Sequence features associated with microRNA strand selection in humans and flies (2009)
Hu, Hai, Yan, Zheng, Xu, Ying, Hu, Hao, Menzel, Corinna, Zhou, Yan, ...
Abstract Background During microRNA (miRNA) maturation in humans and flies, Drosha and Dicer cut the precursor transcript, thereby producing a short RNA duplex. One strand of this duplex becomes a...
Entanglement in Valence-Bond-Solid States (2009)
Korepin, Vladimir E., Xu, Ying
This article reviews the quantum entanglement in Valence-Bond-Solid (VBS) states defined on a lattice or a graph. The subject is presented in a self-contained and pedagogical way. The VBS state was...
Deterministic Decentralized Search in Random Graphs (2009)
Esteban Arcaute, Ning Chen, Ravi Kumar, David Liben-nowell, Mohammad Mahdian, Hamid Nazerzadeh, ...
Abstract. We study a general framework for decentralized search in random graphs. Our main focus is on deterministic memoryless search algorithms that use only local information to reach their...
The cellulose synthase superfamily in fully sequenced plants and algae (2009)
Yin, Yanbin, Huang, Jinling, Xu, Ying
Abstract Background The cellulose synthase superfamily has been classified into nine cellulose synthase-like (Csl) families and one cellulose synthase (CesA) family. The Csl families have been...
Emissions of Phthalate Plasticizer from Polymeric Building Materials (2009)
Modern indoor environments contain a vast array of contaminating sources. Emissions from these sources produce contaminant concentrations that are substantially higher indoors than outside. Because...
Emissions of Phthalate Plasticizer from Polymeric Building Materials (2009)
Modern indoor environments contain a vast array of contaminating sources. Emissions from these sources produce contaminant concentrations that are substantially higher indoors than outside. Because...
Estimating accuracy of RNA-Seq and microarrays with proteomics (2009)
Fu, Xing, Fu, Ning, Guo, Song, Yan, Zheng, Xu, Ying, Hu, Hao, ...
Abstract Background Microarrays revolutionized biological research by enabling gene expression comparisons on a transcriptome-wide scale. Microarrays, however, do not estimate absolute expression...
Analyses of domains and domain fusions in human proto-oncogenes (2009)
Liu, Qi, Huang, Jinling, Liu, Huiqing, Wan, Ping, Ye, Xiuzi, Xu, Ying
Abstract Background Understanding the constituent domains of oncogenes, their origins and their fusions may shed new light about the initiation and the development of cancers. Results We have...
Pricing strategies for viral marketing on Social Networks (2009)
Arthur, David, Motwani, Rajeev, Sharma, Aneesh, Xu, Ying
We study the use of viral marketing strategies on social networks to maximize revenue from the sale of a single product. We propose a model in which the decision of a buyer to buy the product is...
Bo Yan, Tong Zhou, Peng Wang, Zhijie Liu, Victor Olman, ...
Post-translational modifications (PTMs) are very important to biological function, and yet are notoriously difficult to detect and identify, especially in a high-throughput manner. Most of the...
RepPop: a database for repetitive elements in Populus trichocarpa (2009)
Abstract Background Populus trichocarpa is the first tree genome to be completed, and its whole genome is currently being assembled. No functional annotation about the repetitive elements in the...
2-Chloropyridine-3-carboxamide (2009)
Yu-Peng Hua, Ying Xu, Xue-Hong Wei, Hong-Bo Tong
In the crystal structure of the title compound, C6H5ClN2O, the dihedral angle between the pyridine ring and the carboxamine group is 63.88 (8)°. Intermolecular N—H...N and...
Diisopropyl [(benzoylamino)(phenyl)methyl]phosphonate (2009)
Hua Fang, Mei-Juan Fang, Ying Xu, Wen-Cheng Yu, Yu-Fen Zhao
The title compound, C20H26NO4P, has been obtained by the reaction of benzoyl chloride and diisopropyl[amino(phenyl)methyl]phosphonate. The dihedral angle between the planes of the benzoylamino group...
The transcriptional repressor DEC2 regulates sleep length in mammals (2009)
He, Ying, Jones, Christopher R., Fujiki, Nobuhiro, Xu, Ying, Guo, Bin, Holder, Jimmy L., ...
DOOR: a database for prokaryotic operons (2009)
Mao, Fenglou, Dam, Phuongan, Chou, Jacky, Olman, Victor, Xu, Ying
We present a database DOOR (Database for prOkaryotic OpeRons) containing computationally predicted operons of all the sequenced prokaryotic genomes. All the operons in DOOR are predicted using our...
Xu, Ying, Henning, Rob H., Sandovici, Maria, Van Der Want, Johannes J., Van Gilst, Wiek H., Buikema, Hendrik
Aims We previously showed that enhanced myogenic constriction (MC) of peripheral resistance arteries involves active AT1 receptors in chronic heart failure (CHF). Recent data suggest both...
Antifouling compounds from deep-sea bacteria and their potential mode of action (2009)
Thesis (Ph.D.)--Hong Kong University of Science and Technology, 2009
QUBIC: a qualitative biclustering algorithm for analyses of gene expression data (2009)
Li, Guojun, Ma, Qin, Tang, Haibao, Paterson, Andrew H., Xu, Ying
Biclustering extends the traditional clustering techniques by attempting to find (all) subgroups of genes with similar expression patterns under to-be-identified subsets of experimental conditions...
Kong, Yingzhen, Zhou, Gongke, Avci, Utku, Gu, Xiaogang, Jones, Chelsea, Yin, Yanbin, ...
Several genes in Arabidopsis, including PARVUS/AtGATL1, have been implicated in xylan synthesis. However, the biosynthesis of xylan in woody plants, where this polysaccharide is a major component of...
De novo computational prediction of non-coding RNA genes in prokaryotic genomes (2009)
Tran, Thao T., Zhou, Fengfeng, Marshburn, Sarah, Stead, Mark, Kushner, Sidney R., Xu, Ying
Motivation: The computational identification of non-coding RNA (ncRNA) genes represents one of the most important and challenging problems in computational biology. Existing methods for ncRNA gene...
which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Background: Populus trichocarpa is the first tree genome to be completed,...
Chunmei Liu, Bo Yan, Yinglei Song, Ying Xu, Liming Cai
An important but difficult problem in proteomics is the identification of post-translational modifications (PTMs) in a protein. In general, the process of PTM identification by aligning experimental...
Both authors contributed equally to this work (2008)
Bo Yan, Chongle Pan, Victor N Olman, Robert L Hettich, Ying Xu
Mass spectrometry is one of the most popular analytical techniques for identification of individual proteins in a protein mixture, one of the basic problems in proteomics. It identifies a protein...
Ying Xu, Dong Xu, Oakley H. Crawford, J. Ralph Einstein, Engin Serpersu
It zs well known that the NMR method for protein struc-ture determinatwn apphes to small proteins and that zts effectweness decreases very rapidly as the molecular weight increases beyond about 30...
Barcodes for genomes and applications (2008)
Zhou, Fengfeng, Olman, Victor, Xu, Ying
Abstract Background Each genome has a stable distribution of the combined frequency for each k -mer and its reverse complement measured in sequence fragments as short as 1000 bps across the whole...
Low-Dose Radiation Does Not Induce Proliferation in Tumor Cells In Vitro and In Vivo (2008)
Hongyu Jiang, Ying Xu, Wei Li, Kewei Ma, Lu Cai, Guanjun Wang
Jiang, H., Xu, Y., Li, W., Ma, K., Cai, L. and Wang, G. Low-Dose Radiation Does Not Induce Proliferation in Tumor Cells In Vitro and In Vivo. Radiat. Res. 170, 477–487 (2008).We have demonstrated...
BIOINFORMATICS ORIGINAL PAPER (2008)
Genome Analysis, Bo Yan, Chongle Pan, Victor N. Olman, Robert L. Hettich, Ying Xu
A graph-theoretic approach for the separation of b and y ions in tandem mass spectra
CUBIC: Search for Binding Sites (2008)
Victor Olman, Jizhu Lu, Phuongan Dam, Zhengchang Su, Ying Xu
The regulation of gene transcription is achieved through specific interactions between transcription factors and their binding sites in the upstream region of the gene being regulated. Correct...
Glansdorff, Nicolas, Xu, Ying, Labedan, Bernard
Abstract Background Since the reclassification of all life forms in three Domains (Archaea, Bacteria, Eukarya), the identity of their alleged forerunner (Last Universal Common Ancestor or LUCA) has...
