Pesquisa | Biblioteca Virtual em Saúde

1.

KaryoCreate: A CRISPR-based technology to study chromosome-specific aneuploidy by targeting human centromeres.

Bosco, Nazario; Goldberg, Aleah; Zhao, Xin; Mays, Joseph C; Cheng, Pan; Johnson, Adam F; Bianchi, Joy J; Toscani, Cecilia; Di Tommaso, Elena; Katsnelson, Lizabeth; Annuar, Dania; Mei, Sally; Faitelson, Roni E; Pesselev, Ilan Y; Mohamed, Kareem S; Mermerian, Angela; Camacho-Hernandez, Elaine M; Gionco, Courtney A; Manikas, Julie; Tseng, Yi-Shuan; Sun, Zhengxi; Fani, Somayeh; Keegan, Sarah; Lippman, Scott M; Fenyö, David; Giunta, Simona; Santaguida, Stefano; Davoli, Teresa.

Cell ; 186(9): 1985-2001.e19, 2023 04 27.

Artigo em Inglês | MEDLINE | ID: mdl-37075754

2.

Proteogenomic analysis of chemo-refractory high-grade serous ovarian cancer.

Chowdhury, Shrabanti; Kennedy, Jacob J; Ivey, Richard G; Murillo, Oscar D; Hosseini, Noshad; Song, Xiaoyu; Petralia, Francesca; Calinawan, Anna; Savage, Sara R; Berry, Anna B; Reva, Boris; Ozbek, Umut; Krek, Azra; Ma, Weiping; da Veiga Leprevost, Felipe; Ji, Jiayi; Yoo, Seungyeul; Lin, Chenwei; Voytovich, Uliana J; Huang, Yajue; Lee, Sun-Hee; Bergan, Lindsay; Lorentzen, Travis D; Mesri, Mehdi; Rodriguez, Henry; Hoofnagle, Andrew N; Herbert, Zachary T; Nesvizhskii, Alexey I; Zhang, Bing; Whiteaker, Jeffrey R; Fenyo, David; McKerrow, Wilson; Wang, Joshua; Schürer, Stephan C; Stathias, Vasileios; Chen, X Steven; Barcellos-Hoff, Mary Helen; Starr, Timothy K; Winterhoff, Boris J; Nelson, Andrew C; Mok, Samuel C; Kaufmann, Scott H; Drescher, Charles; Cieslik, Marcin; Wang, Pei; Birrer, Michael J; Paulovich, Amanda G.

Cell ; 186(16): 3476-3498.e35, 2023 08 03.

Artigo em Inglês | MEDLINE | ID: mdl-37541199

3.

Pan-cancer proteogenomics connects oncogenic drivers to functional states.

Li, Yize; Porta-Pardo, Eduard; Tokheim, Collin; Bailey, Matthew H; Yaron, Tomer M; Stathias, Vasileios; Geffen, Yifat; Imbach, Kathleen J; Cao, Song; Anand, Shankara; Akiyama, Yo; Liu, Wenke; Wyczalkowski, Matthew A; Song, Yizhe; Storrs, Erik P; Wendl, Michael C; Zhang, Wubing; Sibai, Mustafa; Ruiz-Serra, Victoria; Liang, Wen-Wei; Terekhanova, Nadezhda V; Rodrigues, Fernanda Martins; Clauser, Karl R; Heiman, David I; Zhang, Qing; Aguet, Francois; Calinawan, Anna P; Dhanasekaran, Saravana M; Birger, Chet; Satpathy, Shankha; Zhou, Daniel Cui; Wang, Liang-Bo; Baral, Jessika; Johnson, Jared L; Huntsman, Emily M; Pugliese, Pietro; Colaprico, Antonio; Iavarone, Antonio; Chheda, Milan G; Ricketts, Christopher J; Fenyö, David; Payne, Samuel H; Rodriguez, Henry; Robles, Ana I; Gillette, Michael A; Kumar-Sinha, Chandan; Lazar, Alexander J; Cantley, Lewis C; Getz, Gad; Ding, Li.

Cell ; 186(18): 3921-3944.e25, 2023 08 31.

Artigo em Inglês | MEDLINE | ID: mdl-37582357

4.

Proteogenomic characterization of pancreatic ductal adenocarcinoma.

