Article
Biochemistry & Molecular Biology
Brad T. Sherman, Ming Hao, Ju Qiu, Xiaoli Jiao, Michael W. Baseler, H. Clifford Lane, Tomozumi Imamichi, Weizhong Chang
Summary: DAVID, a popular bioinformatics resource system, has undergone updates in 2021, including the rebuilding of the DAVID Gene system, increasing the number of gene-term records for annotation types, adding new annotations, assigning specific subgroups, and adding a species parameter for improved user experience.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Biotechnology & Applied Microbiology
Siqi Zhang, Qikai Niu, Lin Tong, Sihong Liu, Pengqian Wang, Haiyu Xu, Bing Li, Huamin Zhang
Summary: This study identified risk genes for the comorbid presence of coronary artery disease (CAD) and rheumatoid arthritis (RA) using a gene network modularization approach, providing insights into clinical therapy and drug development for these diseases.
Article
Medicine, Research & Experimental
Jinting Guan, Yiping Lin, Yang Wang, Junchao Gao, Guoli Ji
Summary: Identifying cell type-specific disease gene modules can provide new insights into the pathogenesis and progression of diseases, leading to the development of more targeted treatments and biomarkers. The study also highlights the importance of studying different disorders and their similarities and differences at the molecular level to better understand the underlying mechanisms of diseases.
JOURNAL OF TRANSLATIONAL MEDICINE
(2021)
Article
Medicine, General & Internal
Yanning Wei, Qisheng Su, Xiaohong Li
Summary: Weighted gene co-expression network analysis identified SERPING1, F13A1, C1S, C1R, and HLA-DPA1 as hub genes in Duchenne muscular dystrophy (DMD), and they play a role in the development of DMD by regulating innate immunity and inflammation, making them potential biomarkers and therapeutic targets.
Article
Thermodynamics
Yujian Gong, Zuo Wang, Zeyu Lai, Minlin Jiang
Summary: The time-varying acceleration coefficients particle swarm optimization method is used to extract the physical parameters of the single diode PV model, which shows good accuracy in most ranges. The introduction of the time-varying mechanism helps mitigate premature convergence issues and establish a proper balance between exploratory and exploitative capabilities.
Article
Biotechnology & Applied Microbiology
Jun Lin, Wenqian Jiang, Lin Chen, Huilian Zhang, Yang Shi, Xin Liu, Weiwen Cai
Summary: Banknotes can serve as a valuable genetic resource for discovering novel microbial gene sequences, including potentially economically valuable enzymes. High-throughput genomic sequencing technology was used to characterize the microbial diversity on US dollars and Chinese Renminbis, leading to the discovery of a significant number of novel gene sequences, one of which was experimentally verified for its catalytic activity.
Article
Genetics & Heredity
Ying Ma, Snehal Patil, Xiang Zhou, Bhramar Mukherjee, Lars G. Fritsche
Summary: Complex traits are influenced by genetic risk factors, lifestyle, and environmental variables. ExPRSs offer an alternative method to study the influence of exposures on different phenotypes. By applying four common PRS methods, ExPRSs were generated and shown to be applicable in phenome-wide association studies and as predictors for common chronic conditions. Combining multiple ExPRSs improved the prediction of chronic conditions compared to traditional disease-focused PRS models.
AMERICAN JOURNAL OF HUMAN GENETICS
(2022)
Article
Biochemical Research Methods
Guoxin Cai, Wenyi Zhao, Zhan Zhou, Xun Gu
Summary: In this study, a novel approach called MATTE was introduced to analyze transcriptomics data and identify differences in a modular manner. MATTE assumes that gene interactions modulate a phenotype and models phenotype differences as gene location changes. The results demonstrate that MATTE outperformed state-of-the-art methods in identifying differentially expressed genes and could also handle single-cell RNA-seq data.
BRIEFINGS IN BIOINFORMATICS
(2023)
Article
Plant Sciences
Lixin Cheng, Yonglun Zeng, Shuai Hu, Ning Zhang, Kenneth C. P. Cheung, Baiying Li, Kwong-Sak Leung, Liwen Jiang
Summary: This study identified autophagy-related modules in Arabidopsis using a systems-level algorithm, revealing that newly identified genes in these modules are upregulated and coexpressed during senescence. Additionally, the Golgi apparatus autophagy-related module, ARM13, was found to function in the autophagy process through module clustering and functional analysis.
Review
Gastroenterology & Hepatology
Antoine Gardin, Katharina Remih, Emmanuel Gonzales, Emma Rachel Andersson, Pavel Strnad
Summary: The liver plays a crucial role in health and its dysfunction can lead to various diseases. Genetic approaches, enzyme substitution therapy, and siRNA drugs have been developed for the treatment of liver-related disorders. These methods have shown promising results but still face challenges such as immune response and long-term stability of treatment.
