Article
Biochemical Research Methods
Nuwan Goonasekera, Alexandru Mahmoud, John Chilton, Enis Afgan
Summary: The presence of over 100 public Galaxy servers with service quotas highlights the demand for increased compute resources for Galaxy. The GalaxyCloudRunner allows a Galaxy server to easily expand its compute capacity through sending user jobs to cloud resources, which can be dynamically acquired from four popular cloud providers.
Review
Oncology
Natalie Jaeger
Summary: High-throughput molecular profiling of tumors is crucial for precision oncology, allowing the identification of genomic alterations for targeted therapy. However, effectively translating molecular findings into personalized treatment recommendations remains challenging, requiring the use of extensive bioinformatics methodologies and workflows.
SEMINARS IN CANCER BIOLOGY
(2022)
Article
Entomology
Surya Saha, Amanda M. Cooksey, Anna K. Childers, Monica F. Poelchau, Fiona M. McCarthy
Summary: This article presents a fast workflow for functional annotation of whole proteomes to generate Gene Ontology and pathways information, with applications to diverse arthropod genomes and comparisons to reference genomes. The performance of the predictions remains consistent across various arthropod genomes with different assembly and annotation qualities.
Article
Chemistry, Multidisciplinary
Patricia Inoue Nakagawa, Luis Ferreira Pires, Joao Luiz Rebelo Moreira, Luiz Olavo Bonino da Silva Santos, Faiza Bukhsh
Summary: The study introduces an ontology for representing explainable machine learning experiments and evaluates its applicability and effectiveness through a case study in the context of the COVID-19 pandemic.
APPLIED SCIENCES-BASEL
(2021)
Article
Computer Science, Information Systems
Christopher Bondy, Linlin Chen, Pamela Grover, Vicki Hanson, Rui Li, Pengcheng Shi
Summary: This paper introduces a cross-disciplinary evaluation method - Collaborative Space - Analysis Framework (CS-AF), designed to evaluate technology-mediated collaborative workflows. Through a 5-step meta-process, the CS-AF systematically analyzes gains and gaps of collaborative workflows, providing critical data for continuous workflow improvement.
IEEE JOURNAL OF BIOMEDICAL AND HEALTH INFORMATICS
(2021)
Article
Biochemistry & Molecular Biology
Zunaira Munir, Giuliana Banche, Lorenza Cavallo, Narcisa Mandras, Janira Roana, Raffaele Pertusio, Eleonora Ficiara, Roberta Cavalli, Caterina Guiot
Summary: In the search for non-chemical and green methods to counteract bacterial contamination of foods, the combination of natural substances with antimicrobial properties and light irradiation, known as photodynamic inactivation (PDI), has been extensively studied. Curcumin, in particular, has shown to be a potent natural antibacterial and effective photosensitizer that can activate under visible light, particularly blue light. Practical applications have been investigated for food preservation and prevention of bacterial contaminants.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Biochemistry & Molecular Biology
Emidio Capriotti, Piero Fariselli
Summary: One of the major challenges in human genetics is determining the functional impact of different types of genetic variations. CADD is a widely used algorithm that predicts the effects of genome variations by combining sequence conservation and functional features. We developed a machine-learning tool called PhD-SNPg, which relies solely on sequence-based features and is easy to install and use. The updated version of PhD-SNPg can also predict the impact of insertion and deletion variations, and performs similarly to CADD, making it useful for rapid genome interpretation and tool development benchmarking.
NUCLEIC ACIDS RESEARCH
(2023)
Review
Microbiology
Carlos Andre dos Santos-Silva, Paola Maura Tricarico, Livia Maria Batista Vilela, Ricardo Salas Roldan-Filho, Vinicius Costa Amador, Adamo Pio d'Adamo, Mireli de Santana Rego, Ana Maria Benko-Iseppon, Sergio Crovella
Summary: Hidradenitis Suppurativa (HS) is a chronic skin autoinflammatory disease characterized by suppurative skin lesions, including painful nodules, abscesses, draining sinus, and bridged scars, with significant impact on patients' quality of life. Medical treatments aim to reduce the incidence, infection, and pain of the lesions, with various classes of drugs being used, including anti-inflammatory molecules, antibiotics, and biological drugs. Antimicrobial peptides (AMPs) are emerging as a new therapeutic option with broad-spectrum antimicrobial action, potentially beneficial for HS patients.
