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Widespread Expansion of Protein Interaction Capabilities by Alternative Splicing
Yang, Xinping, Coulombe-Huntington, Jasmin, Kang, Shuli, Sheynkman, Gloria M., Hao, Tong, Richardson, Aaron, Sun, Song, Yang, Fan, Shen, Yun A., Murray, Ryan R., Spirohn, Kerstin, Begg, Bridget E., Duran-Frigola, Miquel, MacWilliams, Andrew, Pevzner, Samuel J., Zhong, Quan, Wanamaker, Shelly A., Tam, Stanley, Ghamsari, Lila, Sahni, Nidhi, Yi, Song, Rodriguez, Maria D., Balcha, Dawit, Tan, Guihong, Costanzo, Michael, Andrews, Brenda, Boone, Charles, Zhou, Xianghong J., Salehi-Ashtiani, Kourosh, Charloteaux, Benoit, Chen, Alyce A., Calderwood, Michael A., Aloy, Patrick, Roth, Frederick P., Hill, David E., Iakoucheva, Lilia M., Xia, Yu, Vidal, Marc
Published in Cell (11.02.2016)
Published in Cell (11.02.2016)
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An empirical framework for binary interactome mapping
Venkatesan, Kavitha, Rual, Jean-François, Vazquez, Alexei, Stelzl, Ulrich, Lemmens, Irma, Hirozane-Kishikawa, Tomoko, Hao, Tong, Zenkner, Martina, Xin, Xiaofeng, Goh, Kwang-Il, Yildirim, Muhammed A, Simonis, Nicolas, Heinzmann, Kathrin, Gebreab, Fana, Sahalie, Julie M, Cevik, Sebiha, Simon, Christophe, de Smet, Anne-Sophie, Dann, Elizabeth, Smolyar, Alex, Vinayagam, Arunachalam, Yu, Haiyuan, Szeto, David, Borick, Heather, Dricot, Amélie, Klitgord, Niels, Murray, Ryan R, Lin, Chenwei, Lalowski, Maciej, Timm, Jan, Rau, Kirstin, Boone, Charles, Braun, Pascal, Cusick, Michael E, Roth, Frederick P, Hill, David E, Tavernier, Jan, Wanker, Erich E, Barabási, Albert-László, Vidal, Marc
Published in Nature methods (01.01.2009)
Published in Nature methods (01.01.2009)
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An inter‐species protein–protein interaction network across vast evolutionary distance
Zhong, Quan, Pevzner, Samuel J, Hao, Tong, Wang, Yang, Mosca, Roberto, Menche, Jörg, Taipale, Mikko, Taşan, Murat, Fan, Changyu, Yang, Xinping, Haley, Patrick, Murray, Ryan R, Mer, Flora, Gebreab, Fana, Tam, Stanley, MacWilliams, Andrew, Dricot, Amélie, Reichert, Patrick, Santhanam, Balaji, Ghamsari, Lila, Calderwood, Michael A, Rolland, Thomas, Charloteaux, Benoit, Lindquist, Susan, Barabási, Albert‐László, Hill, David E, Aloy, Patrick, Cusick, Michael E, Xia, Yu, Roth, Frederick P, Vidal, Marc
Published in Molecular systems biology (01.04.2016)
Published in Molecular systems biology (01.04.2016)
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Evidence for Transcript Networks Composed of Chimeric RNAs in Human Cells
Djebali, Sarah, Lagarde, Julien, Kapranov, Philipp, Lacroix, Vincent, Borel, Christelle, Mudge, Jonathan M., Howald, Cédric, Foissac, Sylvain, Ucla, Catherine, Chrast, Jacqueline, Ribeca, Paolo, Martin, David, Murray, Ryan R., Yang, Xinping, Ghamsari, Lila, Lin, Chenwei, Bell, Ian, Dumais, Erica, Drenkow, Jorg, Tress, Michael L., Gelpí, Josep Lluís, Orozco, Modesto, Valencia, Alfonso, van Berkum, Nynke L., Lajoie, Bryan R., Vidal, Marc, Stamatoyannopoulos, John, Batut, Philippe, Dobin, Alex, Harrow, Jennifer, Hubbard, Tim, Dekker, Job, Frankish, Adam, Salehi-Ashtiani, Kourosh, Reymond, Alexandre, Antonarakis, Stylianos E., Guigó, Roderic, Gingeras, Thomas R.
