Diverse BRCA1 and BRCA2 Reversion Mutations in Circulating Cell-Free DNA of Therapy-Resistant Breast or Ovarian Cancer
Weigelt, Britta, Comino-Méndez, Iñaki, de Bruijn, Ino, Tian, Lei, Meisel, Jane L, García-Murillas, Isaac, Fribbens, Charlotte, Cutts, Ros, Martelotto, Luciano G, Ng, Charlotte K Y, Lim, Raymond S, Selenica, Pier, Piscuoglio, Salvatore, Aghajanian, Carol, Norton, Larry, Murali, Rajmohan, Hyman, David M, Borsu, Laetitia, Arcila, Maria E, Konner, Jason, Reis-Filho, Jorge S, Greenberg, Roger A, Robson, Mark E, Turner, Nicholas C
Published in Clinical cancer research (01.11.2017)
Published in Clinical cancer research (01.11.2017)
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The Fennoscandian Shield deep terrestrial virosphere suggests slow motion ‘boom and burst’ cycles
Holmfeldt, Karin, Nilsson, Emelie, Simone, Domenico, Lopez-Fernandez, Margarita, Wu, Xiaofen, de Bruijn, Ino, Lundin, Daniel, Andersson, Anders F., Bertilsson, Stefan, Dopson, Mark
Published in Communications biology (08.03.2021)
Published in Communications biology (08.03.2021)
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Genomic and transcriptomic heterogeneity in metaplastic carcinomas of the breast
Piscuoglio, Salvatore, Ng, Charlotte K. Y., Geyer, Felipe C., Burke, Kathleen A., Cowell, Catherine F., Martelotto, Luciano G., Natrajan, Rachael, Popova, Tatiana, Maher, Christopher A., Lim, Raymond S., Bruijn, Ino de, Mariani, Odette, Norton, Larry, Vincent-Salomon, Anne, Weigelt, Britta, Reis-Filho, Jorge S.
Published in NPJ breast cancer (01.12.2017)
Published in NPJ breast cancer (01.12.2017)
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Binning metagenomic contigs by coverage and composition
Alneberg, Johannes, Bjarnason, Brynjar Smári, de Bruijn, Ino, Schirmer, Melanie, Quick, Joshua, Ijaz, Umer Z, Lahti, Leo, Loman, Nicholas J, Andersson, Anders F, Quince, Christopher
Published in Nature methods (01.11.2014)
Published in Nature methods (01.11.2014)
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High-intensity sequencing reveals the sources of plasma circulating cell-free DNA variants
Razavi, Pedram, Li, Bob T., Brown, David N., Jung, Byoungsok, Hubbell, Earl, Shen, Ronglai, Abida, Wassim, Juluru, Krishna, De Bruijn, Ino, Hou, Chenlu, Venn, Oliver, Lim, Raymond, Anand, Aseem, Maddala, Tara, Gnerre, Sante, Vijaya Satya, Ravi, Liu, Qinwen, Shen, Ling, Eattock, Nicholas, Yue, Jeanne, Blocker, Alexander W., Lee, Mark, Sehnert, Amy, Xu, Hui, Hall, Megan P., Santiago-Zayas, Angie, Novotny, William F., Isbell, James M., Rusch, Valerie W., Plitas, George, Heerdt, Alexandra S., Ladanyi, Marc, Hyman, David M., Jones, David R., Morrow, Monica, Riely, Gregory J., Scher, Howard I., Rudin, Charles M., Robson, Mark E., Diaz, Luis A., Solit, David B., Aravanis, Alexander M., Reis-Filho, Jorge S.
