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Education
August 2007 - December 2012
September 2004 - July 2007
September 2000 - July 2004
Publications
Publications (36)
Non-synonymous mutations linked to the complex diseases often have a global impact on a biological system, affecting large biomolecular networks and pathways. However, the magnitude of the mutation-driven effects on the macromolecular network is yet to be fully explored. In this work, we present an systematic multi-level characterization of human m...
Non-synonymous mutations linked to the complex diseases often have a global impact on a biological system, affecting large biomolecular networks and pathways. However, the magnitude of the mutation-driven effects on the macromolecular network is yet to be fully explored. In this work, we present an systematic multi-level characterization of human m...
Vaccination is the primary strategy for influenza prevention and control. However, egg-based vaccines, the predominant production platform, have several disadvantages, including the emergence of viral antigenic variants that can be induced during egg passage. These limitations have prompted the development of cell-based vaccines, which themselves a...
Subtype H6 influenza A viruses (IAVs) are commonly detected in wild birds and domestic poultry and can infect humans. In 2010, a H6N6 virus emerged in southern China, and since then, it has caused sporadic infections among swine. We show that this virus binds to α2,6-linked and α2,3-linked sialic acids. Mutations at residues 222 (alanine to valine)...
Besides humans, H3 subtypes of influenza A viruses (IAVs) can infect various animal hosts, including avian, swine, equine, canine, and sea mammal species. These H3 viruses are both antigenically and genetically diverse. Here, we characterized the antigenic diversity of contemporary H3 avian IAVs recovered from migratory birds in North America. Hema...
Influenza A viruses can infect a wide variety of animal species and, occasionally, humans. Infection occurs through the binding formed by viral surface glycoprotein hemagglutinin and certain types of glycan receptors on host cell membranes. Studies have shown that the α2,3-linked sialic acid motif (SA2,3Gal) in avian, equine, and canine species; th...
The poor performance of 2014–15 Northern Hemisphere (NH) influenza vaccines was attributed to mismatched H3N2 component with circulating epidemic strains. Using human serum samples collected from 2009–10, 2010–11 and 2014–15 NH influenza vaccine trials, we assessed their cross-reactive hemagglutination inhibition (HAI) antibody responses against re...
Vaccination is the primary strategy for the prevention and control of influenza outbreaks. However, the manufacture of influenza vaccine requires a high-yield seed strain, and the conventional methods for generating such strains are time consuming. In this study, we developed a novel method to rapidly generate high-yield candidate vaccine strains b...
Single nucleotide polymorphisms (SNPs) are among the most common types of genetic variation in complex genetic disorders. A growing number of studies link the functional role of SNPs with the networks and pathways mediated by the disease-associated genes. For example, many non-synonymous missense SNPs (nsSNPs) have been found near or inside the pro...
Increased risk for autism spectrum disorders (ASD) is attributed to hundreds of genetic loci. The convergence of ASD variants have been investigated using various approaches, including protein interactions extracted from the published literature. However, these datasets are frequently incomplete, carry biases and are limited to interactions of a si...
As species evolve, they become adapted to their local environments. Detecting the genetic signature of selection and connecting that to the phenotype of the organism, however, is challenging. Here we report using an integrative approach that combines DNA sequencing with structural biology analyses to assess the effect of selection on residues in th...
Accurate alignment of protein-protein binding sites can aid in protein docking studies and constructing templates for predicting structure of protein complexes, along with in-depth understanding of evolutionary and functional relationships. However, over the past three decades, structural alignment algorithms have focused predominantly on global al...
Accurate alignment of protein-protein binding sites can aid in protein docking studies and constructing templates for predicting structure of protein complexes, along with in-depth understanding of evolutionary and functional relationships. However, over the past three decades, structural alignment algorithms have focused predominantly on global al...
Community-wide blind prediction experiments such as CAPRI and CASP provide an objective measure of the current state of predictive methodology. Here we describe a community-wide assessment of methods to predict the effects of mutations on protein-protein interactions. Twenty-two groups predicted the effects of comprehensive saturation mutagenesis f...
