SEDA 2024 update: enhancing the SEquence DAtaset builder for seamless integration into automated data analysis pipelines

Authors: Miguel Reboiro-Jato, Daniel Pérez-Rodríguez, Miguel José Da Silva, David Vila-Fernández, Cristina P. Vieira, Jorge Vieira, Hugo López-Fernández

Source: BMC Bioinformatics, Vol 25, Iss 1, Pp 1-9 (2024)

Subject Terms: FASTA, Reproducibility, Pipelines, Workflows, Docker, Computer applications to medicine. Medical informatics, R858-859.7, Biology (General), QH301-705.5

File Description: electronic resource

Relation: https://doaj.org/toc/1471-2105

Access URL: https://doaj.org/article/ba9b47851a8b41a6b6c4b4f4579d89a0

PolyDeep Advance 1: Clinical Validation of a Computer-Aided Detection System for Colorectal Polyp Detection with a Second Observer Design

Authors: Pedro Davila-Piñón, Teresa Pedrido, Astrid Irene Díez-Martín, Jesús Herrero, Manuel Puga, Laura Rivas, Eloy Sánchez, Sara Zarraquiños, Noel Pin, Pablo Vega, Santiago Soto, David Remedios, Rubén Domínguez-Carbajales, Florentino Fdez-Riverola, Alba Nogueira-Rodríguez, Daniel Glez-Peña, Miguel Reboiro-Jato, Hugo López-Fernández, Joaquín Cubiella

Source: Diagnostics, Vol 15, Iss 4, p 458 (2025)

Subject Terms: colonoscopy, computer-aided detection, detection, polyps, performance, screening colonoscopy, Medicine (General), R5-920

File Description: electronic resource

Relation: https://www.mdpi.com/2075-4418/15/4/458; https://doaj.org/toc/2075-4418

Access URL: https://doaj.org/article/97f00d30c713427e9fbe5226dca584c0

Optical diagnosis in still images of colorectal polyps: comparison between expert endoscopists and PolyDeep, a Computer-Aided Diagnosis system

Authors: Pedro Davila-Piñón, Alba Nogueira-Rodríguez, Astrid Irene Díez-Martín, Laura Codesido, Jesús Herrero, Manuel Puga, Laura Rivas, Eloy Sánchez, Florentino Fdez-Riverola, Daniel Glez-Peña, Miguel Reboiro-Jato, Hugo López-Fernández, Joaquín Cubiella

Source: Frontiers in Oncology, Vol 14 (2024)

Subject Terms: colorectal polyps, colonoscopy, deep learning, CADe/x, artificial intelligence, screening, Neoplasms. Tumors. Oncology. Including cancer and carcinogens, RC254-282

File Description: electronic resource

Relation: https://www.frontiersin.org/articles/10.3389/fonc.2024.1393815/full; https://doaj.org/toc/2234-943X

Access URL: https://doaj.org/article/01de0aa34aa74df4971e7b303a0dabed

Pathway-guided monitoring of the disease course in bladder cancer with longitudinal urine proteomics

Authors: Luís Botelho Carvalho, José Luis Capelo, Carlos Lodeiro, Rajiv Dhir, Luis Campos Pinheiro, Hugo López-Fernández, Gonçalo Martins, Mariana Medeiros, Fernando Díaz, Hugo Miguel Santos

Source: Communications Medicine, Vol 3, Iss 1, Pp 1-10 (2023)

Subject Terms: Medicine

File Description: electronic resource

Relation: https://doaj.org/toc/2730-664X

Access URL: https://doaj.org/article/085877129f5a4c0aac521dc42edb3860

MyBrain-Seq: A Pipeline for MiRNA-Seq Data Analysis in Neuropsychiatric Disorders

Authors: Daniel Pérez-Rodríguez, Roberto Carlos Agís-Balboa, Hugo López-Fernández

Source: Biomedicines, Vol 11, Iss 4, p 1230 (2023)

