protein interaction mapping

Summary

Summary: Methods for determining interaction between proteins.

Top Publications

  1. pmc The IntAct molecular interaction database in 2010
    B Aranda
    EMBL Outstation, European Bioinformatics Institute, Wellcome Trust Genome Campus Hinxton, Cambridge CB10 1SD, UK
    Nucleic Acids Res 38:D525-31. 2010
  2. pmc Network organization of the human autophagy system
    Christian Behrends
    Department of Pathology, Harvard Medical School, Boston, Massachusetts 02115, USA
    Nature 466:68-76. 2010
  3. pmc The STRING database in 2011: functional interaction networks of proteins, globally integrated and scored
    Damian Szklarczyk
    Faculty of Health Sciences, Novo Nordisk Foundation Centre for Protein Research, University of Copenhagen, Denmark
    Nucleic Acids Res 39:D561-8. 2011
  4. pmc Human Protein Reference Database--2009 update
    T S Keshava Prasad
    Institute of Bioinformatics, International Tech Park, Bangalore 560 066, India
    Nucleic Acids Res 37:D767-72. 2009
  5. ncbi The genetic landscape of a cell
    Michael Costanzo
    Banting and Best Department of Medical Research, Terrence Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario M5S 3E1, Canada
    Science 327:425-31. 2010
  6. pmc The BioGRID Interaction Database: 2011 update
    Chris Stark
    Samuel Lunenfeld Research Institute, Mount Sinai Hospital, Toronto M5G 1X5, Canada
    Nucleic Acids Res 39:D698-704. 2011
  7. pmc The IntAct molecular interaction database in 2012
    Samuel Kerrien
    EMBL Outstation, European Bioinformatics Institute, Wellcome Trust Genome Campus Hinxton, Cambridge CB10 1SD, UK
    Nucleic Acids Res 40:D841-6. 2012
  8. pmc Interactome networks and human disease
    Marc Vidal
    Center for Cancer Systems Biology and Department of Cancer Biology, Dana Farber Cancer Institute, Boston, MA 02215, USA
    Cell 144:986-98. 2011
  9. pmc MINT, the molecular interaction database: 2012 update
    Luana Licata
    Department of Biology, University of Rome Tor Vergata, Via della Ricerca Scientifica, 00133 Rome, Italy
    Nucleic Acids Res 40:D857-61. 2012
  10. pmc MINT, the molecular interaction database: 2009 update
    Arnaud Ceol
    Department of Biology, University of Rome Tor Vergata, Via della Ricerca Scientifica, 00133 Rome
    Nucleic Acids Res 38:D532-9. 2010

Detail Information

Publications279 found, 100 shown here

  1. pmc The IntAct molecular interaction database in 2010
    B Aranda
    EMBL Outstation, European Bioinformatics Institute, Wellcome Trust Genome Campus Hinxton, Cambridge CB10 1SD, UK
    Nucleic Acids Res 38:D525-31. 2010
    ..Specialized views then allows 'zooming in' on the full annotation of interactions, interactors and their properties. IntAct source code and data are freely available at http://www.ebi.ac.uk/intact...
  2. pmc Network organization of the human autophagy system
    Christian Behrends
    Department of Pathology, Harvard Medical School, Boston, Massachusetts 02115, USA
    Nature 466:68-76. 2010
    ..These studies provide a global view of the mammalian autophagy interaction landscape and a resource for mechanistic analysis of this critical protein homeostasis pathway...
  3. pmc The STRING database in 2011: functional interaction networks of proteins, globally integrated and scored
    Damian Szklarczyk
    Faculty of Health Sciences, Novo Nordisk Foundation Centre for Protein Research, University of Copenhagen, Denmark
    Nucleic Acids Res 39:D561-8. 2011
    ..Version 9.0 of STRING covers more than 1100 completely sequenced organisms; the resource can be reached at http://string-db.org...
  4. pmc Human Protein Reference Database--2009 update
    T S Keshava Prasad
    Institute of Bioinformatics, International Tech Park, Bangalore 560 066, India
    Nucleic Acids Res 37:D767-72. 2009
    ..Since the last update, more than 5500 new protein sequences have been added, making HPRD a comprehensive resource for studying the human proteome...
  5. ncbi The genetic landscape of a cell
    Michael Costanzo
    Banting and Best Department of Medical Research, Terrence Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario M5S 3E1, Canada
    Science 327:425-31. 2010
    ..We also demonstrate that extensive and unbiased mapping of the genetic landscape provides a key for interpretation of chemical-genetic interactions and drug target identification...
  6. pmc The BioGRID Interaction Database: 2011 update
    Chris Stark
    Samuel Lunenfeld Research Institute, Mount Sinai Hospital, Toronto M5G 1X5, Canada
    Nucleic Acids Res 39:D698-704. 2011
    ..The entire BioGRID 3.0 data collection may be downloaded in multiple file formats, including PSI MI XML. Source code for BioGRID 3.0 is freely available without any restrictions...
  7. pmc The IntAct molecular interaction database in 2012
    Samuel Kerrien
    EMBL Outstation, European Bioinformatics Institute, Wellcome Trust Genome Campus Hinxton, Cambridge CB10 1SD, UK
    Nucleic Acids Res 40:D841-6. 2012
    ..IntAct is an active contributor to the IMEx consortium (http://www.imexconsortium.org). IntAct source code and data are freely available at http://www.ebi.ac.uk/intact...
  8. pmc Interactome networks and human disease
    Marc Vidal
    Center for Cancer Systems Biology and Department of Cancer Biology, Dana Farber Cancer Institute, Boston, MA 02215, USA
    Cell 144:986-98. 2011
    ....
  9. pmc MINT, the molecular interaction database: 2012 update
    Luana Licata
    Department of Biology, University of Rome Tor Vergata, Via della Ricerca Scientifica, 00133 Rome, Italy
    Nucleic Acids Res 40:D857-61. 2012
    ..bio.uniroma2.it/mint/download.do. We report here the growth of the database, the major changes in curation policy and a new algorithm to assign a confidence to each interaction...
  10. pmc MINT, the molecular interaction database: 2009 update
    Arnaud Ceol
    Department of Biology, University of Rome Tor Vergata, Via della Ricerca Scientifica, 00133 Rome
    Nucleic Acids Res 38:D532-9. 2010
    ..MINT has adopted the PSI-MI standards for the annotation and for the representation of molecular interactions and is a member of the IMEx consortium...
  11. pmc PID: the Pathway Interaction Database
    Carl F Schaefer
    National Cancer Institute, Center for Biomedical Informatics and Information Technology, Rockville MD, USA
    Nucleic Acids Res 37:D674-9. 2009
    ..The database is updated with new pathway content every month and supplemented by specially commissioned articles on the practical uses of other relevant online tools...
