinformatics. Interdiscip Sci – Comput Life Sci. 2017;9(1) IF2017: 0.796; Q4. https://link.springer.com/journal/12539/9/1/page/1
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Fdez-Riverola F, Rocha M. Selected Extended Papers of the 11th International Conference on Practical Applications of Computational Biology and Bioinformatics (PACBB). J Integr Bioinform. 2017 Dec;14(4) DOI: 10.1515/jib-2017-0071. IF2017: N/A. http://www.degruyter.com/view/j/jib.2017.14.issue-4/jib-2017-0071/jib-2017-0071.xml
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Hidalgo-Cantabrana C, Moro-García MA, Blanco-Míguez A, Fdez-Riverola F, Lourenço A, Alonso-Arias R, Sánchez B. In Silico Screening of the Human Gut Metaproteome Identifies Th17-Promoting Peptides Encrypted in Proteins of Commensal Bacteria. Front Microbiol. 2017 Sep;8:1726. PMID: 28943872. DOI: 10.3389/fmicb.2017.01726. IF2017: 4.019; Q2. http://www.ncbi.nlm.nih.gov/pubmed/28943872
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Jorge P, Grzywacz D, Kamysz W, Lourenço A, Pereira MO. Searching for new strategies against biofilm infections: Colistin-AMP combinations against Pseudomonas aeruginosa and Staphylococcus aureus single- and double-species biofilms. Kaufmann GF (ed.). PLoS One. 2017 Mar;12(3):e0174654. DOI: 10.1371/journal.pone.0174654. https://dx.plos.org/10.1371/journal.pone.0174654
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Jorge P, Pérez-Pérez M, Pérez Rodríguez G, Pereira MO, Lourenço A. A network perspective on antimicrobial peptide combination therapies: the potential of colistin, polymyxin B and nisin. Int J Antimicrob Agents. 2017 Jun;49(6):668–76. PMID: 28457834. DOI: 10.1016/j.ijantimicag.2017.02.012. IF2017: 4.253; Q1. http://www.ncbi.nlm.nih.gov/pubmed/28457834
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Krallinger M, Rabal O, Lourenço A, Oyarzabal J, Valencia A. Information Retrieval and Text Mining Technologies for Chemistry. Chem Rev. 2017 Jun;117(12):7673–761. PMID: 28475312. DOI: 10.1021/acs.chemrev.6b00851. IF2017: 52.613; D1. http://www.ncbi.nlm.nih.gov/pubmed/28475312
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Pérez-Pérez M, Jorge P, Pérez Rodríguez G, Pereira MO, Lourenço A. Quorum sensing inhibition in Pseudomonas aeruginosa biofilms: new insights through network mining. Biofouling. 2017 Feb;33(2):128–42. DOI: 10.1080/08927014.2016.1272104. https://www.tandfonline.com/doi/full/10.1080/08927014.2016.1272104
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Pérez-Pérez M, Pérez-Rodríguez G, Fdez-Riverola F, Lourenço A. Collaborative relation annotation and quality analysis in Markyt environment. Database. 2017 Jan;2017(BAX090):1–12. PMID: 25619558. DOI: 10.1093/database/bax090. IF2017: 3.978; D1. http://www.ncbi.nlm.nih.gov/pubmed/25619558
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Rodrigues ME, Lopes SP, Pereira CR, Azevedo NF, Lourenço A, Henriques M, Pereira MO. Polymicrobial Ventilator-Associated Pneumonia: Fighting In Vitro Candida albicans-Pseudomonas aeruginosa Biofilms with Antifungal-Antibacterial Combination Therapy. PLoS One. 2017;12(1):e0170433. PMID: 28114348. DOI: 10.1371/journal.pone.0170433. http://www.ncbi.nlm.nih.gov/pubmed/28114348
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Rubio-Camarillo M, López-Fernández H, Gómez-López G, Carro Á, Fernández JM, Torre CF, Fdez-Riverola F, Glez-Peña D. RUbioSeq+: A multiplatform application that executes parallelized pipelines to analyse next-generation sequencing data. Comput Methods Programs Biomed. 2017 Jan;138:73–81. DOI: 10.1016/j.cmpb.2016.10.008. https://linkinghub.elsevier.com/retrieve/pii/S0169260716307386
