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Horizontal Gene Transfer (HGT) refers to the sharing of genetic materials between distant species that are not in a parent-offspring relationship. The HGT insertion sites are important to understand the HGT me...
Presently, there is no comprehensive analysis of the transcription regulation network in hematopoiesis. Comparison of networks arising from gene co-expression across species can facilitate an understanding of ...
Single-cell sequencing enables us to better understand genetic diseases, such as cancer or autoimmune disorders, which are often affected by changes in rare cells. Currently, no existing software is aimed at i...
Long-read RNA-Seq techniques can generate reads that encompass a large proportion or the entire mRNA/cDNA molecules, so they are expected to address inherited limitations of short-read RNA-Seq techniques that ...
Understanding the molecular mechanisms of platelet activation and aggregation is of high interest for basic and clinical hemostasis and thrombosis research. The central platelet protein interaction network is ...
Third-generation single molecule sequencing technologies can sequence long reads, which is advancing the frontiers of genomics research. However, their high error rates prohibit accurate and efficient downstre...
Microbe-microbe and host-microbe interactions in a microbiome play a vital role in both health and disease. However, the structure of the microbial community and the colonization patterns are highly complex to...
Next-generation sequencing (NGS) enables unbiased detection of pathogens by mapping the sequencing reads of a patient sample to the known reference sequence of bacteria and viruses. However, for a new pathogen...
Analysis of heterogeneous populations such as viral quasispecies is one of the most challenging bioinformatics problems. Although machine learning models are becoming to be widely employed for analysis of sequ...
An amendment to this paper has been published and can be accessed via the original article.
Current peak callers for identifying RNA-binding protein (RBP) binding sites from CLIP-seq data take into account genomic read profiles, but they ignore the underlying transcript information, that is informati...
Researchers discover LncRNA–miRNA regulatory paradigms modulate gene expression patterns and drive major cellular processes. Identification of lncRNA-miRNA interactions (LMIs) is critical to reveal the mechani...
RNA binding proteins (RBPs) play a vital role in post-transcriptional processes in all eukaryotes, such as splicing regulation, mRNA transport, and modulation of mRNA translation and decay. The identification ...
Many transcripts have been generated due to the development of sequencing technologies, and lncRNA is an important type of transcript. Predicting lncRNAs from transcripts is a challenging and important task. T...
RNA viruses mutate at extremely high rates, forming an intra-host viral population of closely related variants, which allows them to evade the host’s immune system and makes them particularly dangerous. Viral ...
Comparative genomics methods enable the reconstruction of bacterial regulatory networks using available experimental data. In spite of their potential for accelerating research into the composition and evoluti...
One possible approach how to economically facilitate gene expression profiling is to use the L1000 platform which measures the expression of ∼1,000 landmark genes and uses a computational method to infer the e...
Codon usage is an important determinant of gene expression levels that can help us understand codon biology, evolution and mRNA translation of species. The majority of previous codon usage studies have focused...
High throughput single-cell transcriptomic technology produces massive high-dimensional data, enabling high-resolution cell type definition and identification. To uncover the expressional patterns beneath the ...
In marine invertebrate life cycles, which often consist of planktonic larval and benthonic adult stages, settlement of the free-swimming larva to the sea floor in response to environmental cues is a key life c...
Porcine epidemic diarrhea virus (PEDV) is a causative agent of serious viral enteric disease in suckling pigs. Such diseases cause considerable economic losses in the global swine industry. Enhancing our knowl...
There are challenges in generating mRNA-Seq data from whole-blood derived RNA as globin gene and rRNA are frequent contaminants. Given the abundance of erythrocytes in whole blood, globin genes comprise some 8...
Voice disorders are a worldwide problem impacting human health, particularly for occupational voice users. Avoidance of surface dehydration is commonly prescribed as a protective factor against the development...
Brassica nigra (BB), also called black mustard, is grown as a condiment crop in India. B. nigra represents the B genome of U’s triangle and is one of the progenitor species of B. juncea (AABB), an important oilse...
Ophiocordyceps sinensis is an important traditional Chinese medicine for its comprehensive active ingredients, such as cordycepin, cordycepic acid, and Cordyceps polysaccharide. O. sinensis zjut, a special strain...
The degradation of cellulose and hemicellulose molecules into simpler sugars such as glucose is part of the second generation biofuel production process. Hydrolysis of lignocellulosic substrates is usually per...
