Article
Biochemistry & Molecular Biology
Mihaly Varadi, Stephen Anyango, Sri Devan Appasamy, David Armstrong, Marcus Bage, John Berrisford, Preeti Choudhary, Damian Bertoni, Mandar Deshpande, Grisell Diaz Leines, Joseph Ellaway, Genevieve Evans, Romana Gaborova, Deepti Gupta, Aleksandras Gutmanas, Deborah Harrus, Gerard J. Kleywegt, Weslley Morellato Bueno, Nurul Nadzirin, Sreenath Nair, Lukas Pravda, Marcelo Querino Lima Afonso, David Sehnal, Ahsan Tanweer, James Tolchard, Charlotte Abrams, Roisin Dunlop, Sameer Velankar
Summary: The archiving and dissemination of protein and nucleic acid structures are crucial for impactful research in life sciences. The Protein Data Bank in Europe (PDBe) provides databases, web services, and visualizations to facilitate basic and applied research and education.
Editorial Material
Multidisciplinary Sciences
Luke M. M. Evans, Pamela N. Romero N. Villela
Summary: An analysis of rare genetic variants shows their impact on human traits is mediated through similar biological pathways as common variants, enhancing our understanding of their influence on complex traits.
Editorial Material
Multidisciplinary Sciences
Anthony J. Hannan
Summary: The study found a link between tandem repeats in DNA and autism spectrum disorder, which could provide insights into other human disorders. Bioinformatic analysis was used to study tandem repeat mutations in autism.
Article
Cell Biology
Duncan Wei, Xiaopu Chen, Jing Xu, Wenzhen He
Summary: The immune system is known to play a crucial role in the development of ischaemic stroke, but the exact immune-related mechanism remains unclear. Gene expression data of ischaemic stroke patients and healthy controls were analyzed to identify differentially expressed genes (DEGs). Immune-related genes (IRGs) data was also utilized for further analysis. Based on IRGs and weighted co-expression network analysis (WGCNA), two molecular subtypes of ischaemic stroke were identified. Nine hub genes, including IL7R, ITK, SOD1, CD3D, LEF1, FBL, MAF, DNMT1, and SLAMF1, were found to potentially distinguish between the two subtypes and be associated with immune regulation.
IET SYSTEMS BIOLOGY
(2023)
Article
Biology
Dagoberto Armenta-Medina, Christian Diaz de Leon Castaneda, Alma Armenta-Medina, Ernesto Perez-Rueda
Summary: This study analyzes the development of Bioinformatics research in Mexico by examining articles published in the field-specific database, PubMed. The findings reveal the strong correlation between research themes and outstanding researchers, as well as the influence of geographic proximity and collaborations with foreign institutions. There is also a focus on health issues driven by public health financing and philanthropic organizations. The significant increase in publications since 2012 is attributed to the availability of information in public databases. The study suggests the need for improved funding and academic collaborations in the informatics discipline. This work provides a diagnostic of the strengths and weaknesses of bioinformatics research development, which can be applied in other countries.
Review
Plant Sciences
Sydney Everhart, Nikita Gambhir, Remco Stam
Summary: This article provides a brief overview of topics relevant to the study of population genomics of filamentous plant pathogens, including different research question types, sampling strategies, sequencing strategies, data processing options, and population genomic data analysis tools. It highlights some of the hurdles along the population genomic workflow, offers cautionary warnings relative to assumptions and technical challenges, and presents future perspectives of the field.
Review
Cardiac & Cardiovascular Systems
Tejas P. Singh, Matt A. Field, Matthew J. Bown, Gregory T. Jones, Jonathan Golledge
Summary: This study systematically reviewed previous AAA GWAS and identified 33 SNPs associated with AAA diagnosis at genome-wide significance. However, the association between SNPs and AAA growth was not adequately examined. Previous GWAS have various design limitations, such as inconsistent case and control ascertainment and limited phenotyping of the AAAs.
