Search Results - "Liefeld, Ted"

Correlating chemical sensitivity and basal gene expression reveals mechanism of action by Rees, Matthew G, Seashore-Ludlow, Brinton, Cheah, Jaime H, Adams, Drew J, Price, Edmund V, Gill, Shubhroz, Javaid, Sarah, Coletti, Matthew E, Jones, Victor L, Bodycombe, Nicole E, Soule, Christian K, Alexander, Benjamin, Li, Ava, Montgomery, Philip, Kotz, Joanne D, Hon, C Suk-Yee, Munoz, Benito, Liefeld, Ted, Dančík, Vlado, Haber, Daniel A, Clish, Clary B, Bittker, Joshua A, Palmer, Michelle, Wagner, Bridget K, Clemons, Paul A, Shamji, Alykhan F, Schreiber, Stuart L

“…A computational tool provides a systematic approach to determine the mechanisms of action of small molecules by examining correlations between basal gene…”
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Cytoscape: the network visualization tool for GenomeSpace workflows by Demchak, Barry, Hull, Tim, Reich, Michael, Liefeld, Ted, Smoot, Michael, Ideker, Trey, Mesirov, Jill P

“…Modern genomic analysis often requires workflows incorporating multiple best-of-breed tools. GenomeSpace is a web-based visual workbench that combines a…”
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Harnessing Connectivity in a Large-Scale Small-Molecule Sensitivity Dataset by Seashore-Ludlow, Brinton, Rees, Matthew G, Cheah, Jaime H, Cokol, Murat, Price, Edmund V, Coletti, Matthew E, Jones, Victor, Bodycombe, Nicole E, Soule, Christian K, Gould, Joshua, Alexander, Benjamin, Li, Ava, Montgomery, Philip, Wawer, Mathias J, Kuru, Nurdan, Kotz, Joanne D, Hon, C Suk-Yee, Munoz, Benito, Liefeld, Ted, Dančík, Vlado, Bittker, Joshua A, Palmer, Michelle, Bradner, James E, Shamji, Alykhan F, Clemons, Paul A, Schreiber, Stuart L

“…Identifying genetic alterations that prime a cancer cell to respond to a particular therapeutic agent can facilitate the development of precision cancer…”
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Densely Interconnected Transcriptional Circuits Control Cell States in Human Hematopoiesis by Novershtern, Noa, Subramanian, Aravind, Lawton, Lee N., Mak, Raymond H., Haining, W. Nicholas, McConkey, Marie E., Habib, Naomi, Yosef, Nir, Chang, Cindy Y., Shay, Tal, Frampton, Garrett M., Drake, Adam C.B., Leskov, Ilya, Nilsson, Bjorn, Preffer, Fred, Dombkowski, David, Evans, John W., Liefeld, Ted, Smutko, John S., Chen, Jianzhu, Friedman, Nir, Young, Richard A., Golub, Todd R., Regev, Aviv, Ebert, Benjamin L.

“…Though many individual transcription factors are known to regulate hematopoietic differentiation, major aspects of the global architecture of hematopoiesis…”
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Parallel genome-scale loss of function screens in 216 cancer cell lines for the identification of context-specific genetic dependencies by Cowley, Glenn S, Weir, Barbara A, Vazquez, Francisca, Tamayo, Pablo, Scott, Justine A, Rusin, Scott, East-Seletsky, Alexandra, Ali, Levi D, Gerath, William FJ, Pantel, Sarah E, Lizotte, Patrick H, Jiang, Guozhi, Hsiao, Jessica, Tsherniak, Aviad, Dwinell, Elizabeth, Aoyama, Simon, Okamoto, Michael, Harrington, William, Gelfand, Ellen, Green, Thomas M, Tomko, Mark J, Gopal, Shuba, Wong, Terence C, Li, Hubo, Howell, Sara, Stransky, Nicolas, Liefeld, Ted, Jang, Dongkeun, Bistline, Jonathan, Hill Meyers, Barbara, Armstrong, Scott A, Anderson, Ken C, Stegmaier, Kimberly, Reich, Michael, Pellman, David, Boehm, Jesse S, Mesirov, Jill P, Golub, Todd R, Root, David E, Hahn, William C