Published in Nature medicine (01.12.2019)
Published in Nature medicine (01.12.2019)
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Reconstructing a hydrogen-driven microbial metabolic network in Opalinus Clay rock
Bagnoud, Alexandre, Chourey, Karuna, Hettich, Robert L., de Bruijn, Ino, Andersson, Anders F., Leupin, Olivier X., Schwyn, Bernhard, Bernier-Latmani, Rizlan
Published in Nature communications (14.10.2016)
Published in Nature communications (14.10.2016)
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Genetic Heterogeneity in Therapy-Naïve Synchronous Primary Breast Cancers and Their Metastases
Ng, Charlotte K Y, Bidard, Francois-Clement, Piscuoglio, Salvatore, Geyer, Felipe C, Lim, Raymond S, de Bruijn, Ino, Shen, Ronglai, Pareja, Fresia, Berman, Samuel H, Wang, Lu, Pierga, Jean-Yves, Vincent-Salomon, Anne, Viale, Agnes, Norton, Larry, Sigal, Brigitte, Weigelt, Britta, Cottu, Paul, Reis-Filho, Jorge S
Published in Clinical cancer research (01.08.2017)
Published in Clinical cancer research (01.08.2017)
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Massively parallel sequencing of phyllodes tumours of the breast reveals actionable mutations, and TERT promoter hotspot mutations and TERT gene amplification as likely drivers of progression
Piscuoglio, Salvatore, Ng, Charlotte KY, Murray, Melissa, Burke, Kathleen A, Edelweiss, Marcia, Geyer, Felipe C, Macedo, Gabriel S, Inagaki, Akiko, Papanastasiou, Anastasios D, Martelotto, Luciano G, Marchio, Caterina, Lim, Raymond S, Ioris, Rafael A, Nahar, Pooja K, Bruijn, Ino De, Smyth, Lillian, Akram, Muzaffar, Ross, Dara, Petrini, John H, Norton, Larry, Solit, David B, Baselga, Jose, Brogi, Edi, Ladanyi, Marc, Weigelt, Britta, Reis-Filho, Jorge S
Published in The Journal of pathology (01.03.2016)
Published in The Journal of pathology (01.03.2016)
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Uterine adenosarcomas are mesenchymal neoplasms
Piscuoglio, Salvatore, Burke, Kathleen A, Ng, Charlotte KY, Papanastasiou, Anastasios D, Geyer, Felipe C, Macedo, Gabriel S, Martelotto, Luciano G, de Bruijn, Ino, De Filippo, Maria R, Schultheis, Anne M, Ioris, Rafael A, Levine, Douglas A, Soslow, Robert A, Rubin, Brian P, Reis-Filho, Jorge S, Weigelt, Britta
Published in The Journal of pathology (01.02.2016)
Published in The Journal of pathology (01.02.2016)
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Multiomic Integration of Public Oncology Databases in Bioconductor
Ramos, Marcel, Geistlinger, Ludwig, Oh, Sehyun, Schiffer, Lucas, Azhar, Rimsha, Kodali, Hanish, de Bruijn, Ino, Gao, Jianjiong, Carey, Vincent J, Morgan, Martin, Waldron, Levi
Published in JCO clinical cancer informatics (01.11.2020)
Published in JCO clinical cancer informatics (01.11.2020)
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Genomic characterization of small cell carcinomas of the uterine cervix
Schultheis, Anne M., Bruijn, Ino, Selenica, Pier, Macedo, Gabriel S., Silva, Edaise M., Piscuoglio, Salvatore, Jungbluth, Achim A., Park, Kay J., Klimstra, David S., Wardelmann, Eva, Hartmann, Wolfgang, Gerharz, Claus Dieter, Petersdorff, Mareike, Buettner, Reinhard, Reis‐Filho, Jorge S., Weigelt, Britta
Published in Molecular oncology (01.02.2022)
Published in Molecular oncology (01.02.2022)
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Author Correction: The evolution of RET inhibitor resistance in RET-driven lung and thyroid cancers
