Editorial Material
Green & Sustainable Science & Technology
Brian Leung
Summary: A paper reports a workable and effective solution for the management of introduced species, such as kudzu or zebra mussels, which harnesses network analyses of ecological phenomena.
NATURE SUSTAINABILITY
(2022)
Article
Multidisciplinary Sciences
Danielle Welter, Nick Juty, Philippe Rocca-Serra, Fuqi Xu, David Henderson, Wei Gu, Jolanda Strubel, Robert T. Giessmann, Ibrahim Emam, Yojana Gadiya, Tooba Abbassi-Daloii, Ebtisam Alharbi, Alasdair J. G. Gray, Melanie Courtot, Philip Gribbon, Vassilios Ioannidis, Dorothy S. Reilly, Nick Lynch, Jan-Willem Boiten, Venkata Satagopam, Carole Goble, Susanna-Assunta Sansone, Tony Burdett
Summary: The COVID-19 pandemic has emphasized the importance of FAIR data. We developed a flexible FAIRification framework that improves data accessibility and reusability in clinical and molecular datasets. Through collaboration with various projects, our framework demonstrated its reproducibility and applicability across different datasets and contexts.
Review
Genetics & Heredity
Alan Taylor, Zeinab Alloub, Ahmad Abou Tayoun
Summary: As genetic testing becomes more prevalent in medical specialties, healthcare providers often lack the necessary support to order appropriate tests for their patients. Educating providers on genetic testing concepts and proper utilization is crucial for timely diagnoses and cost-effective testing strategies.
Article
Biochemistry & Molecular Biology
Kevin Yauy, Charles Van Goethem, Henri Pegeot, David Baux, Thomas Guignard, Corinne Theze, Olivier Ardouin, Anne-Francoise Roux, Michel Koenig, Anne Bergougnoux, Mireille Cossee
Summary: The transition from targeted sequencing to exome or genome sequencing in clinical contexts lacks clear recommendations or methodology. This study developed a method for evaluating the performance of exome sequencing strategies based on specific sequencing metrics. The study compared different exome kits and a targeted sequencing method, finding significant differences in coverage and PCR duplicates. This study is important for assisting molecular diagnostic laboratories in adopting and evaluating exome sequencing kits in a diagnostic context.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Biochemistry & Molecular Biology
Genis Garcia-Erill, Kristian Hanghoj, Rasmus Heller, Carsten Wiuf, Anders Albrechtsen
Summary: The genome of recently admixed individuals or hybrids has characteristic genetic patterns that can be used to learn about their recent admixture history. We implemented maximum likelihood estimation of interancestry heterozygosity patterns using two complementary models. We also developed a software, apoh, to detect recently admixed individuals or hybrids, and suggest possible admixture pedigrees.
MOLECULAR ECOLOGY RESOURCES
(2023)
Review
Oncology
Nicholas Bradley Larson, Ann L. Oberg, Alex A. Adjei, Liguo Wang
Summary: Next-generation sequencing (NGS) technologies, widely used in cancer research, generate vast and diverse data that require sophisticated computational methods and bioinformatics expertise. This review provides background details of NGS technology and basic bioinformatics concepts for clinicians interested in cancer research applications, with a focus on DNA-based approaches. It introduces principles of library preparation, alignment, variant calling, variant annotations, and NGS applications for other molecular data types. The review also discusses the utility of NGS methods in NSCLC research and study design considerations for leveraging NGS technologies in clinical care.
JOURNAL OF THORACIC ONCOLOGY
(2023)
Review
Multidisciplinary Sciences
Kirsten Grorud-Colvert, Jenna Sullivan-Stack, Callum Roberts, Vanessa Constant, Barbara Horta E Costa, Elizabeth P. Pike, Naomi Kingston, Dan Laffoley, Enric Sala, Joachim Claudet, Alan M. Friedlander, David A. Gill, Sarah E. Lester, Jon C. Day, Emanuel J. Goncalves, Gabby N. Ahmadia, Matt Rand, Angelo Villagomez, Natalie C. Ban, Georgina G. Gurney, Ana K. Spalding, Nathan J. Bennett, Johnny Briggs, Lance E. Morgan, Russell Moffitt, Marine Deguignet, Ellen K. Pikitch, Emily S. Darling, Sabine Jessen, Sarah O. Hameed, Giuseppe Di Carlo, Paolo Guidetti, Jean M. Harris, Jorge Torre, Zafer Kizilkaya, Tundi Agardy, Philippe Cury, Nirmal J. Shah, Karen Sack, Ling Cao, Miriam Fernandez, Jane Lubchenco
Summary: Marine Protected Areas (MPAs) are tools for conserving marine ecosystems and biodiversity. However, confusion over the various MPA types has led to inconsistent outcomes. The MPA Guide provides a science-driven framework to improve the design, implementation, and evaluation of MPAs for achieving conservation goals.