  12. pmc KEGG for representation and analysis of molecular networks involving diseases and drugs
    Minoru Kanehisa
    Bioinformatics Center, Institute for Chemical Research, Kyoto University, Uji, Kyoto 611 0011, Japan
    Nucleic Acids Res 38:D355-60. 2010
    ..The new disease/drug information resource named KEGG MEDICUS can be used as a reference knowledge base for computational analysis of molecular networks, especially, by integrating large-scale experimental datasets...
  13. ncbi Link communities reveal multiscale complexity in networks
    Yong Yeol Ahn
    Center for Complex Network Research, Department of Physics, Northeastern University, Boston, Massachusetts 02115, USA
    Nature 466:761-4. 2010
    ..Our results imply that link communities are fundamental building blocks that reveal overlap and hierarchical organization in networks to be two aspects of the same phenomenon...
  14. pmc Global landscape of HIV-human protein complexes
    Stefanie Jäger
    Department of Cellular and Molecular Pharmacology, University of California, San Francisco, California 94158, USA
    Nature 481:365-70. 2012
    ..This data set facilitates a more comprehensive and detailed understanding of how the host machinery is manipulated during the course of HIV infection...
  15. pmc A global protein kinase and phosphatase interaction network in yeast
    Ashton Breitkreutz
    Centre for Systems Biology, Samuel Lunenfeld Research Institute, 600 University Avenue, Toronto, Ontario, M5G 1X5, Canada
    Science 328:1043-6. 2010
    ..An extensive backbone of kinase-kinase interactions cross-connects the proteome and may serve to coordinate diverse cellular responses...
  16. pmc An empirical framework for binary interactome mapping
    Kavitha Venkatesan
    Center for Cancer Systems Biology and Department of Cancer Biology, Dana Farber Cancer Institute, 1 Jimmy Fund Way, Boston, MA 02115, USA
    Nat Methods 6:83-90. 2009
    ....
  17. ncbi Computing topological parameters of biological networks
    Yassen Assenov
    Department of Computational Biology and Applied Algorithmics, Max Planck Institute for Informatics, Stuhlsatzenhausweg 85, 66123 Saarbrucken, Germany
    Bioinformatics 24:282-4. 2008
    ..It is an interactive and highly customizable application that requires no expert knowledge in graph theory from the user...
  18. pmc Detecting overlapping protein complexes in protein-protein interaction networks
    Tamás Nepusz
    Department of Computer Science, Centre for Systems and Synthetic Biology, Royal Holloway, University of London, Egham Hill, Egham, UK
    Nat Methods 9:471-2. 2012
    ..The results also showed a high extent of functional homogeneity...
  19. pmc Independently evolved virulence effectors converge onto hubs in a plant immune system network
    M Shahid Mukhtar
    Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
    Science 333:596-601. 2011
    ..Thus, pathogens from different kingdoms deploy independently evolved virulence proteins that interact with a limited set of highly connected cellular hubs to facilitate their diverse life-cycle strategies...
  20. pmc A protein complex network of Drosophila melanogaster
    K G Guruharsha
    Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
    Cell 147:690-703. 2011
    ..The DPiM represents, to our knowledge, the largest metazoan protein complex map and provides a valuable resource for analysis of protein complex evolution...
  21. pmc STRING 8--a global view on proteins and their functional interactions in 630 organisms
    Lars J Jensen
    European Molecular Biology Laboratory, Heidelberg, Germany
    Nucleic Acids Res 37:D412-6. 2009
    ..Version 8.0 of STRING covers about 2.5 million proteins from 630 organisms, providing the most comprehensive view on protein-protein interactions currently available. STRING can be reached at http://string-db.org/...
  22. pmc Walking the interactome for prioritization of candidate disease genes
    Sebastian Kohler
    Institute for Medical Genetics, Charite Universitatsmedizin Berlin, Augustenburger Platz 1, 13353 Berlin, Germany
    Am J Hum Genet 82:949-58. 2008
    ....
  23. pmc Protein interaction data curation: the International Molecular Exchange (IMEx) consortium
    Sandra Orchard
    European Molecular Biology Laboratory European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, UK
    Nat Methods 9:345-50. 2012
    ..We discuss the advantages of such a service to the user, our quality-control measures and our data-distribution practices...
  24. pmc BioGRID: a general repository for interaction datasets
    Chris Stark
    Ontario Cancer Institute, Princess Margaret Hospital, 610 University Avenue, Toronto, Ontario, Canada M5G 2M9
    Nucleic Acids Res 34:D535-9. 2006
    ..User-customized graphs with embedded protein, gene and interaction attributes can be constructed with a visualization system called Osprey that is dynamically linked to the BioGRID...
  25. ncbi Q-SiteFinder: an energy-based method for the prediction of protein-ligand binding sites
    Alasdair T R Laurie
    School of Biochemistry and Microbiology, University of Leeds, UK
    Bioinformatics 21:1908-16. 2005
    ..Energetically favourable probe sites are clustered according to their spatial proximity and clusters are then ranked according to the sum of interaction energies for sites within each cluster...
  26. pmc iRefIndex: a consolidated protein interaction database with provenance
    Sabry Razick
    The Biotechnology Centre of Oslo, University of Oslo, PO Box 1125 Blindern, 0317 Oslo, Norway
    BMC Bioinformatics 9:405. 2008
    ..We set out to create a unifying index that would facilitate searching for these data and that would group together redundant interaction data while recording the methods used to perform this grouping...
  27. pmc Rewiring of genetic networks in response to DNA damage
    Sourav Bandyopadhyay
    Department of Medicine, University of California, San Diego, La Jolla, CA 92093, USA
    Science 330:1385-9. 2010
    ..Differential networks chart a new type of genetic landscape that is invaluable for mapping cellular responses to stimuli...
  28. pmc The BioGRID Interaction Database: 2008 update
    Bobby Joe Breitkreutz
    Samuel Lunenfeld Research Institute, Mount Sinai Hospital, Toronto, Canada
    Nucleic Acids Res 36:D637-40. 2008
    ..Source code for the BioGRID and the linked Osprey network visualization system is now freely available without restriction...
  29. pmc Associating genes and protein complexes with disease via network propagation
    Oron Vanunu
    School of Computer Science, Tel Aviv University, Tel Aviv, Israel
    PLoS Comput Biol 6:e1000641. 2010
    ..PRINCE's predictions for these diseases highly match the known literature, suggesting several novel causal genes and protein complexes for further investigation...
  30. pmc An automated method for finding molecular complexes in large protein interaction networks
    Gary D Bader
    Samuel Lunenfeld Research Institute, MT, Sinai Hospital, Toronto ON Canada M5G 1X5, Dept, of Biochemistry, University of Toronto, Toronto ON Canada M5S 1A8
    BMC Bioinformatics 4:2. 2003
    ..As the size of the interaction set increases, databases and computational methods will be required to store, visualize and analyze the information in order to effectively aid in knowledge discovery...
