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204. Open collaborative writing with Manubot

Author

Himmelstein, Daniel S., primary, Rubinetti, Vincent, additional, Slochower, David R., additional, Hu, Dongbo, additional, Malladi, Venkat S., additional, Greene, Casey S., additional, and Gitter, Anthony, additional

Published
2019
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205. The CAFA challenge reports improved protein function prediction and new functional annotations for hundreds of genes through experimental screens

Author

Zhou, Naihui, primary, Jiang, Yuxiang, additional, Bergquist, Timothy R, additional, Lee, Alexandra J, additional, Kacsoh, Balint Z, additional, Crocker, Alex W, additional, Lewis, Kimberley A, additional, Georghiou, George, additional, Nguyen, Huy N, additional, Hamid, Md Nafiz, additional, Davis, Larry, additional, Dogan, Tunca, additional, Atalay, Volkan, additional, Rifaioglu, Ahmet S, additional, Dalkiran, Alperen, additional, Cetin-Atalay, Rengul, additional, Zhang, Chengxin, additional, Hurto, Rebecca L, additional, Freddolino, Peter L, additional, Zhang, Yang, additional, Bhat, Prajwal, additional, Supek, Fran, additional, Fernández, José M, additional, Gemovic, Branislava, additional, Perovic, Vladimir R, additional, Davidović, Radoslav S, additional, Sumonja, Neven, additional, Veljkovic, Nevena, additional, Asgari, Ehsaneddin, additional, Mofrad, Mohammad RK, additional, Profiti, Giuseppe, additional, Savojardo, Castrense, additional, Martelli, Pier Luigi, additional, Casadio, Rita, additional, Boecker, Florian, additional, Kahanda, Indika, additional, Thurlby, Natalie, additional, McHardy, Alice C, additional, Renaux, Alexandre, additional, Saidi, Rabie, additional, Gough, Julian, additional, Freitas, Alex A, additional, Antczak, Magdalena, additional, Fabris, Fabio, additional, Wass, Mark N, additional, Hou, Jie, additional, Cheng, Jianlin, additional, Wang, Zheng, additional, Romero, Alfonso E, additional, Paccanaro, Alberto, additional, Yang, Haixuan, additional, Goldberg, Tatyana, additional, Zhao, Chenguang, additional, Holm, Liisa, additional, Törönen, Petri, additional, Medlar, Alan J, additional, Zosa, Elaine, additional, Borukhov, Itamar, additional, Novikov, Ilya, additional, Wilkins, Angela, additional, Lichtarge, Olivier, additional, Chi, Po-Han, additional, Tseng, Wei-Cheng, additional, Linial, Michal, additional, Rose, Peter W, additional, Dessimoz, Christophe, additional, Vidulin, Vedrana, additional, Dzeroski, Saso, additional, Sillitoe, Ian, additional, Das, Sayoni, additional, Lees, Jonathan Gill, additional, Jones, David T, additional, Wan, Cen, additional, Cozzetto, Domenico, additional, Fa, Rui, additional, Torres, Mateo, additional, Vesztrocy, Alex Wiarwick, additional, Rodriguez, Jose Manuel, additional, Tress, Michael L, additional, Frasca, Marco, additional, Notaro, Marco, additional, Grossi, Giuliano, additional, Petrini, Alessandro, additional, Re, Matteo, additional, Valentini, Giorgio, additional, Mesiti, Marco, additional, Roche, Daniel B, additional, Reeb, Jonas, additional, Ritchie, David W, additional, Aridhi, Sabeur, additional, Alborzi, Seyed Ziaeddin, additional, Devignes, Marie-Dominique, additional, Emily Koo, Da Chen, additional, Bonneau, Richard, additional, Gligorijević, Vladimir, additional, Barot, Meet, additional, Fang, Hai, additional, Toppo, Stefano, additional, Lavezzo, Enrico, additional, Falda, Marco, additional, Berselli, Michele, additional, Tosatto, Silvio CE, additional, Carraro, Marco, additional, Piovesan, Damiano, additional, Rehman, Hafeez Ur, additional, Mao, Qizhong, additional, Zhang, Shanshan, additional, Vucetic, Slobodan, additional, Black, Gage S, additional, Jo, Dane, additional, Larsen, Dallas J, additional, Omdahl, Ashton R, additional, Sagers, Luke W, additional, Suh, Erica, additional, Dayton, Jonathan B, additional, McGuffin, Liam J, additional, Brackenridge, Danielle A, additional, Babbitt, Patricia C, additional, Yunes, Jeffrey M, additional, Fontana, Paolo, additional, Zhang, Feng, additional, Zhu, Shanfeng, additional, You, Ronghui, additional, Zhang, Zihan, additional, Dai, Suyang, additional, Yao, Shuwei, additional, Tian, Weidong, additional, Cao, Renzhi, additional, Chandler, Caleb, additional, Amezola, Miguel, additional, Johnson, Devon, additional, Chang, Jia-Ming, additional, Liao, Wen-Hung, additional, Liu, Yi-Wei, additional, Pascarelli, Stefano, additional, Frank, Yotam, additional, Hoehndorf, Robert, additional, Kulmanov, Maxat, additional, Boudellioua, Imane, additional, Politano, Gianfranco, additional, Di Carlo, Stefano, additional, Benso, Alfredo, additional, Hakala, Kai, additional, Ginter, Filip, additional, Mehryary, Farrokh, additional, Kaewphan, Suwisa, additional, Björne, Jari, additional, Moen, Hans, additional, Tolvanen, Martti E E, additional, Salakoski, Tapio, additional, Kihara, Daisuke, additional, Jain, Aashish, additional, Šmuc, Tomislav, additional, Altenhoff, Adrian, additional, Ben-Hur, Asa, additional, Rost, Burkhard, additional, Brenner, Steven E, additional, Orengo, Christine A, additional, Jeffery, Constance J, additional, Bosco, Giovanni, additional, Hogan, Deborah A, additional, Martin, Maria J, additional, O’Donovan, Claire, additional, Mooney, Sean D, additional, Greene, Casey S, additional, Radivojac, Predrag, additional, and Friedberg, Iddo, additional

Published
2019
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207. Genomic profiling of childhood tumor patient-derived xenograft models to enable rational clinical trial design

Author

Rokita, Jo Lynne, primary, Rathi, Komal S., additional, Cardenas, Maria F., additional, Upton, Kristen A., additional, Jayaseelan, Joy, additional, Cross, Katherine L., additional, Pfeil, Jacob, additional, Ritenour, Laura E., additional, Modi, Apexa, additional, Farrel, Alvin, additional, Way, Gregory P., additional, Kendsersky, Nathan M., additional, Patel, Khushbu, additional, Lopez, Gonzalo, additional, Vaksman, Zalman, additional, Mayoh, Chelsea, additional, Nance, Jonas, additional, McCoy, Kristyn, additional, Haber, Michelle, additional, Evans, Kathryn, additional, McCalmont, Hannah, additional, Bendak, Katerina, additional, Böhm, Julia W., additional, Marshall, Glenn M., additional, Tyrrell, Vanessa, additional, Kalletla, Karthik, additional, Braun, Frank K., additional, Qi, Lin, additional, Du, Yunchen, additional, Zhang, Huiyuan, additional, Lindsay, Holly B., additional, Zhao, Sibo, additional, Shu, Jack, additional, Baxter, Patricia, additional, Morton, Christopher, additional, Kurmashev, Dias, additional, Zheng, Siyuan, additional, Chen, Yidong, additional, Bowen, Jay, additional, Bryan, Anthony C., additional, Leraas, Kristen M., additional, Coppens, Sara E., additional, Doddapaneni, HarshaVardhan, additional, Momin, Zeineen, additional, Zhang, Wendong, additional, Sacks, Gregory I., additional, Hart, Lori S., additional, Krytska, Kateryna, additional, Mosse, Yael P., additional, Gatto, Gregory J., additional, Sanchez, Yolanda, additional, Greene, Casey S., additional, Diskin, Sharon J., additional, Vaske, Olena Morozova, additional, Haussler, David, additional, Gastier-Foster, Julie M., additional, Kolb, E. Anders, additional, Gorlick, Richard, additional, Li, Xiao-Nan, additional, Reynolds, C. Patrick, additional, Kurmasheva, Raushan T., additional, Houghton, Peter J., additional, Smith, Malcolm A., additional, Lock, Richard B., additional, Raman, Pichai, additional, Wheeler, David A., additional, and Maris, John M., additional

Published
2019
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210. Evolving hard problems: Generating human genetics datasets with a complex etiology

Author

Himmelstein Daniel S, Greene Casey S, and Moore Jason H

Subjects
Computer applications to medicine. Medical informatics, R858-859.7, Analysis, QA299.6-433
Abstract

Abstract Background A goal of human genetics is to discover genetic factors that influence individuals' susceptibility to common diseases. Most common diseases are thought to result from the joint failure of two or more interacting components instead of single component failures. This greatly complicates both the task of selecting informative genetic variants and the task of modeling interactions between them. We and others have previously developed algorithms to detect and model the relationships between these genetic factors and disease. Previously these methods have been evaluated with datasets simulated according to pre-defined genetic models. Results Here we develop and evaluate a model free evolution strategy to generate datasets which display a complex relationship between individual genotype and disease susceptibility. We show that this model free approach is capable of generating a diverse array of datasets with distinct gene-disease relationships for an arbitrary interaction order and sample size. We specifically generate eight-hundred Pareto fronts; one for each independent run of our algorithm. In each run the predictiveness of single genetic variation and pairs of genetic variants have been minimized, while the predictiveness of third, fourth, or fifth-order combinations is maximized. Two hundred runs of the algorithm are further dedicated to creating datasets with predictive four or five order interactions and minimized lower-level effects. Conclusions This method and the resulting datasets will allow the capabilities of novel methods to be tested without pre-specified genetic models. This allows researchers to evaluate which methods will succeed on human genetics problems where the model is not known in advance. We further make freely available to the community the entire Pareto-optimal front of datasets from each run so that novel methods may be rigorously evaluated. These 76,600 datasets are available from http://discovery.dartmouth.edu/model_free_data/.

Published
2011
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211. Spatially Uniform ReliefF (SURF) for computationally-efficient filtering of gene-gene interactions

Author

Greene Casey S, Penrod Nadia M, Kiralis Jeff, and Moore Jason H

Subjects
Computer applications to medicine. Medical informatics, R858-859.7, Analysis, QA299.6-433
Abstract

Abstract Background Genome-wide association studies are becoming the de facto standard in the genetic analysis of common human diseases. Given the complexity and robustness of biological networks such diseases are unlikely to be the result of single points of failure but instead likely arise from the joint failure of two or more interacting components. The hope in genome-wide screens is that these points of failure can be linked to single nucleotide polymorphisms (SNPs) which confer disease susceptibility. Detecting interacting variants that lead to disease in the absence of single-gene effects is difficult however, and methods to exhaustively analyze sets of these variants for interactions are combinatorial in nature thus making them computationally infeasible. Efficient algorithms which can detect interacting SNPs are needed. ReliefF is one such promising algorithm, although it has low success rate for noisy datasets when the interaction effect is small. ReliefF has been paired with an iterative approach, Tuned ReliefF (TuRF), which improves the estimation of weights in noisy data but does not fundamentally change the underlying ReliefF algorithm. To improve the sensitivity of studies using these methods to detect small effects we introduce Spatially Uniform ReliefF (SURF). Results SURF's ability to detect interactions in this domain is significantly greater than that of ReliefF. Similarly SURF, in combination with the TuRF strategy significantly outperforms TuRF alone for SNP selection under an epistasis model. It is important to note that this success rate increase does not require an increase in algorithmic complexity and allows for increased success rate, even with the removal of a nuisance parameter from the algorithm. Conclusion Researchers performing genetic association studies and aiming to discover gene-gene interactions associated with increased disease susceptibility should use SURF in place of ReliefF. For instance, SURF should be used instead of ReliefF to filter a dataset before an exhaustive MDR analysis. This change increases the ability of a study to detect gene-gene interactions. The SURF algorithm is implemented in the open source Multifactor Dimensionality Reduction (MDR) software package available from http://www.epistasis.org.

