Article
Multidisciplinary Sciences
Elliott J. Price, Chiara M. Vitale, Gary W. Miller, Arthur David, Robert Barouki, Karine Audouze, Douglas I. Walker, Jean-Philippe Antignac, Xavier Coumoul, Vincent Bessonneau, Jana Klanova
Summary: The exposome concept encourages consideration of non-genetic factors that influence an individual's health, but different interpretations of the concept have led to confusion. A reattribution of the exposome and introduction of the term "functional exposomics" can provide a more integrable dataset for multiomics and systems biology research.
Article
Plant Sciences
Pei-Hsiu Kao, Supaporn Baiya, Zheng-Yuan Lai, Chih-Min Huang, Li-Hsin Jhan, Chian-Jiun Lin, Ya-Syuan Lai, Chung-Feng Kao
Summary: This study proposes an advanced systems biology framework for the discovery of cold tolerance genes in soybean using integrated omics and non-omics data. The study identifies cold tolerance genes and uncovers relevant physiological pathways, advancing the understanding of soybean cold-stress response.
FRONTIERS IN PLANT SCIENCE
(2022)
Editorial Material
Hematology
Visith Thongboonkerd
Summary: This study conducted a comprehensive analysis of chronic lymphocytic leukemia using a multidimensional approach, obtaining both confirmatory and novel data that offer opportunities for improving therapeutic outcomes for the disease.
Article
Biochemistry & Molecular Biology
Peng Zhou, Li Wang, Hai Liu, Chunyan Li, Zhimin Li, Jinxiang Wang, Xiaoming Tan
Summary: CyanoOmicsDB is a database aiming to provide comprehensive functional information for cyanobacterial genes, with over 8 million entries from 928 genomes. It integrates transcriptional and translational profiles, gene function predictions, protein sequences, homologs, and more, offering researchers in this field a convenient way to access functional information on cyanobacterial genes. Compared to other existing databases, CyanoOmicsDB stands out for its extensive datasets and comprehensive functional information.
NUCLEIC ACIDS RESEARCH
(2022)
Review
Chemistry, Multidisciplinary
Tae Hwan Shin, Saraswathy Nithiyanandam, Da Yeon Lee, Do Hyeon Kwon, Ji Su Hwang, Seok Gi Kim, Yong Eun Jang, Shaherin Basith, Sungsu Park, Jung-Soon Mo, Gwang Lee
Summary: Nanoparticles in biomedical applications offer advantages due to their small size, but evaluating their potential adverse effects on health is necessary and challenging. Omics approaches, in combination with machine learning techniques, provide a more comprehensive and sensitive way to assess nanotoxicity. Additionally, mechanobiology methods can be applied to evaluate the biophysical changes induced by nanoparticles, enhancing the overall understanding of their safety implications.
Review
Biotechnology & Applied Microbiology
Parminder S. Reel, Smarti Reel, Ewan Pearson, Emanuele Trucco, Emily Jefferson
Summary: With the advancement of high-throughput omics technologies, it is crucial for biomedical research to adopt integrative approaches to analyze diverse omics data using machine learning algorithms. This can lead to the discovery of novel biomarkers and improve disease prediction and precision medicine delivery.-Methods in machine learning have enabled researchers to gain a deeper insight into biological systems and provide recommendations for interdisciplinary professionals looking to incorporate machine learning skills in multi-omics studies.
BIOTECHNOLOGY ADVANCES
(2021)
Article
Biochemistry & Molecular Biology
Denes Tuerei, Alberto Valdeolivas, Lejla Gul, Nicolas Palacio-Escat, Michal Klein, Olga Ivanova, Marton Oelbei, Attila Gabor, Fabian Theis, Tamas Korcsmaros, Julio Saez-Rodriguez
Summary: Molecular knowledge of biological processes is crucial for omics data analysis, with OmniPath providing a comprehensive resource for researchers to access information on both intracellular and intercellular processes. This resource facilitates the study of cell-cell interactions and downstream signaling processes, demonstrated in applications investigating SARS-CoV-2 infection and ulcerative colitis.
MOLECULAR SYSTEMS BIOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Su Yon Jung, Jeanette C. Papp, Matteo Pellegrini, Herbert Yu, Eric M. Sobel
Summary: The study utilized an integrated genomic network approach to explore the role of CRP/IL6 in disease pathogenesis. It identified shared gene networks and regulatory mechanisms between CRP/IL6 and diseases like breast cancer, offering potential novel genetic targets for prevention and treatment strategies for associated disorders.
