Review
Biochemical Research Methods
Anna Niarakis, Martin Kuiper, Marek Ostaszewski, Rahuman S. Malik Sheriff, Cristina Casals-Casas, Denis Thieffry, Tom C. Freeman, Paul Thomas, Vasundra Toure, Vincent Noel, Gautier Stoll, Julio Saez-Rodriguez, Aurelien Naldi, Eugenia Oshurko, Ioannis Xenarios, Sylvain Soliman, Claudine Chaouiya, Tomas Helikar, Laurence Calzone
Summary: The rapid accumulation of biological data requires systematic integration, analysis, and the generation of relevant hypotheses. Logical models play a crucial role in answering questions about regulatory networks, and there is a growing need for standardized annotation and curation of these models.
BRIEFINGS IN BIOINFORMATICS
(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
Computer Science, Information Systems
Waleed Bin Shahid, Baber Aslam, Haider Abbas, Hammad Afzal, Saad Bin Khalid
Summary: This paper proposes a complete high interaction web deception system that utilizes a hybrid attack detection module and containerization to counter web attacks. The system provides attacker behavior analysis and efficient session management, and has high accuracy and competitive advantages over other solutions. It is also suitable for IoT networks.
JOURNAL OF INFORMATION SECURITY AND APPLICATIONS
(2022)
Article
Multidisciplinary Sciences
Marcel Friedrichs, Cassandra Koenigs
Summary: Biological databases are crucial for life science research, but it can be challenging to find and select the most relevant and up-to-date databases. This article presents a web-based platform that annotates and analyzes databases published in the Nucleic Acids Research (NAR) journal. The platform provides researchers with additional information and insights to facilitate database selection.
Article
Engineering, Electrical & Electronic
Shaoyong Guo, Fan Zhang, Song Guo, Siya Xu, Feng Qi
Summary: This article proposes a blockchain-assisted privacy-preserving distributed data computing architecture to overcome the limitations of existing research. The architecture ensures secure and trustworthy computing and incorporates a sandbox location obfuscation method based on onion routing technology, making it difficult for attackers to infer user privacy.
IEEE COMMUNICATIONS MAGAZINE
(2023)
Article
Biochemistry & Molecular Biology
Martin Diaz-Rodriguez, Oscar Lithgow-Serrano, Francisco Guadarrama-Garcia, Victor H. Tierrafria, Socorro Gama-Castro, Hilda Solano-Lira, Heladia Salgado, Fabio Rinaldi, Carlos-Francisco Mendez-Cruz, Julio Collado-Vides
Summary: Manually curated databases are helpful for researchers to access knowledge. The Lisen&Curate system facilitates linking content in articles with curated objects, providing rich additional information.
BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS
(2021)
Article
Computer Science, Information Systems
Muhammad Aasim Qureshi, Muhammad Asif, Mohd Fadzil Hassan, Ghulam Mustafa, Muhammad Khurram Ehsan, Aasim Ali, Unaza Sajid
Summary: This study proposes a fully automated annotation technique for aspect level sentiment analysis and validates it using a dataset of YouTube comments. The results show that the proposed technique achieves annotation quality comparable to manual annotation, while requiring significantly less computational cost.
CMC-COMPUTERS MATERIALS & CONTINUA
(2022)
Article
Chemistry, Multidisciplinary
Alessandro Bombini, Ahmad Alkhansa, Laura Cappelli, Achille Felicetti, Francesco Giacomini, Alessandro Costantini
Summary: The Competence Centre for the Conservation of Cultural Heritage (4CH) project has initiated the design and deployment of a platform-as-a-service cloud infrastructure for the first European competence centre of cultural heritage, integrating web services such as THESPIAN-Mask for scientific analysis storage and THESPIAN-NER for named entity recognition. Both services aim to simplify metadata generation and data injection processes for users.
APPLIED SCIENCES-BASEL
(2022)
Article
Engineering, Electrical & Electronic
Yu Qiu, Haijun Zhang, Kai Sun, Keping Long, Arumugam Nallanathan
Summary: Web3, as the next generation Internet, is rapidly developing and has attracted extensive attention. This article proposes a new network architecture called FogBC-RAN, which can support stable connections on a global scale and enable new services. The article also introduces the cross-chain information transfer process and computing offloading strategy in the future Web3, which can effectively support its development.