FRONTIERS IN MICROBIOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Carlos Pintado-Grima, Valentin Iglesias, Jaime Santos, Vladimir N. Uversky, Salvador Ventura
Summary: Proteins are sensitive to environmental fluctuations, with disordered regions experiencing solvent-dependent conformational switches. The computational tool DispHScan is introduced to predict pH-induced disorder-order transitions in large protein datasets, offering insights into the physiological and pathological roles of pH-modulated conditional disorder.
Article
Biochemical Research Methods
Gokhan Ozsari, Ahmet Sureyya Rifaioglu, Ahmet Atakan, Tunca Dogan, Maria Jesus Martin, Rengul Cetin Atalay, Volkan Atalay
Summary: In this study, the researchers propose SLPred, an ensemble-based multi-view and multi-label protein subcellular localization prediction tool, which provides predictions for nine main subcellular locations using independent machine-learning models. The results show that SLPred outperforms other tools in most cases.
Article
Astronomy & Astrophysics
Julius Wons, Emanuela Dimastrogiovanni, Matteo Fasiello, Jan Hamann, Matthew C. Johnson
Summary: We forecast the ability of bispectrum estimators to constrain primordial non-Gaussianity using future photometric galaxy redshift surveys. We find that such surveys can provide constraints on primordial non-Gaussianities competitive to those from the cosmic microwave background. We also derive scaling relations for the constraints on the amplitude of primordial non-Gaussianity as a function of redshift error, depth, sky coverage, and nonlinear scale cutoff. Additionally, we investigate the impact of photometric calibration errors on the constraining power of future experiments and propose a method to mitigate their effects using kinetic Sunyaev Zel'dovich tomography.
Article
Biochemistry & Molecular Biology
Yanhui Hu, Aram Comjean, Helen Attrill, Giulia Antonazzo, Jim Thurmond, Weihang Chen, Fangge Li, Tiffany Chao, Stephanie E. Mohr, Nicholas H. Brown, Norbert Perrimon
Summary: PANGEA is a new GSEA tool that allows flexible and configurable data analysis using various classification sets. It enables GO analysis on different sets of GO annotations and provides visualization of results and comparison of multiple input gene lists.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Biochemical Research Methods
Carolyn Allen, Rico Meinl, J. Sebastian Paez, Brian C. Searle, Seth Just, Lindsay K. Pino, William E. Fondrie
Summary: This study presents an open-source NextFlow pipeline, nf-encyclopedia, which connects three open-source tools (MSConvert, EncyclopeDIA, and MSstats) for analyzing DIA proteomics experiments with or without chromatogram libraries. The pipeline is reproducible and provides robust peptide and protein quantification. MSstats improves protein-level quantification performance over EncyclopeDIA alone.
JOURNAL OF PROTEOME RESEARCH
(2023)
Article
Oncology
Ilias Glogovitis, Galina Yahubyan, Thomas Wurdinger, Danijela Koppers-Lalic, Vesselin Baev
Summary: miRGalaxy is an open-source framework based on Galaxy for comprehensive analysis of microRNAs and their sequence variants, focusing on classifying human microRNAs and isomiRs, detecting deregulated microRNAs and isomiRs, and summarizing output through visualization. It provides biologist-user-friendly tools and workflows for analyzing isomiR-ome, allowing customization for advanced users, and accessible through Docker image or Toolshed installation. Studies on miRs and isomiRs have shown their potential as diagnostic biomarkers, especially with the discovery of miRs in biofluids. MiRGalaxy can be applied for in-depth analysis of sRNA-seq data from different biofluids to identify specific differentially expressed miRs and isomiRs.
Article
Engineering, Electrical & Electronic
Ji Yoon Han, Ohyun Jo, Juyeop Kim
Summary: This study examines how machine learning technology can enhance the performance of 5G cell and beam index search. By proposing and implementing new channel-learning schemes, the experimental results demonstrate that these schemes outperform traditional correlation-based schemes in real 5G channel environments.
IEEE TRANSACTIONS ON VEHICULAR TECHNOLOGY
(2022)
Article
Plant Sciences
Marta-Marina Perez-Alonso, Paloma Ortiz-Garcia, Jose Moya-Cuevas, Thomas Lehmann, Beatriz Sanchez-Parra, Robert G. Bjork, Sazzad Karim, Mohammad R. Amirjani, Henrik Aronsson, Mark D. Wilkinson, Stephan Pollmann
Summary: AMI1 plays a crucial role in plant growth by helping plants adapt to abiotic stresses through balancing auxin. Functional impairment of AMI1 leads to increased susceptibility to stress, with mutant plants showing slightly repressed growth but enhanced ABA accumulation, suggesting a role for AMI1 in the crosstalk between auxin and ABA.
