Article
Biochemistry & Molecular Biology
Takeshi Obayashi, Shun Kodate, Himiko Hibara, Yuki Kagaya, Kengo Kinoshita
Summary: Gene coexpression refers to the synchronization of gene expression across multiple conditions and is used to infer gene function. COXPRESdb is an animal gene expression database that provides coexpression data and analysis tools. The latest version, COXPRESdb version 8, introduces new features for overview, summary, and examination of coexpression relationships, as well as bridging coexpression and existing knowledge. It also supports interspecies comparisons by integrating different types of coexpression data.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Physics, Multidisciplinary
Lukasz Huminiecki
Summary: Mendel's paradigm of particle-based heredity has been influential for over 150 years, and with the accumulation of omics data, the concept of virtual gene has emerged. This concept has already inspired a practical research program related to systems genetics.
Article
Medicine, General & Internal
Xiangyu Li, Koeun Shong, Woonghee Kim, Meng Yuan, Hong Yang, Yusuke Sato, Haruki Kume, Seishi Ogawa, Hasan Turkez, Saeed Shoaie, Jan Boren, Jens Nielsen, Mathias Uhlen, Cheng Zhang, Adil Mardinoglu
Summary: In this study, a systematic approach was proposed to reposition drugs for the treatment of clear cell renal cell carcinoma (ccRCC). Using gene co-expression network analysis and drug-perturbed signature profiles, potential drug targets were identified and effective drugs were repurposed. The study demonstrated the usefulness and efficiency of the approach in improving drug repositioning for cancer treatment.
Article
Biology
Raissa Coelho Andrade, Mariana Boroni, Marion Kielmanowicz Amazonas, Fernando Regla Vargas
Summary: This study conducted a meta-analysis of gene expression signature of primary osteosarcoma and proposed potential small molecules to reverse this signature. Through further verification, a final gene expression signature of 266 genes was obtained, providing potential new therapeutic genetic targets and drug options for osteosarcoma.
COMPUTERS IN BIOLOGY AND MEDICINE
(2021)
Article
Plant Sciences
Jonas Blomme, Thomas Wichard, Thomas B. Jacobs, Olivier De Clerck
Summary: Green seaweeds, particularly Ulva species, have various morphologies and ecological roles, making them important for research in carbon assimilation, bacteria interactions, life cycle, and economic benefits. Ulva mutabilis/compressa is suggested as a model species and the article highlights available molecular data and tools for further research. Exciting developments in other Ulva species are also discussed.
JOURNAL OF PHYCOLOGY
(2023)
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.
Article
Biology
Hongran Li, Yan Peng, Yansong Wang, Bryce Summerhays, Xiaohan Shu, Yumary Vasquez, Hannah Vansant, Christy Grenier, Nicolette Gonzalez, Khyati Kansagra, Ryan Cartmill, Edison Ryoiti Sujii, Ling Meng, Xuguo Zhou, Gabor L. Loevei, John J. Obrycki, Arun Sethuraman, Baoping Li
Summary: This study provides new insights into the invasion processes of the harlequin ladybird into other continents from its native range in Asia. It identifies a population in eastern China as the source of non-native populations and identifies potential adaptive genomic loci related to body color variation, visual perception, and hemolymph synthesis. The study also reveals asymmetric migration, varying population sizes, historical bottlenecks, and different mitochondrial haplotypes between native and non-native populations.
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)
Article
Biochemistry & Molecular Biology
William Andres Lopez-Arboleda, Stephan Reinert, Magnus Nordborg, Arthur Korte
Summary: The study demonstrates that sampling locations have an impact on GWAS results in the model plant Arabidopsis thaliana, showing that certain traits are influenced by unique genetic effects in local populations. While using gene expression as a molecular phenotype, some genes are affected by shared variants globally, while others are affected by variants specific to subpopulations.
MOLECULAR BIOLOGY AND EVOLUTION
(2021)
Article
Biochemistry & Molecular Biology
V. M. Datta Darshan, Venketesh Sivaramakrishnan, K. Arvind Kumar
Summary: This study aims to investigate the effects of missense and nonsense SNPs on protein degradation and functional consequences. Computational tools and models are used to analyze the impact of these SNPs on protein-protein interactions and functional networks.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2022)
Article
Oncology
Fazlur Rahman Talukdar, Sheila C. Soares Lima, Rita Khoueiry, Ruhina Shirin Laskar, Cyrille Cuenin, Bruna Pereira Sorroche, Anne-Claire Boisson, Behnoush Abedi-Ardekani, Christine Carreira, Diana Menya, Charles P. Dzamalala, Mathewos Assefa, Abraham Aseffa, Vera Miranda-Goncalves, Carmen Jeronimo, Rui M. Henrique, Ramin Shakeri, Reza Malekzadeh, Nagla Gasmelseed, Mona Ellaithi, Nitin Gangane, Daniel R. S. Middleton, Florence Le Calvez-Kelm, Akram Ghantous, Maria Leon Roux, Joachim Schuz, Valerie McCormack, M. Iqbal Parker, Luis Felipe Ribeiro Pinto, Zdenko Herceg
Summary: This study investigated tumor-specific DNA methylation in ESCC cases from high-incidence countries, identifying thousands of differentially methylated positions and regions, particularly in gene regions associated with transcription activation. Prioritized genes for replication showed consistent methylation differences and downregulation in tumors. The study highlights the potential of these DNA methylation events as tumor-specific markers for further biomarker discovery.
Article
Biochemistry & Molecular Biology
Caitlin A. Finney, Fabien Delerue, Wendy A. Gold, David A. Brown, Artur Shvetcov
Summary: Alzheimer's disease is the most common form of dementia with no effective treatment. Thousands of dysregulated genes have been identified in the brains of patients with Alzheimer’s disease. A study using meta-analysis and artificial intelligence techniques suggests that mitochondrial dysfunction may play a crucial role in Alzheimer's disease.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2023)
Article
Multidisciplinary Sciences
Mohammad Ali Mohammadi, Ali Afgar, Ashkan Faridi, Seyed Mohammad Mousavi, Ali Derakhshani, Mehdi Borhani, Majid Fasihi Harandi
Summary: This study demonstrates the potential of lentiviral gene transient transduction in tapeworms and shows promising outcomes with potential implications in experimental studies on flatworm biology.
JOVE-JOURNAL OF VISUALIZED EXPERIMENTS
(2022)
Review
Biotechnology & Applied Microbiology
Sunita, Yogendra Singh, Gillian Beamer, Xingmin Sun, Pratyoosh Shukla
Summary: Tuberculosis is a prevalent global disease, and current vaccines are not sufficient in protection. Despite many vaccines being evaluated in clinical trials, none have proven significantly successful yet. Therefore, new strategies are urgently needed to design more effective TB vaccines, and the emergence of new technologies will accelerate this process.
CRITICAL REVIEWS IN BIOTECHNOLOGY
(2022)
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.
