Article
Environmental Sciences
Marlene Gamelon, Stephanie Jenouvrier, Melanie Lindner, Bernt-Erik Saether, Marcel E. Visser
Summary: The authors define the time of emergence, known as 'time of emergence' (ToE), as the time at which the signal of climate change in ecological processes emerges from the noise of ecosystem variability. They found that the time of emergence differs across different levels of biological organization, occurring earlier at the population level rather than at the trait or vital rate levels. This finding suggests that the population size of the great tit will experience an amplified climate change signal compared to its laying date and vital rates under the RCP 8.5 scenario.
NATURE CLIMATE CHANGE
(2023)
Article
Medicine, General & Internal
Byung-Keun Kim, Hyun-Seung Lee, Suh-Young Lee, Heung-Woo Park
Summary: This study investigates gene regulatory networks in adult asthma patients to determine the factors influencing responsiveness to inhaled corticosteroids. The top-10 transcription factors and their associated genes were found to be significantly enriched in distinct biological pathways, providing potential targets to enhance corticosteroid sensitivity in asthma patients.
FRONTIERS IN MEDICINE
(2021)
Article
Genetics & Heredity
Malik Yousef, Gokhan Goy, Burcu Bakir-Gungor
Summary: Increasing evidence has shown that miRNAs play a crucial role in carcinogenesis, highlighting the need to understand their regulation mechanisms and roles in gene-regulatory networks. In this study, the researchers developed miRModuleNet, a tool that groups mRNA correlated with each miRNA to identify miRNA-mRNA regulatory modules. This tool provides a hierarchical list of significant miRNA-mRNA regulatory modules, aiding in the identification of functional relationships and essential pathways involved in cancer pathogenesis.
FRONTIERS IN GENETICS
(2022)
Article
Multidisciplinary Sciences
Qian Zhao, Yan Zhang, Shichun Shao, Yeqing Sun, Zhengkui Lin
Summary: This study identified hub genes and key biological pathways for hepatocellular carcinoma (HCC) through integrated bioinformatics analysis. The 11 hub genes MCM3, TRMT6, AURKA, CDC20, TOP2A, ECT2, TK1, MCM2, FEN1, NCAPD2, and KPNA2 were found to play crucial roles in HCC, with high diagnostic efficiency to distinguish tumors from normal tissues. The cell cycle and mitotic pathway were highlighted as important in the progression of HCC.
Article
Biochemical Research Methods
Marco Pensalfini, Adrian Buganza Tepole
Summary: Wound healing involves coordinated action of fibroblasts, extracellular matrix deposition, remodeling, and wound contraction. A computational model is calibrated using local tissue stiffness measurements in murine wounds, enabling the recapitulation of temporal evolution of inflammatory signal, fibroblast infiltration, collagen buildup, and wound contraction. The model challenges the current understanding of wound biomechanics and mechanobiology, while offering a versatile tool to explore and control scar fibrosis.
PLOS COMPUTATIONAL BIOLOGY
(2023)
Article
Oncology
Chang Woo Kim, Jae Myung Cha, Min Seob Kwak
Summary: In colorectal cancer, patients with mucinous adenocarcinoma (MAC) have a poorer prognosis compared to those with traditional adenocarcinoma (TAC), especially in Stage II. The study findings suggest that identifying potential biomarkers and biological pathways can be useful in predicting the prognosis of colorectal cancer.
Article
Mathematical & Computational Biology
Xu Qiao, Xianru Zhang, Wei Chen, Xin Xu, Yen-Wei Chen, Zhi-Ping Liu
Summary: Detecting significant signaling pathways in disease progression is important for understanding complex disease development. This paper introduces a tensor-based gene set enrichment analysis method, called tensorGSEA, that identifies relevant pathways during disease development by reconstructing multi-dimensional gene expression data. The experiments show that tensorGSEA is efficient in identifying critical pathways with diabetes-specific functions.
