Search Results - "Sunshine, Margot"

CellMiner: A Web-Based Suite of Genomic and Pharmacologic Tools to Explore Transcript and Drug Patterns in the NCI-60 Cell Line Set by REINHOLD, William C, SUNSHINE, Margot, HONGFANG LIU, VARMA, Sudhir, KOHN, Kurt W, MORRIS, Joel, DOROSHOW, James, POMMIER, Yves

“…High-throughput and high-content databases are increasingly important resources in molecular medicine, systems biology, and pharmacology. However, the…”
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CellMiner: a relational database and query tool for the NCI-60 cancer cell lines by Shankavaram, Uma T, Varma, Sudhir, Kane, David, Sunshine, Margot, Chary, Krishna K, Reinhold, William C, Pommier, Yves, Weinstein, John N

“…Advances in the high-throughput omic technologies have made it possible to profile cells in a large number of ways at the DNA, RNA, protein, chromosomal,…”
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The NCI-60 Methylome and Its Integration into CellMiner by Reinhold, William C, Varma, Sudhir, Sunshine, Margot, Rajapakse, Vinodh, Luna, Augustin, Kohn, Kurt W, Stevenson, Holly, Wang, Yonghong, Heyn, Holger, Nogales, Vanesa, Moran, Sebastian, Goldstein, David J, Doroshow, James H, Meltzer, Paul S, Esteller, Manel, Pommier, Yves

“…A unique resource for systems pharmacology and genomic studies is the NCI-60 cancer cell line panel, which provides data for the largest publicly available…”
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CellMinerCDB for Integrative Cross-Database Genomics and Pharmacogenomics Analyses of Cancer Cell Lines by Rajapakse, Vinodh N, Luna, Augustin, Yamade, Mihoko, Loman, Lisa, Varma, Sudhir, Sunshine, Margot, Iorio, Francesco, Sousa, Fabricio G, Elloumi, Fathi, Aladjem, Mirit I, Thomas, Anish, Sander, Chris, Kohn, Kurt W, Benes, Cyril H, Garnett, Mathew, Reinhold, William C, Pommier, Yves

“…CellMinerCDB provides a web-based resource (https://discover.nci.nih.gov/cellminercdb/) for integrating multiple forms of pharmacological and genomic analyses,…”
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High resolution copy number variation data in the NCI-60 cancer cell lines from whole genome microarrays accessible through CellMiner by Varma, Sudhir, Pommier, Yves, Sunshine, Margot, Weinstein, John N, Reinhold, William C

“…Array-based comparative genomic hybridization (aCGH) is a powerful technique for detecting gene copy number variation. It is generally considered to be robust…”
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NCI-60 whole exome sequencing and pharmacological CellMiner analyses by Reinhold, William C, Varma, Sudhir, Sousa, Fabricio, Sunshine, Margot, Abaan, Ogan D, Davis, Sean R, Reinhold, Spencer W, Kohn, Kurt W, Morris, Joel, Meltzer, Paul S, Doroshow, James H, Pommier, Yves

“…Exome sequencing provides unprecedented insights into cancer biology and pharmacological response. Here we assess these two parameters for the NCI-60, which is…”
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High-Throughput GoMiner, an 'industrial-strength' integrative gene ontology tool for interpretation of multiple-microarray experiments, with application to studies of Common Variable Immune Deficiency (CVID) by Zeeberg, Barry R, Qin, Haiying, Narasimhan, Sudarshan, Sunshine, Margot, Cao, Hong, Kane, David W, Reimers, Mark, Stephens, Robert M, Bryant, David, Burt, Stanley K, Elnekave, Eldad, Hari, Danielle M, Wynn, Thomas A, Cunningham-Rundles, Charlotte, Stewart, Donn M, Nelson, David, Weinstein, John N

