WorldCat Identities

Aquadro, Charles F.

Works: 5 works in 8 publications in 2 languages and 30 library holdings
Genres: Bibliography  Textbooks  Study guides  Software 
Roles: Thesis advisor
Publication Timeline
Most widely held works by Charles F Aquadro
Genetics : from genes to genomes by Leland Hartwell( Book )

4 editions published between 2014 and 2016 in English and held by 26 WorldCat member libraries worldwide

CD-ROM contains: Animations of basic genetic processes -- Interactive exercises and simulations -- Self-tests -- Glossary definitions
Population and evolutionary genomic analysis of the Drosophila germline stem cell and its coevolution with Wolbachia by Jae Young Choi( Book )

1 edition published in 2015 in English and held by 1 WorldCat member library worldwide

In Drosophila, studies of reproductive protein evolution have shown evidence of elevated levels of adaptive evolution compared to the genomic background. Few, however, have studied the molecular evolution of genes involved in the regulation of the germline stem cell (GSC). My dissertation examines the population genetics of a larger class of genes regulating the GSC, and using a comparative genomic approach to test the hypothesis that infection by the endosymbiotic bacteria Wolbachia pipientis is a selective driver causing the rapid evolution at some of the GSC genes. First, following up on previous observations of adaptive evolution of several GSC genes (particularly bam and bgcn) in D. melanogaster and D. simulans, I have studied the population genetics of these genes in D. ananassae because this species also shows evidence of infection by W. pipientis. However, despite what I show to be a comparable W. pipientis infectious history among D. melanogaster, D. simulans, and D. ananassae; neither bam nor bgcn were evolving under positive selection in D. ananassae. Thus, a simple W. pipientis driven rapid evolution at these genes was not supported by my results. Second, I expanded the population genetic analysis of GSC genes to include all genes that show evidence of involvement in D. melanogaster GSC regulation. Results for these were then compared to genes involved in neural stem cell regulation. My results showed that both germline and neural stem cell are enriched for genes with evidence of recent selective sweeps, but not long-term recurrent adaptive evolution, compared to a randomly chosen group of control genes. Further, overall inferences of rates of adaptive fixation for germline and neural stem cells showed levels comparable to most classes of genes for D. melanogaster and D. simulans. Lastly, I have used whole-genome sequencing to gain deeper insight into the evolutionary history of W. pipientis infecting D. ananassae. D. ananassae has unique evidence of the whole genome of W. pipientis integrated into the host nuclear genome. My results showed that the infectious W. pipientis genome has a stable maternally inherited evolutionary history while the integrated W. pipientis genome had become a potentially functionless pseudogenome
Bibliography of electrophoretic studies of biochemical variation in natural vertebrate populations( Book )

in English and held by 1 WorldCat member library worldwide

Hateuwel ui yujeonhak( Book )

1 edition published in 2016 in Korean and held by 1 WorldCat member library worldwide

High-throughput sequencing and natural selection : studies of recent sweep inferences and a new computational approach for transcription identification by Zhen Wang( Book )

1 edition published in 2014 in English and held by 1 WorldCat member library worldwide

Short-read high-throughput sequencing is the most popular approach to collect massive amount of DNA sequence data at declining cost in nearly all fields of current biological studies. Its many varieties have been employed for different research purposes, e.g. genomic sequencing for variant detection, RNA-seq for transcriptome profiling, etc. However, the individual reads and the resulting called sequences frequently have missing and errorprone base calls, and appropriate corrections and evaluations are necessary for drawing conclusions. I examined how missing data and sequence errors affect the power and prediction accuracy of two frequently used methods for the inference of recent positive selection from such datasets. I showed that variant-frequency based method, SweepFinder, is very sensitive to data quality and its sensitivity and prediction accuracy are greatly compromised by missing data or sequence errors. In contrast, the haplotype-based method, iHS, is very robust to missing data and sequence errors and is able to efficiently detect signals of recent selective sweeps with very low false discovery rate. I then applied four different computational approaches on the high-throughput resequencing data of a 2.1 Mbp segment of Drosophila melanogaster X chromosome to compare and discuss their performances. The study emphasized the relative advantages of linkage disequilibrium-based methods in detecting recent sweeps relative to site frequency-based approaches when applied on incomplete data. There are also many challenges in other applications of high-throughput sequencing, including discoveries of novel transcription active regions (TARs) in RNA-seq analysis. Here, I present a flexible statistical program, HPIBD (HMM-based Peak Identification and Boundary Definition) for de novo analysis of RNA-seq datasets. It avoids the use of arbitrary read-depth cutoffs and has built-in tolerance to read gaps. It is able to statistically make TARs predictions, estimate peak boundaries and evaluate the confidence in the prediction. I implemented the model and showed that HPIBD has robust performance under various validations and with benchmark to Cufflinks
Audience Level
Audience Level
  Kids General Special  
Audience level: 0.58 (from 0.55 for Genetics : ... to 0.99 for Hateuwel u ...)

Alternative Names
아쿠아드로, 찰스 F