A5102781094- Genomics and Phylogenetic Studies
- RNA and protein synthesis mechanisms
- Cancer-related molecular mechanisms research
- MicroRNA in disease regulation
- RNA modifications and cancer
- Circular RNAs in diseases
- Genetic diversity and population structure
- Chromosomal and Genetic Variations
- RNA Research and Splicing
- Radiomics and Machine Learning in Medical Imaging
- Bioinformatics and Genomic Networks
- Machine Learning in Bioinformatics
- Ferroptosis and cancer prognosis
- Amphibian and Reptile Biology
- Mitochondrial Function and Pathology
- Gene expression and cancer classification
- MRI in cancer diagnosis
- Bacteriophages and microbial interactions
- Plant and animal studies
- Biological Research and Disease Studies
- 14-3-3 protein interactions
- vaccines and immunoinformatics approaches
- Tuberculosis Research and Epidemiology
- Renal cell carcinoma treatment
- Ion channel regulation and function
Nanjing University of Chinese Medicine
2021-2025
University of California, San Francisco
2025
Guizhou University
2025
State Key Laboratory of Digital Medical Engineering
2017-2022
Southeast University
2013-2022
Jiangsu Provincial Center for Disease Control and Prevention
2021
University of Colorado Anschutz Medical Campus
2007-2012
The University of Texas at Arlington
2012
University of Calgary
2012
University of Colorado Denver
2007-2011
Using next-generation sequencing technology alone, we have successfully generated and assembled a draft sequence of the giant panda genome. The contigs (2.25 gigabases (Gb)) cover approximately 94% whole genome, remaining gaps (0.05 Gb) seem to contain carnivore-specific repeats tandem repeats. Comparisons with dog human showed that genome has lower divergence rate. assessment genes potentially underlying some its unique traits indicated bamboo diet might be more dependent on gut microbiome...
Transposable elements (TEs) are conventionally identified in eukaryotic genomes by alignment to consensus element sequences. Using this approach, about half of the human genome has been previously as TEs and low-complexity repeats. We recently developed a highly sensitive alternative de novo strategy, P-clouds, that instead searches for clusters high-abundance oligonucleotides related sequence space (oligo "clouds"). show here P-clouds predicts >840 Mbp additional repetitive sequences...
The genome of the zebra finch — a songbird and model for study vertebrate brain, behaviour evolution has been sequenced. Its comparison with chicken genome, only other bird available, shows that genes neural function implicated in cognitive processing song have rapidly evolving lineage. also vocal communication engages much brain transcriptome identifies potential integrator microRNA signals linked to communication. studying Comparison are Moreover, brain. is an important organism several...
Documented cases of convergent molecular evolution due to selection are fairly unusual, and examples date have involved only a few amino acid positions. However, because convergence mimics shared ancestry is not accommodated by current phylogenetic methods, it can strongly mislead inference when does occur. Here, we present case extensive between snake agamid lizard mitochondrial genomes that overcomes an otherwise strong signal. Evidence from morphology, nuclear genes, most sites in the...
Recent studies have suggested that the thermodynamic stability of mRNA secondary structure near start codon can regulate translation efficiency in Escherichia coli, and is more efficient less stable structure. We survey complete genomes 340 species for signals reduced codon. Our analysis includes bacteria, archaea, fungi, plants, insects, fishes, birds, mammals. find nearly all show evidence The reduction generally increases with increasing genomic GC content. In prokaryotes, also decreasing...
Snakes possess many extreme morphological and physiological adaptations. Identification of the molecular basis these traits can provide novel understanding for vertebrate biology medicine. Here, we study snake using genome sequence Burmese python (Python molurus bivittatus), a model metabolic adaptation. We compare king cobra genomes along with genomic samples from other snakes perform transcriptome analysis to gain insights into phenotypes python. discovered rapid massive transcriptional...
Optimal integration of next-generation sequencing into mainstream research requires re-evaluation how problems can be reasonably overcome and what questions asked. One potential application is the rapid acquisition genomic information to identify microsatellite loci for evolutionary, population genetic chromosome linkage mapping on non-model not previously sequenced organisms. Here, we report results using high-throughput obtain a large number from venomous snake Agkistrodon contortrix,...
Recent studies have suggested that the secondary structure of 5′ untranslated region (5′ UTR) messenger RNA (mRNA) is important for microRNA (miRNA)-mediated gene regulation in humans. mRNAs are targeted by miRNA tend to a higher degree local their UTR; however, general role UTR miRNA-mediated remains unknown. We systematically surveyed UTRs both plant and animal species found universal trend increased mRNA stability near cap regulated animals, but not plants. Intra-genome comparison showed...
