Research on Artificial Psychology Based on Multimodal Interactive Service Robot (2009)
Jun Yu, Zhiliang Wang, Lun Xie, Yongxiang Xia
Abstract—In the field of human robot interaction (HRI), providing robot with emotions and psychology like human can be useful to achieve natural interaction. Previous HRI research focused on issues...
Wang, Da-Peng, Wan, Hao-Lei, Zhang, Song, Yu, Jun
Abstract Background Over the past two decades, there have been several approximate methods that adopt different mutation models and used for estimating nonsynonymous and synonymous substitution rates...
Ding, Feng, Tang, Petrus, Hsu, Mei-Hua, Cui, Peng, Hu, Songnian, Yu, Jun, ...
Abstract Background Streptococcus pneumoniae serotype 14 is one of the most common pneumococcal serotypes that cause invasive pneumococcal diseases worldwide. Serotype 14 often expresses resistance...
Zhu, Jingui, Sun, Yongqiao, Zhao, Fa-Qing, Yu, Jun, Craig, Roger, Hu, Songnian
Abstract Background Tarantula has been used as a model system for studying skeletal muscle structure and function, yet data on the genes expressed in tarantula muscle are lacking. Results We...
Abstract Background Divergently-paired genes (DPGs) are defined as two adjacent genes that are transcribed toward the opposite direction (or from different DNA strands) and shared their transcription...
Chen, Wie-Hua, Ge, Xiaomeng, Wang, Weiwei, Yu, Jun, Hu, Songnian
Abstract Background Diapause is a reversible state of developmental suspension and found among diverse taxa, from plants to animals, including marsupials and some other mammals. Although previous...
Symmetric subgroups of automorphism groups of compact simple Lie algebras (2009)
Thesis (M.Phil.)--Hong Kong University of Science and Technology, 2009
A Prototype Sketch-Based Architectural Design (2008)
Widely used for architectural design, CAD systems such as AutoCAD, provide powerful modeling functionalities. However, they are often too complex for an architect to use, especially during the...
LIM only 4is overexpressed in late stage pancreas cancer (2008)
Yu, Jun, Ohuchida, Kenoki, Nakata, Kohei, Mizumoto, Kazuhiro, Cui, Lin, Fujita, Hayato, ...
Abstract Background LIM-only 4 (LMO4), a member of the LIM-only (LMO) subfamily of LIM domain-containing transcription factors, was initially reported to have an oncogenic role in breast cancer. We...
Ge, Xiaomeng, Chen, Weihua, Song, Shuhui, Wang, Weiwei, Hu, Songnian, Yu, Jun
Abstract Background The mature embryo of rice ( Oryza sativa, L .) is a synchronized and integrated tissue mass laying the foundation at molecular level for its growth, development, and...
Li, Limei, Fei, Zhaoliang, Ren, Jianke, Sun, Ruilin, Liu, Zhihui, Sheng, Zhejin, ...
Abstract Background Interleukin 1 beta (IL-1β) plays an important role in a number of chronic and acute inflammatory diseases. To understand the role of IL-1β in disease processes and develop an in...
How many human genes can be defined as housekeeping with current expression data? (2008)
Zhu, Jiang, He, Fuhong, Song, Shuhui, Wang, Jing, Yu, Jun
Abstract Background Housekeeping (HK) genes are ubiquitously expressed in all tissue/cell types and constitute a basal transcriptome for the maintenance of basic cellular functions. Partitioning...
Centre Of Biostochastics, Bo Ranneby, Jun Yu, Bo Ranneby, Jun Yu
In this paper, a new approach for classification of multitemporal satellite data sets, combining multispectral and change detection techniques is proposed. The algorithm is based on the nearest...
An Algorithm for VLSI Implementation of Highly Efficient Cubic-Polynomial Evaluation (2008)
Fan Mo, Yihua Zhang, Jun Yu, Qianling Zhang
Abstract ⎯ In this paper, we present a novel cubic-polynomial evaluation algorithm. It is suitable for VLSI implementation and the computational cost is reduced to about 66 % of the previously...
Interval Testing Strategies Applied to COSY’s Interval and Taylor Model Arithmetic (2008)
Abstract. The COSY Infinity software package by Berz et al. is widely used in the beam physics community. We report execution-based testing of its interval and Taylor model arithmetics. The testing...
Letter Origin and evolution of new exons in rodents (2008)
Wen Wang, Hongkun Zheng, Shuang Yang, Haijing Yu, Jun Li, Huifeng Jiang, ...
Gene number difference among organisms demonstrates that new gene origination is a fundamental biological process in evolution. Exon shuffling has been universally observed in the formation of new...
A Development of the Recoil Rod Pull Force Measurement System Using the Load Cell with Sleeve (2008)
Park, Ju-Ho, Hong, Sung-Soo, Yu, Jun
This paper presents a development of the recoil rod pull force measurement system suing the load cell with a sleeve normally available in the recoil system test. The commercial load cell cannot be...
Velocity and DCM Partial Matching Methods for Ship Flexure Compensation of Transfer Alignment (2008)
Park, You--Lim, Song, Ki-Won, Yu, Jun
This paper is concerned with a transfer alignment of SDINS under ship motions. To reduce alignment errors induced by the ship body flexure, an error compensation method is suggested based on velocity...
VFDB 2008 release: an enhanced web-based resource for comparative pathogenomics (2008)
Yang, Jian, Chen, Lihong, Sun, Lilian, Yu, Jun, Jin, Qi
Virulence factor database (VFDB) was set up in 2004 dedicated for providing current knowledge of virulence factors (VFs) from various medical significant bacterial pathogens to facilitate...
A novel DNA sequence periodicity decodes nucleosome positioning (2008)
Chen, Kaifu, Meng, Qingshu, Ma, Lina, Liu, Qingyou, Tang, Petrus, Chiu, Chungshung, ...
There have been two types of well-characterized DNA sequence periodicities; both are found to be associated with important molecular mechanisms. One is a 3-nt periodicity corresponding to codon...
Leung, Wai K., Wu, Kai-chun, Wong, Christine Y. P., Cheng, Alfred S. L., Ching, Arthur K. K., Chan, Anthony W. H., ...
Cyclooxoygenase (COX)-2 overexpression is involved in gastric carcinogenesis. While high-salt intake is a known risk factor for gastric cancer development, we determined the effects of high salt on...
Do Stock Returns Follow A Finite Variance Distribution? 1 (2007)
In this paper we propose a test statistic to discriminate between models with nite variance and models with in nite variance. The test statistic is the ratio of the sample standard deviation and the...
Summary This paper reviews the general Bayesian approach to parameter estimation in stochastic volatility models with posterior computations performed by Gibbs sampling. The main purpose is to...
One of the key open problems in large-scale DNA sequence assembly is the correct reconstruction of sequences that contain repeats. A long repeat can confound a sequence assembler into falsely...
A second generation human haplotype map of over 3.1 million SNPs (2007)
Frazer, Kelly A., Ballinger, Dennis G., Cox, David R., Hinds, David A., Stuve, Laura L., Gibbs, Richard A., ...
We describe the Phase II HapMap, which characterizes over 3.1 million human single nucleotide polymorphisms (SNPs) genotyped in 270 individuals from four geographically diverse populations and...
Song, Shuhui, Qu, Hongzhu, Chen, Chen, Hu, Songnian, Yu, Jun
Abstract Background It was proposed that differentially-expressed genes, aside from genetic variations affecting protein processing and functioning, between hybrid and its parents provide essential...
Chen, Ailiang, Guo, Min, Yu, Jun
A non-invasive electrorotation (ROT) technique was used to monitor the apoptosis-induced changes in HL-60 cells. The specific membrane capacitance of the cells fell from 15.6 +/- 0.9 mF/cm(2) stop to...
Cui, Peng, Ji, Rimutu, Ding, Feng, Qi, Dan, Gao, Hongwei, Meng, He, ...
Abstract Background The family Camelidae that evolved in North America during the Eocene survived with two distinct tribes, Camelini and Lamini. To investigate the evolutionary relationship between...
Chen, Ailiang, Wang, Lei, Guo, Min, Yu, Jun
The specific membrane capacitance and conductance of mammalian cells reflect the surface morphological complexities and barrier functions of cell membrane, respectively, and could potentially respond...
A Genome-wide Microsatellite Polymorphism Database for the Indica and Japonica Rice (2007)
Zhang, Zhonghua, Deng, Yajun, Tan, Jun, Hu, Songnian, Yu, Jun, Xue, Qingzhong
Microsatellite (MS) polymorphism is an important source of genetic diversity, providing support for map-based cloning and molecular breeding. We have developed a new database that contains 52 845...
Existence of Universal Entangler (2007)
Chen, Jianxin, Duan, Runyao, Ji, Zhengfeng, Ying, Mingsheng, Yu, Jun
A gate is called entangler if it transforms some (pure) product states to entangled states. A universal entangler is a gate which transforms all product states to entangled states. In practice, a...
Gorodkin, Jan, Cirera, Susanna, Hedegaard, Jakob, Gilchrist, Michael J, Panitz, Frank, Jørgensen, Claus, ...
Background Knowledge of the structure of gene expression is essential for mammalian transcriptomics research. We analyzed a collection of more than one million porcine expressed sequence tags (ESTs),...
Yu, Jun, Guo, Qing-Long, You, Qi-Dong, Zhao, Li, Gu, Hong-Yan, Yang, Yong, ...
Molecular mechanisms of cell-cycle arrest caused by gambogic acid (GA), a natural product isolated from the gamboge resin of Garcinia hanburryi tree, have been investigated using BGC-823 human...
Reverse-Engineering a Watermark Detector Using an Oracle (2007)
Scott Craver, Idris Atakli, Jun Yu
The Break Our Watermarking System (BOWS) contest gave researchers three months to defeat an unknown watermark, given three marked images and online access to a watermark detector. The authors...
Indirect Inference for Dynamic Panel Models ∗ (2007)
It is well-known that maximum likelihood (ML) estimation of the autoregressive parameter of a dynamic panel data model with fixed effectsisinconsistent under...
2007 Gorodkin et Volume al. 8, Issue 4, Article R45 Open Access (2007)
Jan Gorodkin, Susanna Cirera, Jakob Hedegaard, Michael J Gilchrist, Frank Panitz, Claus Jørgensen, ...
Porcine transcriptome analysis based on 97 non-normalized cDNA libraries and assembly of 1,021,891 expressed sequence tags
Chen, Ying, Chen, Hua, Yu, Jun, Williams, James S., Craig, Vince
Focused ion beam (FIB) milling system has been used to create nanosized patterns as the template for patterned growth of carbon nanotubes on Si substrate surface without predeposition of metal...
Aligned carbon nanotubes (CNTs) can be readily synthesized on quartz or silicon-oxide-coated Si substrates using a chemical vapor deposition method, but it is difficult to grow them on pure Si...
Influence of nitriding gases on the growth of boron nitride nanotubes (2007)
Yu, Jun, Li, Bill C.P., Zou, Jin, Chen, Ying
Boron nitride (BN) nanotubes of different sizes and tubular structures exhibit very different mechanical and chemical properties, as well as different applications. BN nanotubes of different sizes...
Reverse-Engineering a Watermark Detector Using an Oracle (2007)
Scott Craver, Idris Atakli, Jun Yu
The Break Our Watermarking System (BOWS) contest gave researchers three months to defeat an unknown watermark, given three marked images and online access to a watermark detector. The authors...