Published
2009
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212. Accelerating epistasis analysis in human genetics with consumer graphics hardware

Author

Cancare Fabio, Greene Casey S, Sinnott-Armstrong Nicholas A, and Moore Jason H

Subjects
Medicine, Biology (General), QH301-705.5, Science (General), Q1-390
Abstract

Abstract Background Human geneticists are now capable of measuring more than one million DNA sequence variations from across the human genome. The new challenge is to develop computationally feasible methods capable of analyzing these data for associations with common human disease, particularly in the context of epistasis. Epistasis describes the situation where multiple genes interact in a complex non-linear manner to determine an individual's disease risk and is thought to be ubiquitous for common diseases. Multifactor Dimensionality Reduction (MDR) is an algorithm capable of detecting epistasis. An exhaustive analysis with MDR is often computationally expensive, particularly for high order interactions. This challenge has previously been met with parallel computation and expensive hardware. The option we examine here exploits commodity hardware designed for computer graphics. In modern computers Graphics Processing Units (GPUs) have more memory bandwidth and computational capability than Central Processing Units (CPUs) and are well suited to this problem. Advances in the video game industry have led to an economy of scale creating a situation where these powerful components are readily available at very low cost. Here we implement and evaluate the performance of the MDR algorithm on GPUs. Of primary interest are the time required for an epistasis analysis and the price to performance ratio of available solutions. Findings We found that using MDR on GPUs consistently increased performance per machine over both a feature rich Java software package and a C++ cluster implementation. The performance of a GPU workstation running a GPU implementation reduces computation time by a factor of 160 compared to an 8-core workstation running the Java implementation on CPUs. This GPU workstation performs similarly to 150 cores running an optimized C++ implementation on a Beowulf cluster. Furthermore this GPU system provides extremely cost effective performance while leaving the CPU available for other tasks. The GPU workstation containing three GPUs costs $2000 while obtaining similar performance on a Beowulf cluster requires 150 CPU cores which, including the added infrastructure and support cost of the cluster system, cost approximately $82,500. Conclusion Graphics hardware based computing provides a cost effective means to perform genetic analysis of epistasis using MDR on large datasets without the infrastructure of a computing cluster.

Published
2009
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215. Genomic Profiling of Childhood Tumor Patient-Derived Xenograft Models to Enable Rational Clinical Trial Design.

Author

Rokita, Jo Lynne, Rokita, Jo Lynne, Rathi, Komal S, Cardenas, Maria F, Upton, Kristen A, Jayaseelan, Joy, Cross, Katherine L, Pfeil, Jacob, Egolf, Laura E, Way, Gregory P, Farrel, Alvin, Kendsersky, Nathan M, Patel, Khushbu, Gaonkar, Krutika S, Modi, Apexa, Berko, Esther R, Lopez, Gonzalo, Vaksman, Zalman, Mayoh, Chelsea, Nance, Jonas, McCoy, Kristyn, Haber, Michelle, Evans, Kathryn, McCalmont, Hannah, Bendak, Katerina, Böhm, Julia W, Marshall, Glenn M, Tyrrell, Vanessa, Kalletla, Karthik, Braun, Frank K, Qi, Lin, Du, Yunchen, Zhang, Huiyuan, Lindsay, Holly B, Zhao, Sibo, Shu, Jack, Baxter, Patricia, Morton, Christopher, Kurmashev, Dias, Zheng, Siyuan, Chen, Yidong, Bowen, Jay, Bryan, Anthony C, Leraas, Kristen M, Coppens, Sara E, Doddapaneni, HarshaVardhan, Momin, Zeineen, Zhang, Wendong, Sacks, Gregory I, Hart, Lori S, Krytska, Kateryna, Mosse, Yael P, Gatto, Gregory J, Sanchez, Yolanda, Greene, Casey S, Diskin, Sharon J, Vaske, Olena Morozova, Haussler, David, Gastier-Foster, Julie M, Kolb, E Anders, Gorlick, Richard, Li, Xiao-Nan, Reynolds, C Patrick, Kurmasheva, Raushan T, Houghton, Peter J, Smith, Malcolm A, Lock, Richard B, Raman, Pichai, Wheeler, David A, Maris, John M, Rokita, Jo Lynne, Rokita, Jo Lynne, Rathi, Komal S, Cardenas, Maria F, Upton, Kristen A, Jayaseelan, Joy, Cross, Katherine L, Pfeil, Jacob, Egolf, Laura E, Way, Gregory P, Farrel, Alvin, Kendsersky, Nathan M, Patel, Khushbu, Gaonkar, Krutika S, Modi, Apexa, Berko, Esther R, Lopez, Gonzalo, Vaksman, Zalman, Mayoh, Chelsea, Nance, Jonas, McCoy, Kristyn, Haber, Michelle, Evans, Kathryn, McCalmont, Hannah, Bendak, Katerina, Böhm, Julia W, Marshall, Glenn M, Tyrrell, Vanessa, Kalletla, Karthik, Braun, Frank K, Qi, Lin, Du, Yunchen, Zhang, Huiyuan, Lindsay, Holly B, Zhao, Sibo, Shu, Jack, Baxter, Patricia, Morton, Christopher, Kurmashev, Dias, Zheng, Siyuan, Chen, Yidong, Bowen, Jay, Bryan, Anthony C, Leraas, Kristen M, Coppens, Sara E, Doddapaneni, HarshaVardhan, Momin, Zeineen, Zhang, Wendong, Sacks, Gregory I, Hart, Lori S, Krytska, Kateryna, Mosse, Yael P, Gatto, Gregory J, Sanchez, Yolanda, Greene, Casey S, Diskin, Sharon J, Vaske, Olena Morozova, Haussler, David, Gastier-Foster, Julie M, Kolb, E Anders, Gorlick, Richard, Li, Xiao-Nan, Reynolds, C Patrick, Kurmasheva, Raushan T, Houghton, Peter J, Smith, Malcolm A, Lock, Richard B, Raman, Pichai, Wheeler, David A, and Maris, John M

Abstract

Accelerating cures for children with cancer remains an immediate challenge as a result of extensive oncogenic heterogeneity between and within histologies, distinct molecular mechanisms evolving between diagnosis and relapsed disease, and limited therapeutic options. To systematically prioritize and rationally test novel agents in preclinical murine models, researchers within the Pediatric Preclinical Testing Consortium are continuously developing patient-derived xenografts (PDXs)-many of which are refractory to current standard-of-care treatments-from high-risk childhood cancers. Here, we genomically characterize 261 PDX models from 37 unique pediatric cancers; demonstrate faithful recapitulation of histologies and subtypes; and refine our understanding of relapsed disease. In addition, we use expression signatures to classify tumors for TP53 and NF1 pathway inactivation. We anticipate that these data will serve as a resource for pediatric oncology drug development and will guide rational clinical trial design for children with cancer.

Published
2019

216. The CAFA challenge reports improved protein function prediction and new functional annotations for hundreds of genes through experimental screens

Author

Zhou, Naihui, Jiang, Yuxiang, Bergquist, Timothy R, Lee, Alexandra J, Kacsoh, Balint Z, Crocker, Alex W, Lewis, Kimberley A, Georghiou, George, Nguyen, Huy N, Hamid, Md Nafiz, Davis, Larry, Dogan, Tunca, Atalay, Volkan, Rifaioglu, Ahmet S, Dalkıran, Alperen, Cetin Atalay, Rengul, Zhang, Chengxin, Hurto, Rebecca L, Freddolino, Peter L, Zhang, Yang, Bhat, Prajwal, Supek, Fran, Fernández, José M, Gemović, Branislava S., Perović, Vladimir R., Davidović, Radoslav S., Šumonja, Neven, Veljković, Nevena V., Asgari, Ehsaneddin, Mofrad, Mohammad R.K., Profiti, Giuseppe, Savojardo, Castrense, Martelli, Pier Luigi, Casadio, Rita, Boecker, Florian, Schoof, Heiko, Kahanda, Indika, Thurlby, Natalie, McHardy, Alice C, Renaux, Alexandre, Saidi, Rabie, Gough, Julian, Freitas, Alex A, Antczak, Magdalena, Fabris, Fabio, Wass, Mark N, Hou, Jie, Cheng, Jianlin, Wang, Zheng, Romero, Alfonso E, Paccanaro, Alberto, Yang, Haixuan, Goldberg, Tatyana, Zhao, Chenguang, Holm, Liisa, Törönen, Petri, Medlar, Alan J, Zosa, Elaine, Borukhov, Itamar, Novikov, Ilya, Wilkins, Angela, Lichtarge, Olivier, Chi, Po-Han, Tseng, Wei-Cheng, Linial, Michal, Rose, Peter W, Dessimoz, Christophe, Vidulin, Vedrana, Dzeroski, Saso, Sillitoe, Ian, Das, Sayoni, Lees, Jonathan Gill, Jones, David T, Wan, Cen, Cozzetto, Domenico, Fa, Rui, Torres, Mateo, Warwick Vesztrocy, Alex, Rodriguez, Jose Manuel, Tress, Michael L, Frasca, Marco, Notaro, Marco, Grossi, Giuliano, Petrini, Alessandro, Re, Matteo, Valentini, Giorgio, Mesiti, Marco, Roche, Daniel B, Reeb, Jonas, Ritchie, David W, Aridhi, Sabeur, Alborzi, Seyed Ziaeddin, Devignes, Marie-Dominique, Koo, Da Chen Emily, Bonneau, Richard, Gligorijević, Vladimir, Barot, Meet, Fang, Hai, Toppo, Stefano, Lavezzo, Enrico, Falda, Marco, Berselli, Michele, Tosatto, Silvio C.E., Carraro, Marco, Piovesan, Damiano, Ur Rehman, Hafeez, Mao, Qizhong, Zhang, Shanshan, Vucetic, Slobodan, Black, Gage S, Jo, Dane, Suh, Erica, Dayton, Jonathan B, Larsen, Dallas J, Omdahl, Ashton R, McGuffin, Liam J, Brackenridge, Danielle A, Babbitt, Patricia C, Yunes, Jeffrey M, Fontana, Paolo, Zhang, Feng, Zhu, Shanfeng, You, Ronghui, Zhang, Zihan, Dai, Suyang, Yao, Shuwei, Tian, Weidong, Cao, Renzhi, Chandler, Caleb, Amezola, Miguel, Johnson, Devon, Chang, Jia-Ming, Liao, Wen-Hung, Liu, Yi-Wei, Pascarelli, Stefano, Frank, Yotam, Hoehndorf, Robert, Kulmanov, Maxat, Boudellioua, Imane, Politano, Gianfranco, Di Carlo, Stefano, Benso, Alfredo, Hakala, Kai, Ginter, Filip, Mehryary, Farrokh, Kaewphan, Suwisa, Björne, Jari, Moen, Hans, Tolvanen, Martti E.E., Salakoski, Tapio, Kihara, Daisuke, Jain, Aashish, Šmuc, Tomislav, Altenhoff, Adrian, Ben-Hur, Asa, Rost, Burkhard, Brenner, Steven E, Orengo, Christine A, Jeffery, Constance J, Bosco, Giovanni, Hogan, Deborah A, Martin, Maria J, O’Donovan, Claire, Mooney, Sean D, Greene, Casey S, Radivojac, Predrag, Friedberg, Iddo, Zhou, Naihui, Jiang, Yuxiang, Bergquist, Timothy R, Lee, Alexandra J, Kacsoh, Balint Z, Crocker, Alex W, Lewis, Kimberley A, Georghiou, George, Nguyen, Huy N, Hamid, Md Nafiz, Davis, Larry, Dogan, Tunca, Atalay, Volkan, Rifaioglu, Ahmet S, Dalkıran, Alperen, Cetin Atalay, Rengul, Zhang, Chengxin, Hurto, Rebecca L, Freddolino, Peter L, Zhang, Yang, Bhat, Prajwal, Supek, Fran, Fernández, José M, Gemović, Branislava S., Perović, Vladimir R., Davidović, Radoslav S., Šumonja, Neven, Veljković, Nevena V., Asgari, Ehsaneddin, Mofrad, Mohammad R.K., Profiti, Giuseppe, Savojardo, Castrense, Martelli, Pier Luigi, Casadio, Rita, Boecker, Florian, Schoof, Heiko, Kahanda, Indika, Thurlby, Natalie, McHardy, Alice C, Renaux, Alexandre, Saidi, Rabie, Gough, Julian, Freitas, Alex A, Antczak, Magdalena, Fabris, Fabio, Wass, Mark N, Hou, Jie, Cheng, Jianlin, Wang, Zheng, Romero, Alfonso E, Paccanaro, Alberto, Yang, Haixuan, Goldberg, Tatyana, Zhao, Chenguang, Holm, Liisa, Törönen, Petri, Medlar, Alan J, Zosa, Elaine, Borukhov, Itamar, Novikov, Ilya, Wilkins, Angela, Lichtarge, Olivier, Chi, Po-Han, Tseng, Wei-Cheng, Linial, Michal, Rose, Peter W, Dessimoz, Christophe, Vidulin, Vedrana, Dzeroski, Saso, Sillitoe, Ian, Das, Sayoni, Lees, Jonathan Gill, Jones, David T, Wan, Cen, Cozzetto, Domenico, Fa, Rui, Torres, Mateo, Warwick Vesztrocy, Alex, Rodriguez, Jose Manuel, Tress, Michael L, Frasca, Marco, Notaro, Marco, Grossi, Giuliano, Petrini, Alessandro, Re, Matteo, Valentini, Giorgio, Mesiti, Marco, Roche, Daniel B, Reeb, Jonas, Ritchie, David W, Aridhi, Sabeur, Alborzi, Seyed Ziaeddin, Devignes, Marie-Dominique, Koo, Da Chen Emily, Bonneau, Richard, Gligorijević, Vladimir, Barot, Meet, Fang, Hai, Toppo, Stefano, Lavezzo, Enrico, Falda, Marco, Berselli, Michele, Tosatto, Silvio C.E., Carraro, Marco, Piovesan, Damiano, Ur Rehman, Hafeez, Mao, Qizhong, Zhang, Shanshan, Vucetic, Slobodan, Black, Gage S, Jo, Dane, Suh, Erica, Dayton, Jonathan B, Larsen, Dallas J, Omdahl, Ashton R, McGuffin, Liam J, Brackenridge, Danielle A, Babbitt, Patricia C, Yunes, Jeffrey M, Fontana, Paolo, Zhang, Feng, Zhu, Shanfeng, You, Ronghui, Zhang, Zihan, Dai, Suyang, Yao, Shuwei, Tian, Weidong, Cao, Renzhi, Chandler, Caleb, Amezola, Miguel, Johnson, Devon, Chang, Jia-Ming, Liao, Wen-Hung, Liu, Yi-Wei, Pascarelli, Stefano, Frank, Yotam, Hoehndorf, Robert, Kulmanov, Maxat, Boudellioua, Imane, Politano, Gianfranco, Di Carlo, Stefano, Benso, Alfredo, Hakala, Kai, Ginter, Filip, Mehryary, Farrokh, Kaewphan, Suwisa, Björne, Jari, Moen, Hans, Tolvanen, Martti E.E., Salakoski, Tapio, Kihara, Daisuke, Jain, Aashish, Šmuc, Tomislav, Altenhoff, Adrian, Ben-Hur, Asa, Rost, Burkhard, Brenner, Steven E, Orengo, Christine A, Jeffery, Constance J, Bosco, Giovanni, Hogan, Deborah A, Martin, Maria J, O’Donovan, Claire, Mooney, Sean D, Greene, Casey S, Radivojac, Predrag, and Friedberg, Iddo

