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1. Full Text High-Quality Binary Protein Interaction Map of the Yeast Interactome Network
by Haiyuan Yu and Pascal Braun and Muhammed A. Yildirim and Irma Lemmens and Kavitha Venkatesan and Julie Sahalie and Tomoko Hirozane-Kishikawa and Fana Gebreab and Na Li and Nicolas Simonis and Tong Hao and Jean-François Rual and Amélie Dricot and Alexei Vazquez and Ryan R. Murray and Christophe Simon and Leah Tardivo and Stanley Tam and Nenad Svrzikapa and Changyu Fan and Anne-Sophie de Smet and Adriana Motyl and Michael E. Hudson and Juyong Park and Xiaofeng Xin and Michael E. Cusick and Troy Moore and Charlie Boone and Michael Snyder and Frederick P. Roth and Albert-László Barabási and Jan Tavernier and David E. Hill and Marc Vidal
Science, ISSN 0036-8075, 10/2008, Volume 322, Issue 5898, pp. 104 - 110
Current yeast interactome network maps contain several hundred molecular complexes with limited and somewhat controversial representation of direct binary... 
Datasets | Yeasts | Screening tests | Drug interactions | Molecular interactions | Principal components analysis | Connectivity | Reports | Open reading frames | Grants | Protein interaction mapping | 2-HYBRID SCREENS | REGULATORY NETWORKS | ANNOTATION | MULTIDISCIPLINARY SCIENCES | ESCHERICHIA-COLI | COMPLEXES | GENOMIC ANALYSIS | C-ELEGANS | SCALE | SACCHAROMYCES-CEREVISIAE | MASS-SPECTROMETRY | Signal Transduction | Saccharomyces cerevisiae - genetics | Computational Biology | Saccharomyces cerevisiae Proteins - genetics | Gene Regulatory Networks | Protein Interaction Mapping - standards | Saccharomyces cerevisiae - metabolism | Transcription Factors - metabolism | Protein Interaction Mapping - methods | Two-Hybrid System Techniques | Metabolic Networks and Pathways | Mass Spectrometry | Proteomics | Saccharomyces cerevisiae Proteins - metabolism | Protein Array Analysis | Protein Binding | Saccharomyces cerevisiae Proteins - isolation & purification | Proteome - metabolism | Physiological aspects | Genetic aspects | Research | Yeast fungi | Protein-protein interactions | Data analysis | Yeast | Cellular biology | Molecular biology | Spectrum analysis | Index Medicus
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2. Full Text An empirical framework for binary interactome mapping
by Gebreab, Fana and Vinayagam, Arunachalam and Murray, Ryan R and Rau, Kirstin and Timm, Jan and Boone, Charles and Braun, Pascal and Lalowski, Maciej and Szeto, David and Yu, Haiyuan and Zenkner, Martina and Tavernier, Jan and Heinzmann, Kathrin and Wanker, Erich E and Simonis, Nicolas and Vazquez, Alexei and Xin, Xiaofeng and Hao, Tong and Borick, Heather and Klitgord, Niels and Lin, Chenwei and Lemmens, Irma and Barabási, Albert-László and Venkatesan, Kavitha and Stelzl, Ulrich and Hill, David E and Cusick, Michael E and Simon, Christophe and Hirozane-Kishikawa, Tomoko and Dann, Elizabeth and Cevik, Sebiha and Sahalie, Julie M and Roth, Frederick P and Dricot, Amélie and Smolyar, Alex and Vidal, Marc and Yildirim, Muhammed A and Rual, Jean-François and de Smet, Anne-Sophie and Goh, Kwang-Il
Nature Methods, ISSN 1548-7091, 01/2009, Volume 6, Issue 1, pp. 83 - 90
Several attempts have been made to systematically map protein-protein interaction, or 'interactome', networks. However, it remains difficult to assess the... 
