Article
Biochemical Research Methods
Manuel Rueda, Roberto Ariosa, Mauricio Moldes, Jordi Rambla
Summary: Beacon v2 is an API specification that defines a standard for federated discovery of genomic and phenotypic data. B2RI is a set of open-source software tools that allow quick setup of a local Beacon instance.
Review
Physiology
Jianzheng He, Botong Li, Shuzhen Han, Yuan Zhang, Kai Liu, Simeng Yi, Yongqi Liu, Minghui Xiu
Summary: This article provides an overview of the conserved genetics and evaluation methods of nociceptive mechanisms, as well as the progress in developing anti-pain drugs using the fruit fly model.
FRONTIERS IN PHYSIOLOGY
(2022)
Article
Agronomy
Jessica Delfini, Vania Moda-Cirino, Jose dos Santos Neto, Douglas Mariani Zeffa, Alison Fernando Nogueira, Luriam Aparecida Brandao Ribeiro, Paulo Mauricio Ruas, Paul Gepts, Leandro Simoes Azeredo Goncalves
Summary: This study identified QTNs associated with mineral content in common beans, showcasing the potential for biofortification efforts to enhance nutritional value. Results demonstrated the reliability of markers and the valuable resource of the BDP for association studies. The loci identified have the potential to improve common bean varieties, particularly those consumed in Brazil.
THEORETICAL AND APPLIED GENETICS
(2021)
Review
Neurosciences
Florian P. P. Fischer, Robin A. A. Karge, Yvonne G. G. Weber, Henner Koch, Stefan Wolking, Aaron Voigt
Summary: Epilepsy affects more than 45 million people worldwide and advances in genetic techniques have increased our understanding of its molecular and cellular mechanisms. Model organisms, such as the fruit fly, Drosophila melanogaster, have played a significant role in studying genetic epilepsies and can be used to explore new therapeutic targets.
FRONTIERS IN MOLECULAR NEUROSCIENCE
(2023)
Article
Ophthalmology
Xiaotong Han, Siyu Pan, Jialin Liu, Xiaohu Ding, Xingyan Lin, Decai Wang, Zhi Xie, Changqing Zeng, Fan Liu, Mingguang He, Xiangtian Zhou, Tianzi Liu, Lixia Luo, Yizhi Liu
Summary: Two novel loci associated with ocular axial length were identified, explaining 29.63% of the variation in the Chinese population. The study also suggested a role of the nervous system and glucose metabolism in the development of myopia.
BRITISH JOURNAL OF OPHTHALMOLOGY
(2023)
Article
Biology
Matthew W. Parker, Jonchee A. Kao, Alvin Huang, James M. Berger, Michael R. Botchan
Summary: Researchers demonstrate that phase separation is driven by a synergy between electrostatic DNA-bridging interactions and hydrophobic inter-IDR contacts, dependent on sequence composition but not order. These interactions are resistant to 1,6-hexanediol and independent of aromaticity, revealing distinct mechanisms underlying condensate formation and specificity in different phase-separating systems.
Article
Evolutionary Biology
Zachery Tiedeman, Sarah Signor
Summary: Transposable elements (TEs) are crucial components of the genome, with population genetics and the rate and mode of transposition being essential for understanding genome evolution. In the model Drosophila species Drosophila serrata, TE families show variation among genotypes and some TEs exhibit little diversification between individuals, suggesting recent spread.
GENOME BIOLOGY AND EVOLUTION
(2021)
Article
Multidisciplinary Sciences
Deena Jalal, Mariam G. Elzayat, Hend E. El-Shqanqery, Aya A. Diab, Abdelrahman Yahia, Omar Samir, Usama Bakry, Khaled Amer, Mostafa ElNaqeeb, Wael Hassan, Hala S. Talat, Hala M. Farawela, Mona S. Hamdy, May S. Soliman, Maha H. El Sissy, Moushira H. Ezzelarab, Sara M. El Khateeb, Lamyaa H. Soliman, Sara E. Haddad, Ashraf Hatem, Mohamed S. Ismail, Maha Hossam, Tarek Mansour, Lobna Shalaby, Sonia Soliman, Reem Hassan, Mahmoud Hammad, Ibrahim Abdo, Sameh Magdeldin, Alaa ElHaddad, Sherif Abouelnaga, Ahmed A. Sayed
Summary: This study provides genetic, phylogenetic, and clinical correlation data about the spread of the SARS-CoV-2 pandemic in Egypt. The analyzed samples belonged mostly to clades 20A and 20D, which were present since May 2020. The study also identified four mutations associated with higher disease severity.