IEEE COMMUNICATIONS MAGAZINE
(2023)
Article
Computer Science, Artificial Intelligence
Enwei Zhu, Qilin Sheng, Huanwan Yang, Yiyang Liu, Ting Cai, Jinpeng Li
Summary: Medical information extraction is a group of NLP tasks that convert clinical text to structured formats for electronic medical records. This study presents an engineering framework consisting of three tasks, and demonstrates the entire workflow from data collection to model evaluation. Using a large scale and high quality corpus of Chinese clinical data, the medical information extraction system achieves human-level performance. The annotation scheme, annotated corpus subset, and code are publicly released for further research.
ARTIFICIAL INTELLIGENCE IN MEDICINE
(2023)
Article
Computer Science, Software Engineering
Andres Segura-Tinoco, Ivan Cantador
Summary: This paper presents ARGAEL, an open-source desktop tool designed to facilitate the manual annotation of related arguments in text documents. ARGAEL supports the use of configurable argument models, labeling of argument components and relations, and assessment of argument annotations from multiple annotators, making it suitable for large-scale, collaborative argument annotation processes.
Article
Computer Science, Information Systems
Yanrui Zhai, Xiran Zhou, Honghao Li
Summary: The emergence of the third information wave allows for the generation of extensive maps through volunteered methods, rather than solely relying on professional institutes. These volunteered maps, created by the public, provide abundant geographical information but present a challenge in recognizing unstructured text compared to previous approaches for standard map text detection.
ISPRS INTERNATIONAL JOURNAL OF GEO-INFORMATION
(2023)
Article
Biochemical Research Methods
Daoyu Duan, Sijia He, Emina Huang, Ziyi Li, Hao Feng
Summary: Correctly annotating cell types is crucial in scRNA-seq data analysis. NeuCA web server, a neural network-based tool, offers a user-friendly interface for automated cell labeling and provides a variety of pre-trained classifiers.
Article
Environmental Sciences
Shizheng Zhou, Juntao Jiang, Xiaohan Hong, Pengcheng Fu, Hong Yan
Summary: Marine microalgae are important organisms in the ocean ecosystem, and their automatic identification and location in microscopy images can contribute to marine ecological environment monitoring. This study presents a new dataset and various detection methods for marine microalgae detection, including different genus and states of algae. Both one-stage and two-stage object detection models showed high performance in detecting microalgae, highlighting the potential of computer vision in multi-object detection of microalgae cells.
FRONTIERS IN MARINE SCIENCE
(2023)
Article
Genetics & Heredity
Gislenne da Silva Moia, Antonio Sergio Cruz Gaia, Monica Silva de Oliveira, Victoria Cardoso dos Santosa, Jorianne Thyeska Castro Alves, Pablo Henrique Caracciolo Gomes de Sa, Adonney Allan de Oliveira Veras
Summary: The reduction in the cost and time of DNA sequencing has led to an increase in biological information in public databases. Algorithms and tools have been developed to handle large volumes of data and automate the analysis and annotation of genomes. The ReNoteWeb web tool provides assistance in the assembly enhancement and annotation processes, reducing the time required for manual curation. The tool has been validated on 23 organisms and compared to existing databases and platforms for efficiency.
Article
Multidisciplinary Sciences
Julie Melendez, Daniel Sieiro, David Salgado, Valerie Morin, Marie-Julie Dejardin, Chan Zhou, Alan C. Mullen, Christophe Marcelle
Summary: Fusion of myoblasts is essential for muscle development and repair, with TGF-beta signaling regulating the pace of fusion through a receptor complementation mechanism and endocytic degradation of activated receptors.
NATURE COMMUNICATIONS
(2021)
Article
Biochemistry & Molecular Biology
Elena Gargaun, Sestina Falcone, Guilhem Sole, Julien Durigneux, Andoni Urtizberea, Jean Marie Cuisset, Sofia Benkhelifa-Ziyyat, Laura Julien, Anne Boland, Florian Sandron, Vincent Meyer, Jean Francois Deleuze, David Salgado, Jean-Pierre Desvignes, Christophe Beroud, Anatole Chessel, Alexia Blesius, Martin Krahn, Nicolas Levy, France Leturcq, France Pietri-Rouxel
Summary: This study found that long noncoding RNAs play important roles in Duchenne and Becker muscular dystrophy, particularly in regulating myocyte proliferation and differentiation with potential therapeutic implications. The research suggests that lncRNA44s2 may serve as an accelerator in muscle differentiation process and is associated with a favorable clinical phenotype.