  31. ncbi Exploiting indirect neighbours and topological weight to predict protein function from protein-protein interactions
    Hon Nian Chua
    Graduate School for Integrated Sciences and Engineering, National University of Singapore, Singapore
    Bioinformatics 22:1623-30. 2006
    ..We are interested in finding out how significant is functional association between level-2 neighbours and how they can be exploited for protein function prediction...
  32. pmc ATTED-II provides coexpressed gene networks for Arabidopsis
    Takeshi Obayashi
    Human Genome Center, Institute of Medical Science, The University of Tokyo, 4 6 1 Shirokane dai, Minato ku, Tokyo 108 8639, Japan
    Nucleic Acids Res 37:D987-91. 2009
    ..With these enhanced functions for gene network representation, ATTED-II can help researchers to clarify the functional and regulatory networks of genes in Arabidopsis...
  33. ncbi COPASI--a COmplex PAthway SImulator
    Stefan Hoops
    Virginia Bioinformatics Institute, Virginia Tech, Washington St 0477, Blacksburg, VA 24061, USA
    Bioinformatics 22:3067-74. 2006
    ..Therefore, there is a big need for software tools that allow access to diverse simulation and modeling methods as well as support for the usage of these methods...
  34. pmc Up-to-date catalogues of yeast protein complexes
    Shuye Pu
    Molecular Structure and Function Program, Hospital for Sick Children, Toronto ON, M5G 1X8
    Nucleic Acids Res 37:825-31. 2009
    ..Some of these partially supported and as yet unsupported complexes may be interesting candidates for experimental follow up. Both catalogues are freely available at: http://wodaklab.org/cyc2008/...
  35. pmc Using manifold embedding for assessing and predicting protein interactions from high-throughput experimental data
    Zhu Hong You
    Intelligent Computing Laboratory, Institute of Intelligent Machines, Chinese Academy of Sciences, Hefei, Anhui, China
    Bioinformatics 26:2744-51. 2010
    ..Most previous works for assessing and predicting protein interactions either need supporting evidences from multiple information resources or are severely impacted by the sparseness of PPI networks...
  36. pmc A genetic interaction map of RNA-processing factors reveals links between Sem1/Dss1-containing complexes and mRNA export and splicing
    Gwendolyn M Wilmes
    Department of Biochemistry and Biophysics, University of California, San Francisco, 600 16th Street, Genentech Hall, San Francisco, CA 94143 2200, USA
    Mol Cell 32:735-46. 2008
    ..Finally, we show that Csn12 plays a role in pre-mRNA splicing, which is independent of other signalosome components. Thus, Sem1 is involved in three separate and functionally distinct complexes...
  37. pmc SMART 6: recent updates and new developments
    Ivica Letunic
    EMBL, Meyerhofstrasse 1, 69012 Heidelberg, Germany
    Nucleic Acids Res 37:D229-32. 2009
    ..In addition to the standard web access to the database, users can now query SMART using distributed annotation system (DAS) or through a simple object access protocol (SOAP) based web service...
  38. ncbi Relating protein pharmacology by ligand chemistry
    Michael J Keiser
    Department of Pharmaceutical Chemistry, University of California San Francisco, 1700 4th St, San Francisco California 94143 2550, USA
    Nat Biotechnol 25:197-206. 2007
    ..These predictions were subsequently confirmed experimentally. Relating receptors by ligand chemistry organizes biology to reveal unexpected relationships that may be assayed using the ligands themselves...
  39. ncbi ZDOCK: an initial-stage protein-docking algorithm
    Rong Chen
    Bioinformatics Program, Boston University, Boston, Massachusetts, USA
    Proteins 52:80-7. 2003
    ..All four scoring functions have been integrated into our Fast Fourier Transform based docking algorithm ZDOCK, which is freely available to academic users at http://zlab.bu.edu/~ rong/dock...
  40. ncbi Event extraction for systems biology by text mining the literature
    Sophia Ananiadou
    University of Manchester, Manchester M13 9PL, UK
    Trends Biotechnol 28:381-90. 2010
    ..The approaches described will be of considerable value in associating particular pathways and their components with higher-order physiological properties, including disease states...
  41. pmc Prediction of drug-target interaction networks from the integration of chemical and genomic spaces
    Yoshihiro Yamanishi
    Bioinformatics Center, Institute for Chemical Research, Kyoto University, Gokasho, Uji, Kyoto 611 0011, Japan
    Bioinformatics 24:i232-40. 2008
    ..Therefore, there is a strong incentive to develop new methods capable of detecting these potential drug-target interactions efficiently...
  42. pmc DOMINE: a comprehensive collection of known and predicted domain-domain interactions
    Sailu Yellaboina
    Biostatistics Branch, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709, USA
    Nucleic Acids Res 39:D730-5. 2011
    ..The contents of the DOMINE are available at http://domine.utdallas.edu...
  43. pmc The power of protein interaction networks for associating genes with diseases
    Saket Navlakha
    Center for Bioinformatics and Computational Biology, Institute for Advanced Computer Studies and Department of Computer Science, University of Maryland College Park, College Park, MD 20742, USA
    Bioinformatics 26:1057-63. 2010
    ..Despite the recent interest in this problem, however, there is little understanding of the relative benefits and drawbacks underlying the proposed techniques...
  44. pmc ConsensusPathDB: toward a more complete picture of cell biology
    Atanas Kamburov
    Vertebrate Genomics Department, Max Planck Institute for Molecular Genetics, Ihnestr 63 73, 14195 Berlin, Germany
    Nucleic Acids Res 39:D712-7. 2011
    ....
  45. pmc STITCH 2: an interaction network database for small molecules and proteins
    Michael Kuhn
    Biotechnology Center, TU Dresden, 01062 Dresden, Germany
    Nucleic Acids Res 38:D552-6. 2010
    ..STITCH 2.0 connects proteins from 630 organisms to over 74,000 different chemicals, including 2200 drugs. STITCH can be accessed at http://stitch.embl.de/...
  46. pmc A human functional protein interaction network and its application to cancer data analysis
    Guanming Wu
    Ontario Institute for Cancer Research, MaRS Centre, South Tower, 101 College Street, Suite 800, Toronto, ON M5G 0A3, Canada
    Genome Biol 11:R53. 2010
    ..A pathway-based analysis may shed light by projecting candidate genes onto protein functional relationship networks. We are building such a pathway-based analysis system...