“…Using a genome-scale, lentivirally delivered shRNA library, we performed massively parallel pooled shRNA screens in 216 cancer cell lines to identify genes…”
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Integrative genomic analysis by interoperation of bioinformatics tools in GenomeSpace by Qu, Kun, Garamszegi, Sara, Wu, Felix, Thorvaldsdottir, Helga, Liefeld, Ted, Ocana, Marco, Borges-Rivera, Diego, Pochet, Nathalie, Robinson, James T, Demchak, Barry, Hull, Tim, Ben-Artzi, Gil, Blankenberg, Daniel, Barber, Galt P, Lee, Brian T, Kuhn, Robert M, Nekrutenko, Anton, Segal, Eran, Ideker, Trey, Reich, Michael, Regev, Aviv, Chang, Howard Y, Mesirov, Jill P

“…GenomeSpace is an open-source, cloud-based interoperability platform that facilitates integrative genomic analyses, allowing users to transition seamlessly…”
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NASA GeneLab RNA-seq consensus pipeline: Standardized processing of short-read RNA-seq data by Overbey, Eliah G., Saravia-Butler, Amanda M., Zhang, Zhe, Rathi, Komal S., Fogle, Homer, da Silveira, Willian A., Barker, Richard J., Bass, Joseph J., Beheshti, Afshin, Berrios, Daniel C., Blaber, Elizabeth A., Cekanaviciute, Egle, Costa, Helio A., Davin, Laurence B., Fisch, Kathleen M., Gebre, Samrawit G., Geniza, Matthew, Gilbert, Rachel, Gilroy, Simon, Hardiman, Gary, Herranz, Raúl, Kidane, Yared H., Kruse, Colin P.S., Lee, Michael D., Liefeld, Ted, Lewis, Norman G., McDonald, J. Tyson, Meller, Robert, Mishra, Tejaswini, Perera, Imara Y., Ray, Shayoni, Reinsch, Sigrid S., Rosenthal, Sara Brin, Strong, Michael, Szewczyk, Nathaniel J., Tahimic, Candice G.T., Taylor, Deanne M., Vandenbrink, Joshua P., Villacampa, Alicia, Weging, Silvio, Wolverton, Chris, Wyatt, Sarah E., Zea, Luis, Costes, Sylvain V., Galazka, Jonathan M.

“…With the development of transcriptomic technologies, we are able to quantify precise changes in gene expression profiles from astronauts and other organisms…”
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A phenotypically supervised single-cell analysis protocol to study within-cell-type heterogeneity of cultured mammalian cells by Chen, Kevin, Ozturk, Kivilcim, Liefeld, Ted, Reich, Michael, Mesirov, Jill P., Carter, Hannah, Fraley, Stephanie I.

“…Here, we describe a protocol combining functional metrics with genomic data to elucidate drivers of within-cell-type heterogeneity via the…”
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Cytoscape: the network visualization tool for GenomeSpace workflows [version 1; peer review: 3 approved] by Demchak, Barry, Hull, Tim, Reich, Michael, Liefeld, Ted, Smoot, Michael, Ideker, Trey, Mesirov, Jill P

“…Modern genomic analysis often requires workflows incorporating multiple best-ofbreed tools. GenomeSpace is a web-based visual workbench that combines a…”
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GenePattern flow cytometry suite by Spidlen, Josef, Barsky, Aaron, Breuer, Karin, Carr, Peter, Nazaire, Marc-Danie, Hill, Barbara Allen, Qian, Yu, Liefeld, Ted, Reich, Michael, Mesirov, Jill P, Wilkinson, Peter, Scheuermann, Richard H, Sekaly, Rafick-Pierre, Brinkman, Ryan R

“…Traditional flow cytometry data analysis is largely based on interactive and time consuming analysis of series two dimensional representations of up to 20…”
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GenePattern 2.0 by Reich, Michael, Liefeld, Ted, Gould, Joshua, Lerner, Jim, Tamayo, Pablo, Mesirov, Jill P

