Not logged in 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, Aine; Scher, Emily; Perry, Marc D.; Turakhia, Yatish; De Maio, Nicola; Hughes, Scott; Corbett-Detig, Russ Share Save
The 5-Hydroxymethylcytosine Landscape of Prostate Cancer Sjostrom, Martin; Zhao, Shuang G.; Levy, Samuel; Zhang, Meng; Ning, Yuhong; Shrestha, Raunak; Lundberg, Arian; Herberts, Cameron; Foye, Adam; Aggarwal, Rahul; Hua, Junjie T.; Li, Haolong; Bergamaschi, Anna; Maurice-Dror, Corinne; Maheshwari, Ashutosh; Chen, Sujun; Ng, Sarah W. S.; Ye, Wenbin; Petricca, Jessica; Fraser, Michael; Chesner, Lisa; Perry, Marc D.; Moreno-Rodriguez, Thaidy; Chen, William S.; Alumkal, Joshi J.; Chou, Jonathan; Morgans, Alicia K.; Beer, Tomasz M.; Thomas, George, V; Gleave, Martin; Lloyd, Paul; Phillips, Tierney; McCarthy, Erin; Haffner, Michael C.; Zoubeidi, Amina; Annala, Matti; Reiter, Robert E.; Rettig, Matthew B.; Witte, Owen N.; Fong, Lawrence; Bose, Rohit; Huang, Franklin W.; Luo, Jianhua; Bjartell, Anders; Lang, Joshua M.; Mahajan, Nupam P.; Lara, Primo N.; Evans, Christopher P.; Tran, Phuoc T.; Posadas, Edwin M.; He, Chuan; Cui, Xiao-Long; Huang, Jiaoti; Zwart, Wilbert; Gilbert, Luke A.; Maher, Christopher A.; Boutros, Paul C.; Chi, Kim N.; Ashworth, Alan; Small, Eric J.; He, Housheng H.; Wyatt, Alexander W.; Quigley, David A.; Feng, Felix Y. Share Save
Residual ctDNA after treatment predicts early relapse in patients with early-stage non-small cell lung cancer Gale, D.; Heider, K.; Ruiz-Valdepenas, A.; Hackinger, S.; Perry, M.; Marsico, G.; Rundell, V; Wulff, J.; Sharma, G.; Knock, H.; Castedo, J.; Cooper, W.; Zhao, H.; Smith, C. G.; Garg, S.; Anand, S.; Howarth, K.; Gilligan, D.; Harden, S., V; Rassl, D. M.; Rintoul, R. C.; Rosenfeld, N. Share Save
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; Huebschmann, Daniel; Hutter, Barbara; Livitz, Dimitri; Perry, Marc D.; Rosenberg, Mara; Saksena, Gordon; Trotta, Jean-Remi; Eils, Roland; Gerhard, Daniela S.; Campbell, Peter J.; Schlesner, Matthias; Gut, Ivo G. Share Save
Butler enables rapid cloud-based analysis of thousands of human genomes (vol 79, pg 134, 2019) Yakneen, Sergei; Waszak, Sebastian M.; Gertz, Michael; Korbel, Jan O.; Aminou, Brice; Bartolome, Javier; Boroevich, Keith A.; Boyce, Rich; Brooks, Angela N.; Buchanan, Alex; Buchhalter, Ivo; Butler, Adam P.; Byrne, Niall J.; Cafferkey, Andy; Campbell, Peter J.; Chen, Zhaohong; Cho, Sunghoon; Choi, Wan; Clapham, Peter; Davis-Dusenbery, Brandi N.; De La Vega, Francisco M.; Demeulemeester, Jonas; Dow, Michelle T.; Dursi, Lewis Jonathan; Eils, Juergen; Eils, Roland; Ellrott, Kyle; Farcas, Claudiu; Favero, Francesco; Fayzullaev, Nodirjon; Ferretti, Vincent; Flicek, Paul; Fonseca, Nuno A.; Gelpi, Josep Ll.; Getz, Gad; Gibson, Bob; Grossman, Robert L.; Harismendy, Olivier; Heath, Allison P.; Heinold, Michael C.; Hess, Julian M.; Hofmann, Oliver; Hong, Jongwhi H.; Hudson, Thomas J.; Hutter, Barbara; Hutter, Carolyn