RNA-binding proteins (RBPs) play crucial roles in various biological processes. Deep learning-based methods have been demonstrated powerful on predicting RBP sites on RNAs. However, the training of deep learni...
Women account for 60% of all stroke deaths and are more often permanently disabled than men, despite their higher observed stroke incidence. Considering the clinical population affected by stroke, an obvious d...
Whole mitogenomes or short fragments (i.e., 300–700 bp of the cox1 gene) are the markers of choice for revealing within- and among-species genealogies. Protocols for sequencing and assembling mitogenomes include ...
Bisphenol S (BPS) is a common bisphenol A (BPA) substitute, since BPA is virtually banned worldwide. However, BPS and BPA have both endocrine disrupting properties. Their effects appear mostly in adulthood fol...
Late blight disease (LBD) caused by the pathogen Phytophthora infestans (PI), is the most devastating disease limiting potato (Solanum tuberosum) production globally. Currently, this disease pathogen is re-emergi...
The RNA interference (RNAi) pathway is a gene regulation mechanism that utilizes small RNA (sRNA) and Argonaute (Ago) proteins to silence target genes. Our previous work identified a functional RNAi pathway in...
An amendment to this paper has been published and can be accessed via the original article.
Planarians reliably regenerate all body parts after injury, including a fully functional head and central nervous system. But until now, the expression dynamics and functional role of miRNAs and other small RN...
The electrosensory ampullary organs (AOs) and mechanosensory neuromasts (NMs) found in sturgeon and some other non-neopterygian fish or amphibians are both originated from lateral line placodes. However, these...
Bird mitogenomes differ from other vertebrates in gene rearrangement. The most common avian gene order, identified first in Gallus gallus, is considered ancestral for all Aves. However, other rearrangements inclu...
Orang-utans comprise three critically endangered species endemic to the islands of Borneo and Sumatra. Though whole-genome sequencing has recently accelerated our understanding of their evolutionary history, t...
Gonad development and differentiation is an essential function for all sexually reproducing species, and many aspects of these developmental processes are highly conserved among the metazoa. However, the mecha...
NITRATE TRANSPORTER 1/PEPTIDE TRANSPORTER (NRT1/PTR) family (NPF) members are essential transporters for many substrates in plants, including nitrate, hormones, peptides, and secondary metabolites. Here, we re...
Unlike mammals, zebrafish have a remarkable capacity to regenerate a variety of tissues, including central nervous system tissue. The function of macrophages in tissue regeneration is of great interest, as mac...
Humpless Bos taurus cattle are one of the earliest domestic cattle in Africa, followed by the arrival of humped Bos indicus cattle. The diverse indigenous cattle breeds of Africa are derived from these migrations...
Calcineurin B-like protein (CBL)-interacting protein kinases (CIPKs) are the primary components of calcium sensors, and play crucial roles in plant developmental processes, hormone signaling transduction, and ...
The parasitoid wasp, Trichogramma dendrolimi, can enter diapause at the prepupal stage. Thus, diapause is an efficient preservation method during the mass production of T. dendrolimi. Previous studies on diapause...
The global COVID-19 pandemic has led to an urgent need for scalable methods for clinical diagnostics and viral tracking. Next generation sequencing technologies have enabled large-scale genomic surveillance of...
Over the last decade, the rapid development of high-throughput sequencing platforms has accelerated species description and assisted morphological classification through DNA barcoding. However, the current hig...
As a heavy metal, manganese (Mn) can be toxic to plants. Stylo (Stylosanthes) is an important tropical legume that exhibits tolerance to high levels of Mn. However, little is known about the adaptive responses of...
Ginkgo (Ginkgo biloba L.) is an excellent landscape species. Its yellow-green leaf mutants are ideal materials for research on pigment synthesis, but the regulatory mechanism of leaf coloration in these ginkgo mu...
Ammonia is one of the most common toxicological environment factors affecting shrimp health. Although ammonia tolerance in shrimp is closely related to successful industrial production, few genetic studies of ...
The development and application of CRISPR technologies for the modification of the genome are rapidly expanding. Advances in the field describe new CRISPR components that are strategically engineered to improv...
The invasive species Xanthium spinosum has been used as a traditional Chinese medicine for many years. Unfortunately, no extensive molecular studies of this plant have been conducted.
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