Article
Biochemistry & Molecular Biology
Fabricio Almeida-Silva, Yves Van de Peer
Summary: Angiosperms have a complex history of whole-genome duplications, with varying numbers and ages of duplication events across different clades. These duplications have impacted plant genomes by selectively retaining genes involved in specific functions. Protein-protein interaction networks and gene regulatory networks enriched in these duplicated genes show strong selection pressure on gene sequences and interactions. Duplicated genes are predominantly involved in dosage-sensitive processes such as transcription regulation, cell cycle, translation, photosynthesis, and carbon metabolism.
MOLECULAR BIOLOGY AND EVOLUTION
(2023)
Article
Biotechnology & Applied Microbiology
Yanlin Mi, Stefan-Bogdan Marcu, Sabin Tabirca, Venkata V. B. Yallapragada
Summary: In the field of bioinformatics and computational biology, protein structure modelling and analysis is crucial. To address the lack of user-friendly tools, we developed PROFASA, a protein workstation that combines state-of-the-art visualisation techniques with cutting-edge tools for analysis. PROFASA provides a comprehensive platform for protein sequence and structure analysis, simplifying complex workflows and offering customization options.
FRONTIERS IN BIOENGINEERING AND BIOTECHNOLOGY
(2023)
Article
Biology
Ryan Christian Mailem, Lemmuel L. Tayo
Summary: This paper utilizes computational biology techniques to identify possible repurposed drugs for post-COVID-19 treatment. By analyzing the genetic similarities and differences in symptoms associated with COVID-19, the study identifies seven candidate drugs that have been shown to treat immune-system related ailments. The findings have the potential to drive drug design and discovery for more effective post-COVID-19 therapeutics, and demonstrate the importance of computational techniques in speeding up the drug development process.
Article
Biochemistry & Molecular Biology
Deborah Giordano, Cassiano Langini, Amedeo Caflisch, Anna Marabotti, Angelo Facchiano
Summary: The study compares the structures and flexibility of transglutaminase enzymes from Kutzneria albida (KalbTGase) and Streptomyces mobaraensis (MTGase). It is found that KalbTGase is more rigid and has a more closed catalytic site at room temperature, indicating higher selectivity compared to MTGase. Preliminary results at higher temperature suggest enhanced flexibility of KalbTGase, potentially allowing it to adapt to different substrates, while MTGase shows reduced adaptability and catalytic activity at higher temperatures.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2022)
Article
Biochemistry & Molecular Biology
Carmen Hoffbeck, Danielle M. R. L. Middleton, Nicola J. Nelson, Michael W. Taylor
Summary: An animal's gut microbiota plays a crucial role in their health, reproduction, and digestion. By analyzing 745 gut microbiota samples from 91 reptile species, this study identified the key factors influencing gut microbiota diversity, including host order and diet. The study also identified core microbial communities and highlighted the impact of taxonomy, environment, and conservation status on reptile gut microbiota.
Article
Cell Biology
Khadijeh Sadegh, Amirhossein Ahmadi
Summary: The use of healthy or normal adjacent tissues as calibrator tissues can have an impact on pathway enrichment data and hub gene selection in Gastric cancer (GC). In this study, gene expression datasets containing normal adjacent tissues and healthy tissues were analyzed using various bioinformatics methods. The results showed that there were some shared pathways between the two types of tissues, but selecting normal adjacent tissues as calibrator tissues could miss some inflammation-related pathways.
IET SYSTEMS BIOLOGY
(2023)
Article
Biochemical Research Methods
Tianshu Feng, Jaime Davila, Yuanhang Liu, Sangdi Lin, Shuai Huang, Chen Wang
Summary: Topological data analysis is a powerful method for dimensionality reduction, data relationship mining, and data structure representation, but current TDA modeling frameworks do not take into account domain context information and prior knowledge. The developed semi-supervised topological analysis (STA) framework, validated with simulation data, has been successfully applied to real gene expression and ovarian cancer data.