“…We previously developed GoMiner, an application that organizes lists of 'interesting' genes (for example, under-and overexpressed genes from a microarray…”
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A formal MIM specification and tools for the common exchange of MIM diagrams: an XML-Based format, an API, and a validation method by Luna, Augustin, Karac, Evrim I, Sunshine, Margot, Chang, Lucas, Nussinov, Ruth, Aladjem, Mirit I, Kohn, Kurt W

“…The Molecular Interaction Map (MIM) notation offers a standard set of symbols and rules on their usage for the depiction of cellular signaling network…”
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Gene expression profiles of the NCI-60 human tumor cell lines define molecular interaction networks governing cell migration processes by Kohn, Kurt W, Zeeberg, Barry R, Reinhold, William C, Sunshine, Margot, Luna, Augustin, Pommier, Yves

“…Although there is extensive information on gene expression and molecular interactions in various cell types, integrating those data in a functionally coherent…”
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PathVisio-MIM: PathVisio plugin for creating and editing Molecular Interaction Maps (MIMs) by Luna, Augustin, Sunshine, Margot L., van Iersel, Martijn P., Aladjem, Mirit I., Kohn, Kurt W.

“…Motivation: A plugin for the Java-based PathVisio pathway editor has been developed to help users draw diagrams of bioregulatory networks according to the…”
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GoMiner: a resource for biological interpretation of genomic and proteomic data by Zeeberg, Barry R, Feng, Weimin, Wang, Geoffrey, Wang, May D, Fojo, Anthony T, Sunshine, Margot, Narasimhan, Sudarshan, Kane, David W, Reinhold, William C, Lababidi, Samir, Bussey, Kimberly J, Riss, Joseph, Barrett, J Carl, Weinstein, John N

“…We have developed GoMiner, a program package that organizes lists of 'interesting' genes (for example, under- and overexpressed genes from a microarray…”
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AbMiner: a bioinformatic resource on available monoclonal antibodies and corresponding gene identifiers for genomic, proteomic, and immunologic studies by Major, Sylvia M, Nishizuka, Satoshi, Morita, Daisaku, Rowland, Rick, Sunshine, Margot, Shankavaram, Uma, Washburn, Frank, Asin, Daniel, Kouros-Mehr, Hosein, Kane, David, Weinstein, John N

“…Monoclonal antibodies are used extensively throughout the biomedical sciences for detection of antigens, either in vitro or in vivo. We, for example, have used…”
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MatchMiner: a tool for batch navigation among gene and gene product identifiers by Bussey, Kimberly J, Kane, David, Sunshine, Margot, Narasimhan, Sudar, Nishizuka, Satoshi, Reinhold, William C, Zeeberg, Barry, Ajay, Weinstein, Weinstein, John N

“…MatchMiner is a freely available program package for batch navigation among gene and gene product identifier types commonly encountered in microarray studies…”
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Using CellMiner 1.6 for Systems Pharmacology and Genomic Analysis of the NCI-60 by Reinhold, William C, Sunshine, Margot, Varma, Sudhir, Doroshow, James H, Pommier, Yves

“…The NCI-60 cancer cell line panel provides a premier model for data integration, and systems pharmacology being the largest publicly available database of…”
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RNA Sequencing of the NCI-60: Integration into CellMiner and CellMiner CDB by Reinhold, William C, Varma, Sudhir, Sunshine, Margot, Elloumi, Fathi, Ofori-Atta, Kwabena, Lee, Sunmin, Trepel, Jane B, Meltzer, Paul S, Doroshow, James H, Pommier, Yves