Chang, Suhua, Zhang, Jiajie, Liao, Xiaoyun, Zhu, Xinxing, Wang, Dahai, Zhu, Jiang, ...
Frequent outbreaks of highly pathogenic avian influenza and the increasing data available for comparative analysis require a central database specialized in influenza viruses (IVs). We have...
Chen, Ying, Chen, Hua, Yu, Jun, Williams, James S., Craig, Vince
Focused ion beam (FIB) milling system has been used to create nanosized patterns as the template for patterned growth of carbon nanotubes on Si substrate surface without predeposition of metal...
Aligned carbon nanotubes (CNTs) can be readily synthesized on quartz or silicon-oxide-coated Si substrates using a chemical vapor deposition method, but it is difficult to grow them on pure Si...
Influence of nitriding gases on the growth of boron nitride nanotubes (2007)
Yu, Jun, Li, Bill C.P., Zou, Jin, Chen, Ying
Boron nitride (BN) nanotubes of different sizes and tubular structures exhibit very different mechanical and chemical properties, as well as different applications. BN nanotubes of different sizes...
Design and fabrication of an automated microchip-based cell separation device (2007)
Yu, Jun, Zhu, Jiang, Wang, Lei, Guo, Min
A microchip-based cell separation system was developed and fabricated by integrating traveling-wave dielectrophoresis and laminar flow on a single biochip-based device. Numerical simulations...
Critical function of Bmx/Etk in ischemia-mediated arteriogenesis and angiogenesis (2006)
Luo, Yan, Tang, Shibo, Rajantie, Iiro, Salven, Petri, Heil, Matthias, ...
Bmx/Etk non-receptor tyrosine protein kinase has been implicated in endothelial cell migration and tube formation in vitro. However, the role of Bmx in vivo is not known. Bmx is highly induced in the...
The evolution of Chinese consumers on the internet and its implications for marketing (2006)
China, with its rapid economic development, has become an important consumer market. A fast growing component of this market is its increasingly large internet population. This study examines the...
The evolution of Chinese consumers on the internet and its implications for marketing (2006)
China, with its rapid economic development, has become an important consumer market. A fast growing component of this market is its increasingly large internet population. This study examines the...
Zhang, Bing, Liu, Qinghua, Yin, Wei, Zhang, Xiaowei, Huang, Yijun, Luo, Yingfeng, ...
Abstract Background The snake venom gland is a specialized organ, which synthesizes and secretes the complex and abundant toxin proteins. Though gene expression in the snake venom gland has been...
Computing Ka and Ks with a consideration of unequal transitional substitutions (2006)
Zhang, Zhang, Li, Jun, Yu, Jun
Abstract Background Approximate methods for estimating nonsynonymous and synonymous substitution rates (Ka and Ks) among protein-coding sequences have adopted different mutation (substitution)...
Ma, Zongyuan, Yu, Jun, Kang, Le
Abstract Background The migratory locust ( Locusta migratoria ) is an orthopteran pest and a representative member of hemimetabolous insects for biological studies. Its transcriptomic data provide...
The DNA sequence, annotation and analysis of human chromosome 3 (2006)
Muzny, Donna M., Scherer, Steven E., Kaul, Rajinder, Wang, Jing, Yu, Jun, ...
The DNA sequence, annotation and analysis of human chromosome 3 (2006)
Muzny, Donna M., Scherer, Steven E., Kaul, Rajinder, Wang, Jing, Yu, Jun, ...
The DNA sequence, annotation and analysis of human chromosome 3 (2006)
Muzny, Donna M., Scherer, Steven E., Kaul, Rajinder, Wang, Jing, Yu, Jun, ...
Yu, Jun, Bergaya, Sonia, Murata, Takahisa, Alp, Ilkay F, Bauer, Michael P, Lin, Michelle I, ...
Caveolae in endothelial cells have been implicated as plasma membrane microdomains that sense or transduce hemodynamic changes into biochemical signals that regulate vascular function. Therefore we...
Yu, Jun, Ip, Emilia, Pena, Aileen Dela, Hou, Jing Yun, Sesha, Jayshree, Pera, Natasha, ...
Yes
Yu, Jun, Ip, Emilia, Pena, Aileen Dela, Hou, Jing Yun, Sesha, Jayshree, Pera, Natasha, ...
Yes
Jinghui Huang, Libing Liu, Yumei Zhou, Jun Yu, Jiao Deng
Using an animal model of colonic inflammation, the effects of intrathecal (i.t.) diazepam (0.02mg/kg, 0.08mg/kg and 0.15mg/kg) on visceral pain-related behaviors and hyperalgesia associated with...
Purification of boron nitride nanotubes (2006)
Chen, Hua, Chen, Ying, Yu, Jun, Williams, James S.
A purification process was developed for the first time for boron nitride (BN) nanotubes. BN nanotubes, prepared using a ball milling and annealing method, contain a high yield of nanotubes and a...
Scratching carbon nanotubes onto Si substrates (2006)
Large-scale, high-density, and patterned carbon nanotubes (CNTs) on both pure Si and quartz (SiO2) substrates have been produced using different approaches. The CNTs were synthesized by pyrolysis of...
Conical boron nitride nanorods synthesized via the ball-milling and annealing method (2006)
Zhang, Hongzhou, Yu, Jun, Chen, Ying, Fitz Gerald, John
A boron nitride (BN) nanostructure, conical BN nanorod, has been synthesized in a large quantity on Si substrates for the first time via the ball-milling and annealing method. Nitridation of milled...
Growth and structure of prismatic boron nitride nanorods (2006)
Zhang, Hongzhou, FitzGerald, John D., Chadderton, Lewis T., Yu, Jun, Chen, Ying
Prismatic boron nitride nanorods have been grown on single crystal silicon substrates by mechanical ball-milling followed by annealing at 1300 °C. Growth takes place by rapid surface diffusion of...
Chang, Suhua, Zhang, Jiajie, Liao, Xiaoyun, Zhu, Xinxing, Wang, Dahai, Zhu, Jiang, ...
Frequent outbreaks of highly pathogenic avian influenza and the increasing data available for comparative analysis require a central database specialized in influenza viruses (IVs). We have...
Chang, Suhua, Zhang, Jiajie, Liao, Xiaoyun, Zhu, Xinxing, Wang, Dahai, Zhu, Jiang, ...
Frequent outbreaks of highly pathogenic avian influenza and the increasing data available for comparative analysis require a central database specialized in influenza viruses (IVs). We have...
ShiBASE: an integrated database for comparative genomics of Shigella (2006)
Yang, Jian, Chen, Lihong, Yu, Jun, Sun, Lilian, Jin, Qi
Among the major enteric bacterial pathogens, Shigella is found to display extreme genome diversity and dynamics, which imposes a challenge in comparative genomic studies. To facilitate further...
Purification of boron nitride nanotubes (2006)
Chen, Hua, Chen, Ying, Yu, Jun, Williams, James S.
A purification process was developed for the first time for boron nitride (BN) nanotubes. BN nanotubes, prepared using a ball milling and annealing method, contain a high yield of nanotubes and a...
Scratching carbon nanotubes onto Si substrates (2006)
Large-scale, high-density, and patterned carbon nanotubes (CNTs) on both pure Si and quartz (SiO2) substrates have been produced using different approaches. The CNTs were synthesized by pyrolysis of...
Conical boron nitride nanorods synthesized via the ball-milling and annealing method (2006)
Zhang, Hongzhou, Yu, Jun, Chen, Ying, Fitz Gerald, John
A boron nitride (BN) nanostructure, conical BN nanorod, has been synthesized in a large quantity on Si substrates for the first time via the ball-milling and annealing method. Nitridation of milled...
Growth and structure of prismatic boron nitride nanorods (2006)
Zhang, Hongzhou, FitzGerald, John D., Chadderton, Lewis T., Yu, Jun, Chen, Ying
Prismatic boron nitride nanorods have been grown on single crystal silicon substrates by mechanical ball-milling followed by annealing at 1300 °C. Growth takes place by rapid surface diffusion of...
Chang, Suhua, Zhang, Jiajie, Liao, Xiaoyun, Zhu, Xinxing, Wang, Dahai, Zhu, Jiang, ...
Frequent outbreaks of highly pathogenic avian influenza and the increasing data available for comparative analysis require a central database specialized in influenza viruses (IVs). We have...
Chang, Suhua, Zhang, Jiajie, Liao, Xiaoyun, Zhu, Xinxing, Wang, Dahai, Zhu, Jiang, ...
Frequent outbreaks of highly pathogenic avian influenza and the increasing data available for comparative analysis require a central database specialized in influenza viruses (IVs). We have...
Comment: A Selective Overview of Nonparametric Methods in Financial Econometrics (2005)
Phillips, Peter C. B., Yu, Jun
These comments concentrate on two issues arising from Fan’s overview. The first concerns the importance of finite sample estimation bias relative to the specification and discretization biases that...
Dwyer, Rex A., Huitema, Edgar, Beyer, Katinka, Cvitanich, Cristina, Kelkar, Hemant, ...
To overview the gene content of the important pathogen Phytophthora infestans, large-scale cDNA and genomic sequencing was performed. A set of 75,757 high-quality expressed sequence tags (ESTs) from...
Dwyer, Rex A., Huitema, Edgar, Beyer, Katinka, Cvitanich, Cristina, Kelkar, Hemant, ...
To overview the gene content of the important pathogen Phytophthora infestans, large-scale cDNA and genomic sequencing was performed. A set of 75,757 high-quality expressed sequence tags (ESTs) from...
Ruiqiang Li, Jia Ye, Songgang Li, Jing Wang, Yujun Han, Chen Ye, ...
We describe an algorithm, ReAS, to recover ancestral sequences for transposable elements (TEs) from the unassembled reads of a whole genome shotgun. The main assumptions are that these TEs must exist...
Ruiqiang Li, Jia Ye, Songgang Li, Jing Wang, Yujun Han, Chen Ye, ...
We describe an algorithm ReAS to recover ancestral sequences for transposable elements (TEs) from the unassembled reads of a whole genome shotgun. The main assumptions are that these TEs must exist...
Pigs in sequence space: A 0.66X coverage pig genome survey based on shotgun sequencing (2005)
Wernersson, Rasmus, Schierup, Mikkel H, Jørgensen, Frank G, Gorodkin, Jan, Panitz, Frank, Stærfeldt, Hans-Henrik, ...
Abstract Background Comparative whole genome analysis of Mammalia can benefit from the addition of more species. The pig is an obvious choice due to its economic and medical importance as well as its...
The Genomes of Oryza sativa: A History of Duplications (2005)
Jun Yu, Jun Wang, Wei Lin, Songgang Li, Heng Li, Jun Zhou, ...
Comparative genome sequencing of indica and japonica rice reveals that duplication of genes and genomic regions has played a major part in the evolution of grass genomes.
The Genomes of Oryza sativa: A History of Duplications (2005)
Jun Yu, Jun Wang, Wei Lin, Songgang Li, Heng Li, Jun Zhou, ...
We report improved whole-genome shotgun sequences for the genomes of indica and japonica rice, both with multimegabase contiguity, or almost 1,000-fold improvement over the drafts of 2002. Tested...
This work is an attempt to develop a robust and practical methodology to identify structural systems with a limited number of sensors and actuators (incomplete set of measurements), particularly for...
