Browsing by Author "Doman, Thompson N."

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    Academic laboratory information management system: a tool for science and computer science students
    (2011-07-08) Lerch, Spencer; Merchant, Mahesh; Wild, David; Doman, Thompson N.
    Proof of Concept - An Academic LIMS application: The aim of this project is the creation of an open-source, freeware LIMS application that can be used in an academic setting as a teaching tool for both chemistry and computer science students. The LIMS package will combine an application, developed using VB.NET, to manage the data with other open-source or freeware programs such as MySQL and WEKA. The numerous commercial chemical informatics applications available are useful tools to learn how to manage data from a user's standpoint. However, they are not readily available to the average student, nor do they offer a great understanding into how they were developed from a programmer's frame of mind. There is a great void here that, if filled can greatly help the academic community.
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    Bottom-up, integrated -omics analysis identifies broadly dosage-sensitive genes in breast cancer samples from TCGA
    (PLOS, 2019-01-17) Kechavarzi, Bobak D.; Wu, Huanmei; Doman, Thompson N.; Biohealth Informatics, School of Informatics and Computing
    The massive genomic data from The Cancer Genome Atlas (TCGA), including proteomics data from Clinical Proteomic Tumor Analysis Consortium (CPTAC), provides a unique opportunity to study cancer systematically. While most observations are made from a single type of genomics data, we apply big data analytics and systems biology approaches by simultaneously analyzing DNA amplification, mRNA and protein abundance. Using multiple genomic profiles, we have discovered widespread dosage compensation for the extensive aneuploidy observed in TCGA breast cancer samples. We do identify 11 genes that show strong correlation across all features (DNA/mRNA/protein) analogous to that of the well-known oncogene HER2 (ERBB2). These genes are generally less well-characterized regarding their role in cancer and we advocate their further study. We also discover that shRNA knockdown of these genes has an impact on cancer cell growth, suggesting a vulnerability that could be used for cancer therapy. Our study shows the advantages of systematic big data methodologies and also provides future research directions.
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    Bottom-up, integrated -omics analysis identifies broadly dosage-sensitive genes in breast cancer samples from TCGA
    (PLOS, 2019-01-17) Kechavarzi, Bobak D.; Wu, Huanmei; Doman, Thompson N.; Radiation Oncology, School of Medicine
    The massive genomic data from The Cancer Genome Atlas (TCGA), including proteomics data from Clinical Proteomic Tumor Analysis Consortium (CPTAC), provides a unique opportunity to study cancer systematically. While most observations are made from a single type of genomics data, we apply big data analytics and systems biology approaches by simultaneously analyzing DNA amplification, mRNA and protein abundance. Using multiple genomic profiles, we have discovered widespread dosage compensation for the extensive aneuploidy observed in TCGA breast cancer samples. We do identify 11 genes that show strong correlation across all features (DNA/mRNA/protein) analogous to that of the well-known oncogene HER2 (ERBB2). These genes are generally less well-characterized regarding their role in cancer and we advocate their further study. We also discover that shRNA knockdown of these genes has an impact on cancer cell growth, suggesting a vulnerability that could be used for cancer therapy. Our study shows the advantages of systematic big data methodologies and also provides future research directions.