A5100601932- RNA and protein synthesis mechanisms
- Genomics and Phylogenetic Studies
- Lepidoptera: Biology and Taxonomy
- Plant and animal studies
- Machine Learning in Bioinformatics
- RNA Research and Splicing
- Genetic diversity and population structure
- Genetic Mapping and Diversity in Plants and Animals
- CRISPR and Genetic Engineering
- Bioinformatics and Genomic Networks
- Genomics and Chromatin Dynamics
- Species Distribution and Climate Change
- Renal and related cancers
- Protein Structure and Dynamics
- Plant Reproductive Biology
- Fungal and yeast genetics research
- Cancer Genomics and Diagnostics
- Wheat and Barley Genetics and Pathology
- Evolution and Genetic Dynamics
- Insect Pheromone Research and Control
- Bacterial Genetics and Biotechnology
- RNA modifications and cancer
- Bacteriophages and microbial interactions
- Plant Disease Resistance and Genetics
- RNA regulation and disease
The University of Texas Southwestern Medical Center
2017-2025
Soochow University
2024-2025
Yunnan University
2010-2024
Sichuan Agricultural University
2012-2024
Ministry of Agriculture and Rural Affairs
2023-2024
Southwest Medical University
2021-2024
Southwestern Medical Center
2023
Edward Hines, Jr. VA Hospital
2023
Rice Research Institute
2012-2023
Institute of Biophysics
2023
Protein-protein interactions play critical roles in biology, but the structures of many eukaryotic protein complexes are unknown, and there likely not yet identified. We take advantage advances proteome-wide amino acid coevolution analysis deep-learning–based structure modeling to systematically identify build accurate models core within
As the cost of sequencing continues to decrease and amount sequence data generated grows, new paradigms for storage analysis are increasingly important. The relative scaling behavior these evolving technologies will impact genomics research moving forward.
The Clustered Regularly Interspaced Palindromic Repeats (CRISPR) system is an adaptive immune in prokaryotes. Interference complexes encoded by CRISPR-associated (cas) genes utilize small RNAs for homology-directed detection and subsequent degradation of invading genetic elements, they have been classified into three main types (I–III). Type III share the Cas10 subunit but are subclassifed as type IIIA (CSM) IIIB (CMR), depending on their specificity DNA or RNA targets, respectively. role...
In vivo mapping of transcription-factor binding to the transcriptional output regulated gene is hindered by probabilistic promoter occupancy, presence multiple copies, and cell-to-cell variability. We demonstrate how overcome these obstacles in lysogeny maintenance bacteriophage lambda, P(RM). simultaneously measured concentration lambda repressor CI number messenger RNAs (mRNAs) from P(RM) individual Escherichia coli cells, used a theoretical model identify stochastic activity corresponding...
Recent advances in protein structure prediction have generated accurate structures of previously uncharacterized human proteins. Identifying domains these predicted and classifying them into an evolutionary hierarchy can reveal biological insights. Here, we describe the detection classification from proteome. Our indicates that only 62% residues are located globular domains. We further classify observe majority (65%) be classified among known folds by sequence, with a smaller fraction (33%)...
Protein structure prediction has now been deployed widely across several different large protein sets. Large-scale domain annotation of these predictions can aid in the development biological insights. Using our Evolutionary Classification Domains (ECOD) from experimental structures as a basis for classification, we describe detection and cataloging domains 48 whole proteomes deposited AlphaFold Database. On average, provide positive classification (either or other identifiable non-domain...
Rice yield is an important and complex agronomic trait controlled by multiple genes. In recent decades, dozens of yield-associated genes in rice have been cloned, many which can increase production the form loss or degeneration function. However, mutations occurring randomly under natural conditions provided very limited genetic resources for increases. this study, potentially yield-increasing alleles two closely associated with were edited artificially. The recently developed CRISPR/Cas9...
Abstract The evolutionary classification of protein domains (ECOD) classifies using a combination sequence and structural data (http://prodata.swmed.edu/ecod). Here we present the culmination our previous efforts at classifying from predicted structures, principally AlphaFold Database (AFDB), by integrating these with existing PDB structures. This combined includes both previous, purely experimental, as well provisional 48 proteomes in AFDB model organisms concern to global health. ECOD over...
Multiple breast cancer susceptibility loci have been identified in genome-wide association studies (GWAS) populations of European and Asian ancestry using array chips optimized for ancestry. It is important to examine whether these are associated with risk women African We evaluated 25 single nucleotide polymorphisms (SNPs) at 19 a pooled case–control study cancer, which included 1509 cases 1383 controls. Cases controls were enrolled Nigeria, Barbados the USA; all found significant...