On Leverage in a Stochastic Volatility Model (2005)
This note is concerned with specification for modelling financial leverage e#ect in the context of stochastic volatility (SV) models. Two alternative specifications coexist in the literature. One is...
Pigs in sequence space: a 0.66X coverage pig genome survey based on shotgun sequencing (2005)
Bmc Genomics, Rasmus Wernersson, Mikkel H Schierup, Frank G Jørgensen, Jan Gorodkin, Frank Panitz, ...
Research article
J: SilkDB: a knowledgebase for silkworm biology and genomics (2005)
Jing Wang, Qingyou Xia, Ximiao He, Mingtao Dai, Jue Ruan, Jie Chen, ...
The Silkworm Knowledgebase (SilkDB) is a webbased repository for the curation, integration and study of silkworm genetic and genomic data. With the recent accomplishment of a 6X draft genome sequence...
Heng, Lee Yook, Chou, Alison, Yu, Jun, Chen, Ying, Gooding, J. Justin
The modification of glassy carbon electrodes with random dispersions of nanotubes is currently the most popular approach to the preparation of carbon nanotube modified electrodes. The performance of...
In situ formation of BN nanotubes during nitriding reactions (2005)
Yu, Jun, Chen, Ying, Wuhrer, Richard, Liu, Zongwen, Ringer, Simon P.
High-yield multiwalled boron nitride (BN) nanotubes have been produced using a ball milling-annealing method. The BN nanotubes with a diameter less than 10 nm and a well-crystallized multiwalled...
Department: Civil Engineering and Engineering Mechanics.
VFDB: a reference database for bacterial virulence factors (2005)
Chen, Lihong, Yang, Jian, Yu, Jun, Yao, Zhijian, Sun, Lilian, Shen, Yan, ...
Bacterial pathogens continue to impose a major threat to public health worldwide in the 21st century. Intensified studies on bacterial pathogenesis have greatly expanded our knowledge about the...
SilkDB: a knowledgebase for silkworm biology and genomics (2005)
Wang, Jing, Xia, Qingyou, He, Ximiao, Dai, Mingtao, Ruan, Jue, Chen, Jie, ...
The Silkworm Knowledgebase (SilkDB) is a web-based repository for the curation, integration and study of silkworm genetic and genomic data. With the recent accomplishment of a ∼6X draft genome...
ChickVD: a sequence variation database for the chicken genome (2005)
Wang, Jing, He, Ximiao, Ruan, Jue, Dai, Mingtao, Chen, Jie, Zhang, Yong, ...
Working in parallel with the efforts to sequence the chicken (Gallus gallus) genome, the Beijing Genomics Institute led an international team of scientists from China, USA, UK, Sweden, The...
Jackknifing Bond Option Prices (2005)
Phillips, Peter C. B., Yu, Jun
Prices of interest rate derivative securities depend crucially on the mean reversion parameters of the underlying diffusions. These parameters are subject to estimation bias when standard methods are...
Chiu, Cheng-Hsun, Tang, Petrus, Chu, Chishih, Hu, Songnian, Bao, Qiyu, Yu, Jun, ...
Salmonella enterica serovar Choleraesuis (S.Choleraesuis), a highly invasive serovar among non-typhoidal Salmonella, usually causes sepsis or extra-intestinal focal infections in humans....
Yu, Jun, Wu, Jenny, Francis, Kevin P., Purchio, Tony F., Kadurugamuwa, Jagath L.
Objectives: To investigate in vivo fitness of rifampicin-resistant Staphylococcus aureus mutants in a mouse biofilm model using bioluminescence imaging. Materials and methods: S. aureus was...
Origin and evolution of new exons in rodents (2005)
Wang, Wen, Zheng, Hongkun, Yang, Shuang, Yu, Haijing, Li, Jun, Jiang, Huifeng, ...
Gene number difference among organisms demonstrates that new gene origination is a fundamental biological process in evolution. Exon shuffling has been universally observed in the formation of new...
Evolution of alternative splicing after gene duplication (2005)
Su, Zhixi, Wang, Jianmin, Yu, Jun, Huang, Xiaoqiu, Gu, Xun
Alternative splicing and gene duplication are two major sources of proteomic function diversity. Here, we study the evolutionary trend of alternative splicing after gene duplication by analyzing the...
Yu, Jun, Wu, Jenny, Francis, Kevin P., Purchio, Tony F., Kadurugamuwa, Jagath L.
Objectives: To investigate in vivo fitness of rifampicin-resistant Staphylococcus aureus mutants in a mouse biofilm model using bioluminescence imaging. Materials and methods: S. aureus was...
Jackknifing Bond Option Prices* (2005)
Phillips, Peter C. B., Yu, Jun
Prices of interest rate derivative securities depend crucially on the mean reversion parameters of the underlying diffusions. These parameters are subject to estimation bias when standard methods are...
Yang, Fan, Yang, Jian, Zhang, Xiaobing, Chen, Lihong, Jiang, Yan, Yan, Yongliang, ...
The Shigella bacteria cause bacillary dysentery, which remains a significant threat to public health. The genus status and species classification appear no longer valid, as compelling evidence...
Heng, Lee Yook, Chou, Alison, Yu, Jun, Chen, Ying, Gooding, J. Justin
The modification of glassy carbon electrodes with random dispersions of nanotubes is currently the most popular approach to the preparation of carbon nanotube modified electrodes. The performance of...
In situ formation of BN nanotubes during nitriding reactions (2005)
Yu, Jun, Chen, Ying, Wuhrer, Richard, Liu, Zongwen, Ringer, Simon P.
High-yield multiwalled boron nitride (BN) nanotubes have been produced using a ball milling-annealing method. The BN nanotubes with a diameter less than 10 nm and a well-crystallized multiwalled...
A genetic variation map for chicken with 2.8 million single-nucleotide polymorphisms (2004)
Liu, Bin, Wang, Jun, Zhang, Yong, Yang, Xu, Zhang, Zengjin, ...
We describe a genetic variation map for the chicken genome containing 2.8 million single-nucleotide polymorphisms (SNPs). This map is based on a comparison of the sequences of three domestic chicken...
Complete genome sequence of Yersinia pestis strain 91001, an isolate avirulent to humans (2004)
Tong, Zongzhong, Wang, Jin, Wang, Li, Guo, Zhaobiao, Han, Yanpin, ...
Genomics provides an unprecedented opportunity to probe in minute detail into the genomes of the world's most deadly pathogenic bacteria- Yersinia pestis. Here we report the complete genome sequence...
Content-based temporal and spatial segmentation of motion pictures / (2004)
Thesis (Ph. D. in Electrical Engineering)--Southern Methodist University.
Deviance information criterion for comparing stochastic volatility models (2004)
Andreas Berg, Renate Meyer, Jun Yu
Bayesian methods have been ecient in estimating parameters of stochastic volatility models for analyzing nancial time series. Recent advances made it possible to t stochastic volatility models of...
Deviance Information Criterion for Comparing (2004)
Stochastic Volatility Models, Andreas Berg, Renate Meyer, Jun Yu
Bayesian methods have been e#cient in estimating parameters of stochastic volatility models for analyzing financial time series. Recent advances made it possible to fit stochastic volatility models...
Complete Genome Sequence of Yersinia pestis Strain 91001, an Isolate Avirulent to Humans (2004)
Song, Yajun, Tong, Zongzhong, Wang, Jin, Wang, Li, Guo, Zhaobiao, Han, Yanpin, ...
Genomics provides an unprecedented opportunity to probe in minute detail into the genomes of the world's most deadly pathogenic bacteria-Yersinia pestis. Here we report the complete genome sequence...
Zhao, Wenming, Wang, Jing, He, Ximiao, Huang, Xiaobing, Jiao, Yongzhi, Dai, Mingtao, ...
Rice is a major food staple for the world’s population and serves as a model species in cereal genome research. The Beijing Genomics Institute (BGI) has long been devoting itself to sequencing,...
Loss of beta-catenin expression in metastatic gastric cancer (2003)
Ebert,Matthias P. A., Yu,Jun, Hoffmann,Juliane, Rocco,Alba, Röcken,Christoph, Kahmann,Sabine, ...
Loss of beta-catenin expression in metastatic gastric cancer (2003)
Ebert, Matthias P. A., Yu, Jun, Hoffmann, Juliane, Rocco, Alba, Röcken, Christoph, Kahmann, Sabine, ...
A Population Threshold for Functional Polymorphisms (2003)
Wong, Gane Ka-Shu, Yang, Zhiyong, Passey, Douglas A., Kibukawa, Miho, Paddock, Marcia, Liu, Chun-Rong, ...
We sequenced 114 genes (for DNA repair, cell cycle arrest, apoptosis, and detoxification)in a mixed human population and observed a sudden increase in the number of functional polymorphisms below a...
Dimethyl Ether (DME) Spary Charcteristics in a Common-rail Fuel Injection System (2003)
Fundamental spray characteristics of DME (Dimethyl Ether) and conventional diesel were investigated in a constant volume vessel pressurized by nitrogen gas. A common-rail fuel injection system was...
Dimethyl ether (DME) spray characteristics in a common-rail fuel injection system (2003)
The fundamental spray characteristics of dimethyl ether (DME) and conventional diesel were investigated in a constant-volume vessel pressurized by nitrogen gas. A common-rail fuel injection system...
In this note we represent the well known discrete time stochastic volatility (SV) model with a leverage effect and the SV model of Jacquier, Polson and Rossi (JPR) (2002) using Gaussian nonlinear...
Jacknifing Bond Option Prices (2002)
In continuous time specifications, the prices of interest rate derivative securities depend crucially on the mean reversion parameter of the associated interest rate diffusion equation. This...
Dimethyl ether (DME) Spray Characteristics in Common-Rail High Pressure Injection Equipment (2002)
Bae, Coongsik, Yu, Jun, Lee, Jukwang
14th ISAF (International Symposium on Alcohol Fuels, Phuket, 2002. 11.
Yu, Jun, Lee, Jookwang, Bae, Choongsik
Dimethyl Ether (DME) has been considered as one of the most attractive alternative fuels for compression ignition engine. Its main advantage in compression-ignition engine application is high...
Estimation of Hyperbolic Diffusion using MCMC Method (2002)
Tse, Y.K., Zhang, Bill, Yu, Jun
In this paper we propose a Bayesian method for estimating hyperbolic diffusion models. The approach is based on the Markov Chain Monte Carlo (MCMC) method after discretization via the Milstein...
The Influence of Injector Parameters on Diesel Spray (2002)
Bae, Choongsik, Yu, Jun, Kang, Jinsuk, Kong, Jangsik, Cruenca, Roy, Lee, Kyung Ook
Diesel injection nozzles, incorporated with common-rail high pressure injection system, have the variety in its geometries. The design parameters of injection nozzle need to meet the requirement of...
A Class of Nonlinear Stochastic Volatility Models (2002)
This paper proposes a class of stochastic volatility (SV) models which offers an alternative to the one introduced in Andersen (1994). The class encompasses all standard SV models that have appeared...
Berg, Andreas, Meyer, Renate, Yu, Jun
Bayesian methods have proven very efficient in estimating parameters of stochastic volatility (SV) models for analysing financial time series. Recent work extends the basic stochastic volatility...
Factors affecting diffusion patterns for new products: An hierarchical Bayesian mixture model (2002)
Our major objective is to study the relationship between some variables and new product growth patterns by efficiently utilizing several sources of information, which include: (1)Â sales histories...