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Sánchez B, Delgado S, Blanco-Míguez A, Lourenço A, Gueimonde M, Margolles A. Probiotics, gut microbiota, and their influence on host health and disease. Mol Nutr Food Res. 2017 Jan;61(1):1600240. PMID: 27500859. DOI: 10.1002/mnfr.201600240. IF2017: 5.151; D1. http://www.ncbi.nlm.nih.gov/pubmed/27500859
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Araújo JE, Jorge S, Magriço R, Teixeira e Costa, Ramos A, Reboiro-Jato M, Fdez-Riverola F, Lodeiro C, Capelo JL, Santos HM, Costa TE, Ramos A, Reboiro-Jato M, Fdez-Riverola F, Lodeiro C, Capelo JL, Santos HM. Classifying patients in peritoneal dialysis by mass spectrometry-based profiling. Talanta. 2016 May;152:364–70. PMID: 26992532. DOI: 10.1016/j.talanta.2016.02.026. http://www.ncbi.nlm.nih.gov/pubmed/26992532
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Blanco-Míguez A, Gutiérrez-Jácome A, Fdez-Riverola F, Lourenço A, Sánchez B. A peptidome-based phylogeny pipeline reveals differential peptides at the strain level within Bifidobacterium animalis subsp. lactis. Food Microbiol. 2016 Dec;60:137–41. PMID: 27554155. DOI: 10.1016/j.fm.2016.06.015. http://www.ncbi.nlm.nih.gov/pubmed/27554155
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Jácome AG, Fdez-Riverola F, Lourenço A. BIOMedical Search Engine Framework: Lightweight and customized implementation of domain-specific biomedical search engines. Comput Methods Programs Biomed. 2016 Jul;131:63–77. PMID: 27265049. DOI: 10.1016/j.cmpb.2016.03.030. http://www.ncbi.nlm.nih.gov/pubmed/27265049
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López-Fernández H, de S Pessôa G, Arruda MAZ, Capelo-Martínez JL, Fdez-Riverola F, Glez-Peña D, Reboiro-Jato M. LA-iMageS: a software for elemental distribution bioimaging using LA-ICP-MS data. J Cheminform. Springer International Publishing; 2016 Nov;8(1):65. PMID: 27917244. DOI: 10.1186/s13321-016-0178-7. IF2015: 3.949; D1. http://www.ncbi.nlm.nih.gov/pubmed/27917244
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Pérez-Rodríguez G, Pérez-Pérez M, Fdez-Riverola F, Lourenço A. High performance computing for three-dimensional agent-based molecular models. J Mol Graph Model. 2016 Jul;68:68–77. PMID: 27372059. DOI: 10.1016/j.jmgm.2016.06.001. http://www.ncbi.nlm.nih.gov/pubmed/27372059
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Ruiz L, Hidalgo C, Blanco-Míguez A, Lourenço A, Sánchez B, Margolles A. Tackling probiotic and gut microbiota functionality through proteomics. J Proteomics. 2016 Mar;147:28–39. PMID: 27003613. DOI: 10.1016/j.jprot.2016.03.023. http://www.ncbi.nlm.nih.gov/pubmed/27003613
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Felisberto F, Laza R, Fdez-Riverola F, Pereira A. A distributed multiagent system architecture for body area networks applied to healthcare monitoring. Biomed Res Int. 2015 Jan;2015:192454. PMID: 25874202. DOI: 10.1155/2015/192454. IF: 1.579; Q3. http://www.ncbi.nlm.nih.gov/pubmed/25874202
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López-Fernández H, Santos HM, Capelo JL, Fdez-Riverola F, Glez-Peña D, Reboiro-Jato M. Mass-Up: an all-in-one open software application for MALDI-TOF mass spectrometry knowledge discovery. BMC Bioinformatics. 2015 Oct;16:318. PMID: 26437641. DOI: 10.1186/s12859-015-0752-4. IF2014: 2.576; Q1. http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=4595311&tool=pmcentrez&rendertype=abstract
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Pérez-Pérez M, Glez-Peña D, Fdez-Riverola F, Lourenço A. Marky: a tool supporting annotation consistency in multi-user and iterative document annotation projects. Comput Methods Programs Biomed. 2015 Feb;118(2):242–51. PMID: 25480679. DOI: 10.1016/j.cmpb.2014.11.005. IF: 1.897; Q1. http://www.ncbi.nlm.nih.gov/pubmed/25480679
