解剖学和形态学
麻醉学
听力与言语-语言病理学
行为科学
心脏和心血管系统
细胞和组织工程学
临床神经病学
危重症监护医学
牙科,口腔外科和医学
皮肤病学
急诊医学
内分泌学和新陈代谢
肠胃学和肝脏学
老人病学和老年医学
卫生保健科学和服务
血液学
免疫学
传染病
综合和补充性医学
医学伦理学
医学信息学
医学实验室技术
医学,全科和内科
医学,法律
医学,研究和试验
神经系统科学
护理
营养学和饮食学
产科医学和妇科医学
肿瘤学
眼科学
整形外科学
耳鼻喉科学
病理学
儿科学
周围血管疾病
药理学和药剂学
生理学
基本医疗保健
精神病学
公共、环境和职业卫生
放射学,核医学和医学成像
康复学
生殖生物学
呼吸系统
风湿病学
运动科学
外科学
毒理学
热带医学
泌尿学和肾脏学
病毒学
老年医学
健康政策和服务
心理学,临床
abstract::Recent evidence from proteomics and deep massively parallel sequencing studies have revealed that eukaryotic genomes contain substantial numbers of as-yet-uncharacterized open reading frames (ORFs). We define these uncharacterized ORFs as novel ORFs (nORFs). nORFs in humans are mostly under 100 codons and are found in...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.263202.120
更新日期:2021-01-19 00:00:00
abstract::Transposable elements (TEs) are an integral part of the host transcriptome. TE-containing noncoding RNAs (ncRNAs) show considerable tissue specificity and play important roles during development, including stem cell maintenance and cell differentiation. Recent advances in single-cell RNA-seq (scRNA-seq) revolutionized...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.265173.120
更新日期:2021-01-01 00:00:00
abstract::Somatic transposon expression in neural tissue is commonly considered as a measure of mobilization and has therefore been linked to neuropathology and organismal individuality. We combined genome sequencing data with single-cell mRNA sequencing of the same inbred fly strain to map transposon expression in the Drosophi...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.259200.119
更新日期:2020-11-01 00:00:00
abstract::Rhesus macaque is an Old World monkey that shared a common ancestor with human ∼25 Myr ago and is an important animal model for human disease studies. A deep understanding of its genetics is therefore required for both biomedical and evolutionary studies. Among structural variants, inversions represent a driving force...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.265322.120
更新日期:2020-11-01 00:00:00
abstract::To effectively analyze the increasing amounts of available genomic data, improved comparative analytical tools that are accessible to and applicable by a broad scientific community are essential. We built the "2-n-way" software suite to provide a fundamental and innovative processing framework for revealing and compar...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.262261.120
更新日期:2020-10-01 00:00:00
abstract::Epigenetic modifications on chromatin play important roles in regulating gene expression. Although chromatin states are often governed by multilayered structure, how individual pathways contribute to gene expression remains poorly understood. For example, DNA methylation is known to regulate transcription factor bindi...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.257576.119
更新日期:2020-10-01 00:00:00
abstract::The higher-order structural organization and dynamics of the chromosomes play a central role in gene regulation. To explore this structure-function relationship, it is necessary to directly visualize genomic elements in living cells. Genome imaging based on the CRISPR system is a powerful approach but has limited appl...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.260018.119
更新日期:2020-09-01 00:00:00
abstract::Biological products of importance in food (e.g., milk) and medical (e.g., donor blood-derived products) sciences often correspond to mixtures of samples contributed by multiple individuals. Identifying which individuals contributed to the mixture and in what proportions may be of interest in several circumstances. We ...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.256172.119
更新日期:2020-08-01 00:00:00
abstract::Changes in gene expression drive novel phenotypes, raising interest in how gene expression evolves. In contrast to the static genome, cells modulate gene expression in response to changing environments. Previous comparative studies focused on specific conditions, describing interspecies variation in expression levels,...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.261537.120
更新日期:2020-07-01 00:00:00
abstract::Eukaryotic translation initiation involves preinitiation ribosomal complex 5'-to-3' directional probing of mRNA for codons suitable for starting protein synthesis. The recognition of codons as starts depends on the codon identity and on its immediate nucleotide context known as Kozak context. When the context is weak ...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.257352.119
更新日期:2020-07-01 00:00:00
abstract::Genes with sex-biased expression in Drosophila are thought to underlie sexually dimorphic phenotypes and have been shown to possess unique evolutionary properties. However, the forces and constraints governing the evolution of sex-biased genes in the somatic tissues of Drosophila are largely unknown. By using populati...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.259069.119
更新日期:2020-06-01 00:00:00
abstract::The phenotypic variation of living organisms is shaped by genetics, environment, and their interaction. Understanding phenotypic plasticity under natural conditions is hindered by the apparently complex environment and the interacting genes and pathways. Herein, we report findings from the dissection of rice flowering...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.255703.119
更新日期:2020-05-01 00:00:00
abstract::Centromeres pose an evolutionary paradox: strongly conserved in function but rapidly changing in sequence and structure. However, in the absence of damage, centromere locations are usually conserved within a species. We report here that isolates of the pathogenic yeast species Candida parapsilosis show within-species ...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.257816.119