Ebert,Matthias. P. A., Fei,Guo, Kahmann,Sabine, Müller,Oliver, Yu,Jun, Sung,Joseph J. Y., ...
beta-Catenin is critical for intercellular adhesion and also plays a role as a transcription activating protein in the Wnt signalling pathway. Increased protein levels and mutation of the...
Yu, Jun, Yang, Zhenlin, Zhang, Xibin
This paper proposes a class of stochastic volatility (SV) models which offers an alternative to the one introduced in Andersen (1994). The class encompasses all standard SV models that have appeared...
Estimation of Hyperbolic Diffusion Using Mcmc Method (2002)
Tse, Y.K., Zhang, Xibin, Yu, Jun
In this paper we propose a Bayesian method for estimating hyperbolic diffusion models. The approach is based on the Markov Chain Monte Carlo (MCMC) method after discretization via the Milstein...
Yu, Jun, Yang, Zhenlin, Zhang, Xibin
This paper proposes a class of stochastic volatility (SV) models which offers an alternative to the one introduced in Andersen (1994). The class encompasses all standard SV models that have appeared...
Estimation of Hyperbolic Diffusion Using Mcmc Method (2002)
Tse, Y.K., Zhang, Xibin, Yu, Jun
In this paper we propose a Bayesian method for estimating hyperbolic diffusion models. The approach is based on the Markov Chain Monte Carlo (MCMC) method after discretization via the Milstein...
Ebert, Matthias. P. A., Fei, Guo, Kahmann, Sabine, Müller, Oliver, Yu, Jun, Sung, Joseph J. Y., ...
beta-Catenin is critical for intercellular adhesion and also plays a role as a transcription activating protein in the Wnt signalling pathway. Increased protein levels and mutation of the...
MPEG-4 system development and trial investigation / (2002)
Thesis (M. Sc. (SP))--Nanyang Technological University, School of Electrical and Electronic Engineering, 2002.
Yu, Jun, Yang, Zhenlin, Zhang, Xibin
This paper proposes a class of stochastic volatility (SV) models which offers an alternative to the one introduced in Andersen (1994). The class encompasses all standard SV models that have appeared...
Estimation of Hyperbolic Diffusion Using MCMC Method (2002)
Tse, Y.K., Zhang, Xibin, Yu, Jun
In this paper we propose a Bayesian method for estimating hyperbolic diffusion models. The approach is based on the Markov Chain Monte Carlo (MCMC) method after discretization via the Milstein...
Yu, Jun, Yang, Zhenlin, Zhang, Xibin
This paper proposes a class of stochastic volatility (SV) models which offers an alternative to the one introduced in Andersen (1994). The class encompasses all standard SV models that have appeared...
Estimation of Hyperbolic Diffusion Using MCMC Method (2002)
Tse, Y.K., Zhang, Xibin, Yu, Jun
In this paper we propose a Bayesian method for estimating hyperbolic diffusion models. The approach is based on the Markov Chain Monte Carlo (MCMC) method after discretization via the Milstein...
Abstract—This work presents methods for multispectral image classification using the contextual classifiers based on Markov Random Field (MRF) models. Performance of some conventional...
This paper proposes a class of nonlinear stochastic volatility models. The proposed class encompasses many parametric stochastic volatility models that have appeared in the literature, including the...
Estimation of Hyperbolic Diffusion using MCMC Method (2002)
Y. K. Tse, Xibin Zhang, Jun Yu, Y. K. Tse, Xibin Zhang, Jun Yu
Abstract: In this paper we propose a Bayesian method for estimating hyperbolic diffusion models. The approach is based on the Markov Chain Monte Carlo (MCMC) method after discretization via the...
Estimation of Hyperbolic Diffusion using MCMC Method (2002)
Y. K. Tse, Bill Zhang, Jun Yu, Y. K. Tse, X. B. Zhang, Jun Yu
Abstract: In this paper we propose a Bayesian method for estimating hyperbolic diffusion models. The approach is based on the Markov Chain Monte Carlo (MCMC) method after discretization via the...
A Class of Nonlinear Stochastic Volatility Models (2002)
This paper proposes a class of nonlinear stochastic volatility models based on the Box-Cox transformation which o#ers an alternative to the one introduced in Andersen (1994). The proposed class...
Forecasting volatility in the New Zealand stock (2002)
This paper evaluates the performance of nine alternative models for predicting stock price volatility using daily New Zealand data. The competing models contain both simple models such as the random...
Jun Yu, Jun Yu, Zhenlin Yang, Zhenlin Yang, Xibin Zhang, Xibin Zhang, ...
estimation techniques and did not have the section on option pricing. Jun Yu has benefited greatly from conversations with Ronald Gallant and Genshiro Kitagawa, from comments and suggestions from
Minimal Introns Are Not "Junk" (2002)
Yu, Jun, Yang, Zhiyong, Kibukawa, Miho, Paddock, Marcia, Passey, Douglas A., Wong, Gane Ka-Shu
Ebert, Matthias P.A., Fei, Guo, Kahmann, Sabine, Müller, Oliver, Yu, Jun, Sung, Joseph J.Y., ...
β-Catenin is critical for intercellular adhesion and also plays a role as a transcription activating protein in the Wnt signalling pathway. Increased protein levels and mutation of the β-catenin...
Compositional Gradients in Gramineae Genes (2002)
Wong, Gane Ka-Shu, Wang, Jun, Tao, Lin, Tan, Jun, Zhang, JianGuo, Passey, Douglas A., ...
Jin, Qi, Yuan, Zhenghong, Xu, Jianguo, Wang, Yu, Shen, Yan, Lu, Weichuan, ...
We have sequenced the genome of Shigella flexneri serotype 2a, the most prevalent species and serotype that causes bacillary dysentery or shigellosis in man. The whole genome is composed of a...
A Complete Sequence of the T. tengcongensis Genome (2002)
Bao, Qiyu, Tian, Yuqing, Li, Wei, Xu, Zuyuan, Xuan, Zhenyu, Hu, Songnian, ...
RePS: A Sequence Assembler That Masks Exact Repeats Identified from the Shotgun Data (2002)
Wang, Jun, Wong, Gane Ka-Shu, Ni, Peixiang, Han, Yujun, Huang, Xiangang, Zhang, Jianguo, ...
Yu, Jun, Yang, Zhenlin, Zhang, Xibin
This paper proposes a class of stochastic volatility (SV) models which offers an alternative to the one introduced in Andersen (1994). The class encompasses all standard SV models that have appeared...
Estimation of Hyperbolic Diffusion Using MCMC Method (2002)
Tse, Y.K., Zhang, Xibin, Yu, Jun
In this paper we propose a Bayesian method for estimating hyperbolic diffusion models. The approach is based on the Markov Chain Monte Carlo (MCMC) method after discretization via the Milstein...
Forecasting Volatility:Evidence from the German Stock Market (2001)
In this paper we compare two basic approaches to forecast volatility in the German stock market. The first approach uses various univariate time series techniques while the second approach makes use...
Domain wall resistivity in epitaxial thin film microstructures (2001)
Andrew D., Yu, Jun, Rüdiger, Ulrich, Parkin, Stuart S. P.
This article reviews our recent experimental studies of domain wall (DW) resistivity in epitaxial transition metal ferromagnetic thin film microstructures with stripe domains. The results are...
This paper proposes an exact Gaussian estimator for nonlinear continuous time models of the term structure of interest rates. The approach is based on a stopping time argument that produces a...
BUGS for a Bayesian Analysis of Stochastic Volatility Models (2000)
This paper reviews the general Bayesian approach to parameter estimation in stochastic volatility models with posterior computations performed by Gibbs sampling. The main purpose is to illustrate the...
Micromagnetics of submicron (110) Fe elements (2000)
Thomas, Luc, Parkin, Stuart S. P., Yu, Jun, Rüdiger, Ulrich, Kent, Andrew D.
The magnetization processes and the domain structure of epitaxial (110) Fe submicron-sized elements are studied experimentally and with micromagnetic simulations. Magnetic force microscopy and Kerr...
Magnetotransport and magnetic properties of molecular-beam epitaxy L10 FePt thin films (2000)
Yu, Jun, Ruediger, Ulrich, Kent, Andrew D., Farrow, Robin F. C., Marks, R. F., Weller, D., ...
The magnetotransport and magnetic properties of chemically ordered (001) L10 FePt epitaxial thin films with small scale perpendicularly magnetized stripe domains have been investigated. Film growth...
Is "Junk" DNA Mostly Intron DNA? (2000)
Wong, Gane Ka-Shu, Passey, Douglas A., Huang, Ying-zong, Yang, Zhiyong, Yu, Jun
This paper proposes a new econometric methodology for the estimation of diffusion models that include a jump component. The jump component's arrival time is endogenously determined, reflecting past...
Forecasting Volatility in the New Zealand Stock Market (1999)
This paper evaluates the performance of nine alternative models for predicting stock price volatility using daily New Zealand data. The competing models contain both simple models such as the random...
A Test Statistic and Its Application in Modelling Daily Stock Returns (1999)
Shao, Qi-Man, Yu, Hao, Yu, Jun
In this paper we propose a test statistic to discriminate bctween models with finite variance and models with infinite variance. The test statistic is the ratio of the sample standard deviation and...
Knight, John, Satchell, Stephen, Yu, Jun
This paper estimates the stochastic volatility model using the empirical characteristic function method. This procedure has the same asymptotic efficiency as maximum likelihood, and is thus a...
Empirical Characteristic Function in Time Series Estimation (1999)
Since the empirical characteristic function is the Fourier transformation of the emipirical distribution function, it retains all the information in the sample but can overcome difficulties arising...
Do Topics Diffuse from Core to Periphery Journals? (1999)
Bandyopadhyay, Debasis, Yu, Jun
We examine the interests among competing topics of macroeconomics by tracing publication frequencies of these topics as recorded in the EconLit database over the period from 1969 through 1996. We...
Micromagnetics of mesoscopic epitaxial (110) Fe elements with nanoshaped ends (1999)
Yu, Jun, Rüdiger, Ulrich, Thomas, Luc, Parkin, Stuart S. P., Kent, Andrew D.
The magnetization reversal and magnetic domain configurations of 0.5-μm-wide epitaxial (110) Fe particles with rectangular and needle-shaped ends and competing magnetic anisotropies have been...
Wu, Yan, Suzuki, Yuri, Rüdiger, Ulrich, Yu, Jun, Kent, Andrew D., Nath, Tapan K., ...
We have studied the magnetoresistance (MR) of compressively strained La0.7Sr0.3MnO3 (LSMO) films in various magnetic states in order to understand the role of magnetic domain structure on...
Yu, Jun, Rüdiger, Ulrich, Kent, Andrew, Thomas, Luc, Parkin, Stuart S. P.
Magnetic force microscope (MFM) imaging in conjunction with longitudinal Kerr hysteresis loop measurements have been used to investigate the micromagnetic behavior of micron scale epitaxial (110) bcc...
Magnetoresistance, micromagnetism, and domain-wall scattering in epitaxial hcp Co films (1999)
Rüdiger, Ulrich, Yu, Jun, Kent, Andrew D., Thomas, Luc, Parkin, Stuart S. P.
Large negative magnetoresistance (MR) observed in transport measurements of hcp Co films with stripe domains were recently reported and interpreted in terms of domain-wall (DW) scattering mechanism....
Kent, Andrew D., Rüdiger, Ulrich, Yu, Jun, Thomas, Luc, Parkin, Stuart S. P.