JOURNAL OF EXPERIMENTAL BOTANY
(2021)
Article
Multidisciplinary Sciences
Rosa A. Sola-Martinez, Gema Lozano-Terol, Julia Gallego-Jara, Eva Morales, Esther Cantero-Cano, Manuel Sanchez-Solis, Luis Garcia-Marcos, Pedro Jimenez-Guerrero, Jose A. Noguera-Velasco, Manuel Canovas Diaz, Teresa de Diego Puente
Summary: The study aimed to differentiate between asthmatics with coexisting atopic diseases and non-asthmatics using volatile organic compounds in exhaled breath of women of childbearing age. Analysis revealed discriminants for asthma with other coexisting atopic diseases and refined metabolomic analysis allowed discrimination in women of reproductive age.
SCIENTIFIC REPORTS
(2021)
Article
Biochemistry & Molecular Biology
Belen Juanes Cortes, Jose Antonio Vera-Ramos, Ruth C. Lovering, Pascale Gaudet, Astrid Laegreid, Colin Logie, Stefan Schulz, Maria del Mar Roldan-Garcia, Martin Kuiper, Jesualdo Tomas Fernandez-Breis
Summary: Gene regulation computational research involves handling heterogeneous data by generating knowledge models from gene regulation cartoons using ontologies and semantic tools. These models support data annotation by extracting entities, reusing content from existing ontologies, and implementing the knowledge models. The method was applied to two gene regulation scenarios to illustrate its use in supporting data annotation from research articles.
BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS
(2021)
Article
Biochemistry & Molecular Biology
Martin Kuiper, Joseph Bonello, Jesualdo T. Fernandez-Breis, Philipp Bucher, Matthias E. Futschik, Pascale Gaudet, Ivan V. Kulakovskiy, Luana Licata, Colin Logie, Ruth C. Lovering, Vsevolod J. Makeev, Sandra Orchard, Simona Panni, Livia Perfetto, David Sant, Stefan Schulz, Steven Vercruysse, Daniel R. Zerbino, Astrid Laegreid
Summary: Following nine workshops organized by GREEKC, experts from around the world worked to improve the Gene Regulation Knowledge Commons (GRKC) by standardizing and updating workflows, as well as involving end-users in the design process, leading to significant achievements in enhancing the GRKC.
BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS
(2022)
Article
Allergy
Azahara M. Garcia-Serna, Elena Martin-Orozco, Pedro Jimenez-Guerrero, Trinidad Hernandez-Caselles, Virginia Perez-Fernandez, Esther Cantero-Cano, Maria Munoz-Garcia, Maria Dolores Molina-Ruano, Encarna Rojo-Atenza, Luis Garcia-Marcos, Eva Morales
Summary: This study found that gestational exposure to traffic-related air pollutants may increase the detection rate of pro-inflammatory, Th2-related, and T regulatory cytokines in newborns, which may influence their immune system responses later in life.
PEDIATRIC ALLERGY AND IMMUNOLOGY
(2022)
Article
Plant Sciences
Laura Poza-Viejo, Miriam Paya-Milans, Patxi San Martin-Uriz, Laura Castro-Labrador, David Lara-Astiaso, Mark D. Wilkinson, Manuel Pineiro, Jose A. Jarillo, Pedro Crevillen
Summary: Epigenetic regulation is crucial for optimal development and maintenance of gene expression profiles. This study uncovers the epigenetic mechanisms involved in flowering time regulation in Brassica rapa, shedding light on the conserved and distinct regulatory mechanisms between model and crop species.
PLANT CELL AND ENVIRONMENT
(2022)
Article
Mathematics
Gines Almagro-Hernandez, Juana-Maria Vivo, Manuel Franco, Jesualdo Tomas Fernandez-Breis
Summary: Computational genomics focuses on understanding the impact of genome functionality by analyzing the genetic sequence, structure, and interactions with other factors. The study develops a method based on multivariate models for analyzing ChIP-seq data, providing a novel approach for characterizing and comparing experiments. By using a multivariate hypergeometric distribution, the method is able to handle biological data complexity and uncertainty more effectively than existing dichotomous models.
