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Relevance of Escherichia coli in Fresh Produce Safety
Fresh produceFresh produce demand and consumption have increased due to their nutritional value in the human diet. However, produce has been linked...
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Integrating Genomics and Phenomics Tools to Dissect Climate Resilience Traits in Small Millets
Deployment of advanced tools for trait improvement is imperative to sustain and improve the productivity of food crops. However, over-dependence on...
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Predicting gene expression state and prioritizing putative enhancers using 5hmC signal
BackgroundLike its parent base 5-methylcytosine (5mC), 5-hydroxymethylcytosine (5hmC) is a direct epigenetic modification of cytosines in the context...
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Using k-mer embeddings learned from a Skip-gram based neural network for building a cross-species DNA N6-methyladenine site prediction model
Key messageThis study used k-mer embeddings as effective feature to identify DNA N6-Methyladenine sites in plant genomes and obtained improved...
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Epigenomic insights into common human disease pathology
The epigenome—the chemical modifications and chromatin-related packaging of the genome—enables the same genetic template to be activated or repressed...
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airpg: automatically accessing the inverted repeats of archived plastid genomes
BackgroundIn most flowering plants, the plastid genome exhibits a quadripartite genome structure, comprising a large and a small single copy as well...
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Recovering genotypes and phenotypes using allele-specific genes
With the recent increase in RNA sequencing efforts using large cohorts of individuals, surveying allele-specific gene expression is becoming...
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ChIP-Seq Protocol for In Vitro Cell Differentiation Systems
In vitro differentiation systems provide a flexible platform for understanding complex developmental processes. Here, we provide a comprehensive...
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Functional annotation of the cattle genome through systematic discovery and characterization of chromatin states and butyrate-induced variations
BackgroundThe functional annotation of genomes, including chromatin accessibility and modifications, is important for understanding and effectively...
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In silico analysis and expression profiling revealed Rlm1′ blackleg disease-resistant genes in Chromosome 6 of Brassica oleracea
Blackleg disease caused by Leptosphaeria maculans affects oilseeds and vegetables species of the Brassicaceae family. Several resistant genes have...
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The Exploitation of Recombinant DNA Technology to Induce Biologics Directed to Biocontrol
Plant production losses caused by insects, pests and pathogens are major problems in agricultural production. Over-use of pesticides impacts not only...
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Leading Edge Techniques in the Quest for Characterizing Rare Hematopoietic Stem Cells
Purpose of ReviewHematopoietic stem cells (HSCs) occupy the summit of the intricate hematopoiesis hierarchy, constituting a mere 0.01% of the adult...
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The Population Genetics and Evolutionary Potential of Diatoms
Since the Victorian era, people have remarked on the diversity and abundance of diatoms in marine waters. Diatoms are found across the sunlit ocean,...
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The buzz about honey-based biosurveys
Approximately 1.8 million metric tonnes of honey are produced globally every year. The key source behind this output, the honey bee ( Apis mellifera) ,...
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Dahlia
Dahlias (Dahlia variabilis) are popular Asteraceae ornamental plants cultivated in many countries due to huge variation in flower shapes, sizes and...
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Whole-Genome Identification and Characterization of Bacterial Insertion Sequences Using Bioinformatic Tools
Insertion sequences are small mobile regions of DNA (transposable elements) found primarily in prokaryotes. The identification of insertion sequences...
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How Cells Work: The Basics
Deoxyribonucleic acid—DNA—is perhaps the most famous molecule in the world. If you close your eyes, you can probably picture its iconic double-helix...
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Genomic diversity and biosynthetic capabilities of sponge-associated chlamydiae
Sponge microbiomes contribute to host health, nutrition, and defense through the production of secondary metabolites. Chlamydiae , a phylum of...
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Functions of HP1 proteins in transcriptional regulation
In eukaryotes, DNA is packaged into chromatin, which presents significant barriers to transcription. Non-histone chromatin proteins such as the...
