Article
Plant Sciences
Baoyi Zhang, Yuhan Fei, Jiejie Feng, Xueai Zhu, Rui Wang, Hanqing Xiao, Hongsheng Zhang, Ji Huang
Summary: This study constructed a comprehensive rice ncRNA co-expression atlas, RiceNCexp, which provides expression information and co-expression analysis tools for rice ncRNAs in multiple tissues/organs.
JOURNAL OF EXPERIMENTAL BOTANY
(2022)
Article
Plant Sciences
Yadi Zhou, Abhijit Sukul, John W. Mishler-Elmore, Ahmed Faik, Michael A. Held
Summary: In this study, we constructed global gene co-expression networks (GCNs) for barley and sorghum using existing RNA-seq data sets and manually curated tissue-specific GCNs. We also developed an online tool called PlantNexus for GCN searching and visualization.
PLANT AND CELL PHYSIOLOGY
(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
Biochemical Research Methods
Bin Li, Wen Zhang, Chuang Guo, Hao Xu, Longfei Li, Minghao Fang, Yinlei Hu, Xinye Zhang, Xinfeng Yao, Meifang Tang, Ke Liu, Xuetong Zhao, Jun Lin, Linzhao Cheng, Falai Chen, Tian Xue, Kun Qu
Summary: This study compares 16 integration methods using 45 paired datasets and 32 simulated datasets, finding that Tangram, gimVI, and SpaGE perform best in predicting RNA transcript distribution, while Cell2location, SpatialDWLS, and RCTD are top-performing methods for cell type deconvolution. The benchmark pipeline provided in the study helps researchers in selecting optimal integration methods for their datasets. The comprehensive benchmarking analysis presented in this work evaluates computational methods integrating spatial and single-cell transcriptomics data for transcript distribution prediction and cell type deconvolution.
Article
Biochemistry & Molecular Biology
Sora Yonezawa, Hidemasa Bono
Summary: This study conducted a meta-analysis to explore the expression of heat stress-related genes in humans and mice, identifying common upregulated and downregulated genes and conducting further functional analysis. These findings are important for addressing climate change and technological advancements.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Biochemical Research Methods
Pontus Eriksson, Nour-al-dain Marzouka, Gottfrid Sjodahl, Carina Bernardo, Fredrik Liedberg, Mattias Hoglund
Summary: In this study, we evaluated the behavior of gene-pair-based single sample predictors (SSPs) in gene expression-based multiclass prediction tasks. We found that these methods showed excellent performance, with high accuracy and informative prediction scores, in many expression-based classification tasks. However, the compatibility of gene-pair-based predictors with new datasets still needs to be verified.
Article
Biology
Ana Gutierrez-Franco, Franz Ake, Mohamed N. Hassan, Natalie Chaves Cayuela, Loris Mularoni, Mireya Plass
Summary: The critical step in single-cell transcriptomics is sample preparation. Different preservation methods show varying effects on cell quality and expression biases. In this study, methanol fixation is identified as the preferred method for droplet-based single-cell transcriptomics experiments on neural cell populations derived from induced pluripotent stem cells.
COMMUNICATIONS BIOLOGY
(2023)
Article
Multidisciplinary Sciences
Noor Pratap Singh, Michael I. Love, Rob Patro
Summary: Transcript abundance estimates always come with a certain level of uncertainty, which could pose challenges for downstream analyses like differential testing. TreeTerminus is a data-driven approach that groups transcripts into a tree structure, where leaves represent individual transcripts and internal nodes represent an aggregation of transcript sets. By constructing trees that reduce inferential uncertainty as we move up the topology, TreeTerminus enables flexible data analysis at different levels of resolution within the tree. Evaluations on simulated and experimental datasets show improved performance compared to transcripts (leaves) and other methods across multiple metrics.
