Cloud-based uniform ChIP-Seq processing tools for modENCODE and ENCODE

por 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
Publicado 2013

The modENCODE Data Coordination Center: lessons in harvesting comprehensive experimental details

por 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.
Publicado 2011

modMine: flexible access to modENCODE data

por 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
Publicado 2012

Framework for quality assessment of whole genome cancer sequences

por 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.
Publicado 2020

ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia

por 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
Publicado 2012

Genomic basis for RNA alterations in cancer

por Calabrese, Claudia, Davidson, Natalie R., Demircioğlu, Deniz, Fonseca, Nuno A., He, Yao, Kahles, André, Lehmann, Kjong-Van, Liu, Fenglin, Shiraishi, Yuichi, Soulette, Cameron M., Urban, Lara, Greger, Liliana, Li, Siliang, Liu, Dongbing, Perry, Marc D., Xiang, Qian, Zhang, Fan, Zhang, Junjun, Bailey, Peter, Erkek, Serap, Hoadley, Katherine A., Hou, Yong, Huska, Matthew R., Kilpinen, Helena, Korbel, Jan O., Marin, Maximillian G., Markowski, Julia, Nandi, Tannistha, Pan-Hammarström, Qiang, Pedamallu, Chandra Sekhar, Siebert, Reiner, Stark, Stefan G., Su, Hong, Tan, Patrick, Waszak, Sebastian M., Yung, Christina, Zhu, Shida, Awadalla, Philip, Creighton, Chad J., Meyerson, Matthew, Ouellette, B. F. Francis, Wu, Kui, Yang, Huanming, Brazma, Alvis, Brooks, Angela N., Göke, Jonathan, Rätsch, Gunnar, Schwarz, Roland F., Stegle, Oliver, Zhang, Zemin
Publicado 2020

Author Correction: Genomic basis for RNA alterations in cancer

por Calabrese, Claudia, Davidson, Natalie R., Demircioğlu, Deniz, Fonseca, Nuno A., He, Yao, Kahles, André, Lehmann, Kjong-Van, Liu, Fenglin, Shiraishi, Yuichi, Soulette, Cameron M., Urban, Lara, Greger, Liliana, Li, Siliang, Liu, Dongbing, Perry, Marc D., Xiang, Qian, Zhang, Fan, Zhang, Junjun, Bailey, Peter, Erkek, Serap, Hoadley, Katherine A., Hou, Yong, Huska, Matthew R., Kilpinen, Helena, Korbel, Jan O., Marin, Maximillian G., Markowski, Julia, Nandi, Tannistha, Pan-Hammarström, Qiang, Pedamallu, Chandra Sekhar, Siebert, Reiner, Stark, Stefan G., Su, Hong, Tan, Patrick, Waszak, Sebastian M., Yung, Christina, Zhu, Shida, Awadalla, Philip, Creighton, Chad J., Meyerson, Matthew, Ouellette, B. F. Francis, Wu, Kui, Yang, Huanming, Brazma, Alvis, Brooks, Angela N., Göke, Jonathan, Rätsch, Gunnar, Schwarz, Roland F., Stegle, Oliver, Zhang, Zemin
Publicado 2023

The 5-Hydroxymethylcytosine Landscape of Prostate Cancer

por Sjöström, 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.
Publicado 2022