  47. pmc High-quality binary protein interaction map of the yeast interactome network
    Haiyuan Yu
    Center for Cancer Systems Biology CCSB, Dana Farber Cancer Institute, Boston, MA 02115, USA
    Science 322:104-10. 2008
    ..Rather than correlating with essentiality, protein connectivity correlates with genetic pleiotropy...
  48. ncbi Dynamic protein-protein interaction wiring of the human spliceosome
    Anna Hegele
    Otto Warburg Laboratory, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany
    Mol Cell 45:567-80. 2012
    ..Our data provide extensive information about the spliceosomal protein interaction network and its dynamics...
  49. pmc 3did: identification and classification of domain-based interactions of known three-dimensional structure
    Amelie Stein
    Institute for Research in Biomedicine, Join IRB BSC Program in Computational Biology, 08028 Barcelona, Spain
    Nucleic Acids Res 39:D718-23. 2011
    ..The 3did web server at http://3did.irbbarcelona.org visualizes these interfaces along with atomic details of individual interactions using Jmol. The complete contents are also available for download...
  50. ncbi Complex discovery from weighted PPI networks
    Guimei Liu
    School of Computing, National University of Singapore, Singapore and Institute for Infocomm Research, Singapore
    Bioinformatics 25:1891-7. 2009
    ..However, protein interaction data produced by high-throughput experiments are often associated with high false positive and false negative rates, which makes it difficult to predict complexes accurately...
  51. pmc NetPath: a public resource of curated signal transduction pathways
    Kumaran Kandasamy
    Institute of Bioinformatics, International Tech Park, Bangalore 560066, India
    Genome Biol 11:R3. 2010
    ..We anticipate NetPath to become a consolidated resource for human signaling pathways that should enable systems biology approaches...
  52. ncbi Getting connected: analysis and principles of biological networks
    Xiaowei Zhu
    Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, Connecticut 06520, USA
    Genes Dev 21:1010-24. 2007
    ..Analyzing these networks provides novel insights in understanding basic mechanisms controlling normal cellular processes and disease pathologies...
  53. pmc Measuring the evolutionary rate of protein-protein interaction
    Wenfeng Qian
    Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109, USA
    Proc Natl Acad Sci U S A 108:8725-30. 2011
    ..The extremely slow evolution of protein molecular function may account for the remarkable conservation of life at molecular and cellular levels and allow for studying the mechanistic basis of human disease in much simpler organisms...
  54. pmc HIPPIE: Integrating protein interaction networks with experiment based quality scores
    Martin H Schaefer
    Max Delbruck Center for Molecular Medicine, Berlin, Germany
    PLoS ONE 7:e31826. 2012
    ..The HIPPIE web tool (available at http://cbdm.mdc-berlin.de/tools/hippie) allows researchers to do network analyses focused on likely true PPI sets by generating subnetworks around proteins of interest at a specified confidence level...
  55. pmc PINA v2.0: mining interactome modules
    Mark J Cowley
    Cancer Research Program, Peter Wills Bioinformatics Centre, Garvan Institute of Medical Research, Darlinghurst, Sydney, NSW 2010, Australia
    Nucleic Acids Res 40:D862-5. 2012
    ..The interactome data are also available on the web site for further bioinformatics analysis. PINA is freely accessible at http://cbg.garvan.unsw.edu.au/pina/...
  56. pmc Identification of direct residue contacts in protein-protein interaction by message passing
    Martin Weigt
    Center for Theoretical Biological Physics and Department of Physics, University of California at San Diego, La Jolla, CA 92093 0374, USA
    Proc Natl Acad Sci U S A 106:67-72. 2009
    ....
  57. pmc Genome-wide prioritization of disease genes and identification of disease-disease associations from an integrated human functional linkage network
    Bolan Linghu
    Bioinformatics Program, Boston University, 24 Cummington Street, Boston, MA 02215, USA
    Genome Biol 10:R91. 2009
    ..Many of these disease-disease associations are supported by epidemiology, but with no previous genetic basis. Such associations can drive novel hypotheses on molecular mechanisms of diseases and therapies...
  58. pmc An experimentally derived confidence score for binary protein-protein interactions
    Pascal Braun
    Center for Cancer Systems Biology and Department of Cancer Biology, Dana Farber Cancer Institute, 44 Binney Street, Boston, MA 02115, USA
    Nat Methods 6:91-7. 2009
    ..This general approach will allow a systematic and empirical assignment of confidence scores to all individual protein-protein interactions in interactome networks...
  59. ncbi Evolution of biomolecular networks: lessons from metabolic and protein interactions
    Takuji Yamada
    European Molecular Biology Laboratory, Heidelberg, Germany
    Nat Rev Mol Cell Biol 10:791-803. 2009
    ..However, many evolutionary constraints can be uncovered only if temporal and spatial aspects are included in the network analysis...
  60. pmc GeneCards Version 3: the human gene integrator
    Marilyn Safran
    Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
    Database (Oxford) 2010:baq020. 2010
    ..Finally, we delineate examples of applications and collaborations that have benefited from the GeneCards suite. Database URL: www.genecards.org...
  61. ncbi Modeling interactome: scale-free or geometric?
    N Przulj
    Department of Computer Science, University of Toronto, Toronto, M5S 3G4, Canada
    Bioinformatics 20:3508-15. 2004
    ..Since incorrect models lead to incorrect predictions, it is vital to have as accurate a model as possible. As a result, new techniques and models for analyzing and modeling real-world networks have recently been introduced...
  62. ncbi Reverse engineering of regulatory networks in human B cells
    Katia Basso
    Institute for Cancer Genetics, 1300 St Nicholas Avenue, Room 912, New York, New York 10032, USA
    Nat Genet 37:382-90. 2005
    ..The newly identified MYC targets include some major hubs. This approach can be generally useful for the analysis of normal and pathologic networks in mammalian cells...
  63. pmc DroID 2011: a comprehensive, integrated resource for protein, transcription factor, RNA and gene interactions for Drosophila
    Thilakam Murali
    Center for Molecular Medicine and Genetics, Wayne State University School of Medicine, Detroit, Michigan, USA
    Nucleic Acids Res 39:D736-43. 2011
    ..Improvements have been made to the web and graphical interfaces to help biologists gain a comprehensive view of the interaction networks relevant to the genes and systems that they study...
  64. ncbi ClusPro: an automated docking and discrimination method for the prediction of protein complexes
    Stephen R Comeau
    Bioinformatics Graduate Program and Department, Boston University, 44 Cummington St, Boston, MA 02215, USA
    Bioinformatics 20:45-50. 2004
    ..e. structures with good surface complementarity but far from the native...
  65. pmc Semi-supervised multi-task learning for predicting interactions between HIV-1 and human proteins
    Yanjun Qi
    NEC LABS AMERICA, Princeton, NJ 08540, USA
    Bioinformatics 26:i645-52. 2010
    ..Meanwhile, there exists a considerable amount of protein pairs where an association appears between two partners, but not enough experimental evidence to support it as a direct interaction (partially labeled)...
