Framework for quality assessment of whole genome cancer sequences
Whalley, Justin P., Buchhalter, Ivo, Rheinbay, Esther, Raine, Keiran M., Stobbe, Miranda D., Kleinheinz, Kortine, Werner, Johannes, Beltran, Sergi, Gut, Marta, Hübschmann, Daniel, Hutter, Barbara, Livitz, Dimitri, Perry, Marc D., Rosenberg, Mara, Saksena, Gordon, Trotta, Jean-Rémi, Eils, Roland, Gerhard, Daniela S., Campbell, Peter J., Schlesner, Matthias, Gut, Ivo G.
Published in Nature communications (07.10.2020)
Published in Nature communications (07.10.2020)
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Genomic Hallmarks and Structural Variation in Metastatic Prostate Cancer
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Published in Cell (26.07.2018)
Published in Cell (26.07.2018)
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The DNA methylation landscape of advanced prostate cancer
Zhao, Shuang G., Chen, William S., Li, Haolong, Foye, Adam, Zhang, Meng, Sjöström, Martin, Aggarwal, Rahul, Playdle, Denise, Liao, Arnold, Alumkal, Joshi J., Das, Rajdeep, Chou, Jonathan, Hua, Junjie T., Barnard, Travis J., Bailey, Adina M., Chow, Eric D., Perry, Marc D., Dang, Ha X., Yang, Rendong, Moussavi-Baygi, Ruhollah, Zhang, Li, Alshalalfa, Mohammed, Laura Chang, S., Houlahan, Kathleen E., Shiah, Yu-Jia, Beer, Tomasz M., Thomas, George, Chi, Kim N., Gleave, Martin, Zoubeidi, Amina, Reiter, Robert E., Rettig, Matthew B., Witte, Owen, Yvonne Kim, M., Fong, Lawrence, Spratt, Daniel E., Morgan, Todd M., Bose, Rohit, Huang, Franklin W., Li, Hui, Chesner, Lisa, Shenoy, Tanushree, Goodarzi, Hani, Asangani, Irfan A., Sandhu, Shahneen, Lang, Joshua M., Mahajan, Nupam P., Lara, Primo N., Evans, Christopher P., Febbo, Phillip, Batzoglou, Serafim, Knudsen, Karen E., He, Housheng H., Huang, Jiaoti, Zwart, Wilbert, Costello, Joseph F., Luo, Jianhua, Tomlins, Scott A., Wyatt, Alexander W., Dehm, Scott M., Ashworth, Alan, Gilbert, Luke A., Boutros, Paul C., Farh, Kyle, Chinnaiyan, Arul M., Maher, Christopher A., Small, Eric J., Quigley, David A., Feng, Felix Y.
Published in Nature genetics (01.08.2020)
Published in Nature genetics (01.08.2020)
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ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia
Landt, Stephen G, Marinov, Georgi K, Kundaje, Anshul, Kheradpour, Pouya, Pauli, Florencia, Batzoglou, Serafim, Bernstein, Bradley E, Bickel, Peter, Brown, James B, Cayting, Philip, Chen, Yiwen, DeSalvo, Gilberto, Epstein, Charles, Fisher-Aylor, Katherine I, Euskirchen, Ghia, Gerstein, Mark, Gertz, Jason, Hartemink, Alexander J, Hoffman, Michael M, Iyer, Vishwanath R, Jung, Youngsook L, Karmakar, Subhradip, Kellis, Manolis, Kharchenko, Peter V, Li, Qunhua, Liu, Tao, Liu, X Shirley, Ma, Lijia, Milosavljevic, Aleksandar, Myers, Richard M, Park, Peter J, Pazin, Michael J, Perry, Marc D, Raha, Debasish, Reddy, Timothy E, Rozowsky, Joel, Shoresh, Noam, Sidow, Arend, Slattery, Matthew, Stamatoyannopoulos, John A, Tolstorukov, Michael Y, White, Kevin P, Xi, Simon, Farnham, Peggy J, Lieb, Jason D, Wold, Barbara J, Snyder, Michael
Published in Genome research (01.09.2012)
Published in Genome research (01.09.2012)
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Genomic Hallmarks and Structural Variation in Metastatic Prostate Cancer
Quigley, David A., Dang, Ha X., Zhao, Shuang G., Lloyd, Paul, Aggarwal, Rahul, Alumkal, Joshi J., Foye, Adam, Kothari, Vishal, Perry, Marc D., Bailey, Adina M., Playdle, Denise, Barnard, Travis J., Zhang, Li, Zhang, Jin, Youngren, Jack F., Cieslik, Marcin P., Parolia, Abhijit, Beer, Tomasz M., Thomas, George, Chi, Kim N., Gleave, Martin, Lack, Nathan A., Zoubeidi, Amina, Reiter, Robert E., Rettig, Matthew B., Witte, Owen, Ryan, Charles J., Fong, Lawrence, Kim, Won, Friedlander, Terence, Chou, Jonathan, Li, Haolong, Das, Rajdeep, Li, Hui, Moussavi-Baygi, Ruhollah, Goodarzi, Hani, Gilbert, Luke A., Lara, Primo N., Evans, Christopher P., Goldstein, Theodore C., Stuart, Joshua M., Tomlins, Scott A., Spratt, Daniel E., Cheetham, R. Keira, Cheng, Donavan T., Farh, Kyle, Gehring, Julian S., Hakenberg, Jörg, Liao, Arnold, Febbo, Philip G., Shon, John, Sickler, Brad, Batzoglou, Serafim, Knudsen, Karen E., He, Housheng H., Huang, Jiaoti, Wyatt, Alexander W., Dehm, Scott M., Ashworth, Alan, Chinnaiyan, Arul M., Maher, Christopher A., Small, Eric J., Feng, Felix Y.
