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::CRISPR guide RNA libraries have been iteratively improved to provide increasingly efficient reagents, although their large size is a barrier for many applications. We design an optimised minimal genome-wide human CRISPR-Cas9 library (MinLibCas9) by mining existing large-scale gene loss-of-function datasets, resulting ...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/s13059-021-02268-4
更新日期:2021-01-21 00:00:00
abstract:BACKGROUND:Aberrant activation of the Hedgehog pathway drives tumorigenesis of many cancers, including glioblastoma. However, the sensitization mechanism of the G protein-coupled-like receptor smoothened (SMO), a key component of Hedgehog signaling, remains largely unknown. RESULTS:In this study, we describe a novel p...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/s13059-020-02250-6
更新日期:2021-01-14 00:00:00
abstract::PIWI proteins, a subfamily of PAZ/PIWI Domain family RNA-binding proteins, are best known for their function in silencing transposons and germline development by partnering with small noncoding RNAs called PIWI-interacting RNAs (piRNAs). However, recent studies have revealed multifaceted roles of the PIWI-piRNA pathwa...
journal_title:Genome biology
pub_type: 杂志文章,评审
doi:10.1186/s13059-020-02221-x
更新日期:2021-01-08 00:00:00
abstract:BACKGROUND:Metastatic progress is the primary cause of death in most cancers, yet the regulatory dynamics driving the cellular changes necessary for metastasis remain poorly understood. Multi-omics approaches hold great promise for addressing this challenge; however, current analysis tools have limited capabilities to ...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/s13059-020-02213-x
更新日期:2021-01-07 00:00:00
abstract:BACKGROUND:mRNA processing is critical for gene expression. A challenge in regulating mRNA processing is how to recognize the actual mRNA processing sites, such as splice and polyadenylation sites, when the sequence content is insufficient for this purpose. Previous studies suggested that RNA structure affects mRNA pro...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/s13059-020-02236-4
更新日期:2021-01-04 00:00:00
abstract::Chromosome conformation capture data, particularly from high-throughput approaches such as Hi-C, are typically very complex to analyse. Existing analysis tools are often single-purpose, or limited in compatibility to a small number of data formats, frequently making Hi-C analyses tedious and time-consuming. Here, we p...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/s13059-020-02215-9
更新日期:2020-12-17 00:00:00
abstract::The accurate placement of an ancient whole-genome duplication (WGD) in relation to the lineage divergence is important. Here, we re-investigated the Aquilegia coerulea WGD and found it is more likely lineage-specific rather than shared by all eudicots. ...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/s13059-020-02212-y
更新日期:2020-12-08 00:00:00
abstract::According to a recent article published in Genome Biology, Duggan and coworkers sequenced and partially assembled five genomes of smallpox vaccines from the nineteenth century. No information regarding the ends of genomes was presented, and they are important to understand the evolutionary relationship of the differen...
journal_title:Genome biology
pub_type: 信件
doi:10.1186/s13059-020-02202-0
更新日期:2020-12-04 00:00:00
abstract:BACKGROUND:Chromatin organizes DNA and regulates its transcriptional activity through epigenetic modifications. Heterochromatic regions of the genome are generally transcriptionally silent, while euchromatin is more prone to transcription. During DNA replication, both genetic information and chromatin modifications mus...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/s13059-020-02190-1
更新日期:2020-11-25 00:00:00
abstract:BACKGROUND:Adult T cell acute lymphoblastic leukemia (T-ALL) is a rare disease that affects less than 10 individuals in one million. It has been less studied than its cognate pediatric malignancy, which is more prevalent. A higher percentage of the adult patients relapse, compared to children. It is thus essential to s...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/s13059-020-02192-z
更新日期:2020-11-23 00:00:00
abstract:BACKGROUND:Long noncoding enhancer RNAs (lnc-eRNAs) are a subset of stable eRNAs identified from annotated lncRNAs. They might act as enhancer activity-related therapeutic targets in cancer. However, the underlying mechanism of epigenetic activation and their function in cancer initiation and progression remain largely...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/s13059-020-02186-x
更新日期:2020-11-03 00:00:00
abstract::CRISPR-Cas9 gene editing has transformed our ability to rapidly interrogate the functional impact of somatic mutations in human cancers. Droplet-based technology enables the analysis of Cas9-introduced gene edits in thousands of single cells. Using this technology, we analyze Ba/F3 cells engineered to express single o...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/s13059-020-02174-1
更新日期:2020-10-20 00:00:00
abstract::Stochastic changes in DNA methylation (i.e., spontaneous epimutations) contribute to methylome diversity in plants. Here, we describe AlphaBeta, a computational method for estimating the precise rate of such stochastic events using pedigree-based DNA methylation data as input. We demonstrate how AlphaBeta can be emplo...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/s13059-020-02161-6
更新日期:2020-10-06 00:00:00