SCIENTIFIC REPORTS
(2022)
Article
Agronomy
Qiang Yi, Ana Lopez-Malvar, Lorena Alvarez-Iglesias, Maria Cinta Romay, Pedro Revilla
Summary: This study aimed to elucidate the genetic basis of photosynthesis-related parameters in maize by evaluating a large panel of 731 inbred lines. The results showed significant phenotypic and genotypic variations in this panel, along with fluctuations in heritability for various traits. Twenty-seven minor Quantitative Trait Loci (QTL) were detected, predominantly on chromosomes 5 and 8.
Article
Biology
Claire Burny, Viola Nolte, Marlies Dolezal, Christian Schloetterer
Summary: Experimental evolution combined with whole-genome sequencing is a powerful method to study the adaptive architecture of selected traits. This study shows that the presence of a second stressor affects the genomic selection response, and the combination of temperature and laboratory adaptation results in widespread synergistic effects.
PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES
(2022)
Article
Biochemistry & Molecular Biology
Claudia A. S. Wyer, Lauren J. Cator, Brian Hollis
Summary: This study investigates the mating strategy and sexual selection in the yellow fever mosquito, Aedes aegypti, and reveals the significant impact of sexual selection on the species' genome.
Article
Multidisciplinary Sciences
Bryce T. Bajar, Nguyen T. Phi, Jesse Isaacman-Beck, Jun Reichl, Harpreet Randhawa, Orkun Akin
Summary: Research has found that patterned neural activity during the development of the fruit fly's central nervous system is coordinated by a small population of neurons expressing the Trp gamma gene. This activity is essential for the formation of synaptic connections and the assembly of the brain. The study establishes the fruit fly's brain as a useful model system for investigating how neural activity contributes to the formation of synapses and circuits.
Article
Genetics & Heredity
Thibault Dekeyser, Emmanuelle F. Genin, Anthony Herzig
Summary: Genotype imputation is a widely used method to enrich genetic datasets. Choosing a reference panel that matches the individuals who require imputation is essential, and including diversity in the panel can improve imputation accuracy. However, there can be instances where including more diverse haplotypes leads to incorrect imputation. We demonstrate a technique to retain diversity in the reference panel while avoiding adverse effects on imputation accuracy, and provide a clearer understanding of the role of diversity in a reference panel.
Article
Biology
Eric Wesley Wice, Julia Barbara Saltz
Summary: The position an individual holds in a social network is influenced by both direct and indirect social interactions. The genotype of individuals within a social group impacts their network positions, and studying how genetic effects shape social network positions is crucial for understanding social environment and evolution.
PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES
(2023)
Article
Chemistry, Multidisciplinary
Cheonji Lee, Seungmuk Ji, Sunjong Oh, Seungchul Park, Youngdo Jung, Jinkee Lee, Hyuneui Lim
Summary: This study successfully achieved dual functions of superhydrophobicity and transparency by fabricating nano-hierarchical structured glass surfaces, exhibiting excellent non-wetting properties and transmittance. The hierarchical nanostructures showed better water bouncing performance and transmittance for wide angles of incidence compared to mono-nanostructures.
