Review
Pharmacology & Pharmacy
Yasmin Abdelkader, Luis Perez-Davalos, Richard LeDuc, Rene P. Zahedi, Hagar I. Labouta
Summary: Nanotechnology has revolutionized the development of therapeutics, diagnostics, and drug delivery systems by utilizing nanoparticles (NPs) that can impact various cellular processes. Omics approaches, including transcriptomics, proteomics, metabolomics, lipidomics, and multi-omics, provide comprehensive analysis of molecular changes upon NP exposure. This review highlights the importance of bioinformatics tools in interpreting large omics data and suggests that interdisciplinary multi-omics analyses will enhance our understanding of cell responses to NPs, ultimately improving the development of nanomedicine therapies.
ADVANCED DRUG DELIVERY REVIEWS
(2023)
Review
Chemistry, Analytical
Roger M. Pallares, Yanchen Li, Rebecca J. Abergel
Summary: Lanthanides and actinides are critical elements widely used in multiple industries. Recent omics approaches have improved our understanding of their biological behavior and toxicity mechanisms, leading to the identification of key genes and proteins that mediate their toxicity. This knowledge informs the development of new strategies to prevent and treat the potential harmful effects of these elements.
TRAC-TRENDS IN ANALYTICAL CHEMISTRY
(2023)
Review
Biochemical Research Methods
Stephen Doran, Muhammad Arif, Simon Lam, Abdulahad Bayraktar, Hasan Turkez, Mathias Uhlen, Jan Boren, Adil Mardinoglu
Summary: The development and progression of cardiovascular disease is mainly attributed to factors such as atherosclerosis, thrombosis, cardiac remodelling, and gut microbiota. Understanding the underlying molecular mechanisms and utilizing systems biology approaches are crucial in identifying novel drug targets and biomarkers for CVD treatment strategies. Recent advances in gut microbiota research have shed light on the impact of diet and microbial composition on CVD development.
BRIEFINGS IN BIOINFORMATICS
(2021)
Review
Biochemistry & Molecular Biology
Kumar Saurabh Singh, Justin J. J. van der Hooft, Saskia C. M. van Wees, Marnix H. Medema
Summary: With the increase in omics data, computational approaches for identifying plant natural product biosynthetic pathways have become crucial. Transcriptomics and metabolomics provide complementary information to link genes and metabolites. Recent advances in technology allow for integration of multiple omics types and untargeted pathway discovery.
NATURAL PRODUCT REPORTS
(2022)
Review
Biochemistry & Molecular Biology
Violaine Saint-Andre
Summary: The review discusses the main approaches and tools for mapping Transcriptional Regulatory Networks (TRNs) from high-throughput data, highlighting their advantages and limitations. It summarizes the main principles defining the topology and structure-function relationships in TRNs, and presents an overview of the work done to map TRNs from bulk transcriptomic data by methodological approach. Additionally, it touches upon recent modeling of TRNs using different types of molecular data and concludes with expected improvements in the field.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2021)
Review
Multidisciplinary Sciences
Xu Wang, Dian Fan, Yuqing Yang, Ryan C. Gimple, Shengtao Zhou
Summary: As biological sciences progress, there is a growing focus on combining genomics with other omics technologies to understand specific biological or pathological processes. Single cell sequencing analysis derived from these multi-omics technologies provides insights into immune cell heterogeneity. In this review, advances in multi-omics tools for studying immune cell functions and analyzing clinical immune disorders are summarized, highlighting the potential opportunities and challenges in future immunology research.
Article
Biochemical Research Methods
Anna Pacinkova, Vlad Popovici
Summary: This study presents IntOMICS, an integrative framework based on Bayesian networks, for the integration of multi-omics data and inference of regulatory networks. The framework provides a deeper understanding of the complex flow of genetic information in biological systems and outperforms existing algorithms designed solely for gene expression data in terms of accuracy.