We review our recent magnetotransport and micromagnetic studies of lithographically defined epitaxial thin film structures of bcc Fe and hcp Co with stripe domains. Micromagnetic structure and...
Magnetoresistance due to domain walls in an epitaxial microfabricated Fe wire (1998)
Rüdiger, Ulrich, Yu, Jun, Kent, Andrew D., Parkin, Stuart S. P.
The domain wall (DW) contribution to magnetoresistance has been investigated using an epitaxial microfabricated bcc (110) Fe wires of 2 μm linewidth. A strong in-plane uniaxial component to the...
Negative Domain Wall Contribution to the Resistivity of Microfabricated Fe Wires (1998)
Rüdiger, Ulrich, Yu, Jun, Zhang, S., Kent, Andrew D., Parkin, Stuart S. P.
The effect of domain walls on electron transport has been investigated in microfabricated Fe wires(0.65 to 20 my m linewidths) with controlled stripe domains. Magnetoresistance (MR) measurements as a...
Response analysis of structures including effects of soil-structure interaction (1995)
The objective of the study is to determine the structural response to external force and earthquake excitations with consideration of soil-structure interaction. The physical model concerned herein...
Response analysis of structures including effects of soil-structure interaction / (1995)
Typescript (Photocopy).
Dwivedi, Upendra N., Campbell, Wilbur H., Yu, Jun, Datla, Ruju S.S., Bogos, Robert C., Chiang, Vincent L., ...
Isothermal reaction kinetics of kraft delignification of Douglas-fir /--by Jun Yu. (1991)
Dissertation (Ph. D.)--Michigan Technological University, 1991.
Empirical Characteristic Function Estimation and Its Applications
This paper reviews the method of model-fitting via the empirical characteristic function. The advantage of using this procedure is that one can avoid difficulties inherent in calculating or...
Estimation of Hyperbolic Diffusion Using MCMC Method
In this paper we propose a Bayesian method for estimating hyperbolic diffusion models. The approach is based on the Markov Chain Monte Carlo (MCMC) method after discretization via the Milstein...
Indirect Inference for Dynamic Panel Models
It is well-known that maximum likelihood (ML) estimation of the autoregressive parameter of a dynamic panel data model with fixed effects is inconsistent under fixed time series sample size (T) and...
This paper motivates and introduces a two-stage method for estimating diffusion processes based on discretely sampled observations. In the first stage we make use of the feasible central limit theory...
Deviance Information Criterion for Comparing Stochastic Volatility Models.
Berg, Andreas, Meyer, Renate, Yu, Jun
Bayesian methods have been efficient in estimating parameters of stochastic volatility models for analyzing financial time series. Recent advances made it possible to fit stochastic volatility models...
Abstracts.
Wong, Gane K.-S., Yu, Jun, Thayer, Edward C., Olson, Maynard V.
Multiple-complete-digest mapping is a DNA mapping technique based on complete-restriction-digest fingerprints of a set of clones that provides highly redundant coverage of the mapping target. The...
Yu, Jun, Edwards-Jones, Bryn, Neyrolles, Olivier, Kroll, J. Simon
DsbA, a disulfide bond catalyst, is necessary for realization of the pathogenic potential of Shigella flexneri. Sh42, a mutant strain differing from wild-type M90TS solely because it expresses...
Francis, Kevin P., Yu, Jun, Bellinger-Kawahara, Carolyn, Joh, Danny, Hawkinson, Matthew J., Xiao, Grace, ...
Animal studies with Streptococcus pneumoniae have provided valuable models for drug development. In order to monitor long-term pneumococcal infections noninvasively in living mice, a novel...
In this study, three mutants, dsbA::kan, dsbC-kan, and dsbD-kan, of Shigella flexneri serotype 5 were constructed and characterized to investigate the role of the periplasmic thiol:disulfide...
Jin, Qi, Yuan, Zhenghong, Xu, Jianguo, Wang, Yu, Shen, Yan, Lu, Weichuan, ...
We have sequenced the genome of Shigella flexneri serotype 2a, the most prevalent species and serotype that causes bacillary dysentery or shigellosis in man. The whole genome is composed of a...
Direct Continuous Method for Monitoring Biofilm Infection in a Mouse Model
Kadurugamuwa, Jagath L., Sin, Lin, Albert, Eddie, Yu, Jun, Francis, Kevin, DeBoer, Monica, ...
We have developed a rapid, continuous method for real-time monitoring of biofilms, both in vitro and in a mouse infection model, through noninvasive imaging of bioluminescent bacteria colonized on...
Kuklin, Nelly A., Pancari, Gregory D., Tobery, Timothy W., Cope, Leslie, Jackson, Jesse, Gill, Charles, ...
Staphylococcal infections associated with catheter and prosthetic implants are difficult to eradicate and often lead to chronic infections. Development of novel antibacterial therapies requires...
RePS: A Sequence Assembler That Masks Exact Repeats Identified from the Shotgun Data
Wang, Jun, Wong, Gane Ka-Shu, Ni, Peixiang, Han, Yujun, Huang, Xiangang, Zhang, Jianguo, ...
We describe a sequence assembler, RePS (repeat-masked Phrap with scaffolding), that explicitly identifies exact 20mer repeats from the shotgun data and removes them prior to the assembly. The...
A Complete Sequence of the T. tengcongensis Genome
Bao, Qiyu, Tian, Yuqing, Li, Wei, Xu, Zuyuan, Xuan, Zhenyu, Hu, Songnian, ...
Thermoanaerobacter tengcongensis is a rod-shaped, gram-negative, anaerobic eubacterium that was isolated from a freshwater hot spring in Tengchong, China. Using a whole-genome-shotgun method, we...
Minimal Introns Are Not “Junk”
Yu, Jun, Yang, Zhiyong, Kibukawa, Miho, Paddock, Marcia, Passey, Douglas A., Wong, Gane Ka-Shu
Intron-size distributions for most multicellular (and some unicellular) eukaryotes have a sharp peak at their “minimal intron” size. Across the human population, these minimal introns exhibit an...
Rapid Direct Method for Monitoring Antibiotics in a Mouse Model of Bacterial Biofilm Infection
Kadurugamuwa, Jagath L., Sin, Lin V., Yu, Jun, Francis, Kevin P., Kimura, Richard, Purchio, Tony, ...
We have developed a rapid, continuous method for monitoring the effectiveness of several antibacterial agents in real time, noninvasively, by using a recently described mouse model of chronic biofilm...
BGI-RIS: an integrated information resource and comparative analysis workbench for rice genomics
Zhao, Wenming, Wang, Jing, He, Ximiao, Huang, Xiaobing, Jiao, Yongzhi, Dai, Mingtao, ...
Rice is a major food staple for the world’s population and serves as a model species in cereal genome research. The Beijing Genomics Institute (BGI) has long been devoting itself to sequencing,...
Is “Junk” DNA Mostly Intron DNA?
Wong, Gane Ka-Shu, Passey, Douglas A., Huang, Ying-zong, Yang, Zhiyong, Yu, Jun
Among higher eukaryotes, very little of the genome codes for protein. What is in the rest of the genome, or the “junk” DNA, that, in Homo sapiens, is estimated to be almost 97% of the genome? Is...
Mundy, Rosanna, Petrovska, Liljana, Smollett, Katherine, Simpson, Nandi, Wilson, Rebecca K., Yu, Jun, ...
Citrobacter rodentium is a member of a group of pathogens that colonize the lumen of the host gastrointestinal tract via attaching and effacing (A/E) lesion formation. C. rodentium, which causes...
A Population Threshold for Functional Polymorphisms
Wong, Gane Ka-Shu, Yang, Zhiyong, Passey, Douglas A., Kibukawa, Miho, Paddock, Marcia, Liu, Chun-Rong, ...
We sequenced 114 genes (for DNA repair, cell cycle arrest, apoptosis, and detoxification)in a mixed human population and observed a sudden increase in the number of functional polymorphisms below a...
Noninvasive Optical Imaging Method To Evaluate Postantibiotic Effects on Biofilm Infection In Vivo
Kadurugamuwa, Jagath L., Sin, Lin V., Yu, Jun, Francis, Kevin P., Purchio, Tony F., Contag, Pamela R.
Eradication of Staphylococcus aureus biofilms after rifampin treatment was tested in a mouse model of device-related infection by using biophotonic imaging. Following treatment, the bioluminescent...
A Comparison of Rice Chloroplast Genomes1[w]
Tang, Jiabin, Xia, Hong'ai, Cao, Mengliang, Zhang, Xiuqing, Zeng, Wanyong, Hu, Songnian, ...
Using high quality sequence reads extracted from our whole genome shotgun repository, we assembled two chloroplast genome sequences from two rice (Oryza sativa) varieties, one from 93-11 (a typical...
Zhou, Dongsheng, Han, Yanping, Song, Yajun, Tong, Zongzhong, Wang, Jin, Guo, Zhaobiao, ...
Genomics research provides an unprecedented opportunity for us to probe into the pathogenicity and evolution of the world's most deadly pathogenic bacterium, Yersinia pestis, in minute detail. In our...
The analysis of large-scale gene expression correlated to the phase changes of the migratory locust
Kang, Le, Chen, XiangYong, Zhou, Yan, Liu, BoWan, Zheng, Wei, Li, RuiQiang, ...
The migratory locust is one of the most notorious agricultural pests that undergo a well known reversible, density-dependent phase transition from the solitary to the gregarious. To demonstrate the...
Xiong, Yan Q., Willard, Julie, Kadurugamuwa, Jagath L., Yu, Jun, Francis, Kevin P., Bayer, Arnold S.
Therapeutic options for invasive Staphylococcus aureus infections have become limited due to rising antimicrobial resistance, making relevant animal model testing of new candidate agents more crucial...
Lucchini, Sacha, Liu, Hong, Jin, Qi, Hinton, Jay C. D., Yu, Jun
Shigella flexneri, the etiologic agent of bacillary dysentery, invades epithelial cells as well as macrophages and dendritic cells and escapes into the cytosol soon after invasion. Dissection of the...
VFDB: a reference database for bacterial virulence factors
Chen, Lihong, Yang, Jian, Yu, Jun, Yao, Zhijian, Sun, Lilian, Shen, Yan, ...
Bacterial pathogens continue to impose a major threat to public health worldwide in the 21st century. Intensified studies on bacterial pathogenesis have greatly expanded our knowledge about the...
ChickVD: a sequence variation database for the chicken genome
Wang, Jing, He, Ximiao, Ruan, Jue, Dai, Mingtao, Chen, Jie, Zhang, Yong, ...
Working in parallel with the efforts to sequence the chicken (Gallus gallus) genome, the Beijing Genomics Institute led an international team of scientists from China, USA, UK, Sweden, The...
SilkDB: a knowledgebase for silkworm biology and genomics
Wang, Jing, Xia, Qingyou, He, Ximiao, Dai, Mingtao, Ruan, Jue, Chen, Jie, ...
The Silkworm Knowledgebase (SilkDB) is a web-based repository for the curation, integration and study of silkworm genetic and genomic data. With the recent accomplishment of a ∼6X draft genome...
Endothelial-specific expression of caveolin-1 impairs microvascular permeability and angiogenesis
Bauer, Philip M., Yu, Jun, Chen, Yan, Hickey, Reed, Bernatchez, Pascal N., Looft-Wilson, Robin, ...