JOURNAL OF HEPATOLOGY
(2022)
Article
Biology
Foteini Thanati, Evangelos Karatzas, Fotis A. Baltoumas, Dimitrios J. Stravopodis, Aristides G. Eliopoulos, Georgios A. Pavlopoulos
Summary: In this article, FLAME, a web application for combining multiple gene lists prior to enrichment analysis, is introduced. Users can upload several lists and utilize interactive UpSet plots to handle unions or intersections among the given input files.
Article
Biology
Tzu-Hsien Yang, Chia-Wei Hsu, Yan-Xiang Wang, Chien-Hung Yu, Jagat Rathod, Yan-Yuan Tseng, Wei-Sheng Wu
Summary: In this research, the YMLA (Yeast Multiple List Analyzer) platform was constructed for comparative analysis among multiple gene lists, offering 39 yeast features for analysis and customized feature set reanalysis to help form mechanism hypotheses based on enriched feature subsets. The biological applicability of YMLA was demonstrated using example lists consisting of genes with top/bottom translation efficiency values.
COMPUTERS IN BIOLOGY AND MEDICINE
(2022)
Article
Biochemistry & Molecular Biology
Roozbeh Heidarzadehpilehrood, Maryam Pirhoushiaran, Malina Binti Osman, Habibah Abdul Hamid, King-Hwa Ling
Summary: Polycystic ovary syndrome (PCOS) is a condition that affects reproductive-age women, causing infertility, insulin resistance, obesity, and heart difficulties. This study used bioinformatic methods to identify nine novel dysregulated long non-coding RNAs (lncRNAs) in PCOS and determined their co-expression genes and enriched pathways using weighted gene co-expression network analysis (WGCNA) and pathway enrichment analysis. Hub genes CCT7, EFTUD2, ESR1, JUN, NDUFAB1, CTTNB1, GRB2, and CTNNB1 were also identified. Further functional studies are needed to understand the role of these lncRNAs in translational modification in PCOS.
Article
Neurosciences
Karl Li, Tanweer Rashid, Jinqi Li, Nicolas Honnorat, Anoop Benet Nirmala, Elyas Fadaee, Di Wang, Sokratis Charisis, Hangfan Liu, Crystal Franklin, Mallory Maybrier, Haritha Katragadda, Leen Abazid, Vinutha Ganapathy, Vijaya Lakshmi Valaparla, Pradeepthi Bagudu, Eliana Vasquez, Leigh Solano, Geoffrey Clarke, Gladys Maestre, Tim Richardson, Jamie Walker, Peter T. Fox, Kevin Bieniek, Sudha Seshadri, Mohamad Habes
Summary: This article introduces a new data repository, the South Texas Alzheimer's Disease research center repository, designed to study and validate the relationship between neuroimaging markers and neurological changes. The repository includes a diverse range of dementia samples, spans a wide age range, and utilizes advanced imaging protocols and MRI-guided histopathological analysis to improve diagnosis and understanding of neurodegenerative disorders.
JOURNAL OF ALZHEIMERS DISEASE
(2023)
Article
Chemistry, Physical
Tibor Furtenbacher, Samuel T. Hegedus, Jonathan Tennyson, Attila G. Csaszar
Summary: The empirical rovibronic energy levels of (CH)-C-12 and (OH)-O-16 radicals are reported, which are crucial for modeling efforts in various chemical, combustion, astrophysical, and atmospheric environments.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2022)
Article
Cell Biology
Dang Vinh Do, Bernhard Strauss, Engin Cukuroglu, Iain Macaulay, Keng Boon Wee, Tim Xiaoming Hu, Ruiz De Los Mozos Igor, Caroline Lee, Andrew Harrison, Richard Butler, Sabine Dietmann, Ule Jernej, John Marioni, Christopher W. J. Smith, Jonathan Goke, M. Azim Surani
Article
Neurosciences
Sonia Olivia Spitzer, Sergey Sitnikov, Yasmine Kamen, Kimberley Anne Evans, Deborah Kronenberg-Versteeg, Sabine Dietmann, Omar de Faria, Sylvia Agathou, Ragnhildur Thora Karadottir
Article
Biochemistry & Molecular Biology
Hans-Werner Mewes
Article
Biochemistry & Molecular Biology
Thomas Burgold, Michael Barber, Susan Kloet, Julie Cramard, Sarah Gharbi, Robin Floyd, Masaki Kinoshita, Meryem Ralser, Michiel Vermeulen, Nicola Reynolds, Sabine Dietmann, Brian Hendrich
Article
Biochemistry & Molecular Biology
