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Fast, parallel, and cache-friendly suffix array construction
PurposeString indexes such as the suffix array ( sa ) and the closely related longest common prefix ( lcp ) array are fundamental objects in...
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Pangenomic genoty** with the marker array
We present a new method and software tool called
rowbowt that applies a pangenome index to the problem of inferring genotypes from short-read...
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CRISPR-array-mediated imaging of non-repetitive and multiplex genomic loci in living cells
Dynamic imaging of genomic loci is key for understanding gene regulation, but methods for imaging genomes, in particular non-repetitive DNAs, are...
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Rapid, tunable, and multiplexed detection of RNA using convective array PCR
Detection of RNA targets is typically achieved through RT-qPCR or RNAseq. RT-qPCR is rapid but limited in number and complexity of targets detected,...
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An optrode array for spatiotemporally-precise large-scale optogenetic stimulation of deep cortical layers in non-human primates
Optogenetics has transformed studies of neural circuit function, but remains challenging to apply to non-human primates (NHPs). A major challenge is...
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Griddient: a microfluidic array to generate reconfigurable gradients on-demand for spatial biology applications
Biological tissues are highly organized structures where spatial-temporal gradients (e.g., nutrients, hypoxia, cytokines) modulate multiple...
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Correlative montage parallel array cryo-tomography for in situ structural cell biology
Imaging large fields of view while preserving high-resolution structural information remains a challenge in low-dose cryo-electron tomography. Here...
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Effect of dietary protein, vitamin E, and vitamin C levels on the growth and gonad development of hybrid male abalone (Haliotis fulgens ♂ × H. discus hannai ♀) by the orthogonal array design
A natural feed of fresh seaweed and sixteen diets designed by L16 (4 3 ) orthogonal array were formulated to contain different levels of protein (200,...
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Determining effective acoustic array design for monitoring presence of white sharks Carcharodon carcharias in nearshore habitats
Inferences regarding animal presence from passive acoustic receiver arrays are driven by the spatial configuration of receivers. Large, dense arrays...
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Environmental factors influencing detection efficiency of an acoustic telemetry array and consequences for data interpretation
BackgroundAcoustic telemetry is a commonly used technology to monitor animal occupancy and infer movement in aquatic environments. The information...
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Assessment of genoty** array performance for genome-wide association studies and imputation in African cattle
BackgroundIn cattle, genome-wide association studies (GWAS) have largely focused on European or Asian breeds, using genoty** arrays that were...
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Application of Array-Based Oligonucleotides for Synthesis of Genetic Designs
AbstractThe application of array-based oligonucleotides in biological studies is described. These oligonucleotides are mainly used to design large...
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Dissection of the practical soybean breeding pipeline by develo** ZDX1, a high-throughput functional array
Key messageWe developed the ZDX1 high-throughput functional soybean array for high accuracy evaluation and selection of both parents and progeny,...
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GAWMerge expands GWAS sample size and diversity by combining array-based genoty** and whole-genome sequencing
Genome-wide association studies (GWAS) have made impactful discoveries for complex diseases, often by amassing very large sample sizes. Yet, GWAS of...
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Who’s afraid of the X? Incorporating the X and Y chromosomes into the analysis of DNA methylation array data
BackgroundMany human disease phenotypes manifest differently by sex, making the development of methods for incorporating X and Y-chromosome data into...
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A Wheat 660 K SNP array-based high-density genetic map facilitates QTL map** of flag leaf-related traits in wheat
Key messageA high-density genetic map containing 122,620 SNP markers was constructed, which facilitated the identification of eight major flag...
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Discovery of NSD2 non-histone substrates and design of a super-substrate
The human protein lysine methyltransferase NSD2 catalyzes dimethylation at H3K36. It has very important roles in development and disease but many...
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Minimally sufficient experimental design using identifiability analysis
Mathematical models are increasingly being developed and calibrated in tandem with data collection, empowering scientists to intervene in real time...
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Automatic design of gene regulatory mechanisms for spatial pattern formation
Gene regulatory mechanisms (GRMs) control the formation of spatial and temporal expression patterns that can serve as regulatory signals for the...
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Opportunities and challenges in design and optimization of protein function
The field of protein design has made remarkable progress over the past decade. Historically, the low reliability of purely structure-based design...