更新日期:2020-05-01 00:00:00
abstract::A time course experiment is a widely used design in the study of cellular processes such as differentiation or response to stimuli. In this paper, we propose time course regulatory analysis (TimeReg) as a method for the analysis of gene regulatory networks based on paired gene expression and chromatin accessibility da...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.257063.119
更新日期:2020-04-01 00:00:00
abstract::Plant endogenous small RNAs (sRNAs) are important regulators of gene expression. There are two broad categories of plant sRNAs: microRNAs (miRNAs) and endogenous short interfering RNAs (siRNAs). MicroRNA loci are relatively well-annotated but compose only a small minority of the total sRNA pool; siRNA locus annotation...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.256750.119
更新日期:2020-03-01 00:00:00
abstract::Detecting and estimating DNA sample contamination are important steps to ensure high-quality genotype calls and reliable downstream analysis. Existing methods rely on population allele frequency information for accurate estimation of contamination rates. Correctly specifying population allele frequencies for each indi...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.246934.118
更新日期:2020-02-01 00:00:00
abstract::The most widely appreciated role of DNA is to encode protein, yet the exact portion of the human genome that is translated remains to be ascertained. We previously developed PhyloCSF, a widely used tool to identify evolutionary signatures of protein-coding regions using multispecies genome alignments. Here, we present...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.246462.118
更新日期:2019-12-01 00:00:00
abstract::Aging is a pleiotropic process affecting many aspects of mammalian physiology. Mammals are composed of distinct cell type identities and tissue environments, but the influence of these cell identities and environments on the trajectory of aging in individual cells remains unclear. Here, we performed single-cell RNA-se...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.253880.119
更新日期:2019-12-01 00:00:00
abstract::The Atlantic herring is a model species for exploring the genetic basis for ecological adaptation, due to its huge population size and extremely low genetic differentiation at selectively neutral loci. However, such studies have so far been hampered because of a highly fragmented genome assembly. Here, we deliver a ch...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.253435.119
更新日期:2019-11-01 00:00:00
abstract::RNA sequencing (RNA-seq) is a sensitive and accurate method for quantifying gene expression. Small samples or those whose RNA is degraded, such as formalin-fixed paraffin-embedded (FFPE) tissue, remain challenging to study with nonspecialized RNA-seq protocols. Here, we present a new method, Smart-3SEQ, that accuratel...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.234807.118
更新日期:2019-11-01 00:00:00
abstract::In cancer cells, aberrant DNA methylation is commonly associated with transcriptional alterations, including silencing of tumor suppressor genes. However, multiple epigenetic mechanisms, including polycomb repressive marks, contribute to gene deregulation in cancer. To dissect the relative contribution of DNA methylat...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.249219.119
更新日期:2019-10-01 00:00:00
abstract::The world of noncoding RNAs (ncRNAs) is composed of an enormous and growing number of transcripts, ranging in length from tens of bases to tens of kilobases, involved in all biological processes and altered in expression and/or function in many types of human disorders. The premise of this review is the concept that n...
journal_title:Genome research
pub_type: 杂志文章,评审
doi:10.1101/gr.247239.118
更新日期:2019-09-01 00:00:00
abstract::How pathogens evolve their virulence to humans in nature is a scientific issue of great medical and biological importance. Shiga toxin (Stx)-producing Escherichia coli (STEC) and enteropathogenic E. coli (EPEC) are the major foodborne pathogens that can cause hemolytic uremic syndrome and infantile diarrhea, respectiv...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.249268.119
更新日期:2019-09-01 00:00:00
abstract::The repressive capacity of cytosine DNA methylation is mediated by recruitment of silencing complexes by methyl-CpG binding domain (MBD) proteins. Despite MBD proteins being associated with silencing, we discovered that a family of arthropod Copia retrotransposons have incorporated a host-derived MBD. We functionally ...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.243774.118
更新日期:2019-08-01 00:00:00
abstract::In interphase eukaryotic cells, almost all heterochromatin is located adjacent to the nucleolus or to the nuclear lamina, thus defining nucleolus-associated domains (NADs) and lamina-associated domains (LADs), respectively. Here, we determined the first genome-scale map of murine NADs in mouse embryonic fibroblasts (M...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.247072.118
更新日期:2019-08-01 00:00:00
abstract::Caenorhabditis elegans was the first multicellular eukaryotic genome sequenced to apparent completion. Although this assembly employed a standard C. elegans strain (N2), it used sequence data from several laboratories, with DNA propagated in bacteria and yeast. Thus, the N2 assembly has many differences from any C. el...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.244830.118
更新日期:2019-06-01 00:00:00
