Article
Horticulture
D. S. Kishor, Yoonji Noh, Woon-Ho Song, Gung Pyo Lee, Younghoon Park, Jin-Kee Jung, Eun-Jo Shim, Sung-Chur Sim, Sang-Min Chung
Summary: East Asia's Oriental melon serves as an important fruit crop, with SNP genotyping proving useful in detecting genetic diversity and protecting breeders' rights. Through GBS, 5640 SNPs were detected in 48 melon varieties, with 164 successfully validated and used to classify 87 varieties into distinct groups. GWAS analyses revealed 18 significant SNPs associated with morphological traits, including potential candidate genes for sex expression.
SCIENTIA HORTICULTURAE
(2021)
Article
Plant Sciences
Wei Yan, Xing Wang Deng, Chengwei Yang, Xiaoyan Tang
Summary: By investigating 52 rice EMS mutants, it was found that EMS exhibits a preference for G/C sites with higher GC contents in flanking sequences. The composition of local dinucleotides and trinucleotides is also associated with the efficiency of EMS mutagenesis.
FRONTIERS IN PLANT SCIENCE
(2021)
Article
Computer Science, Artificial Intelligence
Marcelo B. A. Veras, Bishnu Sarker, Sabeur Aridhi, Joao P. P. Gomes, Jose A. F. Macedo, Engelbert Mephu Nguifo, Marie-Dominique Devignes, Malika Smail-Tabbone
Summary: Automatic protein function annotation is crucial for disease understanding and drug design. Similarity functions play an important role in protein function prediction, but there is a lack of specifically designed similarity functions for protein function annotation. This study analyzes the best similarity functions for the task and proposes a new one.
KNOWLEDGE-BASED SYSTEMS
(2022)
Article
Genetics & Heredity
Yachun Han, Tao Tan, Zixin Li, Zheng Ma, Ganqiu Lan, Jing Liang, Kui Li, Lijing Bai
Summary: This study analyzed the genetic diversity and selection signatures associated with important economic traits in Huainan (HN) pigs and Yunan (YN) black pigs. The results identified specific genetic regions and potential candidate genes related to these traits, as well as tissue-specific regulatory elements in YN black pigs.
Article
Microbiology
Md-Mafizur Rahman, Sang-Jin Lim, Yung-Chul Park
Summary: A rapid and high-quality method based on single-nucleotide polymorphisms (SNPs) was developed to improve detection and reduce the burden of salmonellosis.
Article
Biotechnology & Applied Microbiology
Thiruvothur Venkatesan Raja, Rani Alex, Umesh Singh, Sushil Kumar, Achintya Kumar Das, Gyanendra Sengar, Amit Kumar Singh, Abhirupa Ghosh, Sudipto Saha, Abhijit Mitra
Summary: Frieswal is a crossbred cattle developed by ICAR-Central Institute for Research on Cattle using more than 15,000 cattle from military farms. The ddRAD sequencing method was used to identify and annotate the SNPs and INDELs, revealing 1,487,851 SNPs and 128,175 INDELs. The majority of effects were found in the intron region of the genome (66.41%), followed by intergenic regions (21.87%). A significant number of SNPs were annotated in candidate genes related to milk production and reproduction traits.
Article
Genetics & Heredity
G. Ramya, Abhijit Mitra, P. K. Vinod
Summary: RNAs are essential in regulating gene expression, and their secondary structures have significant roles. This study identified disease-associated SNPs, known as RiboSNitches, that can alter the pre-mRNA secondary structure. It also demonstrated the potential importance of splice site mutations in alternative splicing. The workflow developed in this study provides a novel approach to predict riboSNitches associated with alternative splicing and enables future experimental validation.
Article
Biology
Markus J. Sommer, Sooyoung Cha, Ales Varabyou, Natalia Rincon, Sukhwan Park, Ilia Minkin, Mihaela Pertea, Martin Steinegger, Steven L. Salzberg
Summary: The development of three-dimensional protein structure prediction methods has provided new opportunities for research on genomes and proteomes. By utilizing computational predictions of protein structures, it is possible to identify the functional protein product among multiple gene isoforms. In this study, we evaluated over 230,000 isoforms of human protein-coding genes using protein structure predictions, and identified several isoforms with more confidently predicted structures and potentially superior function compared to the canonical isoforms in the latest human gene database. We demonstrated the potential of protein structure prediction as a genome annotation tool and provided a resource of protein structures for better understanding the function of human genes and their isoforms.