abstract:BACKGROUND:A key step in domestication of the grapevine was the transition from separate sexes (dioecy) in wild Vitis vinifera ssp. sylvestris (V. sylvestris) to hermaphroditism in cultivated Vitis vinifera ssp. sativa (V. vinifera). It is known that V. sylvestris has an XY system and V. vinifera a modified Y haplotype...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/s13059-020-02131-y
更新日期:2020-09-07 00:00:00
abstract::Fine-tuning quantitative traits for continuous subtle phenotypes is highly advantageous. We engineer the highly conserved upstream open reading frame (uORF) of FvebZIPs1.1 in strawberry (Fragaria vesca), using base editor A3A-PBE. Seven novel alleles are generated. Sugar content of the homozygous T1 mutant lines is 33...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/s13059-020-02146-5
更新日期:2020-09-03 00:00:00
abstract:BACKGROUND:The Asian tiger mosquito Aedes albopictus is globally expanding and has become the main vector for human arboviruses in Europe. With limited antiviral drugs and vaccines available, vector control is the primary approach to prevent mosquito-borne diseases. A reliable and accurate DNA sequence of the Ae. albop...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/s13059-020-02141-w
更新日期:2020-08-26 00:00:00
abstract::Many existing pipelines for scRNA-seq data apply pre-processing steps such as normalization or imputation to account for excessive zeros or "drop-outs." Here, we extensively analyze diverse UMI data sets to show that clustering should be the foremost step of the workflow. We observe that most drop-outs disappear once ...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/s13059-020-02096-y
更新日期:2020-08-06 00:00:00
abstract:BACKGROUND:The current bovine genomic reference sequence was assembled from a Hereford cow. The resulting linear assembly lacks diversity because it does not contain allelic variation, a drawback of linear references that causes reference allele bias. High nucleotide diversity and the separation of individuals by hundr...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/s13059-020-02105-0
更新日期:2020-07-27 00:00:00
abstract:BACKGROUND:Despite their regional economic importance and being increasingly reared globally, the origins and evolution of the llama and alpaca remain poorly understood. Here we report reference genomes for the llama, and for the guanaco and vicuña (their putative wild progenitors), compare these with the published alp...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/s13059-020-02080-6
更新日期:2020-07-02 00:00:00
abstract::We describe here a CRISPR simultaneous and wide-editing induced by a single system (SWISS), in which RNA aptamers engineered in crRNA scaffold recruit their cognate binding proteins fused with cytidine deaminase and adenosine deaminase to Cas9 nickase target sites to generate multiplexed base editing. By using paired ...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/s13059-020-02051-x
更新日期:2020-06-16 00:00:00
abstract::To discover driver fusions beyond canonical exon-to-exon chimeric transcripts, we develop CICERO, a local assembly-based algorithm that integrates RNA-seq read support with extensive annotation for candidate ranking. CICERO outperforms commonly used methods, achieving a 95% detection rate for 184 independently validat...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/s13059-020-02043-x
更新日期:2020-05-28 00:00:00
abstract:BACKGROUND:Epigenomic studies that use next generation sequencing experiments typically rely on the alignment of reads to a reference sequence. However, because of genetic diversity and the diploid nature of the human genome, we hypothesize that using a generic reference could lead to incorrectly mapped reads and bias ...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/s13059-020-02038-8
更新日期:2020-05-25 00:00:00
abstract:BACKGROUND:Tumors comprise a complex microenvironment of interacting malignant and stromal cell types. Much of our understanding of the tumor microenvironment comes from in vitro studies isolating the interactions between malignant cells and a single stromal cell type, often along a single pathway. RESULT:To develop a...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/s13059-020-02019-x
更新日期:2020-05-07 00:00:00
abstract:BACKGROUND:Polyploidy is ubiquitous in eukaryotic plant and fungal lineages, and it leads to the co-existence of several copies of similar or related genomes in one nucleus. In plants, polyploidy is considered a major factor in successful domestication. However, polyploidy challenges chromosome folding architecture in ...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/s13059-020-01998-1
更新日期:2020-04-29 00:00:00
abstract::Existing circular RNA (circRNA) databases have become essential for transcriptomics. However, most are unsuitable for mining in-depth information for candidate circRNA prioritization. To address this, we integrate circular transcript collections to develop the circAtlas database based on 1070 RNA-seq samples collected...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/s13059-020-02018-y
更新日期:2020-04-28 00:00:00
abstract:BACKGROUND:Early single-cell RNA-seq (scRNA-seq) studies suggested that it was unusual to see more than one isoform being produced from a gene in a single cell, even when multiple isoforms were detected in matched bulk RNA-seq samples. However, these studies generally did not consider the impact of dropouts or isoform ...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/s13059-020-01981-w
更新日期:2020-03-23 00:00:00
abstract::Many differential gene expression analyses are conducted with an inadequate number of biological replicates. We describe an easy and effective RNA-seq approach using molecular barcoding to enable profiling of a large number of replicates simultaneously. This approach significantly improves the performance of different...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/s13059-020-01966-9