Genomic sequencing and analysis of worldwide skipper butterfly (Lepidoptera: Hesperiidae) fauna points to imperfections in their current classification. Some tribes, subtribes genera as they are circumscribed today not monophyletic. Rationalizing genomic results from the perspective phenotypic characters suggests two new 50 that named here: Ceratrichiini Grishin, trib. n., Gretnini Falgina subtr. Apaustina Flattoides gen. Aurivittia Viuria Clytius Incisus Perus Livida Festivia Hoodus Anaxas...
Biologists marvel at the powers of adaptive convergence, when distantly related animals look alike. While mimetic wing patterns butterflies have fooled predators for millennia, entomologists inferred that mimics were distant relatives despite similar appearance. However, obverse question has not been frequently asked. Who are close and what their features? As opposed to divergence from a non-mimetic relative would also be extreme. When closely unalike, it is challenging pair them. Genomic...
Recent development of deep-learning methods has led to a breakthrough in the prediction accuracy 3D protein structures. Extending these pairs is expected allow large-scale detection protein-protein interactions (PPIs) and modeling complexes at proteome level.We applied RoseTTAFold AlphaFold, two latest for structure predictions, analyze coevolution human proteins residing mitochondria, an organelle vital importance many cellular processes including energy production, metabolism, cell death...
Summary Rhizomes are modified stems that grow underground and produce new individuals genetically identical to the mother plant. Recently, a breakthrough has been made in efforts convert annual grains into perennial ones by utilizing wild rhizomatous species as donors, yet developmental biology of this organ is rarely studied. Oryza longistaminata , rice featuring strong rhizomes, provides valuable model for exploration rhizome development. Here, we first assembled double‐haplotype genome O....
Protein-protein interactions (PPI) are essential for biological function. Recent advances in coevolutionary analysis and Deep Learning (DL) based protein structure prediction have enabled comprehensive PPI identification bacterial yeast proteomes, but these approaches limited success to date the more complex human proteome. Here, we overcome this challenge by 1) enhancing signals with 7-fold deeper multiple sequence alignments harvested from 30 petabytes of unassembled genomic data, 2)...
Association mapping has been widely used to map the significant associated loci responsible for natural variation in complex traits and are valuable crop improvement. Sugars organic acids most important metabolites tomato fruits. We a collection of 174 accessions composed Solanum lycopersicum (123 accessions) S. var cerasiforme (51 detect significantly controlling main sugars acids. The were genotyped with 182 SSRs spreading over genome. was conducted on detected by gas chromatography-mass...
Salmonella enterica is a pathogenic bacterium known for causing severe typhoid fever in humans, making it important to study due its potential health risks and significant impact on public health. This provides evolutionary classification of proteins from pangenome. We classified 17,238 domains 13,147 79,758 strains studied detail 272 14 characterized pathogenicity islands (SPIs). Among SPIs-related proteins, 90 function the secretion machinery. 41% SPI have no previous sequence annotation....
Although some preliminary work has revealed the potential transcriptional regulatory function of introns in eukaryotes, additional evidences are needed to support this conjecture. In study, we perform systemic analyses sequence characteristics human introns. The results show that first generally longer and C, G their dinucleotide compositions over-represented relative other introns, which consistent with previous findings. addition, new phenomena concerned regulation found: i) enriched CpG...
Rice (Oryza sativa) is very sensitive to chilling stress at seedling and reproductive stages, whereas wild rice, O. longistaminata, tolerates non-freezing cold temperatures has overwintering ability. Elucidating the molecular mechanisms of tolerance (CT) in longistaminata should thus provide a basis for rice CT improvement through breeding. In this study, high-throughput RNA sequencing was performed profile global transcriptome alterations crucial genes involved response long-term low...
Protein-protein interactions (PPIs) are involved in almost all essential cellular processes. Perturbation of PPI networks plays critical roles tumorigenesis, cancer progression, and metastasis. While numerous high-throughput experiments have produced a vast amount data for PPIs, these sets suffer from high false positive rates exhibit degree discrepancy. Coevolution amino acid positions between protein pairs has proven to be useful identifying interacting proteins providing structural...
The precise identification and efficient in situ eradication of intracellular bacteria can not only prevent the from persisting spreading within host but also accelerate healing infected wounds decrease caused complications. In this study, we designed a multifunctional quantum dot (QD) killer equipped with aggregation-induced emission (AIE) photosensitizers heterobivalent DNA sequences capability to specifically target, fluorescently image, efficiently eliminate bacteria. These QD killers...
Abstract Domain classification of protein predictions released in the AlphaFold Database (AFDB) has been a recent focus Evolutionary Classification Domains (ECOD). Although primary our work partition and assignment domains from these predictions, we here show how diverse can be used to examine reference domain set more closely. Using results DPAM, AlphaFold‐specific parsing algorithm, hierarchical groupings that share significant levels homologous links, both between groups were not...