Browsing by Author "Calderwood, Michael"

Now showing items 1-10 of 10

    • The EBNA3 Family of Epstein-Barr Virus Nuclear Proteins Associates with the USP46/USP12 Deubiquitination Complexes to Regulate Lymphoblastoid Cell Line Growth 

      Ohashi, Makoto; Holthaus, Amy M.; Calderwood, Michael A.; Lai, Chiou-Yan; Krastins, Bryan; Sarracino, David; Johannsen, Eric (Public Library of Science, 2015)
      The Epstein-Barr virus (EBV) nuclear proteins EBNA3A, EBNA3B, and EBNA3C interact with the cell DNA binding protein RBPJ and regulate cell and viral genes. Repression of the CDKN2A tumor suppressor gene products p16INK4A ...

    • Identification of FAM111A as an SV40 Host Range Restriction and Adenovirus Helper Factor 

      Fine, Debrah A.; Rozenblatt-Rosen, Orit; Padi, Megha; Korkhin, Anna; James, Robert L.; Adelmant, Guillaume; Yoon, Rosa; Guo, Luxuan; Berrios, Christian Jose; Zhang, Ying; Calderwood, Michael A.; Velmurgan, Soundarapandian; Cheng, Jingwei; Marto, Jarrod; Hill, David E.; Cusick, Michael; Vidal, Marc; Florens, Laurence; Washburn, Michael P.; Litovchick, Larisa; DeCaprio, James A. (Public Library of Science, 2012)
      The small genome of polyomaviruses encodes a limited number of proteins that are highly dependent on interactions with host cell proteins for efficient viral replication. The SV40 large T antigen (LT) contains several ...

    • Interpreting Cancer Genomes Using Systematic Host Perturbations by Tumour Virus Proteins 

      Rozenblatt-Rosen, Orit; Deo, Rahul C.; Dricot, Amélie; Askenazi, Manor; Tavares, Maria; Abderazzaq, Fieda; Byrdsong, Danielle; Correll, Mick; Fan, Changyu; Feltkamp, Mariet C.; Franchi, Rachel; Garg, Brijesh K.; Gulbahce, Natali; Hao, Tong; Korkhin, Anna; Litovchick, Larisa; Mar, Jessica C.; Pak, Theodore R.; Rabello, Sabrina; Rubio, Renee; Shen, Yun; Tasan, Murat; Wanamaker, Shelly; Roecklein-Canfield, Jennifer; Johannsen, Eric; Barabási, Albert-László; Padi, Megha; Adelmant, Guillaume; Calderwood, Michael A; Rolland, Thomas; Grace, Miranda; Pevzner, Samuel; Carvunis, Anne-Ruxandra; Chen, Alyce Aura; Cheng, Jingwei; Duarte, Melissa; Ficarro, Scott; Holthaus, Amy Marie; James, Robert; Singh, Saurav; Spangle, Jennifer Marie; Webber, James T.; Beroukhim, Rameen; Kieff, Elliott D.; Cusick, Michael; Hill, David E.; Munger, Karl; Marto, Jarrod; Quackenbush, John; Roth, Frederick Phillip; DeCaprio, James A.; Vidal, Marc (Nature Publishing Group, 2012)
      Genotypic differences greatly influence susceptibility and resistance to disease. Understanding genotype-phenotype relationships requires that phenotypes be viewed as manifestations of network properties, rather than simply ...

    • An inter‐species protein–protein interaction network across vast evolutionary distance 

      Zhong, Quan; Pevzner, Samuel J; Hao, Tong; Wang, Yang; Mosca, Roberto; Menche, Jörg; Taipale, Mikko; Taşan, Murat; Fan, Changyu; Yang, Xinping; Haley, Patrick; Murray, Ryan R; Mer, Flora; Gebreab, Fana; Tam, Stanley; MacWilliams, Andrew; Dricot, Amélie; Reichert, Patrick; Santhanam, Balaji; Ghamsari, Lila; Calderwood, Michael A; Rolland, Thomas; Charloteaux, Benoit; Lindquist, Susan; Barabási, Albert‐László; Hill, David E; Aloy, Patrick; Cusick, Michael E; Xia, Yu; Roth, Frederick P; Vidal, Marc (John Wiley and Sons Inc., 2016)
      Abstract In cellular systems, biophysical interactions between macromolecules underlie a complex web of functional interactions. How biophysical and functional networks are coordinated, whether all biophysical interactions ...