Managing Information Security in Healthcare: A Case Study in Region Skåne (2008)
Information security is vital to organizations. This is particularly evident in healthcare where patient information is regarded as very sensitive. The patient is the most important actor in...
Entanglement of Valence-Bond-Solid on an Arbitrary Graph (2008)
The Affleck-Kennedy-Lieb-Tasaki (AKLT) spin interacting model can be defined on an arbitrary graph. We explain the construction of the AKLT Hamiltonian. Given certain conditions, the ground state is...
Block Spin Density Matrix of the Inhomogeneous AKLT Model (2008)
Xu, Ying, Katsura, Hosho, Hirano, Takaaki, Korepin, Vladimir E.
We study the inhomogeneous generalization of a 1-dimensional AKLT spin chain model. Spins at each lattice site could be different. Under certain conditions, the ground state of this AKLT model is...
Lusheng Wang, Louxin Zhang, Ying Xu
Motivation: Genomes are replete with short sequences repeated consecutively called tandem repeats. Reconstructing duplication histories for tandem repeats may yield valuable insights into their...
Better Approximation Algorithms for NMR Spectral Peak Assignment (2008)
Zhi-zhong Chen, Tao Jiang, Guohui Lin, Jianjun Wen, Dong Xu, Ying Xu
Abstract. We study a constrained bipartite matching problem where the input is a weighted bipartite graph G = (U, V, E), U is a set of vertices following a sequential order, V is another set of...
DOI: 10.1093/bioinformatics/btg239 (2008)
Haplotype inference by maximum parsimony
The wealth of genomic sequence data generated through the worldwide se... (2008)
Hongwei Wu, Victor Olman, Ying Xu
We present a computational method for prediction of functional modules that can be directly applied to the newly sequenced microbial genomes for predicting gene functions and the component genes of...
Deterministic Decentralized Search in Random Graphs (2008)
Esteban Arcaute, Ning Chen, Ravi Kumar, David Liben-nowell, Mohammad Mahdian, Hamid Nazerzadeh, ...
Abstract. We study a general framework for decentralized search in random graphs. Our main focus is on deterministic memoryless search algorithms that use only local information to reach their...
Fractional Matching via Balls-and-Bins (2008)
Rajeev Motwani, Rina Panigrahy, Ying Xu
In this paper we relate the problem of finding structures related to perfect matchings in bipartite graphs to a stochastic process similar to throwing balls into bins. Given a bipartite graph with n...
Structural Analysis of FGFR1 Kinase Activation through Molecular Dynamics Simulation (2008)
Peng Wang, Zhengchang Su, Juntao Guo, Ying Xu
Receptor tyrokine kinases are critical regulators of signal transduction pathways mediating cellular homeostasis. Enhanced kinase activities via mutation and other genetic alternations have been...
Chunmei Liu, Bo Yan, Yinglei Song, Ying Xu, Liming Cai
doi:10.1093/bioinformatics/btl226 Peptide sequence tag-based blind identification of
ABSTRACT Estimating Corpus Size via Queries (2008)
Andrei Broder, Marcus Fontura, Vanja Josifovski, Ravi Kumar, Rajeev Motwani, Shubha Nabar, ...
We consider the problem of estimating the size of a collection of documents using only a standard query interface. Our main idea is to construct an unbiased and low-variance estimator that can...
Cooperative Caching in Linux Clusters 1 (2008)
Abstract. Most operating systems used in cluster systems manage memory locally without the benefits of cluster-wide cooperation. During typical use there will be some computers in a cluster that are...
Estimating Sum by Weighted Sampling (2008)
Rajeev Motwani, Rina Panigrahy, Ying Xu
Abstract. We study the classic problem of estimating the sum of n variables. The traditional uniform sampling approach requires a linear number of samples to provide any non-trivial guarantees on the...
Entanglement and Density Matrix of a Block of Spins in AKLT Model (2008)
Xu, Ying, Katsura, Hosho, Hirano, Takaaki, Korepin, Vladimir E.
We study a 1-dimensional AKLT spin chain, consisting of spins $S$ in the bulk and $S/2$ at both ends. The unique ground state of this AKLT model is described by the Valence-Bond-Solid (VBS) state. We...
Design and Performance Evaluation of a Proxy-based Java Rewriting Security System (2008)
Yougang Song, Ying Xu, Brett D. Fleisch
Binary rewriting techniques have been developed to allow users to enforce security policies directly on mobile code. However, the performance overheads incurred for improved security, particularly in...
Insertion Sequencesshow diverse recent activities in Cyanobacteria and Archaea (2008)
Zhou, Fengfeng, Olman, Victor, Xu, Ying
Abstract Background Mobile genetic elements (MGEs) play an essential role in genome rearrangement and evolution, and are widely used as an important genetic tool. Results In this article, we present...
N′-Ferrocenyl-2-hydroxybenzohydrazide (2008)
Ying Xu, Chun-Ling Chen, Jing Zhou, Ming-Xue Li
The title complex, [Fe(C5H5)(C13H11N2O3)], was prepared via self-assembly using ferrocenyl hydrazide and ethyl salicylate. The compound is potentially a tridentate ferrocene-based ligand. The...
A new constrained shape deformation operator with applications in footwear design (2008)
Thesis (M.Phil.)--Hong Kong University of Science and Technology, 2008
Deletion of Yeast CWP Genes Enhances Cell Permeability to Genotoxic Agents (2008)
Zhang, Min, Liang, Yuping, Zhang, Xiaohua, Xu, Ying, Dai, Heping, Xiao, Wei
We have previously reported the development of a novel genotoxic testing system based on the transcriptional response of the yeast RNR3-lacZ reporter gene to DNA damage. This system appears to be...
Myocardial infarction does not further impair renal damage in 5/6 nephrectomized rats (2008)
Henning, Robert H., Kluppel, Alex C. A., Xu, Ying, De Zeeuw, Dick
Background. Recent observational studies show that reduced renal function is an independent risk factor for the development of cardiovascular disease. Previously, we reported that myocardial...
Han, Fei, Xiao, Wenbo, Xu, Ying, Wu, Jianyong, Wang, Qidong, Wang, Huiping, ...
Background. Blood oxygen level-dependent MRI (BOLD MRI) can be used to assess intra-renal oxygen bioavailability by measuring the R2* level, which reflects tissue deoxyhaemoglobin levels. This study...
Computational prediction of human proteins that can be secreted into the bloodstream (2008)
Cui, Juan, Liu, Qi, Puett, David, Xu, Ying
We present a novel computational method for predicting which proteins from highly and abnormally expressed genes in diseased human tissues, such as cancers, can be secreted into the bloodstream,...
The focus of this paper is on developing and evaluating a practical methodology for determining if and when different types of traffic can be safely multiplexed within the same service class. The use...
Characterizing Pure-strategy Equilibria in Large Games (2007)
Fu, Haifeng, Xu, Ying, Zhang, Luyi
In this paper, we divide the players of a large game into countable different groups and assume that each player’s payoff depends on her own action and the distribution of actions in each of the...
Characterizing Pure-strategy Equilibria in Large Games (2007)
Fu, Haifeng, Xu, Ying, Zhang, Luyi
In this paper, we consider a generalized large game model where the agent space is divided into countable subgroups and each player's payoff depends on her own action and the action distribution in...
Computational prediction of Pho regulons in cyanobacteria (2007)
Su, Zhengchang, Olman, Victor, Xu, Ying
Abstract Background Phosphorus is an essential element for all life forms. However, it is limiting in most ecological environments where cyanobacteria inhabit. Elucidation of the phosphorus...
Database search has wide applications and is used as a subroutine in many important algorithms. We shall consider a database with one target item. Quantum algorithm finds the target item in a...
Hierarchical classification of functionally equivalent genes in prokaryotes (2007)
Wu, Hongwei, Mao, Fenglou, Olman, Victor, Xu, Ying
Functional classification of genes represents a fundamental problem to many biological studies. Most of the existing classification schemes are based on the concepts of homology and orthology, which...
Caveolae and vasomotor dysfunction : its relationship in experimental chronic heart failure (2007)
Hartfalen is een conditie waarbij het hart niet in staat is om voldoende bloed naar de weefsels te pompen om in de behoeften van het lichaam te voorzien. Wanneer deze aandoening optreedt, zal het...
Qi, Jinbo, Xu, Ying, Tolk, Norman
In this report, we present our observation of optically excited nonequilibrium spin dynamics in (Ga,Mn)As at room temperature. Our observation demonstrates two different regimes: 1) an initial...
Stochastic kronecker graphs (2007)
A random graph model based on Kronecker products of probability matrices has been recently proposed as a generative model for large-scale real-world networks such as the web. This model...
