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Open AccessAuthor Correction: Perspectives on ENCODE
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Open AccessAuthor Correction: Expanded encyclopaedias of DNA elements in the human and mouse genomes
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Author Correction: Functional genomics data: privacy risk assessment and technological mitigation
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Functional genomics data: privacy risk assessment and technological mitigation
The generation of functional genomics data by next-generation sequencing has increased greatly in the past decade. Broad sharing of these data is essential for research advancement but poses notable privacy ch...
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Open AccessCross-platform transcriptomic profiling of the response to recombinant human erythropoietin
RNA-seq has matured and become an important tool for studying RNA biology. Here we compared two RNA-seq (MGI DNBSEQ and Illumina NextSeq 500) and two microarray platforms (GeneChip Human Transcriptome Array 2....
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Establishing a Global Standard for Wearable Devices in Sport and Exercise Medicine: Perspectives from Academic and Industry Stakeholders
Millions of consumer sport and fitness wearables (CSFWs) are used worldwide, and millions of datapoints are generated by each device. Moreover, these numbers are rapidly growing, and they contain a heterogenei...
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Open AccessNetwork propagation-based prioritization of long tail genes in 17 cancer types
The diversity of genomic alterations in cancer poses challenges to fully understanding the etiologies of the disease. Recent interest in infrequent mutations, in genes that reside in the “long tail” of the mut...
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Article
Quantum computing at the frontiers of biological sciences
Computing plays a critical role in the biological sciences but faces increasing challenges of scale and complexity. Quantum computing, a computational paradigm exploiting the unique properties of quantum mecha...
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Open AccessAuthor Correction: Retrospective evaluation of whole exome and genome mutation calls in 746 cancer samples
Correction to this paper has been published: https://doi.org/10.1038/s41467-020-20128-w
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Open AccessSVFX: a machine learning framework to quantify the pathogenicity of structural variants
There is a lack of approaches for identifying pathogenic genomic structural variants (SVs) although they play a crucial role in many diseases. We present a mechanism-agnostic machine learning-based workflow, c...
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Open AccessRetrospective evaluation of whole exome and genome mutation calls in 746 cancer samples
The Cancer Genome Atlas (TCGA) and International Cancer Genome Consortium (ICGC) curated consensus somatic mutation calls using whole exome sequencing (WES) and whole genome sequencing (WGS), respectively. Her...
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Open AccessUsing sigLASSO to optimize cancer mutation signatures jointly with sampling likelihood
Multiple mutational processes drive carcinogenesis, leaving characteristic signatures in tumor genomes. Determining the active signatures from a full repertoire of potential ones helps elucidate mechanisms of ...
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Article
Perspectives on ENCODE
The Encylopedia of DNA Elements (ENCODE) Project launched in 2003 with the long-term goal of develo** a comprehensive map of functional elements in the human genome. These included genes, biochemical regions...
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Article
Open AccessExpanded encyclopaedias of DNA elements in the human and mouse genomes
The human and mouse genomes contain instructions that specify RNAs and proteins and govern the timing, magnitude, and cellular context of their production. To better delineate these elements, phase III of the ...
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Open AccessMulti-platform discovery of haplotype-resolved structural variation in human genomes
The incomplete identification of structural variants (SVs) from whole-genome sequencing data limits studies of human genetic diversity and disease association. Here, we apply a suite of long-read, short-read, ...
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Article
A multiregional proteomic survey of the postnatal human brain
Detailed observations of transcriptional, translational and post-translational events in the human brain are essential to improving our understanding of its development, function and vulnerability to disease. ...
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Open AccessGaining comprehensive biological insight into the transcriptome by performing a broad-spectrum RNA-seq analysis
RNA-sequencing (RNA-seq) is an essential technique for transcriptome studies, hundreds of analysis tools have been developed since it was debuted. Although recent efforts have attempted to assess the latest av...
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Open AccessExtending gene ontology in the context of extracellular RNA and vesicle communication
To address the lack of standard terminology to describe extracellular RNA (exRNA) data/metadata, we have launched an inter-community effort to extend the Gene Ontology (GO) with subcellular structure concepts ...
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Article
The PsychENCODE project
Recent research on disparate psychiatric disorders has implicated rare variants in genes involved in global gene regulation and chromatin modification, as well as many common variants located primarily in regu...
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Open AccessAn integrated map of structural variation in 2,504 human genomes
Structural variants are implicated in numerous diseases and make up the majority of varying nucleotides among human genomes. Here we describe an integrated set of eight structural variant classes comprising bo...