NANOSCALE ADVANCES
(2022)
Review
Developmental Biology
Trudy F. C. Mackay, Wen Huang
WILEY INTERDISCIPLINARY REVIEWS-DEVELOPMENTAL BIOLOGY
(2018)
Article
Ecology
Fabio Morgante, Wen Huang, Christian Maltecca, Trudy F. C. Mackay
Article
Genetics & Heredity
Daniel R. Matute, Aaron A. Comeault, Eric Earley, Antonio Serrato-Capuchina, David Peede, Anais Monroy-Eklund, Wen Huang, Corbin D. Jones, Trudy F. C. Mackay, Jerry A. Coyne
Article
Genetics & Heredity
Zhijun Dai, Nanye Long, Wen Huang
G3-GENES GENOMES GENETICS
(2020)
Article
Biotechnology & Applied Microbiology
Jinding Liu, Suxu Tan, Shuiqing Huang, Wen Huang
Article
Genetics & Heredity
Grace A. Parker, Nathan Kohn, Ally Spirina, Anna McMillen, Wen Huang, Trudy F. C. Mackay
G3-GENES GENOMES GENETICS
(2020)
Article
Genetics & Heredity
Aya Yanagawa, Wen Huang, Akihiko Yamamoto, Ayako Wada-Katsumata, Coby Schal, Trudy F. C. Mackay
G3-GENES GENOMES GENETICS
(2020)
Article
Genetics & Heredity
Fabio Morgante, Wen Huang, Peter Sorensen, Christian Maltecca, Trudy F. C. Mackay
G3-GENES GENOMES GENETICS
(2020)
Article
Multidisciplinary Sciences
Brandon M. Baker, Mary Anna Carbone, Wen Huang, Robert R. H. Anholt, Trudy F. C. Mackay
Summary: This study used Drosophila melanogaster to map the genetic basis of voluntary consumption of cocaine and methamphetamine. Significant phenotypic variation in drug consumption was found in both sexes, with genes associated with nervous system implicated. The genetic basis of voluntary drug consumption in fruit flies is polygenic and involves genes with human orthologs and sex-and drug-specific effects.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Genetics & Heredity
Ergi D. Ozsoy, Murat Yilmaz, Bahar Patlar, Guzin Emecen, Esra Durmaz, Michael M. Magwire, Shanshan Zhou, Wen Huang, Robert R. H. Anholt, Trudy F. C. Mackay
Summary: Epistasis, or gene-gene interaction, is common in mutations with large phenotypic effects in humans and model organisms, impacting various aspects of genetic studies. However, the significance of epistasis between alleles with small quantitative phenotypic effects remains controversial and challenging to assess. This study used the Drosophila melanogaster Genetic Reference Panel to evaluate the epistasis modifying the effects of mutations in two transcription factors, identifying candidate modifier loci affecting head morphology.
G3-GENES GENOMES GENETICS
(2021)
Article
Agriculture, Dairy & Animal Science
Rongrong Ding, Zhanwei Zhuang, Yibin Qiu, Donglin Ruan, Jie Wu, Jian Ye, Lu Cao, Shenping Zhou, Enqin Zheng, Wen Huang, Zhenfang Wu, Jie Yang
Summary: Backfat thickness (BFT) is an economically important trait in the pig industry, and genetic markers and candidate genes related to BFT were identified through genotyping and genome-wide association analysis in two Duroc populations. Most candidate genes can be directly used for genetic improvement through molecular markers. New insights gained from this study will contribute to genetic studies aiming to increase carcass lean meat percentage in pigs.
JOURNAL OF ANIMAL SCIENCE
(2022)
Article
Biochemistry & Molecular Biology
Jinding Liu, Fei Yin, Kun Lang, Wencai Jie, Suxu Tan, Rongjing Duan, Shuiqing Huang, Wen Huang
Summary: MetazExp is a database for gene expression and alternative splicing profiles based on 53,615 uniformly processed publicly available RNA-seq samples from 72 metazoan species. Users can conveniently query gene expression and alternative splicing profiles by gene IDs, symbols, functional terms, and sequence similarity, and flexibly customize experimental groups for differential and specific analyses. With data visualization tools and comprehensive links with external databases, users can efficiently explore results and gain insights.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Biotechnology & Applied Microbiology
Jinding Liu, Kun Lang, Suxu Tan, Wencai Jie, Yihua Zhu, Shiqing Huang, Wen Huang
Summary: LivestockExp is a web-based database server for exploring gene expression and alternative splicing, containing a large number of livestock animals and RNA-seq samples. It provides diverse analysis modules and visualization tools, serving as a valuable data resource and analysis platform.
Article
Biochemistry & Molecular Biology
Jinding Liu, Yaru Zhang, Yiqing Zheng, Yali Zhu, Yapin Shi, Zhuoran Guan, Kun Lang, Danyu Shen, Wen Huang, Daolong Dou
Summary: PlantExp is a platform for plant gene expression and alternative splicing analysis based on public RNA-seq datasets. It provides online analysis tools and visualization tools to allow users to reanalyze public datasets and gain new research insights.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Plant Sciences
Zhiyuan Yin, Qingjie Yang, Danyu Shen, Jinding Liu, Wen Huang, Daolong Dou
Summary: Soybean is an important crop and the newly established SoyTIPdb database provides a valuable resource for researchers to explore structural variations caused by transposon insertions. The database contains processed whole-genome resequencing data from a wide range of soybean germplasm accessions, allowing for easy query and analysis.