Protein structure-structure alignment with discrete Fréchet distance (2007)
Minghui Jiang, Ying Xu, Binhai Zhu
Matching two geometric objects in 2D and 3D spaces is a central problem in computer vision, pattern recognition and protein structure prediction. In particular, the problem of aligning two polygonal...
Stochastic kronecker graphs (2007)
Abstract. A random graph model based on Kronecker products of probability matrices has been recently proposed as a generative model for large-scale real-world networks such as the web. This model...
Stochastic kronecker graphs (2007)
A random graph model based on Kronecker products of probability matrices has been recently proposed as a generative model for large-scale real-world networks such as the web. This model...
Operon prediction in Pyrococcus furiosus (2007)
Tran, Thao T., Dam, Phuongan, Su, Zhengchang, Poole, Farris L., Adams, Michael W. W., Zhou, G. Tong, ...
Identification of operons in the hyperthermophilic archaeon Pyrococcus furiosus represents an important step to understanding the regulatory mechanisms that enable the organism to adapt and thrive in...
Operon prediction using both genome-specific and general genomic information (2007)
Dam, Phuongan, Olman, Victor, Harris, Kyle, Su, Zhengchang, Xu, Ying
We have carried out a systematic analysis of the contribution of a set of selected features that include three new features to the accuracy of operon prediction. Our analyses have led to a number of...
Hierarchical classification of functionally equivalent genes in prokaryotes (2007)
Wu, Hongwei, Mao, Fenglou, Olman, Victor, Xu, Ying
Functional classification of genes represents a fundamental problem to many biological studies. Most of the existing classification schemes are based on the concepts of homology and orthology, which...
Conductance oscillation and quantization in monoatomic Al wires (2006)
Xu, Ying, Shi, Xingqiang, Zeng, Zhi, Zeng, Zhao Yang, Li, Baowen
We present first-principles calculations for the transport properties of monoatomic Al wires sandwiched between Al(100) electrodes. The conductance of the monoatomic Al wires oscillates with the...
Current rectification by asymmetric molecules: An ab initio study (2006)
Zhou, Yan-hong, Zheng, Xiao-hong, Xu, Ying, Zeng, Zhao Yang
We study current rectification effect in an asymmetric molecule HOOC-C$_6$H$_4$-(CH$_2$)$_n$ sandwiched between two Aluminum electrodes using an {\sl ab initio} nonequilibrium Green function method....
Effects of relative orientation of the molecules on electron transport in molecular devices (2006)
Zhou, Yan-Hong, Zheng, Xiao-Hong, Xu, Ying, Zeng, Zhao Yang, Zeng, Zhi
Effects of relative orientation of the molecules on electron transport in molecular devices are studied by non-equilibrium Green's function method based on density functional theory. In particular,...
A Double Horizon Defense Design for Robust Regulation of Malicious Traffic (2006)
Deploying defense mechanisms in routers holds promises for protecting infrastructure resources such as link bandwidth or router buffers against network Denial-of-Service (DoS) attacks. However, in...
Shiow, Lawrence R, Rosen, David B, Brdicková, Nadezda, Xu, Ying, An, Jinping, Lanier, Lewis L, ...
Naive lymphocytes continually enter and exit lymphoid organs in a recirculation process that is essential for immune surveillance. During immune responses, the egress process can be shut down...
Xu, Ying, Glansdorff, Nicolas, Labedan, Bernard
Abstract Background The N-acetylation of L-glutamate is regarded as a universal metabolic strategy to commit glutamate towards arginine biosynthesis. Until recently, this reaction was thought to be...
Compositional analysis of teas from Australian supermarkets (2006)
Lihu Yao, Xu Liu, Yueming Jiang, Nola Caffin, Bruce D'Arcy, Riantong Singanusong, ...
This paper is the first study of the chemical composition of teas marketed in Australian supermarkets, and provides data on the quality of such teas for the tea industry and government health...
Pak, Alireza, Boutin, Michel, Xu, Ying, Maubert, Marie-Anne, Afonso, Carlos, Fournier, Françoise, ...
Xu, Ying, Glansdorff, Nicolas, Labedan, Bernard
BACKGROUND: The N-acetylation of L-glutamate is regarded as a universal metabolic strategy to commit glutamate towards arginine biosynthesis. Until recently, this reaction was thought to be catalyzed...
Xu, Ying, Glansdorff, Nicolas, Labedan, Bernard
BACKGROUND: The N-acetylation of L-glutamate is regarded as a universal metabolic strategy to commit glutamate towards arginine biosynthesis. Until recently, this reaction was thought to be catalyzed...
Prediction in dynamic SDRAM controller policy / (2006)
Thesis (M.S.)--Michigan Technological University, 2006.
English and Chinese students' use of morphemes in spelling English pseudo words / (2006)
Thesis (M.Sc. ERM)--University of Oxford, 2006.
Compositional analysis of teas from Australian supermarkets (2006)
Lihu Yao, Xu Liu, Yueming Jiang, Nola Caffin, Bruce D'Arcy, Riantong Singanusong, ...
This paper is the first study of the chemical composition of teas marketed in Australian supermarkets, and provides data on the quality of such teas for the tea industry and government health...
Thao T. Tran, Phuongan Dam, Zhengchang Su, G. Tong Zhou, ...
Identification of operons in the hyperthermophilic archaeon Pyrococcus furiosus represents an important step to understanding the regulatory mechanisms that enable the organism to adapt and thrive in...
and general genomic information (2006)
Phuongan Dam, Victor Olman, Kyle Harris, Zhengchang Su, Ying Xu
Operon prediction using both genome-specific
Hierarchical classification of functionally equivalent (2006)
Hongwei Wu, Fenglou Mao, Victor Olman, Ying Xu
genes in prokaryotes
doi:10.1093/nar/gkl974 Operon prediction in Pyrococcus furiosus (2006)
Thao T. Tran, Phuongan Dam, Zhengchang Su, G. Tong Zhou, ...
Identification of operons in the hyperthermophilic archaeon Pyrococcus furiosus represents an important step to understanding the regulatory mechanisms that enable the organism to adapt and thrive in...
doi:10.1093/nar/gkl294 Detecting uber-operons in prokaryotic genomes (2006)
Dongsheng Che, Guojun Li, Fenglou Mao, Hongwei Wu, Ying Xu
We present a study on computational identification of uber-operons in a prokaryotic genome, each of which represents a group of operons that are evolutionarily or functionally associated through...
12 Protein Structure Prediction by Protein Threading (2006)
Ying Xu, Zhijie Liu, Liming Cai, Dong Xu
protein folding problem ” laid the foundation of protein structure prediction by protein threading. By using simple measures for fitness of different amino acid types to local structural...
CSS-Palm: Palmitoylation Site Prediction with a Clustering and Scoring Strategy (CSS) (2006)
Fengfeng Zhou, Yu Xue, Xuebiao Yao, Ying Xu
The online version of this article has been published under an open access model. Users are entitled to use, reproduce, disseminate, or display the open access version of this article for...
doi:10.1093/nar/gkl207 SUMOsp: a web server for sumoylation site prediction (2006)
Yu Xue, Fengfeng Zhou, Chuanhai Fu, Ying Xu, Xuebiao Yao
Systematic dissection of the sumoylation proteome is emerging as an appealing but challenging research topic because of the significant roles sumoylation plays in cellular dynamics and plasticity....
SUMOsp: a web server for sumoylation site prediction (2006)
Xue, Yu, Zhou, Fengfeng, Fu, Chuanhai, Xu, Ying, Yao, Xuebiao
Systematic dissection of the sumoylation proteome is emerging as an appealing but challenging research topic because of the significant roles sumoylation plays in cellular dynamics and plasticity....
Su, Zhengchang, Mao, Fenglou, Dam, Phuongan, Wu, Hongwei, Olman, Victor, Paulsen, Ian T., ...
Deciphering the regulatory networks encoded in the genome of an organism represents one of the most interesting and challenging tasks in the post-genome sequencing era. As an example of this problem,...
CSS-Palm: palmitoylation site prediction with a clustering and scoring strategy (CSS) (2006)
Zhou, Fengfeng, Xue, Yu, Yao, Xuebiao, Xu, Ying
Summary: Palmitoylation is an important post-translational lipid modification of proteins. Unlike prenylation and myristoylation, palmitoylation is a reversible covalent modification, allowing for...