Article
Plant Sciences
Jiangyan Xiong, Danyi Chen, Tingting Su, Qiufang Shen, Dezhi Wu, Guoping Zhang
Summary: This study investigated the SnRK family in barley, identifying 46 members classified into 3 sub-families. Through phylogenetic and conserved motif analyses, insights into the gene structures and evolutionary features of HvSnRKs were obtained. The researchers also found that HvSnRKs play a crucial role in responding to abiotic stress in barley.
Article
Plant Sciences
Roopali Bhoite, Rosemary Smith, Urmil Bansal, Mirza Dowla, Harbans Bariana, Darshan Sharma
Summary: This study used t-GBS technology to detect SNPs and haplotypes in gene-rich regions, and identified 39 novel SNPs and 18 haplotypes. The locations of these SNPs/haplotypes were determined by aligning allelic sequences on chromosomes. Eighteen out of the 39 target SNPs produced PCR markers, of which only eight showed polymorphic signals. These markers were validated for their association with yield, plant density, head number, and harvest index. The functional effects of these markers on closely associated genes were confirmed using high-throughput genotyping, and their regulatory roles in gene expression and protein-coding were annotated. This integrated approach offers potential solutions for crop improvement programs.
Article
Immunology
Roan E. Zaied, Tayaza Fadason, Justin M. O'Sullivan
Summary: In this study, a network analysis approach was used to construct tissue-specific spatial gene regulatory networks for asthma and identify asthma-associated diseases and their molecular mechanisms. The study also analyzed the comorbidity of asthma with other diseases and identified possible therapeutic targets.
FRONTIERS IN IMMUNOLOGY
(2023)
Article
Plant Sciences
Jianjun Li, Xiaopei Chang, Qian Huang, Pengfei Liu, Xiting Zhao, Fengmei Li, Yungang Wang, Cuifang Chang
Summary: This study used simplified genome sequencing technology to evaluate the population structure, genetic relationships, and genetic fingerprints of 39 germplasm resources of Lonicera in China. Through the selection and validation of hundreds of thousands of single nucleotide polymorphisms, 15 high-quality DNA fingerprints were identified, which can effectively identify the 39 Lonicera varieties. These results provide a scientific basis and reference data for the analysis of genetic diversity, species identification, property rights disputes, and molecular breeding of Lonicera.
FRONTIERS IN PLANT SCIENCE
(2023)
Article
Ecology
Shuichi Kitada, Hirohisa Kishino
Summary: Genetic stock identification (GSI) is an important management tool for Pacific salmon, providing rich genetic baseline data across the Pacific Rim. Analyzing data from chum salmon populations, it was observed that Japanese/Korean populations had the greatest impact and SNP selection was based on predicted structures.
ECOLOGY AND EVOLUTION
(2021)
Article
Plant Sciences
B. Franz Lang, Natacha Beck, Samuel Prince, Matt Sarrasin, Pierre Rioux, Gertraud Burger
Summary: Compared to nuclear genomes, mitochondrial genomes (mitogenomes) are small and usually code for only a few dozen genes. Identifying genes and their structure in mitogenomes can be challenging, requiring manual analysis and curation by experts. The development of the MFannot annotator addresses these challenges by providing accurate gene model inference, intron identification and classification. MFannot is applicable to a broad taxonomic scope and has been available as a web-accessible service for nearly 16 years.
FRONTIERS IN PLANT SCIENCE
(2023)
Article
Mathematics
Maria D. Torres, Barbara M. Brizuela, Maria C. Canadas, Antonio Moreno
Summary: This study focuses on how second-grade elementary school students use tables when working with functions. The research reveals that students are capable of organizing the data in tables to identify regularities between variables, with more accurate identifications in the second interview.
Article
Biochemical Research Methods
Corrado Pancotti, Silvia Benevenuta, Giovanni Birolo, Virginia Alberini, Valeria Repetto, Tiziana Sanavia, Emidio Capriotti, Piero Fariselli
Summary: Predicting the difference in thermodynamic stability between protein variants is important for protein design and understanding genotype-phenotype relationships. This study introduces a new dataset and evaluates the prediction performance of 21 different tools. The results suggest that considering both direct and reverse variants improves the prediction accuracy.