Review
Biochemical Research Methods
Timothy D. Veenstra
Summary: Biological research has shifted from focusing on single molecules to analyzing thousands simultaneously, giving rise to various omics fields. These omics fields are laying the groundwork for the development of systems biology, which aims to understand complex interactions within biological systems.
Review
Medicine, General & Internal
Lili Niu, Karolina Sulek, Catherine G. Vasilopoulou, Alberto Santos, Nicolai J. Wewer Albrechtsen, Simon Rasmussen, Florian Meier, Matthias Mann
Summary: NASH is a chronic liver disease affecting a significant portion of the general population, with a molecular mechanism that remains elusive. Multi-omics analysis shows potential in uncovering new biological insights into the disease.
JOURNAL OF CLINICAL MEDICINE
(2021)
Review
Plant Sciences
Muhammad-Redha Abdullah-Zawawi, Nisha Govender, Sarahani Harun, Nor Azlan Nor Muhammad, Zamri Zainal, Zeti-Azura Mohamed-Hussein
Summary: Omics technologies are used to understand the complexity of plant systems and components. Integration of multi-omics datasets allows for comprehensive understanding of organism life processes. Open-source datasets and computational tools aid in silico functional prediction of unknown genes, proteins, and metabolites. The systems biology approach involves data collection, modeling, experimentation, and hypothesis generation for validation. Informatics technologies enhance gene function prediction at a minimal cost and effort. This article provides a comprehensive view and resources for gene function prediction in plants.
Article
Biochemistry & Molecular Biology
Maxime Francois, Avinash Karpe, Jian-Wei Liu, David J. Beale, Maryam Hor, Jane Hecker, Jeff Faunt, John Maddison, Sally Johns, James D. Doecke, Stephen Rose, Wayne R. Leifert
Summary: The metabolomic and proteomic basis of mild cognitive impairment (MCI) and Alzheimer's disease (AD) is not well understood. This study examined the plasma samples of individuals with MCI or AD, as well as age- and gender-matched cognitively normal individuals, to identify cellular pathways and biomarkers associated with the diseases. The analysis revealed specific proteins that distinguish AD from MCI and cognitively normal groups, and identified various metabolic pathways affected in AD. These findings contribute to the understanding of the diseases and may be useful for future clinical trials.
Article
Biochemistry & Molecular Biology
Judith Canto-Santos, Laura Valls-Roca, Ester Tobias, Clara Oliva, Francesc Josep Garcia-Garcia, Mariona Guitart-Mampel, Felix Andujar-Sanchez, Anna Esteve-Codina, Beatriz Martin-Mur, Joan Padrosa, Raquel Aranega, Pedro J. Moreno-Lozano, Jose Cesar Milisenda, Rafael Artuch, Josep M. Grau-Junyent, Gloria Garrabou
Summary: In this study, an omics analysis of multiple samples from IBM patients was conducted to gain insights into the pathophysiology of the disease. The presence of amyloid beta peptide 1-42, imbalanced organic acid profile, and abnormal expression of metabolites and gene regulators were observed in various samples. The findings reported in this study provide novel insights into IBM and suggest potential biomarkers that need to be validated in larger cohorts.
Review
Biochemical Research Methods
Peter D. Karp, Peter E. Midford, Richard Billington, Anamika Kothari, Markus Krummenacker, Mario Latendresse, Wai Kit Ong, Pallavi Subhraveti, Ron Caspi, Carol Fulcher, Ingrid M. Keseler, Suzanne M. Paley
Summary: The development of Pathway Tools software enables researchers to construct biological knowledge resources more efficiently, develop metabolic flux models, and interpret high-throughput data using pathway information.
BRIEFINGS IN BIOINFORMATICS
(2021)
Review
Cell Biology
Harald Hampel, Robert Nistico, Nicholas T. Seyfried, Allan I. Levey, Erica Modeste, Pablo Lemercier, Filippo Baldacci, Nicola Toschi, Francesco Garaci, George Perry, Enzo Emanuele, Pedro L. Valenzuela, Alejandro Lucia, Andrea Urbani, Giulia M. Sancesario, Mark Mapstone, Massimo Corbo, Andrea Vergallo, Simone Lista
Summary: Alzheimer's disease is characterized by complex pathophysiology with high heterogeneity, requiring a holistic approach to fully capture its multifaceted nature. Integrating omics sciences and systems biology network approaches can help detect and describe the biological changes occurring in the progression of AD.
AGEING RESEARCH REVIEWS
(2021)