High-resolution human core-promoter prediction with CoreBoost_HM (2009)
Wang, Xiaowo, Xuan, Zhenyu, Zhao, Xiaoyue, Li, Yanda, Zhang, Michael Q.
Correctly locating the gene transcription start site and the core-promoter is important for understanding transcriptional regulation mechanism. Here we have integrated specific genome-wide histone...
Kamalakaran, Sitharthan, Kendall, Jude, Zhao, Xiaoyue, Tang, Chunlao, Khan, Sohail, Ravi, Kandasamy, ...
Methylation of CpG islands associated with genes can affect the expression of the proximal gene, and methylation of non-associated CpG islands correlates to genomic instability. This epigenetic...
Chapter 11 Functional in silico analysis of gene regulatory polymorphism (2008)
Chaolin Zhang, Xiaoyue Zhao, Michael Q. Zhang
Regulatory polymorphisms play important roles in determining phenotypes and disease susceptibilities through perturbing gene expression. After genetic markers with LD have been mapped, an important...
Prediction of Transcription Start Sites Based on Feature Selection Using AMOSA (2008)
Xi Wang, Sanghamitra B, Zhenyu Xuan, Xiaoyue Zhao, Michael Q. Zhang, Xuegong Zhang
To understand the regulation of the gene expression, the identification of transcription start sites (TSSs) is a primary and important step. With the aim to improve the computational prediction...
Boosting with stumps for predicting transcription start sites (2007)
Zhao, Xiaoyue, Xuan, Zhenyu, Zhang, Michael Q
Abstract Promoter prediction is a difficult but important problem in gene finding, and it is critical for elucidating the regulation of gene expression. We introduce a new promoter prediction...
Disclosure Statement: The authors have nothing to declare. (2007)
Nitzan Levy, Xiaoyue Zhao, Hui Tang, Robert B. Jaffe, Terence P. Speed, Dale C
mobility shift assay; LBD, ligand binding domain; NKG2E, killer cell lectin-like receptor; Q-RT-PCR, quantitative real-time polymerase chain reaction; SDS, sodium dodecyl sulfate; siRNA, small...
Statistical methods for elucidating DNA motifs and modules / (2005)
Thesis (Ph.D. in Statistics)--University of California, Berkeley, Spring 2005.
Finding Anchors for Genomic Sequence Comparison (2004)
Xiaoyue Zhao, Liliana Florea, Clark Mobarry, Sorin Istrail
Recent sequencing of the human and other mammalian genomes has brought about the necessity to align them, to identify and characterize their commonalities and differences. Programs that align whole...
Boosting with stumps for predicting transcription start sites
Zhao, Xiaoyue, Xuan, Zhenyu, Zhang, Michael Q
CoreBoost applies a boosting technique to select important features for predicting core promoters with diverse patterns.
A unified genetic theory for sporadic and inherited autism
Zhao, Xiaoyue, Leotta, Anthony, Kustanovich, Vlad, Lajonchere, Clara, Geschwind, Daniel H., Law, Kiely, ...
Autism is among the most clearly genetically determined of all cognitive-developmental disorders, with males affected more often than females. We have analyzed autism risk in multiplex families from...
On the Ranked-Set Sampling M-Estimates for Symmetric Location Families
Asymptotic normality, asymptotic relative efficiency, M-estimates, optimal sampling design, ranked-set sampling, robustness,
Levy, Nitzan, Tatomer, Dierdre, Herber, Candice B., Zhao, Xiaoyue, Tang, Hui, Sargeant, Toby, ...
Estrogen receptors (ERs) regulate gene transcription by interacting with regulatory elements. Most information regarding how ER activates genes has come from studies using a small set of target genes...
Kamalakaran, Sitharthan, Kendall, Jude, Zhao, Xiaoyue, Tang, Chunlao, Khan, Sohail, Ravi, Kandasamy, ...
Methylation of CpG islands associated with genes can affect the expression of the proximal gene, and methylation of non-associated CpG islands correlates to genomic instability. This epigenetic...
Paruthiyil, Sreenivasan, Cvoro, Aleksandra, Zhao, Xiaoyue, Wu, Zhijin, Sui, Yunxia, Staub, Richard E., ...
Estrogens produce biological effects by interacting with two estrogen receptors, ERα and ERβ. Drugs that selectively target ERα or ERβ might be safer for conditions that have been traditionally...
High-resolution human core-promoter prediction with CoreBoost_HM
Wang, Xiaowo, Xuan, Zhenyu, Zhao, Xiaoyue, Li, Yanda, Zhang, Michael Q.
Correctly locating the gene transcription start site and the core-promoter is important for understanding transcriptional regulation mechanism. Here we have integrated specific genome-wide histone...