Now showing items 1-20 of 28

    • Bayesian Modeling of the Yeast SH3 Domain Interactome Predicts Spatiotemporal Dynamics of Endocytosis Proteins 

      Tonikian, Raffi; Xin, Xiaofeng; Toret, Christopher P.; Gfeller, David; Landgraf, Christiane; Panni, Simona; Paoluzi, Serena; Castagnoli, Luisa; Currell, Bridget; Seshagiri, Somasekar; Winsor, Barbara; Gerstein, Mark B.; Bader, Gary D.; Volkmer, Rudolf; Cesareni, Gianni; Drubin, David G.; Kim, Philip M.; Sidhu, Sachdev S.; Boone, Charles; Yu, Haiyuan; Vidal, Marc (Public Library of Science, 2009)
      SH3 domains are peptide recognition modules that mediate the assembly of diverse biological complexes. We scanned billions of phage-displayed peptides to map the binding specificities of the SH3 domain family in the budding ...
    • 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 ...
    • Evidence for Transcript Networks Composed of Chimeric RNAs in Human Cells 

      Djebali, Sarah; Lagarde, Julien; Kapranov, Philipp; Lacroix, Vincent; Borel, Christelle; Mudge, Jonathan M.; Howald, Cédric; Foissac, Sylvain; Ucla, Catherine; Chrast, Jacqueline; Ribeca, Paolo; Murray, Ryan R.; Lin, Chenwei; Bell, Ian; Dumais, Erica; Drenkow, Jorg; Tress, Michael L.; Gelpí, Josep Lluís; Orozco, Modesto; Valencia, Alfonso; van Berkum, Nynke L.; Lajoie, Bryan R.; Stamatoyannopoulos, John; Batut, Philippe; Dobin, Alex; Harrow, Jennifer; Hubbard, Tim; Dekker, Job; Frankish, Adam; Salehi-Ashtiani, Kourosh; Reymond, Alexandre; Antonarakis, Stylianos E.; Guigó, Roderic; Gingeras, Thomas R.; Martin, David; Yang, Xinping; Ghamsari, Lila; Vidal, Marc (Public Library of Science, 2012)
      The classic organization of a gene structure has followed the Jacob and Monod bacterial gene model proposed more than 50 years ago. Since then, empirical determinations of the complexity of the transcriptomes found in yeast ...
    • A Gene Expression Fingerprint of C. elegans Embryonic Motor Neurons 

      Fox, Rebecca M; Von Stetina, Stephen; Barlow, Susan J; Shaffer, Christian; Olszewski, Kellen L; Moore, Jason H; Dupuy, Denis; Vidal, Marc; Miller, David M. (BioMed Central, 2005)
      Background: Differential gene expression specifies the highly diverse cell types that constitute the nervous system. With its sequenced genome and simple, well-defined neuroanatomy, the nematode C. elegans is a useful model ...
    • A Global Protein–Lipid Interactome Map 

      Brehme, Marc J; Vidal, Marc (Nature Publishing Group, 2010)
    • Hepatitis C Virus Infection Protein Network 

      de Chassey, B; Navratil, V; Tafforeau, L; Hiet, M S; Aublin-Gex, A; Agaugué, S; Meiffren, G; Pradezynski, F; Faria, B F; Chantier, T; Le Breton, M; Pellet, J; Davoust, N; Mangeot, P E; Chaboud, A; Penin, F; Jacob, Y; Vidalain, P O; Vidal, Marc; André, P; Rabourdin-Combe, C; Lotteau, V (Nature Publishing Group, 2008)
      A proteome-wide mapping of interactions between hepatitis C virus (HCV) and human proteins was performed to provide a comprehensive view of the cellular infection. A total of 314 protein–protein interactions between HCV ...
    • 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 ...
    • Insight into transcription factor gene duplication from Caenorhabditis elegans Promoterome-driven expression patterns 