  66. ncbi Chemical and structural lessons from recent successes in protein-protein interaction inhibition (2P2I)
    Xavier Morelli
    Interactions et Modulateurs de Réponses UPR3243, Centre National de la Recherche Scientifique CNRS and Université de Provence, 31 Chemin Joseph Aiguier, 13402 Marseille Cedex 20, France
    Curr Opin Chem Biol 15:475-81. 2011
    ..Finally, ligand efficiency analyses permit us to relate potency to size and polarity and to discuss the need to co-develop nanoparticle drug delivery systems...
  67. pmc HINT: High-quality protein interactomes and their applications in understanding human disease
    Jishnu Das
    Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, NY 14853, USA
    BMC Syst Biol 6:92. 2012
    ..A repository of well-validated high-quality protein-protein interactions can be used in both large- and small-scale studies to generate and validate a wide range of functional hypotheses...
  68. pmc IBIS (Inferred Biomolecular Interaction Server) reports, predicts and integrates multiple types of conserved interactions for proteins
    Benjamin A Shoemaker
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, 8600 Rockville Pike, Building 38A, Bethesda, MD 20894, USA
    Nucleic Acids Res 40:D834-40. 2012
    ..The IBIS server is available at http://www.ncbi.nlm.nih.gov/Structure/ibis/ibis.cgi and updated biweekly...
  69. pmc The ConsensusPathDB interaction database: 2013 update
    Atanas Kamburov
    Department of Vertebrate Genomics, Max Planck Institute for Molecular Genetics, Ihnestrasse 63 73, 14195 Berlin, Germany
    Nucleic Acids Res 41:D793-800. 2013
    ..To facilitate the interactive, visual interpretation of interaction and pathway data, we have re-implemented the graph visualization feature of ConsensusPathDB using the Cytoscape.js library...
  70. pmc Analysis of the human endogenous coregulator complexome
    Anna Malovannaya
    Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, USA
    Cell 145:787-99. 2011
    ..This resource will effectively fill a void in linking correlative genomic studies with an understanding of transcriptional regulatory protein functions within the proteome for formulation and testing of future hypotheses...
  71. pmc A comprehensive benchmark of kernel methods to extract protein-protein interactions from literature
    Domonkos Tikk
    Knowledge Management in Bioinformatics, Computer Science Department, Humboldt Universitat zu Berlin, Berlin, Germany
    PLoS Comput Biol 6:e1000837. 2010
    ..Nevertheless, our study shows that three kernels are clearly superior to the other methods...
  72. pmc Why do hubs in the yeast protein interaction network tend to be essential: reexamining the connection between the network topology and essentiality
    Elena Zotenko
    Max Planck Institute for Informatics, Saarbruecken, Germany
    PLoS Comput Biol 4:e1000140. 2008
    ....
  73. pmc Network modeling identifies molecular functions targeted by miR-204 to suppress head and neck tumor metastasis
    Younghee Lee
    Section of Genetic Medicine and Center for Biomedical Informatics, Department of Medicine, The University of Chicago, Chicago, Illinois, United States of America
    PLoS Comput Biol 6:e1000730. 2010
    ....
  74. pmc Using support vector machine combined with auto covariance to predict protein-protein interactions from protein sequences
    Yanzhi Guo
    College of Chemistry, Sichuan University, Chengdu 610064 and State Key Laboratory of Biotherapy, Sichuan University, Chengdu 610041, P R China
    Nucleic Acids Res 36:3025-30. 2008
    ..The prediction software and all data sets used in this article are freely available at http://www.scucic.cn/Predict_PPI/index.htm...
  75. pmc The impact of multifunctional genes on "guilt by association" analysis
    Jesse Gillis
    Department of Psychiatry, University of British Columbia, Centre for High Throughput Biology, Vancouver, British Columbia, Canada
    PLoS ONE 6:e17258. 2011
    ..We suggest that this source of bias due to multifunctionality is important to control for, with widespread implications for the interpretation of genomics studies...
  76. pmc Next-generation sequencing to generate interactome datasets
    Haiyuan Yu
    Center for Cancer Systems Biology, Department of Cancer Biology, Dana Farber Cancer Institute, Boston, Massachusetts, USA
    Nat Methods 8:478-80. 2011
    ..Stitch-seq is applicable to various interaction assays and should help expand interactome network mapping...
  77. pmc ClusPro: a fully automated algorithm for protein-protein docking
    Stephen R Comeau
    Bioinformatics Graduate Program, Boston University, 44 Cummington Street, Boston, MA 02215, USA
    Nucleic Acids Res 32:W96-9. 2004
    ..The program output is a short list of putative complexes ranked according to their clustering properties, which is automatically sent back to the user via email...
  78. pmc Inferring cellular networks--a review
    Florian Markowetz
    Max Planck Institute for Molecular Genetics, Ihnestrasse 63 73, 14195 Berlin, Germany
    BMC Bioinformatics 8:S5. 2007
    ..The second part discusses probabilistic and graph-based methods for data from experimental interventions and perturbations...
  79. pmc VirusMINT: a viral protein interaction database
    Andrew Chatr-Aryamontri
    Department of Biology, University of Rome Tor Vergata, Via della Ricerca Scientifica, 00133 Rome, Italy
    Nucleic Acids Res 37:D669-73. 2009
    ....
  80. pmc A comprehensive resource of interacting protein regions for refining human transcription factor networks
    Etsuko Miyamoto-Sato
    Advanced Research Centers, Keio University, Yokohama, Japan
    PLoS ONE 5:e9289. 2010
    ..Accordingly, this domain-based interaction resource represents an important step in refining protein interactions and networks at the domain level and in associating network analysis with biological structure and function...
  81. pmc Disease candidate gene identification and prioritization using protein interaction networks
    Jing Chen
    Division of Biomedical Informatics, Cincinnati Children s Hospital Medical Center, Cincinnati, OH, USA
    BMC Bioinformatics 10:73. 2009
    ..In the current study, we describe a candidate gene prioritization method that is entirely based on protein-protein interaction network (PPIN) analyses...
  82. pmc Structure-based prediction of protein-protein interactions on a genome-wide scale
    Qiangfeng Cliff Zhang
    Howard Hughes Medical Institute, Columbia University, New York, New York 10032, USA
    Nature 490:556-60. 2012
    ..The surprising effectiveness of three-dimensional structural information can be attributed to the use of homology models combined with the exploitation of both close and remote geometric relationships between proteins...