Article
Biochemistry & Molecular Biology
Miguel Vazquez, Martin Krallinger, Florian Leitner, Martin Kuiper, Alfonso Valencia, Astrid Laegreid
Summary: This article describes a method to construct a knowledge graph of transcription factor-target gene relationships using text mining tools, with an accuracy close to 75%. It covers 80% of the relationships annotated in existing databases and adds around 11,000 potential interactions.
BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS
(2022)
Article
Genetics & Heredity
Steven Laurie, Davide Piscia, Leslie Matalonga, Alberto Corvo, Marcos Fernandez-Callejo, Carles Garcia-Linares, Carles Hernandez-Ferrer, Cristina Luengo, Ines Martinez, Anastasios Papakonstantinou, Daniel Pico-Amador, Joan Protasio, Rachel Thompson, Raul Tonda, Monica Bayes, Gemma Bullich, Jordi Camps-Puchadas, Ida Paramonov, Jean-Remi Trotta, Angel Alonso, Marcella Attimonelli, Christophe Beroud, Virginie Bros-Facer, Orion J. Buske, Andres Canada-Pallares, Jose M. Fernandez, Mats G. Hansson, Rita Horvath, Julius O. B. Jacobsen, Rajaram Kaliyaperumal, Severine Lair-Preterre, Luana Licata, Pedro Lopes, Estrella Lopez-Martin, Deborah Mascalzoni, Lucia Monaco, Luis A. Perez-Jurado, Manuel Posada de la Paz, Jordi Rambla, Ana Rath, Olaf Riess, Peter N. Robinson, David Salgado, Damian Smedley, Dylan Spalding, Peter A. C. 't Hoen, Ana Topf, Irina Zaharieva, Holm Graessner, Ivo G. Gut, Hanns Lochmuller, Sergi Beltran
Summary: Rare disease patients are now more likely to receive rapid molecular diagnosis, but some cases still remain undiagnosed. The RD-Connect GPAP provides a standardized platform for data collection, sharing, and analysis to aid in diagnosing cases and discovering new disease causing genes.
Article
Biochemistry & Molecular Biology
Emilie Pihan, Martin Kotev, Obdulia Rabal, Claudia Beato, Constantino Diaz Gonzalez
Summary: Structure-based virtual screening is crucial in drug discovery, allowing for the selection of potential ligands for experimental testing. By developing an automated calibration process, it is possible to significantly reduce the duration of the calibration phase and choose the best protocol effectively.
JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN
(2021)
Article
Biochemical Research Methods
Carlos A. Garcia-Prieto, Francisco Martinez-Jimenez, Alfonso Valencia, Eduard Porta-Pardo
Summary: This study highlights the significant impact of variant calling decisions on key analyses of cancer genomic data, such as the identification of cancer driver genes, quantification of mutational signatures, and detection of clinically actionable variants. The choice of somatic variant caller or strategy to combine them can lead to important differences in results, potentially impacting treatment decisions for patients. The widely used Consensus of three calling strategy may result in the loss of important cancer driver genes and actionable mutations, emphasizing the importance of careful consideration in variant calling for critical analyses of tumor sequencing data.
Article
Computer Science, Artificial Intelligence
Charilaos Akasiadis, Miguel Ponce-de-Leon, Arnau Montagud, Evangelos Michelioudakis, Alexia Atsidakou, Elias Alevizos, Alexander Artikis, Alfonso Valencia, Georgios Paliouras
Summary: Computational systems and methods play an important role in biological research, particularly in the understanding and treatment of cancer. This study combines a simulator for tumor cell growth and a genetic algorithm to find effective parameter configurations for drug treatments. Experimental results demonstrate the effectiveness and computational efficiency of the approach.
COMPUTATIONAL INTELLIGENCE
(2022)
Article
Medicine, General & Internal
Ferran Catala-Lopez, Jane A. Driver, Matthew J. Page, Brian Hutton, Manuel Ridao, Clara Berrozpe-Villabona, Adolfo Alonso-Arroyo, Cristina A. Fraga-Medin, Enrique Bernal-Delgado, Alfonso Valencia, Rafael Tabares-Seisdedos
Summary: This study aims to evaluate the design, methods, and reporting of studies conducted using routine health data to investigate the link between cancer and neurodegenerative diseases. The study will search electronic databases and use standardized data extraction forms. The findings will be summarized using tables and graphs. No ethical approval is required, and the full study will be published in an open access journal.
