The real cost of sequencing: higher than you think
Sboner, Andrea, Mu, Xinmeng Jasmine, Greenbaum, Dov, Auerbach, Raymond K, Gerstein, Mark B
Published in Genome biology (25.08.2011)
Published in Genome biology (25.08.2011)
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Journal Article
Genomic Correlates of Immune-Cell Infiltrates in Colorectal Carcinoma
Giannakis, Marios, Mu, Xinmeng Jasmine, Shukla, Sachet A., Qian, Zhi Rong, Cohen, Ofir, Nishihara, Reiko, Bahl, Samira, Cao, Yin, Amin-Mansour, Ali, Yamauchi, Mai, Sukawa, Yasutaka, Stewart, Chip, Rosenberg, Mara, Mima, Kosuke, Inamura, Kentaro, Nosho, Katsuhiko, Nowak, Jonathan A., Lawrence, Michael S., Giovannucci, Edward L., Chan, Andrew T., Ng, Kimmie, Meyerhardt, Jeffrey A., Van Allen, Eliezer M., Getz, Gad, Gabriel, Stacey B., Lander, Eric S., Wu, Catherine J., Fuchs, Charles S., Ogino, Shuji, Garraway, Levi A.
Published in Cell reports (Cambridge) (26.04.2016)
Published in Cell reports (Cambridge) (26.04.2016)
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Journal Article
RNF43 is frequently mutated in colorectal and endometrial cancers
Giannakis, Marios, Hodis, Eran, Jasmine Mu, Xinmeng, Yamauchi, Mai, Rosenbluh, Joseph, Cibulskis, Kristian, Saksena, Gordon, Lawrence, Michael S, Qian, Zhi Rong, Nishihara, Reiko, Van Allen, Eliezer M, Hahn, William C, Gabriel, Stacey B, Lander, Eric S, Getz, Gad, Ogino, Shuji, Fuchs, Charles S, Garraway, Levi A
Published in Nature genetics (01.12.2014)
Published in Nature genetics (01.12.2014)
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Journal Article
FunSeq2: a framework for prioritizing noncoding regulatory variants in cancer
Fu, Yao, Liu, Zhu, Lou, Shaoke, Bedford, Jason, Mu, Xinmeng Jasmine, Yip, Kevin Y, Khurana, Ekta, Gerstein, Mark
Published in Genome biology (01.01.2014)
Published in Genome biology (01.01.2014)
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Journal Article
Expanding control of the tumor cell cycle with a CDK2/4/6 inhibitor
Freeman-Cook, Kevin, Hoffman, Robert L., Miller, Nichol, Almaden, Jonathan, Chionis, John, Zhang, Qin, Eisele, Koleen, Liu, Chaoting, Zhang, Cathy, Huser, Nanni, Nguyen, Lisa, Costa-Jones, Cinthia, Niessen, Sherry, Carelli, Jordan, Lapek, John, Weinrich, Scott L., Wei, Ping, McMillan, Elizabeth, Wilson, Elizabeth, Wang, Tim S., McTigue, Michele, Ferre, Rose Ann, He, You-Ai, Ninkovic, Sacha, Behenna, Douglas, Tran, Khanh T., Sutton, Scott, Nagata, Asako, Ornelas, Martha A., Kephart, Susan E., Zehnder, Luke R., Murray, Brion, Xu, Meirong, Solowiej, James E., Visswanathan, Ravi, Boras, Britton, Looper, David, Lee, Nathan, Bienkowska, Jadwiga R., Zhu, Zhou, Kan, Zhengyan, Ding, Ying, Mu, Xinmeng Jasmine, Oderup, Cecilia, Salek-Ardakani, Shahram, White, Michael A., VanArsdale, Todd, Dann, Stephen G.
