Search Results - "John F. McDonald"

Open source machine-learning algorithms for the prediction of optimal cancer drug therapies by Huang, Cai, Mezencev, Roman, McDonald, John F, Vannberg, Fredrik

“…Precision medicine is a rapidly growing area of modern medical science and open source machine-learning codes promise to be a critical component for the…”
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Leveraging TCGA gene expression data to build predictive models for cancer drug response by Clayton, Evan A, Pujol, Toyya A, McDonald, John F, Qiu, Peng

“…Abstract Background Machine learning has been utilized to predict cancer drug response from multi-omics data generated from sensitivities of cancer cell lines…”
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Gold nanorod assisted near-infrared plasmonic photothermal therapy (PPTT) of squamous cell carcinoma in mice by Dickerson, Erin B, Dreaden, Erik C, Huang, Xiaohua, El-Sayed, Ivan H, Chu, Hunghao, Pushpanketh, Sujatha, McDonald, John F, El-Sayed, Mostafa A

“…Abstract Plasmonic photothermal therapy (PPTT) is a minimally-invasive oncological treatment strategy in which photon energy is selectively administered and…”
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The Clinical Significance of Genetic Variation in Ovarian Cancer by Ban, Dongjo, Housley, Stephen N, McDonald, John F

“…Genetic variation is a well-known contributor to the onset and progression of cancer. The goal of this study is to provide a comprehensive examination of the…”
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An atlas of transposable element-derived alternative splicing in cancer by Clayton, Evan A, Rishishwar, Lavanya, Huang, Tzu-Chuan, Gulati, Saurabh, Ban, Dongjo, McDonald, John F, Jordan, I King

“…Transposable element (TE)-derived sequences comprise more than half of the human genome, and their presence has been documented to alter gene expression in a…”
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Changes in gene-gene interactions associated with cancer onset and progression are largely independent of changes in gene expression by Arshad, Zainab, McDonald, John F.

“…Recent findings indicate that changes underlying cancer onset and progression are not only attributable to changes in DNA structure and expression of…”
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Magnetic Nanoparticle−Peptide Conjugates for in Vitro and in Vivo Targeting and Extraction of Cancer Cells by Scarberry, Kenneth E, Dickerson, Erin B, McDonald, John F, Zhang, Z. John

“…Magnetic cobalt spinel ferrite nanoparticles coated with biocompatible polygalacturonic acid were functionalized with ligands specific for targeting expressed…”
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Overexpression of miR-429 induces mesenchymal-to-epithelial transition (MET) in metastatic ovarian cancer cells by Chen, Jing, Wang, Lijuan, Matyunina, Lilya V, Hill, Christopher G, McDonald, John F

“…Abstract Objective Ovarian cancer (OC) is the most lethal of all gynecological malignancies primarily due to the sloughing-off of highly metastatic cells from…”
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Optimization of a Direct Analysis in Real Time/Time-of-Flight Mass Spectrometry Method for Rapid Serum Metabolomic Fingerprinting by Zhou, Manshui, McDonald, John F., Fernández, Facundo M.

“…Metabolomic fingerprinting of bodily fluids can reveal the underlying causes of metabolic disorders associated with many diseases, and has thus been recognized…”
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High throughput, label-free isolation of circulating tumor cell clusters in meshed microwells by Boya, Mert, Ozkaya-Ahmadov, Tevhide, Swain, Brandi E., Chu, Chia-Heng, Asmare, Norh, Civelekoglu, Ozgun, Liu, Ruxiu, Lee, Dohwan, Tobia, Sherry, Biliya, Shweta, McDonald, L. DeEtte, Nazha, Bassel, Kucuk, Omer, Sanda, Martin G., Benigno, Benedict B., Moreno, Carlos S., Bilen, Mehmet A., McDonald, John F., Sarioglu, A. Fatih

“…Extremely rare circulating tumor cell (CTC) clusters are both increasingly appreciated as highly metastatic precursors and virtually unexplored. Technologies…”
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SNAIL‐induced epithelial‐to‐mesenchymal transition produces concerted biophysical changes from altered cytoskeletal gene expression by McGrail, Daniel J., Mezencev, Roman, Kieu, Quang Minh N., McDonald, John F., Dawson, Michelle R.

“…A growing body of evidence suggests that the developmental process of epithelial‐to‐mesenchymal transition (EMT) is co‐opted by cancer cells to metastasize to…”
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A computational approach to generate highly conserved gene co-expression networks with RNA-seq data by Arshad, Zainab, McDonald, John F.

“…We describe a consensus approach for network construction based on fully conserved gene-gene interactions from randomly downsampled data subsets for an…”
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Functional and evolutionary significance of human microRNA seed region mutations by Hill, Christopher G, Jabbari, Neda, Matyunina, Lilya V, McDonald, John F

“…MicroRNAs have emerged in recent years as important regulators of cell function in both normal and diseased cells. MiRNAs coordinately regulate large suites of…”
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Chemosensitization of cancer cells by siRNA using targeted nanogel delivery by Dickerson, Erin B, Blackburn, William H, Smith, Michael H, Kapa, Laura B, Lyon, L Andrew, McDonald, John F

“…Chemoresistance is a major obstacle in cancer treatment. Targeted therapies that enhance cancer cell sensitivity to chemotherapeutic agents have the potential…”
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Isolation and characterization of stem-like cells from a human ovarian cancer cell line by Wang, Lijuan, Mezencev, Roman, Bowen, Nathan J., Matyunina, Lilya V., McDonald, John F.

“…Increasing evidence supports the existence of a subpopulation of cancer cells capable of self-renewal and differentiation into diverse cell lineages. These…”
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OVCAR-3 spheroid-derived cells display distinct metabolic profiles by Vermeersch, Kathleen A, Wang, Lijuan, Mezencev, Roman, McDonald, John F, Styczynski, Mark P

“…Recently, multicellular spheroids were isolated from a well-established epithelial ovarian cancer cell line, OVCAR-3, and were propagated in vitro. These…”
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De novo assembly and characterization of breast cancer transcriptomes identifies large numbers of novel fusion-gene transcripts of potential functional significance by Mittal, Vinay K, McDonald, John F

“…Gene-fusion or chimeric transcripts have been implicated in the onset and progression of a variety of cancers. Massively parallel RNA sequencing (RNA-Seq) of…”
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Elevation of sulfatides in ovarian cancer: an integrated transcriptomic and lipidomic analysis including tissue-imaging mass spectrometry by Liu, Ying, Chen, Yanfeng, Momin, Amin, Shaner, Rebecca, Wang, Elaine, Bowen, Nathan J, Matyunina, Lilya V, Walker, L Deette, McDonald, John F, Sullards, M Cameron, Merrill, Jr, Alfred H

“…Sulfatides (ST) are a category of sulfated galactosylceramides (GalCer) that are elevated in many types of cancer including, possibly, ovarian cancer. Previous…”
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Gene expression profiling supports the hypothesis that human ovarian surface epithelia are multipotent and capable of serving as ovarian cancer initiating cells by Bowen, Nathan J, Walker, L DeEtte, Matyunina, Lilya V, Logani, Sanjay, Totten, Kimberly A, Benigno, Benedict B, McDonald, John F

“…Accumulating evidence suggests that somatic stem cells undergo mutagenic transformation into cancer initiating cells. The serous subtype of ovarian…”
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LTR_STRUC: a novel search and identification program for LTR retrotransposons by McCarthy, Eugene M., McDonald, John F.

“…Motivation: Long terminal repeat (LTR) retrotransposons constitute a substantial fraction of most eukaryotic genomes and are believed to have a significant…”
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