BRIEFINGS IN BIOINFORMATICS
(2022)
Article
Genetics & Heredity
Emidio Capriotti, Piero Fariselli
Summary: Evolutionary information is crucial for detecting functional conservation and predicting structure, interactions, and functions in macromolecules. In pathogenicity prediction, the conservation of reference and variant plays a important role.
Article
Biochemistry & Molecular Biology
Joseph H. Lubin, Christine Zardecki, Elliott M. Dolan, Changpeng Lu, Zhuofan Shen, Shuchismita Dutta, John D. Westbrook, Brian P. Hudson, David S. Goodsell, Jonathan K. Williams, Maria Voigt, Vidur Sarma, Lingjun Xie, Thejasvi Venkatachalam, Steven Arnold, Luz Helena Alfaro Alvarado, Kevin Catalfano, Aaliyah Khan, Erika McCarthy, Sophia Staggers, Brea Tinsley, Alan Trudeau, Jitendra Singh, Lindsey Whitmore, Helen Zheng, Matthew Benedek, Jenna Currier, Mark Dresel, Ashish Duvvuru, Britney Dyszel, Emily Fingar, Elizabeth M. Hennen, Michael Kirsch, Ali A. Khan, Charlotte Labrie-Cleary, Stephanie Laporte, Evan Lenkeit, Kailey Martin, Marilyn Orellana, Melanie Ortiz-Alvarez de la Campa, Isaac Paredes, Baleigh Wheeler, Allison Rupert, Andrew Sam, Katherine See, Santiago Soto Zapata, Paul A. Craig, Bonnie L. Hall, Jennifer Jiang, Julia R. Koeppe, Stephen A. Mills, Michael J. Pikaart, Rebecca Roberts, Yana Bromberg, J. Steen Hoyer, Siobain Duffy, Jay Tischfield, Francesc X. Ruiz, Eddy Arnold, Jean Baum, Jesse Sandberg, Grace Brannigan, Sagar D. Khare, Stephen K. Burley
Summary: Understanding the molecular evolution of SARS-CoV-2 through analyzing protein structures and amino acid changes provides insights for potential drug discovery and identification of drug resistance mutations.
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS
(2022)
Article
Multidisciplinary Sciences
Yana Bromberg, Ariel A. Aptekmann, Yannick Mahlich, Linda Cook, Stefan Senn, Maximillian Miller, Vikas Nanda, Diego U. Ferreiro, Paul G. Falkowski
Summary: Biological redox reactions are driven by enzymes with similar structural geometry and amino acid sequences, reflecting the availability of key transition metals over geological time. The earliest biologically functional peptides may have existed before the assembly of fully functional protein domains over 3.8 billion years ago.
Article
Biochemical Research Methods
A. A. Aptekmann, J. Buongiorno, D. Giovannelli, M. Glamoclija, D. U. Ferreiro, Y. Bromberg
Summary: Metal-binding proteins play a central role in maintaining life processes, but experimental annotation is lacking and computational techniques are often imprecise. In this study, we developed a machine learning-based method, mebipred, which accurately identifies metal-binding proteins and annotates metal ions. Mebipred can also identify metal-binding capabilities from short sequence stretches, making it useful for metagenomic samples. Analysis of microbiome data revealed different metal preferences and the impact of ion concentration changes on metal-binding protein abundance.
Article
Genetics & Heredity
Siqi Sun, Maximilian Miller, Yanran Wang, Katarzyna M. Tyc, Xiaolong Cao, Richard T. Scott, Xin Tao, Yana Bromberg, Karen Schindler, Jinchuan Xing
Summary: Infertility is a significant health issue affecting a considerable number of women in the United States. This study utilized machine learning-based classifiers to predict the risk of embryonic aneuploidy in female IVF patients using whole-exome sequencing data. The results demonstrated high accuracy and specificity of this approach, as well as identified candidate genes and pathways associated with aneuploidy risk. These findings offer potential targets for future research in aneuploidy studies.
