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Full-Text Articles in Mathematics
Processdriver: A Computational Pipeline To Identify Copy Number Drivers And Associated Disrupted Biological Processes In Cancer, Brittany Baur, Serdar Bozdag
Processdriver: A Computational Pipeline To Identify Copy Number Drivers And Associated Disrupted Biological Processes In Cancer, Brittany Baur, Serdar Bozdag
Mathematics, Statistics and Computer Science Faculty Research and Publications
Copy number amplifications and deletions that are recurrent in cancer samples harbor genes that confer a fitness advantage to cancer tumor proliferation and survival. One important challenge in computational biology is to separate the causal (i.e., driver) genes from passenger genes in large, aberrated regions. Many previous studies focus on the genes within the aberration (i.e., cis genes), but do not utilize the genes that are outside of the aberrated region and dysregulated as a result of the aberration (i.e., trans genes). We propose a computational pipeline, called ProcessDriver, that prioritizes candidate drivers by relating cis genes to …
A Feature Selection Algorithm To Compute Gene Centric Methylation From Probe Level Methylation Data, Brittany Baur, Serdar Bozdag
A Feature Selection Algorithm To Compute Gene Centric Methylation From Probe Level Methylation Data, Brittany Baur, Serdar Bozdag
Mathematics, Statistics and Computer Science Faculty Research and Publications
DNA methylation is an important epigenetic event that effects gene expression during development and various diseases such as cancer. Understanding the mechanism of action of DNA methylation is important for downstream analysis. In the Illumina Infinium HumanMethylation 450K array, there are tens of probes associated with each gene. Given methylation intensities of all these probes, it is necessary to compute which of these probes are most representative of the gene centric methylation level. In this study, we developed a feature selection algorithm based on sequential forward selection that utilized different classification methods to compute gene centric DNA methylation using probe …
The Inferred Cardiogenic Gene Regulatory Network In The Mammalian Heart, Jason Bazil, Karl D. Stamm, Xing Li, Raghuram Thiagarajan, Timonthy J. Nelson, Aoy Tomita-Mitchell, Daniel A. Beard
The Inferred Cardiogenic Gene Regulatory Network In The Mammalian Heart, Jason Bazil, Karl D. Stamm, Xing Li, Raghuram Thiagarajan, Timonthy J. Nelson, Aoy Tomita-Mitchell, Daniel A. Beard
Mathematics, Statistics and Computer Science Faculty Research and Publications
Cardiac development is a complex, multiscale process encompassing cell fate adoption, differentiation and morphogenesis. To elucidate pathways underlying this process, a recently developed algorithm to reverse engineer gene regulatory networks was applied to time-course microarray data obtained from the developing mouse heart. Approximately 200 genes of interest were input into the algorithm to generate putative network topologies that are capable of explaining the experimental data via model simulation. To cull specious network interactions, thousands of putative networks are merged and filtered to generate scale-free, hierarchical networks that are statistically significant and biologically relevant. The networks are validated with known gene …
Age-Specific Signatures Of Glioblastoma At The Genomic, Genetic, And Epigenetic Levels, Serdar Bozdag, Aiguo Li, Gregory Riddick, Yuri Kotliarov, Mehmet Baysan, Fabio M. Iwamoto, Margaret C. Cam, Svetlana Kotliarova, Howard A. Fine
Age-Specific Signatures Of Glioblastoma At The Genomic, Genetic, And Epigenetic Levels, Serdar Bozdag, Aiguo Li, Gregory Riddick, Yuri Kotliarov, Mehmet Baysan, Fabio M. Iwamoto, Margaret C. Cam, Svetlana Kotliarova, Howard A. Fine
Mathematics, Statistics and Computer Science Faculty Research and Publications
Age is a powerful predictor of survival in glioblastoma multiforme (GBM) yet the biological basis for the difference in clinical outcome is mostly unknown. Discovering genes and pathways that would explain age-specific survival difference could generate opportunities for novel therapeutics for GBM. Here we have integrated gene expression, exon expression, microRNA expression, copy number alteration, SNP, whole exome sequence, and DNA methylation data sets of a cohort of GBM patients in The Cancer Genome Atlas (TCGA) project to discover age-specific signatures at the transcriptional, genetic, and epigenetic levels and validated our findings on the REMBRANDT data set. We found major …