IEEE-ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS
(2021)
Article
Biochemical Research Methods
Asmita Tripathi, Rajkrishna Mondal, Tapobrata Lahiri, Deepak Chaurasiya, Manoj Kumar Pal
Summary: The AlphaFold predictor and the homology model both rely on proteins with known structure, but the structures predicted by AlphaFold are often not acceptable. This study used a new similarity criteria to identify template proteins and developed a template search engine which produced better results than traditional search engines. It highlights the need for a combined approach to obtain better protein structure models.
IEEE-ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS
(2023)
Article
Multidisciplinary Sciences
Ari Z. Klein, Arjun Magge, Graciela Gonzalez-Hernandez
Summary: This study developed and evaluated a method for automatically identifying the exact age of users based on self-reports in their tweets. They achieved high accuracy in age identification using natural language processing and a deep neural network classifier, and successfully applied the method to a large Twitter dataset.
Article
Psychology, Developmental
Shelby H. Davies, Miriam D. Langer, Ari Klein, Graciela Gonzalez-Hernandez, Nadia Dowshen
Summary: This study examines youth perceptions about menstruation on Twitter and finds that there is a negative expectation and shame surrounding menstruation. A significant portion of tweets are related to advocacy or education, supporting the potential use of Twitter as a platform to improve public health messaging, health outcomes, and equity for youth who menstruate.
JOURNAL OF ADOLESCENT HEALTH
(2022)
Review
Health Care Sciences & Services
Su Golder, Robin Stevens, Karen O'Connor, Richard James, Graciela Gonzalez-Hernandez
Summary: Social media data is increasingly used in health research. This study aims to identify different methods to extract race or ethnicity from social media and report on the challenges of using these methods. Through a scoping review, the study found that there is currently no standard approach to extract or infer the race or ethnicity of Twitter users, and there are challenges in terms of accuracy and ethical issues.
JOURNAL OF MEDICAL INTERNET RESEARCH
(2022)
Article
Public, Environmental & Occupational Health
Ari Z. Klein, Steven Meanley, Karen O'Connor, Jose A. Bauermeister, Graciela Gonzalez-Hernandez
Summary: By developing an automated natural language processing (NLP) pipeline, MSM at risk of HIV acquisition can be identified on Twitter, laying the groundwork for targeted PrEP-related interventions for this population on a large scale.
JMIR PUBLIC HEALTH AND SURVEILLANCE
(2022)
Article
Public, Environmental & Occupational Health
Su Golder, Davy Weissenbacher, Karen O'Connor, Sean Hennessy, Robert Gross, Graciela Gonzalez Hernandez
Summary: Social media analysis revealed that the main reason for discontinuation of statin therapy was patient experience of adverse events, with musculoskeletal and connective tissue disorders being the most common. 60% of posters identified as female, with the most common age category being 55-64 years. The unique patient perspectives found on social media may provide valuable insights for interventions to reduce medication discontinuation.
Article
Immunology
Jeb Jones, Justin Knox, Steven Meanley, Cui Yang, David W. Lounsbury, Terry T. Huang, Jose Bauermeister, Graciela Gonzalez-Hernandez, Victoria Frye, Christian Grov, Viraj Patel, Stefan D. Baral, Patrick S. Sullivan, Sheree R. Schwartz
Summary: The use of digital technology in HIV-related interventions and implementation strategies is significant and presents both challenges and opportunities. This article explores five case studies that highlight the role of technology in HIV-related implementation research, emphasizing the importance of study design, outcome measurement, and equity.
JAIDS-JOURNAL OF ACQUIRED IMMUNE DEFICIENCY SYNDROMES
(2022)
Article
Psychology, Clinical
Melanie L. Kornides, Sarah Badlis, Katharine J. Head, Mary Putt, Joseph Cappella, Graciela Gonzalez-Hernadez
Summary: Nearly a quarter of #HPV Tweets contain disinformation or misinformation about the HPV vaccine, with adverse health effects, mandatory vaccination, and vaccine inefficacy being the most prevalent categories. These misleading tweets are more likely to be retweeted than supportive tweets.