Article
Mathematical & Computational Biology
Rajaram Kaliyaperumal, Mark D. Wilkinson, Pablo Alarcon Moreno, Nirupama Benis, Ronald Cornet, Bruna dos Santos Vieira, Michel Dumontier, Cesar Henrique Bernabe, Annika Jacobsen, Clemence M. A. Le Cornec, Mario Prieto Godoy, Nuria Queralt-Rosinach, Leo J. Schultze Kool, Morris A. Swertz, Philip van Damme, K. Joeri van der Velde, Nawel Lalout, Shuxin Zhang, Marco Roos
Summary: The European Platform on Rare Disease Registration aims to address the fragmentation of rare disease patient data in Europe by establishing standards for integration and interoperability. Through the creation of semantically grounded models and the use of domain ontologies, they have successfully mapped and transformed the data. They have also developed a reusable ETL pipeline to assist rare disease data repositories in creating FAIR data.
JOURNAL OF BIOMEDICAL SEMANTICS
(2022)
Article
Pediatrics
Azahara M. Garcia-Serna, Eva Morales, Ester Cantero-Cano, Maria Norte-Munoz, Ma Angeles Gil-Buendia, Josefa Velazquez-Marin, Trinidad Hernandez-Caselles, Virginia Perez-Fernandez, Antonia E. Martinez-Torres, Luis Garcia-Marcos, Elena Martin-Orozco
Summary: The cytokine signatures in newborns are influenced by sex and season of birth, with male newborns showing higher levels of certain cytokines and summer-born children displaying increased immune response. These signatures may be associated with the development of clinical outcomes in the future.
PEDIATRIC RESEARCH
(2023)
Article
Mathematical & Computational Biology
Philip van Damme, Jesualdo Tomas Fernandez-Breis, Nirupama Benis, Jose Antonio Minarro-Gimenez, Nicolette F. de Keizer, Ronald Cornet
Summary: This experimental study assessed the performance of ontology matching systems in the context of a real-life application from the rare disease domain. The results showed that the systems produced mappings that were modestly accurate, and the hierarchical analysis of mappings seems promising when no reference alignments are available. These systems show potential to be implemented as part of an ontology matching service for querying FAIR data.
JOURNAL OF BIOMEDICAL SEMANTICS
(2022)
Article
Multidisciplinary Sciences
Javier Cuenca-Guardiola, Belen de la Morena-Barrio, Juan L. Garcia, Alba Sanchis-Juan, Javier Corral, Jesualdo T. Fernandez-Breis
Summary: Whole-genome sequencing using nanopore technologies can detect large structural variants with high accuracy. However, existing software for nanopore sequencing data analysis still has limitations in reporting complete and accurate variant sets, hindering molecular diagnosis and genotyping.
JOURNAL OF ADVANCED RESEARCH
(2023)
Article
Computer Science, Information Systems
J. Castell-Diaz, F. Abad-Navarro, M. E. de la Morena-Barrio, J. Corral, J. T. Fernandez-Breis
Summary: Traditional methods are ineffective in predicting mutations in the translation initiation codon, therefore we propose a method to predict the effect of such mutations using a biological model and machine learning algorithms.
IEEE JOURNAL OF BIOMEDICAL AND HEALTH INFORMATICS
(2022)
Article
Multidisciplinary Sciences
Eduardo Illueca Fernandez, Carlos Fernandez Llatas, Antonio Jesus Jara Valera, Jesualdo Tomas Fernandez Breis, Fernando Seoane Martinez
Summary: The World Health Organization predicts that air pollution will be one of the most significant challenges in the environment in the coming years. Due to its impact on mortality risk, air quality monitoring and climate change mitigation actions have been promoted. Therefore, it is important to develop a methodology that supports experts in making decisions based on exposure data, identifying exposure-related activities, and proposing mitigation scenarios. A new methodology based on human knowledge, using interactive process mining, is proposed to achieve this.
Article
Computer Science, Information Systems
Francisco Abad-Navarro, Catalina Martinez-Costa, Jesualdo Tomas Fernandez-Breis
Summary: The paper discusses human readability in ontology quality assurance and proposes the HURON framework for evaluating the human readability of ontology content. Through applied research on a collection of biomedical ontologies, it was found that while most ontologies meet the expected number of descriptions and names, there is still room for improvement, especially in systematic naming conventions.
Article
Biochemistry & Molecular Biology
Juan Mulero Hernandez, Jesualdo Tomas Fernandez-Breis
Summary: Gene regulation involves a complex network where transcription plays a key role, with enhancers playing an important role in regulating gene transcription. While research has made progress in understanding the relationship between enhancers and diseases, there are still challenges and gaps in the computational exploitation of enhancer data in current public databases.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2022)