Rosen, Ezra Y., Won, Helen H., Zheng, Youyun, Cocco, Emiliano, Selcuklu, Duygu, Gong, Yixiao, Friedman, Noah D., de Bruijn, Ino, Sumer, Onur, Bielski, Craig M., Savin, Casey, Bourque, Caitlin, Falcon, Christina, Clarke, Nikeysha, Jing, Xiaohong, Meng, Fanli, Zimel, Catherine, Shifman, Sophie, Kittane, Srushti, Wu, Fan, Ladanyi, Marc, Ebata, Kevin, Kherani, Jennifer, Brandhuber, Barbara J., Fagin, James, Sherman, Eric J., Rekhtman, Natasha, Berger, Michael F., Scaltriti, Maurizio, Hyman, David M., Taylor, Barry S., Drilon, Alexander
Published in Nature communications (05.04.2022)
Published in Nature communications (05.04.2022)
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Abstract 5277: The cBioPortal for cancer genomics and its application in precision oncology
Gao, Jianjiong, Lindsay, James, Watt, Stuart, Bahceci, Istemi, Lukasse, Pieter, Abeshouse, Adam, Chen, Hsiao-Wei, de Bruijn, Ino, Gross, Benjamin, Li, Dong, Kundra, Ritika, Heins, Zachary, Reis-Filho, Jorge, Sumer, Onur, Sun, Yichao, Wang, Jiaojiao, Wang, Qingguo, Zhang, Hongxin, Kumari, Priti, Sahin, M. Furkan, de Ridder, Sander, Schaeffer, Fedde, van Bochove, Kees, Dogrusoz, Ugur, Pugh, Trevor, Sander, Chris, Cerami, Ethan, Schultz, Nikolaus
Published in Cancer research (Chicago, Ill.) (15.07.2016)
Published in Cancer research (Chicago, Ill.) (15.07.2016)
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Integration and Analysis of CPTAC Proteomics Data in the Context of Cancer Genomics in the cBioPortal[S]
Wu, Pamela, Heins, Zachary J., Muller, James T., Katsnelson, Lizabeth, de Bruijn, Ino, Abeshouse, Adam A., Schultz, Nikolaus, Fenyö, David, Gao, Jianjiong
Published in Molecular & cellular proteomics (01.09.2019)
Published in Molecular & cellular proteomics (01.09.2019)
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The Immune Landscape of Cancer
Bortone, Dante S., Eddy, James A., Liu, Yuexin, Weinstein, John N., Holt, Robert A., Zenklusen, Jean C., Cho, Juok, Reynolds, Sheila, Liu, Wenbin, Ryan, Michael, Chakravarty, Debyani, Schultz, Nikolaus, Stuart, Joshua M., Wilkerson, Matthew D., Balasundaram, Miruna, Carlsen, Rebecca, Chuah, Eric, Holt, Robert, Lee, Darlene, Ha, Gavin, Schumacher, Steven E., Cope, Leslie, Balu, Saianand, Shi, Yan, Hinoue, Toshinori, Glenn, Robert, Miller, Christopher A., Curley, Erin, Mallery, David, Morris, Scott, Longatto-Filho, Adhemar, Reis, Rui M., Scapulatempo-Neto, Cristovam, Singh, Rosy, Le, Xuan, Thorp, Richard, Setdikova, Galiya, Shabunin, Alexey, Barrett, Wendi, Ostrom, Quinn T., Karlan, Beth Y., Hu, Hai, Latour, Mathieu, Lacombe, Louis, Su, Tao, Signoretti, Sabina, Marks, Jeffrey, Olson, Jeffrey J., Sica, Gabriel, Stoop, Hans, Pollo, Bianca, Aymerich, Marta, Stepa, Serghei, Moser, Catherine, Roberts, Lewis, Czerniak, Bogdan, Lazar, Alexander J., Jakrot, Valerie, Scolyer, Richard, Thompson, John, Wilmott, James, Reuter, Victor, Tien, Nguyen Viet, Park, Joong-Won, Pinto, Peter A., Moncrieff, Marc, Botnariuc, Natalia, Pirtac, Maria, Parfitt, Jeremy, Bifulco, Carlo, Antenucci, Anna, Grazi, Gianluca, Marino, Mirella, Chevalier, Simone, McKercher, Ginette, Naska, Theresa, Borgia, Jeffrey A., Pool, Mark, Junker, Kerstin, Moiseenko, Fedor, Hilty, Joe, Pilarski, Robert, Porten, Sima, Asa, Sylvia L., Schadendorf, Dirk, Disaia, Philip, Kelley, Robin K., Sifri, Suzanne, Mannelli, Massimo, Knutson, Tina, Sigmund, Rita, Postier, Russel, Walker, Joan, Feldman, Michael, Luketich, James, Rozek, Laura, Fong, Kwun M., Hooke, Jeffrey A., Govindan, Ramaswamy, Aredes, Natália D.
