Search Results - Sivachenko, Andrey

ProteoLens: a visual analytic tool for multi-scale database-driven biological network data mining by Huan, Tianxiao, Sivachenko, Andrey Y, Harrison, Scott H, Chen, Jake Y

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RNA-SeQC: RNA-seq metrics for quality control and process optimization by DeLuca, David S., Levin, Joshua Z., Sivachenko, Andrey, Fennell, Timothy, Nazaire, Marc-Danie, Williams, Chris, Reich, Michael, Winckler, Wendy, Getz, Gad

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Sensitive detection of somatic point mutations in impure and heterogeneous cancer samples by Cibulskis, Kristian, Lawrence, Michael S., Carter, Scott L., Sivachenko, Andrey, Jaffe, David, Sougnez, Carrie, Gabriel, Stacey, Meyerson, Matthew, Lander, Eric S., Getz, Gad

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Massively Parallel Sequencing of Human Urinary Exosome/Microvesicle RNA Reveals a Predominance of Non-Coding RNA by Miranda, Kevin C., Bond, Daniel T., Levin, Joshua Z., Adiconis, Xian, Sivachenko, Andrey, Russ, Carsten, Brown, Dennis, Nusbaum, Chad, Russo, Leileata M.

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The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data by McKenna, Aaron, Hanna, Matthew, Banks, Eric, Sivachenko, Andrey, Cibulskis, Kristian, Kernytsky, Andrew, Garimella, Kiran, Altshuler, David, Gabriel, Stacey, Daly, Mark, DePristo, Mark A.

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PRADA: pipeline for RNA sequencing data analysis by Torres-García, Wandaliz, Zheng, Siyuan, Sivachenko, Andrey, Vegesna, Rahulsimham, Wang, Qianghu, Yao, Rong, Berger, Michael F., Weinstein, John N., Getz, Gad, Verhaak, Roel G.W.

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RNA-Seq methods for imperfect samples: development, evaluation and applications by Adiconis, Xian, Fan, Lin, DeLuca, David, Sivachenko, Andrey, Pochet, Nathalie, Berlin, Aaron, Young, Sarah, Getz, Gad, Regev, Aviv, Nusbaum, Chad, Gnirke, Andreas, Levin, Joshua Z

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Genome-scale DNA methylation maps of pluripotent and differentiated cells by Meissner, Alexander, Mikkelsen, Tarjei S., Gu, Hongcang, Wernig, Marius, Hanna, Jacob, Sivachenko, Andrey, Zhang, Xiaolan, Bernstein, Bradley E., Nusbaum, Chad, Jaffe, David B., Gnirke, Andreas, Jaenisch, Rudolf, Lander, Eric S.

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A Pan-Cancer Analysis of Transcriptome Changes Associated with Somatic Mutations in U2AF1 Reveals Commonly Altered Splicing Events by Brooks, Angela N., Choi, Peter S., de Waal, Luc, Sharifnia, Tanaz, Imielinski, Marcin, Saksena, Gordon, Pedamallu, Chandra Sekhar, Sivachenko, Andrey, Rosenberg, Mara, Chmielecki, Juliann, Lawrence, Michael S., DeLuca, David S., Getz, Gad, Meyerson, Matthew

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Comprehensive comparative analysis of RNA sequencing methods for degraded or low input samples by Adiconis, Xian, Borges-Rivera, Diego, Satija, Rahul, DeLuca, David S., Busby, Michele A., Berlin, Aaron M., Sivachenko, Andrey, Thompson, Dawn Anne, Wysoker, Alec, Fennell, Timothy, Gnirke, Andreas, Pochet, Nathalie, Regev, Aviv, Levin, Joshua Z.

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Inhibitor-sensitive FGFR2 and FGFR3 mutations in lung squamous cell carcinoma by Liao, Rachel G., Jung, Joonil, Tchaicha, Jeremy, Wilkerson, Matthew D., Sivachenko, Andrey, Beauchamp, Ellen M., Liu, Qingsong, Pugh, Trevor J., Pedamallu, Chandra Sekhar, Hayes, D. Neil, Gray, Nathanael S., Getz, Gad, Wong, Kwok-Kin, Haddad, Robert I., Meyerson, Matthew, Hammerman, Peter S.