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The Cancer Cell Line Encyclopedia enables predictive modelling of anticancer drug sensitivity by Barretina, Jordi, Caponigro, Giordano, Stransky, Nicolas, Venkatesan, Kavitha, Margolin, Adam A., Kim, Sungjoon, Wilson, Christopher J., Lehár, Joseph, Kryukov, Gregory V., Sonkin, Dmitriy, Reddy, Anupama, Liu, Manway, Murray, Lauren, Berger, Michael F., Monahan, John E., Morais, Paula, Meltzer, Jodi, Korejwa, Adam, Jané-Valbuena, Judit, Mapa, Felipa A., Thibault, Joseph, Bric-Furlong, Eva, Raman, Pichai, Shipway, Aaron, Engels, Ingo H., Cheng, Jill, Yu, Guoying K., Yu, Jianjun, Aspesi, Peter, de Silva, Melanie, Jagtap, Kalpana, Jones, Michael D., Wang, Li, Hatton, Charles, Palescandolo, Emanuele, Gupta, Supriya, Mahan, Scott, Sougnez, Carrie, Onofrio, Robert C., Liefeld, Ted, MacConaill, Laura, Winckler, Wendy, Reich, Michael, Li, Nanxin, Mesirov, Jill P., Gabriel, Stacey B., Getz, Gad, Ardlie, Kristin, Chan, Vivien, Myer, Vic E., Weber, Barbara L., Porter, Jeff, Warmuth, Markus, Finan, Peter, Harris, Jennifer L., Meyerson, Matthew, Golub, Todd R., Morrissey, Michael P., Sellers, William R., Schlegel, Robert, Garraway, Levi A.

“…The Cancer Cell Line Encyclopedia presents the first results from a large-scale screen of some 947 cancer cell lines with 24 anticancer drugs, with the aim of…”
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An Interactive Resource to Identify Cancer Genetic and Lineage Dependencies Targeted by Small Molecules by Basu, Amrita, Bodycombe, Nicole E., Cheah, Jaime H., Price, Edmund V., Liu, Ke, Schaefer, Giannina I., Ebright, Richard Y., Stewart, Michelle L., Ito, Daisuke, Wang, Stephanie, Bracha, Abigail L., Liefeld, Ted, Wawer, Mathias, Gilbert, Joshua C., Wilson, Andrew J., Stransky, Nicolas, Kryukov, Gregory V., Dancik, Vlado, Barretina, Jordi, Garraway, Levi A., Hon, C. Suk-Yee, Munoz, Benito, Bittker, Joshua A., Stockwell, Brent R., Khabele, Dineo, Stern, Andrew M., Clemons, Paul A., Shamji, Alykhan F., Schreiber, Stuart L.

“…The high rate of clinical response to protein-kinase-targeting drugs matched to cancer patients with specific genomic alterations has prompted efforts to use…”
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Abstract 5106: The GenePattern Notebook environment for reproducible cancer research by Reich, Michael M., Tabor, Thorin T., Liefeld, Ted, Hill, Barbara, Thorvaldsdottir, Helga, Mesirov, Jill P.

“…Abstract As the availability of genetic and genomic data and analysis tools from large-scale cancer initiatives continues to increase, the need has become more…”
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The landscape of somatic copy-number alteration across human cancers by Yecies, Derek, Gabriel, Stacey, Porter, Dale, Nucera, Carmelo, Antonescu, Cristina R, Chiang, Derek Y, Janne, Pasi A, Greulich, Heidi, Loo, Alice, Prensner, John, Maher, Elizabeth, Rustgi, Anil K, Ligon, Azra H, Tanaka, Kumiko E, Kaye, Frederic J, Ebert, Benjamin L, Pomeroy, Scott L, Lander, Eric S, Fletcher, Jonathan A, Okamoto, Aikou, Signoretti, Sabina, Haery, Leila, Reich, Michael, Dobson, Jennifer, Raychaudhuri, Soumya, Wei, Guo, Baselga, José, Tsao, Ming-Sound, Letai, Anthony, Getz, Gad, Liefeld, Ted, Donovan, Jerry, Levine, Ross L, Beer, David G, Daly, Mark J, Sasaki, Hidefumi, Pinchback, Reid M, Bass, Adam J, Hoffman, Carter, Ladanyi, Marc, True, Lawrence D, Cho, Yoon-Jae, Sellers, William R, Tabernero, Josep, Demichelis, Francesca, Tepper, Joel E, Golub, Todd R, Meyerson, Matthew, Boehm, Jesse S, Mermel, Craig H, Loda, Massimo, Weir, Barbara A, Beroukhim, Rameen, Singer, Samuel, Urashima, Mitsuyoshi, Gao, Qing, Lawrence, Michael S, Rubin, Mark A, Barretina, Jordi, Garraway, Levi A, Winckler, Wendy, Mc Henry, Kevin T

