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Biotechnology & Applied Microbiology
Erica L. Lyons, Daniel Watson, Mohammad S. Alodadi, Sharie J. Haugabook, Gregory J. Tawa, Fady Hannah-Shmouni, Forbes D. Porter, Jack R. Collins, Elizabeth A. Ottinger, Uma S. Mudunuri
Summary: Rare diseases are difficult to diagnose and treat. Genetic sequencing has the potential to improve the diagnostic process, but there are challenges in interpreting variant pathogenicity and communicating known causative variants. This study investigated the translation of variant knowledge from published manuscripts to public databases and found that some pathogenic variants were inaccessible, limiting the use of this information for diagnosis and treatment. Developing text mining workflows that combine natural language processing and impact prediction algorithms could be a promising approach to address this issue.
Article
Biochemistry & Molecular Biology
Noemi del Toro, Anjali Shrivastava, Eliot Ragueneau, Birgit Meldal, Colin Combe, Elisabet Barrera, Livia Perfetto, Karyn How, Prashansa Ratan, Gautam Shirodkar, Odilia Lu, Balint Meszaros, Xavier Watkins, Sangya Pundir, Luana Licata, Marta Iannuccelli, Matteo Pellegrini, Maria Jesus Martin, Simona Panni, Margaret Duesbury, Sylvain D. Vallet, Juri Rappsilber, Sylvie Ricard-Blum, Gianni Cesareni, Lukasz Salwinski, Sandra Orchard, Pablo Porras, Kalpana Panneerselvam, Henning Hermjakob
Summary: IntAct is a curated database of molecular interactions derived from scientific literature, containing over one million binary interactions curated by twelve global partners. The IMEx curation policy emphasizes fine-grained data and curation model to capture essential experimental details for interpretation of the molecular interaction data. Recently, IntAct has introduced a completely redeveloped website to present data in a more user-friendly and detailed way.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Biochemistry & Molecular Biology
John A. Bachman, Benjamin M. Gyori, Peter K. Sorger
Summary: This study presents an approach to accurately assemble molecular mechanisms by using multiple natural language processing systems and INDRA, which improves the reliability of machine reading and assembles non-redundant mechanistic knowledge. Through this approach, the study extends protein-protein interaction databases and provides explanations for co-dependencies in the Cancer Dependency Map.
MOLECULAR SYSTEMS BIOLOGY
(2023)
Article
Multidisciplinary Sciences
Arthur Viode, Patrick van Zalm, Kinga K. Smolen, Benoit Fatou, David Stevenson, Meenakshi Jha, Ofer Levy, Judith Steen, Hanno Steen
Summary: We present a cost-effective, robust high-throughput-compatible method for depleting plasma, enabling comprehensive profiling of plasma with detection of >1300 proteins per run and throughput of 60 samples per day. The method has been extensively validated, processing >3000 samples with no apparent batch effect, and costs around $2.5 per sample for the depletion step.
Article
Engineering, Environmental
Emma H. Palm, Parviel Chirsir, Jessy Krier, Paul A. Thiessen, Jian Zhang, Evan E. Bolton, Emma L. Schymanski
Summary: Transformation product (TP) information is crucial for assessing the hazards of compounds, but the availability and usability of TP data are often limited. FAIRifying existing TP knowledge can improve data accessibility for identification workflows. ShinyTPs is an application that curates and visualizes text-mined chemical names to validate automatically extracted reactions. The application was successful in retrieving and adding newly curated reactions to the PubChem Transformations library, supporting TP identification in non-target analysis workflows.
ENVIRONMENTAL SCIENCE & TECHNOLOGY LETTERS
(2023)
Article
Cell Biology
Xiaohua Jiang, Daren Zhao, Asim Ali, Bo Xu, Wei Liu, Jie Wen, Huan Zhang, Qinghua Shi, Yuanwei Zhang
Summary: MeiosisOnline is a comprehensive database containing known functional genes and potential candidates, providing a wealth of information and classification related to meiosis. 165 mouse genes were predicted as potential candidates for meiosis. The database's search tools and user-friendly interface greatly assist researchers in studying meiosis efficiently and easily.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2021)
Article
Biotechnology & Applied Microbiology
Igor A. Podolsky, Susanna Seppala, Haiqing Xu, Yong-Su Jin, Michelle A. O'Malley
Summary: The study identified a novel fungal SWEET transporter, NcSWEET1, from anaerobic fungi that can enhance glucose and xylose co-utilization. By constructing single cross-over chimeras and studying protein structure and function, enhanced variants were identified, offering potential applications in improving sugar transport efficiency.