Ion channels play a critical role in wide variety of biological processes, including the development human cancer. However, overall impact ion on tumorigenicity breast cancer remains controversial.We conduct microarray meta-analysis 280 channel genes. We identify candidate that are implicated based gene expression profiling. test relationship between genes and p53 mutation status, ER histological tumor grade discovery cohort. A molecular signature consisting (IC30) is identified by...
We conducted a comprehensive assessment of genomic repeat content in two snake genomes, the venomous copperhead (Agkistrodon contortrix) and Burmese python (Python molurus bivittatus). These genomes are both relatively small (∼1.4 Gb) but have surprisingly extensive differences abundance expansion histories their elements. In python, readily identifiable element is low (21%), similar to bird whereas that higher (45%), mammalian genomes. The copperhead's greater arises from recent many...
Background To gain insight into potential roles of isomiR spectrum and isomiRs with 3′ additions in pre-eclampsia, we performed a comprehensive survey miRNA repertoire addition events from placental samples different degrees pre-eclampsia by applying SOLiD sequencing platform. Principal Findings Over 30% were detected non-template additional nucleotides, especially for nucleotide adenosine. However, these modified showed lower percentage total expression (<15%). Generally, 1-3 abundant given...
Synonymous codons are widely selected for various biological mechanisms in both prokaryotes and eukaryotes. Recent evidence suggests that microRNA (miRNA) function may affect synonymous codon choices near miRNA target sites. To better understand this, we perform genome-wide analysis on usage around sites four plant genomes. We observed a general trend of increased site accessibility plants. Guanine-cytosine (GC)–poor preferred the flank region Within-genome analyses show significant...
BackgroundPenguins are flightless aquatic birds widely distributed in the Southern Hemisphere. The distinctive morphological and physiological features of penguins allow them to live an life, some have successfully adapted hostile environments Antarctica. To study phylogenetic population history molecular basis their adaptations Antarctica, we sequenced genomes two Antarctic dwelling penguin species, Adélie [Pygoscelis adeliae] emperor [Aptenodytes forsteri].
BackgroundCircular RNAs (circRNAs) are a class of novel with important biological functions, and aberrant expression circRNAs has been implicated in human diseases. However, the feasibility using blood as disease biomarkers is largely unknown.MethodsWe explored potential peripheral mononuclear cell (PBMC) marker molecules to diagnose active pulmonary tuberculosis (TB).FindingsFirst, we demonstrated that widely expressed PBMCs many abundant enough be detected. Second, found magnitude PBMC TB...
Circular RNAs (circRNAs) are a class of non-coding that widely expressed in various cell lines and tissues many organisms. Although the exact function circRNAs is largely unknown, type-and tissue-specific circRNA expression has implicated their crucial functions biological processes. Hence, quantification from high-throughput RNA-seq data becoming important to ascertain. model-based methods have been developed quantify linear RNA data, these not applicable quantification.Here, we proposed...
Abstract One unmet challenge in lung cancer diagnosis is to accurately differentiate from other diseases with similar clinical symptoms and radiological features, such as pulmonary tuberculosis (TB). To identify reliable biomarkers for screening, we leverage the recently discovered non-canonical small non-coding RNAs (i.e., tRNA-derived [tsRNAs], rRNA-derived [rsRNAs], YRNA-derived [ysRNAs]) human peripheral blood mononuclear cells develop a molecular signature composed of distinct...
Abstract We aim to develop machine learning (ML) models for predicting the complexity and mortality of polytrauma patients using clinical features, including physician diagnoses physiological data. conducted a retrospective analysis cohort comprising 756 admitted intensive care unit (ICU) at Pizhou People’s Hospital Trauma Center, Jiangsu, China between 2020 2022. Clinical parameters encompassed demographics, vital signs, laboratory values, scores diagnoses. The two primary outcomes...
We present a new computational method to identify positive and purifying selection at synonymous sites in yeast worm. define substitutions that change codons from preferred unpreferred or vice versa as nonconservative all other conservative. Using maximum-likelihood framework, we then test whether conservative occur equal rates. Our approach replaces the standard rate of per site, dS, with two rates, substitution (dSC) (dSN). Based on ratio dSN/dSC, find 0.05% genes none worm show evidence...