Operon prediction using both genome-specific and general genomic information (2006)
Dam, Phuongan, Olman, Victor, Harris, Kyle, Su, Zhengchang, Xu, Ying
We have carried out a systematic analysis of the contribution of a set of selected features that include three new features to the accuracy of operon prediction. Our analyses have led to a number of...
Operon prediction in Pyrococcus furiosus (2006)
Tran, Thao T., Dam, Phuongan, Su, Zhengchang, Poole, Farris L., Adams, Michael W. W., Zhou, G. Tong, ...
Identification of operons in the hyperthermophilic archaeon Pyrococcus furiosus represents an important step to understanding the regulatory mechanisms that enable the organism to adapt and thrive in...
libSRES: a C library for stochastic ranking evolution strategy for parameter estimation (2006)
Summary: Estimation of kinetic parameters in a biochemical pathway or network represents a common problem in systems studies of biological processes. We have implemented a C library, named libSRES,...
Liu, Chunmei, Yan, Bo, Song, Yinglei, Xu, Ying, Cai, Liming
An important but difficult problem in proteomics is the identification of post-translational modifications (PTMs) in a protein. In general, the process of PTM identification by aligning experimental...
Operon prediction using both genome-specific and general genomic information (2006)
Dam, Phuongan, Olman, Victor, Harris, Kyle, Su, Zhengchang, Xu, Ying
We have carried out a systematic analysis of the contribution of a set of selected features that include three new features to the accuracy of operon prediction. Our analyses have led to a number of...
Operon prediction in Pyrococcus furiosus (2006)
Tran, Thao T., Dam, Phuongan, Su, Zhengchang, Poole, Farris L., Adams, Michael W. W., Zhou, G. Tong, ...
Identification of operons in the hyperthermophilic archaeon Pyrococcus furiosus represents an important step to understanding the regulatory mechanisms that enable the organism to adapt and thrive in...
Seasonal Variations of Phenolic Compounds in Australia-Grown Tea (Camellia sinensis) (2005)
Lihu Yao, Nola Caffin, Bruce D'Arcy, Yueming Jiang, John Shi, Riantong Singanusong, ...
This is the first detailed study of phenolic compounds in Australian-grown tea, in green leaves and the resulting black tea, over a season. This important information is assisting the Australian tea...
On the Robustness of Router-based Denial-of-Service (DoS) Defense Systems (2005)
This paper focuses on "router-based" defense mechanisms, and whether they can provide effective solutions to network Denial-of-Service (DoS) attacks. Router-based defenses operate either on traffic...
Individual QoS versus aggregate QoS: A loss performance study (2005)
This paper explores the differences that can exist between individual and aggregate loss guarantees in an environment where guarantees are only provided at an aggregate level. The focus is on...
Robust network service delivery in shared resources environments (2005)
This dissertation is aimed at understanding how to design effective resource management schemes in shared resources network environments. We consider two well-known network service models: the "best...
Seasonal Variations of Phenolic Compounds in Australia-Grown Tea (Camellia sinensis) (2005)
Lihu Yao, Nola Caffin, Bruce D'Arcy, Yueming Jiang, John Shi, Riantong Singanusong, ...
This is the first detailed study of phenolic compounds in Australian-grown tea, in green leaves and the resulting black tea, over a season. This important information is assisting the Australian tea...
Pei Hao, Wei-zhong He, Yin Huang, Liang-xiao Ma, Ying Xu, Hong Xi, ...
an integrated database system for surveying a set of proteins
Accurate prediction of orthologous gene groups in microbes (2005)
Hongwei Wu, Fenglou Mao, Victor Olman, Ying Xu
We present a new computational method for the prediction of orthologous gene groups for microbial genomes based on the prediction of co-occurrences of homologous genes. The method is inspired by the...
Efficient Parameterized Algorithm for Biopolymer Structure-Sequence Alignment (2005)
Yinglei Song, Chunmei Liu, Xiuzhen Huang, Russell L. Malmberg, Ying Xu, Liming Cai
Abstract. Computational alignment of a biopolymer sequence (e.g., an RNA or a protein) to a structure is an effective approach to predict and search for the structure of new sequences. To identify...
Computational inference and experimental validation (2005)
Zhengchang Su, Fenglou Mao, Phuongan Dam, Hongwei Wu, Victor Olman, Ian T. Paulsen, ...
of the nitrogen assimilation regulatory network in cyanobacterium Synechococcus sp. WH 8102
Efficient Parameterized Algorithm for Biopolymer Structure-Sequence Alignment (2005)
Yinglei Song, Chunmei Liu, Xiuzhen Huang, Russell L. Malmberg, Ying Xu, Liming Cai
Abstract. Computational alignment of a biopolymer sequence (e.g., an RNA or a protein) to a structure is an effective approach to predict and search for the structure of new sequences. To identify...
Individual QoS versus aggregate QoS: A loss performance study (2005)
Abstract — This papers explores, primarily by means of analysis, the differences that can exist between individual and aggregate loss guarantees in an environment where guarantees are only provided...
Sluggish and Brisk Ganglion Cells Detect Contrast With Similar Sensitivity (2005)
Ying Xu Narender, Ying Xu, Narender K. Dhingra, Robert G. Smith, Peter Sterling, Narender K. Dhingra, ...
this article were defrayed in part by the payment of page charges. The article must therefore be hereby marked "advertisement" in accordance with 18 U.S.C. Section 1734 solely to indicate...
Efficient Parameterized Algorithm for Biopolymer Structure-Sequence Alignment (2005)
Yinglei Song, Chunmei Liu, Xiuzhen Huang, Russell L. Malmberg, Ying Xu, Liming Cai
Abstract—Computational alignment of a biopolymer sequence (e.g., an RNA or a protein) to a structure is an effective approach to predict and search for the structure of new sequences. To identify...
Huang, Jinling, Xu, Ying, Gogarten, Johann Peter
Lateral gene transfer plays an important role in the evolution of life. Events of ancient gene transfer can transmit genetic novelties to descendent lineages and subsequently shape their genetic...
A graph-theoretic approach for the separation of b and y ions in tandem mass spectra (2005)
Yan, Bo, Pan, Chongle, Olman, Victor N., Hettich, Robert L., Xu, Ying
Motivation: Ion-type identification is a fundamental problem in computational proteomics. Methods for accurate identification of ion types provide the basis for many mass spectrometry data...
Su, Zhengchang, Olman, Victor, Mao, Fenglou, Xu, Ying
We have developed a new method for prediction of cis-regulatory binding sites and applied it to predicting NtcA regulated genes in cyanobacteria. The algorithm rigorously utilizes concurrence...
Huang, Jinling, Xu, Ying, Gogarten, Johann Peter
Lateral gene transfer plays an important role in the evolution of life. Events of ancient gene transfer can transmit genetic novelties to descendent lineages and subsequently shape their genetic...
Wu, Hongwei, Su, Zhengchang, Mao, Fenglou, Olman, Victor, Xu, Ying
We present a computational method for the prediction of functional modules encoded in microbial genomes. In this work, we have also developed a formal measure to quantify the degree of consistency...
MPSS: an integrated database system for surveying a set of proteins (2005)
Hao, Pei, He, Wei-Zhong, Huang, Yin, Ma, Liang-Xiao, Xu, Ying, Xi, Hong, ...
Summary: We design and implement an integrated database system called ‘multi-protein survey system’ (MPSS), which provides a platform to retrieve information about many proteins at a time. This...
MPSS: an integrated database system for surveying a set of proteins (2005)
Hao, Pei, He, Wei-Zhong, Huang, Yin, Ma, Liang-Xiao, Xu, Ying, Xi, Hong, ...
Summary: We design and implement an integrated database system MPSS, which provides a platform to retrieve information about many proteins at a time. This system integrates several important and...
libSRES: a C library for stochastic ranking evolution strategy for parameter estimation (2005)
Summary: Estimation of kinetic parameters in a biochemical pathway or network represents a common problem in systems studies of biological processes. We have implemented a C library, named libSRES,...
Liu, Zhijie, Mao, Fenglou, Guo, Jun-tao, Yan, Bo, Wang, Peng, Qu, Youxing, ...
Computational evaluation of protein–DNA interaction is important for the identification of DNA-binding sites and genome annotation. It could validate the predicted binding motifs by sequence-based...
Huang, Jinling, Xu, Ying, Gogarten, Johann Peter
Lateral gene transfer plays an important role in the evolution of life. Events of ancient gene transfer can transmit genetic novelties to descendent lineages and subsequently shape their genetic...
Exploring the Performance Benefits of End-to-End Path Switching (2004)
Tao, Shu, Xu, Kuai, Xu, Ying, Fei, Teng, Gao, Lixin, Guérin, Roch A, ...
