A5100683466- Genomics and Phylogenetic Studies
- Bioinformatics and Genomic Networks
- RNA modifications and cancer
- Advanced Numerical Analysis Techniques
- Gene expression and cancer classification
- 3D Shape Modeling and Analysis
- Chromosomal and Genetic Variations
- Computer Graphics and Visualization Techniques
- RNA and protein synthesis mechanisms
- Genetic Mapping and Diversity in Plants and Animals
- Hate Speech and Cyberbullying Detection
- Gene Regulatory Network Analysis
- Plant Virus Research Studies
- Plant Gene Expression Analysis
- Advanced DC-DC Converters
- Photosynthetic Processes and Mechanisms
- Rice Cultivation and Yield Improvement
- Food composition and properties
- Epigenetics and DNA Methylation
- Fungal and yeast genetics research
- Microbial Community Ecology and Physiology
- Bioenergy crop production and management
- Microbial Metabolic Engineering and Bioproduction
- Complex Network Analysis Techniques
- Phytoplasmas and Hemiptera pathogens
Clemson University
2016-2025
CCCC Highway Consultants (China)
2020-2024
Southwest University
2020-2024
Sichuan University
2022-2024
Tianjin Agricultural University
2010-2024
Anhui Normal University
2023-2024
State Key Laboratory of Oral Diseases
2024
Harbin Institute of Technology
2024
East China University of Technology
2023
Kunming Third People's Hospital
2022-2023
Understanding the interaction among different species within a community and their responses to environmental changes is central goal in ecology. However, defining network structure microbial very challenging due extremely high diversity as-yet uncultivated status. Although recent advance of metagenomic technologies, such as throughout sequencing functional gene arrays, provide revolutionary tools for analyzing structure, it still difficult examine interactions based on high-throughput...
Biodiversity and its responses to environmental changes are central issues in ecology for society. Almost all microbial biodiversity research focuses on "species" richness abundance but not their interactions. Although a network approach is powerful describing ecological interactions among species, defining the structure community great challenge. Also, although stimulating effects of elevated CO(2) (eCO(2)) plant growth primary productivity well established, influences belowground...
Understanding the interactions among different species and their responses to environmental changes, such as elevated atmospheric concentrations of CO(2), is a central goal in ecology but poorly understood microbial ecology. Here we describe novel random matrix theory (RMT)-based conceptual framework discern phylogenetic molecular ecological networks using metagenomic sequencing data 16S rRNA genes from grassland soil communities, which were sampled long-term free-air CO(2) enrichment...
Long nanopore reads are advantageous in de novo genome assembly. However, usually have broad error distribution and high-error-rate subsequences. Existing correction tools cannot correct efficiently effectively. Most methods trim subsequences during correction, which reduces both the length of contiguity final Here, we develop an assembly tool designed to overcome complex errors reads. We propose adaptive read selection two-step progressive method quickly high accuracy. introduce a two-stage...
Accumulating evidences indicate that long non-coding RNAs (lncRNAs) play pivotal roles in various biological processes. Mutations and dysregulations of lncRNAs are implicated miscellaneous human diseases. Predicting lncRNA–disease associations is beneficial to disease diagnosis as well treatment. Although many computational methods have been developed, precisely identifying associations, especially for novel lncRNAs, remains challenging. In this study, we propose a method (named SIMCLDA)...
Abstract Motivation The Oxford Nanopore sequencing enables to directly detect methylation states of bases in DNA from reads without extra laboratory techniques. Novel computational methods are required improve the accuracy and robustness state prediction using reads. Results In this study, we develop DeepSignal, a deep learning method Testing on Homo sapiens (H. sapiens), Escherichia coli (E. coli) pUC19 shows that DeepSignal can achieve higher performance at both read level genome detecting...
Abstract The current human reference genome, GRCh38, represents over 20 years of effort to generate a high-quality assembly, which has benefitted society 1,2 . However, it still many gaps and errors, does not represent biological genome as is blend multiple individuals 3,4 Recently, telomere-to-telomere reference, CHM13, was generated with the latest long-read technologies, but derived from hydatidiform mole cell line nearly homozygous 5 To address these limitations, Human Pangenome...
Large-scale sequencing of entire genomes has ushered in a new age biology. One the next grand challenges is to dissect cellular networks consisting many individual functional modules. Defining co-expression without ambiguity based on genome-wide microarray data difficult and current methods are not robust consistent with different sets. This particularly problematic for little understood organisms since much existing biological knowledge can be exploited determining threshold differentiate...
