• By Genome Biology   -   May 11, 2021

    PROMOTER G-QUADRUPLEX FOLDING PRECEDES TRANSCRIPTION AND IS CONTROLLED BY CHROMATIN

    Four-stranded G-quadruplexes are DNA secondary structures in the human genome that are primarily found in active promoters associated...

    Human Genome, Genome, DNA, Genomics, Research
  • By Genome Biology   -   May 11, 2021

    SCSNV: ACCURATE DSCRNA-SEQ SNV CO-EXPRESSION ANALYSIS USING DUPLICATE TAG COLLAPSING

    Identifying single nucleotide variants has become common practice for droplet-based single-cell RNA-seq experiments; however, presently,...

    RNA, Nucleotide, Nucleotides, Method
  • By Genome Biology   -   May 11, 2021

    LIMITED HAPLOTYPE DIVERSITY UNDERLIES POLYGENIC TRAIT ARCHITECTURE ACROSS 70 YEARS OF WHEAT BREEDING

    Selection has dramatically shaped genetic and phenotypic variation in bread wheat. We can assess the genomic basis of historical phenotypic...

    Genome, Genomics, Genetics, Research
  • By Genome Biology   -   May 11, 2021

    GENETIC AND ENVIRONMENTAL MODULATION OF TRANSPOSITION SHAPES THE EVOLUTIONARY POTENTIAL OF ARABIDOPSIS THALIANA

    How species can adapt to abrupt environmental changes, particularly in the absence of standing genetic variation, is poorly understood...

    Environmental, Genetics, Research
  • By Genome Biology   -   May 11, 2021

    DETERMINATION OF COMPLETE CHROMOSOMAL HAPLOTYPES BY BULK DNA SEQUENCING

    Haplotype phase represents the collective genetic variation between homologous chromosomes and is an essential feature of non-haploid...

    Genome, Genomics, Computers, Chromosomes, DNA, Genetics, Method
  • By Genome Biology   -   May 11, 2021

    EMBRYO CHH HYPERMETHYLATION IS MEDIATED BY RDDM AND IS AUTONOMOUSLY DIRECTED IN BRASSICA RAPA

    RNA-directed DNA methylation initiates cytosine methylation in all contexts and maintains asymmetric CHH methylation. Mature plant...

    RNA, DNA, Plants, Research
  • By Genome Biology   -   May 11, 2021

    TRANSGENERATIONAL EFFECT OF MUTANTS IN THE RNA-DIRECTED DNA METHYLATION PATHWAY ON THE TRIPLOID BLOCK IN ARABIDOPSIS

    Hybridization of plants that differ in number of chromosome sets frequently causes endosperm failure and seed arrest, a phenomenon...

    RNA, Chromosomes, Plants, DNA, Research
  • By Genome Biology   -   May 11, 2021

    A GENERALIZATION OF T-SNE AND UMAP TO SINGLE-CELL MULTIMODAL OMICS

    Emerging single-cell technologies profile multiple types of molecules within individual cells. A fundamental step in the analysis of...

    General, Short Report
  • By Genome Biology   -   May 11, 2021

    SCHEMA: METRIC LEARNING ENABLES INTERPRETABLE SYNTHESIS OF HETEROGENEOUS SINGLE-CELL MODALITIES

    A complete understanding of biological processes requires synthesizing information across heterogeneous modalities, such as age, disease...

    Biology, Biologic, Biological, Genes, Gene, Method
  • By Genome Biology   -   May 11, 2021

    DEEP SEQUENCING OF PRE-TRANSLATIONAL MRNPS REVEALS HIDDEN FLUX THROUGH EVOLUTIONARILY CONSERVED ALTERNATIVE SPLICING NONSENSE-MEDIATED DECAY PATHWAYS

    Alternative splicing, which generates multiple mRNA isoforms from single genes, is crucial for the regulation of eukaryotic gene expression....

    Genes, Gene, Research
  • By Genome Biology   -   May 11, 2021

    FUNCTIONAL AND GENETIC DETERMINANTS OF MUTATION RATE VARIABILITY IN REGULATORY ELEMENTS OF CANCER GENOMES

    Cancer genomes are shaped by mutational processes with complex spatial variation at multiple scales. Entire classes of regulatory elements...

    Genetics, Cancer, Genomics, Genome, Research
  • By Genome Biology   -   May 11, 2021

    GENETIC IMPACTS ON DNA METHYLATION: RESEARCH FINDINGS AND FUTURE PERSPECTIVES

    Multiple recent studies highlight that genetic variants can have strong impacts on a significant proportion of the human DNA methylome....

    Genetics, DNA, Research, Review
  • By Genome Biology   -   May 11, 2021

    MARS: LEVERAGING ALLELIC HETEROGENEITY TO INCREASE POWER OF ASSOCIATION TESTING

    In standard genome-wide association studies , the standard association test is underpowered to detect associations between loci with...

    Genomics, Genome, Method
  • By Genome Biology   -   May 11, 2021

    COMPLETE VERTEBRATE MITOGENOMES REVEAL WIDESPREAD REPEATS AND GENE DUPLICATIONS

    Modern sequencing technologies should make the assembly of the relatively small mitochondrial genomes an easy undertaking. However,...

    Genome, Genes, Gene, Genomics, Research
  • By Genome Biology   -   May 11, 2021

    BEST PRACTICES ON THE DIFFERENTIAL EXPRESSION ANALYSIS OF MULTI-SPECIES RNA-SEQ

    Advances in transcriptome sequencing allow for simultaneous interrogation of differentially expressed genes from multiple species originating...

    RNA, Genes, Gene, Review
  • By Genome Biology   -   May 11, 2021

    THE IMPACT OF CELL TYPE AND CONTEXT-DEPENDENT REGULATORY VARIANTS ON HUMAN IMMUNE TRAITS

    The vast majority of trait-associated variants identified using genome-wide association studies are noncoding, and therefore assumed...

    Immunity, Gene, Genomics, Genes, Genome, Research
  • By Genome Biology   -   May 11, 2021

    NEXT-GENERATION MICROBIOLOGY: FROM COMPARATIVE GENOMICS TO GENE FUNCTION

    Microbiology is at a turning point in its 120-year history. Widespread next-generation sequencing has revealed genetic complexity among...

    Microbiology, Genetics, Genes, Gene, Genomics, Genome, Review
  • By Genome Biology   -   May 11, 2021

    PSEUDOTIMEDE: INFERENCE OF DIFFERENTIAL GENE EXPRESSION ALONG CELL PSEUDOTIME WITH WELL-CALIBRATED P-VALUES FROM SINGLE-CELL RNA SEQUENCING DATA

    To investigate molecular mechanisms underlying cell state changes, a crucial analysis is to identify differentially expressed genes...

    RNA, Genes, Gene, Method
  • By Genome Biology   -   May 11, 2021

    G-QUADRUPLEXES ARE TRANSCRIPTION FACTOR BINDING HUBS IN HUMAN CHROMATIN

    The binding of transcription factors to genomic targets is critical in the regulation of gene expression. Short, double-stranded DNA...

    Genes, DNA, Gene, Genomics, Genome, Research
  • By Genome Biology   -   May 11, 2021

    DROSOPHILA PRIMARY MICRORNA-8 ENCODES A MICRORNA-ENCODED PEPTIDE ACTING IN PARALLEL OF MIR-8

    Recent genome-wide studies of many species reveal the existence of a myriad of RNAs differing in size, coding potential and function....

    Genome, Genomics, Research