    • Pooled‐matrix protein interaction screens using Barcode Fusion Genetics 

      Yachie, Nozomu; Petsalaki, Evangelia; Mellor, Joseph C; Weile, Jochen; Jacob, Yves; Verby, Marta; Ozturk, Sedide B; Li, Siyang; Cote, Atina G; Mosca, Roberto; Knapp, Jennifer J; Ko, Minjeong; Yu, Analyn; Gebbia, Marinella; Sahni, Nidhi; Yi, Song; Tyagi, Tanya; Sheykhkarimli, Dayag; Roth, Jonathan F; Wong, Cassandra; Musa, Louai; Snider, Jamie; Liu, Yi‐Chun; Yu, Haiyuan; Braun, Pascal; Stagljar, Igor; Hao, Tong; Calderwood, Michael A; Pelletier, Laurence; Aloy, Patrick; Hill, David E; Vidal, Marc; Roth, Frederick P (John Wiley and Sons Inc., 2016)
      Abstract High‐throughput binary protein interaction mapping is continuing to extend our understanding of cellular function and disease mechanisms. However, we remain one or two orders of magnitude away from a complete ...

    • Protein interaction network of alternatively spliced isoforms from brain links genetic risk factors for autism 

      Corominas, Roser; Yang, Xinping; Lin, Guan Ning; Kang, Shuli; Shen, Yun; Ghamsari, Lila; Broly, Martin; Rodriguez, Maria; Tam, Stanley; Trigg, Shelly A.; Fan, Changyu; Yi, Song; Tasan, Murat; Lemmens, Irma; Kuang, Xingyan; Zhao, Nan; Malhotra, Dheeraj; Michaelson, Jacob J.; Vacic, Vladimir; Calderwood, Michael A.; Roth, Frederick P.; Tavernier, Jan; Horvath, Steve; Salehi-Ashtiani, Kourosh; Korkin, Dmitry; Sebat, Jonathan; Hill, David E.; Hao, Tong; Vidal, Marc; Iakoucheva, Lilia M. (Nature Pub. Group, 2014)
      Increased risk for autism spectrum disorders (ASD) is attributed to hundreds of genetic loci. The convergence of ASD variants have been investigated using various approaches, including protein interactions extracted from ...

    • Proto-genes and De Novo Gene Birth 

      Carvunis, Anne-Ruxandra; Rolland, Thomas; Wapinski, Ilan Neustat; Calderwood, Michael A; Yildirim, Muhammed; Simonis, Nicolas; Charloteaux, Benoit; Hidalgo, César A.; Barbette, Justin; Santhanam, Balaji; Brar, Gloria A.; Weissman, Jonathan S.; Regev, Aviv; Thierry-Mieg, Nicolas; Cusick, Michael; Vidal, Marc (Nature Publishing Group, 2012)
      Novel protein-coding genes can arise either through re-organization of pre-existing genes or de novo. Processes involving re-organization of pre-existing genes, notably following gene duplication, have been extensively ...