INTERACTION NETWORK | YEAST | BIOCHEMICAL RESEARCH METHODS | PROTEIN-PROTEIN INTERACTIONS | MOLECULAR INTERACTION DATABASE | MAP | PROTEOMICS | RESOURCE | Proteins - genetics | Protein Interaction Mapping - methods | Proteins - metabolism | Databases, Protein | Humans | Sensitivity and Specificity | Protein Binding | Proteins - analysis | Usage | Mass spectrometry | Analysis | Protein-protein interactions | Data analysis | Binary system | Research methodology | Proteomics | Quality control | Index Medicus
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3. Full Text Interpreting cancer genomes using systematic host network perturbations by tumour virus proteins
by Rozenblatt-Rosen, Orit and Deo, Rahul C and Padi, Megha and Adelmant, Guillaume and Calderwood, Michael A and Rolland, Thomas and Grace, Miranda and Dricot, Amélie and Askenazi, Manor and Tavares, Maria and Pevzner, Samuel J and Abderazzaq, Fieda and Byrdsong, Danielle and Carvunis, Anne-Ruxandra and Chen, Alyce A and Cheng, Jingwei and Correll, Mick and Duarte, Melissa and Fan, Changyu and Feltkamp, Mariet C and Ficarro, Scott B and Franchi, Rachel and Garg, Brijesh K and Gulbahce, Natali and Hao, Tong and Holthaus, Amy M and James, Robert and Korkhin, Anna and Litovchick, Larisa and Mar, Jessica C and Pak, Theodore R and Rabello, Sabrina and Rubio, Renee and Shen, Yun and Singh, Saurav and Spangle, Jennifer M and Tasan, Murat and Wanamaker, Shelly and Webber, James T and Roecklein-Canfield, Jennifer and Johannsen, Eric and Barabási, Albert-László and Beroukhim, Rameen and Kieff, Elliott and Cusick, Michael E and Hill, David E and Münger, Karl and Marto, Jarrod A and Quackenbush, John and Roth, Frederick P and Decaprio, James A and Vidal, Marc
Nature, ISSN 0028-0836, 07/2012, Volume 487, Issue 7408, pp. 491 - 495
Genotypic differences greatly influence susceptibility and resistance to disease. Understanding genotype-phenotype relationships requires that phenotypes be... 
COMPLEX | ASSOCIATION | MULTIDISCIPLINARY SCIENCES | EPSTEIN-BARR-VIRUS | Neoplasms - metabolism | Papillomaviridae - metabolism | Herpesvirus 4, Human - genetics | Receptors, Notch - metabolism | Humans | Gene Expression Regulation, Neoplastic | Gene Expression Profiling | Adenoviridae - pathogenicity | Viral Proteins - metabolism | Papillomaviridae - genetics | Neoplasms - genetics | Adenoviridae - genetics | Herpesvirus 4, Human - pathogenicity | Oncogenic Viruses - metabolism | Genes, Neoplasm - genetics | Signal Transduction | Polyomavirus - genetics | Viral Proteins - genetics | Polyomavirus - metabolism | Open Reading Frames - genetics | Genome, Human - genetics | Oncogenic Viruses - pathogenicity | Papillomaviridae - pathogenicity | Two-Hybrid System Techniques | Host-Pathogen Interactions - genetics | Polyomavirus - pathogenicity | Oncogenic Viruses - genetics | Adenoviridae - metabolism | Herpesvirus 4, Human - metabolism | Neoplasms - pathology | Viral proteins | Systems biology | Perturbation (Mathematics) | Physiological aspects | Genetic aspects | Research | Health aspects | Computational biology | Cancer | Proteins | Human papillomavirus | Herpes viruses | Genomes | Mutation | Mass spectrometry | Binding sites | Apoptosis | Index Medicus
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4. Full Text Host-pathogen interactome mapping for HTLV-1 and -2 retroviruses
by Simonis, Nicolas and Rual, Jean-François and Lemmens, Irma and Boxus, Mathieu and Hirozane-Kishikawa, Tomoko and Gatot, Jean-Stéphane and Dricot, Amélie and Hao, Tong and Vertommen, Didier and Legros, Sébastien and Daakour, Sarah and Klitgord, Niels and Martin, Maud and Willaert, Jean-François and Dequiedt, Franck and Navratil, Vincent and Cusick, Michael E and Burny, Arsène and Van Lint, Carine and Hill, David E and Tavernier, Jan and Kettmann, Richard and Vidal, Marc and Twizere, Jean-Claude
Retrovirology, ISSN 1742-4690, 03/2012, Volume 9, Issue 1, pp. 26 - 26
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... 