INTERDISCIPLINARY SCIENCES-COMPUTATIONAL LIFE SCIENCES
(2022)
Article
Biochemistry & Molecular Biology
Fang Liu, Allen D. Smith, Thomas T. Y. Wang, Quynhchi Pham, Lumei Cheung, Haiyan Yang, Robert W. Li
Summary: In this study, the antimicrobial properties of blueberry anthocyanin malvidin 3-glucoside (MG) were investigated using a multi-omics approach with Citrobacter rodentium. MG supplementation reversed the negative effects of infection, improved colonic hyperplasia and histopathological scores, and restored microbial dysbiosis caused by C. rodentium. MG also mediated several host- and microbiota-derived metabolites and normalized the dysregulated bioactive lipid oleoylethanolamine.
Article
Computer Science, Artificial Intelligence
Yaqi Wang, Jungang Lou, Hongyan Yan, Jianquan Lu
Summary: This paper investigates the stability of a class of stochastic neural networks with switching signal by analyzing switched systems with potentially unstable subsystems and stable subsystems using the method of limiting average dwell time. By considering stabilizing and destabilizing switchings, the relationship between two successive activated subsystems is described with time-dependent parameters. The obtained results provide stability criteria for switched neural networks with stochastic disturbances, and a numerical example is presented to demonstrate the effectiveness of the results.
Article
Multidisciplinary Sciences
Laura Aliisa Saarimaki, Michele Fratello, Alisa Pavel, Seela Korpilahde, Jenni Leppanen, Angela Serra, Dario Greco
Summary: Adverse outcome pathways (AOPs) serve as a central framework in modern toxicology and biomedicine, depicting biological mechanisms as causally linked sequences of key events (KEs). AOPs guide the development of new approaches and reduction in animal experimentation, and integrating them with toxicogenomics enables better interpretation of molecular mechanisms. Through rigorous curation, we have established a link between AOPs and molecular data interpretation, paving the way for new knowledge in biomedicine.
Article
Biotechnology & Applied Microbiology
Yueyue Wang, Yanfei Shao, Haitao Zhang, Jun Wang, Peng Zhang, Weizhong Zhang, Huanhuan Chen
Summary: Inflammation- and neuromodulation-related pathways were found to be closely associated with TAO. Clinical verification suggested that OSM, CSF3R, CXCL6, DPP4, and PRKCG may serve as biomarkers related to inflammation or neuromodulation in TAO, offering novel insights for TAO diagnosis and treatment.
Article
Biochemical Research Methods
Ellen Reed, Enrico Ferrari, Mikhail Soloviev
Summary: This study aimed to address issues related to the quality of gene expression data and devise improved quality control and data processing procedures. Linear regression analysis was used to process gene expression datasets, resulting in an increase in the number of identifiable differentially regulated genes and a reduction in false positives. The approach reduced technical errors and improved the accuracy and precision of determining the degree of differential gene expression.
CURRENT BIOINFORMATICS
(2023)
Article
Biotechnology & Applied Microbiology
Wenbo Yang, Peng Liu, Yuling Zheng, Zhongtian Wang, Wenhua Huang, Hua Jiang, Qingyu Lv, Yuhao Ren, Yongqiang Jiang, Liping Sun
Summary: This study utilized public microarray datasets from the Gene Expression Omnibus (GEO) database to identify differentially expressed genes between UTI and normal cell samples, uncovering potential biomarkers and signaling pathways associated with UTIs. The findings were validated through animal experiments, providing new targets for exploring treatments for UTIs.
Article
Agriculture, Dairy & Animal Science
Fatemeh Mohammadinejad, Mohammadreza Mohammadabadi, Zahra Roudbari, Tomasz Sadkowski
Summary: This study aimed to identify the hub genes and mechanisms involved in skeletal muscle maturation and hypertrophy in livestock species (Bos taurus, Ovis aries, and Sus scrofa). Gene expression profiles were analyzed, and differentially expressed genes and enriched pathways were identified in each species. Common genes and pathways were also identified, which play important roles in the development and maturation of skeletal muscles. This study provides valuable insights into the relationships between genes and biological pathways in the skeletal muscle maturation process.
Review
Mathematics
Pei Wang, Shunjie Chen, Sijia Yang
Summary: This review focuses on recent advances in penalized regression models, including linear and logistic regression models, and their applications in biological data. The pros and cons of different models in terms of response prediction, sample classification, network construction, and feature selection are also discussed. The performance of different models in a real-world RNA-seq dataset for breast cancer is explored, and future directions are suggested.