M.; Hubschmann, Daniel; Imoto, Seiya; Ivkovic, Sinisa; Jeon, Seung-Hyup; Jiao, Wei; Jung, Jongsun; Kabbe, Rolf; Kahles, Andre; Kerssemakers, Jules N. A.; Kim, Hyung-Lae; Kim, Hyunghwan; Kim, Jihoon; Kim, Youngwook; Kleinheinz, Kortine; Koscher, Michael; Koures, Antonios; Kovacevic, Milena; Lawerenz, Chris; Leshchiner, Ignaty; Liu, Jia; Livitz, Dimitri; Mihaiescu, George L.; Mijalkovic, Sanja; Lazic, Ana Mijalkovic; Miyano, Satoru; Miyoshi, Naoki; Nahal-Bose, Hardeep K.; Nakagawa, Hidewaki; Nastic, Mia; Newhouse, Steven J.; Nicholson, Jonathan; O'Connor, Brian D.; Ocana, David; Ohi, Kazuhiro; Ohno-Machado, Lucila; Omberg, Larsson; Ouellette, B. F. Francis; Paramasivam, Nagarajan; Perry, Marc D.; Pihl, Todd D.; Prinz, Manuel; Puiggros, Montserrat; Radovic, Petar; Raine, Keiran M.; Rheinbay, Esther; Rosenberg, Mara; Royo, Romina; Ratsch, Gunnar; Saksena, Gordon; Schlesner, Matthias; Shorser, Solomon I.; Short, Charles; Sofia, Heidi J.; Spring, Jonathan; Stein, Lincoln D.; Struck, Adam J.; Tiao, Grace; Tijanic, Nebojsa; Torrents, David; Van Loo, Peter; Vazquez, Miguel; Vicente, David; Wala, Jeremiah A.; Wang, Zhining; Waszak, Sebastian M.; Weischenfeldt, Joachim; Werner, Johannes; Williams, Ashley; Woo, Youngchoon; Wright, Adam J.; Xiang, Qian; Yang, Liming; Yuen, Denis; Yung, Christina K.; Zhang, Junjun; Korbel, Jan O. Share Save
Butler enables rapid cloud-based analysis of thousands of human genomes Yakneen, Sergei; Waszak, Sebastian M.; Gertz, Michael; Korbel, Jan O.; Aminou, Brice; Bartolome, Javier; Boroevich, Keith A.; Boyce, Rich; Brooks, Angela N.; Buchanan, Alex; Buchhalter, Ivo; Butler, Adam P.; Byrne, Niall J.; Cafferkey, Andy; Campbell, Peter J.; Chen, Zhaohong; Cho, Sunghoon; Choi, Wan; Clapham, Peter; Davis-Dusenbery, Brandi N.; De La Vega, Francisco M.; Demeulemeester, Jonas; Dow, Michelle T.; Dursi, Lewis Jonathan; Eils, Juergen; Eils, Roland; Ellrott, Kyle; Farcas, Claudiu; Favero, Francesco; Fayzullaev, Nodirjon; Ferretti, Vincent; Flicek, Paul; Fonseca, Nuno A.; Gelpi, Josep Ll; Getz, Gad; Gibson, Bob; Grossman, Robert L.; Harismendy, Olivier; Heath, Allison P.; Heinold, Michael C.; Hess, Julian M.; Hofmann, Oliver; Hong, Jongwhi H.; Hudson, Thomas J.; Hutter, Barbara; Hutter, Carolyn M.; Huebschmann, Daniel; Imoto, Seiya; Ivkovic, Sinisa; Jeon, Seung-Hyup; Jiao, Wei; Jung, Jongsun; Kabbe, Rolf; Kahles, Andre; Kerssemakers, Jules N. A.; Kim, Hyung-Lae; Kim, Hyunghwan; Kim, Jihoon; Kim, Youngwook; Kleinheinz, Kortine; Koscher, Michael; Koures, Antonios; Kovacevic, Milena; Lawerenz, Chris; Leshchiner, Ignaty; Liu, Jia; Livitz, Dimitri; Mihaiescu, George L.; Mijalkovic, Sanja; Lazic, Ana Mijalkovic; Miyano, Satoru; Miyoshi, Naoki; Nahal-Bose, Hardeep K.; Nakagawa, Hidewaki; Nastic, Mia; Newhouse, Steven J.; Nicholson, Jonathan; O'Connor, Brian D.; Ocana, David; Ohi, Kazuhiro; Ohno-Machado, Lucila; Omberg, Larsson; Ouellette, B. F. Francis; Paramasivam, Nagarajan; Perry, Marc D.; Pihl, Todd D.; Prinz, Manuel; Puiggros, Montserrat; Radovic, Petar; Raine, Keiran