Cao, Liwei; Huang, Chen; Cui Zhou, Daniel; Hu, Yingwei; Lih, T Mamie; Savage, Sara R; Krug, Karsten; Clark, David J; Schnaubelt, Michael; Chen, Lijun; da Veiga Leprevost, Felipe; Eguez, Rodrigo Vargas; Yang, Weiming; Pan, Jianbo; Wen, Bo; Dou, Yongchao; Jiang, Wen; Liao, Yuxing; Shi, Zhiao; Terekhanova, Nadezhda V; Cao, Song; Lu, Rita Jui-Hsien; Li, Yize; Liu, Ruiyang; Zhu, Houxiang; Ronning, Peter; Wu, Yige; Wyczalkowski, Matthew A; Easwaran, Hariharan; Danilova, Ludmila; Mer, Arvind Singh; Yoo, Seungyeul; Wang, Joshua M; Liu, Wenke; Haibe-Kains, Benjamin; Thiagarajan, Mathangi; Jewell, Scott D; Hostetter, Galen; Newton, Chelsea J; Li, Qing Kay; Roehrl, Michael H; Fenyö, David; Wang, Pei; Nesvizhskii, Alexey I; Mani, D R; Omenn, Gilbert S; Boja, Emily S; Mesri, Mehdi; Robles, Ana I; Rodriguez, Henry.

Cell ; 184(19): 5031-5052.e26, 2021 09 16.

Artigo em Inglês | MEDLINE | ID: mdl-34534465

5.

Proteogenomic Landscape of Breast Cancer Tumorigenesis and Targeted Therapy.

Krug, Karsten; Jaehnig, Eric J; Satpathy, Shankha; Blumenberg, Lili; Karpova, Alla; Anurag, Meenakshi; Miles, George; Mertins, Philipp; Geffen, Yifat; Tang, Lauren C; Heiman, David I; Cao, Song; Maruvka, Yosef E; Lei, Jonathan T; Huang, Chen; Kothadia, Ramani B; Colaprico, Antonio; Birger, Chet; Wang, Jarey; Dou, Yongchao; Wen, Bo; Shi, Zhiao; Liao, Yuxing; Wiznerowicz, Maciej; Wyczalkowski, Matthew A; Chen, Xi Steven; Kennedy, Jacob J; Paulovich, Amanda G; Thiagarajan, Mathangi; Kinsinger, Christopher R; Hiltke, Tara; Boja, Emily S; Mesri, Mehdi; Robles, Ana I; Rodriguez, Henry; Westbrook, Thomas F; Ding, Li; Getz, Gad; Clauser, Karl R; Fenyö, David; Ruggles, Kelly V; Zhang, Bing; Mani, D R; Carr, Steven A; Ellis, Matthew J; Gillette, Michael A.

Cell ; 183(5): 1436-1456.e31, 2020 11 25.

Artigo em Inglês | MEDLINE | ID: mdl-33212010

6.

Proteogenomic analysis of chemo-refractory high-grade serous ovarian cancer.

Chowdhury, Shrabanti; Kennedy, Jacob J; Ivey, Richard G; Murillo, Oscar D; Hosseini, Noshad; Song, Xiaoyu; Petralia, Francesca; Calinawan, Anna; Savage, Sara R; Berry, Anna B; Reva, Boris; Ozbek, Umut; Krek, Azra; Ma, Weiping; da Veiga Leprevost, Felipe; Ji, Jiayi; Yoo, Seungyeul; Lin, Chenwei; Voytovich, Uliana J; Huang, Yajue; Lee, Sun-Hee; Bergan, Lindsay; Lorentzen, Travis D; Mesri, Mehdi; Rodriguez, Henry; Hoofnagle, Andrew N; Herbert, Zachary T; Nesvizhskii, Alexey I; Zhang, Bing; Whiteaker, Jeffrey R; Fenyo, David; McKerrow, Wilson; Wang, Joshua; Schürer, Stephan C; Stathias, Vasileios; Chen, X Steven; Barcellos-Hoff, Mary Helen; Starr, Timothy K; Winterhoff, Boris J; Nelson, Andrew C; Mok, Samuel C; Kaufmann, Scott H; Drescher, Charles; Cieslik, Marcin; Wang, Pei; Birrer, Michael J; Paulovich, Amanda G.

Cell ; 187(4): 1016, 2024 Feb 15.

Artigo em Inglês | MEDLINE | ID: mdl-38364782

7.

CDK-independent role of D-type cyclins in regulating DNA mismatch repair.

Rona, Gergely; Miwatani-Minter, Bearach; Zhang, Qingyue; Goldberg, Hailey V; Kerzhnerman, Marc A; Howard, Jesse B; Simoneschi, Daniele; Lane, Ethan; Hobbs, John W; Sassani, Elizabeth; Wang, Andrew A; Keegan, Sarah; Laverty, Daniel J; Piett, Cortt G; Pongor, Lorinc S; Xu, Miranda Li; Andrade, Joshua; Thomas, Anish; Sicinski, Piotr; Askenazi, Manor; Ueberheide, Beatrix; Fenyö, David; Nagel, Zachary D; Pagano, Michele.

Mol Cell ; 84(7): 1224-1242.e13, 2024 Apr 04.