Article
Biodiversity Conservation
Jessica A. Rowland, Lucie M. Bland, Simon James, Emily Nicholson
Summary: Biodiversity indicators are essential for informing decisions and measuring progress, but uncertainty and variability are often not quantified accurately. This study developed a guide to help select appropriate methods for representing uncertainty or variation in biodiversity indicators, aiding in accurate interpretation by decision makers. Different interval methods provided valuable information about underlying variability and uncertainty, with the choice depending on indicator formulation and data distribution.
CONSERVATION BIOLOGY
(2021)
Review
Oncology
Albrecht Stenzinger, Arndt Vogel, Ulrich Lehmann, Angela Lamarca, Paul Hofman, Luigi Terracciano, Nicola Normanno
Summary: Cholangiocarcinomas are a heterogeneous group of tumors with distinct genomic alterations. Next-generation sequencing is a powerful tool for identifying gene variants and guiding personalized treatment for patients with cholangiocarcinomas. Understanding the use of NGS in molecular profiling is crucial for healthcare professionals to optimize treatment outcomes.
CANCER TREATMENT REVIEWS
(2024)
Article
Immunology
Yi Tian, Bingxuan Wu, Linyi Peng, Jian Wang, Min Shen
Summary: This study reports the clinical characteristics and genetic variants of eight HA20 patients from three Chinese families. Two novel TNFAIP3 variants were identified and validated as pathogenic. The clinical phenotype of Chinese HA20 patients is similar to that of patients from other populations, except for a lower frequency of genital ulcers.
FRONTIERS IN IMMUNOLOGY
(2022)
Review
Cell Biology
Yong-Xin Liu, Yuan Qin, Tong Chen, Meiping Lu, Xubo Qian, Xiaoxuan Guo, Yang Bai
Summary: This article systematically summarizes the advantages and limitations of methods in microbiome research, recommends specific analysis flows and common software, introduces statistical and visualization methods suitable for microbiome analysis, and provides a reproducible analysis guide. The goal is to help researchers conduct data analysis more effectively and efficiently mine the biological significance behind the data.
Review
Biochemical Research Methods
Jiung-Wen Chen, Lisa Shrestha, George Green, Andre Leier, Tatiana T. Marquez-Lago
Summary: DNA and RNA sequencing technologies have greatly advanced biology and biomedical sciences by enabling high-speed and cost-effective sequencing of full genomes and transcriptomes. RNA sequencing (RNA-Seq) has been particularly useful for transcript identification and quantification. However, the analysis of RNA-Seq data presents challenges in terms of interpreting and deriving actionable knowledge from the vast amount of information generated. This paper provides a detailed explanation of the steps involved in RNA-Seq analysis and discusses various options, their advantages, and disadvantages. It also explores additional topics such as non-coding RNA analysis, multi-omics approaches, meta-transcriptomics, and the use of artificial intelligence methods in complementing existing tools. The paper concludes with a complete analysis example, emphasizing the impact of algorithmic decisions on results and interpretation.
BRIEFINGS IN BIOINFORMATICS
(2023)
Article
Public, Environmental & Occupational Health
Mary Lou Manning, Monika Pogorzelska-Maziarz, Cindy Hou, Nikunj Vyas, Marianne Kraemer, Eileen Carter, Elizabeth Monsees
Summary: This study aims to establish an evidence-based framework for antibiotic stewardship nursing practice to guide nurses in participating and leading in antibiotic stewardship practices. Nurses are ideally positioned to provide holistic care, advocate for judicious use of antibiotics, and act as educators in antibiotic stewardship on a global scale.
AMERICAN JOURNAL OF INFECTION CONTROL
(2022)
Article
Genetics & Heredity
Elise A. Ferreira, Annemarijne R. J. Veenvliet, Udo F. H. Engelke, Leo A. J. Kluijtmans, Marleen C. D. G. Huigen, Brechtje Hoegen, Lonneke de Boer, Maaike C. de Vries, Bregje W. van Bon, Erika Leenders, Elisabeth A. M. Cornelissen, Charlotte A. Haaxma, Jolanda H. Schieving, M. Estela Rubio-Gozalbo, Irene M. L. W. Korver-Keularts, Lara M. Marten, Susann Diegmann, Jeroen Mourmans, Alexander J. M. Rennings, Clara D. M. van Karnebeek, Richard J. Rodenburg, Karlien L. M. Coene
Summary: This article discusses the application of gene function tests in the diagnosis of patients with inherited metabolic disorders (IMDs), highlighting the value of metabolomics-based analysis in enhancing diagnostic success and improving clinical management.
GENETICS IN MEDICINE
(2023)
Article
Green & Sustainable Science & Technology
R. Gaillac, S. Marbach
Summary: The article discusses the significant portion of greenhouse gas emissions from meat and dairy products in the food industry and how to reduce their carbon footprint. By comparing the carbon footprint of different meat and dairy products, a method of reducing carbon emissions by adjusting the diet structure is proposed. The study found that a diet mainly consisting of dairy products only slightly reduces carbon emissions compared to current diets, while a tailored diet including small poultry, eggs, and yogurt can achieve a 50% reduction in carbon footprint globally.
JOURNAL OF CLEANER PRODUCTION
(2021)