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 2014

A phenotypically supervised single-cell analysis protocol to study within-cell-type heterogeneity of cultured mammalian cells

por Chen, Kevin, Ozturk, Kivilcim, Liefeld, Ted, Reich, Michael, Mesirov, Jill P., Carter, Hannah, Fraley, Stephanie I.
Publicado 2021

NMFClustering: Accessible NMF-based clustering utilizing GPU acceleration

por Liefeld, Ted, Huang, Edwin, Wenzel, Alexander T., Yoshimoto, Kenneth, Sharma, Ashwyn K, Sicklick, Jason K, Mesirov, Jill P, Reich, Michael
Publicado 2023

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 2013

Imaging-AMARETTO: An Imaging Genomics Software Tool to Interrogate Multiomics Networks for Relevance to Radiography and Histopathology Imaging Biomarkers of Clinical Outcomes

por Gevaert, Olivier, Nabian, Mohsen, Bakr, Shaimaa, Everaert, Celine, Shinde, Jayendra, Manukyan, Artur, Liefeld, Ted, Tabor, Thorin, Xu, Jishu, Lupberger, Joachim, Haas, Brian J., Baumert, Thomas F., Hernaez, Mikel, Reich, Michael, Quintana, Francisco J., Uhlmann, Erik J., Krichevsky, Anna M., Mesirov, Jill P., Carey, Vincent, Pochet, Nathalie
Publicado 2020

GeNets: A unified web platform for network-based analyses of genomic data

por 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
Publicado 2018

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 2016

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 2015

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 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 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 2011

NASA GeneLab RNA-seq consensus pipeline: standardized processing of short-read RNA-seq data

por 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.
Publicado 2021

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 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 2012