Abstract

Background: The Critical Assessment of Functional Annotation (CAFA) is an ongoing, global, community-driven effort to evaluate and improve the computational annotation of protein function. Results: Here, we report on the results of the third CAFA challenge, CAFA3, that featured an expanded analysis over the previous CAFA rounds, both in terms of volume of data analyzed and the types of analysis performed. In a novel and major new development, computational predictions and assessment goals drove some of the experimental assays, resulting in new functional annotations for more than 1000 genes. Specifically, we performed experimental whole-genome mutation screening in Candida albicans and Pseudomonas aureginosa genomes, which provided us with genome-wide experimental data for genes associated with biofilm formation and motility. We further performed targeted assays on selected genes in Drosophila melanogaster, which we suspected of being involved in long-Term memory. Conclusion: We conclude that while predictions of the molecular function and biological process annotations have slightly improved over time, those of the cellular component have not. Term-centric prediction of experimental annotations remains equally challenging; although the performance of the top methods is significantly better than the expectations set by baseline methods in C. albicans and D. melanogaster, it leaves considerable room and need for improvement. Finally, we report that the CAFA community now involves a broad range of participants with expertise in bioinformatics, biological experimentation, biocuration, and bio-ontologies, working together to improve functional annotation, computational function prediction, and our ability to manage big data in the era of large experimental screens. © 2019 The Author(s).

Published
2019

217. Voices in methods development.

Author

Anikeeva, Polina, Anikeeva, Polina, Boyden, Edward, Brangwynne, Clifford, Cissé, Ibrahim I, Fiehn, Oliver, Fromme, Petra, Gingras, Anne-Claude, Greene, Casey S, Heard, Edith, Hell, Stefan W, Hillman, Elizabeth, Jensen, Grant Jay, Karchin, Rachel, Kiessling, Laura L, Kleinstiver, Benjamin P, Knight, Rob, Kukura, Philipp, Lancaster, Madeline A, Loman, Nicholas, Looger, Loren, Lundberg, Emma, Luo, Qingming, Miyawaki, Atsushi, Myers, Eugene W, Nolan, Garry P, Picotti, Paola, Reik, Wolf, Sauer, Markus, Shalek, Alex K, Shendure, Jay, Slavov, Nikolai, Tanay, Amos, Troyanskaya, Olga, van Valen, David, Wang, Hong-Wei, Yi, Chengqi, Yin, Peng, Zernicka-Goetz, Magdalena, Zhuang, Xiaowei, Anikeeva, Polina, Anikeeva, Polina, Boyden, Edward, Brangwynne, Clifford, Cissé, Ibrahim I, Fiehn, Oliver, Fromme, Petra, Gingras, Anne-Claude, Greene, Casey S, Heard, Edith, Hell, Stefan W, Hillman, Elizabeth, Jensen, Grant Jay, Karchin, Rachel, Kiessling, Laura L, Kleinstiver, Benjamin P, Knight, Rob, Kukura, Philipp, Lancaster, Madeline A, Loman, Nicholas, Looger, Loren, Lundberg, Emma, Luo, Qingming, Miyawaki, Atsushi, Myers, Eugene W, Nolan, Garry P, Picotti, Paola, Reik, Wolf, Sauer, Markus, Shalek, Alex K, Shendure, Jay, Slavov, Nikolai, Tanay, Amos, Troyanskaya, Olga, van Valen, David, Wang, Hong-Wei, Yi, Chengqi, Yin, Peng, Zernicka-Goetz, Magdalena, and Zhuang, Xiaowei

Abstract

To mark the 15th anniversary of Nature Methods, we asked scientists from across diverse fields of basic biology research for their views on the most exciting and essential methodological challenges that their communities are poised to tackle in the near future.

Published
2019

218. Sci-Hub provides access to nearly all scholarly literature

Author

Rodgers, Peter A., Himmelstein, Daniel S., Rodriguez Romero, Ariel, Levernier, Jacob, Munro, Thomas Anthony, McLaughlin, Stephen Reid, Tzovaras, Bastian Greshake, Greene, Casey S., Rodgers, Peter A., Himmelstein, Daniel S., Rodriguez Romero, Ariel, Levernier, Jacob, Munro, Thomas Anthony, McLaughlin, Stephen Reid, Tzovaras, Bastian Greshake, and Greene, Casey S.

Abstract

The website Sci-Hub enables users to download PDF versions of scholarly articles, including many articles that are paywalled at their journal’s site. Sci-Hub has grown rapidly since its creation in 2011, but the extent of its coverage has been unclear. Here we report that, as of March 2017, Sci-Hub’s database contains 68.9% of the 81.6 million scholarly articles registered with Crossref and 85.1% of articles published in toll access journals. We find that coverage varies by discipline and publisher, and that Sci-Hub preferentially covers popular, paywalled content. For toll access articles, we find that Sci-Hub provides greater coverage than the University of Pennsylvania, a major research university in the United States. Green open access to toll access articles via licit services, on the other hand, remains quite limited. Our interactive browser at https://greenelab.github.io/scihub allows users to explore these findings in more detail. For the first time, nearly all scholarly literature is available gratis to anyone with an Internet connection, suggesting the toll access business model may become unsustainable.

Published
2019

219. PSB 2019 Workshop on Text Mining and Visualization for Precision Medicine

Author

Gonzalez-Hernandez, Graciela, Lu, Zhiyong, Leaman, Robert, Weissenbacher, Davy, Boland, Mary Regina, Chen, Yong, Du, Jingcheng, Fluck, Juliane, Greene, Casey S., Holmes, John, Kashyap, Aditya, Nielsen, Rikke Linnemann, Ouyang, Zhengqing, Schaaf, Sebastian, Taroni, Jaclyn N., Tao, Cui, Zhang, Yuping, and Liu, Hongfang

Abstract

Precision medicine, an approach for disease treatment and prevention that considers “individual variability in genes, environment, and lifestyle” 1 was endorsed by the National Institutes of Health, aided by the presidential Precision Medicine Initiative (PMI), in 2016. PMI provided funding for cancer research and for building a national cohort of one million or more U.S. participants, now known as the “All of Us” Research Program, which aims to expand its impact to all diseases. PMI was the catalyst to a widespread effort around precision medicine, as evidenced by the more than 1000 grants funded by different NIH institutes in just the last two years. The data being generated by these efforts is growing exponentially, and becomes both the greatest treasure and the greatestchallenge for researchers. This workshop is a continuation of a similar session in PSB 2018, providing a forum for researchers with strong background in text mining or natural language processing (NLP) and/or machine learning (ML) who are actively collaborating with bench scientists and clinicians to tackle the challenges brought about by this explosion of data.

Published
2018

220. Sci-Hub provides access to nearly all scholarly literature [v2]

Author

Himmelstein, Daniel S., Rodriguez Romero, Ariel, McLaughlin, Stephen Reid, Tzovaras, Bastian Greshake, and Greene​, Casey S.

Subjects
ddc:370, ddc:004
Abstract

The website Sci-Hub provides access to scholarly literature via full text PDF downloads. The site enables users to access articles that would otherwise be paywalled. Since its creation in 2011, SciHub has grown rapidly in popularity. However, until now, the extent of Sci-Hub’s coverage was unclear. As of March 2017, we find that Sci-Hub’s database contains 68.9% of all 81.6 million scholarly articles, which rises to 85.2% for those published in toll access journals. Coverage varies by discipline, with 92.8% coverage of articles in chemistry journals compared to 76.3% for computer science. Coverage also varies by publisher, with the coverage of the largest publisher, Elsevier, at 97.3%. Our interactive browser at greenelab.github.io/scihub allows users to explore these findings in more detail. We find Sci-Hub preferentially covers popular, paywalled content, containing 96.2% of citations to toll access journals since 2015. For recently requested articles by Unpaywall users, oaDOI provided access to 48.8% whereas Sci-Hub contained 81.5%. Together, oaDOI and Sci-Hub covered 94.1%, demonstrating that gaps in Sci-Hub’s coverage, especially for open access articles, can be filled using licit services. For the first time, nearly all scholarly literature is available gratis to anyone with an Internet connection. Sci-Hub’s scope suggests the subscription publishing model is becoming unsustainable.

Published
2017

221. International genome-wide meta-analysis identifies new primary biliary cirrhosis risk loci and targetable pathogenic pathways

Author

Cordell, Heather J, Han, Younghun, Mells, George F, Li, Yafang, Hirschfield, Gideon M, Greene, Casey S, Xie, Gang, Juran, Brian D, Zhu, Dakai, Qian, David C, Floyd, James A. B, Morley, Katherine I, Prati, Daniele, Lleo, Ana, Cusi, Daniele, Gershwin, M. Eric, Anderson, Carl A, Lazaridis, Konstantinos N, Invernizzi, Pietro, Seldin, Michael F, Sandford, Richard N, Amos, Christopher I, Siminovitch, Katherine A., MORISCO, FILOMENA, Cordell, Heather J, Han, Younghun, Mells, George F, Li, Yafang, Hirschfield, Gideon M, Greene, Casey S, Xie, Gang, Juran, Brian D, Zhu, Dakai, Qian, David C, Floyd, James A. B, Morley, Katherine I, Prati, Daniele, Lleo, Ana, Cusi, Daniele, Gershwin, M. Eric, Anderson, Carl A, Lazaridis, Konstantinos N, Invernizzi, Pietro, Seldin, Michael F, Sandford, Richard N, Amos, Christopher I, Siminovitch, Katherine A., and Morisco, Filomena

Abstract

Primary biliary cirrhosis (PBC) is a classical autoimmune liver disease for which effective immunomodulatory therapy is lacking. Here we perform meta-analyses of discovery data sets from genome-wide association studies of European subjects (n=2,764 cases and 10,475 controls) followed by validation genotyping in an independent cohort (n=3,716 cases and 4,261 controls). We discover and validate six previously unknown risk loci for PBC (Pcombined

Published
2015
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223. Incorporating biological structure into machine learning models in biomedicine.

Author

Crawford, Jake and Greene, Casey S

Subjects
*MORPHOLOGY, *MACHINE learning, *GENE regulatory networks, *GENE expression, *RNA sequencing, *ONTOLOGIES (Information retrieval)
Abstract

Schematic showing the main categories of models incorporating structured biological data covered in this review. The first panel shows an example of a model operating on sequence data, the second panel shows a model in which dimension reduction is influenced by the connections in a gene network, and the third panel shows a neural network with structure constrained by a phylogeny or ontology. The 'x' values in the data tables represent gene expression measurements. In biomedical applications of machine learning, relevant information often has a rich structure that is not easily encoded as real-valued predictors. Examples of such data include DNA or RNA sequences, gene sets or pathways, gene interaction or coexpression networks, ontologies, and phylogenetic trees. We highlight recent examples of machine learning models that use structure to constrain model architecture or incorporate structured data into model training. For machine learning in biomedicine, where sample size is limited and model interpretability is crucial, incorporating prior knowledge in the form of structured data can be particularly useful. The area of research would benefit from performant open source implementations and independent benchmarking efforts. [ABSTRACT FROM AUTHOR]

Published
2020
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225. Pseudomonas aeruginosa lasR mutant fitness in microoxia is supported by an Anr-regulated oxygen-binding hemerythrin.

