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Article
Open AccessGiotto: a toolbox for integrative analysis and visualization of spatial expression data
Spatial transcriptomic and proteomic technologies have provided new opportunities to investigate cells in their native microenvironment. Here we present Giotto, a comprehensive and open-source toolbox for spat...
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Article
Open AccessFlsnRNA-seq: protoplasting-free full-length single-nucleus RNA profiling in plants
The broad application of single-cell RNA profiling in plants has been hindered by the prerequisite of protoplasting that requires digesting the cell walls from different types of plant tissues. Here, we presen...
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Article
Open AccessClonal tracing reveals diverse patterns of response to immune checkpoint blockade
Immune checkpoint blockade (ICB) therapy has improved patient survival in a variety of cancers, but only a minority of cancer patients respond. Multiple studies have sought to identify general biomarkers of IC...
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Article
Open AccessAn integrated peach genome structural variation map uncovers genes associated with fruit traits
Genome structural variations (SVs) have been associated with key traits in a wide range of agronomically important species; however, SV profiles of peach and their functional impacts remain largely unexplored.
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Article
Correction to: Complex patterns of genetic and morphological differentiation in the Smallmouth Bass subspecies (Micropterus dolomieu dolomieu and M. d. velox) of the Central Interior Highlands
In the original publication of the article, Table 2 was published incorrectly. The correct Table 2 is given in this Correction.
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Article
Open AccesssgBE: a structure-guided design of sgRNA architecture specifies base editing window and enables simultaneous conversion of cytosine and adenosine
We present a base editing system, in which base editors are attached to different sites of sgRNA scaffold (sgBE). Each independent sgBE has its own specific editing pattern for a given target site. Among teste...
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Article
Open AccessIntegrative analyses of single-cell transcriptome and regulome using MAESTRO
We present Model-based AnalysEs of Transcriptome and RegulOme (MAESTRO), a comprehensive open-source computational workflow (http://github.com/liulab-dfci/MAESTRO)...
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Open AccessRepeat-induced point mutation in Neurospora crassa causes the highest known mutation rate and mutational burden of any cellular life
Repeat-induced point (RIP) mutation in Neurospora crassa degrades transposable elements by targeting repeats with C→T mutations. Whether RIP affects core genomic sequence in important ways is unknown.
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Open AccessSWISS: multiplexed orthogonal genome editing in plants with a Cas9 nickase and engineered CRISPR RNA scaffolds
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 deamina...
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Open AccessModulating chromatin accessibility by transactivation and targeting proximal dsgRNAs enhances Cas9 editing efficiency in vivo
The CRISPR/Cas9 system is unable to edit all targetable genomic sites with full efficiency in vivo. We show that Cas9-mediated editing is more efficient in open chromatin regions than in closed chromatin regio...
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Article
Open AccessWhole genomes and transcriptomes reveal adaptation and domestication of pistachio
Pistachio (Pistacia vera), one of the most important commercial nut crops worldwide, is highly adaptable to abiotic stresses and is tolerant to drought and salt stresses.
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Article
Open AccessDNA methylation footprints during soybean domestication and improvement
In addition to genetic variation, epigenetic variation plays an important role in determining various biological processes. The importance of natural genetic variation to crop domestication and improvement has...
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Article
Open AccessAdaptation of Arabidopsis thaliana to the Yangtze River basin
Organisms need to adapt to keep pace with a changing environment. Examining recent range expansion aids our understanding of how organisms evolve to overcome environmental constraints. However, how organisms a...
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Article
Open AccessLong-term balancing selection contributes to adaptation in Arabidopsis and its relatives
In contrast to positive selection, which reduces genetic variation by fixing beneficial alleles, balancing selection maintains genetic variation within a population or species and plays crucial roles in adapta...
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Open AccessPerfectly matched 20-nucleotide guide RNA sequences enable robust genome editing using high-fidelity SpCas9 nucleases
High-fidelity SpCas9 variants (eSpCas9 and SpCas9-HF1) have been engineered to reduce off-target effects. We found that changes in guide RNA length induced significant reductions in the editing activities of S...
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Article
Open AccessData normalization considerations for digital tumor dissection
In a recently published article in Genome Biology, Li and colleagues introduced TIMER, a gene expression deconvolution approach for studying tumor-infiltrating leukocytes (TILs) in 23 cancer types profiled by The...
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Article
Open AccessChallenges and emerging directions in single-cell analysis
Single-cell analysis is a rapidly evolving approach to characterize genome-scale molecular information at the individual cell level. Development of single-cell technologies and computational methods has enable...
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Article
Open AccessGenomic legacy of the African cheetah, Acinonyx jubatus
Patterns of genetic and genomic variance are informative in inferring population history for human, model species and endangered populations.
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Article
Open AccessNew genes drive the evolution of gene interaction networks in the human and mouse genomes
The origin of new genes with novel functions creates genetic and phenotypic diversity in organisms. To acquire functional roles, new genes must integrate into ancestral gene-gene interaction (GGI) networks. Th...
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Article
Open AccessGenome-wide analysis of light-regulated alternative splicing mediated by photoreceptors in Physcomitrella patens
Light is one of the most important factors regulating plant growth and development. Light-sensing photoreceptors tightly regulate gene expression to control photomorphogenic responses. Although many levels of ...