Article
Gastroenterology & Hepatology
Soo Young Cho, Heeyoun Hwang, Yun-Hee Kim, Byong Chul Yoo, Nayoung Han, Sun-Young Kong, Min-Jeong Baek, Kyung-Hee Kim, Mi Rim Lee, Jae Gwang Park, Sung-Sik Han, Woo Jin Lee, Charny Park, Jong Bae Park, Jin Young Kim, Sang-Jae Park, Sang Myung Woo
Summary: Through comprehensive analysis of genomic, transcriptomic, proteomic, and phosphoproteomic data from 102 iCC patients, three clinically supported subtypes were identified (stem-like, poorly immunogenic, and metabolism), and an organoid model was constructed for therapeutic testing. The ALDH1A1 inhibitor NCT-501 showed synergy with nanoparticle albumin-bound-paclitaxel in the organoid model for the stem-like subtype. Dysregulations in oncometabolites were associated with different clinical outcomes in the stem-like and metabolism subtypes. The poorly immunogenic subtype exhibited non-T-cell tumor infiltration. Integrated multiomics analysis reproduced the 3 subtypes and revealed heterogeneity in iCC.
Article
Medicine, Research & Experimental
Chang-Zhu Pei, Lan Jin, Kwang-Hyun Baek
Summary: PCOS is a common gynecological endocrine disease involving multiple genes and pathways, and cannot be explained by a single factor. Omics analysis plays a key role in studying the pathogenesis of PCOS, offering new perspectives for explaining new mechanisms and potential biomarkers discovery.
BIOMEDICINE & PHARMACOTHERAPY
(2021)
Review
Biotechnology & Applied Microbiology
Bashar Amer, Edward E. K. Baidoo
Summary: Biomanufacturing, a key component of biotechnology, utilizes biological systems to produce commercial bioproducts which are of interest to various industries. Technologies like synthetic biology and metabolic engineering heavily rely on omics driven systems biology for research and development, aiding in the establishment of industrial biomanufacturing platforms. These technologies have a significant impact on the production of biofuels, bioproducts, agricultural and food biotechnology, as well as current COVID-19 research.
FRONTIERS IN BIOENGINEERING AND BIOTECHNOLOGY
(2021)
Article
Biochemical Research Methods
Nathaniel Kwok, Zita Aretz, Sumiko Takao, Zheng Ser, Paolo Cifani, Alex Kentsis
Summary: Recent advances in nucleic acid sequencing and mass spectrometry proteomics have enabled genome-scale analysis of genetic variation and transcription as well as whole proteome-scale studies of protein expression. However, most proteomic studies are limited to canonical protein sequences. Here, we develop ProteomeGenerator2 (PG2), which integrates genome and transcriptome sequencing to incorporate protein variants and other non-canonical features caused by genomic and transcriptomic variation. PG2 has been benchmarked using synthetic data and analysis of human leukemia cells and can be used with current and emerging sequencing technologies, assemblers, variant callers, and mass spectral analysis algorithms. It is open-source and available at https://github.com/kentsisresearchgroup/ProteomeGenerator2.
JOURNAL OF PROTEOME RESEARCH
(2023)
Review
Oncology
Miaomiao Ye, Yibin Lin, Shuya Pan, Zhi-wei Wang, Xueqiong Zhu
Summary: Ovarian cancer ranks as the fifth most common cause of cancer-related death in females. Multi-omics approaches have been applied to determine the mechanisms of ovarian oncogenesis at different levels and have identified potential diagnostic and prognostic biomarkers and therapeutic targets. The discovery of molecular signatures and targeted therapy strategies could significantly improve the prognosis of ovarian cancer patients.
FRONTIERS IN ONCOLOGY
(2021)
Review
Microbiology
Juan Jose Gonzalez-Plaza, Cristina Furlan, Tomaz Rijavec, Ales Lapanje, Rocio Barros, Juan Antonio Tamayo-Ramos, Maria Suarez-Diez
Summary: The study of microbial cells interacting with natural and synthetic interfaces has been enriched by the development of advanced omics technologies, allowing for the isolation and analysis of nucleic acids, proteins, and metabolites from complex samples. This review discusses the challenges in analyzing microbial cells at genomic, transcriptomic, proteomic, and metabolomic levels, and describes both experimental and computational approaches to address them. The integration of multi omics datasets is presented as a means to achieve a systems level understanding of these complex interactions.