Author

Clay, Michelle E., Hammond, John H., Fangfang Zhong, Xiaolei Chen, Kowalski, Caitlin H., Lee, Alexandra J., Porter, Monique S., Hampton, Thomas H., Greene, Casey S., Pletneva, Ekaterina V., and Hogan, Deborah A.

Subjects
PSEUDOMONAS aeruginosa, CYTOCHROME oxidase, TRANSCRIPTION factors, CYTOCHROME c, CELL metabolism
Abstract

Pseudomonas aeruginosa strains with loss-of-function mutations in the transcription factor LasR are frequently encountered in the clinic and the environment. Among the characteristics common to LasR-defective (LasR-) strains is increased activity of the transcription factor Anr, relative to their LasR+ counterparts, in low-oxygen conditions. One of the Anr-regulated genes found to be highly induced in LasR- strains was PA14_42860 (PA1673), which we named mhr for microoxic hemerythrin. Purified P. aeruginosa Mhr protein contained the predicted di-iron center and bound molecular oxygen with an apparent Kd of ~1 µM. Both Anr and Mhr were necessary for fitness in lasR+ and lasR mutant strains in colony biofilms grown in microoxic conditions, and the effects were more striking in the lasR mutant. Among genes in the Anr regulon, mhr was most closely coregulated with the Anr-controlled high-affinity cytochrome c oxidase genes. In the absence of high-affinity cytochrome c oxidases, deletion of mhr no longer caused a fitness disadvantage, suggesting that Mhr works in concert with microoxic respiration. We demonstrate that Anr and Mhr contribute to LasR- strain fitness even in biofilms grown in normoxic conditions. Furthermore, metabolomics data indicate that, in a lasR mutant, expression of Anr-regulated mhr leads to differences in metabolism in cells grown on lysogeny broth or artificial sputum medium. We propose that increased Anr activity leads to higher levels of the oxygen-binding protein Mhr, which confers an advantage to lasR mutants in microoxic conditions. [ABSTRACT FROM AUTHOR]

Published
2020
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229. PSB 2019 Workshop on Text Mining and Visualization for Precision Medicine

Author

Gonzalez-Hernandez, Graciela, primary, Lu, Zhiyong, additional, Leaman, Robert, additional, Weissenbacher, Davy, additional, Boland, Mary Regina, additional, Chen, Yong, additional, Du, Jingcheng, additional, Fluck, Juliane, additional, Greene, Casey S., additional, Holmes, John, additional, Kashyap, Aditya, additional, Nielsen, Rikke Linnemann, additional, Ouyang, Zhengqing, additional, Schaaf, Sebastian, additional, Taroni, Jaclyn N., additional, Tao, Cui, additional, Zhang, Yuping, additional, and Liu, Hongfang, additional

Published
2018
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230. Enter the Matrix: Factorization Uncovers Knowledge from Omics

Author

Stein-O’Brien, Genevieve L., primary, Arora, Raman, additional, Culhane, Aedin C., additional, Favorov, Alexander V., additional, Garmire, Lana X., additional, Greene, Casey S., additional, Goff, Loyal A., additional, Li, Yifeng, additional, Ngom, Aloune, additional, Ochs, Michael F., additional, Xu, Yanxun, additional, and Fertig, Elana J., additional

Published
2018
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235. Abstract 5318: High-grade serous ovarian cancer DNA methylation and survival in African-American women

Author

Salas, Lucas A., primary, Peres, Lauren C., additional, Abbott, Sarah E., additional, Greene, Casey S., additional, Marks, Jeffrey R., additional, Alberg, Anthony J., additional, Bandera, Elisa V., additional, Barnholtz-Sloan, Jill S., additional, Schwartz, Ann G., additional, Cote, Michele L., additional, Moorman, Patricia G., additional, Funkhouser, Ellen M., additional, Peters, Edward S., additional, Bondy, Melissa L., additional, Terry, Paul D., additional, Doherty, Jennifer A., additional, Christensen, Brock C., additional, and Schildkraut, Joellen M., additional

Published
2018
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237. Metabolic pathways and immunometabolism in rare kidney diseases

Author

Grayson, Peter C, primary, Eddy, Sean, additional, Taroni, Jaclyn N, additional, Lightfoot, Yaíma L, additional, Mariani, Laura, additional, Parikh, Hemang, additional, Lindenmeyer, Maja T, additional, Ju, Wenjun, additional, Greene, Casey S, additional, Godfrey, Brad, additional, Cohen, Clemens D, additional, Krischer, Jeffrey, additional, Kretzler, Matthias, additional, and Merkel, Peter A, additional

Published
2018
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238. A Multimodal Strategy Used by a Large c-di-GMP Network

Author

Dahlstrom, Kurt M., primary, Collins, Alan J., additional, Doing, Georgia, additional, Taroni, Jaclyn N., additional, Gauvin, Timothy J., additional, Greene, Casey S., additional, Hogan, Deborah A., additional, and O'Toole, George A., additional

Published
2018
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239. Opportunities and obstacles for deep learning in biology and medicine

Author

Ching, Travers, primary, Himmelstein, Daniel S., additional, Beaulieu-Jones, Brett K., additional, Kalinin, Alexandr A., additional, Do, Brian T., additional, Way, Gregory P., additional, Ferrero, Enrico, additional, Agapow, Paul-Michael, additional, Zietz, Michael, additional, Hoffman, Michael M., additional, Xie, Wei, additional, Rosen, Gail L., additional, Lengerich, Benjamin J., additional, Israeli, Johnny, additional, Lanchantin, Jack, additional, Woloszynek, Stephen, additional, Carpenter, Anne E., additional, Shrikumar, Avanti, additional, Xu, Jinbo, additional, Cofer, Evan M., additional, Lavender, Christopher A., additional, Turaga, Srinivas C., additional, Alexandari, Amr M., additional, Lu, Zhiyong, additional, Harris, David J., additional, DeCaprio, Dave, additional, Qi, Yanjun, additional, Kundaje, Anshul, additional, Peng, Yifan, additional, Wiley, Laura K., additional, Segler, Marwin H. S., additional, Boca, Simina M., additional, Swamidass, S. Joshua, additional, Huang, Austin, additional, Gitter, Anthony, additional, and Greene, Casey S., additional

Published
2018
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240. Oncogenic Signaling Pathways in The Cancer Genome Atlas

