Benben Miao

Xiamen University | XMU · State Key Laboratory of Marine Environmental Science

Complex biomedical data generated during clinical, omics and mechanism-based experiments have increasingly been exploited through cloud-and visualization-based data mining techniques. However, the scientific community still lacks an easy-to-use web service for the comprehensive visualization of biomedical data, particularly high-quality and publica...

Simple Summary In this study, a high-quality chromosomal-level genome of male Decapterus maruadsi was assembled based on Illumina, PacBio, and Hi-C technology. Notably, 23 chromosome-level genome sequences with lengths ranging between 21.74 and 44.53 Mb were assembled. A total of 22,716 protein-coding genes with an average transcript and a CDs leng...

The transcription factors of NR1D1 and NR1D2 belong to the nuclear receptor transcription factor family. They participate in many biological processes by regulating the expression of target genes and play an important role in the regulation of circadian rhythm. In this study, we revealed the functional role of NR1D1 and NR1D2 underlying low-tempera...

Simple Summary We constructed a high-quality genome assembly of Eupleurogrammus muticus at the chromosomal level using PacBio SMRT, Illumina Nova-Seq, and Hi-C technologies. By combining genomic annotation, comparative genomic analyses, and species attribute information, we identified many candidate genes related to the whip-like tail, innate immun...

Trachinotus ovatus is an economically important mariculture fish, and hypoxia has become a critical threat to this hypoxia-sensitive species. However, the molecular adaptation mechanism of T. ovatus liver to hypoxia remains unclear. In this study, we investigated the effects of acute hypoxic stress (1.5 ± 0.1 mg·L−1 for 6 h) and re-oxygenation (5.8...

In the era of rapid advancements in high-throughput omics technologies, the visualization of diverse data types with varying orders of magnitude presents a pressing challenge. To bridge this gap, we introduce DataColor, an all-encompassing software solution meticulously crafted to address this challenge. Our aim is to empower users with the ability...

Transcriptomic analysis has been widely used in comparative experiments to uncover biological mechanisms in various species. However, a simple tool is still lacking to optimize and integrate the features from multiple R packages. In this study, we developed TOmicsVis (Transcriptomics Visualization) (CRAN: https://cran.r-project.org/package=TOmicsVi...

With the advancements in high-throughput sequencing technologies such as Illumina, PacBio, and 10X Genomics platforms, and gas/liquid chromatography-mass spectrometry, large volumes of biological data in multiple formats can now be obtained through multi-omics analysis. Bioinformatics is constantly evolving and seeking breakthroughs to solve multi-...

Savalani hairtail Lepturacanthus savala is a widely distributed fish along the Indo-Western Pacific coast, and contributes substantially to trichiurid fishery resources worldwide. In this study, the first chromosome-level genome assembly of L. savala was obtained by PacBio SMRT-Seq, Illumina HiSeq, and Hi-C technologies. The final assembled L. sava...

Pearl gentian grouper is an important new breed of high-density farmed fish with high commercial value on the coast of southeast China. However, frequent hypoxia could suppress growth and increase the mortality of high-density farmed pearl gentian grouper, limiting the application and scope of this farming mode and obstructing the rapid development...

Modern web techniques provide an unprecedented opportunity for leveraging complex biomedical data generating in clinical, omics, and mechanism experiments. Currently, the functions for carrying out publication-ready biomedical data visualization represent primary technical hurdles in the state-of-art omics-based web services, whereas the demand for...

Pearl gentian grouper (Epinephelus fuscoguttatus ♀ × E. lanceolatus ♂) is a hybrid fish with high commercial value. It is widely cultured on the Asian coast; however, it is not cold-tolerant. Although we have previously characterized the liver transcriptomic responses of this grouper to cold stress, the roles of miRNAs and transcription factors (TF...

Pearl gentian grouper (Epinephelus fuscoguttatus ♀ × Epinephelus lanceolatus ♂) is a fish of high commercial value in the aquaculture industry in Asia. However, this hybrid fish is not cold-tolerant, and its molecular regulation mechanism underlying cold stress remains largely elusive. This study thus investigated the liver transcriptomic responses...

In this study, we reported the complete mitogenome of Scolopsis ciliata sampled from the Beibu Gulf, South China Sea. It was 16,734 bp in length and contained 37 canonical mitochondrial genes and 2 non-coding regions. Fifty-one single nucleotide polymorphisms and five insertion and deletions were detected between two S. ciliata mitogenomes, suggest...

In this study, we determined the complete mitogenome of Nemipterus virgatus of which the length was 17,073 bp, including 37 canonical mitochondrial genes and 2 non-coding regions. The control region contained termination associated sequence domain (TAS), central conserved domain (CSB-F, CSB-E, CSB-D, CSB-C, and CSB-A), conserved sequence block doma...

The complete mitochondrial genome of the ornate threadfin bream, Nemipterus hexodon, was first determined by the pairs-walking sequencing in this study. The circular mtDNA molecule was 17,115 bp in size and the overall nucleotide composition of H-stand was A (29.55%), T (27.36%), G (16.08%), and C (27.01%), with a slight bias towards A + T. The com...

The complete mitogenome sequence of Dentex hypselosomus was amplified by designing 15 primer pairs. The circle genome was 16,618 bp in size and the overall base composition was 27.04% of A, 26.38% of T, 17.08% of G, and 29.50 of C, with significant anti-G bias. The complete mitogenome of D. hypselosomus encodes 37 canonical mitochondrial genes, two...