BMC BIOINFORMATICS
(2022)
Review
Biotechnology & Applied Microbiology
Ranjna Sirohi, Jaemin Joun, Hong Ii Choi, Vivek Kumar Gaur, Sang Jun Sim
Summary: This article discusses the potential of microalgae as an energy feedstock and the efforts to increase microalgae productivity using various omics techniques, with a particular focus on the application of genome sequencing and metabolic engineering in this field.
MICROBIAL CELL FACTORIES
(2021)
Review
Immunology
Xiaojing Chu, Bowen Zhang, Valerie A. C. M. Koeken, Manoj Kumar Gupta, Yang Li
Summary: This review emphasizes the importance of applying a multi-omics approach in immunological research to understand the complexity of the immune system. It provides an overview of methodological approaches for different omics data layers, discusses data analysis methods, and highlights the possible applications of multi-omics studies in understanding immune-related diseases.
FRONTIERS IN IMMUNOLOGY
(2021)
Review
Biochemistry & Molecular Biology
Leah Schaffer, Trey Ideker
Summary: Biological systems are inherently multiscale, allowing for the application of diverse technologies to characterize units at different levels and create networks of proximities. By using network proximity measures to build hierarchical maps of biological systems, functionalizing them to create predictive models, and addressing challenges in multiscale modeling, a unified hierarchical approach to biological data can be achieved, spanning from the molecular to macroscopic level.
Article
Biochemistry & Molecular Biology
Zhiquan Yang, Jing Wang, Yiming Huang, Shengbo Wang, Lulu Wei, Dongxu Liu, Yonglin Weng, Jinhai Xiang, Qiang Zhu, Zhaoen Yang, Xinhui Nie, Yu Yu, Zuoren Yang, Qing-Yong Yang
Summary: This study collected and integrated multi-omics data to construct a cotton multi-omics database for identifying and analyzing candidate genes. The results demonstrate the great potential of integrating multi-omics data for cotton genetic breeding and functional genomics research.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Biochemical Research Methods
Robson P. Bonidia, Lucas D. H. Sampaio, Douglas S. Domingues, Alexandre R. Paschoal, Fabricio M. Lopes, Andre C. P. L. F. de Carvalho, Danilo S. Sanches
Summary: This study proposes a research on feature extraction approaches based on mathematical features to address the challenge of extracting significant discriminatory information from biological sequence data. Through case studies and experiments, the effectiveness and robustness of the new algorithm are demonstrated.
BRIEFINGS IN BIOINFORMATICS
(2021)
Review
Biochemistry & Molecular Biology
Jasmin Adriana Schaefer, F. X. Reymond Sutandy, Christian Muench
Summary: Mitochondria play essential roles in cellular metabolism and apoptosis, and they dynamically adjust their contents of proteins, nucleic acids, metabolites, and lipids to adapt to environmental changes. Multiple levels of regulation, including abundance, activity, and interaction, modulate mitochondrial components in response to changes. Omics-based approaches have been developed to systematically investigate mitochondrial adaptation and dysfunction in diseases. This review provides an overview of these methods and showcases how they have contributed to a better understanding of mitochondrial biology.
Review
Genetics & Heredity
Na Zhao, Zachary Quicksall, Yan W. W. Asmann, Yingxue Ren
Summary: Multi-omics approaches have greatly enhanced our understanding of the molecular complexity of the brain and disease states. Network approaches provide critical insights into disease biology, and multi-omics integration connects the underlying information of disease mechanisms.
FRONTIERS IN GENETICS
(2022)
Review
Immunology
Jessica M. Zielinski, Jason J. Luke, Silvia Guglietta, Carsten Krieg
Summary: High throughput single cell multi-omics platforms have enabled unprecedented insights into biological and clinical questions, creating whole atlases of cell types and interaction networks. Combining different -omic workflows on a single cell level can help examine cellular phenotypes and immune effector functions, as well as accelerate cellular biomarker discovery and definition of druggable target pathways. Challenges in the field include sharing disruptive technologies to scientific communities while incorporating new approaches like genomic cytometry and single cell metabolomics.