Published in Immunity (Cambridge, Mass.) (17.04.2018)
Published in Immunity (Cambridge, Mass.) (17.04.2018)
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An Integrated TCGA Pan-Cancer Clinical Data Resource to Drive High-Quality Survival Outcome Analytics
Omberg, Larsson, Wolf, Denise M., Sofia, Heidi J., Chudamani, Sudha, Lolla, Laxmi, Pihl, Todd, Lin, Pei, Chambwe, Nyasha, Kramer, Roger, Thorsson, Vesteinn, Wang, Jing, Armenia, Joshua, Chatila, Walid K., de Bruijn, Ino, Gross, Benjamin E., Brooks, Denise, Tam, Angela, Tse, Kane, Meng, Shaowu, Korchina, Viktoriya, Cordes, Matthew G., McLellan, Michael D., Miller, Christopher A., Shelton, Candace, Yena, Peggy, Wise, Lisa, Costello, Tony, Hovens, Christopher, Silveira, Henrique C.S., Singh, Rosy, Anderson, Matthew L., Duffy, Elizabeth R., Tavobilov, Mikhail, Cramer, Daniel, Horowitz, Neil, Fulop, Jordonna, Wolinsky, Yingli, Sloan, Andrew E., Mural, Richard J., Latour, Mathieu, Lacombe, Louis, Wang, Timothy, Magliocca, Kelly, Pickens, Alan, Shin, Dong M., Van Meir, Erwin G., Zhang, Hongzheng, Cuzzubbo, Stefania, Hartmann, Arndt, Stoehr, Christine, Wach, Sven, Kycler, Witold, Chung, Ki, Martin, Julie, De Rienzo, Assunta, Richards, William G., Kalkanis, Steven, Gabra, Hani, Ahn, Keunsoo, Farnell, Michael, Patel, Tushar, Smallridge, Robert, Rice, David, Troncoso, Patricia, Mann, Graham, Levine, Douglas A., Singer, Samuel, Linehan, W. Marston, Melamed, Jonathan, Parfitt, Jeremy, Sekhon, Harman, Thomas, George, Bifulco, Carlo, Hayward, Nicholas, Grazi, Gianluca, de Krijger, Ronald, Birsoy, Kivanc, Brewer, Cathy, Williams, Felicia, Pool, Mark, Dinkin, Mikhail, Schoenfield, Lynn, Hansen, Paul, Asa, Sylvia L., Glenn, Pat, Jungk, Christin, Ma, Deqin, Milhem, Mohammed, Madan, Rashna, Mannel, Robert, Dos Santos, Jose Sebastião, Moyer, Jeffey, Rozek, Laura, Yang, Ian, Korst, Robert, Rathmell, W. Kimryn, Drake, Bettina, Westervelt, Peter, Lee, Jung Il, Hu, Hai
Published in Cell (05.04.2018)
Published in Cell (05.04.2018)
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Oncogenic Signaling Pathways in The Cancer Genome Atlas
Chatila, Walid K., Luna, Augustin, Kantheti, Havish S., Daian, Foysal, Shmulevich, Ilya, Greene, Casey S., Iavarone, Antonio, Tward, Aaron D., Meyerson, Matthew, Sofia, Heidi J., Zenklusen, Jean C., Pihl, Todd, Meier, Sam, Noble, Michael S., Kramer, Roger, Hegde, Apurva M., Li, Jun, Rao, Arvind, Abeshouse, Adam, Schultz, Nikolaus, Taylor, Barry S., Stuart, Joshua M., Wong, Christopher K., Parker, Joel S., Carlsen, Rebecca, Tam, Angela, Gabriel, Stacey B., Ha, Gavin, Schumacher, Steven