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Evolution and impact of subclonal mutations in chronic lymphocytic leukemia by Landau, Dan A., Carter, Scott L., Stojanov, Petar, McKenna, Aaron, Stevenson, Kristen, Lawrence, Michael S., Sougnez, Carrie, Stewart, Chip, Sivachenko, Andrey, Wang, Lili, Wan, Youzhong, Zhang, Wandi, Shukla, Sachet A., Vartanov, Alexander, Fernandes, Stacey M., Saksena, Gordon, Cibulskis, Kristian, Tesar, Bethany, Gabriel, Stacey, Hacohen, Nir, Meyerson, Matthew, Lander, Eric S., Neuberg, Donna, Brown, Jennifer R., Getz, Gad, Wu, Catherine J.

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Integrative analysis of the melanoma transcriptome by Berger, Michael F., Levin, Joshua Z., Vijayendran, Krishna, Sivachenko, Andrey, Adiconis, Xian, Maguire, Jared, Johnson, Laura A., Robinson, James, Verhaak, Roel G., Sougnez, Carrie, Onofrio, Robert C., Ziaugra, Liuda, Cibulskis, Kristian, Laine, Elisabeth, Barretina, Jordi, Winckler, Wendy, Fisher, David E., Getz, Gad, Meyerson, Matthew, Jaffe, David B., Gabriel, Stacey B., Lander, Eric S., Dummer, Reinhard, Gnirke, Andreas, Nusbaum, Chad, Garraway, Levi A.

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SF3B1 and Other Novel Cancer Genes in Chronic Lymphocytic Leukemia by Wang, Lili, Lawrence, Michael S., Wan, Youzhong, Stojanov, Petar, Sougnez, Carrie, Stevenson, Kristen, Werner, Lillian, Sivachenko, Andrey, DeLuca, David S., Zhang, Li, Zhang, Wandi, Vartanov, Alexander R., Fernandes, Stacey M., Goldstein, Natalie R., Folco, Eric G., Cibulskis, Kristian, Tesar, Bethany, Sievers, Quinlan L., Shefler, Erica, Gabriel, Stacey, Hacohen, Nir, Reed, Robin, Meyerson, Matthew, Golub, Todd R., Lander, Eric S., Neuberg, Donna, Brown, Jennifer R., Getz, Gad, Wu, Catherine J.

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Whole-exome sequencing and clinical interpretation of FFPE tumor samples to guide precision cancer medicine by Allen, Eliezer M. Van, Wagle, Nikhil, Stojanov, Petar, Perrin, Danielle L., Cibulskis, Kristian, Marlow, Sara, Jane-Valbuena, Judit, Friedrich, Dennis C., Kryukov, Gregory, Carter, Scott L., McKenna, Aaron, Sivachenko, Andrey, Rosenberg, Mara, Kiezun, Adam, Voet, Douglas, Lawrence, Michael, Lichtenstein, Lee T., Gentry, Jeff G., Huang, Franklin W., Fostel, Jennifer, Farlow, Deborah, Barbie, David, Gandhi, Leena, Lander, Eric S., Gray, Stacy W., Joffe, Steven, Janne, Pasi, Garber, Judy, MacConaill, Laura, Lindeman, Neal, Rollins, Barrett, Kantoff, Philip, Fisher, Sheila A., Gabriel, Stacey, Getz, Gad, Garraway, Levi A.

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Integrative and Comparative Genomic Analysis of Lung Squamous Cell Carcinomas in East Asian Patients by Kim, Youngwook, Hammerman, Peter S., Kim, Jaegil, Yoon, Ji-ae, Lee, Yoomi, Sun, Jong-Mu, Wilkerson, Matthew D., Pedamallu, Chandra Sekhar, Cibulskis, Kristian, Yoo, Yeong Kyung, Lawrence, Michael S., Stojanov, Petar, Carter, Scott L., McKenna, Aaron, Stewart, Chip, Sivachenko, Andrey Y., Oh, In-Jae, Kim, Hong Kwan, Choi, Yong Soo, Kim, Kwhanmien, Shim, Young Mog, Kim, Kyu-Sik, Song, Sang-Yun, Na, Kook-Joo, Choi, Yoon-La, Hayes, D. Neil, Kim, Jhingook, Cho, Sukki, Kim, Young-Chul, Ahn, Jin Seok, Ahn, Myung-Ju, Getz, Gad, Meyerson, Matthew, Park, Keunchil

