Article
Cardiac & Cardiovascular Systems
Michael Harris, Junhui Sun, Karen Keeran, Angel Aponte, Komudi Singh, Danielle Springer, Marjan Gucek, Mehdi Pirooznia, Matthew E. Cockman, Elizabeth Murphy, Leslie M. Kennedy
Summary: This study demonstrates that deletion of Ogfod1 alters the myocardial proteome and metabolome, providing protection against ischemia-reperfusion injury.
CARDIOVASCULAR RESEARCH
(2022)
Article
Biochemistry & Molecular Biology
Alex Gallinat, Gemma Vilahur, Teresa Padro, Lina Badimon
Summary: Infarct size is a major risk predictor for heart failure after acute myocardial infarction (AMI). The discovery of conditioning phenomena has revealed the existence of endogenous protective mechanisms that can limit infarct size after revascularization. However, most strategies aiming to reduce infarct size have failed in clinical studies, highlighting the need for cardioprotection. This study used a network-assisted systems biology approach to explore the mitochondrial proteomic signature of the myocardium in a swine model of AMI. The results identified cardiac metabolism as a driver of cardioprotection and highlighted the role of post-conditioning in promoting metabolic reprogramming of the myocardium and a protective response mediated by VDAC2 and DJ-1 in the mitochondria.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
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
Biochemical Research Methods
Mohammad Reza Karimi, Amir Hossein Karimi, Shamsozoha Abolmaali, Mehdi Sadeghi, Ulf Schmitz
Summary: Holistic perspectives are crucial in understanding the complexity of tumors and current single-layer analysis has limitations. Integrative multilayer approaches are emerging as effective tools in achieving systemic views on cancer biology.
BRIEFINGS IN BIOINFORMATICS
(2022)
Review
Biotechnology & Applied Microbiology
Girish Kumar Rasineni, Nalinikanta Panigrahy, Subha Narayan Rath, Madhurarekha Chinnaboina, Ramesh Konanki, Dinesh Kumar Chirla, Srinivas Madduri
Summary: Perinatal asphyxia and neonatal encephalopathy contribute to neonatal mortality, and a combination of clinical data, neuroimaging, and biochemical parameters is a strategy for improved diagnosis and prognosis. Omics technologies may help identify biomarkers associated with brain injuries and predict disease severity.
BIOENGINEERING-BASEL
(2022)
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)
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
Genetics & Heredity
Serena Dato, Paolina Crocco, Nicola Rambaldi Migliore, Francesco Lescai
Summary: The omics approach provides new opportunities in understanding the mechanisms of aging, by combining single-cell analysis with systems biology tools to investigate perturbed networks during aging and disease. High-throughput technologies like next-generation sequencing, proteomics, and metabolomics offer a unique opportunity to study biological markers during aging with high accuracy and specificity. Integration, interpretation, and sharing of high-throughput data continue to be major challenges in aging research, highlighting the need for the development of methods focused on integrating different data types. Emphasis on bioinformatics collaboration, diversity, data sharing, and community-driven portable methods is essential for future advancements in aging research.
FRONTIERS IN GENETICS
(2021)
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
Hematology
Mark C. Blaser, Simon Kraler, Thomas F. Luescher, Elena Aikawa
Summary: Despite the devastating clinical consequences of calcific aortic valve disease, the understanding of its molecular mechanisms is limited and effective pharmacotherapies are not available.
ARTERIOSCLEROSIS THROMBOSIS AND VASCULAR BIOLOGY
(2023)
Editorial Material
Microbiology
Jennifer Geddes-McAlister
Summary: The beauty within biological systems can be revealed through advanced technological platforms. Improvements in genome, transcriptome, proteome, and metabolome investigations, as well as data integration, have accelerated our understanding of diverse biological systems. For fungal pathogens, innovation is driven by exploring mechanisms of antifungal resistance, uncovering new relationships and interactions between host and pathogen, improving characterization of virulence determinants, and discovering new antifungal targets.
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)
Review
Marine & Freshwater Biology
Jiaoyun Jiang, Aoqi Wang, Xiangzi Deng, Wenxu Zhou, Qinhua Gan, Yandu Lu
Summary: The health of corals relies on the fragile partnership between coral hosts and endosymbiotic dinoflagellate symbionts, with modern omics techniques providing crucial insights into the symbiotic relationship. Proteomics and metabolomics are complementing genomics and transcriptomics, offering new perspectives on the intrinsic processes of holobionts. A new era of systems biology, coupled with the development of synthetic biology, is anticipated to greatly enhance the understanding of the underlying mechanisms of mutualistic partners.