HBZ | Retrovirus | Tax | Interactome | ORFeome | HTLV | TRANSCRIPTION FACTORS | INTERACTION DATABASE | ANAPHASE-PROMOTING COMPLEX | VIRUS TYPE-1 TAX | T-CELL LEUKEMIA | PROTEIN-INTERACTION NETWORK | FANCONI-ANEMIA | RNA-BINDING | VIROLOGY | GENE-EXPRESSION | NUCLEOTIDE-SEQUENCE | Host-Pathogen Interactions | Human T-lymphotropic virus 2 - pathogenicity | Systems Biology - methods | Two-Hybrid System Techniques | Humans | Human T-lymphotropic virus 1 - pathogenicity | T-Lymphocytes - immunology | Human T-lymphotropic virus 1 - immunology | T-Lymphocytes - virology | Human T-lymphotropic virus 2 - immunology | Physiological aspects | Host-parasite relationships | Genetic aspects | Research | T cells | HTLV-I (Virus) | Index Medicus | Life Sciences | Human health and pathology | Infectious diseases
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5. Full Text Edgetic perturbation models of human inherited disorders
by Hill, David E and Klitgord, Niels and Yan, Han and Cusick, Michael E and Heuze, Fabien and Lin, Chenwei and Vidal, Marc and Venkatesan, Kavitha and Zhong, Quan and Mou, Danny and Simonis, Nicolas and Swearingen, Venus and Yildirim, Muhammed A and Szeto, David and Fan, Changyu and Li, Qian-Ru and Yu, Haiyuan and Dricot, Amélie and Brasseur, Robert and Hao, Tong and Charloteaux, Benoit and Dupuy, Denis and Milstein, Stuart and Tam, Stanley
Molecular Systems Biology, ISSN 1744-4292, 11/2009, Volume 5, Issue 1, pp. 321 - n/a
Cellular functions are mediated through complex systems of macromolecules and metabolites linked through biochemical and physical interactions, represented in... 
genotype‐to‐phenotype relationships | network perturbation | binary protein interaction | human Mendelian disorders | Genotype-to-phenotype relationships | Binary protein interaction | Network perturbation | Human Mendelian disorders | genotype-to-phenotype relationships | WEB TOOLS | CRYSTAL-STRUCTURE | BIOCHEMISTRY & MOLECULAR BIOLOGY | HUMAN GENES | BETA-ACTIN | GENOME | DATABASE | STRUCTURAL BASIS | DISEASE | PROTEIN-PROTEIN INTERACTIONS | IMPROVEMENTS | Models, Genetic | Disease - genetics | Mutation - genetics | Humans | Alleles | Genetic Diseases, Inborn - genetics | Index Medicus
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6. Full Text A Proteome-Scale Map of the Human Interactome Network
by Rolland, Thomas and Taşan, Murat and Charloteaux, Benoit and Pevzner, Samuel J and Zhong, Quan and Sahni, Nidhi and Yi, Song and Lemmens, Irma and Fontanillo, Celia and Mosca, Roberto and Kamburov, Atanas and Ghiassian, Susan D and Yang, Xinping and Ghamsari, Lila and Balcha, Dawit and Begg, Bridget E and Braun, Pascal and Brehme, Marc and Broly, Martin P and Carvunis, Anne-Ruxandra and Convery-Zupan, Dan and Corominas, Roser and Coulombe-Huntington, Jasmin and Dann, Elizabeth and Dreze, Matija and Dricot, Amélie and Fan, Changyu and Franzosa, Eric and Gebreab, Fana and Gutierrez, Bryan J and Hardy, Madeleine F and Jin, Mike and Kang, Shuli and Kiros, Ruth and Lin, Guan Ning and Luck, Katja and MacWilliams, Andrew and Menche, Jörg and Murray, Ryan R and Palagi, Alexandre and Poulin, Matthew M and Rambout, Xavier and Rasla, John and Reichert, Patrick and Romero, Viviana and Ruyssinck, Elien and Sahalie, Julie M and Scholz, Annemarie and Shah, Akash A and Sharma, Amitabh and Shen, Yun and Spirohn, Kerstin and Tam, Stanley and Tejeda, Alexander O and Trigg, Shelly A and Twizere, Jean-Claude and Vega, Kerwin and Walsh, Jennifer and Cusick, Michael E and Xia, Yu and Barabási, Albert-László and Iakoucheva, Lilia M and Aloy, Patrick and De Las Rivas, Javier and Tavernier, Jan and Calderwood, Michael A and Hill, David E and Hao, Tong and Roth, Frederick P and Vidal, Marc
Cell, ISSN 0092-8674, 11/2014, Volume 159, Issue 5, pp. 1212 - 1226
Just as reference genome sequences revolutionized human genetics, reference maps of interactome networks will be critical to fully understand... 