FRONTIERS IN MICROBIOLOGY
(2022)
Review
Oncology
Zijian Zou, Wei Sun, Yu Xu, Wanlin Liu, Jingqin Zhong, Xinyi Lin, Yong Chen
Summary: Sarcomas are rare mesenchymal neoplasms with unique genetic characteristics, and their diagnosis relies heavily on pathological examination. Advanced treatments and multi-omics approaches have shown promise in improving outcomes and understanding sarcomas, but further research is needed to optimize their clinical application.
FRONTIERS IN ONCOLOGY
(2022)
Review
Biotechnology & Applied Microbiology
Alexander Arsov, Kaloyan Petrov, Penka Petrova
Summary: This article discusses the potential of microbial production of butanol as a new fuel and the challenge of butanol toxicity to microbes. Modern omics approaches have made significant progress in addressing the issue of low butanol tolerance, but a strain capable of both synthesis and tolerance at commercializable concentrations has yet to be discovered or produced.
BIOTECHNOLOGY ADVANCES
(2021)
Review
Food Science & Technology
Karolinny Cristiny de Oliveira Vieira, Hevelin Regiane Augusto da Silva, Isabela Poletto Masselli Rocha, Emmanuel Barboza, Lizziane Kretli Winkelstroter Eller
Summary: Outbreaks and deaths related to Foodborne Diseases (FBD) are constantly occurring worldwide, largely due to consumption of contaminated foodstuffs with pathogens. This review discusses the main omic techniques applied in foodborne pathogens and their potential in ensuring food safety. Omics have been shown to integrate variables that contribute to food safety and improve consumer health, costs, and product quality.
CRITICAL REVIEWS IN FOOD SCIENCE AND NUTRITION
(2022)
Article
Cell Biology
Linyan Chen, Hao Zeng, Yu Xiang, Yeqian Huang, Yuling Luo, Xuelei Ma
Summary: In this study, machine learning models based on histopathological image features successfully predicted genetic aberrations, transcriptional subtypes, and survival outcomes of LUAD patients. The combination of histopathological image features with single omics data improved the prognostic power for LUAD patients.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2021)
Review
Cell Biology
Jia-Chen Liu, Shan-Shan Dong, Hui Shen, Dan-Yue Yang, Bin-Bin Chen, Xue-Ying Ma, Yi-Ran Peng, Hong-Mei Xiao, Hong-Wen Deng
Summary: Sarcopenia is a systemic disease characterized by muscle dysfunction, with its genetic architecture and molecular mechanisms still largely unclear. Recent advancements in multi-omics studies offer new insights into the pathogenesis of sarcopenia and may lead to new clinical applications.
AGEING RESEARCH REVIEWS
(2022)
Review
Biochemistry & Molecular Biology
Huan Li, Muhammad Tahir ul Qamar, Li Yang, Junchao Liang, Jun You, Linhai Wang
Summary: Sesame is an important traditional oil crop with high economic and nutritional value. Advances in high throughput sequencing techniques and bioinformatical methods have led to rapid developments in genomics, methylomics, transcriptomics, proteomics, and metabonomics studies of sesame.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Review
Pharmacology & Pharmacy
Mengyuan Kan, Blanca E. Himes
Summary: Glucocorticoid drugs are widely used in the treatment of diseases, but there is still much to learn about their cell type-specific mechanisms and why patients respond differently. Recent studies have used genomics, transcriptomics, and other omics approaches to address these questions, but there are still knowledge gaps to be filled related to glucocorticoid action mechanisms.
PHARMACOLOGY & THERAPEUTICS
(2021)
Editorial Material
Multidisciplinary Sciences
Amber Dance
Summary: Methods that combine imaging with sequencing are revealing the organizational principles of the genome and its impact on cell fates.
Review
Plant Sciences
Yamshi Arif, Priyanka Singh, Andrzej Bajguz, Pravej Alam, Shamsul Hayat
Summary: This review discusses the crucial role of silicon in plant development and stress responses, highlighting its interactions with plant hormones and antioxidants, as well as its application in 'omic approaches. Furthermore, it emphasizes the need for further research on the role of silicon during abiotic stress in plants for a better understanding at a broader level.
PLANT PHYSIOLOGY AND BIOCHEMISTRY
(2021)