“…CellMiner (http://discover.nci.nih.gov/cellminer) and CellMinerCDB (https://discover.nci.nih.gov/cellminercdb/) are web-based applications for mining publicly…”
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The BioPAX community standard for pathway data sharing by Bader, Gary D, Demir, Emek, Cary, Michael P, Paley, Suzanne, Fukuda, Ken, Lemer, Christian, Vastrik, Imre, Wu, Guanming, D'Eustachio, Peter, Schaefer, Carl, Luciano, Joanne, Schacherer, Frank, Martinez-Flores, Irma, Hu, Zhenjun, Jimenez-Jacinto, Veronica, Joshi-Tope, Geeta, Kandasamy, Kumaran, Lopez-Fuentes, Alejandra C, Mi, Huaiyu, Pichler, Elgar, Rodchenkov, Igor, Splendiani, Andrea, Tkachev, Sasha, Zucker, Jeremy, Gopinath, Gopal, Rajasimha, Harsha, Ramakrishnan, Ranjani, Shah, Imran, Syed, Mustafa, Anwar, Nadia, Babur, Özgün, Blinov, Michael, Brauner, Erik, Corwin, Dan, Donaldson, Sylva, Gibbons, Frank, Goldberg, Robert, Hornbeck, Peter, Luna, Augustin, Murray-Rust, Peter, Neumann, Eric, Reubenacker, Oliver, Samwald, Matthias, van Iersel, Martijn, Wimalaratne, Sarala, Allen, Keith, Braun, Burk, Whirl-Carrillo, Michelle, Cheung, Kei-Hoi, Dahlquist, Kam, Finney, Andrew, Gillespie, Marc, Glass, Elizabeth, Gong, Li, Haw, Robin, Honig, Michael, Hubaut, Olivier, Kane, David, Krupa, Shiva, Kutmon, Martina, Leonard, Julie, Marks, Debbie, Merberg, David, Petri, Victoria, Pico, Alex, Ravenscroft, Dean, Ren, Liya, Shah, Nigam, Sunshine, Margot, Tang, Rebecca, Whaley, Ryan, Letovksy, Stan, Buetow, Kenneth H, Rzhetsky, Andrey, Schachter, Vincent, Sobral, Bruno S, Dogrusoz, Ugur, McWeeney, Shannon, Aladjem, Mirit, Birney, Ewan, Collado-Vides, Julio, Goto, Susumu, Hucka, Michael, Novère, Nicolas Le, Maltsev, Natalia, Pandey, Akhilesh, Thomas, Paul, Wingender, Edgar, Karp, Peter D, Sander, Chris

“…Incompatible data storage formats have hindered the sharing and analyses of digital representations of biological pathways. BioPAX is a standardized language…”
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Abstract 75: CellMiner, a systems pharmacological web-application for the NCI-60 cancerous cell-lines: Updates, data integration, and translationally relevant results by Reinhold, William C., Sunshine, Margot, Varma, Sudir, Doroshow, James, Pommier, Yves

“…Abstract Understanding the influences of molecular alterations on pharmacological responses in the omic sense is at the fore of the effort to make oncology…”
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Abstract 3749: Uses and update for CellMiner, a tool for access to and comparison of molecular data and pharmacological response for the NCI-60 by Reinhold, William C., Sunshine, Margot, Varma, Sudir, Rajapakse, Vinodh, Doroshow, James, Morris, Joel, Pmmier, Yves

“…Abstract Integration and understanding of genomic and proteomic data and their relationships with and influences on pharmacology have become key components of…”
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Abstract 5327: Using CellMiner for gene expression, DNA copy number, microRNA transcript levels, variant status, drug activity, and their integration for systems pharmacology for the NCI-60 by Reinhold, William C., Sunshine, Margot, Varma, Sudir, Morris, Joel, Kohn, Kurt, Doroshow, James, Pommier, Yves

“…Abstract Molecular biology and pharmacology are being transformed by high-throughput data. Access, and integration of this data, however, remains difficult…”
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The NCI-60 methylome and its integration into CellMiner by Reinhold, William C, Varma, Sudhir, Sunshine, Margot, Rajapakse, Vinodh, Luna, Augustin, Kohn, Kurt W, Stevenson, Holly, Wang, Yonghong, Heyn, Holger, Nogales, Vanesa, Moran, Sebastian, Goldstein, David J, Doroshow, James H, Meltzer, Paul S, Esteller, Manel, Pommier, Yves

“…A unique resource for systems pharmacology and genomic studies is the NCI-60 cancer cell line panel, which provides data for the largest publicly available…”
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