Article
Biochemistry & Molecular Biology
Pedro L. Baldoni, Yunshun Chen, Soroor Hediyeh-zadeh, Yang Liao, Xueyi Dong, Matthew E. Ritchie, Wei Shi, Gordon K. Smyth
Summary: Differential expression analysis of RNA-seq is commonly used in bioinformatics. However, transcript-level quantifications are more uncertain due to the ambiguity of sequence reads. To address this issue, a new method is proposed to estimate the overdispersion caused by read-to-transcript ambiguity and generate scaled transcript counts, which improves the efficiency and accuracy of differential analysis.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Multidisciplinary Sciences
Amichay Afriat, Vanessa Zuzarte-Luis, Keren Bahar Halpern, Lisa Buchauer, Sofia Marques, Angelo Ferreira Chora, Aparajita Lahree, Ido Amit, Maria M. Mota, Shalev Itzkovitz
Summary: This study characterized the temporal expression programs of the rodent malaria parasite Plasmodium berghei ANKA and the host hepatocyte in a zonally controlled manner using single-cell RNA sequencing and single-molecule transcript imaging. The study identified differences in parasite gene expression in distinct zones and identified a subpopulation of hepatocytes with reduced levels of Plasmodium transcripts and parasitophorous vacuole breakdown. These findings provide insights into the liver stage of Plasmodium infection.
Article
Biochemical Research Methods
Yi Wang, Stephanie C. Hicks, Kasper D. Hansen
Summary: Estimates of correlation between genes in co-expression analysis are commonly used to construct gene networks. However, the distribution of these correlations depends on the observed expression level, resulting in a higher correlation for highly expressed genes. This relationship is not observed in protein-protein interaction data, indicating that it is not biologically relevant. To address this issue, we propose a method called spatial quantile normalization (SpQN) that normalizes local distributions in a correlation matrix, removing the mean-correlation relationship and correcting expression bias in network reconstruction.
PLOS COMPUTATIONAL BIOLOGY
(2022)
Article
Multidisciplinary Sciences
Teruo Akuta, Daisuke Minegishi, Nobuhide Kido, Keitaro Imaizumi, Shinji Nakaoka, Shin-Ichiro Tachibana, Kenji Hikosaka, Fumi Hori, Masataka Nakagawa, Chiaki Sakuma, Yuki Oouchi, Yu Nakajima, Sohei Tanaka, Tomoko Omiya, Kouki Morikaku, Minori Kawahara, Yoshifumi Tada, Hiroshi Tarui, Takafumi Ueda, Takane Kikuchi-Ueda, Yasuo Ono
Summary: A study developed an immunodiagnostic test based on RNA-seq data to detect scabies in infected animals' skin, which has the potential to accurately diagnose scabies in wildlife and humans.
SCIENTIFIC REPORTS
(2021)
Article
Biochemical Research Methods
Thomas Gatter, Peter F. Stadler
Summary: Research shows that multi-sample RNA-Seq experiments exhibit better stability and accuracy in RNA-seq assembly. The extended version of Ryuto can generate consensus transcriptomes and provide a better sensitivity-precision trade-off. Utilizing a (incomplete) reference for multi-sample assembly is an effective way to improve precision.
Article
Biochemistry & Molecular Biology
Miguel Barquin, Ian U. Kouzel, Beat Ehrmann, Michael Basler, Andreas J. Gruber
Summary: This study presents a single cell-based Terminal Exon Annotation database (scTEA-db), which provides yet unannotated terminal exons and associated transcript isoforms for studying their biological role in cell identity and function.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Biology
Richard J. White, Eirinn Mackay, Stephen W. Wilson, Elisabeth M. Busch-Nentwich
Summary: In zebrafish, differentially expressed genes are often over-represented on the same chromosome as the mutation, due to different levels of expression of alleles from different genetic backgrounds. This has implications for interpreting the results and pathways in RNA-seq experiments.
Review
Cell Biology
Simone Borgoni, Ksenia S. Kudryashova, Ksenia Burka, Joao Pedro de Magalhaes
Summary: Human aging is a multifactorial phenomenon that affects various organ systems and cellular processes, with the immune system being one of the most dysregulated. The immune changes that occur during aging, such as immunosenescence and inflammaging, result in increased susceptibility to infections, reduced healing abilities, and the emergence of age-associated diseases. Therapeutic approaches targeting specific immune subpopulations affected by aging have the potential to rejuvenate the immune system and improve healthspan.
