Academic Articles & Research Papers

Calmodulin-binding transcription activator (CAMTA) genes family: Genome-wide survey and phylogenetic analysis in flax (Linum usitatissimum).

Flax (Linum usitatissimum) is a member of family linaceae with annual growth habit. It is included among those crops which were domesticated very early and has been used in development related studies as a model plant. In plants, Calmodulin...

Leveraging human-trained neural networks for cross-species chromatin regulation annotations.

A chromosome-level genome assembly and annotation of the marbled rockfish (Sebastiscus marmoratus).

Whole genome sequencing, assembly, and functional annotation of Hyphopichia burtonii Y951 isolated from Vitis vinifera L. cv Cabernet Sauvignon grape must.

Thirteen quick tips for bacteriophage genome annotation.

LncRNA-Top: Controlled deep learning approaches for lncRNA gene regulatory relationship annotations across different platforms

Summary: By soaking microRNAs (miRNAs), long non-coding RNAs (lncRNAs) have the potential to regulate gene expression. Few methods have been created based on this mechanism to anticipate the lncRNA-gene relationship prediction. Hence, we pr...

Functional annotation of the human retinal pigment epithelium transcriptome

Abstract Background To determine level, variability and functional annotation of gene expression of the human retinal pigment epithelium (RPE), the key tissue involved in retinal diseases like age-related macular degeneration and retinitis ...

Brain transcriptome of the violet-eared waxbill Uraeginthus granatina and recent evolution in the songbird genome

Songbirds are important models for the study of social behaviour and communication. To complement the recent genome sequencing of the domesticated zebra finch, we sequenced the brain transcriptome of a closely related songbird species, the ...

Theoretical Aspects of Industrial Design

A companion to Geometric aspects . . . (see preceding entry). The 10 papers consider traditional applied mathematics emphasizing problems such as control and optimization in industrial design. No index. Acidic paper. Annotation copyright Bo...

ProtoMix: Unified Prototype Learning for Semantic Change Detection in Remote Sensing

As an emerging topic, semantic change detection (SCD) in remote sensing aims to both identify the locations of changes before and after events and determine the land cover (LC) classes of changed regions. While deep learning has demonstrate...

Ontologies as integrative tools for plant science

PREMISE OF THE STUDY: Bio-ontologies are essential tools for accessing and analyzing the rapidly growing pool of plant genomic and phenomic data. Ontologies provide structured vocabularies to support consistent aggregation of data and a sem...

Improved chromosomal-level genome assembly and re-annotation of leopard coral grouper

Abstract Plectropomus leopardus, as known as leopard coral grouper, is a valuable marine fish that has gradually been bred artificially. To promote future conservation, molecular breeding, and comparative studies, we generated an improved h...

SNPPhenA: a corpus for extracting ranked associations of single-nucleotide polymorphisms and phenotypes from literature

Abstract Background Single Nucleotide Polymorphisms (SNPs) are among the most important types of genetic variations influencing common diseases and phenotypes. Recently, some corpora and methods have been developed with the purpose of extra...

G-Aligner: a graph-based feature alignment method for untargeted LC–MS-based metabolomics

Abstract Background Liquid chromatography–mass spectrometry is widely used in untargeted metabolomics for composition profiling. In multi-run analysis scenarios, features of each run are aligned into consensus features by feature alignment ...

A method for automatically extracting infectious disease-related primers and probes from the literature

Abstract Background Primer and probe sequences are the main components of nucleic acid-based detection systems. Biologists use primers and probes for different tasks, some related to the diagnosis and prescription of infectious diseases. Th...

plsMD: a plasmid reconstruction tool from short-read assemblies

Abstract Background While whole genome sequencing has become a cornerstone of antimicrobial resistance surveillance, the reconstruction of plasmid sequences from short-read data remains a challenge due to repetitive sequences and assembly f...

Identifying elemental genomic track types and representing them uniformly

Abstract Background With the recent advances and availability of various high-throughput sequencing technologies, data on many molecular aspects, such as gene regulation, chromatin dynamics, and the three-dimensional organization of DNA, ar...

Ggtree: A serialized data object for visualization of a phylogenetic tree and annotation data

Abstract While phylogenetic trees and associated data have been getting easier to generate, it has been difficult to reuse, combine, and synthesize the information they provided, because published trees are often only available as image fil...

Genetic signatures of exceptional longevity: a comprehensive analysis of coding region single nucleotide polymorphisms (SNPs) in centenarians and supercentenarians

Abstract Aging, a complex biological process, entails sequential changes in organisms that elevate the risk of frailty, disease, and mortality, affecting individuals at the level of cellular, organ, and organism. This process is influenced ...

New trends in natural language processing: statistical natural language processing.

The field of natural language processing (NLP) has seen a dramatic shift in both research direction and methodology in the past several years. In the past, most work in computational linguistics tended to focus on purely symbolic methods. R...