METABOLIC ENGINEERING
(2021)
Article
Microbiology
Corinna Probst, Magnus J. Hallas-Moller, Johan O. Ipsen, Jacob S. Brooks, Karsten Andersen, Mireille Haon, Jean-Guy A. Berrin, Helle Martens, Connie A. Nichols, Katja Johansen, J. Andrew A. Alspaugh
Summary: Fungi adapt to environmental stress by changing their size, shape, or rate of cell division. This study focuses on the role of the CEL1 gene in the fungal pathogen Cryptococcus neoformans, which is involved in cell wall remodeling and adaptation to the host environment. The results indicate that CEL1 is required for stress response phenotypes and virulence in C. neoformans.
Article
Computer Science, Artificial Intelligence
Hyejin Jang, Yujin Jeong, Byungun Yoon
Summary: This study proposes a methodology for designing a TechWord-based lexical database that aims to improve the text mining performance of technological information.
EXPERT SYSTEMS WITH APPLICATIONS
(2021)
Article
Biochemistry & Molecular Biology
Jiajing Hu, Rosalba Lepore, Richard J. B. Dobson, Ammar Al-Chalabi, Daniel M. Bean, Alfredo Iacoangeli
Summary: The rapid progress in understanding genetics underlying biological processes has led to the development of DGLinker, a webserver that uses machine learning models to predict novel genetic factors associated with human diseases. DGLinker allows users to explore biomedical information, generate knowledge graphs, and predict new disease-associated genes, making it a valuable tool for researchers in the field.
NUCLEIC ACIDS RESEARCH
(2021)
Article
Chemistry, Medicinal
Bailu Yan, Xinchun Ran, Anvita Gollu, Zihao Cheng, Xiang Zhou, Yiwen Chen, Zhongyue J. Yang
Summary: Data-driven modeling is crucial for biocatalyst design and discovery, and a biocatalytic database integrating enzyme structure and function data is urgently needed. In this study, we introduce IntEnzyDB as an integrated structure-kinetics database, which allows easy statistical modeling and machine learning. Using this database, we investigated the effects of mutations on enzyme efficiency, and found that efficiency-enhancing mutations are globally encoded. Furthermore, we provide a web interface for public access to enzymology data stored in IntEnzyDB.
JOURNAL OF CHEMICAL INFORMATION AND MODELING
(2022)
Article
Computer Science, Artificial Intelligence
Martin Perez-Perez, Tania Ferreira, Gilberto Igrejas, Florentino Fdez-Riverola
Summary: Discovering relevant biomedical interactions is crucial for biology research. This study proposes a novel vector-space integrated with a deep learning model to assist manual curators in a real curation task. Experimental results show that the proposed workflow is valuable for semi-automatic relation extraction and saves manual annotation efforts.
EXPERT SYSTEMS WITH APPLICATIONS
(2022)
Article
Environmental Sciences
Dinesh Kumar Barupal, Mary K. Schubauer-Berigan, Michael Korenjak, Jiri Zavadil, Kathryn Z. Guyton
Summary: The study utilized database fusion, cheminformatics, and text mining techniques to analyze and prioritize recommended carcinogenic agents through an innovative approach. This method provides crucial information for future evaluations, aiding in understanding the volume and key characteristics of relevant information.
ENVIRONMENT INTERNATIONAL
(2021)
Article
Biotechnology & Applied Microbiology
Tiantian Han, Yingchun Zhou, Danhua Li
Summary: This study identified 199 common genes between HCC and depression, with GO term enrichment analysis showing association with cell death and apoptosis, and KEGG enrichment analysis showing pathways related to inflammatory response. Some genes exhibited statistical differences in expression and survival rates in HCC, possibly linked to associated drugs.
Article
Nursing
Figaro L. Loresto, Lisa Nunez, Lindsey Tarasenko, Marie St Pierre, Kenneth Oja, Mallory Mueller, Bailey Switzer, Katherine Marroquin, Catherine Kleiner
Summary: This study describes the development and function of the Nursing COVID and Historical Epidemic Literature repository, which utilizes text mining algorithms to extract nurse-specific literature from CORD-19 and LitCOVID datasets, providing high-level summaries. The repository contains 760 articles as of July 2020, with summaries indicating the importance of psychological support for nurses and high-impact rapid education.