The functions of caveolae and/or caveolins in intact animals are beginning to be explored. Here, by using endothelial cell-specific transgenesis of the caveolin-1 (Cav-1) gene in mice, we show the...
Bucci, Mariarosaria, Roviezzo, Fiorentina, Posadas, Inmaculada, Yu, Jun, Parente, Luca, Sessa, William C., ...
The role of endothelium-derived nitric oxide (NO) in acute inflammation is not known. Here, we examine acute inflammation in congenic endothelial NO synthase-deficient (eNOS-/-) mice. Intraplantar...
Bernatchez, Pascal N., Bauer, Philip M., Yu, Jun, Prendergast, Jay S., He, Pingnian, Sessa, William C.
In endothelia, NO is synthesized by endothelial NO synthase (eNOS), which is negatively regulated by caveolin-1 (Cav-1), the primary coat protein of caveolae. We show that delivery of Cav-1 amino...
The Genomes of Oryza sativa: A History of Duplications
Yu, Jun, Wang, Jun, Lin, Wei, Li, Songgang, Li, Heng, Zhou, Jun, ...
We report improved whole-genome shotgun sequences for the genomes of indica and japonica rice, both with multimegabase contiguity, or almost 1,000-fold improvement over the drafts of 2002. Tested...
Chiu, Cheng-Hsun, Tang, Petrus, Chu, Chishih, Hu, Songnian, Bao, Qiyu, Yu, Jun, ...
Salmonella enterica serovar Choleraesuis (S.Choleraesuis), a highly invasive serovar among non-typhoidal Salmonella, usually causes sepsis or extra-intestinal focal infections in humans....
Pigs in sequence space: A 0.66X coverage pig genome survey based on shotgun sequencing
Wernersson, Rasmus, Schierup, Mikkel H, Jørgensen, Frank G, Gorodkin, Jan, Panitz, Frank, Stærfeldt, Hans-Henrik, ...
Akt1/protein kinase Bα is critical for ischemic and VEGF-mediated angiogenesis
Ackah, Eric, Yu, Jun, Zoellner, Stefan, Iwakiri, Yasuko, Skurk, Carsten, Shibata, Rei, ...
Akt, or protein kinase B, is a multifunctional serine-threonine protein kinase implicated in a diverse range of cellular functions including cell metabolism, survival, migration, and gene expression....
Yu, Jun, DeMuinck, Ebo D., Zhuang, Zhenwu, Drinane, Mary, Kauser, Katalin, Rubanyi, Gabor M., ...
The genetic loss of endothelial-derived nitric oxide synthase (eNOS) in mice impairs vascular endothelial growth factor (VEGF) and ischemia-initiated blood flow recovery resulting in critical limb...
Origin and evolution of new exons in rodents
Wang, Wen, Zheng, Hongkun, Yang, Shuang, Yu, Haijing, Li, Jun, Jiang, Huifeng, ...
Gene number difference among organisms demonstrates that new gene origination is a fundamental biological process in evolution. Exon shuffling has been universally observed in the formation of new...
Li, Ruiqiang, Ye, Jia, Li, Songgang, Wang, Jing, Han, Yujun, Ye, Chen, ...
We describe an algorithm, ReAS, to recover ancestral sequences for transposable elements (TEs) from the unassembled reads of a whole genome shotgun. The main assumptions are that these TEs must exist...
Genome dynamics and diversity of Shigella species, the etiologic agents of bacillary dysentery
Yang, Fan, Yang, Jian, Zhang, Xiaobing, Chen, Lihong, Jiang, Yan, Yan, Yongliang, ...
The Shigella bacteria cause bacillary dysentery, which remains a significant threat to public health. The genus status and species classification appear no longer valid, as compelling evidence...
ShiBASE: an integrated database for comparative genomics of Shigella
Yang, Jian, Chen, Lihong, Yu, Jun, Sun, Lilian, Jin, Qi
Among the major enteric bacterial pathogens, Shigella is found to display extreme genome diversity and dynamics, which imposes a challenge in comparative genomic studies. To facilitate further...
Compositional Gradients in Gramineae Genes
Wong, Gane Ka-Shu, Wang, Jun, Tao, Lin, Tan, Jun, Zhang, JianGuo, Passey, Douglas A., ...
In this study, we describe a property of Gramineae genes, and perhaps all monocot genes, that is not observed in eudicot genes. Along the direction of transcription, beginning at the junction of the...
Kadurugamuwa, Jagath L., Modi, Kshitij, Yu, Jun, Francis, Kevin P., Purchio, Tony, Contag, Pamela R.
Urinary tract infections (UTIs) are among the most common bacterial infections acquired by humans, particularly in catheterized patients. A major problem with catheterization is the formation of...
Yu, Jun, Bergaya, Sonia, Murata, Takahisa, Alp, Ilkay F., Bauer, Michael P., Lin, Michelle I., ...
Caveolae in endothelial cells have been implicated as plasma membrane microdomains that sense or transduce hemodynamic changes into biochemical signals that regulate vascular function. Therefore we...
Bao, JingYue, Lee, Sanggyu, Chen, Chen, Zhang, XiuQing, Zhang, Yu, Liu, SiQi, ...
Using the serial analysis of gene expression technique, we surveyed transcriptomes of three major tissues (panicles, leaves, and roots) of a super-hybrid rice (Oryza sativa) strain, LYP9, in...
Evolution of alternative splicing after gene duplication
Su, Zhixi, Wang, Jianmin, Yu, Jun, Huang, Xiaoqiu, Gu, Xun
Alternative splicing and gene duplication are two major sources of proteomic function diversity. Here, we study the evolutionary trend of alternative splicing after gene duplication by analyzing the...
Critical function of Bmx/Etk in ischemia-mediated arteriogenesis and angiogenesis
He, Yun, Luo, Yan, Tang, Shibo, Rajantie, Iiro, Salven, Petri, Heil, Matthias, ...
Bmx/Etk non-receptor tyrosine protein kinase has been implicated in endothelial cell migration and tube formation in vitro. However, the role of Bmx in vivo is not known. Bmx is highly induced in the...
Our comments on Fan’s paper will concentrate on two issues that relate in important ways to the paper’s focus on misspecification and discretization bias and the role of nonparametric methods in...
Comment on “Realized Variance and Market Microstructure Noise” by Peter R. Hansen and Asger Lunde
We find ourselves very much in agreement with the thrust of HL’s message concerning the complexity induced by microstructure noise. In particular, we agree that noise is time dependent and...
Jackknifing Bond Option Prices
In continuous time specifications, the prices of interest rate derivative securities depend crucially on the mean reversion parameter of the associated interest rate diffusion equation. This...
This paper examines the asymmetric response of equity volatility to return shocks. We generalize the news impact function (NIF), originally introduced by Engle and Ng (1993) to study asymmetric...
Multivariate Stochastic Volatility Models: Bayesian Estimation and Model Comparison
In this paper we show that fully likelihood-based estimation and comparison of multivariate stochastic volatility (SV) models can be easily performed via a freely available Bayesian software called...
On Leverage in a Stochastic Volatility Model
This paper is concerned with specification for modelling financial leverage effect in the context of stochastic volatility (SV) models. Two alternative specifications coexist in the literature. One...
Wong, Gane K.-S., Yu, Jun, Thayer, Edward C., Olson, Maynard V.
Multiple-complete-digest mapping is a DNA mapping technique based on complete-restriction-digest fingerprints of a set of clones that provides highly redundant coverage of the mapping target. The...
Yu, Jun, Edwards-Jones, Bryn, Neyrolles, Olivier, Kroll, J. Simon
DsbA, a disulfide bond catalyst, is necessary for realization of the pathogenic potential of Shigella flexneri. Sh42, a mutant strain differing from wild-type M90TS solely because it expresses...
Francis, Kevin P., Yu, Jun, Bellinger-Kawahara, Carolyn, Joh, Danny, Hawkinson, Matthew J., Xiao, Grace, ...
Animal studies with Streptococcus pneumoniae have provided valuable models for drug development. In order to monitor long-term pneumococcal infections noninvasively in living mice, a novel...
In this study, three mutants, dsbA::kan, dsbC-kan, and dsbD-kan, of Shigella flexneri serotype 5 were constructed and characterized to investigate the role of the periplasmic thiol:disulfide...
Jin, Qi, Yuan, Zhenghong, Xu, Jianguo, Wang, Yu, Shen, Yan, Lu, Weichuan, ...
We have sequenced the genome of Shigella flexneri serotype 2a, the most prevalent species and serotype that causes bacillary dysentery or shigellosis in man. The whole genome is composed of a...
Direct Continuous Method for Monitoring Biofilm Infection in a Mouse Model
Kadurugamuwa, Jagath L., Sin, Lin, Albert, Eddie, Yu, Jun, Francis, Kevin, DeBoer, Monica, ...
We have developed a rapid, continuous method for real-time monitoring of biofilms, both in vitro and in a mouse infection model, through noninvasive imaging of bioluminescent bacteria colonized on...
Kuklin, Nelly A., Pancari, Gregory D., Tobery, Timothy W., Cope, Leslie, Jackson, Jesse, Gill, Charles, ...
Staphylococcal infections associated with catheter and prosthetic implants are difficult to eradicate and often lead to chronic infections. Development of novel antibacterial therapies requires...
RePS: A Sequence Assembler That Masks Exact Repeats Identified from the Shotgun Data
Wang, Jun, Wong, Gane Ka-Shu, Ni, Peixiang, Han, Yujun, Huang, Xiangang, Zhang, Jianguo, ...
We describe a sequence assembler, RePS (repeat-masked Phrap with scaffolding), that explicitly identifies exact 20mer repeats from the shotgun data and removes them prior to the assembly. The...
A Complete Sequence of the T. tengcongensis Genome
Bao, Qiyu, Tian, Yuqing, Li, Wei, Xu, Zuyuan, Xuan, Zhenyu, Hu, Songnian, ...
Thermoanaerobacter tengcongensis is a rod-shaped, gram-negative, anaerobic eubacterium that was isolated from a freshwater hot spring in Tengchong, China. Using a whole-genome-shotgun method, we...
Minimal Introns Are Not “Junk”
Yu, Jun, Yang, Zhiyong, Kibukawa, Miho, Paddock, Marcia, Passey, Douglas A., Wong, Gane Ka-Shu
Intron-size distributions for most multicellular (and some unicellular) eukaryotes have a sharp peak at their “minimal intron” size. Across the human population, these minimal introns exhibit an...
Rapid Direct Method for Monitoring Antibiotics in a Mouse Model of Bacterial Biofilm Infection
Kadurugamuwa, Jagath L., Sin, Lin V., Yu, Jun, Francis, Kevin P., Kimura, Richard, Purchio, Tony, ...
We have developed a rapid, continuous method for monitoring the effectiveness of several antibacterial agents in real time, noninvasively, by using a recently described mouse model of chronic biofilm...
BGI-RIS: an integrated information resource and comparative analysis workbench for rice genomics
Zhao, Wenming, Wang, Jing, He, Ximiao, Huang, Xiaobing, Jiao, Yongzhi, Dai, Mingtao, ...
Rice is a major food staple for the world’s population and serves as a model species in cereal genome research. The Beijing Genomics Institute (BGI) has long been devoting itself to sequencing,...
Is “Junk” DNA Mostly Intron DNA?