HUMAN-DISEASE | CANCER GENES | BIOCHEMISTRY & MOLECULAR BIOLOGY | COMPREHENSIVE RESOURCE | DISORDERS | POSTTRANSLATIONAL MODIFICATIONS | UPDATE | PROTEINS | MOLECULAR INTERACTION DATABASE | EXPRESSION | GENOME-WIDE ASSOCIATION | CELL BIOLOGY | Neoplasms - metabolism | Genome-Wide Association Study | Animals | Databases, Protein | Humans | Mice | Proteome - metabolism | Protein Interaction Maps | Analysis | Genomics | Protein-protein interactions | Computer science | Index Medicus
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7. Full Text Viral perturbations of host networks reflect disease etiology
by Gulbahce, Natali and Yan, Han and Dricot, Amélie and Padi, Megha and Byrdsong, Danielle and Franchi, Rachel and Lee, Deok-Sun and Rozenblatt-Rosen, Orit and Mar, Jessica C and Calderwood, Michael A and Baldwin, Amy and Zhao, Bo and Santhanam, Balaji and Braun, Pascal and Simonis, Nicolas and Huh, Kyung-Won and Hellner, Karin and Grace, Miranda and Chen, Alyce and Rubio, Renee and Marto, Jarrod A and Christakis, Nicholas A and Kieff, Elliott and Roth, Frederick P and Roecklein-Canfield, Jennifer and DeCaprio, James A and Cusick, Michael E and Quackenbush, John and Hill, David E and Münger, Karl and Vidal, Marc and Barabási, Albert-László
PLoS Computational Biology, ISSN 1553-734X, 06/2012, Volume 8, Issue 6, pp. e1002531 - e1002531
Many human diseases, arising from mutations of disease susceptibility genes (genetic diseases), are also associated with viral infections (virally implicated... 
PROTEIN INTERACTION NETWORK | INTERACTION DATABASE | CELLS | RETINOBLASTOMA | GENE | PATHWAY | TYPE-16 E7 ONCOPROTEIN | BIOLOGY | BIOCHEMICAL RESEARCH METHODS | MATHEMATICAL & COMPUTATIONAL BIOLOGY | HUMAN-PAPILLOMAVIRUS | EPSTEIN-BARR-VIRUS | Fanconi Anemia - virology | Genetic Predisposition to Disease | Human papillomavirus 16 - pathogenicity | Disease - genetics | Humans | Computational Biology | Virus Diseases - complications | Viral Proteins - metabolism | Human papillomavirus 16 - metabolism | Protein Interaction Maps | Disease - etiology | Host-Pathogen Interactions - genetics | Models, Biological | Fanconi Anemia - etiology | Fanconi Anemia - genetics | Herpesvirus 4, Human - pathogenicity | Herpesvirus 4, Human - metabolism | Host-Pathogen Interactions - physiology | Virus diseases | Plant diseases | Perturbation (Mathematics) | Host-parasite relationships | Physiological aspects | Development and progression | Research | Proteins | Health sciences | Human papillomavirus | Hypotheses | Medicare | Disease | Viruses | Genomes | Lymphomas | Grants | Family medical history | Viral infections | Index Medicus
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8. Full Text Systematic screening reveals a role for BRCA1 in the response to transcription-associated DNA damage
by Hill, Sarah J and Rolland, Thomas and Adelmant, Guillaume and Xia, Xianfang and Owen, Matthew S and Dricot, Amélie and Zack, Travis I and Sahni, Nidhi and Jacob, Yves and Hao, Tong and McKinney, Kristine M and Clark, Allison P and Reyon, Deepak and Tsai, Shengdar Q and Joung, J. Keith and Beroukhim, Rameen and Marto, Jarrod A and Vidal, Marc and Gaudet, Suzanne and Hill, David E and Livingston, David M
Genes and Development, ISSN 0890-9369, 09/2014, Volume 28, Issue 17, pp. 1957 - 1975
BRCA1 is a breast and ovarian tumor suppressor. Given its numerous incompletely understood functions and the possibility that more exist, we performed... 