Author

Sanchez-Vega, Francisco, primary, Mina, Marco, additional, Armenia, Joshua, additional, Chatila, Walid K., additional, Luna, Augustin, additional, La, Konnor C., additional, Dimitriadoy, Sofia, additional, Liu, David L., additional, Kantheti, Havish S., additional, Saghafinia, Sadegh, additional, Chakravarty, Debyani, additional, Daian, Foysal, additional, Gao, Qingsong, additional, Bailey, Matthew H., additional, Liang, Wen-Wei, additional, Foltz, Steven M., additional, Shmulevich, Ilya, additional, Ding, Li, additional, Heins, Zachary, additional, Ochoa, Angelica, additional, Gross, Benjamin, additional, Gao, Jianjiong, additional, Zhang, Hongxin, additional, Kundra, Ritika, additional, Kandoth, Cyriac, additional, Bahceci, Istemi, additional, Dervishi, Leonard, additional, Dogrusoz, Ugur, additional, Zhou, Wanding, additional, Shen, Hui, additional, Laird, Peter W., additional, Way, Gregory P., additional, Greene, Casey S., additional, Liang, Han, additional, Xiao, Yonghong, additional, Wang, Chen, additional, Iavarone, Antonio, additional, Berger, Alice H., additional, Bivona, Trever G., additional, Lazar, Alexander J., additional, Hammer, Gary D., additional, Giordano, Thomas, additional, Kwong, Lawrence N., additional, McArthur, Grant, additional, Huang, Chenfei, additional, Tward, Aaron D., additional, Frederick, Mitchell J., additional, McCormick, Frank, additional, Meyerson, Matthew, additional, Van Allen, Eliezer M., additional, Cherniack, Andrew D., additional, Ciriello, Giovanni, additional, Sander, Chris, additional, Schultz, Nikolaus, additional, Caesar-Johnson, Samantha J., additional, Demchok, John A., additional, Felau, Ina, additional, Kasapi, Melpomeni, additional, Ferguson, Martin L., additional, Hutter, Carolyn M., additional, Sofia, Heidi J., additional, Tarnuzzer, Roy, additional, Wang, Zhining, additional, Yang, Liming, additional, Zenklusen, Jean C., additional, Zhang, Jiashan (Julia), additional, Chudamani, Sudha, additional, Liu, Jia, additional, Lolla, Laxmi, additional, Naresh, Rashi, additional, Pihl, Todd, additional, Sun, Qiang, additional, Wan, Yunhu, additional, Wu, Ye, additional, Cho, Juok, additional, DeFreitas, Timothy, additional, Frazer, Scott, additional, Gehlenborg, Nils, additional, Getz, Gad, additional, Heiman, David I., additional, Kim, Jaegil, additional, Lawrence, Michael S., additional, Lin, Pei, additional, Meier, Sam, additional, Noble, Michael S., additional, Saksena, Gordon, additional, Voet, Doug, additional, Zhang, Hailei, additional, Bernard, Brady, additional, Chambwe, Nyasha, additional, Dhankani, Varsha, additional, Knijnenburg, Theo, additional, Kramer, Roger, additional, Leinonen, Kalle, additional, Liu, Yuexin, additional, Miller, Michael, additional, Reynolds, Sheila, additional, Thorsson, Vesteinn, additional, Zhang, Wei, additional, Akbani, Rehan, additional, Broom, Bradley M., additional, Hegde, Apurva M., additional, Ju, Zhenlin, additional, Kanchi, Rupa S., additional, Korkut, Anil, additional, Li, Jun, additional, Ling, Shiyun, additional, Liu, Wenbin, additional, Lu, Yiling, additional, Mills, Gordon B., additional, Ng, Kwok-Shing, additional, Rao, Arvind, additional, Ryan, Michael, additional, Wang, Jing, additional, Weinstein, John N., additional, Zhang, Jiexin, additional, Abeshouse, Adam, additional, de Bruijn, Ino, additional, Gross, Benjamin E., additional, Heins, Zachary J., additional, La, Konnor, additional, Ladanyi, Marc, additional, Nissan, Moriah G., additional, Phillips, Sarah M., additional, Reznik, Ed, additional, Sanchez-Vega, Francisco, additional, Sheridan, Robert, additional, Sumer, S. Onur, additional, Sun, Yichao, additional, Taylor, Barry S., additional, Wang, Jioajiao, additional, Anur, Pavana, additional, Peto, Myron, additional, Spellman, Paul, additional, Benz, Christopher, additional, Stuart, Joshua M., additional, Wong, Christopher K., additional, Yau, Christina, additional, Hayes, D. Neil, additional, Parker, Joel S., additional, Wilkerson, Matthew D., additional, Ally, Adrian, additional, Balasundaram, Miruna, additional, Bowlby, Reanne, additional, Brooks, Denise, additional, Carlsen, Rebecca, additional, Chuah, Eric, additional, Dhalla, Noreen, additional, Holt, Robert, additional, Jones, Steven J.M., additional, Kasaian, Katayoon, additional, Lee, Darlene, additional, Ma, Yussanne, additional, Marra, Marco A., additional, Mayo, Michael, additional, Moore, Richard A., additional, Mungall, Andrew J., additional, Mungall, Karen, additional, Robertson, A. Gordon, additional, Sadeghi, Sara, additional, Schein, Jacqueline E., additional, Sipahimalani, Payal, additional, Tam, Angela, additional, Thiessen, Nina, additional, Tse, Kane, additional, Wong, Tina, additional, Berger, Ashton C., additional, Beroukhim, Rameen, additional, Cibulskis, Carrie, additional, Gabriel, Stacey B., additional, Gao, Galen F., additional, Ha, Gavin, additional, Schumacher, Steven E., additional, Shih, Juliann, additional, Kucherlapati, Melanie H., additional, Kucherlapati, Raju S., additional, Baylin, Stephen, additional, Cope, Leslie, additional, Danilova, Ludmila, additional, Bootwalla, Moiz S., additional, Lai, Phillip H., additional, Maglinte, Dennis T., additional, Van Den Berg, David J., additional, Weisenberger, Daniel J., additional, Auman, J. Todd, additional, Balu, Saianand, additional, Bodenheimer, Tom, additional, Fan, Cheng, additional, Hoadley, Katherine A., additional, Hoyle, Alan P., additional, Jefferys, Stuart R., additional, Jones, Corbin D., additional, Meng, Shaowu, additional, Mieczkowski, Piotr A., additional, Mose, Lisle E., additional, Perou, Amy H., additional, Perou, Charles M., additional, Roach, Jeffrey, additional, Shi, Yan, additional, Simons, Janae V., additional, Skelly, Tara, additional, Soloway, Matthew G., additional, Tan, Donghui, additional, Veluvolu, Umadevi, additional, Fan, Huihui, additional, Hinoue, Toshinori, additional, Bellair, Michelle, additional, Chang, Kyle, additional, Covington, Kyle, additional, Creighton, Chad J., additional, Dinh, Huyen, additional, Doddapaneni, HarshaVardhan, additional, Donehower, Lawrence A., additional, Drummond, Jennifer, additional, Gibbs, Richard A., additional, Glenn, Robert, additional, Hale, Walker, additional, Han, Yi, additional, Hu, Jianhong, additional, Korchina, Viktoriya, additional, Lee, Sandra, additional, Lewis, Lora, additional, Li, Wei, additional, Liu, Xiuping, additional, Morgan, Margaret, additional, Morton, Donna, additional, Muzny, Donna, additional, Santibanez, Jireh, additional, Sheth, Margi, additional, Shinbrot, Eve, additional, Wang, Linghua, additional, Wang, Min, additional, Wheeler, David A., additional, Xi, Liu, additional, Zhao, Fengmei, additional, Hess, Julian, additional, Appelbaum, Elizabeth L., additional, Bailey, Matthew, additional, Cordes, Matthew G., additional, Fronick, Catrina C., additional, Fulton, Lucinda A., additional, Fulton, Robert S., additional, Mardis, Elaine R., additional, McLellan, Michael D., additional, Miller, Christopher A., additional, Schmidt, Heather K., additional, Wilson, Richard K., additional, Crain, Daniel, additional, Curley, Erin, additional, Gardner, Johanna, additional, Lau, Kevin, additional, Mallery, David, additional, Morris, Scott, additional, Paulauskis, Joseph, additional, Penny, Robert, additional, Shelton, Candace, additional, Shelton, Troy, additional, Sherman, Mark, additional, Thompson, Eric, additional, Yena, Peggy, additional, Bowen, Jay, additional, Gastier-Foster, Julie M., additional, Gerken, Mark, additional, Leraas, Kristen M., additional, Lichtenberg, Tara M., additional, Ramirez, Nilsa C., additional, Wise, Lisa, additional, Zmuda, Erik, additional, Corcoran, Niall, additional, Costello, Tony, additional, Hovens, Christopher, additional, Carvalho, Andre L., additional, de Carvalho, Ana C., additional, Fregnani, José H., additional, Longatto-Filho, Adhemar, additional, Reis, Rui M., additional, Scapulatempo-Neto, Cristovam, additional, Silveira, Henrique C.S., additional, Vidal, Daniel O., additional, Burnette, Andrew, additional, Eschbacher, Jennifer, additional, Hermes, Beth, additional, Noss, Ardene, additional, Singh, Rosy, additional, Anderson, Matthew L., additional, Castro, Patricia D., additional, Ittmann, Michael, additional, Huntsman, David, additional, Kohl, Bernard, additional, Le, Xuan, additional, Thorp, Richard, additional, Andry, Chris, additional, Duffy, Elizabeth R., additional, Lyadov, Vladimir, additional, Paklina, Oxana, additional, Setdikova, Galiya, additional, Shabunin, Alexey, additional, Tavobilov, Mikhail, additional, McPherson, Christopher, additional, Warnick, Ronald, additional, Berkowitz, Ross, additional, Cramer, Daniel, additional, Feltmate, Colleen, additional, Horowitz, Neil, additional, Kibel, Adam, additional, Muto, Michael, additional, Raut, Chandrajit P., additional, Malykh, Andrei, additional, Barnholtz-Sloan, Jill S., additional, Barrett, Wendi, additional, Devine, Karen, additional, Fulop, Jordonna, additional, Ostrom, Quinn T., additional, Shimmel, Kristen, additional, Wolinsky, Yingli, additional, Sloan, Andrew E., additional, De Rose, Agostino, additional, Giuliante, Felice, additional, Goodman, Marc, additional, Karlan, Beth Y., additional, Hagedorn, Curt H., additional, Eckman, John, additional, Harr, Jodi, additional, Myers, Jerome, additional, Tucker, Kelinda, additional, Zach, Leigh Anne, additional, Deyarmin, Brenda, additional, Hu, Hai, additional, Kvecher, Leonid, additional, Larson, Caroline, additional, Mural, Richard J., additional, Somiari, Stella, additional, Vicha, Ales, additional, Zelinka, Tomas, additional, Bennett, Joseph, additional, Iacocca, Mary, additional, Rabeno, Brenda, additional, Swanson, Patricia, additional, Latour, Mathieu, additional, Lacombe, Louis, additional, Têtu, Bernard, additional, Bergeron, Alain, additional, McGraw, Mary, additional, Staugaitis, Susan M., additional, Chabot, John, additional, Hibshoosh, Hanina, additional, Sepulveda, Antonia, additional, Su, Tao, additional, Wang, Timothy, additional, Potapova, Olga, additional, Voronina, Olga, additional, Desjardins, Laurence, additional, Mariani, Odette, additional, Roman-Roman, Sergio, additional, Sastre, Xavier, additional, Stern, Marc-Henri, additional, Cheng, Feixiong, additional, Signoretti, Sabina, additional, Berchuck, Andrew, additional, Bigner, Darell, additional, Lipp, Eric, additional, Marks, Jeffrey, additional, McCall, Shannon, additional, McLendon, Roger, additional, Secord, Angeles, additional, Sharp, Alexis, additional, Behera, Madhusmita, additional, Brat, Daniel J., additional, Chen, Amy, additional, Delman, Keith, additional, Force, Seth, additional, Khuri, Fadlo, additional, Magliocca, Kelly, additional, Maithel, Shishir, additional, Olson, Jeffrey J., additional, Owonikoko, Taofeek, additional, Pickens, Alan, additional, Ramalingam, Suresh, additional, Shin, Dong M., additional, Sica, Gabriel, additional, Van Meir, Erwin G., additional, Zhang, Hongzheng, additional, Eijckenboom, Wil, additional, Gillis, Ad, additional, Korpershoek, Esther, additional, Looijenga, Leendert, additional, Oosterhuis, Wolter, additional, Stoop, Hans, additional, van Kessel, Kim E., additional, Zwarthoff, Ellen C., additional, Calatozzolo, Chiara, additional, Cuppini, Lucia, additional, Cuzzubbo, Stefania, additional, DiMeco, Francesco, additional, Finocchiaro, Gaetano, additional, Mattei, Luca, additional, Perin, Alessandro, additional, Pollo, Bianca, additional, Chen, Chu, additional, Houck, John, additional, Lohavanichbutr, Pawadee, additional, Hartmann, Arndt, additional, Stoehr, Christine, additional, Stoehr, Robert, additional, Taubert, Helge, additional, Wach, Sven, additional, Wullich, Bernd, additional, Kycler, Witold, additional, Murawa, Dawid, additional, Wiznerowicz, Maciej, additional, Chung, Ki, additional, Edenfield, W. Jeffrey, additional, Martin, Julie, additional, Baudin, Eric, additional, Bubley, Glenn, additional, Bueno, Raphael, additional, De Rienzo, Assunta, additional, Richards, William G., additional, Kalkanis, Steven, additional, Mikkelsen, Tom, additional, Noushmehr, Houtan, additional, Scarpace, Lisa, additional, Girard, Nicolas, additional, Aymerich, Marta, additional, Campo, Elias, additional, Giné, Eva, additional, Guillermo, Armando López, additional, Van Bang, Nguyen, additional, Hanh, Phan Thi, additional, Phu, Bui Duc, additional, Tang, Yufang, additional, Colman, Howard, additional, Evason, Kimberley, additional, Dottino, Peter R., additional, Martignetti, John A., additional, Gabra, Hani, additional, Juhl, Hartmut, additional, Akeredolu, Teniola, additional, Stepa, Serghei, additional, Hoon, Dave, additional, Ahn, Keunsoo, additional, Kang, Koo Jeong, additional, Beuschlein, Felix, additional, Breggia, Anne, additional, Birrer, Michael, additional, Bell, Debra, additional, Borad, Mitesh, additional, Bryce, Alan H., additional, Castle, Erik, additional, Chandan, Vishal, additional, Cheville, John, additional, Copland, John A., additional, Farnell, Michael, additional, Flotte, Thomas, additional, Giama, Nasra, additional, Ho, Thai, additional, Kendrick, Michael, additional, Kocher, Jean-Pierre, additional, Kopp, Karla, additional, Moser, Catherine, additional, Nagorney, David, additional, O’Brien, Daniel, additional, O’Neill, Brian Patrick, additional, Patel, Tushar, additional, Petersen, Gloria, additional, Que, Florencia, additional, Rivera, Michael, additional, Roberts, Lewis, additional, Smallridge, Robert, additional, Smyrk, Thomas, additional, Stanton, Melissa, additional, Thompson, R. Houston, additional, Torbenson, Michael, additional, Yang, Ju Dong, additional, Zhang, Lizhi, additional, Brimo, Fadi, additional, Ajani, Jaffer A., additional, Gonzalez, Ana Maria Angulo, additional, Behrens, Carmen, additional, Bondaruk, Jolanta, additional, Broaddus, Russell, additional, Czerniak, Bogdan, additional, Esmaeli, Bita, additional, Fujimoto, Junya, additional, Gershenwald, Jeffrey, additional, Guo, Charles, additional, Logothetis, Christopher, additional, Meric-Bernstam, Funda, additional, Moran, Cesar, additional, Ramondetta, Lois, additional, Rice, David, additional, Sood, Anil, additional, Tamboli, Pheroze, additional, Thompson, Timothy, additional, Troncoso, Patricia, additional, Tsao, Anne, additional, Wistuba, Ignacio, additional, Carter, Candace, additional, Haydu, Lauren, additional, Hersey, Peter, additional, Jakrot, Valerie, additional, Kakavand, Hojabr, additional, Kefford, Richard, additional, Lee, Kenneth, additional, Long, Georgina, additional, Mann, Graham, additional, Quinn, Michael, additional, Saw, Robyn, additional, Scolyer, Richard, additional, Shannon, Kerwin, additional, Spillane, Andrew, additional, Stretch, Jonathan, additional, Synott, Maria, additional, Thompson, John, additional, Wilmott, James, additional, Al-Ahmadie, Hikmat, additional, Chan, Timothy A., additional, Ghossein, Ronald, additional, Gopalan, Anuradha, additional, Levine, Douglas A., additional, Reuter, Victor, additional, Singer, Samuel, additional, Singh, Bhuvanesh, additional, Tien, Nguyen Viet, additional, Broudy, Thomas, additional, Mirsaidi, Cyrus, additional, Nair, Praveen, additional, Drwiega, Paul, additional, Miller, Judy, additional, Smith, Jennifer, additional, Zaren, Howard, additional, Park, Joong-Won, additional, Hung, Nguyen Phi, additional, Kebebew, Electron, additional, Linehan, W. Marston, additional, Metwalli, Adam R., additional, Pacak, Karel, additional, Pinto, Peter A., additional, Schiffman, Mark, additional, Schmidt, Laura S., additional, Vocke, Cathy D., additional, Wentzensen, Nicolas, additional, Worrell, Robert, additional, Yang, Hannah, additional, Moncrieff, Marc, additional, Goparaju, Chandra, additional, Melamed, Jonathan, additional, Pass, Harvey, additional, Botnariuc, Natalia, additional, Caraman, Irina, additional, Cernat, Mircea, additional, Chemencedji, Inga, additional, Clipca, Adrian, additional, Doruc, Serghei, additional, Gorincioi, Ghenadie, additional, Mura, Sergiu, additional, Pirtac, Maria, additional, Stancul, Irina, additional, Tcaciuc, Diana, additional, Albert, Monique, additional, Alexopoulou, Iakovina, additional, Arnaout, Angel, additional, Bartlett, John, additional, Engel, Jay, additional, Gilbert, Sebastien, additional, Parfitt, Jeremy, additional, Sekhon, Harman, additional, Thomas, George, additional, Rassl, Doris M., additional, Rintoul, Robert C., additional, Bifulco, Carlo, additional, Tamakawa, Raina, additional, Urba, Walter, additional, Hayward, Nicholas, additional, Timmers, Henri, additional, Antenucci, Anna, additional, Facciolo, Francesco, additional, Grazi, Gianluca, additional, Marino, Mirella, additional, Merola, Roberta, additional, de Krijger, Ronald, additional, Gimenez-Roqueplo, Anne-Paule, additional, Piché, Alain, additional, Chevalier, Simone, additional, McKercher, Ginette, additional, Birsoy, Kivanc, additional, Barnett, Gene, additional, Brewer, Cathy, additional, Farver, Carol, additional, Naska, Theresa, additional, Pennell, Nathan A., additional, Raymond, Daniel, additional, Schilero, Cathy, additional, Smolenski, Kathy, additional, Williams, Felicia, additional, Morrison, Carl, additional, Borgia, Jeffrey A., additional, Liptay, Michael J., additional, Pool, Mark, additional, Seder, Christopher W., additional, Junker, Kerstin, additional, Omberg, Larsson, additional, Dinkin, Mikhail, additional, Manikhas, George, additional, Alvaro, Domenico, additional, Bragazzi, Maria Consiglia, additional, Cardinale, Vincenzo, additional, Carpino, Guido, additional, Gaudio, Eugenio, additional, Chesla, David, additional, Cottingham, Sandra, additional, Dubina, Michael, additional, Moiseenko, Fedor, additional, Dhanasekaran, Renumathy, additional, Becker, Karl-Friedrich, additional, Janssen, Klaus-Peter, additional, Slotta-Huspenina, Julia, additional, Abdel-Rahman, Mohamed H., additional, Aziz, Dina, additional, Bell, Sue, additional, Cebulla, Colleen M., additional, Davis, Amy, additional, Duell, Rebecca, additional, Elder, J. Bradley, additional, Hilty, Joe, additional, Kumar, Bahavna, additional, Lang, James, additional, Lehman, Norman L., additional, Mandt, Randy, additional, Nguyen, Phuong, additional, Pilarski, Robert, additional, Rai, Karan, additional, Schoenfield, Lynn, additional, Senecal, Kelly, additional, Wakely, Paul, additional, Hansen, Paul, additional, Lechan, Ronald, additional, Powers, James, additional, Tischler, Arthur, additional, Grizzle, William E., additional, Sexton, Katherine C., additional, Kastl, Alison, additional, Henderson, Joel, additional, Porten, Sima, additional, Waldmann, Jens, additional, Fassnacht, Martin, additional, Asa, Sylvia L., additional, Schadendorf, Dirk, additional, Couce, Marta, additional, Graefen, Markus, additional, Huland, Hartwig, additional, Sauter, Guido, additional, Schlomm, Thorsten, additional, Simon, Ronald, additional, Tennstedt, Pierre, additional, Olabode, Oluwole, additional, Nelson, Mark, additional, Bathe, Oliver, additional, Carroll, Peter R., additional, Chan, June M., additional, Disaia, Philip, additional, Glenn, Pat, additional, Kelley, Robin K., additional, Landen, Charles N., additional, Phillips, Joanna, additional, Prados, Michael, additional, Simko, Jeffry, additional, Smith-McCune, Karen, additional, VandenBerg, Scott, additional, Roggin, Kevin, additional, Fehrenbach, Ashley, additional, Kendler, Ady, additional, Sifri, Suzanne, additional, Steele, Ruth, additional, Jimeno, Antonio, additional, Carey, Francis, additional, Forgie, Ian, additional, Mannelli, Massimo, additional, Carney, Michael, additional, Hernandez, Brenda, additional, Campos, Benito, additional, Herold-Mende, Christel, additional, Jungk, Christin, additional, Unterberg, Andreas, additional, von Deimling, Andreas, additional, Bossler, Aaron, additional, Galbraith, Joseph, additional, Jacobus, Laura, additional, Knudson, Michael, additional, Knutson, Tina, additional, Ma, Deqin, additional, Milhem, Mohammed, additional, Sigmund, Rita, additional, Godwin, Andrew K., additional, Madan, Rashna, additional, Rosenthal, Howard G., additional, Adebamowo, Clement, additional, Adebamowo, Sally N., additional, Boussioutas, Alex, additional, Beer, David, additional, Mes-Masson, Anne-Marie, additional, Saad, Fred, additional, Bocklage, Therese, additional, Landrum, Lisa, additional, Mannel, Robert, additional, Moore, Kathleen, additional, Moxley, Katherine, additional, Postier, Russel, additional, Walker, Joan, additional, Zuna, Rosemary, additional, Feldman, Michael, additional, Valdivieso, Federico, additional, Dhir, Rajiv, additional, Luketich, James, additional, Pinero, Edna M. Mora, additional, Quintero-Aguilo, Mario, additional, Carlotti, Carlos Gilberto, additional, Dos Santos, Jose Sebastião, additional, Kemp, Rafael, additional, Sankarankuty, Ajith, additional, Tirapelli, Daniela, additional, Catto, James, additional, Agnew, Kathy, additional, Swisher, Elizabeth, additional, Creaney, Jenette, additional, Robinson, Bruce, additional, Shelley, Carl Simon, additional, Godwin, Eryn M., additional, Kendall, Sara, additional, Shipman, Cassaundra, additional, Bradford, Carol, additional, Carey, Thomas, additional, Haddad, Andrea, additional, Moyer, Jeffey, additional, Peterson, Lisa, additional, Prince, Mark, additional, Rozek, Laura, additional, Wolf, Gregory, additional, Bowman, Rayleen, additional, Fong, Kwun M., additional, Yang, Ian, additional, Korst, Robert, additional, Rathmell, W. Kimryn, additional, Fantacone-Campbell, J. Leigh, additional, Hooke, Jeffrey A., additional, Kovatich, Albert J., additional, Shriver, Craig D., additional, DiPersio, John, additional, Drake, Bettina, additional, Govindan, Ramaswamy, additional, Heath, Sharon, additional, Ley, Timothy, additional, Van Tine, Brian, additional, Westervelt, Peter, additional, Rubin, Mark A., additional, Lee, Jung Il, additional, Aredes, Natália D., additional, and Mariamidze, Armaz, additional