Wong, Gane Ka-Shu, Passey, Douglas A., Huang, Ying-zong, Yang, Zhiyong, Yu, Jun
Among higher eukaryotes, very little of the genome codes for protein. What is in the rest of the genome, or the “junk” DNA, that, in Homo sapiens, is estimated to be almost 97% of the genome? Is...
Mundy, Rosanna, Petrovska, Liljana, Smollett, Katherine, Simpson, Nandi, Wilson, Rebecca K., Yu, Jun, ...
Citrobacter rodentium is a member of a group of pathogens that colonize the lumen of the host gastrointestinal tract via attaching and effacing (A/E) lesion formation. C. rodentium, which causes...
A Population Threshold for Functional Polymorphisms
Wong, Gane Ka-Shu, Yang, Zhiyong, Passey, Douglas A., Kibukawa, Miho, Paddock, Marcia, Liu, Chun-Rong, ...
We sequenced 114 genes (for DNA repair, cell cycle arrest, apoptosis, and detoxification)in a mixed human population and observed a sudden increase in the number of functional polymorphisms below a...
Noninvasive Optical Imaging Method To Evaluate Postantibiotic Effects on Biofilm Infection In Vivo
Kadurugamuwa, Jagath L., Sin, Lin V., Yu, Jun, Francis, Kevin P., Purchio, Tony F., Contag, Pamela R.
Eradication of Staphylococcus aureus biofilms after rifampin treatment was tested in a mouse model of device-related infection by using biophotonic imaging. Following treatment, the bioluminescent...
A Comparison of Rice Chloroplast Genomes1[w]
Tang, Jiabin, Xia, Hong'ai, Cao, Mengliang, Zhang, Xiuqing, Zeng, Wanyong, Hu, Songnian, ...
Using high quality sequence reads extracted from our whole genome shotgun repository, we assembled two chloroplast genome sequences from two rice (Oryza sativa) varieties, one from 93-11 (a typical...
Zhou, Dongsheng, Han, Yanping, Song, Yajun, Tong, Zongzhong, Wang, Jin, Guo, Zhaobiao, ...
Genomics research provides an unprecedented opportunity for us to probe into the pathogenicity and evolution of the world's most deadly pathogenic bacterium, Yersinia pestis, in minute detail. In our...
The analysis of large-scale gene expression correlated to the phase changes of the migratory locust
Kang, Le, Chen, XiangYong, Zhou, Yan, Liu, BoWan, Zheng, Wei, Li, RuiQiang, ...
The migratory locust is one of the most notorious agricultural pests that undergo a well known reversible, density-dependent phase transition from the solitary to the gregarious. To demonstrate the...
Xiong, Yan Q., Willard, Julie, Kadurugamuwa, Jagath L., Yu, Jun, Francis, Kevin P., Bayer, Arnold S.
Therapeutic options for invasive Staphylococcus aureus infections have become limited due to rising antimicrobial resistance, making relevant animal model testing of new candidate agents more crucial...
Lucchini, Sacha, Liu, Hong, Jin, Qi, Hinton, Jay C. D., Yu, Jun
Shigella flexneri, the etiologic agent of bacillary dysentery, invades epithelial cells as well as macrophages and dendritic cells and escapes into the cytosol soon after invasion. Dissection of the...
VFDB: a reference database for bacterial virulence factors
Chen, Lihong, Yang, Jian, Yu, Jun, Yao, Zhijian, Sun, Lilian, Shen, Yan, ...
Bacterial pathogens continue to impose a major threat to public health worldwide in the 21st century. Intensified studies on bacterial pathogenesis have greatly expanded our knowledge about the...
ChickVD: a sequence variation database for the chicken genome
Wang, Jing, He, Ximiao, Ruan, Jue, Dai, Mingtao, Chen, Jie, Zhang, Yong, ...
Working in parallel with the efforts to sequence the chicken (Gallus gallus) genome, the Beijing Genomics Institute led an international team of scientists from China, USA, UK, Sweden, The...
SilkDB: a knowledgebase for silkworm biology and genomics
Wang, Jing, Xia, Qingyou, He, Ximiao, Dai, Mingtao, Ruan, Jue, Chen, Jie, ...
The Silkworm Knowledgebase (SilkDB) is a web-based repository for the curation, integration and study of silkworm genetic and genomic data. With the recent accomplishment of a ∼6X draft genome...
Endothelial-specific expression of caveolin-1 impairs microvascular permeability and angiogenesis
Bauer, Philip M., Yu, Jun, Chen, Yan, Hickey, Reed, Bernatchez, Pascal N., Looft-Wilson, Robin, ...
The functions of caveolae and/or caveolins in intact animals are beginning to be explored. Here, by using endothelial cell-specific transgenesis of the caveolin-1 (Cav-1) gene in mice, we show the...
Bucci, Mariarosaria, Roviezzo, Fiorentina, Posadas, Inmaculada, Yu, Jun, Parente, Luca, Sessa, William C., ...
The role of endothelium-derived nitric oxide (NO) in acute inflammation is not known. Here, we examine acute inflammation in congenic endothelial NO synthase-deficient (eNOS-/-) mice. Intraplantar...
Bernatchez, Pascal N., Bauer, Philip M., Yu, Jun, Prendergast, Jay S., He, Pingnian, Sessa, William C.
In endothelia, NO is synthesized by endothelial NO synthase (eNOS), which is negatively regulated by caveolin-1 (Cav-1), the primary coat protein of caveolae. We show that delivery of Cav-1 amino...
The Genomes of Oryza sativa: A History of Duplications
Yu, Jun, Wang, Jun, Lin, Wei, Li, Songgang, Li, Heng, Zhou, Jun, ...
We report improved whole-genome shotgun sequences for the genomes of indica and japonica rice, both with multimegabase contiguity, or almost 1,000-fold improvement over the drafts of 2002. Tested...
Chiu, Cheng-Hsun, Tang, Petrus, Chu, Chishih, Hu, Songnian, Bao, Qiyu, Yu, Jun, ...
Salmonella enterica serovar Choleraesuis (S.Choleraesuis), a highly invasive serovar among non-typhoidal Salmonella, usually causes sepsis or extra-intestinal focal infections in humans....
Pigs in sequence space: A 0.66X coverage pig genome survey based on shotgun sequencing
Wernersson, Rasmus, Schierup, Mikkel H, Jørgensen, Frank G, Gorodkin, Jan, Panitz, Frank, Stærfeldt, Hans-Henrik, ...
Kadurugamuwa, Jagath L., Modi, Kshitij, Yu, Jun, Francis, Kevin P., Purchio, Tony, Contag, Pamela R.
Urinary tract infections (UTIs) are among the most common bacterial infections acquired by humans, particularly in catheterized patients. A major problem with catheterization is the formation of...
Bao, JingYue, Lee, Sanggyu, Chen, Chen, Zhang, XiuQing, Zhang, Yu, Liu, SiQi, ...
Using the serial analysis of gene expression technique, we surveyed transcriptomes of three major tissues (panicles, leaves, and roots) of a super-hybrid rice (Oryza sativa) strain, LYP9, in...
Akt1/protein kinase Bα is critical for ischemic and VEGF-mediated angiogenesis
Ackah, Eric, Yu, Jun, Zoellner, Stefan, Iwakiri, Yasuko, Skurk, Carsten, Shibata, Rei, ...
Akt, or protein kinase B, is a multifunctional serine-threonine protein kinase implicated in a diverse range of cellular functions including cell metabolism, survival, migration, and gene expression....
Yu, Jun, DeMuinck, Ebo D., Zhuang, Zhenwu, Drinane, Mary, Kauser, Katalin, Rubanyi, Gabor M., ...
The genetic loss of endothelial-derived nitric oxide synthase (eNOS) in mice impairs vascular endothelial growth factor (VEGF) and ischemia-initiated blood flow recovery resulting in critical limb...
Origin and evolution of new exons in rodents
Wang, Wen, Zheng, Hongkun, Yang, Shuang, Yu, Haijing, Li, Jun, Jiang, Huifeng, ...
Gene number difference among organisms demonstrates that new gene origination is a fundamental biological process in evolution. Exon shuffling has been universally observed in the formation of new...
Li, Ruiqiang, Ye, Jia, Li, Songgang, Wang, Jing, Han, Yujun, Ye, Chen, ...
We describe an algorithm, ReAS, to recover ancestral sequences for transposable elements (TEs) from the unassembled reads of a whole genome shotgun. The main assumptions are that these TEs must exist...
Genome dynamics and diversity of Shigella species, the etiologic agents of bacillary dysentery
Yang, Fan, Yang, Jian, Zhang, Xiaobing, Chen, Lihong, Jiang, Yan, Yan, Yongliang, ...
The Shigella bacteria cause bacillary dysentery, which remains a significant threat to public health. The genus status and species classification appear no longer valid, as compelling evidence...
ShiBASE: an integrated database for comparative genomics of Shigella
Yang, Jian, Chen, Lihong, Yu, Jun, Sun, Lilian, Jin, Qi
Among the major enteric bacterial pathogens, Shigella is found to display extreme genome diversity and dynamics, which imposes a challenge in comparative genomic studies. To facilitate further...
Evolution of alternative splicing after gene duplication
Su, Zhixi, Wang, Jianmin, Yu, Jun, Huang, Xiaoqiu, Gu, Xun
Alternative splicing and gene duplication are two major sources of proteomic function diversity. Here, we study the evolutionary trend of alternative splicing after gene duplication by analyzing the...
Compositional Gradients in Gramineae Genes
Wong, Gane Ka-Shu, Wang, Jun, Tao, Lin, Tan, Jun, Zhang, JianGuo, Passey, Douglas A., ...
In this study, we describe a property of Gramineae genes, and perhaps all monocot genes, that is not observed in eudicot genes. Along the direction of transcription, beginning at the junction of the...
Yu, Jun, Bergaya, Sonia, Murata, Takahisa, Alp, Ilkay F., Bauer, Michael P., Lin, Michelle I., ...
Caveolae in endothelial cells have been implicated as plasma membrane microdomains that sense or transduce hemodynamic changes into biochemical signals that regulate vascular function. Therefore we...
Critical function of Bmx/Etk in ischemia-mediated arteriogenesis and angiogenesis
He, Yun, Luo, Yan, Tang, Shibo, Rajantie, Iiro, Salven, Petri, Heil, Matthias, ...
Bmx/Etk non-receptor tyrosine protein kinase has been implicated in endothelial cell migration and tube formation in vitro. However, the role of Bmx in vivo is not known. Bmx is highly induced in the...
Miao, Robert Qing, Gao, Yuan, Harrison, Kenneth D., Prendergast, Jay, Acevedo, Lisette M., Yu, Jun, ...
Nogo isoforms (Nogo-A and -B) have been implicated in regulating neural and cardiovascular functions, such as cell spreading and chemotaxis. Unlike the loop domain (Nogo-66) found in all Nogo...
The Rice Mitochondrial Genomes and Their Variations1[W]
Tian, Xiangjun, Zheng, Jing, Hu, Songnian, Yu, Jun
Based on highly redundant and high-quality sequences, we assembled rice (Oryza sativa) mitochondrial genomes for two cultivars, 93-11 (an indica variety) and PA64S (an indica-like variety with...
Chang, Suhua, Zhang, Jiajie, Liao, Xiaoyun, Zhu, Xinxing, Wang, Dahai, Zhu, Jiang, ...
Frequent outbreaks of highly pathogenic avian influenza and the increasing data available for comparative analysis require a central database specialized in influenza viruses (IVs). We have...
