Search Results - "Murray, Ryan R."

Widespread Expansion of Protein Interaction Capabilities by Alternative Splicing by 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

“…While alternative splicing is known to diversify the functional characteristics of some genes, the extent to which protein isoforms globally contribute to…”
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An empirical framework for binary interactome mapping by Tavernier, Jan, Wanker, Erich E, Barabási, Albert-László, Vidal, Marc, 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

“…A framework based on numerous empirical data, including protein-protein interaction reference sets, provides parameters for assessing the quality and coverage…”
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An inter‐species protein–protein interaction network across vast evolutionary distance by 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

“…In cellular systems, biophysical interactions between macromolecules underlie a complex web of functional interactions. How biophysical and functional networks…”
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Evidence for transcript networks composed of chimeric RNAs in human cells by 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

“…The classic organization of a gene structure has followed the Jacob and Monod bacterial gene model proposed more than 50 years ago. Since then, empirical…”
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A Proteome-Scale Map of the Human Interactome Network by 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

“…Just as reference genome sequences revolutionized human genetics, reference maps of interactome networks will be critical to fully understand…”
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A public genome-scale lentiviral expression library of human ORFs by 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

“…Two sequence-verified, clonal, publicly available collections of human open reading frames are reported. One collection is in a lentiviral vector for…”
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Isoform discovery by targeted cloning, 'deep-well' pooling and parallel sequencing by Salehi-Ashtiani, Kourosh, Roth, Frederick P, Vidal, Marc, 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

“…Describing the 'ORFeome' of an organism, including all major isoforms, is essential for a system-level understanding of any species; however, conventional…”
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High-Quality Binary Protein Interaction Map of the Yeast Interactome Network by 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

“…Current yeast interactome network maps contain several hundred molecular complexes with limited and somewhat controversial representation of direct binary…”
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An experimentally derived confidence score for binary protein-protein interactions by Braun, Pascal, Tavernier, Jan, Wrana, Jeffrey L, Roth, Frederick P, Vidal, Marc, 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

“…Use of the protein-protein interaction reference sets reported in this issue in Venkatesan et al . to benchmark four complementary protein-protein interaction…”
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COT drives resistance to RAF inhibition through MAP kinase pathway reactivation by Emery, Caroline M, Hieronymus, Haley, Zhao, Jean J, Boehm, Jesse S, Golub, Todd, Yang, Xiaoping, Root, David E, Roberts, Thomas M, Hahn, William C, Hill, David E, Wilson, Christopher J, Weber, Barbara L, Garraway, Levi A, Johnson, Laura A, Kim, Sungjoon, Harris, Jennifer L, Kim, So Young, Vidal, Marc, Finan, Peter M, Myer, Vic E, Sellers, William R, Barretina, Jordi, Alkan, Ozan, Thomas, Sapana R, Wardwell, Leslie, Cogdill, Alexandria P, Dummer, Reinhard, Schlegel, Robert, Stransky, Nicolas, Flaherty, Keith T, Wargo, Jennifer A, Murray, Ryan R, Johannessen, Cory M, Salehi-Ashtiani, Kourosh, Caponigro, Giordano

“…Oncogenic mutations in the serine/threonine kinase B-RAF (also known as BRAF) are found in 50-70% of malignant melanomas. Pre-clinical studies have…”
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Metabolic network analysis integrated with transcript verification for sequenced genomes by Salehi-Ashtiani, Kourosh, Papin, Jason A, 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

“…With sequencing of thousands of organisms completed or in progress, there is a growing need to integrate gene prediction with metabolic network analysis. Using…”
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Efficient targeted transcript discovery via array-based normalization of RACE libraries by Guigó, Roderic, 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

“…Rapid amplification of cDNA ends (RACE) is a widely used approach for transcript identification. Random clone selection from the RACE mixture, however, is an…”
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Large-scale RACE approach for proactive experimental definition of C. elegans ORFeome by 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

“…Although a highly accurate sequence of the Caenorhabditis elegans genome has been available for 10 years, the exact transcript structures of many of its…”
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The completion of the Mammalian Gene Collection (MGC) by 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

“…Since its start, the Mammalian Gene Collection (MGC) has sought to provide at least one full-protein-coding sequence cDNA clone for every human and mouse gene…”
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Evidence for transcript networks composed of chimeric RNAs in human cells by 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

“…The classic organization of a gene structure has followed the Jacob and Monod bacterial gene model proposed more than 50 years ago. Since then, empirical…”
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Evidence for transcript networks composed of chimeric RNAs in human cells by Djebali, Sarah, Lagarde, Julien, Lacroix, Vincent, Foissac, Sylvain, Ribeca, Paolo, Martin, David, Guigó Serra, Roderic, Gingeras, Thomas R

“…The classic organization of a gene structure has followed the Jacob and Monod bacterial gene model proposed more than 50 years ago. Since then, empirical…”
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COT/MAP3K8 drives resistance to RAF inhibition through MAP kinase pathway reactivation by 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.

“…Oncogenic mutations in the serine/threonine kinase B-RAF are found in 50–70% of malignant melanomas 1 . Pre-clinical studies have demonstrated that the B-RAF…”
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