FRONTIERS IN IMMUNOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Jacqueline Stockli, Kelsey H. Fisher-Wellman, Rima Chaudhuri, Xiao-Yi Zeng, Daniel J. Fazakerley, Christopher C. Meoli, Kristen C. Thomas, Nolan J. Hoffman, Salvatore P. Mangiafico, Chrysovalantou E. Xirouchaki, Chieh-Hsin Yang, Olga Ilkayeva, Kari Wong, Gregory J. Cooney, Sofianos Andrikopoulos, Deborah M. Muoio, David E. James
JOURNAL OF BIOLOGICAL CHEMISTRY
(2017)
Article
Biochemistry & Molecular Biology
Jill J. Leckey, Nolan J. Hoffman, Evelyn B. Parr, Brooke L. Devlin, Adam J. Trewin, Nigel K. Stepto, James P. Morton, Louise M. Burke, John A. Hawley
Article
Biochemistry & Molecular Biology
James G. Burchfield, Melkam A. Kebede, Christopher C. Meoli, Jacqueline Stockli, P. Tess Whitworth, Amanda L. Wright, Nolan J. Hoffman, Annabel Y. Minard, Xiuquan Ma, James R. Krycer, Marin E. Nelson, Shi-Xiong Tan, Belinda Yau, Kristen C. Thomas, Natalie K. Y. Wee, Ee-Cheng Khor, Ronaldo F. Enriquez, Bryce Vissel, Trevor J. Biden, Paul A. Baldock, Kyle L. Hoehn, James Cantley, Gregory J. Cooney, David E. James, Daniel J. Fazakerley
JOURNAL OF BIOLOGICAL CHEMISTRY
(2018)
Article
Biology
Daniel J. Fazakerley, Rima Chaudhuri, Pengyi Yang, Ghassan J. Maghzal, Kristen C. Thomas, James R. Krycer, Sean J. Humphrey, Benjamin L. Parker, Kelsey H. Fisher-Wellman, Christopher C. Meoli, Nolan J. Hoffman, Cina Diskin, James G. Burchfield, Mark J. Cowley, Warren Kaplan, Zora Modrusan, Ganesh Kolumam, Jean Y. H. Yang, Daniel L. Chen, Dorit Samocha-Bonet, Jerry R. Greenfield, Kyle L. Hoehn, Roland Stocker, David E. James
Review
Biochemistry & Molecular Biology
Natalie R. Janzen, Jamie Whitfield, Nolan J. Hoffman
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2018)
Article
Biochemistry & Molecular Biology
Marin E. Nelson, Benjamin L. Parker, James G. Burchfield, Nolan J. Hoffman, Elise J. Needham, Kristen C. Cooke, Timur Naim, Lykke Sylow, Naomi X. Y. Ling, Deanne Francis, Dougall M. Norris, Rima Chaudhuri, Jonathan S. Oakhill, Erik A. Richter, Gordon S. Lynch, Jacqueline Stockli, David E. James
Article
Physiology
Bill Tachtsis, Jamie Whitfield, John A. Hawley, Nolan J. Hoffman
FRONTIERS IN PHYSIOLOGY
(2020)
Article
Cell Biology
Hani Jieun Kim, Taiyun Kim, Nolan J. Hoffman, Di Xiao, David E. James, Sean J. Humphrey, Pengyi Yang
Summary: Mass spectrometry-based phosphoproteomics allows for comprehensive analysis of phosphorylation-based signaling in cells and tissues. PhosR, a suite of R packages, facilitates in-depth analysis of phosphoproteomic data including data imputation, normalization, and functional analysis for inferring active kinases and signaling pathways. The introduction of a "signalome" construction method aids in identifying signaling modules and visualizing kinase interactions for generating biological knowledge.