E., Maglinte, Dennis T., Balu, Saianand, Skelly, Tara, Laird, Peter W., Lewis, Lora, Muzny, Donna, Santibanez, Jireh, Wang, Min, Morris, Scott, Shelton, Candace, Gerken, Mark, Costello, Tony, Reis, Rui M., Scapulatempo-Neto, Cristovam, Singh, Rosy, Duffy, Elizabeth R., Setdikova, Galiya, Devine, Karen, Ostrom, Quinn T., Deyarmin, Brenda, Kvecher, Leonid, Mural, Richard J., Latour, Mathieu, Lacombe, Louis, Lipp, Eric, Marks, Jeffrey, Pickens, Alan, Shin, Dong M., Zhang, Hongzheng, Calatozzolo, Chiara, Cuzzubbo, Stefania, Kycler, Witold, Giné, Eva, Beuschlein, Felix, Borad, Mitesh, Chandan, Vishal, Farnell, Michael, Torbenson, Michael, Logothetis, Christopher, Rice, David, Jakrot, Valerie, Mann, Graham, Moncrieff, Marc, Doruc, Serghei, Bartlett, John, Parfitt, Jeremy, Bifulco, Carlo, Hayward, Nicholas, Grazi, Gianluca, Marino, Mirella, Naska, Theresa, Borgia, Jeffrey A., Pool, Mark, Gaudio, Eugenio, Bell, Sue, Hilty, Joe, Sexton, Katherine C., Asa, Sylvia L., Schlomm, Thorsten, Prados, Michael, Smith-McCune, Karen, Bossler, Aaron, Moxley, Katherine, Carlotti, Carlos Gilberto, Swisher, Elizabeth, Korst, Robert, Rathmell, W. Kimryn, Heath, Sharon, Aredes, Natália D., Mariamidze, Armaz, Van Allen, Eliezer M.
Published in Cell (05.04.2018)
Published in Cell (05.04.2018)
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Cell-of-Origin Patterns Dominate the Molecular Classification of 10,000 Tumors from 33 Types of Cancer
Wolf, Denise M., Cherniack, Andrew D., Sanchez-Vega, Francisco, Sun, Qiang, Wu, Ye, Gehlenborg, Nils, Zhang, Hailei, Akbani, Rehan, Ling, Shiyun, Rao, Arvind, Phillips, Sarah M., Sun, Yichao, Benz, Christopher, Dhalla, Noreen, Robertson, A. Gordon, Sipahimalani, Payal, Wong, Tina, Weisenberger, Daniel J., Bodenheimer, Tom, Roach, Jeffrey, Simons, Janae V., Fan, Huihui, Zhou, Wanding, Dinh, Huyen, Doddapaneni, HarshaVardhan, Han, Yi, Lee, Sandra, Liu, Xiuping, Hess, Julian, Ding, Li, Fulton, Lucinda A., Shelton, Troy, Zmuda, Erik, de Carvalho, Ana C., Vidal, Daniel O., Eschbacher, Jennifer, Hermes, Beth, Noss, Ardene, Shabunin, Alexey, Eckman, John, Bennett, Joseph, Rabeno, Brenda, Swanson, Patricia, Bergeron, Alain, Staugaitis, Susan M., Chabot, John, McCall, Shannon, Behera, Madhusmita, Brat, Daniel J., Force, Seth, Eijckenboom, Wil, Zwarthoff, Ellen C., Cuppini, Lucia, Murawa, Dawid, Mikkelsen, Tom, Hanh, Phan Thi, Phu, Bui Duc, Tang, Yufang, Colman, Howard, Birrer, Michael, Ho, Thai, Nagorney, David, Meric-Bernstam, Funda, Moran, Cesar, Hersey, Peter, Synott, Maria, Mirsaidi, Cyrus, Metwalli, Adam R., Vocke, Cathy