Article
Biochemistry & Molecular Biology
Ludovica Montanucci, Emidio Capriotti, Giovanni Birolo, Silvia Benevenuta, Corrado Pancotti, Dennis Lal, Piero Fariselli
Summary: The DDGun method is an untrained method for predicting the effect of single amino acid variants on the thermodynamic stability of proteins. It demonstrates comparable prediction performance to trained methods and has been validated through database updates and blind testing.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Multidisciplinary Sciences
A. Hoarfrost, A. Aptekmann, G. Farfanuk, Y. Bromberg
Summary: Computational methods for analyzing microbial systems often rely on reference databases that do not fully capture the functional diversity of these systems. In this study, the authors develop a deep learning model that is capable of transferring its learned knowledge to multiple tasks, resulting in biologically relevant models. The model, called LookingGlass, can provide useful representations of unknown and unannotated sequences, shedding light on the microbial dark matter that dominates life on Earth.
NATURE COMMUNICATIONS
(2022)
Article
Genetics & Heredity
Zishuo Zeng, Yana Bromberg
Summary: The study found that screening sSNVs for recurrence among patients, conservation of the affected genomic position, and synVep prediction could identify cancer driver variants and previously unknown potential cancer genes. This computational guidance in prioritizing the experimental evaluation of synonymous mutations found in cancers and may highlight unexplored cancer mechanisms.
Editorial Material
Genetics & Heredity
Yana Bromberg, Predrag Radivojac
Article
Biochemistry & Molecular Biology
Silvia Benevenuta, Giovanni Birolo, Tiziana Sanavia, Emidio Capriotti, Piero Fariselli
Summary: An open challenge in computational and experimental biology is to understand the impact of non-synonymous DNA variations on protein function and human health. Predictive tools for protein stability are less accurate in predicting stabilizing variations compared to destabilizing ones, possibly due to the abundance of destabilizing variants in the available datasets. New methods should consider input features highly correlated with stabilizing variants and be tested on unbalanced datasets.
FRONTIERS IN MOLECULAR BIOSCIENCES
(2023)
Article
Biochemistry & Molecular Biology
Emidio Capriotti, Piero Fariselli
Summary: One of the major challenges in human genetics is determining the functional impact of different types of genetic variations. CADD is a widely used algorithm that predicts the effects of genome variations by combining sequence conservation and functional features. We developed a machine-learning tool called PhD-SNPg, which relies solely on sequence-based features and is easy to install and use. The updated version of PhD-SNPg can also predict the impact of insertion and deletion variations, and performs similarly to CADD, making it useful for rapid genome interpretation and tool development benchmarking.
NUCLEIC ACIDS RESEARCH
(2023)
Review
Biochemistry & Molecular Biology
Luana Licata, Allegra Via, Paola Turina, Giulia Babbi, Silvia Benevenuta, Claudio Carta, Rita Casadio, Andrea Cicconardi, Angelo Facchiano, Piero Fariselli, Deborah Giordano, Federica Isidori, Anna Marabotti, Pier Luigi Martelli, Stefano Pascarella, Michele Pinelli, Tommaso Pippucci, Roberta Russo, Castrense Savojardo, Bernardina Scafuri, Lucrezia Valeriani, Emidio Capriotti
Summary: Rare genetic disorders affect a significant portion of the global population, and the diagnosis and genetic characterization of these conditions are often challenging. However, recent advancements in genome sequencing/analysis technologies and computer-aided tools can greatly improve our understanding of these diseases and the development of therapeutic treatments.
FRONTIERS IN MOLECULAR BIOSCIENCES
(2023)
Article
Biochemistry & Molecular Biology
Paola Turina, Piero Fariselli, Emidio Capriotti
Summary: The study of protein folding is crucial for understanding protein function and the relationship between genetics and phenotypes. K-Pro is a new database that collects experimental kinetic data on monomeric proteins with a two-state folding mechanism. It provides a user-friendly interface for browsing and downloading relevant data.
JOURNAL OF MOLECULAR BIOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Yannick Mahlich, Chengsheng Zhu, Henri Chung, Pavan K. Velaga, M. Clara De Paolis Kaluza, Predrag Radivojac, Iddo Friedberg, Yana Bromberg
Summary: This study describes a novel approach to exploring bacterial functional repertoires without reference databases, which outperforms marker genes in assigning taxonomic clades. The Fusion-taxa method is robust to the addition of novel organisms and can capture environment-driven bacterial diversity. The Siamese Neural Network model created using Fusion functions allows finding shared functionality of very distant microbial homologs. This study helps annotate functional repertoires of bacterial organisms and guide our understanding of microbial communities.
NUCLEIC ACIDS RESEARCH
(2023)