Artigo em Inglês | MEDLINE | ID: mdl-38458201

8.

Integrated Proteogenomic Characterization of Human High-Grade Serous Ovarian Cancer.

Zhang, Hui; Liu, Tao; Zhang, Zhen; Payne, Samuel H; Zhang, Bai; McDermott, Jason E; Zhou, Jian-Ying; Petyuk, Vladislav A; Chen, Li; Ray, Debjit; Sun, Shisheng; Yang, Feng; Chen, Lijun; Wang, Jing; Shah, Punit; Cha, Seong Won; Aiyetan, Paul; Woo, Sunghee; Tian, Yuan; Gritsenko, Marina A; Clauss, Therese R; Choi, Caitlin; Monroe, Matthew E; Thomas, Stefani; Nie, Song; Wu, Chaochao; Moore, Ronald J; Yu, Kun-Hsing; Tabb, David L; Fenyö, David; Bafna, Vineet; Wang, Yue; Rodriguez, Henry; Boja, Emily S; Hiltke, Tara; Rivers, Robert C; Sokoll, Lori; Zhu, Heng; Shih, Ie-Ming; Cope, Leslie; Pandey, Akhilesh; Zhang, Bing; Snyder, Michael P; Levine, Douglas A; Smith, Richard D; Chan, Daniel W; Rodland, Karin D.

Cell ; 166(3): 755-765, 2016 Jul 28.

Artigo em Inglês | MEDLINE | ID: mdl-27372738

9.

Much ado about zero.

Boeke, Jef D; Fenyo, David.

Cell ; 163(3): 534-5, 2015 Oct 22.

Artigo em Inglês | MEDLINE | ID: mdl-26496595

10.

Dissecting the Structural Dynamics of the Nuclear Pore Complex.

Hakhverdyan, Zhanna; Molloy, Kelly R; Keegan, Sarah; Herricks, Thurston; Lepore, Dante M; Munson, Mary; Subbotin, Roman I; Fenyö, David; Aitchison, John D; Fernandez-Martinez, Javier; Chait, Brian T; Rout, Michael P.

Mol Cell ; 81(1): 153-165.e7, 2021 01 07.

Artigo em Inglês | MEDLINE | ID: mdl-33333016

11.

The role of retrotransposable elements in ageing and age-associated diseases.

Gorbunova, Vera; Seluanov, Andrei; Mita, Paolo; McKerrow, Wilson; Fenyö, David; Boeke, Jef D; Linker, Sara B; Gage, Fred H; Kreiling, Jill A; Petrashen, Anna P; Woodham, Trenton A; Taylor, Jackson R; Helfand, Stephen L; Sedivy, John M.

Nature ; 596(7870): 43-53, 2021 08.

Artigo em Inglês | MEDLINE | ID: mdl-34349292

12.

CRL4^AMBRA1 is a master regulator of D-type cyclins.

Simoneschi, Daniele; Rona, Gergely; Zhou, Nan; Jeong, Yeon-Tae; Jiang, Shaowen; Milletti, Giacomo; Arbini, Arnaldo A; O'Sullivan, Alfie; Wang, Andrew A; Nithikasem, Sorasicha; Keegan, Sarah; Siu, Yik; Cianfanelli, Valentina; Maiani, Emiliano; Nazio, Francesca; Cecconi, Francesco; Boccalatte, Francesco; Fenyö, David; Jones, Drew R; Busino, Luca; Pagano, Michele.

Nature ; 592(7856): 789-793, 2021 04.

Artigo em Inglês | MEDLINE | ID: mdl-33854235

13.

PhosphoDisco: A Toolkit for Co-regulated Phosphorylation Module Discovery in Phosphoproteomic Data.

Schraink, Tobias; Blumenberg, Lili; Hussey, Grant; George, Sabrina; Miller, Brecca; Mathew, Nithu; González-Robles, Tania J; Sviderskiy, Vladislav; Papagiannakopoulos, Thales; Possemato, Richard; Fenyö, David; Ruggles, Kelly V.

Mol Cell Proteomics ; 22(8): 100596, 2023 08.

Artigo em Inglês | MEDLINE | ID: mdl-37394063

14.

LINE-1 retrotransposon expression in cancerous, epithelial and neuronal cells revealed by 5' single-cell RNA-Seq.

McKerrow, Wilson; Kagermazova, Larisa; Doudican, Nicole; Frazzette, Nicholas; Kaparos, Efiyenia Ismini; Evans, Shane A; Rocha, Azucena; Sedivy, John M; Neretti, Nicola; Carucci, John; Boeke, Jef D; Fenyö, David.

Nucleic Acids Res ; 51(5): 2033-2045, 2023 03 21.

Artigo em Inglês | MEDLINE | ID: mdl-36744437

15.