Subject Terms: miRNA-Seq, miRNAs, differential expression, functional analysis, neuropsychiatry, reproducibility, Biology (General), QH301-705.5

File Description: electronic resource

Relation: https://www.mdpi.com/2227-9059/11/4/1230; https://doaj.org/toc/2227-9059

Access URL: https://doaj.org/article/c2804862a0e74bab9975f1d0884a7ec5

Negative Samples for Improving Object Detection—A Case Study in AI-Assisted Colonoscopy for Polyp Detection

Authors: Alba Nogueira-Rodríguez, Daniel Glez-Peña, Miguel Reboiro-Jato, Hugo López-Fernández

Source: Diagnostics, Vol 13, Iss 5, p 966 (2023)

Subject Terms: colorectal cancer, deep learning, convolutional neural network (CNN), polyp detection, polyp localization, Medicine (General), R5-920

File Description: electronic resource

Relation: https://www.mdpi.com/2075-4418/13/5/966; https://doaj.org/toc/2075-4418

Access URL: https://doaj.org/article/cd0137fb912d408095245d90b5ee09c0

ATXN1 N-terminal region explains the binding differences of wild-type and expanded forms

Authors: Sara Rocha, Jorge Vieira, Noé Vázquez, Hugo López-Fernández, Florentino Fdez-Riverola, Miguel Reboiro-Jato, André D. Sousa, Cristina P. Vieira

Source: BMC Medical Genomics, Vol 12, Iss 1, Pp 1-14 (2019)

Subject Terms: Protein-protein interaction, Wild-type ATXN1, Expanded ATXN1, Binding interface, Internal medicine, RC31-1245, Genetics, QH426-470

File Description: electronic resource

Relation: http://link.springer.com/article/10.1186/s12920-019-0594-4; https://doaj.org/toc/1755-8794

Access URL: https://doaj.org/article/58539774873847b3b9304bef0d7ca09d

Multiple independent L-gulonolactone oxidase (GULO) gene losses and vitamin C synthesis reacquisition events in non-Deuterostomian animal species

Authors: Sílvia F. Henriques, Pedro Duque, Hugo López-Fernández, Noé Vázquez, Florentino Fdez-Riverola, Miguel Reboiro-Jato, Cristina P. Vieira, Jorge Vieira

Source: BMC Evolutionary Biology, Vol 19, Iss 1, Pp 1-12 (2019)

Subject Terms: GULO, Ascorbic acid, D. melanogaster, Microbiome, Synthesis, Evolution, QH359-425

File Description: electronic resource

Relation: http://link.springer.com/article/10.1186/s12862-019-1454-8; https://doaj.org/toc/1471-2148

Access URL: https://doaj.org/article/ff34edc980c146b3b5f3bccea5869115

Compi: a framework for portable and reproducible pipelines

Authors: Hugo López-Fernández, Osvaldo Graña-Castro, Alba Nogueira-Rodríguez, Miguel Reboiro-Jato, Daniel Glez-Peña

Source: PeerJ Computer Science, Vol 7, p e593 (2021)

Subject Terms: Computational pipelines, Workflow management systems, Application development framework, Electronic computers. Computer science, QA75.5-76.95

File Description: electronic resource

Relation: https://peerj.com/articles/cs-593.pdf; https://peerj.com/articles/cs-593/; https://doaj.org/toc/2376-5992

Access URL: https://doaj.org/article/faeccdfd60c9443e876aa18359bdc2ea

An RNA-seq Based Machine Learning Approach Identifies Latent Tuberculosis Patients With an Active Tuberculosis Profile

Authors: Olivia Estévez, Luis Anibarro, Elina Garet, Ángeles Pallares, Laura Barcia, Laura Calviño, Cremildo Maueia, Tufária Mussá, Florentino Fdez-Riverola, Daniel Glez-Peña, Miguel Reboiro-Jato, Hugo López-Fernández, Nuno A. Fonseca, Rajko Reljic, África González-Fernández

Source: Frontiers in Immunology, Vol 11 (2020)

