Detecting gene clusters under evolutionary constraint in a large number of genomes (2009)
Motivation: Spatial clusters of genes conserved across multiple genomes provide important clues to gene functions and evolution of genome organization. Existing methods of identifying these clusters...
Abstract Language Models for Genomics Information Retrieval: UIUC at TREC 2007 Genomics Track (2008)
Yue Lu, Jing Jiang, Xu Ling, Xin He, Chengxiang Zhai
goal of participation is to apply language modelbased approaches to the genomics retrieval task and study how we may extend the standard language models to accommodate two special needs for this...
Xu Ling, Jing Jiang, Xin He, Qiaozhu Mei, Chengxiang Zhai, Bruce Schatz
Most knowledge accumulated through scientific discoveries in genomics and related biomedical disciplines is buried in the vast amount of biomedical literature. Since understanding gene regulations is...
Qiaozhu Mei, Xu Ling, Matthew Wondra, Hang Su, Chengxiang Zhai
In this paper, we define the problem of topic-sentiment analysis on Weblogs and propose a novel probabilistic model to capture the mixture of topics and sentiments simultaneously. The proposed...
Xu Ling, Jing Jiang, Xin He, Qiaozhu Mei, Chengxiang Zhai, Bruce Schatz
Most knowledge accumulated through scientific discoveries in genomics and related biomedical disciplines is buried in the vast amount of biomedical literature. Since understanding gene regulations is...
UIUC/MUSC at TREC 2005 Genomics Track (2008)
Chengxiang Zhai, Xinghua Lu, Xu Ling, Xin He, Atulya Velivelli, Xuanhui Wang, ...
We report experiment results from the collaborative participation of UIUC and MUSC in the TREC 2005 Genomics Track. We participated in both the adhoc task and the categorization task, and studied the...
Xu Ling, Wang Yan, Collins Charles, Tang Shenglan
Abstract Background In 1997 there was a major reform of the government run urban health insurance system in China. The principal aims of the reform were to widen coverage of health insurance for the...
Topic sentiment mixture: modeling facets and opinions in weblogs (2007)
Qiaozhu Mei, Xu Ling, Matthew Wondra, Hang Su, Chengxiang Zhai
In this paper, we define the problem of topic-sentiment analysis on Weblogs and propose a novel probabilistic model to capture the mixture of topics and sentiments simultaneously. The proposed...
Insights into social insects from the genome of the honeybee Apis mellifera (2006)
Robinson, Gene E, Gibbs, Richard A, Worley, Kim C, Evans, Jay D, Maleszka, Ryszard, ...
Here we report the genome sequence of the honeybee Apis mellifera, a key model for social behaviour and essential to global ecology through pollination. Compared with other sequenced insect genomes,...
Design clues from functional constraints and broadly neutralizing antibodies (2006)
Zhou Tongqing, Xu Ling, Dey Barna, Hessell Ann, Majeed Shahzad, Van Ryk Donald, ...
Functional CpG methylation system in a social insect (2006)
Wang, Ying, Jorda, Mireia, Jones, Peter L., Maleszka, Ryszard, Ling, Xu, Robertson, Hugh M., ...
DNA methylation systems are well characterized in vertebrates, but methylation in Drosophila melanogaster and other invertebrates remains controversial. Using the recently sequenced honey bee genome,...
Functional CpG methylation system in a social insect (2006)
Wang, Ying, Jorda, Mireia, Jones, Peter L., Maleszka, Ryszard, Ling, Xu, Robertson, Hugh M., ...
DNA methylation systems are well characterized in vertebrates, but methylation in Drosophila melanogaster and other invertebrates remains controversial. Using the recently sequenced honey bee genome,...
Automatically generating gene summaries from biomedical literature (2006)
Xu Ling, Jing Jiang, Xin He, Qiaozhu Mei, Chengxiang Zhai, Bruce Schatz
Biologists often need to find information about genes whose function is not described in the genome databases. Currently they must try to search disparate biomedical literature to locate relevant...
Automatically generating gene summaries from biomedical literature (2006)
In this project, we address the problem of automatic gene summarization from biomedical literature. The ultimate goal is to automatically extract relevant statements from biomedical literature to...
Automatically generating gene summaries from biomedical literature (2006)
Xu Ling, Xu Ling, Jing Jiang, Jing Jiang, Xin He, Xin He, ...
Biologists often need to find information about genes whose function is not described in the genome databases. Currently they must try to search disparate biomedical literature to locate relevant...
Chan, Sherri Y., Louie, Marisa C., Piccotti, Joseph R., Iyer, Gaitry, Ling, Xu, Yang, Zhi-Yong, ...
Overview summary The immune system poses a major obstacle to the long-term success of in vivo gene therapies. Immune responses to foreign transgene products and/or the vectors that facilitate gene...
Ling, Xu, Aimin, Lu, Xihe, Zhao, Xiaoshu, Chen, Cummings, Steven R.
One third of the world's hip fractures are said to occur in Asia, mostly in China. However, there have as yet been no validated studies of hip fracture rates in China. The authors estimated the...
Chakrabarti, Bimal K., Kong, Wing-pui, Wu, Bei-yue, Yang, Zhi-Yong, Friborg, Jacques, Ling, Xu, ...
In this study, we have investigated the effect of specific mutations in human immunodeficiency virus type 1 (HIV-1) envelope (Env) on antibody production in an effort to improve humoral immune...
Lemiale, Franck, Kong, Wing-pui, Akyürek, Levent M., Ling, Xu, Huang, Yue, Chakrabarti, Bimal K., ...
Replication-defective adenovirus (ADV) vectors represent a promising potential platform for the development of a vaccine for AIDS. Although this vector is typically administered intramuscularly, it...
Chakrabarti, Bimal K., Kong, Wing-pui, Wu, Bei-yue, Yang, Zhi-Yong, Friborg, Jacques, Ling, Xu, ...
In this study, we have investigated the effect of specific mutations in human immunodeficiency virus type 1 (HIV-1) envelope (Env) on antibody production in an effort to improve humoral immune...
Lemiale, Franck, Kong, Wing-pui, Akyürek, Levent M., Ling, Xu, Huang, Yue, Chakrabarti, Bimal K., ...
Replication-defective adenovirus (ADV) vectors represent a promising potential platform for the development of a vaccine for AIDS. Although this vector is typically administered intramuscularly, it...
Wagstaff, Adam, Lindelow, Magnus, Gao Jun, Xu Ling, Qian Juncheng
In 2003, after over 20 years of minimal health insurance coverage in rural areas, China launched a heavily subsidized voluntary health insurance program for rural residents. The authors use program...
Genome scan for cis-regulatory DNA motifs associated with social behavior in honey bees
Sinha, Saurabh, Ling, Xu, Whitfield, Charles W., Zhai, Chengxiang, Robinson, Gene E.
Honey bees (Apis mellifera) undergo an age-related, socially regulated transition from working in the hive to foraging, which is associated with changes in the expression of thousands of genes in the...
Wagstaff, Adam, Lindelow, Magnus, Jun, Gao, Ling, Xu, Juncheng, Qian
In 2003, China launched a heavily subsidized voluntary health insurance program for rural residents. We combine differences-in-differences with matching methods to obtain impact estimates, using data...
Alignment and Prediction of cis-Regulatory Modules Based on a Probabilistic Model of Evolution
He, Xin, Ling, Xu, Sinha, Saurabh
Cross-species comparison has emerged as a powerful paradigm for predicting cis-regulatory modules (CRMs) and understanding their evolution. The comparison requires reliable sequence alignment, which...