Published in Cell (18.10.2018)
Published in Cell (18.10.2018)
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modMine: flexible access to modENCODE data
Contrino, Sergio, Smith, Richard N., Butano, Daniela, Carr, Adrian, Hu, Fengyuan, Lyne, Rachel, Rutherford, Kim, Kalderimis, Alex, Sullivan, Julie, Carbon, Seth, Kephart, Ellen T., Lloyd, Paul, Stinson, E. O., Washington, Nicole L., Perry, Marc D., Ruzanov, Peter, Zha, Zheng, Lewis, Suzanna E., Stein, Lincoln D., Micklem, Gos
Published in Nucleic acids research (01.01.2012)
Published in Nucleic acids research (01.01.2012)
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Prognosis Associated With Luminal and Basal Subtypes of Metastatic Prostate Cancer
Aggarwal, Rahul, Rydzewski, Nicholas R, Zhang, Li, Foye, Adam, Kim, Won, Helzer, Kyle T, Bakhtiar, Hamza, Chang, S Laura, Perry, Marc D, Gleave, Martin, Reiter, Robert E, Huang, Jiaoti, Evans, Christopher P, Alumkal, Joshi J, Lang, Joshua M, Yu, Menggang, Quigley, David A, Sjöström, Martin, Small, Eric J, Feng, Felix Y, Zhao, Shuang G
Published in JAMA oncology (01.11.2021)
Published in JAMA oncology (01.11.2021)
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SARS-CoV-2 lineage assignments using phylogenetic placement/UShER are superior to pangoLEARN machine-learning method
de Bernardi Schneider, Adriano, Su, Michelle, Hinrichs, Angie S, Wang, Jade, Amin, Helly, Bell, John, Wadford, Debra A, O’Toole, Áine, Scher, Emily, Perry, Marc D, Turakhia, Yatish, De Maio, Nicola, Hughes, Scott, Corbett-Detig, Russ
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Published in Virus evolution (2024)
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Cloud-based uniform ChIP-Seq processing tools for modENCODE and ENCODE
Trinh, Quang M, Jen, Fei-Yang Arthur, Zhou, Ziru, Chu, Kar Ming, Perry, Marc D, Kephart, Ellen T, Contrino, Sergio, Ruzanov, Peter, Stein, Lincoln D
Published in BMC genomics (22.07.2013)
Published in BMC genomics (22.07.2013)
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The modENCODE Data Coordination Center: lessons in harvesting comprehensive experimental details
Washington, Nicole L, Stinson, E O, Perry, Marc D, Ruzanov, Peter, Contrino, Sergio, Smith, Richard, Zha, Zheng, Lyne, Rachel, Carr, Adrian, Lloyd, Paul, Kephart, Ellen, McKay, Sheldon J, Micklem, Gos, Stein, Lincoln D, Lewis, Suzanna E
Published in Database : the journal of biological databases and curation (01.01.2011)
Published in Database : the journal of biological databases and curation (01.01.2011)
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Inducible expression of an hsp68-lacZ hybrid gene in transgenic mice
Kothary, R, Clapoff, S, Darling, S, Perry, M D, Moran, L A, Rossant, J
Published in Development (Cambridge) (01.04.1989)
Published in Development (Cambridge) (01.04.1989)
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