Published in PloS one (04.01.2012)
Published in PloS one (04.01.2012)
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A Proteome-Scale Map of the Human Interactome Network
Rolland, Thomas, Taşan, Murat, Charloteaux, Benoit, Pevzner, Samuel J., Zhong, Quan, Sahni, Nidhi, Yi, Song, Lemmens, Irma, Fontanillo, Celia, Mosca, Roberto, Kamburov, Atanas, Ghiassian, Susan D., Yang, Xinping, Ghamsari, Lila, Balcha, Dawit, Begg, Bridget E., Braun, Pascal, Brehme, Marc, Broly, Martin P., Carvunis, Anne-Ruxandra, Convery-Zupan, Dan, Corominas, Roser, Coulombe-Huntington, Jasmin, Dann, Elizabeth, Dreze, Matija, Dricot, Amélie, Fan, Changyu, Franzosa, Eric, Gebreab, Fana, Gutierrez, Bryan J., Hardy, Madeleine F., Jin, Mike, Kang, Shuli, Kiros, Ruth, Lin, Guan Ning, Luck, Katja, MacWilliams, Andrew, Menche, Jörg, Murray, Ryan R., Palagi, Alexandre, Poulin, Matthew M., Rambout, Xavier, Rasla, John, Reichert, Patrick, Romero, Viviana, Ruyssinck, Elien, Sahalie, Julie M., Scholz, Annemarie, Shah, Akash A., Sharma, Amitabh, Shen, Yun, Spirohn, Kerstin, Tam, Stanley, Tejeda, Alexander O., Wanamaker, Shelly A., Twizere, Jean-Claude, Vega, Kerwin, Walsh, Jennifer, Cusick, Michael E., Xia, Yu, Barabási, Albert-László, Iakoucheva, Lilia M., Aloy, Patrick, De Las Rivas, Javier, Tavernier, Jan, Calderwood, Michael A., Hill, David E., Hao, Tong, Roth, Frederick P., Vidal, Marc
Published in Cell (20.11.2014)
Published in Cell (20.11.2014)
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Pervasive mislocalization of pathogenic coding variants underlying human disorders
Lacoste, Jessica, Haghighi, Marzieh, Haider, Shahan, Reno, Chloe, Lin, Zhen-Yuan, Segal, Dmitri, Qian, Wesley Wei, Xiong, Xueting, Teelucksingh, Tanisha, Miglietta, Esteban, Shafqat-Abbasi, Hamdah, Ryder, Pearl V., Senft, Rebecca, Cimini, Beth A., Murray, Ryan R., Nyirakanani, Chantal, Hao, Tong, McClain, Gregory G., Roth, Frederick P., Calderwood, Michael A., Hill, David E., Vidal, Marc, Yi, S. Stephen, Sahni, Nidhi, Peng, Jian, Gingras, Anne-Claude, Singh, Shantanu, Carpenter, Anne E., Taipale, Mikko
Published in Cell (14.11.2024)
Published in Cell (14.11.2024)
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A public genome-scale lentiviral expression library of human ORFs
Yang, Xiaoping, Boehm, Jesse S, Yang, Xinping, Salehi-Ashtiani, Kourosh, Hao, Tong, Shen, Yun, Lubonja, Rakela, Thomas, Sapana R, Alkan, Ozan, Bhimdi, Tashfeen, Green, Thomas M, Johannessen, Cory M, Silver, Serena J, Nguyen, Cindy, Murray, Ryan R, Hieronymus, Haley, Balcha, Dawit, Fan, Changyu, Lin, Chenwei, Ghamsari, Lila, Vidal, Marc, Hahn, William C, Hill, David E, Root, David E
Published in Nature methods (01.08.2011)
Published in Nature methods (01.08.2011)
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High-Quality Binary Protein Interaction Map of the Yeast Interactome Network
Yu, Haiyuan, Braun, Pascal, Yıldırım, Muhammed A, Lemmens, Irma, Venkatesan, Kavitha, Sahalie, Julie, Hirozane-Kishikawa, Tomoko, Gebreab, Fana, Li, Na, Simonis, Nicolas, Hao, Tong, Rual, Jean-François, Dricot, Amélie, Vazquez, Alexei, Murray, Ryan R, Simon, Christophe, Tardivo, Leah, Tam, Stanley, Svrzikapa, Nenad, Fan, Changyu, de Smet, Anne-Sophie, Motyl, Adriana, Hudson, Michael E, Park, Juyong, Xin, Xiaofeng, Cusick, Michael E, Moore, Troy, Boone, Charlie, Snyder, Michael, Roth, Frederick P, Barabási, Albert-László, Tavernier, Jan, Hill, David E, Vidal, Marc
Published in Science (American Association for the Advancement of Science) (03.10.2008)