Review
Biochemistry & Molecular Biology
Mehdi R. Belhaj, Nathan G. Lawler, Nolan J. Hoffman
Summary: Dynamic changes in metabolism and lipid profiles during exercise provide insights into the metabolic responses to different types of exercise. Advances in metabolomics and lipidomics have allowed for a better understanding of the molecular mechanisms underlying the health-promoting effects of exercise, with a focus on human biofluids and tissues in recent years.
Article
Biochemistry & Molecular Biology
Natalie R. Janzen, Jamie Whitfield, Lisa Murray-Segal, Bruce E. Kemp, John A. Hawley, Nolan J. Hoffman
Summary: By studying AMPK beta double knock-in mice, it was found that DKI mice displayed increased whole-body fat mass and glucose intolerance, along with reduced fat oxidation compared to wild-type. DKI mice had reduced liver glycogen content in the fed state, increased utilization of skeletal muscle glycogen in response to fasting but no repletion during refeeding, and also showed reductions in AMPK protein content in liver and skeletal muscle compared to WT.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Biochemistry & Molecular Biology
Ashley J. Ovens, Yi Sing Gee, Naomi X. Y. Ling, Dingyi Yu, Justin P. Hardee, Jin D. Chung, Kevin R. W. Ngoei, Nicholas J. Waters, Nolan J. Hoffman, John W. Scott, Kim Loh, Katrin Spengler, Regine Heller, Michael W. Parker, Gordon S. Lynch, Fei Huang, Sandra Galic, Bruce E. Kemp, Jonathan B. Baell, Jonathan S. Oakhill, Christopher G. Langendorf
Summary: AMPK is a cellular energy sensor and regulator of energy homeostasis. Activating AMPK shows potential for treating type 2 diabetes and insulin resistance. Recent studies suggest that the ??202??1 isoform combination is primarily responsible for these effects. Structure/function analysis of SC4 activator led to the discovery of MSG010 and MSG011, which show greater potency in activating ??202??1 AMPK compared to MK-8722. These findings guide the development of selective AMPK activators.
BIOCHEMICAL JOURNAL
(2022)
Article
Physiology
Natalie R. Janzen, Jamie Whitfield, Lisa Murray-Segal, Bruce E. Kemp, John A. Hawley, Nolan J. Hoffman
Summary: Disrupting AMPK-glycogen interaction reduces maximal exercise capacity and skeletal muscle AMPK alpha and beta 2 content, and increases glycogen utilization.
FRONTIERS IN PHYSIOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Mehdi R. R. Belhaj, Nathan G. G. Lawler, John A. A. Hawley, David I. I. Broadhurst, Nolan J. J. Hoffman, Stacey N. N. Reinke
Summary: The study found that disruptions in AMPK-glycogen binding in mice led to decreased exercise capacity and alterations in plasma metabolite profiles during rest and exercise. Differences in metabolite responses were observed between wild type and disrupted AMPK mice, suggesting a potential role for AMPK-glycogen interactions in fuel utilization during exercise.
FRONTIERS IN MOLECULAR BIOSCIENCES
(2022)
Article
Biochemistry & Molecular Biology
David J. Bishop, Nolan J. Hoffman, Dale F. Taylor, Nicholas J. Saner, Matthew J. -C. Lee, John A. Hawley
Summary: The ability of skeletal muscle to adapt to repeated contractile stimuli involves various molecular processes, including increased protein activity and/or expression. Recent studies challenge the common assumption of a direct relationship between changes in the skeletal muscle transcriptome and proteome induced by repeated muscle contractions (e.g., exercise).
TRENDS IN BIOCHEMICAL SCIENCES
(2023)
Article
Endocrinology & Metabolism
Nolan J. Hoffman, Jamie Whitfield, Natalie R. Janzen, Mehdi R. Belhaj, Sandra Galic, Lisa Murray-Segal, William J. Smiles, Naomi X. Y. Ling, Toby A. Dite, John W. Scott, Jonathan S. Oakhill, Robert Brink, Bruce E. Kemp, John A. Hawley
MOLECULAR METABOLISM
(2020)
