Article
Multidisciplinary Sciences
Peng Wu, Dongsheng Chen, Wencheng Ding, Ping Wu, Hongyan Hou, Yong Bai, Yuwen Zhou, Kezhen Li, Shunian Xiang, Panhong Liu, Jia Ju, Ensong Guo, Jia Liu, Bin Yang, Junpeng Fan, Liang He, Ziyong Sun, Ling Feng, Jian Wang, Tangchun Wu, Hao Wang, Jin Cheng, Hui Xing, Yifan Meng, Yongsheng Li, Yuanliang Zhang, Hongbo Luo, Gang Xie, Xianmei Lan, Ye Tao, Jiafeng Li, Hao Yuan, Kang Huang, Wan Sun, Xiaobo Qian, Zhichao Li, Mingxi Huang, Peiwen Ding, Haoyu Wang, Jiaying Qiu, Feiyue Wang, Shiyou Wang, Jiacheng Zhu, Xiangning Ding, Chaochao Chai, Langchao Liang, Xiaoling Wang, Lihua Luo, Yuzhe Sun, Ying Yang, Zhenkun Zhuang, Tao Li, Lei Tian, Shaoqiao Zhang, Linnan Zhu, Ashley Chang, Lei Chen, Yiquan Wu, Xiaoyan Ma, Fang Chen, Yan Ren, Xun Xu, Siqi Liu, Huanming Yang, Lin Wang, Chaoyang Sun, Ding Ma, Xin Jin, Gang Chen
Summary: The authors conducted blood sampling and multi-omics analysis on COVID-19 patients of various disease severities, reporting a trans-omics landscape of COVID-19. The study found differences in characteristics between patients with different disease severities, suggesting potential clues for pathophysiology and therapeutic strategies of COVID-19.
NATURE COMMUNICATIONS
(2021)
Article
Multidisciplinary Sciences
Akira Terakawa, Yanhui Hu, Toshiya Kokaji, Katsuyuki Yugi, Keigo Morita, Satoshi Ohno, Yifei Pan, Yunfan Bai, Andrey A. Parkhitko, Xiaochun Ni, John M. Asara, Martha L. Bulyk, Norbert Perrimon, Shinya Kuroda
Summary: This study constructed a transgenic network to investigate the role of insulin in Drosophila cells. The findings suggest that insulin promotes cell growth and proliferation by regulating gene expression, especially genes involved in anabolic metabolism.
Article
Environmental Sciences
Pallavi Gautam, Anand Kumar Pandey, Ankush Gupta, Suresh Kumar Dubey
Summary: Imidacloprid, a widely used insecticide, has toxic effects on non-targeted organisms. This study investigated the potential of Sphingobacterium sp. InxBP1 in degrading imidacloprid through genomic, proteomic, bioinformatic, and metabolomic analyses. The findings identified genes and enzymes involved in the oxidative degradation of imidacloprid, as well as their affinity and binding to the degradation intermediates. The metabolomic study validated the proposed degradation mechanism. These findings suggest that Sphingobacterium sp. InxBP1 can be utilized in developing in-situ remediation technologies for imidacloprid.
ENVIRONMENTAL POLLUTION
(2023)
Review
Chemistry, Analytical
Maria A. Woerheide, Jan Krumsiek, Gabi Kastenmueller, Matthias Arnold
Summary: Recent advances in high-throughput technologies have enabled the profiling of multiple layers of a biological system, generating vast amounts of data that can be integrated in multi-omics studies. Integrative analysis of such datasets is complicated by the high dimensionality, heterogeneity, and lack of universal protocols. While previous reviews focused on integrating two omics layers with a phenotype, this review highlights methods to combine metabolomics data with two or more omics layers without focusing on a specific phenotype.
ANALYTICA CHIMICA ACTA
(2021)
Article
Biochemical Research Methods
Ahmed A. Metwally, Tom Zhang, Si Wu, Ryan Kellogg, Wenyu Zhou, Kevin Contrepois, Hua Tang, Michael Snyder
Summary: This study developed a statistical method called OmicsLonDA that robustly identifies time intervals of temporal omics biomarkers. The method uses a semi-parametric approach to model longitudinal data and infer significant time intervals based on an empirical distribution. Through testing on simulated datasets and real datasets, the method demonstrated high accuracy and sensitivity.