This paper explores the feasibility of improving the performance of end-to-end data transfers between different sites through path switching. Our study is focused on both the logic that controls path...
Naumoff, Daniil G, Xu, Ying, Glansdorff, Nicolas, Labedan, Bernard
Abstract Background Annotating genomes remains an hazardous task. Mistakes or gaps in such a complex process may occur when relevant knowledge is ignored, whether lost, forgotten or overlooked. This...
Detection of delamination in composites with fiber optic sensor / (2004)
Thesis (Ph. D.)--Hong Kong University of Science and Technology, 2004.
Detection of delamination in composites with fiber optic sensor (2004)
Thesis (Ph.D.)--Hong Kong University of Science and Technology, 2004
Detection of delamination in composites with fiber optic sensor / (2004)
Thesis (Ph. D.)--Hong Kong University of Science and Technology, 2004.
Fresnel-Kirchhoff integral for path loss prediction in outdoor urban environments / (2004)
Thesis (Ph. D. in Electrical and Computer Engineering)--University of Illinois at Chicago, 2004.
Detection of delamination in composites with fiber optic sensor / (2004)
Thesis (Ph. D.)--Hong Kong University of Science and Technology, 2004.
Jun-tao Guo, Kyle Ellrott, Won Jae Chung, Dong Xu, Serguei Passovets, Ying Xu
Knowledge of the detailed structure of a protein is crucial to our understanding of the biological functions of that protein. The gap between the number of solved protein structures and the number of...
Mapping of Microbial Pathways through Constrained Mapping of Orthologous Genes (2004)
Victor Olman, Hanchuan Peng, Zhengchang Su, Ying Xu
We present a novel computer algorithm for mapping biological pathways from one prokaryotic genome to another. The algorithm maps genes in a known pathway to their homologous genes (if any) in a...
Exploring the Performance Benefits of End-to-End Path (2004)
Switching Extend Ed, Shu Tao, Kuai Xu, Ying Xu, Teng Fei, Lixin Gao, ...
Shu Tao, Kuai Xu, Ying Xu, Teng Fei Lixin Gao, Roch Guerin, Jim Kurose, Don Towsley, Zhi-Li Zhang Categories and Subject Descriptors: C.2[Computer Systems Organization]:Computer Communication...
Computational Prediction of Operons in Synechococcus sp. WH8102 (2004)
Synechococcus Sp. Wh, Xin Chen, Zhengchang Su, Ying Xu, Tao Jiang
We computationally predict operons in the Synechococcus sp. WH8102 genome based on three types of genomic data: intergenic distances, COG gene functions and phylogenetic profiles. In the proposed...
In silico reconstruction of the carbon fixation pathway in Synechococcus sp. WH8102 (2004)
Phuongan Dam, Zhengchang Su, Victor Olman, Ying Xu
The carbon fixation pathway plays an essential role in the primary production and natural carbon recycling process. In this paper, we present a computational model of the carbon fixation pathway in...
Language anxiety in a senior middle school in China / (2004)
Supervisor: Dr Ernesto Macaro.
Lee, Hsien-Yang, Xu, Ying, Huang, Yong, Ahn, Andy H., Auburger, Georg W.J., Pandolfo, Massimo, ...
Paroxysmal Nonkinesigenic Dyskinesia (PNKD) is characterized by spontaneous hyperkinetic attacks that are precipitated by alcohol, coffee, stress, and fatigue. We report mutations in the...
Lee, Hsien-Yang, Xu, Ying, Huang, Yong, Ahn, Andy H., Auburger, Georg W.J., Pandolfo, Massimo, ...
Paroxysmal Nonkinesigenic Dyskinesia (PNKD) is characterized by spontaneous hyperkinetic attacks that are precipitated by alcohol, coffee, stress, and fatigue. We report mutations in the...
Lee, Hsien-Yang, Xu, Ying, Huang, Yong, Ahn, Andy H., Auburger, Georg W.J., Pandolfo, Massimo, ...
Paroxysmal Nonkinesigenic Dyskinesia (PNKD) is characterized by spontaneous hyperkinetic attacks that are precipitated by alcohol, coffee, stress, and fatigue. We report mutations in the...
Labedan, Bernard, Xu, Ying, Naumoff, Daniil G., Glansdorff, Nicolas
Many evolutionary scenarios describing the history of proteins are based solely on phylogenetic studies. We have designed a new approach that allows ascertainment of such questionable scenarios by...
A graph-theoretic approach to separation of b and y ions in tandem mass spectra (2004)
Yan, Bo, Pan, Chongle, Olman, Victor N., Hettich, Robert L., Xu, Ying
Motivation: Ion-type identification is a fundamental problem in computational proteomics. Methods for accurate identification of ion types provide the basis for many mass spectrometry data...
Protein structure prediction using sparse dipolar coupling data (2004)
Qu, Youxing, Guo, Jun-tao, Olman, Victor, Xu, Ying
Residual dipolar coupling (RDC) represents one of the most exciting emerging NMR techniques for protein structure studies. However, solving a protein structure using RDC data alone is still a highly...
PROSPECT-PSPP: an automatic computational pipeline for protein structure prediction (2004)
Guo, Jun-tao, Ellrott, Kyle, Chung, Won Jae, Xu, Dong, Passovets, Serguei, Xu, Ying
Knowledge of the detailed structure of a protein is crucial to our understanding of the biological functions of that protein. The gap between the number of solved protein structures and the number of...
Lee, Hsien-Yang, Xu, Ying, Huang, Yong, Ahn, Andrew H., Auburger, Georg W.J., Pandolfo, Massimo, ...
Paroxysmal non-kinesigenic dyskinesia (PNKD) is characterized by spontaneous hyperkinetic attacks that are precipitated by alcohol, coffee, stress and fatigue. We report mutations in the...
Model Checking for a First-Order Temporal Logic Using Multiway Decision Graphs (MDGs) (2004)
Xu, Ying, Song, Xiaoyu, Cerny, Eduard, Mohamed, Otmane Ait
We study model checking for a first-order linear-time temporal logic. We present the computation model: abstract description of state machines (ASMs), in which data and data operations are described...
Lee, Hsien-Yang, Xu, Ying, Huang, Yong, Ahn, Andy H., Auburger, Georg W.J., Pandolfo, Massimo, ...
Paroxysmal Nonkinesigenic Dyskinesia (PNKD) is characterized by spontaneous hyperkinetic attacks that are precipitated by alcohol, coffee, stress, and fatigue. We report mutations in the...
Lee, Hsien-Yang, Xu, Ying, Huang, Yong, Ahn, Andy H., Auburger, Georg W.J., Pandolfo, Massimo, ...
Paroxysmal Nonkinesigenic Dyskinesia (PNKD) is characterized by spontaneous hyperkinetic attacks that are precipitated by alcohol, coffee, stress, and fatigue. We report mutations in the...
Lee, Hsien-Yang, Xu, Ying, Huang, Yong, Ahn, Andy H., Auburger, Georg W.J., Pandolfo, Massimo, ...
Paroxysmal Nonkinesigenic Dyskinesia (PNKD) is characterized by spontaneous hyperkinetic attacks that are precipitated by alcohol, coffee, stress, and fatigue. We report mutations in the...
A graph-theoretic approach to separation of b and y ions in tandem mass spectra (2004)
Yan, Bo, Pan, Chongle, Olman, Victor N., Hettich, Robert L., Xu, Ying
Motivation: Ion-type identification is a fundamental problem in computational proteomics. Methods for accurate identification of ion types provide the basis for many mass spectrometry data...
Xu, Ying, Lu, Meng, Su, Ru-Keng
An approximation method, namely, the Extended Wronskian Determinant Approach, is suggested to study the one-dimensional Dirac equation. An integral equation which can be solved by iterative procedure...
On Evaluating Loss Performance Deviation: A Simple Tool and Its Practical Applications (2003)
The focus of this paper is on developing and evaluating a practical methodology for determining if and when different types of traffic can be safely multiplexed within the same service class. The use...
Lin, Juan, Chen, Yu, Xu, Ying, Yan, Fang, Tang, Lin, Chen, Fang
Curcin, a ribosome-inactivating protein with a molecular weight of about 28.2 kD, which stronglyinhibits the protein synthesisin rabbit reticulocytelysate system with an IC50 value of about (0.19 ±...
Approximation algorithms for NMR spectral peak assignment (2003)
Zhi-zhong Chen, Tao Jiang, Guohui Lin, Jianjun Wen, Dong Xu, Jinbo Xu, ...