  83. pmc Geometric de-noising of protein-protein interaction networks
    Oleksii Kuchaiev
    Department of Computer Science, University of California, Irvine, California, USA
    PLoS Comput Biol 5:e1000454. 2009
    ..The data and Matlab code implementing the methods are freely available from the web site: http://www.kuchaev.com/Denoising...
  84. pmc PepX: a structural database of non-redundant protein-peptide complexes
    Peter Vanhee
    VIB Switch Laboratory, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium
    Nucleic Acids Res 38:D545-51. 2010
    ..Moreover, we provide an additional source of data for peptide design by annotating peptides with naturally occurring backbone variations using fragment clusters from the BriX database...
  85. pmc COXPRESdb: a database to compare gene coexpression in seven model animals
    Takeshi Obayashi
    Graduate School of Information Science, Tohoku University, 6 3 09 Aramaki Aza Aoba, Aoba ku, Sendai 980 8679, Japan
    Nucleic Acids Res 39:D1016-22. 2011
    ..With the functions for gene network representation, COXPRESdb can help researchers to clarify the functional and regulatory networks of genes in a broad array of animal species...
  86. ncbi BioNet: an R-Package for the functional analysis of biological networks
    Daniela Beisser
    Department of Bioinformatics, Biocenter, University of Wurzburg, Am Hubland, 97074 Wurzburg, Germany
    Bioinformatics 26:1129-30. 2010
    ..Here, we present a comprehensive R-package for the analysis of biological networks including an exact and a heuristic approach to identify functional modules...
  87. pmc Computational approaches for detecting protein complexes from protein interaction networks: a survey
    Xiaoli Li
    Institute for Infocomm Research, 1 Fusionopolis Way, Singapore
    BMC Genomics 11:S3. 2010
    ..They can be used together with the experimental methods for mapping the interactions of proteins to understand how different proteins are organized into higher-level substructures to perform various cellular functions...
  88. pmc Inferred Biomolecular Interaction Server--a web server to analyze and predict protein interacting partners and binding sites
    Benjamin A Shoemaker
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    Nucleic Acids Res 38:D518-24. 2010
    ..IBIS is updated regularly and is freely accessible via http://www.ncbi.nlm.nih.gov/Structure/ibis/ibis.html...
  89. ncbi Protein-protein docking with backbone flexibility
    Chu Wang
    Department of Biochemistry and Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, USA
    J Mol Biol 373:503-19. 2007
    ..The explicit treatment of backbone flexibility improves both sampling in the vicinity of the native docked conformation and the energetic discrimination between near-native and incorrect models...
  90. pmc Evaluating contributions of natural language parsers to protein-protein interaction extraction
    Yusuke Miyao
    Department of Computer Science, University of Tokyo, Tokyo, Japan
    Bioinformatics 25:394-400. 2009
    ..We measure how each parser, and its output representation, contributes to accuracy improvement when the parser is used as a component in a PPI system...
  91. pmc Protein-protein docking benchmark version 3.0
    Howook Hwang
    Bioinformatics Program, Boston University, Boston, Massachusetts 02215, USA
    Proteins 73:705-9. 2008
    ..0 will facilitate the development of new algorithms that require a large number of training examples. Benchmark 3.0 is available to the public at http://zlab.bu.edu/benchmark...
  92. pmc 3did Update: domain-domain and peptide-mediated interactions of known 3D structure
    Amelie Stein
    Institute for Research in Biomedicine, Barcelona Supercomputing Center, c Baldiri Reixac 10 12, 08028 Barcelona, Spain
    Nucleic Acids Res 37:D300-4. 2009
    ..A web-based tool to query 3did is available at http://3did.irbbarcelona.org...
  93. pmc AtPIN: Arabidopsis thaliana protein interaction network
    Marcelo M Brandão
    Departamento de Genetica, Escola Superior de Agricultura Luiz de Queiroz, Universidade de Sao Paulo, 13400 970 Piracicaba, SP, Brazil
    BMC Bioinformatics 10:454. 2009
    ..To study PPI in Arabidopsis thaliana we have developed AtPIN, a database and web interface for searching and building interaction networks based on publicly available protein-protein interaction datasets...
  94. pmc Proteome scanning to predict PDZ domain interactions using support vector machines
    Shirley Hui
    Donnelly Center for Cellular and Biomolecular Research, Banting and Best Department of Medical Research, University of Toronto, Toronto ON, Canada
    BMC Bioinformatics 11:507. 2010
    ..Once validated these predictions will help to increase the coverage of current PDZ domain interaction networks and further our understanding of the roles that PDZ domains play in a variety of biological processes...
  95. pmc Functional modules in the Arabidopsis core cell cycle binary protein-protein interaction network
    Joanna Boruc
    Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium
    Plant Cell 22:1264-80. 2010
    ..The obtained interaction map constitutes a framework for further in-depth analysis of the cell cycle machinery...
  96. pmc DroID: the Drosophila Interactions Database, a comprehensive resource for annotated gene and protein interactions
    Jingkai Yu
    Center for Molecular Medicine and Genetics, Wayne State University School of Medicine, 540 East Canfield Ave, Detroit, MI 48201, USA
    BMC Genomics 9:461. 2008
    ..No single database, for example, includes all available interactions, integrated gene expression data, and comprehensive and searchable gene information for the important model organism, Drosophila melanogaster...
  97. pmc ConsensusPathDB--a database for integrating human functional interaction networks
    Atanas Kamburov
    Max Planck Institute for Molecular Genetics, Ihnestr 63 73, 14195 Berlin, Germany
    Nucleic Acids Res 37:D623-8. 2009
    ..The ConsensusPathDB database is available at: http://cpdb.molgen.mpg.de...
  98. pmc Protein-protein docking benchmark version 4.0
    Howook Hwang
    Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA
    Proteins 78:3111-4. 2010
    ..Benchmark 4.0 listings and processed structure files are publicly accessible at http://zlab.umassmed.edu/benchmark/...
  99. ncbi Docking and scoring protein interactions: CAPRI 2009
    Marc F Lensink
    Genome and Network Bioinformatics, CP 263, BC6, Universite Libre de Bruxelles, Blvd du Triomphe, 1050 Bruxelles, Belgium
    Proteins 78:3073-84. 2010
    ....
  100. pmc The landscape of human proteins interacting with viruses and other pathogens
    Matthew D Dyer
    Genetics, Bioinformatics, and Computational Biology Program, Virginia Polytechnic Institute and State University, Blacksburg, Virginia, United States of America
    PLoS Pathog 4:e32. 2008
    ..Supplementary data accompanying this paper is available at http://staff.vbi.vt.edu/dyermd/publications/dyer2008a.html...

Research Grants68

  1. Integrating computation and genetics to quantify specificity in protein networks
    Nevan J Krogan; Fiscal Year: 2013
    ..protein modeling and design (Tanja Kortemme) and in large-scale, quantitative genetic and protein-protein interaction mapping strategies (Nevan Krogan)...