Information Loss in Volatility Measurement with Flat Price Trading
A model of price determination is proposed that incorporates flat trading features into an efficient price process. The model involves the superposition of a Brownian semimartingale process for the...
Maximum Likelihood and Gaussian Estimation of Continuous Time Models in Finance
This paper overviews maximum likelihood and Gaussian methods of estimating continuous time models used in finance. Since the exact likelihood can be constructed only in special cases, much attention...
Simulation-based Estimation of Contingent-claims Prices
A new methodology is proposed to estimate theoretical prices of financial contingent-claims whose values are dependent on some other underlying financial assets. In the literature the preferred...
Gorodkin, Jan, Cirera, Susanna, Hedegaard, Jakob, Gilchrist, Michael J, Panitz, Frank, Jørgensen, Claus, ...
A resource consisting of one million porcine ESTs is described, providing an essential resource for annotation, comparative genomics, assembly of the pig genome sequence, and further porcine...
Cui, Peng, Ji, Rimutu, Ding, Feng, Qi, Dan, Gao, Hongwei, Meng, He, ...
Mundy, Rosanna, Petrovska, Liljana, Smollett, Katherine, Simpson, Nandi, Wilson, Rebecca K., Yu, Jun, ...
VFDB 2008 release: an enhanced web-based resource for comparative pathogenomics
Yang, Jian, Chen, Lihong, Sun, Lilian, Yu, Jun, Jin, Qi
Virulence factor database (VFDB) was set up in 2004 dedicated for providing current knowledge of virulence factors (VFs) from various medical significant bacterial pathogens to facilitate...
Murata, Takahisa, Lin, Michelle I., Huang, Yan, Yu, Jun, Bauer, Phillip Michael, Giordano, Frank J., ...
Caveolin-1 (Cav-1) is the principal structural component of caveolae organelles in smooth muscle cells, adipocytes, fibroblasts, epithelial cells, and endothelial cells (ECs). Cav-1–deficient...
Wang, Fengping, Wang, Jianbin, Jian, Huahua, Zhang, Bing, Li, Shengkang, Wang, Feng, ...
Shewanella species are widespread in various environments. Here, the genome sequence of Shewanella piezotolerans WP3, a piezotolerant and psychrotolerant iron reducing bacterium from deep-sea...
On leverage in a stochastic volatility model
This paper is concerned with specification for modelling financial leverage effect in the context of stochastic volatility (SV) models. Two alternative specifications co-exist in the literature. One...
A Class of Nonlinear Stochastic Volatility Models and Its Implications on Pricing Currency Options
Jun Yu, Zhenlin Yang, Xibin Zhang
This paper proposes a class of stochastic volatility (SV) models which offers an alternative to the one introduced in Andersen (1994). The class encompasses all standard SV models that have appeared...
A Gaussian approach for continuous time models of the short-term interest rate
This paper proposes a Gaussian estimator for nonlinear continuous time models of the short-term interest rate. The approach is based on a stopping time argument that produces a normalizing...
BUGS for a Bayesian analysis of stochastic volatility models
This paper reviews the general Bayesian approach to parameter estimation in stochastic volatility models with posterior computations performed by Gibbs sampling. The main purpose is to illustrate the...
EMPIRICAL CHARACTERISTIC FUNCTION IN TIME SERIES ESTIMATION
Because the empirical characteristic function (ECF) is the Fourier transform of the empirical distribution function, it retains all the information in the sample but can overcome difficulties arising...
Jackknifing Bond Option Prices
In continuous time specifications, the prices of interest rate derivative securities depend crucially on the mean reversion parameter of the associated interest rate diffusion equation. This...
Gaussian Estimation of Continuous Time Models of the Short Term Interest Rate
This paper proposes a Gaussian estimator for nonlinear continuous time models of the short term interest rate. The approach is based on a stopping time argument that produces a normalizing...
On Leverage in a Stochastic Volatility Model
This paper is concerned with specification for modelling financial leverage effect in the context of stochastic volatility (SV) models. Two alternative specifications co-exist in the literature. One...
Forecasting Volatility in the New Zealand Stock Market.
This study evaluates the performance of nine alternative models for predicting stock price volatility using daily New Zealand data. The competing models contain both simple models such as the random...
Multivariate Stochastic Volatility Models: Bayesian Estimation and Model Comparison
In this paper we show that fully likelihood-based estimation and comparison of multivariate stochastic volatility (SV) models can be easily performed via a freely available Bayesian software called...
Multivariate Stochastic Volatility: A Review
Manabu Asai, Michael McAleer, Jun Yu
The literature on multivariate stochastic volatility (MSV) models has developed significantly over the last few years. This paper reviews the substantial literature on specification, estimation, and...
Schleicher, Michael, Shepherd, Benjamin R., Suarez, Yajaira, Fernandez-Hernando, Carlos, Yu, Jun, Pan, Yong, ...
Prohibitin 1 (PHB1) is a highly conserved protein that is mainly localized to the inner mitochondrial membrane and has been implicated in regulating mitochondrial function in yeast. Because...
A comprehensive crop genome research project: the Superhybrid Rice Genome Project in China
Yu, Jun, Liu, Siqi, Wang, Jian, Yang, Huanming
In May 2000, the Beijing Institute of Genomics formally announced the launch of a comprehensive crop genome research project on rice genomics, the Chinese Superhybrid Rice Genome Project. SRGP is not...
The Silkworm (Bombyx mori) microRNAs and Their Expressions in Multiple Developmental Stages
Yu, Xiaomin, Zhou, Qing, Li, Sung-Chou, Luo, Qibin, Cai, Yimei, Lin, Wen-chang, ...
Explosive Behavior in the 1990s Nasdaq: When Did Exuberance Escalate Asset Values?
A recursive test procedure is suggested that provides a mechanism for testing explosive behavior, date-stamping the origination and collapse of economic exuberance, and providing valid confidence...
A novel DNA sequence periodicity decodes nucleosome positioning
Chen, Kaifu, Meng, Qingshu, Ma, Lina, Liu, Qingyou, Tang, Petrus, Chiu, Chungshung, ...
There have been two types of well-characterized DNA sequence periodicities; both are found to be associated with important molecular mechanisms. One is a 3-nt periodicity corresponding to codon...
EMPIRICAL CHARACTERISTIC FUNCTION IN TIME SERIES ESTIMATION
Because the empirical characteristic function (ECF) is the Fourier transform of the empirical distribution function, it retains all the information in the sample but can overcome difficulties arising...
A Systematic Survey of Mini-Proteins in Bacteria and Archaea
Wang, Fengyu, Xiao, Jingfa, Pan, Linlin, Yang, Ming, Zhang, Guoqiang, Jin, Shouguang, ...
LIM only 4 is overexpressed in late stage pancreas cancer
Yu, Jun, Ohuchida, Kenoki, Nakata, Kohei, Mizumoto, Kazuhiro, Cui, Lin, Fujita, Hayato, ...
Trade Retaliation in a Monetary-Trade Model
John Whalley, Jun Yu, Shunming Zhang
We explore how outcomes of trade policy retaliation (Nash tariff games) are affected when trade simultaneously takes places geographically across countries and through time via financial...
A gene catalogue for post-diapause development of an anhydrobiotic arthropod Artemia franciscana
Chen, Wie-Hua, Ge, Xiaomeng, Wang, Weiwei, Yu, Jun, Hu, Songnian
Thrombospondin-2 Modulates Extracellular Matrix Remodeling during Physiological Angiogenesis
Krady, Marie M., Zeng, Jianmin, Yu, Jun, MacLauchlan, Susan, Skokos, Eleni A., Tian, Weiming, ...
Thrombospondin 2 (TSP2) can inhibit angiogenesis in vitro by limiting proliferation and inducing apoptosis of endothelial cells (ECs). TSP2 can also modulate the extracellular levels of gelatinases...
Dicer-dependent endothelial microRNAs are necessary for postnatal angiogenesis
Suárez, Yajaira, Fernández-Hernando, Carlos, Yu, Jun, Gerber, Scott A., Harrison, Kenneth D., Pober, Jordan S., ...
Posttranscriptional gene regulation by microRNAs (miRNAs) is important for many aspects of development, homeostasis, and disease. Here, we show that reduction of endothelial miRNAs by cell-specific...
Information Loss in Volatility Measurement with Flat Price Trading
A model of financial asset price determination is proposed that incorporates flat trading features into an efficient price process. The model involves the superposition of a Brownian semimartingale...
Temporal Aggregation and Risk-Return Relation
The function form of a linear intertemporal relation between risk and return is suggested by Merton’s (1973) analytical work for instantaneous returns, whereas empirical studies have examined the...
Explosive Behavior in the 1990s Nasdaq: When Did Exuberance Escalate Asset Values?
A recursive test procedure is suggested that provides a mechanism for testing explosive behavior, date-stamping the origination and collapse of economic exuberance, and providing valid confidence...
Zhang, Li-Jing, Wang, Shi-Yan, Huo, Xiao-Hui, Zhu, Zhen-Long, Chu, Jian-Kun, Ma, Jin-Cheng, ...
AIM: To evaluate whether celecoxib, a selective cyclooxygenase 2 (COX-2) inhibitor, could reduce the severity of gastric precancerous lesions following Helicobacter pylori (H pylori) eradication.
LMO2 Is a Novel Predictive Marker for a Better Prognosis in Pancreatic Cancer1
Nakata, Kohei, Ohuchida, Kenoki, Nagai, Eishi, Hayashi, Akifumi, Miyasaka, Yoshihiro, Kayashima, Tadashi, ...
Wang, Limin, Yu, Jun, Walzem, Rosemary L
High-carbohydrate diets reduce plasma low-density lipoprotein (LDL)–cholesterol but also provoke the appearance of an atherogenic lipoprotein profile (ALP). Characterized by high plasma...
Interaction of Enteric Bacterial Pathogens with Murine Embryonic Stem Cells ▿ †
Yu, Jun, Rossi, Raffaella, Hale, Christine, Goulding, David, Dougan, Gordon
Embryonic stem (ES) cells are susceptible to genetic manipulation and retain the potential to differentiate into diverse cell types, which are factors that make them potentially attractive cells for...
Yu, Jun, Mϋller, Helena, Hehn, Sina, Koschmieder, Steffen, Schönig, Kai, Berdel, Wolfgang E., ...
Stringently controlled conditional expressing systems are crucial for the functional characterization of genes. Currently, screening of multiple clones to identify the tightly controlled ones is...
A two-stage realized volatility approach to estimation of diffusion processes with discrete data
This paper motivates and introduces a two-stage method of estimating diffusion processes based on discretely sampled observations. In the first stage we make use of the feasible central limit theory...
Simulation-Based Estimation of Contingent-Claims Prices
A new methodology is proposed to estimate theoretical prices of financial contingent claims whose values are dependent on some other underlying financial assets. In the literature, the preferred...
Interaction of Enteric Bacterial Pathogens with Murine Embryonic Stem Cells
Yu, Jun, Rossi, Raffaella, Hale, Christine, Goulding, David, Dougan, Gordon
A transcriptomic analysis of superhybrid rice LYP9 and its parents
Wei, Gang, Tao, Yong, Liu, Guozhen, Chen, Chen, Luo, Renyuan, Xia, Hongai, ...
By using a whole-genome oligonucleotide microarray, designed based on known and predicted indica rice genes, we investigated transcriptome profiles in developing leaves and panicles of superhybrid...