We study a constrained bipartite matching problem where the input is a weighted bipartite graph G = (U, V, E), U is a set of vertices following a sequential order, V is another set of vertices...
AnÇÒ��deterministic gossiping algorithm for radio networks (2003)
We consider the problem of distributed gossiping in radio networks of unknown topology. For radio networks of size n and diameter D, we present an adaptive deterministic gossiping algorithm of time O...
Dong Xu, Dongsup Kim, Phuongan Dam, Manesh Shah, Edward C. Uberbacher, Ying Xu
Recent advances in high-throughput production capabilities for biological data such as genomic sequence (Lander et al., 2001; Venter et al., 2001), large-scale gene expression data (DeRisi et al,...
Protein threading by linear programming (2003)
Jinb Xu, Ming Li, Guohui Lin, Dongsup Kim, Ying Xu
Protein three-dimensional structure prediction through threading approach has been extensively studied and various models and algorithms have been proposed. In order to further explore ways to...
Excavator: a computer program for efficiently mining gene expression data (2003)
Dong Xu, Victor Olman, Li Wang, Ying Xu
Massive gene-expression data are generated using microarrays, and clustering gene-expression data is useful for studying functional relationship among genes in a biological process. We have developed...
Youxing Qu, Jun-tao Guo, Victor Olman, Ying Xu
Protein structure prediction using sparse dipolar
Raptor: Optimal Protein Threading By Linear Programming (2003)
Jinbo Xu Ming, Ming Li, Dongsup Kim, Ying Xu
This paper presents a novel linear programming approach to do protein 3-dimensional (3D) structure prediction via threading. Based on the contact map graph of the protein 3D structure template, the...
Exploring the Performance Benefits of End-to-End Path Switching (2003)
Shu Tao Kuai, Shu Tao, Kuai Xu, Ying Xu, Teng Fei, Lixin Gao, ...
This paper explores the feasibility of improving the performance of end-to-end data transfers between different sites through path switching. Our study is focused on both the logic that controls path...
Zhengchang Su, Phuongan Dam, Xin Chen, Victor Olman, Tao Jiang, Brian Palenik, ...
We present a computational protocol for inference of regulatory and signaling pathways in a microbial cell, through literature search, mining "high-throughput" biological data of various...
Protein Threading by Linear Programming (2003)
Jinbo Xu, Ming Li, Guohui Lin, Dongsup Kim, Ying Xu
this paper investigates the eectiveness of a new method: protein threading via linear programming. Based on the contact map model of protein 3D structure, we formulate the protein threading problem...
Labedan, Bernard, Xu, Ying, Naumoff, Daniil G., Glansdorff, Nicolas
Many evolutionary scenarios describing the history of proteins are based solely on phylogenetic studies. We have designed a new approach allowing to ascertain such questionable scenarios by taking...
PROSPECT II: protein structure prediction program for genome-scale applications (2003)
Kim, Dongsup, Xu, Dong, Guo, Jun-tao, Ellrott, Kyle, Xu, Ying
A new method for fold recognition is developed and added to the general protein structure prediction package PROSPECT (http://compbio.ornl.gov/PROSPECT/). The new method (PROSPECT II) has four key...
Guo, Jun-tao, Xu, Dong, Kim, Dongsup, Xu, Ying
Structural domains are considered as the basic units of protein folding, evolution, function and design. Automatic decomposition of protein structures into structural domains, though after many years...
SEGID: Identifying Interesting Segments in (Multiple) Sequence Alignments (2003)
Summary: SEGID is a tool for finding conserved regions (regions of high scores) for a given (multiple) sequence alignment. It takes a (multiple) sequence alignment as its input and converts the...
EXCAVATOR: a computer program for efficiently mining gene expression data (2003)
Xu, Dong, Olman, Victor, Wang, Li, Xu, Ying
Massive amounts of gene expression data are generated using microarrays for functional studies of genes and gene expression data clustering is a useful tool for studying the functional relationship...
Haplotype inference by maximum parsimony (2003)
Motivation: Haplotypes have been attracting increasing attention because of their importance in analysis of many fine-scale molecular-genetics data. Since direct sequencing of haplotype via...
A computational pipeline for protein structure prediction and analysis at genome scale (2003)
Shah, Manesh, Passovets, Sergei, Kim, Dongsup, Ellrott, Kyle, Wang, Li, Vokler, Inna, ...
Motivation: Experimental techniques alone cannot keep up with the production rate of protein sequences, while computational techniques for protein structure predictions have matured to such a level...
Labedan, Bernard, Xu, Ying, Naumoff, Daniil G., Glansdorff, Nicolas
Many evolutionary scenarios describing the history of proteins are based solely on phylogenetic studies. We have designed a new approach allowing to ascertain such questionable scenarios by taking...
Carbon Sequestration in Synechococcus Sp.: From Molecular Machines to Hierarchical Modeling (2002)
Heffelfinger, Grant S., Martino, Anthony, Gorin, Andrey, Xu, Ying, Rintoul, Mark D., Geist, Al, ...
The U.S. Department of Energy recently announced the first five grants for the Genomes to Life (GTL) Program. The goal of this program is to "achieve the most far-reaching of all biological goals: a...
Individual QoS versus Aggregate QoS: A Loss Performance Study (2002)
This papers explores, primarily by means of analysis, the differences that can exist between individual and aggregate loss guarantees in an environment where guarantees are only provided at an...
Thesis (Ph. D.)--Arizona State University, 2002.
Thesis (Ph. D.)--Arizona State University, 2002.
Wang, Yue-Dan, Gu, Zong-Jiang, Huang, Jian-An, Zhu, Yi-Bei, Zhou, Zhao-Hua, Xie, Wei, ...
In order to explore the role of gp130‐linked signal transduction in the differentiation and maturation of dendritic cells (DC), the mAb, B‐S12, an agonist of gp130, was used for the...
PRIMEGENS: robust and efficient design of gene-specific probes for microarray analysis (2002)
Xu, Dong, Li, Guangshan, Wu, Liyou, Zhou, Jizhong, Xu, Ying
Motivation: DNA microarray is a powerful high-throughput tool for studying gene function and regulatory networks. Due to the problem of potential cross hybridization, using full-length genes for...
Xu, Ying, Olman, Victor, Xu, Dong
Motivation: Gene expression data clustering provides a powerful tool for studying functional relationships of genes in a biological process. Identifying correlated expression patterns of genes...
Typescript.
Detection of delamination in laminated composites with optic fiber /--by Ying Xu. (2001)
Thesis (M.Phil.)--Hong Kong University of Science and Technology, 2001.
Minimum spanning trees for gene expression data clustering (2001)
Ying Xu, Victor Olman, Dong Xu
This paper describes a new framework for microarray gene-expression data clustering. The foundation of this framework is a minimum spanning tree (MST) representation of a set of multidimensional gene...
Detection of delamination in laminated composites with optic fiber (2001)
Thesis (M.Phil.)--Hong Kong University of Science and Technology, 2001
Xu, Dong, Unseren, Michael A., Xu, Ying, Uberbacher, Edward C.
*To whom correspondence should be addressed. Motivation: This paper investigates the sequence-structure specificity of a representative knowledge based energy function by applying it to threading...
Thesis (M.A.)--Arizona State University, 1999.
Protein threading by PROSPECT: a prediction experiment in CASP3 (1999)
Xu, Ying, Xu, Dong, Crawford, Oakley H., Einstein, J.ralph, Larimer, Frank, Uberbacher, Ed, ...
We present an analysis of the protein fold recognition experiment using PROSPECT in The Third Community Wide Experiment on the Critical Assessment of Techniques for Protein Structure Prediction...
Thesis (M.A.)--University of Texas at Austin, 1996.
A polynomial-time algorithm for a class of protein threading problems (1996)
Xu, Ying, Uberbacher, Edward C.
This paper presents an algorithm for constructing an optimal alignment between a three-dimensional protein structure template and an amino acid sequence. A protein structure template is given as a...
Thesis (M.S.) - Mississippi State University. Department of Chemical Engineering.
A metrological scanning force microscope. (1995)
Thesis (Ph. D.)--University of Warwick, 1995.
Correcting sequencing errors in DNA coding regions using a dynamic programming approach (1995)
Xu, Ying, Mural, Richard J., Uberbacher, Edward C.
This paper presents an algorithm for detecting and ‘correcting’ sequencing errors that occur in DNA coding regions. The types of sequencing errors addressed are insertions and deletions (indels)...
Dynamic Subtrees: a New Data Structure for Manipulating Trees (1994)
This paper presents a new data structure, called dynamic subtrees, which manipulates an undirected forest. The data structure supports three main operations cut, link and comp. A cut operation splits...
