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1.

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.

Cell ; 174(3): 758-769.e9, 2018 07 26.

Artículo en Inglés | MEDLINE | ID: mdl-30033370

2.

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.

Cell ; 175(3): 889, 2018 10 18.

Artículo en Inglés | MEDLINE | ID: mdl-30340047

3.

Genomic basis for RNA alterations in cancer.

Calabrese, Claudia; Davidson, Natalie R; Demircioglu, 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.

Nature ; 578(7793): 129-136, 2020 02.

Artículo en Inglés | MEDLINE | ID: mdl-32025019

4.

Author Correction: Genomic basis for RNA alterations in cancer.

Calabrese, Claudia; Davidson, Natalie R; Demircioglu, 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.

Nature ; 614(7948): E37, 2023 Feb.

Artículo en Inglés | MEDLINE | ID: mdl-36697831

5.

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.

Genome Res ; 22(9): 1813-31, 2012 Sep.

Artículo en Inglés | MEDLINE | ID: mdl-22955991

6.

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.

Nucleic Acids Res ; 40(Database issue): D1082-8, 2012 Jan.

Artículo en Inglés | MEDLINE | ID: mdl-22080565

7.

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.

Virus Evol ; 10(1): vead085, 2024.

Artículo en Inglés | MEDLINE | ID: mdl-38361813

8.

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.

BMC Genomics ; 14: 494, 2013 Jul 22.

Artículo en Inglés | MEDLINE | ID: mdl-23875683

9.

The 5-Hydroxymethylcytosine Landscape of Prostate Cancer.

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.

Cancer Res ; 82(21): 3888-3902, 2022 11 02.

Artículo en Inglés | MEDLINE | ID: mdl-36251389

10.

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.

JAMA Oncol ; 7(11): 1644-1652, 2021 Nov 01.

Artículo en Inglés | MEDLINE | ID: mdl-34554200

11.

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.

Nat Commun ; 11(1): 5040, 2020 10 07.

Artículo en Inglés | MEDLINE | ID: mdl-33028839

12.

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.

Nat Genet ; 52(8): 778-789, 2020 08.

Artículo en Inglés | MEDLINE | ID: mdl-32661416

13.

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.

Database (Oxford) ; 2011: bar023, 2011.

Artículo en Inglés | MEDLINE | ID: mdl-21856757

14.

Extragenic suppressors of a dominant masculinizing her-1 mutation in C. elegans identify two new genes that affect sex determination in different ways.

Manser, James; Wood, William B; Perry, Marc D.

Genesis ; 34(3): 184-95, 2002 Nov.

Artículo en Inglés | MEDLINE | ID: mdl-12395383

15.

Principles of biochemistry

Horton, H. Robert; Moran, Laurence A; Scrimgeour, K. Gray; Perry, Marc D; Rawn, J. David.

New Jersey; Pearson; 4. ed; 2006. 852 p.

Monografía en Inglés | LILACS, Coleciona SUS (Brasil) | ID: biblio-940920

16.

Principles of biochemistry

Horton, H. Robert; Moran, Laurence A; Scrimgeour, K. Gray; Perry, Marc D; Rawn, J. David.

New Jersey; Pearson; 4. ed; 2006. 852 p.

Monografía en Inglés | CPQRR, FIOCRUZ | ID: crr-2387

17.

Principles of biochemistry

Horton, H. Robert; Moran, Laurence A; Scrimgeour, K. Gray; Perry, Marc D; Rawn, J. David.

New Jersey; Pearson; 4. ed; 2006. 852 p.

Monografía en Inglés | LILACS | ID: lil-760555

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Genomic Hallmarks and Structural Variation in Metastatic Prostate Cancer.

Genomic Hallmarks and Structural Variation in Metastatic Prostate Cancer.

Genomic basis for RNA alterations in cancer.

Author Correction: Genomic basis for RNA alterations in cancer.

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

modMine: flexible access to modENCODE data.

SARS-CoV-2 lineage assignments using phylogenetic placement/UShER are superior to pangoLEARN machine-learning method.

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

The 5-Hydroxymethylcytosine Landscape of Prostate Cancer.

Prognosis Associated With Luminal and Basal Subtypes of Metastatic Prostate Cancer.

Framework for quality assessment of whole genome cancer sequences.

The DNA methylation landscape of advanced prostate cancer.

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

Extragenic suppressors of a dominant masculinizing her-1 mutation in C. elegans identify two new genes that affect sex determination in different ways.

Principles of biochemistry

Principles of biochemistry

Principles of biochemistry