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 in a greater than 42% reduction in size compared to other CRISPR-Cas9 libraries while preserving assay sensitivity and specificity. MinLibCas9 provides backward compatibility with existing datasets, increases the dynamic range of CRISPR-Cas9 screens and extends their application to complex models and assays.
journal_name
Genome Bioljournal_title
Genome biologyauthors
Gonçalves E,Thomas M,Behan FM,Picco G,Pacini C,Allen F,Vinceti A,Sharma M,Jackson DA,Price S,Beaver CM,Dovey O,Parry-Smith D,Iorio F,Parts L,Yusa K,Garnett MJdoi
10.1186/s13059-021-02268-4subject
Has Abstractpub_date
2021-01-21 00:00:00pages
40issue
1eissn
1474-7596issn
1474-760Xpii
10.1186/s13059-021-02268-4journal_volume
22pub_type
杂志文章相关文献
GENOME BIOLOGY文献大全abstract::How viruses evolve within hosts can dictate infection outcomes; however, reconstructing this process is challenging. We evaluate our multiplexed amplicon approach, PrimalSeq, to demonstrate how virus concentration, sequencing coverage, primer mismatches, and replicates influence the accuracy of measuring intrahost vir...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/s13059-018-1618-7
更新日期:2019-01-08 00:00:00
abstract:BACKGROUND:There is tremendous potential for genome sequencing to improve clinical diagnosis and care once it becomes routinely accessible, but this will require formalizing research methods into clinical best practices in the areas of sequence data generation, analysis, interpretation and reporting. The CLARITY Challe...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/gb-2014-15-3-r53
更新日期:2014-03-25 00:00:00
abstract::Vascular endothelia comprise a diverse population of cells that specialize in response to genetic programs and environmental cues to take on distinct roles in different vessels, tissues, and organs, and in response to pathophysiological stresses. Characterization of endothelial-cell diversity will facilitate the devel...
journal_title:Genome biology
pub_type: 杂志文章,评审
doi:10.1186/gb-2004-5-2-207
更新日期:2004-01-01 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:Symbiotic bacteria known as rhizobia interact with the roots of legumes and induce the formation of nitrogen-fixing nodules. In rhizobia, essential genes for symbiosis are compartmentalized either in symbiotic plasmids or in chromosomal symbiotic islands. To understand the structure and evolution of the symb...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/gb-2003-4-6-r36
更新日期:2003-01-01 00:00:00
abstract::In a recent study, Petrovski and Goldstein reported that (non-Finnish) Europeans have significantly fewer nonsynonymous singletons in Online Mendelian Inheritance in Man (OMIM) disease genes compared with Africans, Latinos, South Asians, East Asians, and other unassigned non-Europeans. We use simulations of Exome Aggr...
journal_title:Genome biology
pub_type: 评论,信件
doi:10.1186/s13059-017-1172-8
更新日期:2017-02-27 00:00:00
abstract:BACKGROUND:Gene expression signatures indicative of tumor proliferative capacity and tumor-immune cell interactions have emerged as principal biology-driven predictors of breast cancer outcomes. How these signatures relate to one another in biological and prognostic contexts remains to be clarified. RESULTS:To investi...
journal_title:Genome biology
pub_type: 杂志文章,随机对照试验
doi:10.1186/gb-2013-14-4-r34
更新日期:2013-04-29 00:00:00
abstract::We used scaled factorial moments to search for intermittency in the log expression ratios (LERs) for thousands of genes spotted on cDNA microarrays (gene chips). Results indicate varying levels of intermittency in gene expression. The observation of intermittency in the data analyzed provides a complimentary handle on...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/gb-2002-3-7-preprint0005
更新日期:2002-05-29 00:00:00
abstract::We have developed a new strategy for de novo prediction of splice junctions in short-read RNA-seq data, suitable for detection of novel splicing events and chimeric transcripts. When tested on mouse RNA-seq data, >31,000 splice events were predicted, of which 88% bridged between two regions separated by journal_title:Genome biology pub_type: 杂志文章 doi:10.1186/gb-2010-11-3-r34 更新日期:2010-01-01 00:00:00
abstract::We propose a novel approach for finding a list of features that are commonly perturbed in two or more experiments, quantifying the evidence of dependence between the experiments by a ratio. We present a Bayesian analysis of this ratio, which leads us to suggest two rules for choosing a cut-off on the ranked list of p ...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/gb-2007-8-4-r54
更新日期:2007-01-01 00:00:00
abstract:BACKGROUND:The nature of the protein molecular clock, the protein-specific rate of amino acid substitutions, is among the central questions of molecular evolution. Protein expression level is the dominant determinant of the clock rate in a number of organisms. It has been suggested that highly expressed proteins evolve...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/gb-2010-11-9-r98
更新日期:2010-01-01 00:00:00
abstract::A report of the recent EMBO Conference 'From Functional Genomics to Systems Biology' held at the EMBL Advanced Training Centre, Heidelberg, Germany, 13-16 November 2010. ...
journal_title:Genome biology
pub_type:
doi:10.1186/gb-2011-12-1-302
更新日期:2011-01-01 00:00:00
abstract::Completion of fungal, plant and human genomes paved the way to the identification of erythrocytic rhesus proteins and their kidney homologs as ammonium transporters. ...