Transcription | BRCA1 interaction screening | DNA damage | RNA-POLYMERASE-II | PROTEIN INTERACTION NETWORK | transcription | HUMAN-CELLS | MMS22L-NFKBIL2 COMPLEX | DEVELOPMENTAL BIOLOGY | GENOME STABILITY | NEGATIVE BREAST-CANCER | CELL BIOLOGY | MMS22L-TONSL COMPLEX | GENETICS & HEREDITY | PLATINUM-BASED CHEMOTHERAPY | HOMOLOGOUS RECOMBINATION | COPY-NUMBER ALTERATION | Humans | NF-kappa B - metabolism | DNA Repair - genetics | Protein Interaction Mapping | BRCA1 Protein - genetics | Ultraviolet Rays | NF-kappa B - genetics | BRCA1 Protein - metabolism | Cell Line, Tumor | DNA Damage - genetics | Protein Binding | HeLa Cells | Transcription, Genetic - genetics | DNA testing | Genetic transcription | Medical screening | Gene expression | Analysis | Methods | Index Medicus | Resource | Methodology
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9. Full Text Empirically controlled mapping of the Caenorhabditis elegans protein-protein interactome network
by Hill, David E and Tavernier, Jan and Li, Ning and Cusick, Michael E and Ahn, Jin Sook and Dreze, Matija and Kao, Huey-Ling and Braun, Pascal and Lin, Chenwei and Tasan, Murat and Simonis, Nicolas and Cevik, Sebiha and Yildirim, Muhammed A and Boxem, Mike and Bertin, Nicolas and Fan, Changyu and Lemmens, Irma and Hirozane-Kishikawa, Tomoko and Hao, Tong and Tewari, Muneesh and Vandenhaute, Jean and Simon, Christophe and Carvunis, Anne-Ruxandra and Venkatesan, Kavitha and Rual, Jean-François and Milstein, Stuart and Vidal, Marc and Roth, Frederick P and Gunsalus, Kristin C and Gebreab, Fana and Klitgord, Niels and Smolyar, Alex and Sahalie, Julie M and Szeto, David and Dricot, Amélie and Yu, Haiyuan and Ayivi-Guedehoussou, Nono and de Smet, Anne-Sophie and Dann, Elizabeth
Nature Methods, ISSN 1548-7091, 01/2009, Volume 6, Issue 1, pp. 47 - 54
To provide accurate biological hypotheses and elucidate global properties of cellular networks, systematic identification of protein-protein interactions must... 
ANNOTATION | PERTURBATION | SEQUENCE | BIOCHEMICAL RESEARCH METHODS | INTERACTION MAP | C-ELEGANS | EARLY EMBRYOGENESIS | RESOURCE | Cell Line | Protein Interaction Mapping - methods | Animals | Caenorhabditis elegans - metabolism | Caenorhabditis elegans - genetics | Caenorhabditis elegans Proteins - analysis | Humans | Caenorhabditis elegans Proteins - metabolism | Protein Binding | Software | Caenorhabditis elegans Proteins - genetics | Caenorhabditis elegans | Usage | Research | Biological assay | Protein-protein interactions | Cellular control mechanisms | Nematodes | Cellular biology | Standards | Proteomics | Quality control | Index Medicus
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