      Reece-Hoyes, John S; Shingles, Jane; Dupuy, Denis; Grove, Christian A; Walhout, Albertha JM; Vidal, Marc; Hope, Ian A (BioMed Central, 2007)
      Background: The C. elegans Promoterome is a powerful resource for revealing the regulatory mechanisms by which transcription is controlled pan-genomically. Transcription factors will form the core of any systems biology ...
    • InSite: a computational method for identifying protein-protein interaction binding sites on a proteome-wide scale 

      Wang, Haidong; Segal, Eran; Ben-Hur, Asa; Li, Qian-Ru; Vidal, Marc; Koller, Daphne (BioMed Central, 2007)
      We propose InSite, a computational method that integrates high-throughput protein and sequence data to infer the specific binding regions of interacting protein pairs. We compared our predictions with binding sites in ...
    • 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 ...
    • 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 ...
    • Large-Scale RNAi Screens Identify Novel Genes that Interact with the C. Elegans Retinoblastoma Pathway as well as Splicing-Related Components with synMuv B Activity 

      Ceron, Julian; Rual, Jean-François; Chandra, Abha; Dupuy, Denis; Vidal, Marc; van den Heuvel, Sander (BioMed Central, 2007)
      Background: The retinoblastoma tumor suppressor (Rb) acts in a conserved pathway that is deregulated in most human cancers. Inactivation of the single Rb-related gene in Caenorhabditis elegans, lin-35, has only limited ...
    • Mapping differential interactomes by affinity purification coupled with data independent mass spectrometry acquisition 

      Lambert, Jean-Philippe; Ivosev, Gordana; Couzens, Amber L.; Larsen, Brett; Taipale, Mikko; Lin, Zhen-Yuan; Zhong, Quan; Lindquist, Susan; Vidal, Marc; Aebersold, Ruedi; Pawson, Tony; Bonner, Ron; Tate, Stephen; Gingras, Anne-Claude (2013)
      Characterizing changes in protein-protein interactions associated with sequence variants (e.g. disease-associated mutations or splice forms) or following exposure to drugs, growth factors or hormones is critical to ...
    • MECP2 Is a Frequently Amplified Oncogene with a Novel Epigenetic Mechanism That Mimics the Role of Activated RAS in Malignancy 

      Neupane, Manish; Clark, Allison Paige; Landini, S.; Birkbak, N; Eklund, A. C.; Lim, E.; Culhane, Aedin; Barry, William T.; Schumacher, Sandra Kay; Beroukhim, Rameen; Szallasi, Zoltan; Vidal, Marc; Hill, David E.; Silver, Daniel P. (American Association for Cancer Research (AACR), 2015)
      An unbiased genome-scale screen for unmutated genes that drive cancer growth when overexpressed identified MECP2 as a novel oncogene. MECP2 resides in a region of the Xchromosome that is significantly amplified across 18% ...
    • Mycobacterium tuberculosis Type VII Secreted Effector EsxH Targets Host ESCRT to Impair Trafficking 

      Mehra, Alka; Zahra, Aleena; Thompson, Victor; Sirisaengtaksin, Natalie; Wells, Ashley; Porto, Maura; Köster, Stefan; Penberthy, Kristen; Kubota, Yoshihisha; Dricot, Amelie; Rogan, Daniel; Vidal, Marc; Hill, David E.; Bean, Andrew J.; Philips, Jennifer A. (Public Library of Science, 2013)
      Mycobacterium tuberculosis (Mtb) disrupts anti-microbial pathways of macrophages, cells that normally kill bacteria. Over 40 years ago, D'Arcy Hart showed that Mtb avoids delivery to lysosomes, but the molecular mechanisms ...
    • Network-based in silico drug efficacy screening 

      Guney, Emre; Menche, Jörg; Vidal, Marc; Barábasi, Albert-László (Nature Publishing Group, 2016)
      The increasing cost of drug development together with a significant drop in the number of new drug approvals raises the need for innovative approaches for target identification and efficacy prediction. Here, we take advantage ...
    • 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 ...