Cytoscape: the network visualization tool for GenomeSpace workflows

Por Demchak, Barry, Hull, Tim, Reich, Michael, Liefeld, Ted, Smoot, Michael, Ideker, Trey, Mesirov, Jill P.
Publicado em 2014

GenePattern flow cytometry suite

Por 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
Publicado em 2013

Integrative genomic analysis by interoperation of bioinformatics tools in GenomeSpace

Por 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.
Publicado no Nat Methods (2016)

Densely interconnected transcriptional circuits control cell states in human hematopoiesis

Por 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.
Publicado em 2011

Harnessing Connectivity in a Large-Scale Small-Molecule Sensitivity Dataset

Por 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.
Publicado no Cancer Discov (2015)

Correlating chemical sensitivity and basal gene expression reveals mechanism of action

Por 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.
Publicado no Nat Chem Biol (2015)

An interactive resource to identify cancer genetic and lineage dependencies targeted by small molecules

Por 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.
Publicado em 2013

Parallel genome-scale loss of function screens in 216 cancer cell lines for the identification of context-specific genetic dependencies

Por Cowley, Glenn S, Weir, Barbara A, Vazquez, Francisca, Tamayo, Pablo, Scott, Justine A, Rusin, Scott, East-Seletsky, Alexandra, Ali, Levi D, Gerath, William F.J, 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, Meyers, Barbara Hill, 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
Publicado no Sci Data (2014)

Parallel genome-scale loss of function screens in 216 cancer cell lines for the identification of context-specific genetic dependencies

Por 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
Publicado no Sci Data (2014)

Initial genome sequencing and analysis of multiple myeloma

Por Chapman, Michael A., Lawrence, Michael S., Keats, Jonathan J., Cibulskis, Kristian, Sougnez, Carrie, Schinzel, Anna C., Harview, Christina L., Brunet, Jean-Philippe, Ahmann, Gregory J., Adli, Mazhar, Anderson, Kenneth C., Ardlie, Kristin G., Auclair, Daniel, Baker, Angela, Bergsagel, P. Leif, Bernstein, Bradley E., Drier, Yotam, Fonseca, Rafael, Gabriel, Stacey B., Hofmeister, Craig C., Jagannath, Sundar, Jakubowiak, Andrzej J., Krishnan, Amrita, Levy, Joan, Liefeld, Ted, Lonial, Sagar, Mahan, Scott, Mfuko, Bunmi, Monti, Stefano, Perkins, Louise M., Onofrio, Robb, Pugh, Trevor J., Vincent Rajkumar, S., Ramos, Alex H., Siegel, David S., Sivachenko, Andrey, Trudel, Suzanne, Vij, Ravi, Voet, Douglas, Winckler, Wendy, Zimmerman, Todd, Carpten, John, Trent, Jeff, Hahn, William C., Garraway, Levi A., Meyerson, Matthew, Lander, Eric S., Getz, Gad, Golub, Todd R.
Publicado em 2011

The landscape of somatic copy-number alteration across human cancers

Por Beroukhim, Rameen, Mermel, Craig H., Porter, Dale, Wei, Guo, Raychaudhuri, Soumya, Donovan, Jerry, Barretina, Jordi, Boehm, Jesse S., Dobson, Jennifer, Urashima, Mitsuyoshi, Mc Henry, Kevin T., Pinchback, Reid M., Ligon, Azra H., Cho, Yoon-Jae, Haery, Leila, Greulich, Heidi, Reich, Michael, Winckler, Wendy, Lawrence, Michael S., Weir, Barbara A., Tanaka, Kumiko E., Chiang, Derek Y., Bass, Adam J., Loo, Alice, Hoffman, Carter, Prensner, John, Liefeld, Ted, Gao, Qing, Yecies, Derek, Signoretti, Sabina, Maher, Elizabeth, Kaye, Frederic J., Sasaki, Hidefumi, Tepper, Joel E., Fletcher, Jonathan A., Tabernero, Josep, Baselga, Jose, Tsao, Ming-Sound, DeMichelis, Francesca, Rubin, Mark A., Janne, Pasi A., Daly, Mark J., Nucera, Carmelo, Levine, Ross L., Ebert, Benjamin L., Gabriel, Stacey, Rustgi, Anil K., Antonescu, Cristina R., Ladanyi, Marc, Letai, Anthony, Garraway, Levi A., Loda, Massimo, Beer, David G., True, Lawrence D., Okamoto, Aikou, Pomeroy, Scott L., Singer, Samuel, Golub, Todd R., Lander, Eric S., Getz, Gad, Sellers, William R., Meyerson, Matthew
Publicado em 2010

The Cancer Cell Line Encyclopedia enables predictive modeling of anticancer drug sensitivity

Por 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.
Publicado em 2012