Article
Cell Biology
Tian-Qi Gong, Yi-Zhou Jiang, Chen Shao, Wen-Ting Peng, Ming-Wei Liu, Da-Qiang Li, Ben-Yu Zhang, Peng Du, Yin Huang, Fei-Fei Li, Mu-Yun Li, Zhao-Lian Han, Xi Jin, Ding Ma, Yi Xiao, Peng-Yuan Yang, Jun Qin, Zhi-Ming Shao, Weimin Zhu
Summary: This study presents a comprehensive proteomic analysis of paired samples of TNBC, identifying four integrative subtypes with distinct molecular and pathway features. The analysis reveals key pathways and master regulators within and between sub-structures and co-expression communities, providing valuable insights into the molecular mechanisms of TNBC.
Article
Biology
Munhwan Lee, Pil-Jong Kim, Hyunwhan Joe, Hong-Gee Kim
Summary: This study introduces a gene-centric multi-channel architecture to predict cancer drug response by integrating multi-omics. Evaluations on various datasets show the effectiveness of GCMC in improving performance and feature extraction capabilities.
COMPUTERS IN BIOLOGY AND MEDICINE
(2022)
Review
Immunology
Yuya Shirai, Yukinori Okada
Summary: Genome-wide association studies have identified numerous associations between genetic polymorphisms and human traits, but the pathways between genotype and phenotype remain poorly understood. Omics such as the transcriptome, proteome, and metabolome offer valuable information for translating from genotype to phenotype, providing insights into disease causality and personalized medicine through the integration of various omics datasets.
INFLAMMATION AND REGENERATION
(2021)
Article
Biotechnology & Applied Microbiology
Marina de Leeuw, Marta R. A. Matos, Lars Keld Nielsen
Summary: Kinetic models are important for understanding metabolic systems. This paper presents a detailed kinetic model for the central carbon metabolism of Escherichia coli, which has been validated and can be used for studying cellular metabolism and metabolic pathway design.
METABOLIC ENGINEERING
(2023)
Article
Multidisciplinary Sciences
Yameng Li, Lin Zhang, Mingcai Mao, Linjuan He, Tiancai Wang, Yecan Pan, Xiaoyu Zhao, Zishu Li, Xiyan Mu, Yongzhong Qian, Jing Qiu
Summary: Emerging studies showed that inflammation is crucial in the pathogenesis of bipolar disorder, but the underlying mechanism is unclear. By analyzing different -omics data, we unraveled the comprehensive molecular mechanism in the zebrafish model of BD. We found that JNK-mediated neuroinflammation altered metabolic pathways involved in neurotransmission, leading to disturbed serotonergic and dopaminergic synaptic transmission.
Article
Biochemical Research Methods
Ryohei Eguchi, Momoko Hamano, Michio Iwata, Toru Nakamura, Shinya Oki, Yoshihiro Yamanishi
Summary: In this study, a novel computational method, TRANSDIRE, was developed to predict the transcription factors (TFs) that induce direct reprogramming in various human cell types using multiple omics data. The method successfully predicted TFs for most cell conversions with high accuracy, suggesting its potential practical applications in regenerative medicine.
Article
Immunology
Yajuan Fan, Yuan Gao, Qingyan Ma, Zai Yang, Binbin Zhao, Xiaoyan He, Jian Yang, Bin Yan, Fengjie Gao, Li Qian, Wei Wang, Feng Zhu, Xiancang Ma
Summary: Schizophrenia is associated with immune dysfunctions and disturbed intestinal microbiota. This study found that abnormal gut metabolism-immune network exists in schizophrenia, and gut microbiota may influence immune responses by regulating host metabolic processes.
FRONTIERS IN IMMUNOLOGY
(2022)
Article
Oncology
Jiajin Chen, Yunjie Song, Yi Li, Yongyue Wei, Sipeng Shen, Yang Zhao, Dongfang You, Li Su, Maria Moksnes Bjaanaes, Anna Karlsson, Maria Planck, Johan Staaf, Aslaug Helland, Manel Esteller, Hongbing Shen, David C. C. Christiani, Ruyang Zhang, Feng Chen
Summary: This study identified significant gene-gene interactions associated with non-small-cell lung cancer survival through a three-step analytic strategy. Two interactions were found at both the epigenetic and transcriptional levels, providing potential clues for precision treatment of NSCLC.
MOLECULAR ONCOLOGY
(2023)
Editorial Material
Plant Sciences
Elmien Heyneke, Rainer Hoefgen
Summary: Understanding nutrient metabolism in plants is crucial for improving yield and quality, as nutrient imbalances can affect growth and productivity. Modern agriculture relies on supplementing soils with optimal nutrients and using elite crop cultivars adapted to these conditions. Sustainable agriculture aims to reduce inputs by developing novel cultivars that require balanced, but reduced nutrient inputs.