Article
Microbiology
Ferran Tarres-Freixas, Benjamin Trinite, Anna Pons-Grifols, Miguel Romero-Durana, Eva Riveira-Munoz, Carlos avila-Nieto, Monica Perez, Edurne Garcia-Vidal, Daniel Perez-Zsolt, Jordana Munoz-Basagoiti, Dalia Raich-Regue, Nuria Izquierdo-Useros, Cristina Andres, Andres Anton, Tomas Pumarola, Ignacio Blanco, Marc Noguera-Julian, Victor Guallar, Rosalba Lepore, Alfonso Valencia, Victor Urrea, Julia Vergara-Alert, Bonaventura Clotet, Ester Ballana, Jorge Carrillo, Joaquim Segales, Julia Blanco
Summary: The study found that the emerging SARS-CoV-2 variants show heterogeneous infectivity and pathogenesis in mice models, with B.1.351/Beta variant being the most pathogenic and BA.1.1/Omicron leading to lower viral RNA levels.
FRONTIERS IN MICROBIOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Miguel Ponce-de-Leon, Arnau Montagud, Charilaos Akasiadis, Janina Schreiber, Thaleia Ntiniakou, Alfonso Valencia
Summary: The study used multi-scale models to investigate the complex phenomenon of cell resistance in cancer treatment, demonstrating the importance of considering cells' spatial geometry and population variability when optimizing treatment strategies.
FRONTIERS IN MOLECULAR BIOSCIENCES
(2022)
Article
Plant Sciences
Andrei S. Steindorff, Kyungyong Seong, Akiko Carver, Sara Calhoun, Monika S. Fischer, Kyra Stillman, Haowen Liu, Elodie Drula, Bernard Henrissat, Hunter J. Simpson, Jonathan S. Schilling, Anna Lipzen, Guifen He, Mi Yan, Bill Andreopoulos, Jasmyn Pangilinan, Kurt LaButti, Vivian Ng, Matthew Traxler, Thomas D. Bruns, Igor Grigoriev
Summary: Wildfires have a drastic impact on the soil environment, altering soil organic matter and reducing microorganism diversity. This study sequenced six new genomes of post-fire pyrophilous fungi and found enrichment of gene families involved in stress responses and the degradation of pyrolyzed organic matter. The protein sequence lengths and G+C content in pyrophilous fungi fall between those in mesophilic/nonpyrophilous and thermophilic fungi. Comparative transcriptome analysis revealed co-expressed gene modules in charcoal and light-induced sexual development conditions, suggesting a potential connection between charcoal tolerance and fruiting body formation in one pyrophilous fungus.
Article
Infectious Diseases
A. Maisa, G. Spaccaferri, L. Fournier, J. Schaeffer, J. Deniau, P. Rolland, B. Coignard
Summary: This study investigated the first cases of Omicron detected in France and found that most cases presented with mild symptoms, including young individuals and those who were vaccinated. The findings provide important support for the national COVID-19 surveillance system.
INFECTIOUS DISEASES NOW
(2022)
Proceedings Paper
Computer Science, Artificial Intelligence
Anastasios Nentidis, Anastasia Krithara, Georgios Paliouras, Luis Gasco, Martin Krallinger
Summary: The BioASQ Challenge aims to continuously improve approaches and tools for efficient and precise access to the growing field of biomedical knowledge. The annual challenges provide a testbed for investigating and comparing new approaches, aligning with the real needs of biomedical experts.
ADVANCES IN INFORMATION RETRIEVAL, PT II
(2022)
Article
Linguistics
Salvador Lima-Lopez, Eulalia Farre-Maduell, Antonio Miranda-Escalada, Vicent Briva-Iglesias, Martin Krallinger
Summary: Occupations play a significant role in various aspects of health and have an impact on physical and mental well-being. The MEDDOPROF shared task focused on recognizing and normalizing professions in medical documents, with best-performing systems based on deep-learning technologies achieving high F-scores. Future initiatives should consider multilingual aspects and application to other domains like social services and policy making.
PROCESAMIENTO DEL LENGUAJE NATURAL
(2021)