  2. Identifying New Aging and Longevity Genes in Caenorhabditis elegans
    Muneesh Tewari; Fiscal Year: 2007
    ..signaling pathway, will be used as baits in genome-wide yeast two-hybrid screens (an approach termed protein interaction mapping)...
  3. A C. elegans localization-of-expression mapping project
    Marc Vidal; Fiscal Year: 2002
    ..mapping), high-throughput gene knock-out analyses (phoneme mapping) and large-scale protein-protein interaction mapping (interactome mapping) can be used to identify orthologs of potential cancer genes...
  4. CENTER FOR STRUCTURAL BIOLOGY
    Vernon Reinhold; Fiscal Year: 2003
    ..Directed and guided by experienced hands in K-12 through graduate science teaching (Hopkins, Bauer, resp.,), this component of our Program may be the most compelling and long lasting. ..
  5. Tiling Path Microarray Re-amplifable Resource Drosophila
    Kevin White; Fiscal Year: 2006
    ..These arrays can be used for DNA-protein interaction mapping, comprehensive expression profiling, replication origin mapping, comparative genomic hybridization, ..
  6. NEW TECHNOLOGIES FOR PROTEIN INTERACTION MAPPING
    Marc Vidal; Fiscal Year: 1999
    ..to as "functional genomics" include genome-wide expression analysis, gene knock-outs and protein-protein interaction mapping. They are expected to reveal gene functions at a drastically increased rate...
  7. NEW TECHNOLOGIES FOR PROTEIN INTERACTION MAPPING
    Marc Vidal; Fiscal Year: 2002
    ..to as "functional genomics" include genome-wide expression analysis, gene knock-outs and protein-protein interaction mapping. They are expected to reveal gene functions at a drastically increased rate...
  8. Comprehensive Protein Interaction Mapping in Mammals
    STEVEN PRUITT; Fiscal Year: 2004
    ..Based on the utility of similar protein interaction maps in model organisms, this work can be expected to provide an enormous wealth of insight into the function of mammalian cells. ..
  9. Structural Analyses of Fission Yeast Splicing Complexes
    KATHLEEN GOULD; Fiscal Year: 2006
    ..abstract_text> ..
  10. BRANCHED CHAIN AMINO ACID METABOLISM
    SUSAN HUTSON; Fiscal Year: 2008
    ..It is our hope that the ideas put forth in this proposal will bring new ways of thinking into the field of amino acid metabolism and will lead to exciting new research directions. ..
  11. Biology of HHV-8 interactions with host cells
    Bala Chandran; Fiscal Year: 2007
    ..Further understanding of HHV-8-cell signaling will broaden our knowledge of HHV-8 related diseases and eventually lead to new anti-HHV-8 agents, and therapeutic agents against KS. ..
  12. Zebrafish Protein & Antibody Core
    Brian Kay; Fiscal Year: 2008
    ..We propose a sharing plan consisting of a website containing publicly accessible data, presentations at scientific meetings, and distribution of requested reagents and protocols. [unreadable] [unreadable] [unreadable]..
  13. A C. elegans localization-of-expression mapping project
    Marc Vidal; Fiscal Year: 2005
    ..mapping), high-throughput gene knock-out analyses (phoneme mapping) and large-scale protein-protein interaction mapping (interactome mapping) can be used to identify orthologs of potential cancer genes...
  14. In vivo panning for schistosome protective epitopes
    Charles Shoemaker; Fiscal Year: 2005
    ....
  15. MOLECULAR PHYSIOLOGY OF BAND 3 LIKE PROTEINS OF KIDNEY
    Seth Alper; Fiscal Year: 2007
    ..5. Define aspects of transcriptional and translational regulation of AE gene products in kidney of mutant and parental mouse strains and in cultured kidney cells. ..
  16. Mechanisms and Evolutionary Potential of Promiscuous Enzyme Activities
    SHELLEY COPLEY; Fiscal Year: 2007
    ..Thus, the processes by which new enzyme activities evolve are of great interest for both theoretical and practical reasons. ..
  17. Mechanisms of Thrombus Instability
    ZAVERIO RUGGERI; Fiscal Year: 2007
    ..These studies will provide novel insights into the unexpected role of leptin in platelet function, and in the formation and stability of thrombi. ..
  18. Signal Transduction in Models of Fibroblast Invasion
    JASON HAUGH; Fiscal Year: 2007
    ..These efforts will serve as a foundation for more in-depth studies of molecular mechanisms governing physiological processes. [unreadable] [unreadable] [unreadable]..
  19. Function of a-1-Antitrypsin Receptor in Lung Disease
    William Balch; Fiscal Year: 2006
    ..unreadable] [unreadable]..
  20. Initiation and Regulation of Platelet Thrombus Formation
    ZAVERIO RUGGERI; Fiscal Year: 2004
    ..The results of the proposed studies will have an impact on public health by providing novel mechanistic information on processes that are central to normal hemostasis and pathological arterial thrombosis. ..
  21. NFkB Targets and Neural Crest Development
    MICHAEL WILLIAM KLYMKOWSKY; Fiscal Year: 2010
    ..Together these observation should have important implications for understanding the behavior of molecular and inductive networks in general and the prevention and/or amelioration of neural crest defects in particular. ..
  22. Molecular Mechanisms of Natural Killer Cell Activation
    Subramaniam Malarkannan; Fiscal Year: 2010
    ..Mechanisms identified here will not only have practical implications in tumor and graft immunity but will serve as models for other systems in which the responding cell must balance a number of activating and inhibitory inputs. ..
  23. Mapping the Human Binary Interactome Network
    MARC contact VIDAL; Fiscal Year: 2010
    ..Our modified specific aims are to: i) Provide an expanded high-confidence/high-coverage version of the human binary interactome map ii) Validate human binary interaction data iii) Analyze the expanded human interactome model ..
  24. PROFILING AUTOANTIGENS IN UVEITIS
    Wei Li; Fiscal Year: 2010
    ..These efforts will advance our understanding of the disease etiology and prognosis, and improve the diagnosis and therapy. ..
  25. Hierarchical Methods for Large BioMolecular Complexes
    Chandrajit L Bajaj; Fiscal Year: 2010
    ..AIM 4: To implement, test, package and freely distribute our structural feature determination and fast search/fitting techniques. ..
  26. Acquisition of an electrospray TOF mass spectrometer
    IGOR KALTASHOV; Fiscal Year: 2004
    ..The operation of the instrument will be overseen by a Mass Spectrometry Advisory committee comprised of faculty members representing three academic departments and one interdisciplinary research center at UMass. ..