JOURNAL OF BEHAVIORAL MEDICINE
(2023)
Article
Computer Science, Artificial Intelligence
Robert Leaman, Rezarta Islamaj, Alexis Allot, Qingyu Chen, W. John Wilbur, Zhiyong Lu
Summary: A significant percentage of COVID-19 survivors experience ongoing multisystemic symptoms known as Long Covid. Identifying relevant scientific articles on Long Covid is challenging due to lack of standardized terminology. A machine learning framework combining data programming with active learning shows higher specificity and sensitivity compared to other methods. Analysis of the Long Covid Collection reveals that most articles do not refer to Long Covid by any name, and when mentioned, Long Covid is the most frequently used term associated with disorders in various body systems. The Long Covid Collection is regularly updated and searchable on the LitCovid portal.
Letter
Health Care Sciences & Services
Ari Z. Klein, Shriya Kunatharaju, Karen O'Connor, Graciela Gonzalez-Hernandez
JOURNAL OF MEDICAL INTERNET RESEARCH
(2023)
Letter
Health Care Sciences & Services
Ari Z. Klein, Shriya Kunatharaju, Karen O'Connor, Graciela Gonzalez-Hernandez
JOURNAL OF MEDICAL INTERNET RESEARCH
(2023)
Editorial Material
Urology & Nephrology
Qiao Jin, Robert Leaman, Zhiyong Lu
JOURNAL OF THE AMERICAN SOCIETY OF NEPHROLOGY
(2023)
Review
Health Care Sciences & Services
Su Golder, Karen O'Connor, Yunwen Wang, Graciela Gonzalez Hernandez
Summary: This study aims to evaluate and characterize the use of social media in adverse drug event detection and pharmacovigilance compared to other data sources. By comparing social media data with other sources, the added value of social media in monitoring adverse drug events can be concluded.
JMIR RESEARCH PROTOCOLS
(2023)
Article
Biochemical Research Methods
Ling Luo, Chih-Hsuan Wei, Po-Ting Lai, Robert Leaman, Qingyu Chen, Zhiyong Lu
Summary: Biomedical named entity recognition (BioNER) aims to automatically identify biomedical entities in natural language text, providing a necessary foundation for downstream text mining tasks and applications. Due to the expensive and domain-specific expertise required for manual annotation of training data, current BioNER approaches suffer from data scarcity and limitations in generalizability and entity coverage. In this paper, we propose an all-in-one (AIO) scheme that utilizes external annotated resources to enhance the accuracy and stability of BioNER models. We introduce AIONER, a general-purpose BioNER tool based on cutting-edge deep learning and our AIO scheme, and demonstrate its effectiveness, robustness, and advantages over existing methods on 14 BioNER benchmark tasks and three independent tasks.
Article
Mathematical & Computational Biology
Robert Leaman, Rezarta Islamaj, Virginia Adams, Mohammed A. Alliheedi, Joao Rafael Almeida, Rui Antunes, Robert Bevan, Yung-Chun Chang, Arslan Erdengasileng, Matthew Hodgskiss, Ryuki Ida, Hyunjae Kim, Keqiao Li, Robert E. Mercer, Lukrecia Mertova, Ghadeer Mobasher, Hoo-Chang Shin, Mujeen Sung, Tomoki Tsujimura, Wen-Chao Yeh, Zhiyong Lu
Summary: The BioCreative National Library of Medicine (NLM)-Chem track is a community effort to improve automated recognition of chemical names in biomedical literature. The track consists of two tasks: chemical identification and chemical indexing. The community challenge demonstrated the achievements in deep learning technologies and the challenges of the chemical indexing task. Further development of biomedical text-mining methods is expected to respond to the rapid growth of biomedical literature.
DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION
(2023)
Article
Health Care Sciences & Services
Ari Z. Klein, Karen O'Connor, Lisa D. Levine, Graciela Gonzalez-Hernandez
Summary: This study examined the utility of Twitter data for analyzing the outcomes of pregnancies where beta-blockers were taken. The results suggest that Twitter can be a useful resource for cohort studies on drug safety during pregnancy.
JMIR FORMATIVE RESEARCH
(2022)