Article
Microbiology
Bahtiyar Yilmaz, Catherine Mooser, Irene Keller, Hai Li, Jakob Zimmermann, Lars Bosshard, Tobias Fuhrer, Mercedes Gomez de Agueero, Nerea Fernandez Trigo, Heidi Tschanz-Lischer, Julien P. Limenitakis, Wolf-Dietrich Hardt, Kathy D. McCoy, Baerbel Stecher, Laurent Excoffier, Uwe Sauer, Stephanie C. Ganal-Vonarburg, Andrew J. Macpherson
Summary: The study showed that isobiotic mice with stable microbiota can adapt to changes in the intestinal environment through long-term genomic positive selection and short-term transcriptional reprogramming and adjustments in sub-strain proportions.
CELL HOST & MICROBE
(2021)
Article
Biochemistry & Molecular Biology
Ellie E. Armstrong, Anubhab Khan, Ryan W. Taylor, Alexandre Gouy, Gili Greenbaum, Alexandre Thiery, Jonathan T. Kang, Sergio A. Redondo, Stefan Prost, Gregory Barsh, Christopher Kaelin, Sameer Phalke, Anup Chugani, Martin Gilbert, Dale Miquelle, Arun Zachariah, Udayan Borthakur, Anuradha Reddy, Edward Louis, Oliver A. Ryder, Yadvendradev Jhala, Dmitri Petrov, Laurent Excoffier, Elizabeth Hadly, Uma Ramakrishnan
Summary: Species conservation can benefit from understanding evolutionary and genetic history. Tigers, especially Indian tigers with high genomic diversity, may experience recent inbreeding events due to connectivity loss in fragmented habitats. Demographic models suggest subspecies divergence within the last 20,000 years, with Amur and Sumatran tigers showing different patterns of selection for metabolic and body size regulation genes. Further investigation on local adaptation is recommended prior to genetic rescue efforts.
MOLECULAR BIOLOGY AND EVOLUTION
(2021)
Article
Biochemistry & Molecular Biology
Parul Johri, Kellen Riall, Hannes Becher, Laurent Excoffier, Brian Charlesworth, Jeffrey D. Jensen
Summary: Current methods for inferring population history assume neutrality, but neglect the effects of direct and background selection. The study shows that background selection can lead to mis-inferences of population growth, especially with increasing strength of purifying selection and density of directly selected sites.
MOLECULAR BIOLOGY AND EVOLUTION
(2021)
News Item
Biochemistry & Molecular Biology
Nina Marchi, Flavia Schlichta, Laurent Excoffi
Summary: The revolution in next-generation sequencing technology has significantly increased the amount of genetic data for many organisms, allowing researchers to obtain more information about genetic diversity and evolution of the organisms studied.
Article
Multidisciplinary Sciences
Jeremy Choin, Javier Mendoza-Revilla, Lara R. Arauna, Sebastian Cuadros-Espinoza, Olivier Cassar, Maximilian Larena, Albert Min-Shan Ko, Christine Harmant, Romain Laurent, Paul Verdu, Guillaume Laval, Anne Boland, Robert Olaso, Jean-Francois Deleuze, Frederique Valentin, Ying-Chin Ko, Mattias Jakobsson, Antoine Gessain, Laurent Excoffier, Mark Stoneking, Etienne Patin, Lluis Quintana-Murci
Summary: The study analyzed high-coverage genomes of 317 individuals from 20 populations in the Pacific region, revealing a strong bottleneck in the ancestors of Oceanian populations before their settlement and a divergence between East Asian Pacific populations and Taiwanese Indigenous peoples before the Neolithic expansion. The research also showed significant differences in the Denisovan genetic contribution among Pacific groups and highlighted selective sweeps and polygenic adaptation linked to pathogen exposure and lipid metabolism in the region.
Editorial Material
Multidisciplinary Sciences
David A. Marques, Kay Lucek, Vitor C. Sousa, Laurent Excoffier, Ole Seehausen
NATURE COMMUNICATIONS
(2021)
Article
Biochemical Research Methods
Laurent Excofffier, Nina Marchi, David Alexander Marques, Remi Matthey-Doret, Alexandre Gouy, Vitor C. Sousa
Summary: fastsimcoal2 extends fastsimcoal by enabling estimation of demographic parameters under complex scenarios, with improvements such as multi-threading, handling of population inbreeding, extended input file syntax, and more efficient simulations.
