• By Genome Biology   -   Jan 27, 2022

    NANOPORE ADAPTIVE SAMPLING: A TOOL FOR ENRICHMENT OF LOW ABUNDANCE SPECIES IN METAGENOMIC SAMPLES

    Adaptive sampling is a method of software-controlled enrichment unique to nanopore sequencing platforms. To test its potential for...

    Method
  • By Genome Biology   -   Jan 27, 2022

    SPLINK: A HYBRID FEDERATED TOOL AS A ROBUST ALTERNATIVE TO META-ANALYSIS IN GENOME-WIDE ASSOCIATION STUDIES

    Meta-analysis has been established as an effective approach to combining summary statistics of several genome-wide association studies....

    Genome, Genomics, Method
  • By Genome Biology   -   Jan 27, 2022

    IDEAS: INDIVIDUAL LEVEL DIFFERENTIAL EXPRESSION ANALYSIS FOR SINGLE-CELL RNA-SEQ DATA

    We consider an increasingly popular study design where single-cell RNA-seq data are collected from multiple individuals and the question...

    Genes, Gene, RNA, Method
  • By Genome Biology   -   Jan 27, 2022

    OPEN CHROMATIN INTERACTION MAPS REVEAL FUNCTIONAL REGULATORY ELEMENTS AND CHROMATIN ARCHITECTURE VARIATIONS DURING WHEAT EVOLUTION

    Bread wheat is an allohexaploid that is generated by two subsequent allopolyploidization events. The large genome size and polyploid...

    Genomics, Genome, Research
  • By Genome Biology   -   Jan 27, 2022

    GENOME-WIDE ANALYSIS AND FUNCTIONAL ANNOTATION OF CHROMATIN-ENRICHED NONCODING RNAS IN RICE DURING SOMATIC CELL REGENERATION

    Plants have the remarkable ability to generate callus, a pluripotent cell mass that acquires competence for subsequent tissue regeneration....

    Genome, Plants, Tissue, Genomics, Research
  • By Genome Biology   -   Jan 27, 2022

    STRAINLINE: FULL-LENGTH DE NOVO VIRAL HAPLOTYPE RECONSTRUCTION FROM NOISY LONG READS

    Haplotype-resolved de novo assembly of highly diverse virus genomes is critical in prevention, control and treatment of viral diseases....

    Genome, Virus, Genomics, Method
  • By Genome Biology   -   Jan 27, 2022

    BACON: A COMPREHENSIVE COMPUTATIONAL BENCHMARKING FRAMEWORK FOR EVALUATING TARGETED CHROMATIN CONFORMATION CAPTURE-SPECIFIC METHODOLOGIES

    Chromatin conformation capture -based technologies have enabled the accurate detection of topological genomic interactions, and the...

    Computers, Genomics, Genome, Method
  • By Genome Biology   -   Jan 27, 2022

    STATISTICS OR BIOLOGY: THE ZERO-INFLATION CONTROVERSY ABOUT SCRNA-SEQ DATA

    Researchers view vast zeros in single-cell RNA-seq data differently: some regard zeros as biological signals representing no or low...

    RNA, Biologic, Gene, Genes, Biological, Research, Biology, Review
  • By Genome Biology   -   Jan 27, 2022

    COMPARISON AND EVALUATION OF STATISTICAL ERROR MODELS FOR SCRNA-SEQ

    Heterogeneity in single-cell RNA-seq data is driven by multiple sources, including biological variation in cellular state as well as...

    RNA, Cellular, Biologic, Biological, Biology, Research
  • By Genome Biology   -   Jan 27, 2022

    DENA: TRAINING AN AUTHENTIC NEURAL NETWORK MODEL USING NANOPORE SEQUENCING DATA OF ARABIDOPSIS TRANSCRIPTS FOR DETECTION AND QUANTIFICATION OF N6-METHYLADENOSINE ON RNA

    Models developed using Nanopore direct RNA sequencing data from in vitro synthetic RNA with all adenosine replaced by N6-methyladenosine...

    RNA, Method
  • By Genome Biology   -   Jan 27, 2022

    BLOOD-BASED EPIGENOME-WIDE ANALYSES OF COGNITIVE ABILITIES

    Blood-based markers of cognitive functioning might provide an accessible way to track neurodegeneration years prior to clinical manifestation...

    Clinical, Neurodegeneration, Research
  • By Genome Biology   -   Jan 27, 2022

    FUNCTIONAL GENOMICS ANALYSIS IDENTIFIES T AND NK CELL ACTIVATION AS A DRIVER OF EPIGENETIC CLOCK PROGRESSION

    Epigenetic clocks use DNA methylation levels of specific sets of CpG dinucleotides to accurately predict individual chronological age....

    Genomics, Genome, DNA, Research
  • By Genome Biology   -   Jan 27, 2022

    POLYGENIC TRANSCRIPTOME RISK SCORES CAN IMPROVE PORTABILITY OF POLYGENIC RISK SCORES ACROSS ANCESTRIES

    Polygenic risk scores are valuable to translate the results of genome-wide association studies into clinical practice. To date, most...

    Clinical, Genome, Genomics, Research
  • By Genome Biology   -   Jan 27, 2022

    A DEEP GENERATIVE MODEL FOR MULTI-VIEW PROFILING OF SINGLE-CELL RNA-SEQ AND ATAC-SEQ DATA

    Here, we present a multi-modal deep generative model, the single-cell Multi-View Profiler , which is designed for handling sequencing...

    Genes, Gene, RNA, Method
  • By Genome Biology   -   Jan 27, 2022

    THE BLOOMING OF LONG-READ SEQUENCING REFORMS BIOMEDICAL RESEARCH

    Research, Biomedical, BioMedical, Editorial
  • By Genome Biology   -   Jan 27, 2022

    USING SYNTHETIC CHROMOSOME CONTROLS TO EVALUATE THE SEQUENCING OF DIFFICULT REGIONS WITHIN THE HUMAN GENOME

    Next-generation sequencing can identify mutations in the human genome that cause disease and has been widely adopted in clinical diagnosis....

    Genomics, Chromosomes, Human Genome, Polymorphisms, Genome, Clinical, Research
  • By Genome Biology   -   Jan 27, 2022

    THE GENOME OF OIL-CAMELLIA AND POPULATION GENOMICS ANALYSIS PROVIDE INSIGHTS INTO SEED OIL DOMESTICATION

    As a perennial crop, oil-Camellia possesses a long domestication history and produces high-quality seed oil that is beneficial to human...

    Plants, Oil, Genomics, Human health, Genome, Health, Research
  • By Genome Biology   -   Jan 27, 2022

    SYSTEMATIC IDENTIFICATION OF ACE2 EXPRESSION MODULATORS REVEALS CARDIOMYOPATHY AS A RISK FACTOR FOR MORTALITY IN COVID-19 PATIENTS

    Angiotensin-converting enzyme 2 is the cell-entry receptor for SARS-CoV-2. It plays critical roles in both the transmission and the...

    Enzymes, Research
  • By Genome Biology   -   Jan 27, 2022

    KNOCKOUT OF CIRCRNAS BY BASE EDITING BACK-SPLICE SITES OF CIRCULARIZED EXONS

    Many circular RNAs are produced from back-splicing of exons of precursor mRNAs and are generally co-expressed with cognate linear RNAs....

    General, Method
  • By Genome Biology   -   Jan 27, 2022

    EVOLUTION OF THE REPRESSION MECHANISMS IN CIRCADIAN CLOCKS

    Circadian timekeeping is essential to the survival of many organisms. An integral part of all circadian timekeeping systems is negative...

    Research