Published in Science (American Association for the Advancement of Science) (03.10.2008)
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Journal Article
Isoform discovery by targeted cloning, 'deep-well' pooling and parallel sequencing
Salehi-Ashtiani, Kourosh, Yang, Xinping, Derti, Adnan, Tian, Weidong, Hao, Tong, Lin, Chenwei, Makowski, Kathryn, Shen, Lei, Murray, Ryan R, Szeto, David, Tusneem, Nadeem, Smith, Douglas R, Cusick, Michael E, Hill, David E, Roth, Frederick P, Vidal, Marc
Published in Nature methods (01.07.2008)
Published in Nature methods (01.07.2008)
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Journal Article
An experimentally derived confidence score for binary protein-protein interactions
Braun, Pascal, Tasan, Murat, Dreze, Matija, Barrios-Rodiles, Miriam, Lemmens, Irma, Yu, Haiyuan, Sahalie, Julie M, Murray, Ryan R, Roncari, Luba, de Smet, Anne-Sophie, Venkatesan, Kavitha, Rual, Jean-François, Vandenhaute, Jean, Cusick, Michael E, Pawson, Tony, Hill, David E, Tavernier, Jan, Wrana, Jeffrey L, Roth, Frederick P, Vidal, Marc
Published in Nature methods (01.01.2009)
Published in Nature methods (01.01.2009)
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Journal Article
COT drives resistance to RAF inhibition through MAP kinase pathway reactivation
Johannessen, Cory M., Boehm, Jesse S., Kim, So Young, Thomas, Sapana R., Wardwell, Leslie, Johnson, Laura A., Emery, Caroline M., Stransky, Nicolas, Cogdill, Alexandria P., Barretina, Jordi, Caponigro, Giordano, Hieronymus, Haley, Murray, Ryan R., Salehi-Ashtiani, Kourosh, Hill, David E., Vidal, Marc, Zhao, Jean J., Yang, Xiaoping, Alkan, Ozan, Kim, Sungjoon, Harris, Jennifer L., Wilson, Christopher J., Myer, Vic E., Finan, Peter M., Root, David E., Roberts, Thomas M., Golub, Todd, Flaherty, Keith T., Dummer, Reinhard, Weber, Barbara L., Sellers, William R., Schlegel, Robert, Wargo, Jennifer A., Hahn, William C., Garraway, Levi A.
Published in Nature (London) (16.12.2010)
Published in Nature (London) (16.12.2010)
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Metabolic network analysis integrated with transcript verification for sequenced genomes
Manichaikul, Ani, Ghamsari, Lila, Hom, Erik F Y, Lin, Chenwei, Murray, Ryan R, Chang, Roger L, Balaji, S, Hao, Tong, Shen, Yun, Chavali, Arvind K, Thiele, Ines, Yang, Xinping, Fan, Changyu, Mello, Elizabeth, Hill, David E, Vidal, Marc, Salehi-Ashtiani, Kourosh, Papin, Jason A
Published in Nature methods (01.08.2009)
Published in Nature methods (01.08.2009)
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Journal Article
Efficient targeted transcript discovery via array-based normalization of RACE libraries
Djebali, Sarah, Kapranov, Philipp, Foissac, Sylvain, Lagarde, Julien, Reymond, Alexandre, Ucla, Catherine, Wyss, Carine, Drenkow, Jorg, Dumais, Erica, Murray, Ryan R, Lin, Chenwei, Szeto, David, Denoeud, France, Calvo, Miquel, Frankish, Adam, Harrow, Jennifer, Makrythanasis, Periklis, Vidal, Marc, Salehi-Ashtiani, Kourosh, Antonarakis, Stylianos E, Gingeras, Thomas R, Guigó, Roderic
Published in Nature methods (01.07.2008)
Published in Nature methods (01.07.2008)
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Journal Article
Large-scale RACE approach for proactive experimental definition of C. elegans ORFeome
Salehi-Ashtiani, Kourosh, Lin, Chenwei, Hao, Tong, Shen, Yun, Szeto, David, Yang, Xinping, Ghamsari, Lila, Lee, HanJoo, Fan, Changyu, Murray, Ryan R., Milstein, Stuart, Svrzikapa, Nenad, Cusick, Michael E., Roth, Frederick P., Hill, David E., Vidal, Marc