JOURNAL OF EXPERIMENTAL BOTANY
(2021)
Article
Biochemistry & Molecular Biology
Mariia Emelianova, Anastasiia Gainullina, Nikolay Poperechnyi, Alexander Loboda, Maxim Artyomov, Alexey Sergushichev
Summary: This article introduces an updated pipeline GATOM and the corresponding web-service Shiny GATOM, which uses transcriptional and/or metabolomic data to find the most regulated metabolic subnetwork between two conditions. The method features a new metabolic network topology based on atom transition, which improves interpretability of the analysis results, and provides a corresponding exact solver and database analysis capabilities.
NUCLEIC ACIDS RESEARCH
(2022)
Review
Biotechnology & Applied Microbiology
Katsuyuki Yugi, Hiroyuki Kubota, Atsushi Hatano, Shinya Kuroda
TRENDS IN BIOTECHNOLOGY
(2016)
Article
Cell Biology
James R. Krycer, Katsuyuki Yugi, Akiyoshi Hirayama, Daniel J. Fazakerley, Lake-Ee Quek, Richard Scalzo, Satoshi Ohno, Mark P. Hodson, Satsuki Ikeda, Futaba Shoji, Kumi Suzuki, Westa Domanova, Benjamin L. Parker, Marin E. Nelson, Sean J. Humphrey, Nigel Turner, Kyle L. Hoehn, Gregory J. Cooney, Tomoyoshi Soga, Shinya Kuroda, David E. James
Article
Cell Biology
Kentaro Kawata, Katsuyuki Yugi, Atsushi Hatano, Toshiya Kokaji, Yoko Tomizawa, Masashi Fujii, Shinsuke Uda, Hiroyuki Kubota, Masaki Matsumoto, Keiichi I. Nakayama, Shinya Kuroda
Article
Multidisciplinary Sciences
Daisuke Hoshino, Kentaro Kawata, Katsuyuki Kunida, Atsushi Hatano, Katsuyuki Yugi, Takumi Wada, Masashi Fujii, Takanori Sano, Yuki Ito, Yasuro Furuichi, Yasuko Manabe, Yutaka Suzuki, Nobuharu L. Fujii, Tomoyoshi Soga, Shinya Kuroda
Article
Multidisciplinary Sciences
Satoshi Ohno, Lake-Ee Quek, James R. Krycer, Katsuyuki Yugi, Akiyoshi Hirayama, Satsuki Ikeda, Futaba Shoji, Kumi Suzuki, Tomoyoshi Soga, David E. James, Shinya Kuroda
Article
Biochemistry & Molecular Biology
Toshiya Kokaji, Atsushi Hatano, Yuki Ito, Katsuyuki Yugi, Miki Eto, Keigo Morita, Satoshi Ohno, Masashi Fujii, Ken-ichi Hironaka, Riku Egami, Akira Terakawa, Takaho Tsuchiya, Haruka Ozaki, Hiroshi Inoue, Shinsuke Uda, Hiroyuki Kubota, Yutaka Suzuki, Kazutaka Ikeda, Makoto Arita, Masaki Matsumoto, Keiichi Nakayama, Akiyoshi Hirayama, Tomoyoshi Soga, Shinya Kuroda
Correction
Multidisciplinary Sciences
Lake-Ee Quek, James R. Krycer, Satoshi Ohno, Katsuyuki Yugi, Daniel J. Fazakerley, Richard Scalzo, Sarah D. Elkington, Ziwei Dai, Akiyoshi Hirayama, Satsuki Ikeda, Futaba Shoji, Kumi Suzuki, Jason W. Locasale, Tomoyoshi Soga, David E. James, Shinya Kuroda
Article
Multidisciplinary Sciences
Riku Egami, Toshiya Kokaji, Atsushi Hatano, Katsuyuki Yugi, Miki Eto, Keigo Morita, Satoshi Ohno, Masashi Fujii, Ken-ichi Hironaka, Saori Uematsu, Akira Terakawa, Yunfan Bai, Yifei Pan, Takaho Tsuchiya, Haruka Ozaki, Hiroshi Inoue, Shinsuke Uda, Hiroyuki Kubota, Yutaka Suzuki, Masaki Matsumoto, Keiichi Nakayama, Akiyoshi Hirayama, Tomoyoshi Soga, Shinya Kuroda
Summary: The study examined the systemic metabolic disturbances in obesity by analyzing the transcriptome, proteome, and metabolome in liver, skeletal muscle, and blood of obese mice. Potential mechanisms of dysfunction in metabolic cycles between liver and skeletal muscle in obesity were identified, shedding light on the pathological processes associated with obesity.