Published in Cancer cell (11.10.2021)
Published in Cancer cell (11.10.2021)
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Journal Article
First-in-Human Study of Utomilumab, a 4-1BB/CD137 Agonist, in Combination with Rituximab in Patients with Follicular and Other CD20 + Non-Hodgkin Lymphomas
Gopal, Ajay K, Levy, Ronald, Houot, Roch, Patel, Sandip P, Popplewell, Leslie, Jacobson, Caron, Mu, Xinmeng J, Deng, Shibing, Ching, Keith A, Chen, Ying, Davis, Craig B, Huang, Bo, Fly, Kolette D, Thall, Aron, Woolfson, Adrian, Bartlett, Nancy L
Published in Clinical cancer research (01.06.2020)
Published in Clinical cancer research (01.06.2020)
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Journal Article
Genomics and privacy: implications of the new reality of closed data for the field
Greenbaum, Dov, Sboner, Andrea, Mu, Xinmeng Jasmine, Gerstein, Mark
Published in PLoS computational biology (01.12.2011)
Published in PLoS computational biology (01.12.2011)
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Journal Article
Genomic Correlates of Immune-Cell Infiltrates in Colorectal Carcinoma
Giannakis, Marios, Mu, Xinmeng Jasmine, Shukla, Sachet A., Qian, Zhi Rong, Cohen, Ofir, Nishihara, Reiko, Bahl, Samira, Cao, Yin, Amin-Mansour, Ali, Yamauchi, Mai, Sukawa, Yasutaka, Stewart, Chip, Rosenberg, Mara, Mima, Kosuke, Inamura, Kentaro, Nosho, Katsuhiko, Nowak, Jonathan A., Lawrence, Michael S., Giovannucci, Edward L., Chan, Andrew T., Ng, Kimmie, Meyerhardt, Jeffrey A., Van Allen, Eliezer M., Getz, Gad, Gabriel, Stacey B., Lander, Eric S., Wu, Catherine J., Fuchs, Charles S., Ogino, Shuji, Garraway, Levi A.
Published in Cell reports (Cambridge) (18.10.2016)
Published in Cell reports (Cambridge) (18.10.2016)
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Journal Article
Molecular characterization of renal cell carcinoma tumors from a phase III anti-angiogenic adjuvant therapy trial
Motzer, Robert J., Martini, Jean-François, Mu, Xinmeng J., Staehler, Michael, George, Daniel J., Valota, Olga, Lin, Xun, Pandha, Hardev S., Ching, Keith A., Ravaud, Alain
Published in Nature communications (10.10.2022)
Published in Nature communications (10.10.2022)
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Journal Article
GENCODE pseudogene resource
Pei, Baikang, Sisu, Cristina, Frankish, Adam, Howald, Cédric, Habegger, Lukas, Mu, Xinmeng Jasmine, Harte, Rachel, Balasubramanian, Suganthi, Tanzer, Andrea, Diekhans, Mark, Reymond, Alexandre, Hubbard, Tim J, Harrow, Jennifer, Gerstein, Mark B
Published in Genome biology (05.09.2012)
Published in Genome biology (05.09.2012)
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Journal Article
PEMer: a computational framework with simulation-based error models for inferring genomic structural variants from massive paired-end sequencing data
Korbel, Jan O, Abyzov, Alexej, Mu, Xinmeng Jasmine, Carriero, Nicholas, Cayting, Philip, Zhang, Zhengdong, Snyder, Michael, Gerstein, Mark B
Published in Genome biology (23.02.2009)
Published in Genome biology (23.02.2009)
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Journal Article
Identifying therapeutic targets for cancer among 2074 circulating proteins and risk of nine cancers
Smith-Byrne, Karl, Hedman, Åsa, Dimitriou, Marios, Desai, Trishna, Sokolov, Alexandr V., Schioth, Helgi B., Koprulu, Mine, Pietzner, Maik, Langenberg, Claudia, Atkins, Joshua, Penha, Ricardo Cortez, McKay, James, Brennan, Paul, Zhou, Sirui, Richards, Brent J., Yarmolinsky, James, Martin, Richard M., Borlido, Joana, Mu, Xinmeng J., Butterworth, Adam, Shen, Xia, Wilson, Jim, Assimes, Themistocles L., Hung, Rayjean J., Amos, Christopher, Purdue, Mark, Rothman, Nathaniel, Chanock, Stephen, Travis, Ruth C., Johansson, Mattias, Mälarstig, Anders
Published in Nature communications (29.04.2024)
Published in Nature communications (29.04.2024)
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Journal Article
Genomic profiling of ER + breast cancers after short-term estrogen suppression reveals alterations associated with endocrine resistance
Giltnane, Jennifer M, Hutchinson, Katherine E, Stricker, Thomas P, Formisano, Luigi, Young, Christian D, Estrada, Monica V, Nixon, Mellissa J, Du, Liping, Sanchez, Violeta, Ericsson, Paula Gonzalez, Kuba, Maria G, Sanders, Melinda E, Mu, Xinmeng J, Van Allen, Eliezer M, Wagle, Nikhil, Mayer, Ingrid A, Abramson, Vandana, Gόmez, Henry, Rizzo, Monica, Toy, Weiyi, Chandarlapaty, Sarat, Mayer, Erica L, Christiansen, Jason, Murphy, Danielle, Fitzgerald, Kerry, Wang, Kai, Ross, Jeffrey S, Miller, Vincent A, Stephens, Phillip J, Yelensky, Roman, Garraway, Levi, Shyr, Yu, Meszoely, Ingrid, Balko, Justin M, Arteaga, Carlos L
Published in Science translational medicine (09.08.2017)
Published in Science translational medicine (09.08.2017)
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Journal Article
Avelumab plus axitinib versus sunitinib in advanced renal cell carcinoma: biomarker analysis of the phase 3 JAVELIN Renal 101 trial
Motzer, Robert J., Robbins, Paul B., Powles, Thomas, Albiges, Laurence, Haanen, John B., Larkin, James, Mu, Xinmeng Jasmine, Ching, Keith A., Uemura, Motohide, Pal, Sumanta K., Alekseev, Boris, Gravis, Gwenaelle, Campbell, Matthew T., Penkov, Konstantin, Lee, Jae Lyun, Hariharan, Subramanian, Wang, Xiao, Zhang, Weidong, Wang, Jing, Chudnovsky, Aleksander, di Pietro, Alessandra, Donahue, Amber C., Choueiri, Toni K.