journal_title:Genome biology
pub_type: 杂志文章,评审
doi:10.1186/gb-2001-2-3-reviews1010
更新日期:2001-01-01 00:00:00
abstract:BACKGROUND:The vast number of precise intercellular connections within vertebrate nervous systems is only partly explained by the comparatively few known extracellular guidance cues. Large families of neural orphan receptor proteins have been identified and are likely to contribute to these recognition processes but du...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/gb-2009-10-9-r99
更新日期:2009-01-01 00:00:00
abstract:BACKGROUND:DNA replication plays an important role in mutagenesis, yet little is known about how it interacts with other mutagenic processes. Here, we use somatic mutation signatures-each representing a mutagenic process-derived from 3056 patients spanning 19 cancer types to quantify the strand asymmetry of mutational ...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/s13059-018-1509-y
更新日期:2018-09-10 00:00:00
abstract:BACKGROUND:Pluripotency of embryonic stem (ES) cells is controlled in part by chromatin-modifying factors that regulate histone H3 lysine 4 (H3K4) methylation. However, it remains unclear how H3K4 demethylation contributes to ES cell function. RESULTS:Here, we show that KDM5B, which demethylates lysine 4 of histone H3...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/gb-2014-15-2-r32
更新日期:2014-02-04 00:00:00
abstract::Interpretation of the clinical significance of genomic alterations remains the most severe bottleneck preventing the realization of personalized medicine in cancer. We propose a knowledge commons to facilitate collaborative contributions and open discussion of clinical decision-making based on genomic events in cancer...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/s13059-014-0438-7
更新日期:2014-08-27 00:00:00
abstract:BACKGROUND:Processed copies of genes (retrogenes) are duplicate genes that originated through the reverse-transcription of a host transcript and insertion in the genome. This type of gene duplication, as any other, could be a source of new genes and functions. Using whole genome sequence data for 12 Drosophila species,...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/gb-2007-8-1-r11
更新日期:2007-01-01 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::DNA sequence data are being produced at an ever-increasing rate. The Bowtie sequence-alignment algorithm uses advanced data structures to help data analysis keep pace with data generation. ...
journal_title:Genome biology
pub_type: 评论,杂志文章
doi:10.1186/gb-2009-10-3-212
更新日期:2009-01-01 00:00:00
abstract::Two recent publications have demonstrated how delivering CRISPR nucleases provides a promising solution to the growing problem of bacterial antibiotic resistance. ...
journal_title:Genome biology
pub_type: 评论,杂志文章
doi:10.1186/s13059-014-0516-x
更新日期:2014-11-08 00:00:00
abstract:BACKGROUND:Complete genomic sequences of closely related organisms, such as the chlamydiae, afford the opportunity to assess significant strain differences against a background of many shared characteristics. The chlamydiae are ubiquitous intracellular parasites that are important pathogens of humans and other organism...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/gb-2002-3-9-research0051
更新日期:2002-08-29 00:00:00
abstract:BACKGROUND:Rare coding variants constitute an important class of human genetic variation, but are underrepresented in current databases that are based on small population samples. Recent studies show that variants altering amino acid sequence and protein function are enriched at low variant allele frequency, 2 to 5%, b...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/gb-2011-12-9-r84
更新日期:2011-09-14 00:00:00
abstract::We describe an algorithm, multi-species cMonkey, for the simultaneous biclustering of heterogeneous multiple-species data collections and apply the algorithm to a group of bacteria containing Bacillus subtilis, Bacillus anthracis, and Listeria monocytogenes. The algorithm reveals evolutionary insights into the surpris...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/gb-2010-11-9-r96
更新日期:2010-01-01 00:00:00
abstract::Swine production has been an important part of our lives since the late Mesolithic or early Neolithic periods, and ranks number one in world meat production. Pig production also contributes to high-value-added medical markets in the form of pharmaceuticals, heart valves, and surgical materials. Genetic engineering, in...
journal_title:Genome biology
pub_type: 杂志文章,评审
doi:10.1186/gb-2007-8-s1-s13
更新日期:2007-01-01 00:00:00
abstract:BACKGROUND:Circular RNAs (circRNAs) are implicated in various biological processes. As a layer of the gene regulatory network, circRNA expression is also an intermediate phenotype bridging genetic variation and phenotypic changes. Thus, analyzing circRNA expression variation will shed light on molecular fundamentals of...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/s13059-019-1701-8
更新日期:2019-05-20 00:00:00
abstract::A report of the First Golden Helix Symposium 'Copy Number Variation (CNV) and Genomic Alterations in Health and Disease', Athens, Greece, 28-29 November 2008. ...
journal_title:Genome biology
pub_type:
doi:10.1186/gb-2009-10-1-301
更新日期:2009-01-01 00:00:00
abstract::Piwi-interacting RNAs (piRNAs) originate from genomic regions dubbed piRNA clusters. How cluster transcripts are selected for processing into piRNAs is not understood. We discuss evidence for the involvement of chromatin structure and maternally inherited piRNAs in determining their fate. ...
journal_title:Genome biology
pub_type: 杂志文章,评审
doi:10.1186/gb4154
更新日期:2014-01-27 00:00:00
abstract::An elegant, genome-wide approach to define the precise DNA sequences bound by transcription factors has been developed by Rhee and Pugh. ...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/gb-2012-13-1-139
更新日期:2012-01-27 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