This work introduces a unified framework for discrete surface Ricci flow algorithms, including spherical, Euclidean, and hyperbolic flows, which can design Riemannian metrics on surfaces with arbitrary topologies by user-defined Gaussian curvatures. Furthermore, the target are conformal (angle-preserving) to original metrics. A conformally deforms metric according its induced curvature, such that curvature evolves like heat diffusion process. Eventually, becomes user defined curvature....
In this paper, three new algorithms, a greedy algorithm, KL-like and an add-all are proposed to find local optimal community structures in large networks starting from given source vertex. The time complexity for finding l
Accumulating evidence suggests that biological systems are composed of interacting, separable, functional modules. Identifying these modules is essential to understand the organization systems.In this paper, we present a framework identify within networks. In approach, concept degree extended from single vertex sub-graph, and formal definition module in network used. A new agglomerative algorithm was developed by combining with relative edge order generated Girvan-Newman (G-N) algorithm....
Huanglongbing (HLB) is currently the most destructive disease of citrus worldwide. Although there no immune cultivar, field tolerance to HLB within and relatives has been observed at USDA Picos farm Ft. Pierce, Florida, where plants have exposed a very high level pressure since 2006. In this study, we used RNA-Seq evaluate expression differences between two closely related cultivars after infection: HLB-tolerant 'Jackson' grapefruit-like-hybrid trees susceptible 'Marsh' grapefruit trees. A...
Cyberbullying can have a deep and long lasting impact on its victims, who are often adolescents. Accurately detecting cyberbullying helps prevent it. However, the noise errors in social media posts messages make very challenging. In this paper, we propose novel pronunciation based convolutional neural network (PCNN) to address challenge. Upon observing that of misspelled words informal online conversations is unchanged, used phoneme codes text as features for network. This procedure corrects...
The process of crop domestication often consists two stages: initial domestication, where the wild species is first cultivated by humans, followed diversification, when domesticated are subsequently adapted to more environments and specialized uses. Selective pressure increase sugar accumulation in certain varieties cereal Sorghum bicolor an excellent example latter; this has resulted pronounced phenotypic divergence between sweet grain-type sorghums, but genetic mechanisms underlying these...
Many complex networks in the real world have community structures - groups of well-connected nodes with important functional roles. It has been well recognized that identification communities bears numerous practical applications. While existing approaches mainly apply statistical or graph theoretical/combinatorial methods for detection, this paper, we present a novel geometric approach which enables us to borrow powerful classical and properties. By considering as objects network...
Abstract In plants, cytosine DNA methylations (5mCs) can happen in three sequence contexts as CpG, CHG, and CHH (where H = A, C, or T), which play different roles the regulation of biological processes. Although long Nanopore reads are advantageous detection 5mCs comparing to short-read bisulfite sequencing, existing methods only detect CpG context, limits their application plants. Here, we develop DeepSignal-plant, a deep learning tool genome-wide all plants from reads. We Arabidopsis...
Long single-molecular sequencing technologies, such as PacBio circular consensus (CCS) and nanopore sequencing, are advantageous in detecting DNA 5-methylcytosine CpGs (5mCpGs), especially repetitive genomic regions. However, existing methods for 5mCpGs using CCS less accurate robust. Here, we present ccsmeth, a deep-learning method to detect reads. We sequence polymerase-chain-reaction treated M.SssI-methyltransferase of one human sample training ccsmeth. Using long (≥10 Kb) reads, ccsmeth...
Although long-read single-cell RNA isoform sequencing (scISO-Seq) can reveal alternative splicing in individual cells, it suffers from a low read throughput. Here, we introduce HIT-scISOseq, method that removes most artifact cDNAs and concatenates multiple for PacBio circular consensus (CCS) to achieve high-throughput high-accuracy sequencing. HIT-scISOseq yield >10 million long-reads single Sequel II SMRT Cell 8M. We also report the development of scISA-Tools demultiplex concatenated reads...
Abstract Canonical three-dimensional (3D) genome structures represent the ensemble average of pairwise chromatin interactions but not single-allele topologies in populations cells. Recently developed Pore-C can capture multiway contacts that reflect regional single chromosomes. By carrying out high-throughput Pore-C, we reveal extensive regionally restricted clusters aggregate into canonical 3D two human cell types. We show fragments multi-contact reads generally coexist same TAD. In...