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2018
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241. Genomic and Molecular Landscape of DNA Damage Repair Deficiency across The Cancer Genome Atlas

Author

Knijnenburg, Theo A., primary, Wang, Linghua, additional, Zimmermann, Michael T., additional, Chambwe, Nyasha, additional, Gao, Galen F., additional, Cherniack, Andrew D., additional, Fan, Huihui, additional, Shen, Hui, additional, Way, Gregory P., additional, Greene, Casey S., additional, Liu, Yuexin, additional, Akbani, Rehan, additional, Feng, Bin, additional, Donehower, Lawrence A., additional, Miller, Chase, additional, Shen, Yang, additional, Karimi, Mostafa, additional, Chen, Haoran, additional, Kim, Pora, additional, Jia, Peilin, additional, Shinbrot, Eve, additional, Zhang, Shaojun, additional, Liu, Jianfang, additional, Hu, Hai, additional, Bailey, Matthew H., additional, Yau, Christina, additional, Wolf, Denise, additional, Zhao, Zhongming, additional, Weinstein, John N., additional, Li, Lei, additional, Ding, Li, additional, Mills, Gordon B., additional, Laird, Peter W., additional, Wheeler, David A., additional, Shmulevich, Ilya, additional, Monnat, Raymond J., additional, Xiao, Yonghong, additional, Wang, Chen, additional, Caesar-Johnson, Samantha J., additional, Demchok, John A., additional, Felau, Ina, additional, Kasapi, Melpomeni, additional, Ferguson, Martin L., additional, Hutter, Carolyn M., additional, Sofia, Heidi J., additional, Tarnuzzer, Roy, additional, Wang, Zhining, additional, Yang, Liming, additional, Zenklusen, Jean C., additional, Zhang, Jiashan (Julia), additional, Chudamani, Sudha, additional, Liu, Jia, additional, Lolla, Laxmi, additional, Naresh, Rashi, additional, Pihl, Todd, additional, Sun, Qiang, additional, Wan, Yunhu, additional, Wu, Ye, additional, Cho, Juok, additional, DeFreitas, Timothy, additional, Frazer, Scott, additional, Gehlenborg, Nils, additional, Getz, Gad, additional, Heiman, David I., additional, Kim, Jaegil, additional, Lawrence, Michael S., additional, Lin, Pei, additional, Meier, Sam, additional, Noble, Michael S., additional, Saksena, Gordon, additional, Voet, Doug, additional, Zhang, Hailei, additional, Bernard, Brady, additional, Dhankani, Varsha, additional, Knijnenburg, Theo, additional, Kramer, Roger, additional, Leinonen, Kalle, additional, Miller, Michael, additional, Reynolds, Sheila, additional, Thorsson, Vesteinn, additional, Zhang, Wei, additional, Broom, Bradley M., additional, Hegde, Apurva M., additional, Ju, Zhenlin, additional, Kanchi, Rupa S., additional, Korkut, Anil, additional, Li, Jun, additional, Liang, Han, additional, Ling, Shiyun, additional, Liu, Wenbin, additional, Lu, Yiling, additional, Ng, Kwok-Shing, additional, Rao, Arvind, additional, Ryan, Michael, additional, Wang, Jing, additional, Zhang, Jiexin, additional, Abeshouse, Adam, additional, Armenia, Joshua, additional, Chakravarty, Debyani, additional, Chatila, Walid K., additional, de Bruijn, Ino, additional, Gao, Jianjiong, additional, Gross, Benjamin E., additional, Heins, Zachary J., additional, Kundra, Ritika, additional, La, Konnor, additional, Ladanyi, Marc, additional, Luna, Augustin, additional, Nissan, Moriah G., additional, Ochoa, Angelica, additional, Phillips, Sarah M., additional, Reznik, Ed, additional, Sanchez-Vega, Francisco, additional, Sander, Chris, additional, Schultz, Nikolaus, additional, Sheridan, Robert, additional, Sumer, S. Onur, additional, Sun, Yichao, additional, Taylor, Barry S., additional, Wang, Jioajiao, additional, Zhang, Hongxin, additional, Anur, Pavana, additional, Peto, Myron, additional, Spellman, Paul, additional, Benz, Christopher, additional, Stuart, Joshua M., additional, Wong, Christopher K., additional, Hayes, D. Neil, additional, Parker, Joel S., additional, Wilkerson, Matthew D., additional, Ally, Adrian, additional, Balasundaram, Miruna, additional, Bowlby, Reanne, additional, Brooks, Denise, additional, Carlsen, Rebecca, additional, Chuah, Eric, additional, Dhalla, Noreen, additional, Holt, Robert, additional, Jones, Steven J.M., additional, Kasaian, Katayoon, additional, Lee, Darlene, additional, Ma, Yussanne, additional, Marra, Marco A., additional, Mayo, Michael, additional, Moore, Richard A., additional, Mungall, Andrew J., additional, Mungall, Karen, additional, Robertson, A. Gordon, additional, Sadeghi, Sara, additional, Schein, Jacqueline E., additional, Sipahimalani, Payal, additional, Tam, Angela, additional, Thiessen, Nina, additional, Tse, Kane, additional, Wong, Tina, additional, Berger, Ashton C., additional, Beroukhim, Rameen, additional, Cibulskis, Carrie, additional, Gabriel, Stacey B., additional, Ha, Gavin, additional, Meyerson, Matthew, additional, Schumacher, Steven E., additional, Shih, Juliann, additional, Kucherlapati, Melanie H., additional, Kucherlapati, Raju S., additional, Baylin, Stephen, additional, Cope, Leslie, additional, Danilova, Ludmila, additional, Bootwalla, Moiz S., additional, Lai, Phillip H., additional, Maglinte, Dennis T., additional, Van Den Berg, David J., additional, Weisenberger, Daniel J., additional, Auman, J. Todd, additional, Balu, Saianand, additional, Bodenheimer, Tom, additional, Fan, Cheng, additional, Hoadley, Katherine A., additional, Hoyle, Alan P., additional, Jefferys, Stuart R., additional, Jones, Corbin D., additional, Meng, Shaowu, additional, Mieczkowski, Piotr A., additional, Mose, Lisle E., additional, Perou, Amy H., additional, Perou, Charles M., additional, Roach, Jeffrey, additional, Shi, Yan, additional, Simons, Janae V., additional, Skelly, Tara, additional, Soloway, Matthew G., additional, Tan, Donghui, additional, Veluvolu, Umadevi, additional, Hinoue, Toshinori, additional, Zhou, Wanding, additional, Bellair, Michelle, additional, Chang, Kyle, additional, Covington, Kyle, additional, Creighton, Chad J., additional, Dinh, Huyen, additional, Doddapaneni, HarshaVardhan, additional, Drummond, Jennifer, additional, Gibbs, Richard A., additional, Glenn, Robert, additional, Hale, Walker, additional, Han, Yi, additional, Hu, Jianhong, additional, Korchina, Viktoriya, additional, Lee, Sandra, additional, Lewis, Lora, additional, Li, Wei, additional, Liu, Xiuping, additional, Morgan, Margaret, additional, Morton, Donna, additional, Muzny, Donna, additional, Santibanez, Jireh, additional, Sheth, Margi, additional, Wang, Min, additional, Xi, Liu, additional, Zhao, Fengmei, additional, Hess, Julian, additional, Appelbaum, Elizabeth L., additional, Bailey, Matthew, additional, Cordes, Matthew G., additional, Fronick, Catrina C., additional, Fulton, Lucinda A., additional, Fulton, Robert S., additional, Kandoth, Cyriac, additional, Mardis, Elaine R., additional, McLellan, Michael D., additional, Miller, Christopher A., additional, Schmidt, Heather K., additional, Wilson, Richard K., additional, Crain, Daniel, additional, Curley, Erin, additional, Gardner, Johanna, additional, Lau, Kevin, additional, Mallery, David, additional, Morris, Scott, additional, Paulauskis, Joseph, additional, Penny, Robert, additional, Shelton, Candace, additional, Shelton, Troy, 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Thorp, Richard, additional, Andry, Chris, additional, Duffy, Elizabeth R., additional, Lyadov, Vladimir, additional, Paklina, Oxana, additional, Setdikova, Galiya, additional, Shabunin, Alexey, additional, Tavobilov, Mikhail, additional, McPherson, Christopher, additional, Warnick, Ronald, additional, Berkowitz, Ross, additional, Cramer, Daniel, additional, Feltmate, Colleen, additional, Horowitz, Neil, additional, Kibel, Adam, additional, Muto, Michael, additional, Raut, Chandrajit P., additional, Malykh, Andrei, additional, Barnholtz-Sloan, Jill S., additional, Barrett, Wendi, additional, Devine, Karen, additional, Fulop, Jordonna, additional, Ostrom, Quinn T., additional, Shimmel, Kristen, additional, Wolinsky, Yingli, additional, Sloan, Andrew E., additional, De Rose, Agostino, additional, Giuliante, Felice, additional, Goodman, Marc, additional, Karlan, Beth Y., additional, Hagedorn, Curt H., additional, Eckman, John, additional, Harr, Jodi, additional, Myers, Jerome, additional, Tucker, Kelinda, additional, Zach, Leigh Anne, additional, Deyarmin, Brenda, additional, Kvecher, Leonid, additional, Larson, Caroline, additional, Mural, Richard J., additional, Somiari, Stella, additional, Vicha, Ales, additional, Zelinka, Tomas, additional, Bennett, Joseph, additional, Iacocca, Mary, additional, Rabeno, Brenda, additional, Swanson, Patricia, additional, Latour, Mathieu, additional, Lacombe, Louis, additional, Têtu, Bernard, additional, Bergeron, Alain, additional, McGraw, Mary, additional, Staugaitis, Susan M., additional, Chabot, John, additional, Hibshoosh, Hanina, additional, Sepulveda, Antonia, additional, Su, Tao, additional, Wang, Timothy, additional, Potapova, Olga, additional, Voronina, Olga, additional, Desjardins, Laurence, additional, Mariani, Odette, additional, Roman-Roman, Sergio, additional, Sastre, Xavier, additional, Stern, Marc-Henri, additional, Cheng, Feixiong, additional, Signoretti, Sabina, additional, Berchuck, Andrew, additional, Bigner, Darell, additional, Lipp, Eric, additional, Marks, Jeffrey, additional, McCall, Shannon, additional, McLendon, Roger, additional, Secord, Angeles, additional, Sharp, Alexis, additional, Behera, Madhusmita, additional, Brat, Daniel J., additional, Chen, Amy, additional, Delman, Keith, additional, Force, Seth, additional, Khuri, Fadlo, additional, Magliocca, Kelly, additional, Maithel, Shishir, additional, Olson, Jeffrey J., additional, Owonikoko, Taofeek, additional, Pickens, Alan, additional, Ramalingam, Suresh, additional, Shin, Dong M., additional, Sica, Gabriel, additional, Van Meir, Erwin G., additional, Zhang, Hongzheng, additional, Eijckenboom, Wil, additional, Gillis, Ad, additional, Korpershoek, Esther, additional, Looijenga, Leendert, additional, Oosterhuis, Wolter, additional, Stoop, Hans, additional, van Kessel, Kim E., additional, Zwarthoff, Ellen C., additional, Calatozzolo, Chiara, additional, Cuppini, Lucia, additional, Cuzzubbo, Stefania, additional, DiMeco, Francesco, additional, Finocchiaro, Gaetano, additional, Mattei, Luca, additional, Perin, Alessandro, additional, Pollo, Bianca, additional, Chen, Chu, additional, Houck, John, additional, Lohavanichbutr, Pawadee, additional, Hartmann, Arndt, additional, Stoehr, Christine, additional, Stoehr, Robert, additional, Taubert, Helge, additional, Wach, Sven, additional, Wullich, Bernd, additional, Kycler, Witold, additional, Murawa, Dawid, additional, Wiznerowicz, Maciej, additional, Chung, Ki, additional, Edenfield, W. Jeffrey, additional, Martin, Julie, additional, Baudin, Eric, additional, Bubley, Glenn, additional, Bueno, Raphael, additional, De Rienzo, Assunta, additional, Richards, William G., additional, Kalkanis, Steven, additional, Mikkelsen, Tom, additional, Noushmehr, Houtan, additional, Scarpace, Lisa, additional, Girard, Nicolas, additional, Aymerich, Marta, additional, Campo, Elias, additional, Giné, Eva, additional, Guillermo, Armando López, additional, Van Bang, Nguyen, additional, Hanh, Phan Thi, additional, Phu, Bui Duc, additional, Tang, Yufang, additional, Colman, Howard, additional, Evason, Kimberley, additional, Dottino, Peter R., additional, Martignetti, John A., additional, Gabra, Hani, additional, Juhl, Hartmut, additional, Akeredolu, Teniola, additional, Stepa, Serghei, additional, Hoon, Dave, additional, Ahn, Keunsoo, additional, Kang, Koo Jeong, additional, Beuschlein, Felix, additional, Breggia, Anne, additional, Birrer, Michael, additional, Bell, Debra, additional, Borad, Mitesh, additional, Bryce, Alan H., additional, Castle, Erik, additional, Chandan, Vishal, additional, Cheville, John, additional, Copland, John A., additional, Farnell, Michael, additional, Flotte, Thomas, additional, Giama, Nasra, additional, Ho, Thai, additional, Kendrick, Michael, additional, Kocher, Jean-Pierre, additional, Kopp, Karla, additional, Moser, Catherine, additional, Nagorney, David, additional, O’Brien, Daniel, additional, O’Neill, Brian Patrick, additional, Patel, Tushar, additional, Petersen, Gloria, additional, Que, Florencia, additional, Rivera, Michael, additional, Roberts, Lewis, additional, Smallridge, Robert, additional, Smyrk, Thomas, additional, Stanton, Melissa, additional, Thompson, R. 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2018
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242. Machine Learning Detects Pan-cancer Ras Pathway Activation in The Cancer Genome Atlas

