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Full-Text Articles in Life Sciences

Analysis Of G-Quadruplexes As Environmental Sensors: Novel Statistical Models And Computational Algorithms Enable Interpretation Of Complex Gene Expression Patterns For Maize Under Salt Stress Conditions, Mingze He Jan 2018

Analysis Of G-Quadruplexes As Environmental Sensors: Novel Statistical Models And Computational Algorithms Enable Interpretation Of Complex Gene Expression Patterns For Maize Under Salt Stress Conditions, Mingze He

Graduate Theses and Dissertations

The occurrence of G-quadruplex (G4) structures in both genic and non-genic sequences have been well-documented. However, even in genic regions the biological functions of these motifs remains poorly understood, though their potential to act in a regulatory fashion has been hypothesized. With the recent development of next-generation sequencing technology, we have accumulated genomic and transcriptomic sequences from various species and tissues. Coupled with pattern recognition software that can identify putative G4 sequences, the time is right for tackling the question of whether and how G4’s are involved in regulating gene expression. Previous studies suggested that G4 conformation can be ...


Allele-Specific Copy Number Profiling By Next-Generation Dna Sequencing, Hao Chen, John M. Bell, Nicolas A. Zavala, Hanlee P. Ji, Nancy R. Zhang Feb 2015

Allele-Specific Copy Number Profiling By Next-Generation Dna Sequencing, Hao Chen, John M. Bell, Nicolas A. Zavala, Hanlee P. Ji, Nancy R. Zhang

Statistics Papers

The progression and clonal development of tumors often involve amplifications and deletions of genomic DNA. Estimation of allele-specific copy number, which quantifies the number of copies of each allele at each variant loci rather than the total number of chromosome copies, is an important step in the characterization of tumor genomes and the inference of their clonal history. We describe a new method, Falcon, for finding somatic allele-specific copy number changes by next generation sequencing of tumors with matched normals. Falcon is based on a change-point model on a bivariate mixed Binomial process, which explicitly models the copy numbers of ...


Estimation Of Parent Specific Dna Copy Number In Tumors Using High-Density Genotyping Arrays, Hao Chen, Haipeng Xing, Nancy R. Zhang Jan 2011

Estimation Of Parent Specific Dna Copy Number In Tumors Using High-Density Genotyping Arrays, Hao Chen, Haipeng Xing, Nancy R. Zhang

Statistics Papers

Chromosomal gains and losses comprise an important type of genetic change in tumors, and can now be assayed using microarray hybridization-based experiments. Most current statistical models for DNA copy number estimate total copy number, which do not distinguish between the underlying quantities of the two inherited chromosomes. This latter information, sometimes called parent specific copy number, is important for identifying allele-specific amplifications and deletions, for quantifying normal cell contamination, and for giving a more complete molecular portrait of the tumor. We propose a stochastic segmentation model for parent-specific DNA copy number in tumor samples, and give an estimation procedure that ...


Modeling Dna Methylation Tiling Array Data, Gayla Olbricht, Bruce A. Craig, R. W. Doerge Apr 2010

Modeling Dna Methylation Tiling Array Data, Gayla Olbricht, Bruce A. Craig, R. W. Doerge

Conference on Applied Statistics in Agriculture

Epigenetics is the study of heritable changes in gene function that occur without a change in DNA sequence. It has quickly emerged as an essential area for understanding inheritance and variation that cannot be explained by the DNA sequence alone. Epigenetic modifications have the potential to regulate gene expression and may play a role in diseases such as cancer. DNA methylation is a type of epigenetic modification that occurs when a methyl chemical group attaches to a cytosine base on the DNA molecule. To better understand this epigenetic mechanism, DNA methylation profiles can be constructed by identifying all locations of ...


Analyzing Dna Microarrays With Undergraduate Statisticians, Johanna S. Hardin, Laura Hoopes, Ryan Murphy '06 Jan 2006

Analyzing Dna Microarrays With Undergraduate Statisticians, Johanna S. Hardin, Laura Hoopes, Ryan Murphy '06

Pomona Faculty Publications and Research

With advances in technology, biologists have been saddled with high dimensional data that need modern statistical methodology for analysis. DNA microarrays are able to simultaneously measure thousands of genes (and the activity of those genes) in a single sample. Biologists use microarrays to trace connections between pathways or to identify all genes that respond to a signal. The statistical tools we usually teach our undergraduates are inadequate for analyzing thousands of measurements on tens of samples. The project materials include readings on microarrays as well as computer lab activities. The topics covered include image analysis, filtering and normalization techniques, and ...