    • A Reference Map of the Human Binary Protein Interactome 

      Luck, Katja; Kim, Dae-Kyum; Lambourne, Luke; Spirohn, Kerstin; Begg, Bridget E; Bian, Wenting; Brignall, Ruth; Cafarelli, Tiziana; Campos-Laborie, Francisco J.; Charloteaux, Benoit; Choi, Dongsic; Coté, Atina; Daley, Meaghan; Deimling, Steven; Desbuleux, Alice; Dricot, Amélie; Gebbia, Marinella; Hardy, Madeleine; Kishore, Nishka; Knapp, Jennifer; Kovács, István A.; Lemmens, Irma; Mee, Miles W.; Mellor, Joseph C.; Pollis, Carl; Pons, Carles; Richardson, Aaron; Schlabach, Sadie; Teeking, Bridget; Yadav, Anupama; Babor, Mariana; Balcha, Dawit; Basha, Omer; Bowman-Colin, Christian; Chin, Suet-Feung; Choi, Soon Gang; Colabella, Claudia; Coppin, Georges; D'Amata, Cassandra; De Ridder, David; De Rouck, Steffi; Duran-Frigola, Miquel; Ennajdaoui, Hanane; Goebels, Florian; Goehring, Liana; Gopal, Anjali; Haddad, Ghazal; Hatchi, Elodie; Helmy, Mohamed; Jacob, Yves; Kassa, Yoseph; Landini, Serena; Li, Roujia; van Lieshout, Natascha; MacWilliams, Andrew; Markey, Dylan; Paulson, Joseph; Rangarajan, Sudharshan; Rasla, John; Rayhan, Ashyad; Rolland, Thomas; San Miguel Delgadillo, Adriana; Shen, Yun; Sheykhkarimli, Dayag; Sheynkman, Gloria; Simonovsky, Eyal; Taşan, Murat; Tejeda, Alexander; Tropepe, Vincent; Twizere, Jean-Claude; Wang, Yang; Weatheritt, Robert; Weile, Jochen; Xia, Yu; Yang, Xinping; Yeger-Lotem, Esti; Zhong, Quan; Aloy, Patrick; Bader, Gary D.; De Las Rivas, Javier; Gaudet, Suzanne; Hao, Tong; Rak, Janusz; Tavernier, Jan; Hill, David; Vidal, Marc; Roth, Frederick P.; Calderwood, Michael (Nature Research, 2020-04-08)
      Global insights into cellular organization and genome function require comprehensive understanding of the interactome networks that mediate genotype-phenotype relationships. Here, we present a human “all-by-all” reference ...

    • An RS Motif within the Epstein-Barr Virus BLRF2 Tegument Protein Is Phosphorylated by SRPK2 and Is Important for Viral Replication 

      Duarte, Melissa; Wang, Lili; Calderwood, Michael A; Adelmant, Guillaume; Ohashi, Makoto; Roecklein-Canfield, Jennifer; Marto, Jarrod; Hill, David E.; Deng, Hongyu; Johannsen, Eric (Public Library of Science, 2013)
      Epstein-Barr virus (EBV) is a gammaherpesvirus that causes infectious mononucleosis, B cell lymphomas, and nasopharyngeal carcinoma. Many of the genes required for EBV virion morphogenesis are found in all herpesviruses, ...

    • Viral Perturbations of Host Networks Reflect Disease Etiology 

      Gulbahce, Natali; Yan, Han; Dricot, Amélie; Padi, Megha; Byrdsong, Danielle; Franchi, Rachel; Lee, Deok-Sun; Rozenblatt-Rosen, Orit; Mar, Jessica C.; Calderwood, Michael A; Baldwin, Amy; Zhao, Bo; Santhanam, Balaji; Braun, Pascal; Simonis, Nicolas; Huh, Kyung-Won; Hellner, Karin; Grace, Miranda; Chen, Alyce Aura; Rubio, Renee; Marto, Jarrod; Christakis, Nicholas Alexander; Kieff, Elliott D.; Roth, Frederick Phillip; Roecklein-Canfield, Jennifer; DeCaprio, James A.; Cusick, Michael; Quackenbush, John; Hill, David E.; Münger, Karl; Vidal, Marc; Barabási, Albert-László (Public Library of Science, 2012)
      Many human diseases, arising from mutations of disease susceptibility genes (genetic diseases), are also associated with viral infections (virally implicated diseases), either in a directly causal manner or by indirect ...