Browsing by Author "Hill, David"

Now showing items 1-15 of 15

    • 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; 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 ...

    • 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 ...

    • 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% ...

    • Model Comparison and Assessment for Single Particle Tracking in Biological Fluids 

      Lysy, Martin; Pillai, Natesh S; Hill, David E.; Forest, M. Gregory; Mellnik, John W. R.; Vasquez, Paula A.; McKinley, Scott A. (Informa UK Limited, 2016)
      State-of-the-art techniques in passive particle-tracking microscopy provide high-resolution path trajectories of diverse foreign particles in biological fluids. For particles on the order of 1 μm diameter, these paths are ...

    • 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 ...

    • 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 ...

    • R5-SHIV Induces Multiple Defects in T Cell Function during Early Infection of Rhesus Macaques Including Accumulation of T Reg Cells in Lymph Nodes 

      Righi, Elda; Leblanc, Pierre R.; Kodish, Brett; Mylvaganam, Hari N.; Stevceva, Liljana; Hu, Shiu-Lok; Chenine, Agnes-L.; Hovav, Avi-Hai; Unutmaz, Derya; Santosuosso, Michael Robert; Siddappa, Nagadenahalli B.; Ghebremichael, Musie Syum; Ruprecht, Ruth Margrit; Poznansky, Mark; Hill, David E. (Public Library of Science, 2011)
      Background: HIV-1 is a pathogen that T cell responses fail to control. HIV-1gp120 is the surface viral envelope glycoprotein that interacts with CD4 T cells and mediates entry. HIV-1gp120 has been implicated in immune ...

    • 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, ...

    • SH3 interactome conserves general function over specific form 

      Xin, Xiaofeng; Gfeller, David; Cheng, Jackie; Tonikian, Raffi; Sun, Lin; Guo, Ailan; Lopez, Lianet; Pavlenco, Alevtina; Akintobi, Adenrele; Zhang, Yingnan; Rual, Jean-François; Currell, Bridget; Seshagiri, Somasekar; Hao, Tong; Yang, Xinping; Shen, Yun A; Salehi-Ashtiani, Kourosh; Li, Jingjing; Cheng, Aaron T; Bouamalay, Dryden; Lugari, Adrien; Hill, David E.; Grimes, Mark L; Drubin, David G; Grant, Barth D; Vidal, Marc; Boone, Charles; Sidhu, Sachdev S; Bader, Gary D (Nature Publishing Group, 2013)
      Src homology 3 (SH3) domains bind peptides to mediate protein–protein interactions that assemble and regulate dynamic biological processes. We surveyed the repertoire of SH3 binding specificity using peptide phage display ...

    • 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 ...