Now showing items 1-9 of 9

    • Broadening the Horizon – Level 2.5 of the HUPO-PSI Format for Molecular Interactions 

      Kerrien, Samuel; Orchard, Sandra; Montecchi-Palazzi, Luisa; Aranda, Bruno; Quinn, Antony F; Vinod, Nisha; Bader, Gary D; Xenarios, Ioannis; Wojcik, Jérôme; Tyers, Mike; Salama, John J; Ceol, Arnaud; Chatr-aryamontri, Andrew; Oesterheld, Matthias; Stümpflen, Volker; Salwinski, Lukasz; Nerothin, Jason; Cerami, Ethan; Gilson, Michael; Armstrong, John; Woollard, Peter; Hogue, Christopher; Cesareni, Gianni; Apweiler, Rolf; Hermjakob, Henning; Sherman, David Joseph; Moore, Susan; Cusick, Michael; Vidal, Marc; Eisenberg, David Miles (BioMed Central, 2007)
      Background: Molecular interaction Information is a key resource in modern biomedical research. Publicly available data have previously been provided in a broad array of diverse formats, making access to this very difficult. ...
    • Edgetic Perturbation Models of Human Inherited Disorders 

      Simonis, Nicolas; Li, Qian-Ru; Heuze, Fabien; Klitgord, Niels; Tam, Stanley; Venkatesan, Kavitha; Mou, Danny; Swearingen, Venus; Yildirim, Muhammed A; Dricot, Amélie; Szeto, David; Lin, Chenwei; Hao, Tong; Fan, Changyu; Milstein, Stuart; Dupuy, Denis; Brasseur, Robert; Zhong, Quan; Charloteaux, Benoit; Yu, Haiyuan; Yan, Han; Hill, David E.; Cusick, Michael; Vidal, Marc (Nature Publishing Group, 2009)
      Cellular functions are mediated through complex systems of macromolecules and metabolites linked through biochemical and physical interactions, represented in interactome models as ‘nodes' and ‘edges', respectively. Better ...
    • Host-Pathogen Interactome Mapping for HTLV-1 and -2 Retroviruses 

      Simonis, Nicolas; Rual, Jean-François; Lemmens, Irma; Boxus, Mathieu; Hirozane-Kishikawa, Tomoko; Gatot, Jean-Stéphane; Dricot, Amélie; Hao, Tong; Vertommen, Didier; Legros, Sébastien; Daakour, Sarah; Klitgord, Niels; Martin, Maud; Willaert, Jean-François; Dequiedt, Franck; Navratil, Vincent; Burny, Arsène; Van Lint, Carine; Tavernier, Jan; Kettmann, Richard; Twizere, Jean-Claude; Cusick, Michael; Hill, David E.; Vidal, Marc (BioMed Central, 2012)
      Background: Human T-cell leukemia virus type 1 (HTLV-1) and type 2 both target T lymphocytes, yet induce radically different phenotypic outcomes. HTLV-1 is a causative agent of Adult T-cell leukemia (ATL), whereas HTLV-2, ...
    • 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 ...
    • Intrinsic Disorder Is a Common Feature of Hub Proteins from Four Eukaryotic Interactomes 

      Haynes, Chad; Oldfield, Christopher J; Ji, Fei; Klitgord, Niels; Cusick, Michael; Radivojac, Predrag; Uversky, Vladimir N; Vidal, Marc; Iakoucheva, Lilia M (Public Library of Science, 2006)
      Recent proteome-wide screening approaches have provided a wealth of information about interacting proteins in various organisms. To test for a potential association between protein connectivity and the amount of predicted ...
    • Proto-genes and De Novo Gene Birth 

      Carvunis, Anne-Ruxandra; Rolland, Thomas; Wapinski, Ilan Neustat; Calderwood, Michael A; Yildirim, Muhammed A.; 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 ...
    • 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 ...
    • VirusMINT: A Viral Protein Interaction Database 

      Chatr-aryamontri, Andrew; Ceol, Arnaud; Peluso, Daniele; Nardozza, Aurelio; Panni, Simona; Sacco, Francesca; Tinti, Michele; Smolyar, Alex; Castagnoli, Luisa; Cesareni, Gianni; Vidal, Marc; Cusick, Michael (Oxford University Press, 2009)
      Understanding the consequences on host physiology induced by viral infection requires complete understanding of the perturbations caused by virus proteins on the cellular protein interaction network. The VirusMINT database ...