PBSword is a web server designed for efficient and accurate comparisons and searches of geometrically similar protein–protein
binding sites from a large-scale database. The basic idea of PBSword is that each protein binding site is first represented
by a high-dimensional vector of ‘visual words’, which characterizes both the global and local shape...
Motivation:
Finding geometrically similar protein binding sites is crucial for understanding protein functions and can provide valuable information for protein-protein docking and drug discovery. As the number of known protein-protein interaction structures has dramatically increased, a high-throughput and accurate protein binding site comparison...
Large-scale protein structure alignment, an indispensable tool to structural bioinformatics, poses a tremendous challenge on computational resources. To ensure structure alignment accuracy and efficiency, efforts have been made to parallelize traditional alignment algorithms in grid environments. However, these solutions are costly and of limited a...
Figure S1. In this example, one leaf node tjQ from the indexing tree of the target protein Q is used to search the indexing tree of entire protein database Λ and m best matched nodes are returned. In this example, tjQ node is represented by a representative cjQ which is a "structure medium" from three similar substructures {uj, 1, uj, 2, uj, 3} fro...
With the growing number of experimentally resolved structures of macromolecular complexes, it becomes clear that the interactions
that involve protein structures are mediated not only by the protein domains, but also by various non-structured regions,
such as interdomain linkers, or terminal sequences. Here, we present DOMMINO (http://dommino.org),...
Structural knowledge about protein-protein interactions can provide insights to the basic processes underlying cell function. Recent progress in experimental and computational structural biology has led to a rapid growth of experimentally resolved structures and computationally determined near-native models of protein-protein interactions. However,...
Protein-protein interactions play an essential role in the functioning of cell. The importance of charged residues and their diverse role in protein-protein interactions have been well studied using experimental and computational methods. Often, charged residues located in protein interaction interfaces are conserved across the families of homologo...
Interactions between proteins play a key role in many cellular processes.
Studying protein-protein interactions that share similar interaction interfaces
may shed light on their evolution and could be helpful in elucidating the
mechanisms behind stability and dynamics of the protein complexes. When two
complexes share structurally similar subunits,...
The progress in experimental and computational structural biology has led to a rapid growth of experimentally resolved structures and computational models of protein-protein interactions. However, distinguishing between the physiological and non-physiological interactions remains a challenging problem. In this work, two related problems of interfac...
ProteinDBS v2.0 is a web server designed for efficient and accurate comparisons and searches of structurally similar proteins
from a large-scale database. It provides two comparison methods, global-to-global and local-to-local, to facilitate the searches
of protein structures or substructures. ProteinDBS v2.0 applies advanced feature extraction alg...
For the purpose of analyzing gastric tumor pathologic cell images, a novel method is developed with gray-scale edge detection of mathematical morphology in this study. In combination with texture features of the image under investigation, this paper works on edge detection with various structuring elements (SEs) and gray-scale values. The results o...
A histomorphological method has been used universally in the researches on the focused ultrasound modifications on the neural tissues, but the dynamic effect is usually unknown. We report on an electrophysiological method to investigate the time-dependent effect of focused ultrasound on the conduction properties of toad's sciatic nerve. It was noti...
A novel texture detecting analysis for medical pathological tissue images was developed by fractal Brown model. According to fractal Brown random field model, a discrete fractal random field for image texture detection on a definite scale could be derived from the Brown model. Using fractal dimensions in partial region of the image and gray differe...
Two estimating algorithms, time-dependent Tsallis entropy (ETsEn) and time-dependent approximate entropy (EApEn), are provided to analyze the dynamic transformation of cognitive event-related potential complexity in Stroop tasks. It is discovered that ETsEn reflects the differences of ERP complexity between different stimulation types more profitab...
A complexity estimating algorithm, cross approximate entropy (Cross-ApEn), was developed to analyze the instantaneous synchronization of cognitive ERPs, which could indicate the interactions of different brain regions during selective attention tasks. In order to illustrate the validity of Cross-ApEn’s reflection of instantaneous synchronization, c...
A method for calculating dynamic complexity of cognitive event-related potential (ERP) was introduced, which was recognized as time-dependent approximate entropy (ApEn). In addition, two calculating methods, mean of entropy for each trial (Mean of ApEn) and entropy for averaged ERP (ApEn of ERP), were validated and compared through an investigation...