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Telomere-to-telomere Citrullus super-pangenome provides direction for watermelon breeding
To decipher the genetic diversity within the cucurbit genus Citrullus , we generated telomere-to-telomere (T2T) assemblies of 27 distinct genotypes,...
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Navigating bottlenecks and trade-offs in genomic data analysis
Genome sequencing and analysis allow researchers to decode the functional information hidden in DNA sequences as well as to study cell to cell...
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Agricultural Bioinformatics
Agricultural bioinformatics can play a very important role in improving crop productivity. The important areas of agricultural bioinformatics are...
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High throughput sequencing from Angolan citrus accessions discloses the presence of emerging CTV strains
BackgroundCitrus industry is worldwide dramatically affected by outbreaks of Citrus tristeza virus (CTV). Controls should be applied to nurseries,...
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Epigenetic tumor heterogeneity in the era of single-cell profiling with nanopore sequencing
Nanopore sequencing has brought the technology to the next generation in the science of sequencing. This is achieved through research advancing on:...
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Mobile element insertions in rare diseases: a comparative benchmark and reanalysis of 60,000 exome samples
Mobile element insertions (MEIs) are a known cause of genetic disease but have been underexplored due to technical limitations of genetic testing...
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Deciphering the virome of Chunkung (Cnidium officinale) showing dwarfism-like symptoms via a high-throughput sequencing analysis
BackgroundViruses have notable effects on agroecosystems, wherein they can adversely affect plant health and cause problems (e.g., increased...
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Microbiome Data Analysis and Interpretation: Correlation Inference and Dynamic Pattern Discovery
Microbial communities are everywhere within our bodies and in the environments (Byrd et al. n.d.), which play a key role in human health and all...
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The endohyphal microbiome: current progress and challenges for scaling down integrative multi-omic microbiome research
As microbiome research has progressed, it has become clear that most, if not all, eukaryotic organisms are hosts to microbiomes composed of...
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Transcriptomics-proteomics Integration reveals alternative polyadenylation driving inflammation-related protein translation in patients with diabetic nephropathy
BackgroundDiabetic nephropathy (DN) is a complex disease involving the upregulation of many inflammation-related proteins. Alternative...
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The generative grammar of the brain: a critique of internally generated representations
The past decade of progress in neurobiology has uncovered important organizational principles for network preconfiguration and neuronal selection...
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Computational Pipeline for the Detection of Plant RNA Viruses Using High-Throughput Sequencing
In this chapter, we describe a computational pipeline for the in silico detection of plant viruses by high-throughput sequencing (HTS) from total RNA...
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First Insights into the Guar (Cyamopsis tetragonoloba (L.) Taub.) Genome of the ‘Vavilovskij 130’ Accession, Using Second and Third-Generation Sequencing Technologies
AbstractGuar ( Cyamopsis tetragonoloba (L.) Taub.) is becoming a popular industrial crop in response to industry demand for the guar gum extracted...
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A survey of the adaptive immune genes of the polka-dot batfish Ogcocephalus cubifrons
BackgroundThe anglerfish, belonging to the teleost order Lophiiformes , are a diverse and species-rich group of fish that are known to exhibit a...
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RNA-seq Fusion Detection in Clinical Oncology
Gene fusions play a prominent role in the oncogenesis of many cancers and have been extensively targeted as biomarkers for diagnostic, prognostic,...
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Super-pangenome analyses highlight genomic diversity and structural variation across wild and cultivated tomato species
Effective utilization of wild relatives is key to overcoming challenges in genetic improvement of cultivated tomato, which has a narrow genetic...
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Chromatin remodeler Activity-Dependent Neuroprotective Protein (ADNP) contributes to syndromic autism
BackgroundIndividuals affected with autism often suffer additional co-morbidities such as intellectual disability. The genes contributing to autism...
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Software for Drug Discovery and Protein Engineering: A Comparison Between the Alternatives and Recent Advancements in Computational Biology
“Omic” technologies (such as genomics, transcriptomics, proteomics, and metabolomics) generate huge databases that demand computational approaches to...
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Comparing genomes recovered from time-series metagenomes using long- and short-read sequencing technologies
BackgroundOver the past years, sequencing technologies have expanded our ability to examine novel microbial metabolisms and diversity previously...
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Rolling down that mountain: microgeographical adaptive divergence during a fast population expansion along a steep environmental gradient in European beech
Forest tree populations harbour high genetic diversity thanks to large effective population sizes and strong gene flow, allowing them to diversify...