Article
Multidisciplinary Sciences
Kosuke Miyauchi, Yu Adachi, Keisuke Tonouchi, Taiki Yajima, Yasuyo Harada, Hidehiro Fukuyama, Senka Deno, Yoichiro Iwakura, Akihiko Yoshimura, Hideki Hasegawa, Katsuyuki Yugi, Shin-ichiro Fujii, Osamu Ohara, Yoshimasa Takahashi, Masato Kubo
Summary: This study reveals that influenza infection facilitates a broader antibody response by unmasking haemagglutinin epitopes and signaling IL-4 in the germinal center, shedding light on the differences in antibody responses induced by vaccination versus infection.
NATURE COMMUNICATIONS
(2021)
Article
Neurosciences
Lisa Okamoto, Soyoka Watanabe, Senka Deno, Xiang Nie, Junichi Maruyama, Masaru Tomita, Atsushi Hatano, Katsuyuki Yugi
Summary: By reconstructing and comparing the transcriptional regulatory network for lipid metabolism enzymes using transcriptome datasets from schizophrenia patients, this study identifies common and unique transcriptional modes of regulation and reveals associations between SNPs and hematological cell counts as well as other traits/diseases that were not adequately reported in previous studies.
NEUROSCIENCE RESEARCH
(2022)
Article
Multidisciplinary Sciences
Akira Terakawa, Yanhui Hu, Toshiya Kokaji, Katsuyuki Yugi, Keigo Morita, Satoshi Ohno, Yifei Pan, Yunfan Bai, Andrey A. Parkhitko, Xiaochun Ni, John M. Asara, Martha L. Bulyk, Norbert Perrimon, Shinya Kuroda
Summary: This study constructed a transgenic network to investigate the role of insulin in Drosophila cells. The findings suggest that insulin promotes cell growth and proliferation by regulating gene expression, especially genes involved in anabolic metabolism.
Article
Multidisciplinary Sciences
Toshiya Kokaji, Miki Eto, Atsushi Hatano, Katsuyuki Yugi, Keigo Morita, Satoshi Ohno, Masashi Fujii, Ken-ichi Hironaka, Yuki Ito, Riku Egami, Saori Uematsu, Akira Terakawa, Yifei Pan, Hideki Maehara, Dongzi Li, Yunfan Bai, Takaho Tsuchiya, Haruka Ozaki, Hiroshi Inoue, Hiroyuki Kubota, Yutaka Suzuki, Akiyoshi Hirayama, Tomoyoshi Soga, Shinya Kuroda
Summary: Metabolic regulation in skeletal muscle plays a crucial role in maintaining blood glucose levels. Obesity leads to insulin resistance in skeletal muscle, resulting in elevated blood glucose and the development of type 2 diabetes. Through multiomic analysis of skeletal muscle in wild-type and leptin-deficient obese mice, this study constructed regulatory transomic networks to understand the metabolic regulation after oral glucose administration. The findings indicate that glucose-responsive metabolites have a significant impact on metabolic regulation, particularly in carbohydrate metabolic pathways, in wild-type mice. In contrast, the metabolic regulation by glucose-responsive metabolites is largely disrupted in obese mice, with increased reliance on glucose-responsive genes, especially in carbohydrate and lipid metabolic pathways. The study also identified characteristic metabolic regulatory pathways in central carbon, branched amino acids, and ketone body metabolism. These findings provide valuable insights into how skeletal muscle responds to changes in blood glucose and the dysregulation observed in obesity.
SCIENTIFIC REPORTS
(2022)
Article
Multidisciplinary Sciences
Lake-Ee Quek, James R. Krycer, Satoshi Ohno, Katsuyuki Yugi, Daniel J. Fazakerley, Richard Scalzo, Sarah D. Elkington, Ziwei Dai, Akiyoshi Hirayama, Satsuki Ikeda, Futaba Shoji, Kumi Suzuki, Jason W. Locasale, Tomoyoshi Soga, David E. James, Shinya Kuroda
Article
Multidisciplinary Sciences
Kentaro Kawata, Atsushi Hatano, Katsuyuki Yugi, Hiroyuki Kubota, Takanori Sano, Masashi Fujii, Yoko Tomizawa, Toshiya Kokaji, Kaori Y. Tanaka, Shinsuke Uda, Yutaka Suzuki, Masaki Matsumoto, Keiichi Nakayama, Kaori Saitoh, Keiko Kato, Ayano Ueno, Maki Ohishi, Akiyoshi Hirayama, Tomoyoshi Soga, Shinya Kuroda