AGEING RESEARCH REVIEWS
(2021)
Review
Cell Biology
Anne M. Bronikowski, Richard P. Meisel, Peggy R. Biga, James R. Walters, Judith E. Mank, Erica Larschan, Gerald S. Wilkinson, Nicole Valenzuela, Ashley Mae Conard, Joao Pedro de Magalhaes, Jingyue (Ellie) Duan, Amy E. Elias, Tony Gamble, Rita M. Graze, Kristin E. Gribble, Jill A. Kreiling, Nicole C. Riddle
Summary: Sex differences in aging, including lifespan, age-associated decline, and physiological markers, vary greatly across animal species. The underlying causes of these differences remain mostly unknown, highlighting the need for further research on the role of sex-determination mechanisms and their impact on aging.
Editorial Material
Biotechnology & Applied Microbiology
Joao Pedro de Magalhaes, Alejandro Ocampo
Summary: Cells can be rejuvenated and biological clocks reset through cellular reprogramming, and many companies are now developing therapies using this technique to rejuvenate human beings. However, the current research in rejuvenation is mostly based on in vitro studies, and it remains to be seen if it can be translated into clinical applications.
TRENDS IN BIOTECHNOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Emily Shorter, Roberto Avelar, Margarita Zachariou, George M. Spyrou, Priyanka Raina, Aibek Smagul, Yalda Ashraf Kharaz, Mandy Peffers, Kasia Goljanek-Whysall, Joao Pedro de Magalhaes, Blandine Poulet
Summary: This study conducted a systematic meta-analysis of differentially expressed mRNA and micro-RNAs to identify and rank osteoarthritis-associated genes and micro-RNAs. Cellular senescence was identified as an enriched pathway, and a co-expression network was built to prioritize the most integral factors. Experimental confirmation revealed five novel osteoarthritis-associated proteins. Focusing future studies on these novel targets may lead to new therapies for osteoarthritis.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Editorial Material
Genetics & Heredity
Joao Pedro de Magalhaes
Summary: Most human genes have been studied in the context of cancer, which justifies the study of almost any human gene based on existing literature. These findings also have implications for large-scale analyses.
TRENDS IN GENETICS
(2022)
Article
Dermatology
Iqra Fatima, Guodong Chen, Natalia Botchkareva, Andrey A. Sharov, Daniel Thornton, Holly N. Wilkinson, Matthew J. Hardman, Andreas Grutzkau, Joao Pedro de Magalhaes, Andrei Seluanov, Ewan St J. Smith, Vera Gorbunova, Andrei N. Mardaryev, Chris G. Faulkes, Vladimir A. Botchkarev
Summary: Naked mole-rats show similar skin aging characteristics to humans, including a decrease in epidermal thickness and keratinocyte proliferation. However, interestingly, the expression levels of several longevity-associated and tumor-suppressor genes are increased in aged naked mole-rat skin. These findings provide a basis for using naked mole-rats as a model organism to study the biology and disease resistance of human skin.
JOURNAL OF INVESTIGATIVE DERMATOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Daiyun Huang, Kunqi Chen, Bowen Song, Zhen Wei, Jionglong Su, Frans Coenen, Joao Pedro de Magalhaes, Daniel J. Rigden, Jia Meng
Summary: This study developed a transcript encoding scheme that captures the submolecular geographic information of RNA, which can be used to predict m(6)A sites based on geographic information alone or enhance the accuracy of sequence-based models. The scheme also enables isoform- and tissue-specific prediction of m(6)A sites and improves m(6)A signal detection from direct RNA sequencing data.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Biochemistry & Molecular Biology
Bowen Song, Xuan Wang, Zhanmin Liang, Jiongming Ma, Daiyun Huang, Yue Wang, Joao Pedro de Magalhaes, Daniel J. Rigden, Jia Meng, Gang Liu, Kunqi Chen, Zhen Wei
Summary: Recent advances in epitranscriptomics have revealed the functional associations between RNA modifications (RMs) and multiple human diseases. This study presents an updated database, RMDisease v2.0, which identifies RM-associated genetic variants that may affect different types of RNA modifications in various organisms. These variants, including disease- and trait-associated genetic variants, may function through perturbations of epitranscriptomic markers. RMDisease v2.0 serves as a valuable resource for studying the genetic drivers of phenotypes in the epitranscriptome layer circuitry.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Cell Biology
Dominic F. Bennett, Anita Goyala, Cyril Statzer, Charles W. Beckett, Alexander Tyshkovskiy, Vadim N. Gladyshev, Collin Y. Ewald, Joao Pedro de Magalhaes
Summary: Searching for drugs with similar gene expression patterns, rilmenidine was found to extend the lifespan of nematodes and rats, mediated by the I1-imidazoline receptor. This study suggests the potential of rilmenidine as a longevity-promoting drug.