Xu, Ying, Mural, Richard J., Uberbacher, Edward C.
This paper presents a computationally efficient algorithm, the Gene Assembly Program III (GAP III), for constructing gene models from a set of accurately-predicted ‘exons’. The input to the...
Efficient sequential and parallel matroid intersection algorithms /--by Ying Xu. (1991)
Thesis (Ph. D.)--University of Colorado, 1991.
A computational pipeline for protein structure prediction and analysis at genome scale (1985)
Manesh Shah, Sergei Passovets, Dongsup Kim, Kyle Ellrott, Li Wang, Inna Vokler, ...
The tertiary (3D) structure of a protein contains the essential information for understanding the biological function of the protein at the molecular and cellular levels. Traditionally, protein 3D...
Xu, Ying, Liang, Ziyuan, Legrain, Christianne, Rüger, Hans J., Glansdorff, Nicolas
In the arginine biosynthetic pathway of the vast majority of prokaryotes, the formation of ornithine is catalyzed by an enzyme transferring the acetyl group of N-α-acetylornithine to glutamate...
Improving the performance of DomainParser for structural domain partition using neural network
Guo, Jun-tao, Xu, Dong, Kim, Dongsup, Xu, Ying
Structural domains are considered as the basic units of protein folding, evolution, function and design. Automatic decomposition of protein structures into structural domains, though after many years...
Xu, Ying, Feller, Georges, Gerday, Charles, Glansdorff, Nicolas
The enzyme ornithine carbamoyltransferase (OTCase) of Moritella abyssi (OTCaseMab), a new, strictly psychrophilic and piezophilic bacterial species, was purified. OTCaseMab displays maximal activity...
Xu, Ying, Feller, Georges, Gerday, Charles, Glansdorff, Nicolas
Adapting metabolic enzymes of microorganisms to low temperature environments may require a difficult compromise between velocity and affinity. We have investigated catalytic efficiency in a key...
EXCAVATOR: a computer program for efficiently mining gene expression data
Xu, Dong, Olman, Victor, Wang, Li, Xu, Ying
Massive amounts of gene expression data are generated using microarrays for functional studies of genes and gene expression data clustering is a useful tool for studying the functional relationship...
Protein structure prediction using sparse dipolar coupling data
Qu, Youxing, Guo, Jun-tao, Olman, Victor, Xu, Ying
Residual dipolar coupling (RDC) represents one of the most exciting emerging NMR techniques for protein structure studies. However, solving a protein structure using RDC data alone is still a highly...
PROSPECT-PSPP: an automatic computational pipeline for protein structure prediction
Guo, Jun-tao, Ellrott, Kyle, Chung, Won Jae, Xu, Dong, Passovets, Serguei, Xu, Ying
Knowledge of the detailed structure of a protein is crucial to our understanding of the biological functions of that protein. The gap between the number of solved protein structures and the number of...
Quantitative evaluation of protein–DNA interactions using an optimized knowledge-based potential
Liu, Zhijie, Mao, Fenglou, Guo, Jun-tao, Yan, Bo, Wang, Peng, Qu, Youxing, ...
Computational evaluation of protein–DNA interaction is important for the identification of DNA-binding sites and genome annotation. It could validate the predicted binding motifs by sequence-based...
Prediction of functional modules based on comparative genome analysis and Gene Ontology application
Wu, Hongwei, Su, Zhengchang, Mao, Fenglou, Olman, Victor, Xu, Ying
We present a computational method for the prediction of functional modules encoded in microbial genomes. In this work, we have also developed a formal measure to quantify the degree of consistency...
Su, Zhengchang, Olman, Victor, Mao, Fenglou, Xu, Ying
We have developed a new method for prediction of cis-regulatory binding sites and applied it to predicting NtcA regulated genes in cyanobacteria. The algorithm rigorously utilizes concurrence...
Su, Zhengchang, Mao, Fenglou, Dam, Phuongan, Wu, Hongwei, Olman, Victor, Paulsen, Ian T., ...
Deciphering the regulatory networks encoded in the genome of an organism represents one of the most interesting and challenging tasks in the post-genome sequencing era. As an example of this problem,...
He, Guo-qing, Xuan, Guo-dong, Ruan, Hui, Chen, Qi-he, Xu, Ying
Angiotensin I-converting enzyme (ACE) inhibitory peptides have been shown to have antihypertensive effects and have been utilized for physiologically functional foods and pharmaceuticals. The ACE...
Xu, Ying, He, Guo-qing, Li, Jing-jun
This paper presents the evaluation of an aqueous two-phase system (ATPS) for extracting elastase produced by Bacillus sp. EL31410. The elastase and cell partition behavio r in polyethylene glycol...
DNA Damage Recognition of Mutated Forms of UvrB Proteins in Nucleotide Excision Repair
Zou, Yue, Ma, Huaxian, Shell, Steven M., Yang, Zhengguan, Lloyd, R. Stephen, Minko, Irina G., ...
The DNA repair protein UvrB plays an indispensable role in the stepwise and sequential damage recognition of nucleotide excision repair in Escherichia coli. Our previous studies suggested that UvrB...
Detecting uber-operons in prokaryotic genomes
Che, Dongsheng, Li, Guojun, Mao, Fenglou, Wu, Hongwei, Xu, Ying
We present a study on computational identification of uber-operons in a prokaryotic genome, each of which represents a group of operons that are evolutionarily or functionally associated through...
Structural genomics analysis of alternative splicing and application to isoform structure modeling
Wang, Peng, Yan, Bo, Guo, Jun-tao, Hicks, Chindo, Xu, Ying
Alternative splicing is a sophisticated nuclear process that regulates gene expression. It represents an important mechanism for enhancing the functional diversity of proteins. Our current knowledge...
Mao, Fenglou, Su, Zhengchang, Olman, Victor, Dam, Phuongan, Liu, Zhijie, Xu, Ying
Mapping biological pathways across microbial genomes is a highly important technique in functional studies of biological systems. Existing methods mainly rely on sequence-based orthologous gene...
SUMOsp: a web server for sumoylation site prediction
Xue, Yu, Zhou, Fengfeng, Fu, Chuanhai, Xu, Ying, Yao, Xuebiao
Systematic dissection of the sumoylation proteome is emerging as an appealing but challenging research topic because of the significant roles sumoylation plays in cellular dynamics and plasticity....
Xu, Ying, Liang, Ziyuan, Legrain, Christianne, Rüger, Hans J., Glansdorff, Nicolas
In the arginine biosynthetic pathway of the vast majority of prokaryotes, the formation of ornithine is catalyzed by an enzyme transferring the acetyl group of N-α-acetylornithine to glutamate...
Improving the performance of DomainParser for structural domain partition using neural network
Guo, Jun-tao, Xu, Dong, Kim, Dongsup, Xu, Ying
Structural domains are considered as the basic units of protein folding, evolution, function and design. Automatic decomposition of protein structures into structural domains, though after many years...
Xu, Ying, Feller, Georges, Gerday, Charles, Glansdorff, Nicolas
The enzyme ornithine carbamoyltransferase (OTCase) of Moritella abyssi (OTCaseMab), a new, strictly psychrophilic and piezophilic bacterial species, was purified. OTCaseMab displays maximal activity...
Xu, Ying, Feller, Georges, Gerday, Charles, Glansdorff, Nicolas
Adapting metabolic enzymes of microorganisms to low temperature environments may require a difficult compromise between velocity and affinity. We have investigated catalytic efficiency in a key...
EXCAVATOR: a computer program for efficiently mining gene expression data
Xu, Dong, Olman, Victor, Wang, Li, Xu, Ying
Massive amounts of gene expression data are generated using microarrays for functional studies of genes and gene expression data clustering is a useful tool for studying the functional relationship...
Protein structure prediction using sparse dipolar coupling data
Qu, Youxing, Guo, Jun-tao, Olman, Victor, Xu, Ying
Residual dipolar coupling (RDC) represents one of the most exciting emerging NMR techniques for protein structure studies. However, solving a protein structure using RDC data alone is still a highly...
PROSPECT-PSPP: an automatic computational pipeline for protein structure prediction
Guo, Jun-tao, Ellrott, Kyle, Chung, Won Jae, Xu, Dong, Passovets, Serguei, Xu, Ying
Knowledge of the detailed structure of a protein is crucial to our understanding of the biological functions of that protein. The gap between the number of solved protein structures and the number of...