Article
Anesthesiology
Christopher Lotz, Jun Zhang, Caiyun Fang, David Liem, Peipei Ping
ANESTHESIA AND ANALGESIA
(2015)
Article
Cardiac & Cardiovascular Systems
Sarah B. Scruggs, Karol Watson, Andrew I. Su, Henning Hermjakob, John R. Yates, Merry L. Lindsey, Peipei Ping
CIRCULATION RESEARCH
(2015)
Review
Biochemical Research Methods
Edward Lau, Derrick Huang, Quan Cao, T. Umut Dincer, Caitie M. Black, Amanda J. Lin, Jessica M. Lee, Ding Wang, David A. Liem, Maggie P. Y. Lam, Peipei Ping
EXPERT REVIEW OF PROTEOMICS
(2015)
Review
Cardiac & Cardiovascular Systems
X'avia C. Y. Chan, Caitlin M. Black, Amanda J. Lin, Peipei Ping, Edward Lau
JOURNAL OF MOLECULAR AND CELLULAR CARDIOLOGY
(2015)
Review
Cardiac & Cardiovascular Systems
Guillaume Calmettes, Bernard Ribalet, Scott John, Paavo Korge, Peipei Ping, James N. Weiss
JOURNAL OF MOLECULAR AND CELLULAR CARDIOLOGY
(2015)
Article
Cardiac & Cardiovascular Systems
Kin Lung Siu, Christopher Lotz, Peipei Ping, Hua Cai
JOURNAL OF MOLECULAR AND CELLULAR CARDIOLOGY
(2015)
Article
Cardiac & Cardiovascular Systems
David A. Liem, Ali Nsair, Shaun P. Setty, Martin Cadeiras, Ding Wang, Robb Maclellan, Chris Lotz, Amanda J. Lin, Jason Tabaraki, Hua Li, Junbo Ge, Jacob Odeberg, Fredrik Ponten, Erik Larson, Jan Mulder, Emma Lundberg, James N. Weiss, Mathias Uhlen, Peipei Ping, Mario C. Deng
CIRCULATION-HEART FAILURE
(2014)
Article
Medicine, Research & Experimental
Maggie P. Y. Lam, Ding Wang, Edward Lau, David A. Liem, Allen K. Kim, Dominic C. M. Ng, Xiangbo Liang, Brian J. Bleakley, Chenguang Liu, Jason D. Tabaraki, Martin Cadeiras, Yibin Wang, Mario C. Deng, Peipei Ping
JOURNAL OF CLINICAL INVESTIGATION
(2014)
Review
Cardiac & Cardiovascular Systems
Ziyou Cui, Sarah B. Scruggs, Jennifer E. Gilda, Peipei Ping, Aldrin V. Gomes
JOURNAL OF MOLECULAR AND CELLULAR CARDIOLOGY
(2014)
Editorial Material
Cardiac & Cardiovascular Systems
C. Y. X'avia Chan, Ding Wang, Martin Cadeiras, Mario C. Deng, Peipei Ping
JOURNAL OF MOLECULAR AND CELLULAR CARDIOLOGY
(2014)
Article
Biochemical Research Methods
Christopher Lotz, Amanda J. Lin, Caitlin M. Black, Jun Zhang, Edward Lau, Ning Deng, Yueju Wang, Nobel C. Zong, Jeong H. Choi, Tao Xu, David A. Liem, Paavo Korge, James N. Weiss, Henning Hermjakob, John R. Yates, Roll Apweiler, Peipei Ping
JOURNAL OF PROTEOME RESEARCH
(2014)
Article
Multidisciplinary Sciences
Galyna Bondar, Martin Cadeiras, Nicholas Wisniewski, Jetrina Maque, Jay Chittoor, Eleanor Chang, Maral Bakir, Charlotte Starling, Khurram Shahzad, Peipei Ping, Elaine Reed, Mario Deng
Article
Biochemical Research Methods
Ding Wang, David A. Liem, Edward Lau, Dominic C. M. Ng, Brian J. Bleakley, Martin Cadeiras, Mario C. Deng, Maggie P. Y. Lam, Peipei Ping
PROTEOMICS CLINICAL APPLICATIONS
(2014)
Article
Biochemical Research Methods
Nobel Zong, Peipei Ping, Edward Lau, Howard J. H. Choi, Dominic C. M. Ng, David Meyer, Caiyun Fang, Haomin Li, Ding Wang, Ivette M. Zelaya, John R. Yates, Maggie P. Y. Lam
PROTEOMICS CLINICAL APPLICATIONS
(2014)
Article
Cardiac & Cardiovascular Systems
Aijun Sun, Yunzeng Zou, Ping Wang, Danling Xu, Hui Gong, Shijun Wang, Yingjie Qin, Peng Zhang, Yunqin Chen, Mutsuo Harada, Toyoshi Isse, Toshihiro Kawamoto, Huizhi Fan, Pengyuan Yang, Hiroshi Akazawa, Toshio Nagai, Hiroyuki Takano, Peipei Ping, Issei Komuro, Junbo Ge
JOURNAL OF THE AMERICAN HEART ASSOCIATION
(2014)