Volume 9 Supplement 2
IEEE 7th International Conference on Bioinformatics and Bioengineering at Harvard Medical School
Research
Edited by Mary Qu Yang, Jack Y Yang, Hamid R Arabnia and Youping Deng
IEEE 7th International Conference on Bioinformatics and Bioengineering at Harvard Medical School. Go to
conference site.
Boston, MA, USA14-17 October 2007
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Content type: Introductory Review
Supported by National Science Foundation (NSF), International Society of Intelligent Biological Medicine (ISIBM), International Journal of Computational Biology and Drug Design and International Journal of Fun...
Authors: Jack Y Yang, Mary Qu Yang, Hamid R Arabnia and Youping Deng
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Content type: Research
Our first predictor of protein disorder was published just over a decade ago in the Proceedings of the IEEE International Conference on Neural Networks (Romero P, Obradovic Z, Kissinger C, Villafranca JE, Dunker ...
Authors: A Keith Dunker, Christopher J Oldfield, Jingwei Meng, Pedro Romero, Jack Y Yang, Jessica Walton Chen, Vladimir Vacic, Zoran Obradovic and Vladimir N Uversky
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Content type: Research
Structural genomics efforts contribute new protein structures that often lack significant sequence and fold similarity to known proteins. Traditional sequence and structure-based methods may not be sufficient ...
Authors: Inbal Halperin, Dariya S Glazer, Shirley Wu and Russ B Altman
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Content type: Research
Bidirectional promoters lie between adjacent genes, which are transcribed from opposite strands of DNA. The functional mechanisms underlying the activation of bidirectional promoters are currently uncharacteri...
Authors: Mary Qu Yang and Laura L Elnitski
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Content type: Research
To examine the usefulness of protein disorder predictions as a tool for the comparative analysis of viral proteins, a relational database has been constructed. The database includes proteins from influenza A a...
Authors: Gerard Kian-Meng Goh, A Keith Dunker and Vladimir N Uversky
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Content type: Research
Using genomic DNA as common reference in microarray experiments has recently been tested by different laboratories. Conflicting results have been reported with regard to the reliability of microarray results u...
Authors: Yunfeng Yang, Mengxia Zhu, Liyou Wu and Jizhong Zhou
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Content type: Research
Sudden death syndrome (SDS) of soybean (Glycine max L. Merr.) is an economically important disease, caused by the semi-biotrophic fungus Fusarium solani f. sp. glycines, recently renamed Fusarium virguliforme (Fv...
Authors: Jiazheng Yuan, Mengxia Zhu, David A Lightfoot, M Javed Iqbal, Jack Y Yang and Khalid Meksem
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Content type: Research
The growing body of DNA microarray data has the potential to advance our understanding of the molecular basis of disease. However annotating microarray datasets with clinically useful information is not always...
Authors: Cole Harris and Noushin Ghaffari
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Content type: Research
Many protein regions and some entire proteins have no definite tertiary structure, presenting instead as dynamic, disorder ensembles under different physiochemical circumstances. These proteins and regions are...
Authors: Jack Y Yang and Mary Qu Yang
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Content type: Research
Adjuvant Radiotherapy (RT) after surgical removal of tumors proved beneficial in long-term tumor control and treatment planning. For many years, it has been well concluded that radio-sensitivities of tumors up...
Authors: Jack Y Yang, Andrzej Niemierko, Mary Qu Yang and Youping Deng
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Content type: Research
BLAST programs are very efficient in finding similarities for sequences. However for large datasets such as ESTs, manual extraction of the information from the batch BLAST output is needed. This can be time co...
Authors: Mehdi Pirooznia, Edward J Perkins and Youping Deng
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Content type: Research
Microarray technology is widely applied to address complex scientific questions. However, there remain fundamental issues on how to design experiments to ensure that the resulting data enables robust statistic...
Authors: Mehdi Pirooznia, Ping Gong, Jack Y Yang, Mary Qu Yang, Edward J Perkins and Youping Deng
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Content type: Research
As studies of molecular biology system attempt to achieve a comprehensive understanding of a particular system, Type 1 errors may be a significant problem. However, few investigators are inclined to accept the...