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Way, Gregory P., primary, Sanchez-Vega, Francisco, additional, La, Konnor, additional, Armenia, Joshua, additional, Chatila, Walid K., additional, Luna, Augustin, additional, Sander, Chris, additional, Cherniack, Andrew D., additional, Mina, Marco, additional, Ciriello, Giovanni, additional, Schultz, Nikolaus, additional, Sanchez, Yolanda, additional, Greene, Casey S., additional, Caesar-Johnson, Samantha J., additional, Demchok, John A., additional, Felau, Ina, additional, Kasapi, Melpomeni, additional, Ferguson, Martin L., additional, Hutter, Carolyn M., additional, Sofia, Heidi J., additional, Tarnuzzer, Roy, additional, Wang, Zhining, additional, Yang, Liming, additional, Zenklusen, Jean C., additional, Zhang, Jiashan (Julia), additional, Chudamani, Sudha, additional, Liu, Jia, additional, Lolla, Laxmi, additional, Naresh, Rashi, additional, Pihl, Todd, additional, Sun, Qiang, additional, Wan, Yunhu, additional, Wu, Ye, additional, Cho, Juok, additional, DeFreitas, Timothy, additional, Frazer, Scott, additional, Gehlenborg, Nils, additional, Getz, Gad, additional, Heiman, David I., additional, Kim, Jaegil, additional, Lawrence, Michael S., additional, Lin, Pei, additional, Meier, Sam, additional, Noble, Michael S., additional, Saksena, Gordon, additional, Voet, Doug, additional, Zhang, Hailei, additional, Bernard, Brady, additional, Chambwe, Nyasha, additional, Dhankani, Varsha, additional, Knijnenburg, Theo, additional, Kramer, Roger, additional, Leinonen, Kalle, additional, Liu, Yuexin, additional, Miller, Michael, additional, Reynolds, Sheila, additional, Shmulevich, Ilya, additional, Thorsson, Vesteinn, additional, Zhang, Wei, additional, Akbani, Rehan, additional, Broom, Bradley M., additional, Hegde, Apurva M., additional, Ju, Zhenlin, additional, Kanchi, Rupa S., additional, Korkut, Anil, additional, Li, Jun, additional, Liang, Han, additional, Ling, Shiyun, additional, Liu, Wenbin, additional, Lu, Yiling, additional, Mills, Gordon B., additional, Ng, Kwok-Shing, additional, Rao, Arvind, additional, Ryan, Michael, additional, Wang, Jing, additional, Weinstein, John N., additional, Zhang, Jiexin, additional, Abeshouse, Adam, additional, Chakravarty, Debyani, additional, de Bruijn, Ino, additional, Gao, Jianjiong, additional, Gross, Benjamin E., additional, Heins, Zachary J., additional, Kundra, Ritika, additional, Ladanyi, Marc, additional, Nissan, Moriah G., additional, Ochoa, Angelica, additional, Phillips, Sarah M., additional, Reznik, Ed, additional, Sheridan, Robert, additional, Sumer, S. 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Mora, additional, Quintero-Aguilo, Mario, additional, Carlotti, Carlos Gilberto, additional, Dos Santos, Jose Sebastião, additional, Kemp, Rafael, additional, Sankarankuty, Ajith, additional, Tirapelli, Daniela, additional, Catto, James, additional, Agnew, Kathy, additional, Swisher, Elizabeth, additional, Creaney, Jenette, additional, Robinson, Bruce, additional, Shelley, Carl Simon, additional, Godwin, Eryn M., additional, Kendall, Sara, additional, Shipman, Cassaundra, additional, Bradford, Carol, additional, Carey, Thomas, additional, Haddad, Andrea, additional, Moyer, Jeffey, additional, Peterson, Lisa, additional, Prince, Mark, additional, Rozek, Laura, additional, Wolf, Gregory, additional, Bowman, Rayleen, additional, Fong, Kwun M., additional, Yang, Ian, additional, Korst, Robert, additional, Rathmell, W. Kimryn, additional, Fantacone-Campbell, J. Leigh, additional, Hooke, Jeffrey A., additional, Kovatich, Albert J., additional, Shriver, Craig D., additional, DiPersio, John, additional, Drake, Bettina, additional, Govindan, Ramaswamy, additional, Heath, Sharon, additional, Ley, Timothy, additional, Van Tine, Brian, additional, Westervelt, Peter, additional, Rubin, Mark A., additional, Lee, Jung Il, additional, Aredes, Natália D., additional, and Mariamidze, Armaz, additional

Published
2018
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245. Genomic and Molecular Landscape of DNA Damage Repair Deficiency across The Cancer Genome Atlas.

Author

Knijnenburg, Theo A, Knijnenburg, Theo A, Wang, Linghua, Zimmermann, Michael T, Chambwe, Nyasha, Gao, Galen F, Cherniack, Andrew D, Fan, Huihui, Shen, Hui, Way, Gregory P, Greene, Casey S, Liu, Yuexin, Akbani, Rehan, Feng, Bin, Donehower, Lawrence A, Miller, Chase, Shen, Yang, Karimi, Mostafa, Chen, Haoran, Kim, Pora, Jia, Peilin, Shinbrot, Eve, Zhang, Shaojun, Liu, Jianfang, Hu, Hai, Bailey, Matthew H, Yau, Christina, Wolf, Denise, Zhao, Zhongming, Weinstein, John N, Li, Lei, Ding, Li, Mills, Gordon B, Laird, Peter W, Wheeler, David A, Shmulevich, Ilya, Cancer Genome Atlas Research Network, Monnat, Raymond J, Xiao, Yonghong, Wang, Chen, Knijnenburg, Theo A, Knijnenburg, Theo A, Wang, Linghua, Zimmermann, Michael T, Chambwe, Nyasha, Gao, Galen F, Cherniack, Andrew D, Fan, Huihui, Shen, Hui, Way, Gregory P, Greene, Casey S, Liu, Yuexin, Akbani, Rehan, Feng, Bin, Donehower, Lawrence A, Miller, Chase, Shen, Yang, Karimi, Mostafa, Chen, Haoran, Kim, Pora, Jia, Peilin, Shinbrot, Eve, Zhang, Shaojun, Liu, Jianfang, Hu, Hai, Bailey, Matthew H, Yau, Christina, Wolf, Denise, Zhao, Zhongming, Weinstein, John N, Li, Lei, Ding, Li, Mills, Gordon B, Laird, Peter W, Wheeler, David A, Shmulevich, Ilya, Cancer Genome Atlas Research Network, Monnat, Raymond J, Xiao, Yonghong, and Wang, Chen

Abstract

DNA damage repair (DDR) pathways modulate cancer risk, progression, and therapeutic response. We systematically analyzed somatic alterations to provide a comprehensive view of DDR deficiency across 33 cancer types. Mutations with accompanying loss of heterozygosity were observed in over 1/3 of DDR genes, including TP53 and BRCA1/2. Other prevalent alterations included epigenetic silencing of the direct repair genes EXO5, MGMT, and ALKBH3 in ∼20% of samples. Homologous recombination deficiency (HRD) was present at varying frequency in many cancer types, most notably ovarian cancer. However, in contrast to ovarian cancer, HRD was associated with worse outcomes in several other cancers. Protein structure-based analyses allowed us to predict functional consequences of rare, recurrent DDR mutations. A new machine-learning-based classifier developed from gene expression data allowed us to identify alterations that phenocopy deleterious TP53 mutations. These frequent DDR gene alterations in many human cancers have functional consequences that may determine cancer progression and guide therapy.