Article
Medicine, Legal
Michel Bottinelli, Alexandre Gouy, Silvia Utz, Martin Zieger
Summary: X-chromosomal STRs are a powerful tool for assessing complex kinship scenarios. The first Swiss X-STR dataset, based on 1198 individuals, fits well in the European context and shows no apparent intra-national population substructure.
INTERNATIONAL JOURNAL OF LEGAL MEDICINE
(2022)
Article
Medicine, Legal
Martin Zieger, Alexandre Gouy, Silvia Utz
Summary: The research expanded the Swiss autosomal STR dataset to 32 loci by genotyping 1198 individuals using the Qiagen Investigator (R) HDplex Kit, providing additional resources for complex kinship cases. The study also presented high-quality allele frequency datasets for several loci that will be accessible through the ENFSI reference database STRidER.
INTERNATIONAL JOURNAL OF LEGAL MEDICINE
(2021)
Article
Genetics & Heredity
Antoine Moinet, Flavia Schlichta, Stephan Peischl, Laurent Excoffier
Summary: This article investigates the shape of neutral valleys of diversity under a model of population size change and compares it to signals of a selective sweep. The results show that selective sweep valleys of diversity are wider than neutral valleys, but it is possible to find a neutral valley with the same width as a given selective valley by parameterizing the model.
Article
Biology
Josephine T. Daub, Saman Amini, Denise J. E. Kersjes, Xiaotu Ma, Natalie Jager, Jinghui Zhang, Stefan M. Pfister, Frank C. P. Holstege, Patrick Kemmeren
Summary: By analyzing over 2,500 tumors from 23 types of childhood cancer, Josephine Daub, Saman Amini, et al. developed a genetic interaction map of childhood cancers, providing a valuable resource for investigating the biological underpinnings of pediatric cancer.
COMMUNICATIONS BIOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Nina Marchi, Laura Winkelbach, Ilektra Schulz, Maxime Brami, Zuzana Hofmanova, Jens Bloecher, Carlos S. Reyna-Blanco, Yoan Diekmann, Alexandre Thiery, Adamandia Kapopoulou, Vivian Link, Valerie Piuz, Susanne Kreutzer, Sylwia M. Figarska, Elissavet Ganiatsou, Albert Pukaj, Travis J. Struck, Ryan N. Gutenkunst, Necmi Karul, Fokke Gerritsen, Joachim Pechtl, Joris Peters, Andrea Zeeb-Lanz, Eva Lenneis, Maria Teschler-Nicola, Sevasti Triantaphyllou, Sofija Stefanovic, Christina Papageorgopoulou, Daniel Wegmann, Joachim Burger, Laurent Excoffier
Summary: Demogenomic modeling of ancient genomes sheds light on the genetic origins and differentiation process of early farming populations in Europe and Southwest Asia, as well as the genetic drift they experienced during their migration.
Article
Biochemistry & Molecular Biology
Parul Johri, Charles F. Aquadro, Mark Beaumont, Brian Charlesworth, Laurent Excoffier, Adam Eyre-Walker, Peter D. Keightley, Michael Lynch, Gil McVean, Bret A. Payseur, Susanne P. Pfeifer, Wolfgang Stephan, Jeffrey D. Jensen
Summary: The field of population genomics has grown rapidly, but there is a tendency to focus on specific models at the expense of exploring underlying evolutionary processes. We need to pay more attention to statistical inference and theory and establish relevant baseline models for each analysis.
Article
Biochemistry & Molecular Biology
Flavia Schlichta, Stephan Peischl, Laurent Excoffier
Summary: Range expansions lead to a loss of genomic diversity and the occurrence of gene surfing. This study simulated the evolution of whole genomes during range expansions and found that the initial evolution of trough density and width can be predicted, regardless of the expansion condition, by considering the amount of diversity lost since the beginning of the expansion. Troughs are over-represented in regions of low recombination. Therefore, range expansions leave genomic signatures that can be interpreted as evidence of past selective events, providing insights for evolutionary biology studies.
MOLECULAR BIOLOGY AND EVOLUTION
(2022)