LINE-1 expression in cancer correlates with p53 mutation, copy number alteration, and S phase checkpoint.

McKerrow, Wilson; Wang, Xuya; Mendez-Dorantes, Carlos; Mita, Paolo; Cao, Song; Grivainis, Mark; Ding, Li; LaCava, John; Burns, Kathleen H; Boeke, Jef D; Fenyö, David.

Proc Natl Acad Sci U S A ; 119(8)2022 02 22.

Artigo em Inglês | MEDLINE | ID: mdl-35169076

16.

Staphylococcus aureus induces a muted host response in human blood that blunts the recruitment of neutrophils.

Zwack, Erin E; Chen, Ze; Devlin, Joseph C; Li, Zhi; Zheng, Xuhui; Weinstock, Ada; Lacey, Keenan A; Fisher, Edward A; Fenyö, David; Ruggles, Kelly V; Loke, P'ng; Torres, Victor J.

Proc Natl Acad Sci U S A ; 119(31): e2123017119, 2022 08 02.

Artigo em Inglês | MEDLINE | ID: mdl-35881802

17.

Few-shot genes selection: subset of PAM50 genes for breast cancer subtypes classification.

Okimoto, Leandro Y S; Mendonca-Neto, Rayol; Nakamura, Fabíola G; Nakamura, Eduardo F; Fenyö, David; Silva, Claudio T.

BMC Bioinformatics ; 25(1): 92, 2024 Mar 01.

Artigo em Inglês | MEDLINE | ID: mdl-38429657

18.

Cyclin F-Mediated Degradation of SLBP Limits H2A.X Accumulation and Apoptosis upon Genotoxic Stress in G2.

Dankert, John F; Rona, Gergely; Clijsters, Linda; Geter, Phillip; Skaar, Jeffrey R; Bermudez-Hernandez, Keria; Sassani, Elizabeth; Fenyö, David; Ueberheide, Beatrix; Schneider, Robert; Pagano, Michele.

Mol Cell ; 64(3): 507-519, 2016 11 03.

Artigo em Inglês | MEDLINE | ID: mdl-27773672

19.

Proteogenomics Reveal the Overexpression of HLA-I in Cancer.

Wang, Ying; Fenyö, David.

J Proteome Res ; 22(11): 3625-3639, 2023 11 03.

Artigo em Inglês | MEDLINE | ID: mdl-37857377

20.

Longitudinal gut microbiome analyses and blooms of pathogenic strains during lupus disease flares.

Azzouz, Doua F; Chen, Ze; Izmirly, Peter M; Chen, Lea Ann; Li, Zhi; Zhang, Chongda; Mieles, David; Trujillo, Kate; Heguy, Adriana; Pironti, Alejandro; Putzel, Greg G; Schwudke, Dominik; Fenyo, David; Buyon, Jill P; Alekseyenko, Alexander V; Gisch, Nicolas; Silverman, Gregg J.

Ann Rheum Dis ; 82(10): 1315-1327, 2023 10.

Artigo em Inglês | MEDLINE | ID: mdl-37365013

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KaryoCreate: A CRISPR-based technology to study chromosome-specific aneuploidy by targeting human centromeres.

Proteogenomic analysis of chemo-refractory high-grade serous ovarian cancer.

Pan-cancer proteogenomics connects oncogenic drivers to functional states.

Proteogenomic characterization of pancreatic ductal adenocarcinoma.

Proteogenomic Landscape of Breast Cancer Tumorigenesis and Targeted Therapy.

Proteogenomic analysis of chemo-refractory high-grade serous ovarian cancer.

CDK-independent role of D-type cyclins in regulating DNA mismatch repair.

Integrated Proteogenomic Characterization of Human High-Grade Serous Ovarian Cancer.

Much ado about zero.

Dissecting the Structural Dynamics of the Nuclear Pore Complex.

The role of retrotransposable elements in ageing and age-associated diseases.

CRL4^AMBRA1 is a master regulator of D-type cyclins.

PhosphoDisco: A Toolkit for Co-regulated Phosphorylation Module Discovery in Phosphoproteomic Data.

LINE-1 retrotransposon expression in cancerous, epithelial and neuronal cells revealed by 5' single-cell RNA-Seq.

LINE-1 expression in cancer correlates with p53 mutation, copy number alteration, and S phase checkpoint.

Staphylococcus aureus induces a muted host response in human blood that blunts the recruitment of neutrophils.

Few-shot genes selection: subset of PAM50 genes for breast cancer subtypes classification.

Cyclin F-Mediated Degradation of SLBP Limits H2A.X Accumulation and Apoptosis upon Genotoxic Stress in G2.

Proteogenomics Reveal the Overexpression of HLA-I in Cancer.

Longitudinal gut microbiome analyses and blooms of pathogenic strains during lupus disease flares.