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Article
Open AccessDiseaseNet: a transfer learning approach to noncommunicable disease classification
As noncommunicable diseases (NCDs) pose a significant global health burden, identifying effective diagnostic and predictive markers for these diseases is of paramount importance. Epigenetic modifications, such...
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Article
Open AccessPOSMM: an efficient alignment-free metagenomic profiler that complements alignment-based profiling
We present here POSMM (pronounced ‘Possum’), Python-Optimized Standard Markov Model classifier, which is a new incarnation of the Markov model approach to metagenomic sequence analysis. Built on the top of a r...
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Article
Open AccessMolecular signatures in the progression of COVID-19 severity
SARS-CoV-2 is the causative agent of COVID-19 that has infected over 642 million and killed over 6.6 million people around the globe. Underlying a wide range of clinical manifestations of this disease, from mo...
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Article
Analysis of multipartite bacterial genomes using alignment free and alignment-based pipelines
Since the discovery of second chromosome in Rhodobacter sphaeroides 2.4.1 in 1989, multipartite genomes have been reported in over three hundred bacterial species under nine different phyla. This has shattered th...
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Article
Open AccessCancerNet: a unified deep learning network for pan-cancer diagnostics
Despite remarkable advances in cancer research, cancer remains one of the leading causes of death worldwide. Early detection of cancer and localization of the tissue of its origin are key to effective treatmen...
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Article
Open AccessInhaled diesel exhaust particles result in microbiome-related systemic inflammation and altered cardiovascular disease biomarkers in C57Bl/6 male mice
The gut microbiota plays a vital role in host homeostasis and is associated with inflammation and cardiovascular disease (CVD) risk. Exposure to particulate matter (PM) is a known mediator of inflammation and ...
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Protocol
A Protocol for Phylogenetic Reconstruction
The similarity of biological functions and molecular mechanisms in living organisms suggests their common origin. The inference of evolutionary relationships among the extant organisms is primarily based on st...
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Protocol
A Protocol for Prion Discovery in Plants
Recently a likely prion was found in the proteome of Arabidopsis thaliana based on inclusive compositional similarity to known yeast prion-like domains (PrLDs) and gene ontology analysis. A total of 474 proteins ...
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Protocol
A Protocol for Horizontally Acquired Metabolic Gene Detection in Algae
Horizontal gene transfer (HGT) or lateral gene transfer (LGT), the exchange of genetic materials among organisms by means of other than parent-to-offspring (vertical) inheritance, plays a major role in prokary...
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Protocol
RNA-Seq Data Analysis Pipeline for Plants: Transcriptome Assembly, Alignment, and Differential Expression Analysis
In this chapter, we describe methods for analyzing RNA-Seq data, presented as a flow along a pipeline beginning with raw data from a sequencer and ending with an output of differentially expressed genes and th...
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Article
Discovery of mosaic genomic islands in Pseudomonas spp.
Genomic islands, defined as large clusters of genes mobilized through horizontal gene transfer, have a profound impact on evolution of prokaryotes. Recently, we developed a new program, IslandCafe, for identif...
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Article
Age-group-targeted testing for COVID-19 as a new prevention strategy
Robust testing and tracing are key to fighting the menace of coronavirus disease 2019 (COVID-19). This outbreak has progressed with tremendous impact on human life, society and economy. In this paper, we propo...
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Article
Prions: Roles in Development and Adaptive Evolution
Prions are often considered as anomalous proteins associated primarily with disease rather than as a fundamental source of diversity within biological proteomes. Whereas this longstanding viewpoint has its gen...
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Article
Tissue-specific differences in metabolites and transcripts contribute to the heterogeneity of ricinoleic acid accumulation in Ricinus communis L. (castor) seeds
Castor (Ricinus communis L.) seeds are valued for their production of oils which can comprise up to 90% hydroxy-fatty acids (ricinoleic acid). Castor oil contains mono-, di- and tri- ricinoleic acid containing tr...
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Article
Open AccessPhylogenetic analysis of the CDGSH iron-sulfur binding domain reveals its ancient origin
The iron-sulfur (2Fe-2S) binding motif CDGSH appears in many important plant and animal proteins that regulate iron and reactive oxygen metabolism. In human it is found in CISD1-3 proteins involved in diabetes...
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Article
Open AccessPhylogenetic analysis of eukaryotic NEET proteins uncovers a link between a key gene duplication event and the evolution of vertebrates
NEET proteins belong to a unique family of iron-sulfur proteins in which the 2Fe-2S cluster is coordinated by a CDGSH domain that is followed by the “NEET” motif. They are involved in the regulation of iron an...
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Article
Deciphering evolutionary strata on plant sex chromosomes and fungal mating-type chromosomes through compositional segmentation
Sex chromosomes have evolved from a pair of homologous autosomes which differentiated into sex determination systems, such as XY or ZW system, as a consequence of successive recombination suppression between t...
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Article
Open AccessRapid identification of causative insertions underlying Medicago truncatula Tnt1 mutants defective in symbiotic nitrogen fixation from a forward genetic screen by whole genome sequencing
In the model legume Medicago truncatula, the near saturation genome-wide Tnt1 insertion mutant population in ecotype R108 is a valuable tool in functional genomics studies. Forward genetic screens have identified...
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Chapter
Bioinformatics Approaches to Deciphering Alien Gene Transfer: A Comprehensive Analysis
A large number of bioinformatics methods have been developed in recent years for detecting gene transfers between distantly related or unrelated organisms. These have been mainly classified as parametric and p...
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Protocol
Detecting Laterally Transferred Genes
Methods for identifying alien genes in genomes fall into two general classes. Phylogenetic methods examine the distribution of a gene’s homologues among genomes to find those with relationships not consistent ...
