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Showing 1–22 of 22 results
Advanced filters: Author: Serghei Mangul Clear advanced filters

  • Information on immune receptor repertoire provides important insights on disease progression and therapy development, but can be expensive and time-consuming to obtain. Here the authors report ImReP, a computational method that can extract detailed immune repertoire information from existing tissue-specific RNA sequencing data.

    • Igor Mandric
    • Jeremy Rotman
    • Serghei Mangul
    ResearchOpen Access
    Nature Communications
    Volume: 11, P: 1-14

  • Metagenomics describes the analysis of genetic information in a microbial community to provide taxonomic or functional information on the constituent microorganisms. This Primer describes suitable sample types, sampling handling and processing workflows for metagenomics, and gives a detailed discussion of the various analysis techniques to generate meaningful information from metagenomic data.

    • Shaopeng Liu
    • Judith S. Rodriguez
    • Serghei Mangul
    Reviews
    Nature Reviews Methods Primers
    Volume: 5, P: 1-28

  • Attempts to reproduce the computational steps described in published omics research often fail. This review provides guidelines for the packaging and containerization of software so that readers can use the exact programs used in published work.

    • Mohammed Alser
    • Brendan Lawlor
    • Serghei Mangul
    Reviews
    Nature Protocols
    Volume: 19, P: 2529-2539

  • Immunogenomics studies have been largely limited to individuals of European ancestry, restricting the ability to identify variation in human adaptive immune responses across populations. Inclusion of a greater diversity of individuals in immunogenomics studies will substantially enhance our understanding of human immunology.

    • Kerui Peng
    • Yana Safonova
    • Serghei Mangul
    Comments & Opinion
    Nature Methods
    Volume: 18, P: 588-591

  • Benchmarking studies are important for comprehensively understanding and evaluating different computational omics methods. Here, the authors review practices from 25 recent studies and propose principles to improve the quality of benchmarking studies.

    • Serghei Mangul
    • Lana S. Martin
    • Jonathan Flint
    ReviewsOpen Access
    Nature Communications
    Volume: 10, P: 1-11

  • During the COVID-19 pandemic, genomics and bioinformatics have emerged as essential public health tools. The genomic data acquired using these methods have supported the global health response, facilitated the development of testing methods and allowed the timely tracking of novel SARS-CoV-2 variants. Yet the virtually unlimited potential for rapid generation and analysis of genomic data is also coupled with unique technical, scientific and organizational challenges. Here, we discuss the application of genomic and computational methods for efficient data-driven COVID-19 response, the advantages of the democratization of viral sequencing around the world and the challenges associated with viral genome data collection and processing.

    • Sergey Knyazev
    • Karishma Chhugani
    • Serghei Mangul
    Comments & Opinion
    Nature Methods
    Volume: 19, P: 374-380

  • This study presents the results of the second round of the Critical Assessment of Metagenome Interpretation challenges (CAMI II), which is a community-driven effort for comprehensively benchmarking tools for metagenomics data analysis.

    • Fernando Meyer
    • Adrian Fritz
    • Alice Carolyn McHardy
    ResearchOpen Access
    Nature Methods
    Volume: 19, P: 429-440

  • Whole-genome sequencing, transcriptome-wide association and fine-mapping analyses in over 7,000 individuals with critical COVID-19 are used to identify 16 independent variants that are associated with severe illness in COVID-19.

    • Athanasios Kousathanas
    • Erola Pairo-Castineira
    • J. Kenneth Baillie
    ResearchOpen Access
    Nature
    Volume: 607, P: 97-103

  • Using the GTEx data and others, a comprehensive analysis of adenosine-to-inosine RNA editing in mammals is presented; targets of the various ADAR enzymes are identified, as are several potential regulators of editing, such as AIMP2.

    • Meng How Tan
    • Qin Li
    • Jin Billy Li
    Research
    Nature
    Volume: 550, P: 249-254

  • Multiple transcriptome approaches, including single-cell sequencing, demonstrate that escape from X chromosome inactivation is widespread and occasionally variable between cells, chromosomes, and tissues, resulting in sex-biased expression of at least 60 genes and potentially contributing to sex-specific differences in health and disease.

    • Taru Tukiainen
    • Alexandra-Chloé Villani
    • Daniel G. MacArthur
    ResearchOpen Access
    Nature
    Volume: 550, P: 244-248

  • The authors show that rare genetic variants contribute to large gene expression changes across diverse human tissues and provide an integrative method for interpretation of rare variants in individual genomes.

    • Xin Li
    • Yungil Kim
    • Stephen B. Montgomery
    ResearchOpen Access
    Nature
    Volume: 550, P: 239-243

  • Samples of different body regions from hundreds of human donors are used to study how genetic variation influences gene expression levels in 44 disease-relevant tissues.

    • François Aguet
    • Andrew A. Brown
    • Jingchun Zhu
    ResearchOpen Access
    Nature
    Volume: 550, P: 204-213

  • Phenotypic variation and diseases are influenced by factors such as genetic variants and gene expression. Here, Barbeira et al. develop S-PrediXcan to compute PrediXcan results using summary data, and investigate the effects of gene expression variation on human phenotypes in 44 GTEx tissues and >100 phenotypes.

    • Alvaro N. Barbeira
    • Scott P. Dickinson
    • Hae Kyung Im
    ResearchOpen Access
    Nature Communications
    Volume: 9, P: 1-20