Nikoletta A. Gkatza, Cecilia Castro, Robert F. Harvey, Matthias Heiss, Martyna C. Popis, Sandra Blanco, Susanne Bornelov, Abdulrahim A. Sajini, Joseph G. Gleeson, Julian L. Griffin, James A. West, Stefanie Kellner, Anne E. Willie, Sabine Dietmann, Michaels Frye
Article
Cell & Tissue Engineering
Bjorn Neumann, Roey Baror, Chao Zhao, Michael Segel, Sabine Dietmann, Khalil S. Rawji, Sarah Foerster, Crystal R. McClain, Kevin Chalut, Peter van Wijngaarden, Robin J. M. Franklin
Article
Biochemical Research Methods
Paul Hager, Hans-Werner Mewes, Meino Rohlfs, Christoph Klein, Tim Jeske
PLOS COMPUTATIONAL BIOLOGY
(2020)
Article
Cell & Tissue Engineering
Nicholas Bredenkamp, Jian Yang, James Clarke, Giuliano Giuseppe Stirparo, Ferdinand von Meyenn, Sabine Dietmann, Duncan Baker, Rosalind Drummond, Yongming Ren, Dongwei Li, Chuman Wu, Maria Rostovskaya, Sarah Eminli-Meissner, Austin Smith, Ge Guo
Article
Multidisciplinary Sciences
Anastasiya Sybirna, Walfred W. C. Tang, Merrick Pierson Smela, Sabine Dietmann, Wolfram H. Gruhn, Ran Brosh, M. Azim Surani
NATURE COMMUNICATIONS
(2020)
Article
Cell Biology
Dorian Forte, Maria Garcia-Fernandez, Abel Sanchez-Aguilera, Vaia Stavropoulou, Claire Fielding, Daniel Martin-Perez, Juan Antonio Lopez, Ana S. H. Costa, Laura Tronci, Efterpi Nikitopoulou, Michael Barber, Paolo Gallipoli, Ludovica Marando, Carlos Lopez Fernandez de Castillejo, Alexandar Tzankov, Sabine Dietmann, Michele Cavo, Lucia Catani, Antonio Curti, Jesus Vazquez, Christian Frezza, Brian J. Huntly, Juerg Schwaller, Simon Mendez-Ferrer
Article
Cell Biology
Qifan Zhu, Fei Sang, Sarah Withey, Walfred Tang, Sabine Dietmann, Doris Klisch, Priscila Ramos-Ibeas, Haixin Zhang, Cristina E. Requena, Petra Hajkova, Matt Loose, M. Azim Surani, Ramiro Alberio
Summary: Research on pig primordial germ cells has shown large-scale epigenomic reprogramming during early embryonic development, including DNA demethylation, repair, and re-expression of certain genes. Additionally, some gene regions in hypomethylated PGCs exhibit resistance to demethylation, suggesting potential for transgenerational epigenetic inheritance.
Article
Biochemistry & Molecular Biology
Emily M. A. Lewis, Komal Kaushik, Luke A. Sandoval, Irene Antony, Sabine Dietmann, Kristen L. Kroll
Summary: Epigenetic regulation is crucial in neural development, and mutations in genes can lead to neurodevelopmental disorders; in vitro models like differentiation of hPSCs are essential for studying epigenetic regulation in human neural development.
NEUROCHEMISTRY INTERNATIONAL
(2021)
Article
Multidisciplinary Sciences
Fatima Zohra Khamissi, Liang Ning, Eirini Kefaloyianni, Hao Dun, Akshayakeerthi Arthanarisami, Amy Keller, Jeffrey J. Atkinson, Wenjun Li, Brian Wong, Sabine Dietmann, Kory Lavine, Daniel Kreisel, Andreas Herrlich
Summary: This study identifies circulating osteopontin (OPN) released from kidney tubule cells as a novel mediator in acute kidney injury (AKI)-induced acute lung injury (ALI). OPN triggers lung endothelial leakage, inflammation, and respiratory failure. The study also demonstrates the elevated levels of OPN in AKI patients and its correlation with kidney injury.
Article
Multidisciplinary Sciences
Wolfram H. Gruhn, Walfred W. C. Tang, Sabine Dietmann, Joao P. Alves-Lopes, Christopher A. Penfold, Frederick C. K. Wong, Navin B. Ramakrishna, M. Azim Surani
Summary: Epigenetic resetting in the mammalian germ line involves acute DNA demethylation, resulting in reduced repressive histone modifications and acquisition of a neutral or paused epigenetic state in hypomethylated human primordial germ cells (hPGCs). Transcriptional repression in hPGCs relies on local maintenance of heterochromatic features and a lack of inductive cues, with a subset of genomic loci requiring specific histone modifications for efficient repression.
Article
Biotechnology & Applied Microbiology
Susanne Bornelov, Tommaso Selmi, Sophia Flad, Sabine Dietmann, Michaela Frye