M.; Rheinbay, Esther; Rosenberg, Mara; Royo, Romina; Raetsch, Gunnar; Saksena, Gordon; Schlesner, Matthias; Shorser, Solomon, I; Short, Charles; Sofia, Heidi J.; Spring, Jonathan; Stein, Lincoln D.; Struck, Adam J.; Tiao, Grace; Tijanic, Nebojsa; Torrents, David; Van Loo, Peter; Vazquez, Miguel; Vicente, David; Wala, Jeremiah A.; Wang, Zhining; Weischenfeldt, Joachim; Werner, Johannes; Williams, Ashley; Woo, Youngchoon; Wright, Adam J.; Xiang, Qian; Yang, Liming; Yuen, Denis; Yung, Christina K.; Zhang, Junjun Share Save
Pan-cancer study of recurrent and heterogeneous RNA aberrations and association with whole-genome variants Amin, Samirkumar; Awadalla, Philip; Biankin, Andrew; Boutros, Paul; Brazma, Alvis; Brooks, Angela Norie; Calabrese, Claudia; Chang, David; Chateigner, Aurelien; Chen, Ken; Chong, Zechen; Craft, Brian; Creighton, Chad; Demircioglu, Deniz; Fonseca, Nuno; Frenkel-Morgenstern, Milana; Getz, Gad; Goke, Jonathan; Goldman, Mary; Greger, Liliana; Haider, Syed; He, Yao; Hoadley, Katherine; Ji, Yuan; Kahles, Andre; Khurana, Ekta; Korbel, Jan; Lehmann, Kjong; Liang, Han; Liu, Fenglin; Marin, Maximillian; Meyerson, Matthew; Ojesina, Akinyemi; Ouellette, Francis; Pedamallu, Chandra; Perry, Marc; Ratsch, Gunnar; Schwarz, Roland; Shiraishi, Yuichi; Soulette, Cameron; Stegle, Oliver; Tan, Patrick; Valencia, Alfonso; Xiang, Linda; Yung, Christina; Zhang, Junjun; Zhang, Fan; Zhang, Zemin; Zhu, Jingchun Share Save
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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 Share Save
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 Share Save
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. Share Save
An assessment of histone-modification antibody quality Egelhofer, Thea A.; Minoda, Aki; Klugman, Sarit; Lee, Kyungjoon; Kolasinska-Zwierz, Paulina; Alekseyenko, Artyom A.; Cheung, Ming-Sin; Day, Daniel S.; Gadel, Sarah; Gorchakov, Andrey A.; Gu, Tingting; Kharchenko, Peter V.; Kuan, Samantha; Latorre, Isabel; Linder-Basso, Daniela; Luu, Ying; Ngo, Queminh; Perry, Marc; Rechtsteiner, Andreas; Riddle, Nicole C.; Schwartz, Yuri B.; Shanower, Gregory A.; Vielle, Anne; Ahringer, Julie; Elgin, Sarah C. R.; Kuroda, Mitzi I.; Pirrotta, Vincenzo; Ren, Bing; Strome, Susan; Park, Peter J.; Karpen, Gary H.; Hawkins, R. David; Lieb, Jason D. Share Save
Comparative proteomics profiling of a phospholamban mutant mouse model of dilated cardiomyopathy reveals progressive intracellular stress responses Gramolini, Anthony O.; Kislinger, Thomas; Alikhani-Koopaei, Rasoul; Fong, Vincent; Thompson, Natalie J.; Isserlin, Ruth; Sharma, Parveen; Oudit, Gavin Y.; Trivieri, Maria G.; Fagan, Ailis; Kannan, Anitha; Higgins, Desmond G.; Huedig, Hendrik; Hess, George; Arab, Sara; Seidman, Jonathan G.; Seidman, Christine E.; Frey, Brendan; Perry, Marc; Backx, Peter H.; Liu, Peter P.; MacLennan, David H.; Emili, Andrew Share Save
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