更新日期:2020-03-23 00:00:00
abstract:BACKGROUND:Recent advancements in next-generation sequencing have rapidly improved our ability to study genomic material at an unprecedented scale. Despite substantial improvements in sequencing technologies, errors present in the data still risk confounding downstream analysis and limiting the applicability of sequenc...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/s13059-020-01988-3
更新日期:2020-03-17 00:00:00
abstract:BACKGROUND:Hemispheric asymmetry in neuronal processes is a fundamental feature of the human brain and drives symptom lateralization in Parkinson's disease (PD), but its molecular determinants are unknown. Here, we identify divergent epigenetic patterns involved in hemispheric asymmetry by profiling DNA methylation in ...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/s13059-020-01960-1
更新日期:2020-03-09 00:00:00
abstract::Droplet-based microfluidic devices have become widely used to perform single-cell RNA sequencing (scRNA-seq). However, ambient RNA present in the cell suspension can be aberrantly counted along with a cell's native mRNA and result in cross-contamination of transcripts between different cell populations. DecontX is a n...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/s13059-020-1950-6
更新日期:2020-03-05 00:00:00
abstract:BACKGROUND:The initiation and subsequent evolution of cancer are largely driven by a relatively small number of somatic mutations with critical functional impacts, so-called driver mutations. Identifying driver mutations in a patient's tumor cells is a central task in the era of precision cancer medicine. Over the deca...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/s13059-020-01954-z
更新日期:2020-02-20 00:00:00
abstract::Structural variants (SVs) remain challenging to represent and study relative to point mutations despite their demonstrated importance. We show that variation graphs, as implemented in the vg toolkit, provide an effective means for leveraging SV catalogs for short-read SV genotyping experiments. We benchmark vg against...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/s13059-020-1941-7
更新日期:2020-02-12 00:00:00
abstract:BACKGROUND:Host-associated microbiomes, the microorganisms occurring inside and on host surfaces, influence evolutionary, immunological, and ecological processes. Interactions between host and microbiome affect metabolism and contribute to host adaptation to changing environments. Meta-analyses of host-associated bacte...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/s13059-019-1908-8
更新日期:2020-02-03 00:00:00
abstract:BACKGROUND:Many genome-wide collections of candidate cis-regulatory elements (cCREs) have been defined using genomic and epigenomic data, but it remains a major challenge to connect these elements to their target genes. RESULTS:To facilitate the development of computational methods for predicting target genes, we deve...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/s13059-019-1924-8
更新日期:2020-01-22 00:00:00
abstract:BACKGROUND:RNA splicing is a key post-transcriptional mechanism that generates protein diversity and contributes to the fine-tuning of gene expression, which may facilitate adaptation to environmental challenges. Here, we employ a systems approach to study alternative splicing changes upon enteric infection in females ...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/s13059-019-1918-6
更新日期:2020-01-17 00:00:00
abstract:BACKGROUND:CTCF binding contributes to the establishment of a higher-order genome structure by demarcating the boundaries of large-scale topologically associating domains (TADs). However, despite the importance and conservation of TADs, the role of CTCF binding in their evolution and stability remains elusive. RESULTS...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/s13059-019-1894-x
更新日期:2020-01-07 00:00:00
abstract::We develop PIRCh-seq, a method which enables a comprehensive survey of chromatin-associated RNAs in a histone modification-specific manner. We identify hundreds of chromatin-associated RNAs in several cell types with substantially less contamination by nascent transcripts. Non-coding RNAs are found enriched on chromat...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/s13059-019-1880-3
更新日期:2019-12-20 00:00:00
abstract::The spatial organization of chromatin in the nucleus has been implicated in regulating gene expression. Maps of high-frequency interactions between different segments of chromatin have revealed topologically associating domains (TADs), within which most of the regulatory interactions are thought to occur. TADs are not...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/s13059-019-1893-y
更新日期:2019-12-18 00:00:00
abstract:BACKGROUND:The lifelong accumulation of somatic mutations underlies age-related phenotypes and cancer. Mutagenic forces are thought to shape the genome of aging cells in a tissue-specific way. Whole genome analyses of somatic mutation patterns, based on both types and genomic distribution of variants, can shed light on...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/s13059-019-1892-z
更新日期:2019-12-18 00:00:00
abstract:BACKGROUND:Gynecologic malignancy is one of the leading causes of mortality in female adults worldwide. Comprehensive genomic analysis has revealed a list of molecular aberrations that are essential to tumorigenesis, progression, and metastasis of gynecologic tumors. However, targeting such alterations has frequently l...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/s13059-019-1848-3
更新日期:2019-11-26 00:00:00