“…A powerful way to discover key genes with causal roles in oncogenesis is to identify genomic regions that undergo frequent alteration in human cancers. Here we…”
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Abstract 3207: GenePattern Notebook: An integrative analytical environment for cancer research by Reich, Michael M., Tabor, Thorin, Liefeld, Ted, Juarez, Edwin, Hill, Barbara, Thorvaldsdottir, Helga, Tamayo, Pablo, Mesirov, Jill P.

“…Abstract As the availability of genetic and genomic data and analysis tools from large-scale cancer initiatives continues to increase, with single-cell studies…”
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GeNets: a unified web platform for network-based genomic analyses by Li, Taibo, Kim, April, Rosenbluh, Joseph, Horn, Heiko, Greenfeld, Liraz, An, David, Zimmer, Andrew, Liberzon, Arthur, Bistline, Jon, Natoli, Ted, Li, Yang, Tsherniak, Aviad, Narayan, Rajiv, Subramanian, Aravind, Liefeld, Ted, Wong, Bang, Thompson, Dawn, Calvo, Sarah, Carr, Steve, Boehm, Jesse, Jaffe, Jake, Mesirov, Jill, Hacohen, Nir, Regev, Aviv, Lage, Kasper

“…Functional genomics networks are widely used to identify unexpected pathway relationships in large genomic datasets. However, it is challenging to compare the…”
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Abstract 2279: The GenePattern Notebook environment for reproducible cancer research by Reich, Michael M., Tabor, Thorin T., Liefeld, Ted, Hill, Barbara, Thorvaldsdottir, Helga, Mesirov, Jill P.

“…Abstract As the availability of genetic and genomic data and analysis tools from large-scale cancer initiatives continues to increase, the need has become more…”
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Addendum: The Cancer Cell Line Encyclopedia enables predictive modelling of anticancer drug sensitivity by Barretina, Jordi, Caponigro, Giordano, Stransky, Nicolas, Venkatesan, Kavitha, Margolin, Adam A., Kim, Sungjoon, J.Wilson, Christopher, Lehár, Joseph, Kryukov, Gregory V., Sonkin, Dmitriy, Reddy, Anupama, Liu, Manway, Murray, Lauren, Berger, Michael F., Monahan, John E., Morais, Paula, Meltzer, Jodi, Korejwa, Adam, Jané-Valbuena, Judit, Mapa, Felipa A., Thibault, Joseph, Bric-Furlong, Eva, Raman, Pichai, Shipway, Aaron, Engels, Ingo H., Cheng, Jill, Yu, Guoying K., Yu, Jianjun, Aspesi, Peter, de Silva, Melanie, Jagtap, Kalpana, Jones, Michael D., Wang, Li, Hatton, Charles, Palescandolo, Emanuele, Gupta, Supriya, Mahan, Scott, Sougnez, Carrie, Onofrio, Robert C., Liefeld, Ted, MacConaill, Laura, Winckler, Wendy, Reich, Michael, Li, Nanxin, Mesirov, Jill P., Gabriel, Stacey B., Getz, Gad, Ardlie, Kristin, Chan, Vivien, Myer, Vic E., Weber, Barbara L., Porter, Jeff, Warmuth, Markus, Finan, Peter, Harris, Jennifer L., Meyerson, Matthew, Golub, Todd R., Morrissey, Michael P., Sellers, William R., Schlegel, Robert, Garraway, Levi A.

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Abstract 2588: GenePattern Notebook: an environment for reproducible cancer research by Reich, Michael M., Tabor, Thorin T., Liefeld, Ted, Hill, Barbara, Thorvaldsdottir, Helga, Mesirov, Jill P.

“…Abstract As the availability of genetic and genomic data and analysis tools from large-scale cancer initiatives continues to increase, the need has become more…”
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