Authors: Jian Wu, Nataliya I Lenchik and Ivan C Gerling
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Content type: Research
Computational gene prediction tools routinely generate large volumes of predicted coding exons (putative exons). One common limitation of these tools is the relatively low specificity due to the large amount of n...
Authors: Jing Wu
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Content type: Research
Gene expression data extracted from microarray experiments have been used to study the difference between mRNA abundance of genes under different conditions. In one of such experiments, thousands of genes are ...
Authors: Xin Yan and Tian Zheng
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Content type: Research
Because of the advent of high-throughput sequencing and the consequent reduction in the cost of sequencing, many organisms have been completely sequenced and most of their genes identified. It thus has become ...
Authors: Feng Yue, Meng Zhang and Jijun Tang
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Content type: Research
Being formal, declarative knowledge representation models, ontologies help to address the problem of imprecise terminologies in biological and biomedical research. However, ontologies constructed under the aus...
Authors: Jingshan Huang, Jiangbo Dang, Michael N Huhns and W Jim Zheng
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Content type: Research
Array-based comparative genomic hybridization (array CGH) is a highly efficient technique, allowing the simultaneous measurement of genomic DNA copy number at hundreds or thousands of loci and the reliable det...
Authors: Heng Huang, Nha Nguyen, Soontorn Oraintara and An Vo
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Content type: Research
Microarray technology is often used to identify the genes that are differentially expressed between two biological conditions. On the other hand, since microarray datasets contain a small number of samples and...
Authors: Min Xu, Mengxia Zhu and Louxin Zhang
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Content type: Research
To date, the reconstruction of gene regulatory networks from gene expression data has primarily relied on the correlation between the expression of transcription regulators and that of target genes.
Authors: Chieh-Chun Chen and Sheng Zhong
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Content type: Research
Microarrays have the capacity to measure the expressions of thousands of genes in parallel over many experimental samples. The unsupervised classification technique of bicluster analysis has been employed prev...
Authors: Kenneth Bryan and Pádraig Cunningham
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Content type: Research
Gene expression profiles based on microarray data are recognized as potential diagnostic indices of cancer. Molecular tumor classifications resulted from these data and learning algorithms have advanced our un...
Authors: Rattikorn Hewett and Phongphun Kijsanayothin
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Content type: Research
Prostate cancer is one of the leading causes of cancer death in men. Androgen ablation, the most commonly-used therapy for progressive prostate cancer, is ineffective once the cancer cells become androgen-inde...
Authors: Guohua Wang, Yadong Wang, Weixing Feng, Xin Wang, Jack Y Yang, Yuming Zhao, Yue Wang and Yunlong Liu
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Content type: Research
We present a mixture model-based analysis for identifying differences in the distribution of RNA polymerase II (Pol II) in transcribed regions, measured using ChIP-seq (chromatin immunoprecipitation following ...
Authors: Weixing Feng, Yunlong Liu, Jiejun Wu, Kenneth P Nephew, Tim HM Huang and Lang Li
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Content type: Research
Dimension reduction is a critical issue in the analysis of microarray data, because the high dimensionality of gene expression microarray data set hurts generalization performance of classifiers. It consists o...
Authors: Guo-Zheng Li, Hua-Long Bu, Mary Qu Yang, Xue-Qiang Zeng and Jack Y Yang
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Content type: Research
We have previously shown that using multiple prediction methods improves the accuracy of disorder predictions. It is, however, a time-consuming procedure, since individual outputs of multiple predictions have ...
Authors: Philippe Lieutaud, Bruno Canard and Sonia Longhi
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Content type: Research
Protein interactions are essential for most cellular functions. Interactions mediated by domains that appear in a large number of proteins are of particular interest since they are expected to have an impact o...
Authors: Siyuan Ren, Vladimir N Uversky, Zhengjun Chen, A Keith Dunker and Zoran Obradovic
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Content type: Research
Gene expression data usually contains a large number of genes, but a small number of samples. Feature selection for gene expression data aims at finding a set of genes that best discriminate biological samples...
Authors: Yi Zhang, Chris Ding and Tao Li