Published in Genome research (01.12.2009)
Published in Genome research (01.12.2009)
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Journal Article
The completion of the Mammalian Gene Collection (MGC)
Temple, Gary, Gerhard, Daniela S., Rasooly, Rebekah, Feingold, Elise A., Good, Peter J., Robinson, Cristen, Mandich, Allison, Derge, Jeffrey G., Lewis, Jeanne, Shoaf, Debonny, Collins, Francis S., Jang, Wonhee, Wagner, Lukas, Shenmen, Carolyn M., Misquitta, Leonie, Schaefer, Carl F., Buetow, Kenneth H., Bonner, Tom I., Yankie, Linda, Ward, Ming, Phan, Lon, Astashyn, Alex, Brown, Garth, Farrell, Catherine, Hart, Jennifer, Landrum, Melissa, Maidak, Bonnie L., Murphy, Michael, Murphy, Terence, Rajput, Bhanu, Riddick, Lillian, Webb, David, Weber, Janet, Wu, Wendy, Pruitt, Kim D., Maglott, Donna, Siepel, Adam, Brejova, Brona, Diekhans, Mark, Harte, Rachel, Baertsch, Robert, Kent, Jim, Haussler, David, Brent, Michael, Langton, Laura, Comstock, Charles L.G., Stevens, Michael, Wei, Chaochun, van Baren, Marijke J., Salehi-Ashtiani, Kourosh, Murray, Ryan R., Ghamsari, Lila, Mello, Elizabeth, Lin, Chenwei, Pennacchio, Christa, Schreiber, Kirsten, Shapiro, Nicole, Marsh, Amber, Pardes, Elizabeth, Moore, Troy, Lebeau, Anita, Muratet, Mike, Simmons, Blake, Kloske, David, Sieja, Stephanie, Hudson, James, Sethupathy, Praveen, Brownstein, Michael, Bhat, Narayan, Lazar, Joseph, Jacob, Howard, Gruber, Chris E., Smith, Mark R., McPherson, John, Garcia, Angela M., Gunaratne, Preethi H., Wu, Jiaqian, Muzny, Donna, Gibbs, Richard A., Young, Alice C., Bouffard, Gerard G., Blakesley, Robert W., Mullikin, Jim, Green, Eric D., Dickson, Mark C., Rodriguez, Alex C., Grimwood, Jane, Schmutz, Jeremy, Myers, Richard M., Hirst, Martin, Zeng, Thomas, Tse, Kane, Moksa, Michelle, Deng, Merinda, Ma, Kevin, Mah, Diana, Pang, Johnson, Taylor, Greg, Chuah, Eric, Deng, Athena
Published in Genome research (01.12.2009)
Published in Genome research (01.12.2009)
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Evidence for transcript networks composed of chimeric RNAs in human cells
Djebali, Sarah, Lagarde, Julien, Kapranov, Philipp, Lacroix, Vincent, Borel, Christelle, Mudge, Jonathan M, Howald, Cédric, Foissac, Sylvain, Ucla, Catherine, Chrast, Jacqueline, Ribeca, Paolo, Martín, David, Murray, Ryan R, Yang, Xinping, Ghamsari, Lila, Lin, Chenwei, Bell, Ian, Dumais, Erica, Gelpí Buchaca, Josep Lluís, Orozco López, Modesto
Published in PloS one (01.01.2012)
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Published in PloS one (01.01.2012)
Journal Article
COT/MAP3K8 drives resistance to RAF inhibition through MAP kinase pathway reactivation
Johannessen, Cory M., Boehm, Jesse S., Kim, So Young, Thomas, Sapana R., Wardwell, Leslie, Johnson, Laura A., Emery, Caroline M., Stransky, Nicolas, Cogdill, Alexandria P., Barretina, Jordi, Caponigro, Giordano, Hieronymus, Haley, Murray, Ryan R., Salehi-Ashtiani, Kourosh, Hill, David E., Vidal, Marc, Zhao, Jean J., Yang, Xiaoping, Alkan, Ozan, Kim, Sungjoon, Harris, Jennifer L., Wilson, Christopher J., Myer, Vic E., Finan, Peter M., Root, David E., Roberts, Thomas M., Golub, Todd, Flaherty, Keith T., Dummer, Reinhard, Weber, Barbara, Sellers, William R., Schlegel, Robert, Wargo, Jennifer A., Hahn, William C., Garraway, Levi A.
Published in Nature (London) (24.11.2010)
Published in Nature (London) (24.11.2010)
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