Subject Terms: tuberculosis, latent tuberculosis, RNA-seq, machine-learning, TB progression, Immunologic diseases. Allergy, RC581-607

File Description: electronic resource

Relation: https://www.frontiersin.org/article/10.3389/fimmu.2020.01470/full; https://doaj.org/toc/1664-3224

Access URL: https://doaj.org/article/1dc1e9a60b5146ebbcfc937c9bc73ddf

Performance of Convolutional Neural Networks for Polyp Localization on Public Colonoscopy Image Datasets

Authors: Alba Nogueira-Rodríguez, Miguel Reboiro-Jato, Daniel Glez-Peña, Hugo López-Fernández

Source: Diagnostics, Vol 12, Iss 4, p 898 (2022)

Subject Terms: colorectal cancer, deep learning, convolutional neural network (CNN), polyp detection, polyp localization, Medicine (General), R5-920

File Description: electronic resource

Relation: https://www.mdpi.com/2075-4418/12/4/898; https://doaj.org/toc/2075-4418

Access URL: https://doaj.org/article/2d1dc98758484c0b97a1fd5a98e71aa5

Predicting Specificities Under the Non-self Gametophytic Self-Incompatibility Recognition Model

Authors: Jorge Vieira, Sara Rocha, Noé Vázquez, Hugo López-Fernández, Florentino Fdez-Riverola, Miguel Reboiro-Jato, Cristina P. Vieira

Source: Frontiers in Plant Science, Vol 10 (2019)

Subject Terms: Solanaceae, SLFs, S-RNase, self-incompatibility, specificity recognition, positive selection, Plant culture, SB1-1110

File Description: electronic resource

Relation: https://www.frontiersin.org/article/10.3389/fpls.2019.00879/full; https://doaj.org/toc/1664-462X

Access URL: https://doaj.org/article/bc0c2dfdc7794e42bbb9bd5db34b74cd

The Artificial Intelligence Workbench: a retrospective review

Authors: Hugo LÓPEZ-FERNÁNDEZ, Miguel REBOIRO-JATO, José A. PÉREZ RODRÍGUEZ, Florentino FDEZ-RIVEROLA, Daniel GLEZ-PEÑA

Source: Advances in Distributed Computing and Artificial Intelligence Journal, Vol 5, Iss 1, Pp 73-85 (2016)

Subject Terms: scientific software develop-ment, biomedical informatics, open software, application framework, artificial intelli-gence, aibench, Electronic computers. Computer science, QA75.5-76.95

File Description: electronic resource

Relation: https://revistas.usal.es/index.php/2255-2863/article/view/14545; https://doaj.org/toc/2255-2863

Access URL: https://doaj.org/article/8923f791b7c443fa88376777a8d9e0c4

Application of data mining and artificial intelligence techniques to mass spectrometry data for knowledge discovery

Authors: Hugo López-Fernández

Source: Inteligencia Artificial, Vol 19, Iss 57, Pp 22-25 (2016)

Subject Terms: Electronic computers. Computer science, QA75.5-76.95

File Description: electronic resource

Relation: http://journal.iberamia.org/index.php/intartif/article/view/49; https://doaj.org/toc/1137-3601; https://doaj.org/toc/1988-3064

Access URL: https://doaj.org/article/84d6bb60e26f4ac193cf7a2a6d7ef810

GC4S: A bioinformatics-oriented Java software library of reusable graphical user interface components.

Authors: Hugo López-Fernández, Miguel Reboiro-Jato, Daniel Glez-Peña, Rosalía Laza, Reyes Pavón, Florentino Fdez-Riverola

Source: PLoS ONE, Vol 13, Iss 9, p e0204474 (2018)

Subject Terms: Medicine, Science

File Description: electronic resource

Relation: http://europepmc.org/articles/PMC6147514?pdf=render; https://doaj.org/toc/1932-6203

Access URL: https://doaj.org/article/2cbca7c8e5f64703aa16fb6d517006c5