Article
Biochemistry & Molecular Biology
Priyanka Raina, Rodrigo Guinea, Kasit Chatsirisupachai, Ines Lopes, Zoya Farooq, Cristina Guinea, Csaba-Attila Solyom, Joao Pedro de Magalhaes
Summary: Gene co-expression analysis is a powerful method for understanding gene function and regulation. The GeneFriends database provides researchers with updated gene co-expression networks for humans, mice, and other model organisms, based on RNA-seq data. This valuable tool can help researchers decipher the complexity of genomes and assign functions to poorly annotated genes.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Biochemistry & Molecular Biology
Yuxin Zhang, Jie Jiang, Jiongming Ma, Zhen Wei, Yue Wang, Bowen Song, Jia Meng, Guifang Jia, Joao Pedro de Magalhaes, Daniel J. Rigden, Daiyun Hang, Kunqi Chen
Summary: Mapping RNA modifications with advanced technologies has revolutionized our understanding of them. Current modification profiling methods are limited and require selective treatments. Direct RNA sequencing enables the direct study of modifications and has the potential to overcome the limitations of previous methods. The DirectRMDB database provides a fresh perspective on RNA modifications and allows exploration of the epitranscriptome in an isoform-specific manner.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Biochemical Research Methods
Marcelo Rodrigues de Holanda Maia, Alexandre Plastino, Alex Freitas, Joao Pedro de Magalhaes
Summary: This paper proposes two new approaches for dealing with data uncertainty. One approach is to select training instances for each model in an ensemble, and the other is to sample features when splitting a node in a Random Forest training. These approaches are applied to classify ageing-related genes and predict drugs' side effects, and the results show that ensembles based on these approaches achieve better predictive performance.
IEEE-ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS
(2023)
Article
Biochemistry & Molecular Biology
Xuan Wang, Yuxin Zhang, Kunqi Chen, Zhanmin Liang, Jiongming Ma, Rong Xia, Joao Pedro de Magalhaes, Daniel J. Rigden, Jia Meng, Bowen Song
Summary: With the advancement in mapping N7-methylguanosine (m(7)G) RNA methylation sites, a comprehensive resource (m7Ghub v.2.0) has been developed to study m(7)G modification under various physiological contexts. The resource includes the m7GDB database collecting hundreds of thousands of putative m(7)G sites identified in 23 species, the m7GDiseaseDB hosting m(7)G-associated variants including disease-relevant m(7)G-SNPs, and two enhanced analysis modules for interactive analyses.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Biochemistry & Molecular Biology
Joao Pedro de Magalhaes, Zoya Abidi, Gabriel Arantes dos Santos, Roberto A. Avelar, Diogo Barardo, Kasit Chatsirisupachai, Peter Clark, Evandro A. De-Souza, Emily J. Johnson, Ines Lopes, Guy Novoa, Ludovic Senez, Angelo Talay, Daniel Thornton, Paul Ka Po To
Summary: This article introduces the key features and recent enhancements of the Human Ageing Genomic Resources (HAGR), focusing on its six main databases. These databases cover information related to genes and ageing, longevity, life-history, cellular senescence, and genetic variants associated with human longevity. HAGR also provides various tools and gene expression signatures.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Cell Biology
Cyril Lagger, Eugen Ursu, Anais Equey, Roberto A. Avelar, Angela Oliveira Pisco, Robi Tacutu, Joao Pedro de Magalhaes
Summary: Dysregulation of intercellular communication is a hallmark of aging. Here the authors provide a bioinformatics tool to infer changes in cell-cell signaling and an atlas of age-related communication changes in 23 mouse tissues.