abstract::Little is known about the rate of emergence of de novo genes, what their initial properties are, and how they spread in populations. We examined wild yeast populations (Saccharomyces paradoxus) to characterize the diversity and turnover of intergenic ORFs over short evolutionary timescales. We find that hundreds of in...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.239822.118
更新日期:2019-06-01 00:00:00
abstract::Establishment of spatial coordinates during Drosophila embryogenesis relies on differential regulatory activity of axis patterning enhancers. Concentration gradients of activator and repressor transcription factors (TFs) provide positional information to each enhancer, which in turn promotes transcription of a target ...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.242362.118
更新日期:2019-05-01 00:00:00
abstract::Oncoviral infection is responsible for 12%-15% of cancer in humans. Convergent evidence from epidemiology, pathology, and oncology suggests that new viral etiologies for cancers remain to be discovered. Oncoviral profiles can be obtained from cancer genome sequencing data; however, widespread viral sequence contaminat...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.242529.118
更新日期:2019-05-01 00:00:00
abstract::Here we use a chromosome-level genome assembly of a prairie rattlesnake (Crotalus viridis), together with Hi-C, RNA-seq, and whole-genome resequencing data, to study key features of genome biology and evolution in reptiles. We identify the rattlesnake Z Chromosome, including the recombining pseudoautosomal region, and...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.240952.118
更新日期:2019-04-01 00:00:00
abstract::We report on the development of a methylation analysis workflow for optical detection of fluorescent methylation profiles along chromosomal DNA molecules. In combination with Bionano Genomics genome mapping technology, these profiles provide a hybrid genetic/epigenetic genome-wide map composed of DNA molecules spannin...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.240739.118
更新日期:2019-04-01 00:00:00
abstract::Large-scale genetic interaction (GI) screens in yeast have been invaluable for our understanding of molecular systems biology and for characterizing novel gene function. Owing in part to the high costs and long experiment times required, a preponderance of GI data has been generated in a single environmental condition...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.246603.118
更新日期:2019-04-01 00:00:00
abstract::Most mammalian RNA polymerase II initiation events occur at CpG islands, which are rich in CpGs and devoid of DNA methylation. Despite their relevance for gene regulation, it is unknown to what extent the CpG dinucleotide itself actually contributes to promoter activity. To address this question, we determined the tra...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.241653.118
更新日期:2019-04-01 00:00:00
abstract::Despite much research, our understanding of the architecture and cis-regulatory elements of human promoters is still lacking. Here, we devised a high-throughput assay to quantify the activity of approximately 15,000 fully designed sequences that we integrated and expressed from a fixed location within the human genome...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.236075.118
更新日期:2019-02-01 00:00:00
abstract::Gene expression can be regulated at multiple levels, but it is not known if and how there is broad coordination between regulation at the transcriptional and post-transcriptional levels. Transcription factors and chromatin regulate gene expression transcriptionally, whereas microRNAs (miRNAs) are small regulatory RNAs...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.238311.118
更新日期:2019-02-01 00:00:00
abstract::In vivo analyses of the occurrence, subcellular localization, and dynamics of protein-protein interactions (PPIs) are important issues in functional proteomic studies. The bimolecular fluorescence complementation (BiFC) assay has many advantages in that it provides a reliable way to detect PPIs in living cells with mi...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.231860.117
更新日期:2019-01-01 00:00:00
abstract::Mosaic mutations present in the germline have important implications for reproductive risk and disease transmission. We previously demonstrated a phenomenon occurring in the male germline, whereby specific mutations arising spontaneously in stem cells (spermatogonia) lead to clonal expansion, resulting in elevated mut...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.239186.118
更新日期:2018-12-01 00:00:00
abstract::Despite claims that the mammalian Y Chromosome is on a path to extinction, comparative sequence analysis of primate Y Chromosomes has shown the decay of the ancestral single-copy genes has all but ceased in this eutherian lineage. The suite of single-copy Y-linked genes is highly conserved among the majority of euther...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.237586.118
更新日期:2018-12-01 00:00:00
abstract::Targeted genotyping of transcriptome-scale genetic markers is highly attractive for genetic, ecological, and evolutionary studies, but achieving this goal in a cost-effective manner remains a major challenge, especially for laboratories working on nonmodel organisms. Here, we develop a high-throughput, sequencing-base...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.235820.118
更新日期:2018-12-01 00:00:00
abstract::To investigate whether and how CRISPR-Cas9 on-target and off-target activities are affected by chromatin in eukaryotic cells, we first identified a series of identical endogenous DNA sequences present in both open and closed chromatin regions and then measured mutation frequencies at these sites in human cells using C...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.236620.118
更新日期:2018-12-01 00:00:00