Published in Nature medicine (01.11.2020)
Published in Nature medicine (01.11.2020)
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Journal Article
Avelumab maintenance in advanced urothelial carcinoma: biomarker analysis of the phase 3 JAVELIN Bladder 100 trial
Powles, Thomas, Sridhar, Srikala S., Loriot, Yohann, Bellmunt, Joaquim, Mu, Xinmeng Jasmine, Ching, Keith A., Pu, Jie, Sternberg, Cora N., Petrylak, Daniel P., Tambaro, Rosa, Dourthe, Louis M., Alvarez-Fernandez, Carlos, Aarts, Maureen, di Pietro, Alessandra, Grivas, Petros, Davis, Craig B.
Published in Nature medicine (01.12.2021)
Published in Nature medicine (01.12.2021)
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Journal Article
Multi-omics profiling of younger Asian breast cancers reveals distinctive molecular signatures
Kan, Zhengyan, Ding, Ying, Kim, Jinho, Jung, Hae Hyun, Chung, Woosung, Lal, Samir, Cho, Soonweng, Fernandez-Banet, Julio, Lee, Se Kyung, Kim, Seok Won, Lee, Jeong Eon, Choi, Yoon-La, Deng, Shibing, Kim, Ji-Yeon, Ahn, Jin Seok, Sha, Ying, Mu, Xinmeng Jasmine, Nam, Jae-Yong, Im, Young-Hyuck, Lee, Soohyeon, Park, Woong-Yang, Nam, Seok Jin, Park, Yeon Hee
Published in Nature communications (30.04.2018)
Published in Nature communications (30.04.2018)
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Journal Article
Standard machine learning approaches outperform deep representation learning on phenotype prediction from transcriptomics data
Smith, Aaron M, Walsh, Jonathan R, Long, John, Davis, Craig B, Henstock, Peter, Hodge, Martin R, Maciejewski, Mateusz, Mu, Xinmeng Jasmine, Ra, Stephen, Zhao, Shanrong, Ziemek, Daniel, Fisher, Charles K
Published in BMC bioinformatics (20.03.2020)
Published in BMC bioinformatics (20.03.2020)
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Journal Article
The origin, evolution, and functional impact of short insertion-deletion variants identified in 179 human genomes
Montgomery, Stephen B, Goode, David L, Kvikstad, Erika, Albers, Cornelis A, Zhang, Zhengdong D, Mu, Xinmeng Jasmine, Ananda, Guruprasad, Howie, Bryan, Karczewski, Konrad J, Smith, Kevin S, Anaya, Vanessa, Richardson, Rhea, Davis, Joe, MacArthur, Daniel G, Sidow, Arend, Duret, Laurent, Gerstein, Mark, Makova, Kateryna D, Marchini, Jonathan, McVean, Gil, Lunter, Gerton
Published in Genome research (01.05.2013)
Published in Genome research (01.05.2013)
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Journal Article
Analysis of deletion breakpoints from 1,092 humans reveals details of mutation mechanisms
Abyzov, Alexej, Li, Shantao, Kim, Daniel Rhee, Mohiyuddin, Marghoob, Stütz, Adrian M., Parrish, Nicholas F., Mu, Xinmeng Jasmine, Clark, Wyatt, Chen, Ken, Hurles, Matthew, Korbel, Jan O., Lam, Hugo Y. K., Lee, Charles, Gerstein, Mark B.
Published in Nature communications (01.06.2015)
Published in Nature communications (01.06.2015)
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Journal Article
Nucleotide-resolution analysis of structural variants using BreakSeq and a breakpoint library
Korbel, Jan O, Gerstein, Mark B, Lam, Hugo Y K, Mu, Xinmeng Jasmine, Stütz, Adrian M, Tanzer, Andrea, Cayting, Philip D, Snyder, Michael, Kim, Philip M
Published in Nature biotechnology (2010)
Published in Nature biotechnology (2010)
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