Quantitative evaluation of protein–DNA interactions using an optimized knowledge-based potential
Liu, Zhijie, Mao, Fenglou, Guo, Jun-tao, Yan, Bo, Wang, Peng, Qu, Youxing, ...
Computational evaluation of protein–DNA interaction is important for the identification of DNA-binding sites and genome annotation. It could validate the predicted binding motifs by sequence-based...
Prediction of functional modules based on comparative genome analysis and Gene Ontology application
Wu, Hongwei, Su, Zhengchang, Mao, Fenglou, Olman, Victor, Xu, Ying
We present a computational method for the prediction of functional modules encoded in microbial genomes. In this work, we have also developed a formal measure to quantify the degree of consistency...
Su, Zhengchang, Olman, Victor, Mao, Fenglou, Xu, Ying
We have developed a new method for prediction of cis-regulatory binding sites and applied it to predicting NtcA regulated genes in cyanobacteria. The algorithm rigorously utilizes concurrence...
Structural genomics analysis of alternative splicing and application to isoform structure modeling
Wang, Peng, Yan, Bo, Guo, Jun-tao, Hicks, Chindo, Xu, Ying
Alternative splicing is a sophisticated nuclear process that regulates gene expression. It represents an important mechanism for enhancing the functional diversity of proteins. Our current knowledge...
Mao, Fenglou, Su, Zhengchang, Olman, Victor, Dam, Phuongan, Liu, Zhijie, Xu, Ying
Mapping biological pathways across microbial genomes is a highly important technique in functional studies of biological systems. Existing methods mainly rely on sequence-based orthologous gene...
Su, Zhengchang, Mao, Fenglou, Dam, Phuongan, Wu, Hongwei, Olman, Victor, Paulsen, Ian T., ...
Deciphering the regulatory networks encoded in the genome of an organism represents one of the most interesting and challenging tasks in the post-genome sequencing era. As an example of this problem,...
He, Guo-qing, Xuan, Guo-dong, Ruan, Hui, Chen, Qi-he, Xu, Ying
Angiotensin I-converting enzyme (ACE) inhibitory peptides have been shown to have antihypertensive effects and have been utilized for physiologically functional foods and pharmaceuticals. The ACE...
Xu, Ying, He, Guo-qing, Li, Jing-jun
This paper presents the evaluation of an aqueous two-phase system (ATPS) for extracting elastase produced by Bacillus sp. EL31410. The elastase and cell partition behavio r in polyethylene glycol...
Detecting uber-operons in prokaryotic genomes
Che, Dongsheng, Li, Guojun, Mao, Fenglou, Wu, Hongwei, Xu, Ying
We present a study on computational identification of uber-operons in a prokaryotic genome, each of which represents a group of operons that are evolutionarily or functionally associated through...
SUMOsp: a web server for sumoylation site prediction
Xue, Yu, Zhou, Fengfeng, Fu, Chuanhai, Xu, Ying, Yao, Xuebiao
Systematic dissection of the sumoylation proteome is emerging as an appealing but challenging research topic because of the significant roles sumoylation plays in cellular dynamics and plasticity....
Naive CD4 T cells constitutively express CD40L and augment autoreactive B cell survival
Lesley, Robin, Kelly, Lisa M., Xu, Ying, Cyster, Jason G.
Chronic engagement of the B cell receptor by soluble autoantigen leads to reduced B cell survival. Using the Ig and hen egg lysozyme double transgenic mouse model, we demonstrate that the survival of...
Operon prediction in Pyrococcus furiosus
Tran, Thao T., Dam, Phuongan, Su, Zhengchang, Poole, Farris L., Adams, Michael W. W., Zhou, G. Tong, ...
Identification of operons in the hyperthermophilic archaeon Pyrococcus furiosus represents an important step to understanding the regulatory mechanisms that enable the organism to adapt and thrive in...
Operon prediction using both genome-specific and general genomic information
Dam, Phuongan, Olman, Victor, Harris, Kyle, Su, Zhengchang, Xu, Ying
We have carried out a systematic analysis of the contribution of a set of selected features that include three new features to the accuracy of operon prediction. Our analyses have led to a number of...
Hierarchical classification of functionally equivalent genes in prokaryotes
Wu, Hongwei, Mao, Fenglou, Olman, Victor, Xu, Ying
Functional classification of genes represents a fundamental problem to many biological studies. Most of the existing classification schemes are based on the concepts of homology and orthology, which...
Plasma cell S1P1 expression determines secondary lymphoid organ retention versus bone marrow tropism
Kabashima, Kenji, Haynes, Nicole M., Xu, Ying, Nutt, Stephen L., Allende, Maria L., Proia, Richard L., ...
After induction in secondary lymphoid organs, a subset of antibody-secreting cells (ASCs) homes to the bone marrow (BM) and contributes to long-term antibody production. The factors determining...
Xu, Ying, Labedan, Bernard, Glansdorff, Nicolas
Summary: Major aspects of the pathway of de novo arginine biosynthesis via acetylated intermediates in microorganisms must be revised in light of recent enzymatic and genomic investigations. The...
Lo, Charles G., Xu, Ying, Proia, Richard L., Cyster, Jason G.
Sphingosine-1-phosphate receptor 1 (S1P1) was recently shown to be required for lymphocyte egress from lymphoid organs. Here we have examined the relationship between S1P1 abundance on the cell and...
Introduction: Since their invention in the late 1980s and early 1990s, selective serotonin reuptake inhibitors (SSRIs) have become the primary form of pharmaceutical treatment for depression. As the...
Noda, Yasuko, Okada, Yasushi, Saito, Nobuhito, Setou, Mitsutoshi, Xu, Ying, Zhang, Zheizeng, ...
We have identified and characterized a COOH-terminal motor domain–type kinesin superfamily protein (KIFC), KIFC3, in the kidney. KIFC3 is a minus end–directed microtubule motor protein, therefore...
Role of KIFC3 motor protein in Golgi positioning and integration
Xu, Ying, Takeda, Sen, Nakata, Takao, Noda, Yasuko, Tanaka, Yosuke, Hirokawa, Nobutaka
KIFC3, a microtubule (MT) minus end–directed kinesin superfamily protein, is expressed abundantly and is associated with the Golgi apparatus in adrenocortical cells. We report here that disruption...
Characterizing Pure-strategy Equilibria in Large Games
Fu, Haifeng, Xu, Ying, Zhang, Luyi
In this paper, we consider a generalized large game model where the agent space is divided into countable subgroups and each player's payoff depends on her own action and the action distribution in...
Chen, Yong, Zhou, Fengfeng, Li, Guojun, Xu, Ying
Miniature inverted-repeat transposable elements (MITEs) are short DNA transposons with terminal inverted repeat (TIR) signals and have been extensively studied in plants and other eukaryotes. But...
Estimating accuracy of RNA-Seq and microarrays with proteomics
Fu, Xing, Fu, Ning, Guo, Song, Yan, Zheng, Xu, Ying, Hu, Hao, ...
Analyses of domains and domain fusions in human proto-oncogenes
Liu, Qi, Huang, Jinling, Liu, Huiqing, Wan, Ping, Ye, Xiuzi, Xu, Ying
DOOR: a database for prokaryotic operons
Mao, Fenglou, Dam, Phuongan, Chou, Jacky, Olman, Victor, Xu, Ying
We present a database DOOR (Database for prOkaryotic OpeRons) containing computationally predicted operons of all the sequenced prokaryotic genomes. All the operons in DOOR are predicted using our...
QUBIC: a qualitative biclustering algorithm for analyses of gene expression data
Li, Guojun, Ma, Qin, Tang, Haibao, Paterson, Andrew H., Xu, Ying
Biclustering extends the traditional clustering techniques by attempting to find (all) subgroups of genes with similar expression patterns under to-be-identified subsets of experimental conditions...
Sequence features associated with microRNA strand selection in humans and flies
Hu, Hai Yang, Yan, Zheng, Xu, Ying, Hu, Hao, Menzel, Corinna, Zhou, Yan Hong, ...
Computational prediction of human proteins that can be secreted into the bloodstream
Cui, Juan, Liu, Qi, Puett, David, Xu, Ying
We present a novel computational method for predicting which proteins from highly and abnormally expressed genes in diseased human tissues, such as cancers, can be secreted into the bloodstream,...
De novo computational prediction of non-coding RNA genes in prokaryotic genomes
Tran, Thao T., Zhou, Fengfeng, Marshburn, Sarah, Stead, Mark, Kushner, Sidney R., Xu, Ying
Motivation: The computational identification of non-coding RNA (ncRNA) genes represents one of the most important and challenging problems in computational biology. Existing methods for ncRNA gene...