• By Genome Biology   -   Jun 20, 2021

    AUTHOR CORRECTION: HIGHLY RECURRENT CBS EPIMUTATIONS IN GASTRIC CANCER CPG ISLAND METHYLATOR PHENOTYPES AND INFLAMMATION

    Cancer, Author Correction
  • By Genome Biology   -   Jun 20, 2021

    LIQA: LONG-READ ISOFORM QUANTIFICATION AND ANALYSIS

    Long-read RNA sequencing technologies can sequence full-length transcripts, facilitating the exploration of isoform-specific gene expression...

    Genes, Gene, RNA, Method
  • By Genome Biology   -   Jun 20, 2021

    GUNC: DETECTION OF CHIMERISM AND CONTAMINATION IN PROKARYOTIC GENOMES

    Genomes are critical units in microbiology, yet ascertaining quality in prokaryotic genome assemblies remains a formidable challenge....

    Genome, Genomics, Microbiology, Method
  • By Genome Biology   -   Jun 20, 2021

    LEVERAGING BREEDING PROGRAMS AND GENOMIC DATA IN NORWAY SPRUCE FOR GWAS ANALYSIS

    Genome-wide association studies identify loci underlying the variation of complex traits. One of the main limitations of GWAS is the...

    Genomics, Genome, Research
  • By Genome Biology   -   Jun 20, 2021

    POSITIVE NATURAL SELECTION OF N6-METHYLADENOSINE ON THE RNAS OF PROCESSED PSEUDOGENES

    Canonical nonsense-mediated decay is an important splicing-dependent process for mRNA surveillance in mammals. However, processed pseudogenes...

    Nature, Research
  • By Genome Biology   -   Jun 20, 2021

    BUTTERFLY: ADDRESSING THE POOLED AMPLIFICATION PARADOX WITH UNIQUE MOLECULAR IDENTIFIERS IN SINGLE-CELL RNA-SEQ

    The incorporation of unique molecular identifiers in single-cell RNA-seq assays makes possible the identification of duplicated molecules,...

    RNA, Method
  • By Genome Biology   -   Jun 20, 2021

    CHROMOSOME-LEVEL GENOME ASSEMBLY OF A REGENERABLE MAIZE INBRED LINE A188

    The maize inbred line A188 is an attractive model for elucidation of gene function and improvement due to its high embryogenic capacity...

    Genes, Chromosomes, Gene, Genome, Genomics, Research
  • By Genome Biology   -   Jun 20, 2021

    TRANSCRIPTION SHAPES DNA REPLICATION INITIATION TO PRESERVE GENOME INTEGRITY

    Early DNA replication occurs within actively transcribed chromatin compartments in mammalian cells, raising the immediate question...

    DNA, Genomics, Genome, Research
  • By Genome Biology   -   Jun 20, 2021

    PUBLISHER CORRECTION: SCDESIGN2: A TRANSPARENT SIMULATOR THAT GENERATES HIGH-FIDELITY SINGLE-CELL GENE EXPRESSION COUNT DATA WITH GENE CORRELATIONS CAPTURED

    Gene, Genes, Publisher Correction
  • By Genome Biology   -   Jun 20, 2021

    THE GLOBAL AND PROMOTER-CENTRIC 3D GENOME ORGANIZATION TEMPORALLY RESOLVED DURING A CIRCADIAN CYCLE

    Circadian gene expression is essential for organisms to adjust their physiology and anticipate daily changes in the environment. The...

    Physiology, Gene, Genomics, Genome, Environment, Genes, Research
  • By Genome Biology   -   Jun 20, 2021

    GENE SET ENRICHMENT ANALYSIS FOR GENOME-WIDE DNA METHYLATION DATA

    DNA methylation is one of the most commonly studied epigenetic marks, due to its role in disease and development. Illumina methylation...

    Genes, Genome, Genomics, DNA, Gene, Method
  • By Genome Biology   -   Jun 20, 2021

    N6-METHYLADENOSINE RNA MODIFICATION REGULATES STRAWBERRY FRUIT RIPENING IN AN ABA-DEPENDENT MANNER

    Epigenetic mark such as DNA methylation plays pivotal roles in regulating ripening of both climacteric and non-climacteric fruits....

    RNA, DNA, Research
  • By Genome Biology   -   Jun 20, 2021

    DETECTION OF SARS-COV-2 RNA USING RT-LAMP AND MOLECULAR BEACONS

    Rapid spread of SARS-CoV-2 has led to a global pandemic, resulting in the need for rapid assays to allow diagnosis and prevention of...

    RNA, Research
  • By Genome Biology   -   Jun 20, 2021

    TARGETED MUTAGENESIS IN MOUSE CELLS AND EMBRYOS USING AN ENHANCED PRIME EDITOR

    Prime editors, novel genome-editing tools consisting of a CRISPR-Cas9 nickase and an engineered reverse transcriptase, can induce targeted...

    Genome, Engineering, Genomics, Short Report
  • By Genome Biology   -   Jun 20, 2021

    DYNAMICS OF ALTERNATIVE SPLICING DURING SOMATIC CELL REPROGRAMMING REVEALS FUNCTIONS FOR RNA-BINDING PROTEINS CPSF3, HNRNP UL1, AND TIA1

    Somatic cell reprogramming is the process that allows differentiated cells to revert to a pluripotent state. In contrast to the extensively...

    Protein, RNA, Research
  • By Genome Biology   -   Jun 20, 2021

    ANNOTATION OF SNORNA ABUNDANCE ACROSS HUMAN TISSUES REVEALS COMPLEX SNORNA-HOST GENE RELATIONSHIPS

    Small nucleolar RNAs are mid-size non-coding RNAs required for ribosomal RNA modification, implying a ubiquitous tissue distribution...

    Genes, Tissue, Gene, RNA, Research
  • By Genome Biology   -   Jun 20, 2021

    HIGHLY RECURRENT CBS EPIMUTATIONS IN GASTRIC CANCER CPG ISLAND METHYLATOR PHENOTYPES AND INFLAMMATION

    CIMP is an epigenetic molecular subtype, observed in multiple malignancies and associated with the epigenetic silencing of tumor suppressors....

    Cancer, Research
  • By Genome Biology   -   Jun 20, 2021

    IMPACTS OF ALLOPOLYPLOIDIZATION AND STRUCTURAL VARIATION ON INTRASPECIFIC DIVERSIFICATION IN BRASSICA RAPA

    Despite the prevalence and recurrence of polyploidization in the speciation of flowering plants, its impacts on crop intraspecific...

    Genome, Plants, Genomics, Research
  • By Genome Biology   -   Jun 20, 2021

    DIFFBUM-HMM: A ROBUST STATISTICAL MODELING APPROACH FOR DETECTING RNA FLEXIBILITY CHANGES IN HIGH-THROUGHPUT STRUCTURE PROBING DATA

    Advancing RNA structural probing techniques with next-generation sequencing has generated demands for complementary computational tools...

    RNA, Computers, Method
  • By Genome Biology   -   Jun 20, 2021

    GRINCH: SIMULTANEOUS SMOOTHING AND DETECTION OF TOPOLOGICAL UNITS OF GENOME ORGANIZATION FROM SPARSE CHROMATIN CONTACT COUNT MATRICES WITH MATRIX FACTORIZATION

    High-throughput chromosome conformation capture assays, such as Hi-C, have shown that the genome is organized into organizational units...

    Chromosomes, Gene, Genome, Genes, Genomics, Method