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Characterizing Sequencing Artifacts, Kathy Thanh Lam
Characterizing Sequencing Artifacts, Kathy Thanh Lam
Master's Projects
Next Generation Sequencing (NGS) introduces artifactual variants from library preparation methods and errors, which affects the accuracy of variant calling. Whole Exome Sequencing (WES) data from the National Center for Biotechnology Information (NCBI) Sequence Read Archive (SRA) database is processed. Comparison of single nucleotide polymorphism (SNP) calls to Genome In a Bottle (GIAB) provides labels that are used to build machine learning (ML) models. The left and right flanking region (LSEQ and RSEQ) of each SNP is extracted. Nucleotide frequency, kmers of size 4 and their counts, largest homopolymer size, largest palindrome size, and largest hairpin loop size were computed …
Spaceflight And The Differential Gene Expression Of Human Stem Cell-Derived Cardiomyocytes, Eugenie Zhu
Spaceflight And The Differential Gene Expression Of Human Stem Cell-Derived Cardiomyocytes, Eugenie Zhu
Master's Projects
The National Aeronautics and Space Administration (NASA) has performed many experiments on the International Space Station (ISS) to further understand how conditions in space can affect life on Earth. This project analyzed GLDS-258, a gene set from NASA’s GeneLab repository which examines the impact of microgravity on human induced pluripotent stem-cell-derived cardiomyocytes (hiPSC-CMs). While many datasets have been run through NASA’s RNA-Seq Consensus Pipeline (RCP) to study differential gene expression in space, a Homo sapiens dataset has yet to be analyzed using the RCP. The aim of this project was to run the first Homo sapiens dataset, GLDS-258, through the …
Poriferal Vision, Saketh Saxena
Poriferal Vision, Saketh Saxena
Master's Projects
Sponges provide nourishment as well as a habitat for various aquatic organisms. Anatomically, sponges are made up of soft tissue with a silica based exoskeleton which serves both as support and protection for the underlying tissue. The exoskeleton persists after the tissue decomposes, and microscopic parts of the exoskeleton break away to form spicules. Oceanographic studies have shown that the density of the sponge spicules is a good indicator of the sponge population in an area. This measure can be used to study sponge population dynamics over time. The spicule density is measured by imaging spicules from samples of water …
Predicting Pancreatic Cancer Using Support Vector Machine, Akshay Bodkhe
Predicting Pancreatic Cancer Using Support Vector Machine, Akshay Bodkhe
Master's Projects
This report presents an approach to predict pancreatic cancer using Support Vector Machine Classification algorithm. The research objective of this project it to predict pancreatic cancer on just genomic, just clinical and combination of genomic and clinical data. We have used real genomic data having 22,763 samples and 154 features per sample. We have also created Synthetic Clinical data having 400 samples and 7 features per sample in order to predict accuracy of just clinical data. To validate the hypothesis, we have combined synthetic clinical data with subset of features from real genomic data. In our results, we observed that …