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ggcoverage: an R package to visualize and annotate genome coverage for various NGS data
BackgroundVisualizing genome coverage is of vital importance to inspect and interpret various next-generation sequencing (NGS) data. Besides genome...
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Using Gene Ontology to Annotate and Prioritize Microarray Data
The results of high-throughput experiments consist of numerous candidate genes, proteins, or other molecules potentially associated with diseases. A...
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ChromGene: gene-based modeling of epigenomic data
Various computational approaches have been developed to annotate epigenomes on a per-position basis by modeling combinatorial and spatial patterns...
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Using deep learning to annotate the protein universe
Understanding the relationship between amino acid sequence and protein function is a long-standing challenge with far-reaching scientific and...
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FINDER: an automated software package to annotate eukaryotic genes from RNA-Seq data and associated protein sequences
BackgroundGene annotation in eukaryotes is a non-trivial task that requires meticulous analysis of accumulated transcript data. Challenges include...
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Bioinformatics in Gene and Genome Analysis
Gene and genome analysis play important roles in molecular biology research and individualized medicine. Thanks to the development of sequencing...
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A Multi-Label Learning Framework for Predicting Chemical Classes and Biological Activities of Natural Products from Biosynthetic Gene Clusters
Natural products (NP) or secondary metabolites, as a class of small chemical molecules that are naturally synthesized by chromosomally clustered...
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Interpreting Gene Ontology Annotations Derived from Sequence Homology Methods
The Gene Ontology (GO) project describes the functions of the gene products of organisms from all kingdoms of life in a standardized way, enabling...
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annoFuse: an R Package to annotate, prioritize, and interactively explore putative oncogenic RNA fusions
BackgroundGene fusion events are significant sources of somatic variation across adult and pediatric cancers and are some of the most...
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PCR-Based Assembly of Gene Sequences by Thermodynamically Balanced Inside-Out (TBIO) Gene Synthesis
The ability to enzymatically assemble DNA oligonucleotides into longer DNA duplexes in a process known as gene synthesis has wide-ranging...
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The Theory of Gene Family Histories
Most genes are part of larger families of evolutionary-related genes. The history of gene families typically involves duplications and losses of...
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PEATmoss: A Gene Expression Atlas for Bryophytes
PEATmoss is an interactive gene expression atlas for bryophytes, which originally unified Physcomitrium patens RNA-seq and microarray expression data...
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Finding Gene Associations by Text Mining and Annotating it with Gene Ontology
Digitalization of the research articles and their maintenance in a database was the first stage toward the development of biomedical research. With...
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Ocean to Tree: Leveraging Single-Molecule RNA-Seq to Repair Genome Gene Models and Improve Phylogenomic Analysis of Gene and Species Evolution
Understanding gene evolution across genomes and organisms, including ctenophores, can provide unexpected biological insights. It enables powerful...
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Gene Expression in Medicinal Plants in Stress Conditions
Medicinal plants have been in use for hundreds of years for the betterment of mankind against a plethora of ailments in different parts of the world....
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Protein-Coding Gene Families in Prokaryote Genome Comparisons
The identification of orthologous genes is relevant for comparative genomics, phylogenetic analysis, and functional annotation. There are many...
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Map** the common gene networks that underlie related diseases
A longstanding goal of biomedicine is to understand how alterations in molecular and cellular networks give rise to the spectrum of human diseases....
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Crop-GPA: an integrated platform of crop gene-phenotype associations
With the increasing availability of large-scale biology data in crop plants, there is an urgent demand for a versatile platform that fully mines and...
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Gene Ontology Meta Annotator for Plants (GOMAP)
Annotating gene structures and functions to genome assemblies is necessary to make assembly resources useful for biological inference. Gene Ontology...
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AnnoLnc: A One-Stop Portal to Systematically Annotate Novel Human Long Noncoding RNAs
While more than a hundred thousand long noncoding RNAs (lncRNAs) have been identified in human genome, their biological functions and regulation are...