Published
2018

246. Machine Learning Detects Pan-cancer Ras Pathway Activation in The Cancer Genome Atlas.

Author

Way, Gregory P, Way, Gregory P, Sanchez-Vega, Francisco, La, Konnor, Armenia, Joshua, Chatila, Walid K, Luna, Augustin, Sander, Chris, Cherniack, Andrew D, Mina, Marco, Ciriello, Giovanni, Schultz, Nikolaus, Cancer Genome Atlas Research Network, Sanchez, Yolanda, Greene, Casey S, Way, Gregory P, Way, Gregory P, Sanchez-Vega, Francisco, La, Konnor, Armenia, Joshua, Chatila, Walid K, Luna, Augustin, Sander, Chris, Cherniack, Andrew D, Mina, Marco, Ciriello, Giovanni, Schultz, Nikolaus, Cancer Genome Atlas Research Network, Sanchez, Yolanda, and Greene, Casey S

Abstract

Precision oncology uses genomic evidence to match patients with treatment but often fails to identify all patients who may respond. The transcriptome of these "hidden responders" may reveal responsive molecular states. We describe and evaluate a machine-learning approach to classify aberrant pathway activity in tumors, which may aid in hidden responder identification. The algorithm integrates RNA-seq, copy number, and mutations from 33 different cancer types across The Cancer Genome Atlas (TCGA) PanCanAtlas project to predict aberrant molecular states in tumors. Applied to the Ras pathway, the method detects Ras activation across cancer types and identifies phenocopying variants. The model, trained on human tumors, can predict response to MEK inhibitors in wild-type Ras cell lines. We also present data that suggest that multiple hits in the Ras pathway confer increased Ras activity. The transcriptome is underused in precision oncology and, combined with machine learning, can aid in the identification of hidden responders.

Published
2018

247. Oncogenic Signaling Pathways in The Cancer Genome Atlas

Author

Sanchez-Vega, Francisco, Mina, Marco, Armenia, Joshua, Chatila, Walid K., Luna, Augustin, La, Konnor C., Dimitriadoy, Sofia, Liu, David L., Kantheti, Havish S., Saghafinia, Sadegh, Chakravarty, Debyani, Daian, Foysal, Gao, Qingsong, Bailey, Matthew H., Liang, Wen Wei, Foltz, Steven M., Shmulevich, Ilya, Ding, Li, Heins, Zachary J., Ochoa, Angelica, Gross, Benjamin E., Gao, Jianjiong, Zhang, Hongxin, Kundra, Ritika, Kandoth, Cyriac, Bahceci, Istemi, Dervishi, Leonard, Dogrusoz, Ugur, Zhou, Wanding, Shen, Hui, Laird, Peter W., Way, Gregory P., Greene, Casey S., Liang, Han, Xiao, Yonghong, Wang, Chen, Iavarone, Antonio, Berger, Alice H., Bivona, Trever G., Lazar, Alexander J., Hammer, Gary D., Giordano, Thomas, Kwong, Lawrence N., McArthur, Grant, Huang, Chenfei, Tward, Aaron D., Frederick, Mitchell J., McCormick, Frank, Zhang, Jiashan (Julia), de Krijger, Ronald, The Cancer Genome Atlas Research Network, Sanchez-Vega, Francisco, Mina, Marco, Armenia, Joshua, Chatila, Walid K., Luna, Augustin, La, Konnor C., Dimitriadoy, Sofia, Liu, David L., Kantheti, Havish S., Saghafinia, Sadegh, Chakravarty, Debyani, Daian, Foysal, Gao, Qingsong, Bailey, Matthew H., Liang, Wen Wei, Foltz, Steven M., Shmulevich, Ilya, Ding, Li, Heins, Zachary J., Ochoa, Angelica, Gross, Benjamin E., Gao, Jianjiong, Zhang, Hongxin, Kundra, Ritika, Kandoth, Cyriac, Bahceci, Istemi, Dervishi, Leonard, Dogrusoz, Ugur, Zhou, Wanding, Shen, Hui, Laird, Peter W., Way, Gregory P., Greene, Casey S., Liang, Han, Xiao, Yonghong, Wang, Chen, Iavarone, Antonio, Berger, Alice H., Bivona, Trever G., Lazar, Alexander J., Hammer, Gary D., Giordano, Thomas, Kwong, Lawrence N., McArthur, Grant, Huang, Chenfei, Tward, Aaron D., Frederick, Mitchell J., McCormick, Frank, Zhang, Jiashan (Julia), de Krijger, Ronald, and The Cancer Genome Atlas Research Network

Published
2018

248. Sci-Hub provides access to nearly all scholarly literature

Author

Himmelstein, Daniel S, Romero, Ariel Rodriguez, Levernier, Jacob G, Munro, Thomas Anthony, McLaughlin, Stephen Reid, Greshake Tzovaras, Bastian, Greene, Casey S, Himmelstein, Daniel S, Romero, Ariel Rodriguez, Levernier, Jacob G, Munro, Thomas Anthony, McLaughlin, Stephen Reid, Greshake Tzovaras, Bastian, and Greene, Casey S

Abstract

The website Sci-Hub enables users to download PDF versions of scholarly articles, including many articles that are paywalled at their journal's site. Sci-Hub has grown rapidly since its creation in 2011, but the extent of its coverage was unclear. Here we report that, as of March 2017, Sci-Hub's database contains 68.9% of the 81.6 million scholarly articles registered with Crossref and 85.1% of articles published in toll access journals. We find that coverage varies by discipline and publisher, and that Sci-Hub preferentially covers popular, paywalled content. For toll access articles, we find that Sci-Hub provides greater coverage than the University of Pennsylvania, a major research university in the United States. Green open access to toll access articles via licit services, on the other hand, remains quite limited. Our interactive browser at https://greenelab.github.io/scihub allows users to explore these findings in more detail. For the first time, nearly all scholarly literature is available gratis to anyone with an Internet connection, suggesting the toll access business model may become unsustainable.

Published
2018

249. Genomic and Molecular Landscape of DNA Damage Repair Deficiency across The Cancer Genome Atlas

Author

Onderzoeksgroep 6, Regenerative Medicine and Stem Cells, Cancer, Pathologie Pathologen staf, Knijnenburg, Theo, Wang, Linghua, Zimmermann, Michael T., Chambwe, Nyasha, Gao, Galen F., Cherniack, Andrew D., Fan, Huihui, Shen, Hui, Way, Gregory P., Greene, Casey S., Liu, Yuexin, Akbani, Rehan, Feng, Bin, Donehower, Lawrence A., Miller, Chase, Shen, Yang, Karimi, Mostafa, Chen, Haoran, Kim, Pora, Jia, Peilin, Shinbrot, Eve, Zhang, Shaojun, Liu, Jianfang, Hu, Hai, Bailey, Matthew H., Yau, Christina, Wolf, Denise, Zhao, Zhongming, Weinstein, John N., Li, Lei, Ding, Li, Mills, Gordon B., Laird, Peter W., Wheeler, David A., Shmulevich, Ilya, Caesar-Johnson, Samantha J., Demchok, John A., Felau, Ina, Kasapi, Melpomeni, Ferguson, Martin L., Hutter, Carolyn M., Sofia, Heidi J., Tarnuzzer, Roy, Wang, Zhining, Yang, Liming, Zenklusen, Jean C., Zhang, Jiashan (Julia), Chudamani, Sudha, Timmers, Henri, de Krijger, Ronald, The Cancer Genome Atlas Research Network, Onderzoeksgroep 6, Regenerative Medicine and Stem Cells, Cancer, Pathologie Pathologen staf, Knijnenburg, Theo, Wang, Linghua, Zimmermann, Michael T., Chambwe, Nyasha, Gao, Galen F., Cherniack, Andrew D., Fan, Huihui, Shen, Hui, Way, Gregory P., Greene, Casey S., Liu, Yuexin, Akbani, Rehan, Feng, Bin, Donehower, Lawrence A., Miller, Chase, Shen, Yang, Karimi, Mostafa, Chen, Haoran, Kim, Pora, Jia, Peilin, Shinbrot, Eve, Zhang, Shaojun, Liu, Jianfang, Hu, Hai, Bailey, Matthew H., Yau, Christina, Wolf, Denise, Zhao, Zhongming, Weinstein, John N., Li, Lei, Ding, Li, Mills, Gordon B., Laird, Peter W., Wheeler, David A., Shmulevich, Ilya, Caesar-Johnson, Samantha J., Demchok, John A., Felau, Ina, Kasapi, Melpomeni, Ferguson, Martin L., Hutter, Carolyn M., Sofia, Heidi J., Tarnuzzer, Roy, Wang, Zhining, Yang, Liming, Zenklusen, Jean C., Zhang, Jiashan (Julia), Chudamani, Sudha, Timmers, Henri, de Krijger, Ronald, and The Cancer Genome Atlas Research Network

Published
2018

250. Oncogenic Signaling Pathways in The Cancer Genome Atlas

Author

Onderzoeksgroep 6, Pathologie Pathologen staf, Sanchez-Vega, Francisco, Mina, Marco, Armenia, Joshua, Chatila, Walid K., Luna, Augustin, La, Konnor C., Dimitriadoy, Sofia, Liu, David L., Kantheti, Havish S., Saghafinia, Sadegh, Chakravarty, Debyani, Daian, Foysal, Gao, Qingsong, Bailey, Matthew H., Liang, Wen Wei, Foltz, Steven M., Shmulevich, Ilya, Ding, Li, Heins, Zachary J., Ochoa, Angelica, Gross, Benjamin E., Gao, Jianjiong, Zhang, Hongxin, Kundra, Ritika, Kandoth, Cyriac, Bahceci, Istemi, Dervishi, Leonard, Dogrusoz, Ugur, Zhou, Wanding, Shen, Hui, Laird, Peter W., Way, Gregory P., Greene, Casey S., Liang, Han, Xiao, Yonghong, Wang, Chen, Iavarone, Antonio, Berger, Alice H., Bivona, Trever G., Lazar, Alexander J., Hammer, Gary D., Giordano, Thomas, Kwong, Lawrence N., McArthur, Grant, Huang, Chenfei, Tward, Aaron D., Frederick, Mitchell J., McCormick, Frank, Zhang, Jiashan (Julia), de Krijger, Ronald, The Cancer Genome Atlas Research Network, Onderzoeksgroep 6, Pathologie Pathologen staf, Sanchez-Vega, Francisco, Mina, Marco, Armenia, Joshua, Chatila, Walid K., Luna, Augustin, La, Konnor C., Dimitriadoy, Sofia, Liu, David L., Kantheti, Havish S., Saghafinia, Sadegh, Chakravarty, Debyani, Daian, Foysal, Gao, Qingsong, Bailey, Matthew H., Liang, Wen Wei, Foltz, Steven M., Shmulevich, Ilya, Ding, Li, Heins, Zachary J., Ochoa, Angelica, Gross, Benjamin E., Gao, Jianjiong, Zhang, Hongxin, Kundra, Ritika, Kandoth, Cyriac, Bahceci, Istemi, Dervishi, Leonard, Dogrusoz, Ugur, Zhou, Wanding, Shen, Hui, Laird, Peter W., Way, Gregory P., Greene, Casey S., Liang, Han, Xiao, Yonghong, Wang, Chen, Iavarone, Antonio, Berger, Alice H., Bivona, Trever G., Lazar, Alexander J., Hammer, Gary D., Giordano, Thomas, Kwong, Lawrence N., McArthur, Grant, Huang, Chenfei, Tward, Aaron D., Frederick, Mitchell J., McCormick, Frank, Zhang, Jiashan (Julia), de Krijger, Ronald, and The Cancer Genome Atlas Research Network

Published
2018

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