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Article
Open AccessA longer time to relapse is associated with a larger increase in differences between paired primary and recurrent IDH wild-type glioblastomas at both the transcriptomic and genomic levels
Glioblastoma (GBM) is the most common malignant brain tumor in adults, which remains incurable and often recurs rapidly after initial therapy. While large efforts have been dedicated to uncover genomic/transcr...
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Article
Large-scale benchmarking of circRNA detection tools reveals large differences in sensitivity but not in precision
The detection of circular RNA molecules (circRNAs) is typically based on short-read RNA sequencing data processed using computational tools. Numerous such tools have been developed, but a systematic comparison...
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Article
Open AccessTrans-genetic effects of circular RNA expression quantitative trait loci and potential causal mechanisms in autism
Genetic risk variants and transcriptional expression changes in autism spectrum disorder (ASD) were widely investigated, but their causal relationship remains largely unknown. Circular RNAs (circRNAs) are abun...
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Article
Open AccessCircMiMi: a stand-alone software for constructing circular RNA-microRNA-mRNA interactions across species
Circular RNAs (circRNAs) are a class of non-coding RNAs formed by pre-mRNA back-splicing, which are widely expressed in animal/plant cells and often play an important role in regulating microRNA (miRNA) activi...
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Article
Open AccessTranscriptomopathies of pre- and post-symptomatic frontotemporal dementia-like mice with TDP-43 depletion in forebrain neurons
TAR DNA-binding protein (TDP-43) is a ubiquitously expressed nuclear protein, which participates in a number of cellular processes and has been identified as the major pathological factor in amyotrophic lateral s...
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Article
Open AccessNCLcomparator: systematically post-screening non-co-linear transcripts (circular, trans-spliced, or fusion RNAs) identified from various detectors
Non-co-linear (NCL) transcripts consist of exonic sequences that are topologically inconsistent with the reference genome in an intragenic fashion (circular or intragenic trans-spliced RNAs) or in an intergenic f...
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Article
Open AccessAssessment of imprinting- and genetic variation-dependent monoallelic expression using reciprocal allele descendants between human family trios
Genomic imprinting is an important epigenetic process that silences one of the parentally-inherited alleles of a gene and thereby exhibits allelic-specific expression (ASE). Detection of human imprinting event...
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Article
Open AccessPurifying selection shapes the coincident SNP distribution of primate coding sequences
Genome-wide analysis has observed an excess of coincident single nucleotide polymorphisms (coSNPs) at human-chimpanzee orthologous positions and suggested that this is due to cryptic variation in the mutation ...
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Article
Open AccessComparative genomics of grass EST libraries reveals previously uncharacterized splicing events in crop plants
Crop plants such as rice, maize and sorghum play economically-important roles as main sources of food, fuel, and animal feed. However, current genome annotations of crop plants still suffer false-positive pred...
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Article
Open AccessThe evolution of the coding exome of the Arabidopsisspecies - the influences of DNA methylation, relative exon position, and exon length
The evolution of the coding exome is a major driving force of functional divergence both between species and between protein isoforms. Exons at different positions in the transcript or in different transcript ...
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Article
Open AccessLDGIdb: a database of gene interactions inferred from long-range strong linkage disequilibrium between pairs of SNPs
Complex human diseases may be associated with many gene interactions. Gene interactions take several different forms and it is difficult to identify all of the interactions that are potentially associated with...
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Article
Open AccessCAPIH: A Web interface for comparative analyses and visualization of host-HIV protein-protein interactions
The Human Immunodeficiency Virus type one (HIV-1) is the major causing pathogen of the Acquired Immune Deficiency Syndrome (AIDS). A large number of HIV-1-related studies are based on three non-human model ani...
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Article
Open AccessDifferent alternative splicing patterns are subject to opposite selection pressure for protein reading frame preservation
Alternative splicing (AS) has been regarded capable of altering selection pressure on protein subsequences. Particularly, the frequency of reading frame preservation (FRFP), as a measure of selection pressure,...
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Article
Open AccessThe effects of multiple features of alternatively spliced exons on the K A /K S ratio test
The evolution of alternatively spliced exons (ASEs) is of primary interest because these exons are suggested to be a major source of functional diversity of proteins. Many exon features have been suggested to ...
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Article
Open AccessIdentification and evolutionary analysis of novel exons and alternative splicing events using cross-species EST-to-genome comparisons in human, mouse and rat
Alternative splicing (AS) is important for evolution and major biological functions in complex organisms. However, the extent of AS in mammals other than human and mouse is largely unknown, making it difficult...