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Exome and whole genome sequencing of esophageal adenocarcinoma identifies recurrent driver events and mutational complexity by Dulak, Austin M., Stojanov, Petar, Peng, Shouyong, Lawrence, Michael S., Fox, Cameron, Stewart, Chip, Bandla, Santhoshi, Imamura, Yu, Schumacher, Steven E., Shefler, Erica, McKenna, Aaron, Cibulskis, Kristian, Sivachenko, Andrey, Carter, Scott L., Saksena, Gordon, Voet, Douglas, Ramos, Alex H., Auclair, Daniel, Thompson, Kristin, Sougnez, Carrie, Onofrio, Robert C., Guiducci, Candace, Beroukhim, Rameen, Zhou, David, Lin, Lin, Lin, Jules, Reddy, Rishindra, Chang, Andrew, Luketich, James D., Pennathur, Arjun, Ogino, Shuji, Golub, Todd R., Gabriel, Stacey B., Lander, Eric S., Beer, David G., Godfrey, Tony E., Getz, Gad, Bass, Adam J.

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Genomic sequencing of colorectal adenocarcinomas identifies a recurrent VTI1A-TCF7L2 fusion by Bass, Adam J, Lawrence, Michael S, Brace, Lear E, Ramos, Alex H, Drier, Yotam, Cibulskis, Kristian, Sougnez, Carrie, Voet, Douglas, Saksena, Gordon, Sivachenko, Andrey, Jing, Rui, Parkin, Melissa, Pugh, Trevor, Verhaak, Roel G, Stransky, Nicolas, Boutin, Adam T, Barretina, Jordi, Solit, David B, Vakiani, Evi, Shao, Wenlin, Mishina, Yuji, Warmuth, Markus, Jimenez, Jose, Chiang, Derek Y, Signoretti, Sabina, Kaelin, William G, Spardy, Nicole, Hahn, William C, Hoshida, Yujin, Ogino, Shuji, DePinho, Ronald A, Chin, Lynda, Garraway, Levi A, Fuchs, Charles S, Baselga, Jose, Tabernero, Josep, Gabriel, Stacey, Lander, Eric S, Getz, Gad, Meyerson, Matthew

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The genomic complexity of primary human prostate cancer by Berger, Michael F., Lawrence, Michael S., Demichelis, Francesca, Drier, Yotam, Cibulskis, Kristian, Sivachenko, Andrey Y., Sboner, Andrea, Esgueva, Raquel, Pflueger, Dorothee, Sougnez, Carrie, Onofrio, Robert, Carter, Scott L., Park, Kyung, Habegger, Lukas, Ambrogio, Lauren, Fennell, Timothy, Parkin, Melissa, Saksena, Gordon, Voet, Douglas, Ramos, Alex H., Pugh, Trevor J., Wilkinson, Jane, Fisher, Sheila, Winckler, Wendy, Mahan, Scott, Ardlie, Kristin, Baldwin, Jennifer, Simons, Jonathan W., Kitabayashi, Naoki, MacDonald, Theresa Y., Kantoff, Philip W., Chin, Lynda, Gabriel, Stacey B., Gerstein, Mark B., Golub, Todd R., Meyerson, Matthew, Tewari, Ashutosh, Lander, Eric S., Getz, Gad, Rubin, Mark A., Garraway, Levi A.

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The Mutational Landscape of Head and Neck Squamous Cell Carcinoma by Stransky, Nicolas, Egloff, Ann Marie, Tward, Aaron D., Kostic, Aleksandar D., Cibulskis, Kristian, Sivachenko, Andrey, Kryukov, Gregory V., Lawrence, Michael, Sougnez, Carrie, McKenna, Aaron, Shefler, Erica, Ramos, Alex H., Stojanov, Petar, Carter, Scott L., Voet, Douglas, Cortés, Maria L, Auclair, Daniel, Berger, Michael F., Saksena, Gordon, Guiducci, Candace, Onofrio, Robert, Parkin, Melissa, Romkes, Marjorie, Weissfeld, Joel L., Seethala, Raja R., Wang, Lin, Rangel-Escareño, Claudia, Fernandez-Lopez, Juan Carlos, Hidalgo-Miranda, Alfredo, Melendez-Zajgla, Jorge, Winckler, Wendy, Ardlie, Kristin, Gabriel, Stacey B., Meyerson, Matthew, Lander, Eric S., Getz, Gad, Golub, Todd R., Garraway, Levi A., Grandis, Jennifer R.

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