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Pérez-Rodríguez G, Glez-Peña D, Azevedo NF, Pereira MO, Fdez-Riverola F, Lourenço A. Enabling systematic, harmonised and large-scale biofilms data computation: the Biofilms Experiment Workbench. Comput Methods Programs Biomed. 2015 Mar;118(3):309–21. PMID: 25600941. DOI: 10.1016/j.cmpb.2014.12.005. IF: 1.897; Q1. http://www.ncbi.nlm.nih.gov/pubmed/25600941
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Pérez-Rodríguez G, Pérez-Pérez M, Glez-Peña D, Fdez-Riverola F, Azevedo NF, Lourenço A. Agent-based spatiotemporal simulation of biomolecular systems within the open source MASON framework. Biomed Res Int. 2015 Jan;2015:769471. PMID: 25874228. DOI: 10.1155/2015/769471. IF: 1.579; Q3. http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=4385633&tool=pmcentrez&rendertype=abstract
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Costa N, Domingues P, Fdez-Riverola F, Pereira A. A Mobile Virtual Butler to Bridge the Gap between Users and Ambient Assisted Living: A Smart Home Case Study. Sensors. 2014 Aug;14(8):14302–29. PMID: 25102342. DOI: 10.3390/s140814302. IF: 2.245; Q2. http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=4179076&tool=pmcentrez&rendertype=abstract
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Felisberto F, Fdez-Riverola F, Pereira A. A ubiquitous and low-cost solution for movement monitoring and accident detection based on sensor fusion. Sensors (Basel). 2014 Jan;14(5):8961–83. PMID: 24854360. DOI: 10.3390/s140508961. IF: 2.245; Q2. http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=4063039&tool=pmcentrez&rendertype=abstract
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Fernández-Costa C, Reboiro-Jato M, Fdez-Riverola F, Ruiz-Romero C, Blanco FJ, Capelo-Martínez J-L. Sequential depletion coupled to C18 sequential extraction as a rapid tool for human serum multiple profiling. Talanta. 2014 Jul;125:189–95. PMID: 24840432. DOI: 10.1016/j.talanta.2014.02.050. IF: 3.545; Q1. http://www.ncbi.nlm.nih.gov/pubmed/24840432
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Glez-Peña D, Lourenço A, López-Fernández H, Reboiro-Jato M, Fdez-Riverola F. Web scraping technologies in an API world. Brief Bioinform. 2014 Sep;15(5):788–97. PMID: 23632294. DOI: 10.1093/bib/bbt026. IF: 9.617; Q1. http://www.ncbi.nlm.nih.gov/pubmed/23632294
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Nunes-Miranda JD, Núñez C, Santos HM, Vale G, Reboiro-Jato M, Fdez-Riverola F, Lodeiro C, Miró M, Capelo JL. A mesofluidic platform integrating on-chip probe ultrasonication for multiple sample pretreatment involving denaturation, reduction, and digestion in protein identification assays by mass spectrometry. Analyst. 2014 Mar;139(5):992–5. PMID: 24443721. DOI: 10.1039/c3an02178e. IF: 4.107; Q1. http://www.ncbi.nlm.nih.gov/pubmed/24443721
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Reboiro-Jato M, Arrais JP, Oliveira JL, Fdez-Riverola F. geneCommittee: a web-based tool for extensively testing the discriminatory power of biologically relevant gene sets in microarray data classification. BMC Bioinformatics. 2014 Jan;15:31. PMID: 24475928. DOI: 10.1186/1471-2105-15-31. IF: 2.576; Q1; http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3909759&tool=pmcentrez&rendertype=abstract
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Reboiro-Jato M, Díaz F, Glez-Peña D, Fdez-Riverola F. A novel ensemble of classifiers that use biological relevant gene sets for microarray classification. Appl Soft Comput. 2014 Apr;17:117–26. DOI: 10.1016/j.asoc.2014.01.002. IF: 2.810; Q1. http://www.sciencedirect.com/science/article/pii/S1568494614000039
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