D., Goparaju, Chandra, Cernat, Mircea, Gilbert, Sebastien, Timmers, Henri, Schilero, Cathy, Manikhas, George, Chesla, David, Janssen, Klaus-Peter, Slotta-Huspenina, Julia, Davis, Amy, Elder, J. Bradley, Lehman, Norman L., Mandt, Randy, Wakely, Paul, Powers, James, Carroll, Peter R., Chan, June M., Roggin, Kevin, Fehrenbach, Ashley, Galbraith, Joseph, Knudson, Michael, Saad, Fred, Bocklage, Therese, Zuna, Rosemary, Feldman, Michael, Quintero-Aguilo, Mario, Tirapelli, Daniela, Creaney, Jenette, Shelley, Carl Simon, Bradford, Carol, Prince, Mark
Published in Cell (05.04.2018)
Published in Cell (05.04.2018)
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Machine Learning Identifies Stemness Features Associated with Oncogenic Dedifferentiation
Malta, Tathiane M., Gentles, Andrew J., Weinstein, John N., Czerwińska, Patrycja, Heyn, Holger, Godwin, Andrew K., Zhang, Jiashan (Julia), Wu, Ye, Liu, Yuexin, Reynolds, Sheila, Akbani, Rehan, Kanchi, Rupa S., Ladanyi, Marc, Peto, Myron, Bowlby, Reanne, Schein, Jacqueline E., Sipahimalani, Payal, Thiessen, Nina, Cope, Leslie, Weisenberger, Daniel J., Hoyle, Alan P., Mieczkowski, Piotr A., Shi, Yan, Veluvolu, Umadevi, Zhou, Wanding, Bellair, Michelle, Creighton, Chad J., Gibbs, Richard A., Li, Wei, Xi, Liu, Zhao, Fengmei, Mardis, Elaine R., Paulauskis, Joseph, Eschbacher, Jennifer, Ittmann, Michael, Le, Xuan, Thorp, Richard, Lyadov, Vladimir, Setdikova, Galiya, Raut, Chandrajit P., Barrett, Wendi, Karlan, Beth Y., Hu, Hai, Bennett, Joseph, Chabot, John, Hibshoosh, Hanina, Potapova, Olga, Voronina, Olga, Berchuck, Andrew, McCall, Shannon, Olson, Jeffrey J., Ramalingam, Suresh, Stoop, Hans, Guillermo, Armando López, Castle, Erik, Kopp, Karla, Roberts, Lewis, Stanton, Melissa, Yang, Ju Dong, Broaddus, Russell, Guo, Charles, Moran, Cesar, Tamboli, Pheroze, Thompson, Timothy, Tsao, Anne, Wistuba, Ignacio, Haydu, Lauren, Saw, Robyn, Scolyer, Richard, Thompson, John, Reuter, Victor, Drwiega, Paul, Hung, Nguyen Phi, Pass, Harvey, Gorincioi, Ghenadie, Gilbert, Sebastien, Tamakawa, Raina, Chevalier, Simone, Morrison, Carl, Borgia, Jeffrey A., Junker, Kerstin, Bragazzi, Maria Consiglia, Moiseenko, Fedor, Duell, Rebecca, Pilarski, Robert, Senecal, Kelly, Henderson, Joel, Schadendorf, Dirk, Olabode, Oluwole, Nelson, Mark, Roggin, Kevin, Carey, Francis, Carney, Michael, Hernandez, Brenda, Walker, Joan, Valdivieso, Federico, Luketich, James, Tirapelli, Daniela, Catto, James, Kovatich, Albert J.
Published in Cell (05.04.2018)
Published in Cell (05.04.2018)
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