  27. Communication between Kupffer cells and stellate cells
    Natalia Nieto; Fiscal Year: 2009
    ..We hope that this co-culture model will help us to define the effects of Kupffer cells on the stellate cell fibrogenic response and to dissect potential therapeutic targets for preventing liver disease. ..
  28. New Technology for Protein Interaction Network and Topology Analysis
    James Bruce; Fiscal Year: 2009
    ....
  29. HUPO 2nd Annual World Congress Montreal 2003
    Samir Hanash; Fiscal Year: 2003
    ....
  30. RBC Ion Transporters as Hemoglobinopathy Risk Modifiers
    Seth Alper; Fiscal Year: 2009
    ..The proposed experiments will increase understanding of sickle cell disease and thalassemia by providing mouse models for genetic tests of new drug therapies under development for near-term clinical testing. ..
  31. Imaging Vaccina Viral-Host Pathogenesis
    Gary Luker; Fiscal Year: 2007
    ..Collectively, the research is expected to facilitate the development of improved vaccines and treatments for smallpox, thereby enhancing our ability to prevent the use of smallpox for bioterrorism. [unreadable] [unreadable] [unreadable]..
  32. Entry of HHV-8 Into the Target Cells
    Bala Chandran; Fiscal Year: 2009
    ..Further understanding of HHV-8-entry, integrin-dependent cell signaling pathways, and their role in infection would eventually lead to the development of new anti-HHV-8 agents. ..
  33. Physiologic Genomics of Pulmonary Hypertension & RVH
    SINA GHARIB; Fiscal Year: 2008
    ..Ultimately, this mentored research career award will allow the PI to develop into an independent computational molecular biologist and pursue an academic research career in the physiologic genomics of the cardiopulmonary system. ..
  34. REGULATION OF BRAIN NEUROTRANSMITTER SYNTHESIS
    SUSAN HUTSON; Fiscal Year: 2007
    ..unreadable] [unreadable] [unreadable]..
  35. Software Maintenance for Biomolecular Complexes
    Chandrajit L Bajaj; Fiscal Year: 2010
    ..3. Continued documentation and web based dissemination of all the components (libraries and tools) of our MVP. (http://ccvweb.csres.utexas.edu/software/). ..
  36. UL34 and herpes simplex virus envelopment
    Richard J Roller; Fiscal Year: 2010
    ..3. We will fully characterize changes in the host cell nuclear lamina associated with infection and determine the mechanism by which UL34 and other viral proteins accomplish those changes. ..
  37. A New Approach to Rapid Protein-Protein Docking
    Chandrajit Bajaj; Fiscal Year: 2008
    ..abstract_text> ..
  38. Antitumor Mechanisms of SRC Inhibitors in Lung Cancer
    Eric Haura; Fiscal Year: 2008
    ..unreadable] [unreadable] [unreadable]..
  39. Analysis and Statistical Validation of Proteomic Datasets
    Alexey Nesvizhskii; Fiscal Year: 2009
    ....
  40. Structure and function of platelet membrane glycoproteins
    ZAVERIO RUGGERI; Fiscal Year: 2008
    ..abstract_text> ..
  41. Integrating and Disseminating Functional Genomics Data
    David Botstein; Fiscal Year: 2007
    ....
  42. STRUCTURE/FUNCTION OF THE SNARE COMPLEX
    Phyllis Hanson; Fiscal Year: 2002
    ....
  43. ENVELOPE GLYCOPROTEINS OF HHV8
    Bala Chandran; Fiscal Year: 2002
    ..1(A and B) and gB will lead into an important in sight into the development of future control measures. ..
  44. Analysis to enhance sensitivity for membrane proteins
    Samir Hanash; Fiscal Year: 2002
    ....
  45. Sickle Red Cell K+ Transporter Genetics in S. cerevisiae
    Seth Alper; Fiscal Year: 2002
    ..3) (Provisional Aim): Time permitting, to improve, validate, and standardize growth rescue of trk1delta/trk2delta S. cerevisiae by expression in nonpermissive conditions of cDNA encoding the mammalian IK1 K(ca) channel. ..
  46. Purchase of BIAcore 3000 Instrument
    Satya Yadav; Fiscal Year: 2003
    ..In this way, the authentic presentation of the cytoplasmic domain as visualized from the interior of the cell will be maintained. ..
  47. CATENINS, EPITHELIAL BEHAVIOR AND GENE EXPRESSION
    Michael Klymkowsky; Fiscal Year: 2004
    ..We will test whether decreasing the expression of specific SOXs using anti-sense reagents leads to the predicted expansion of TCF regulated target genes and/or increased sensitivity of embryonic cells to Wnt signaling components ..
  48. A Proteome Map of Neutrophil Granules
    KENNETH MCLEISH; Fiscal Year: 2004
    ..These hypotheses will lead to NIH applications to confirm these mechanisms and to identify methods to interrupt neutrophil participation in acute renal injury. ..
  49. STRUCTURE/FUNCTION OF HIV1 CAPSID/CYCLOPHILIN COMPLEX
    Wesley Sundquist; Fiscal Year: 2001
    ..Finally, genetic analysis of mutants of CA in an HIV provirus will be used to test models that arise from the CA and CA-cyclophilin structures. ..
  50. ION CHANNEL REGULATION BY THE CYTOPLASMIC TAIL OF PDK1
    Seth Alper; Fiscal Year: 2005
    ..We will search for novel interacting proteins, and prepare protein suitable for structural analysis. ..
  51. Integrated interactome mapping
    Marc Vidal; Fiscal Year: 2006
    ..abstract_text> ..
  52. Structural Biology of HIV Assembly, Budding, and Entry
    Wesley Sundquist; Fiscal Year: 2006
    ..In summary, our Program will provide significant insights into how the HIV virion functions as a machine that can enter and exit cells, and how these processes can be inhibited. ..
  53. Conference on Systems & Biology
    Marc Vidal; Fiscal Year: 2005
    ..abstract_text> ..
  54. Mapping worm fat gene networks
    ALBERTHA WALHOUT; Fiscal Year: 2006
    ..In addition, we recently developed a version of the yeast one-hybrid system that enables us to map fat TF-fat gene interactions in a high-throughput manner. ..
  55. Recruitment of Enzymes to Serve New Functions
    SHELLEY COPLEY; Fiscal Year: 2006
    ....
  56. INHIBITION OF CELL-MEDIATED PROMMP-2 ACTIVATION IN ORAL CANCER
    Xiaoping Xu; Fiscal Year: 2008
    ..This research project will test new approaches to inhibit MMPs. The goal is to develop MMP inhibitors for treatment of oral cancer. [unreadable] [unreadable] [unreadable]..
  57. Platelet interactions with vessel wall components
    ZAVERIO RUGGERI; Fiscal Year: 2005
    ..These findings will provide a better definition and characterization of several potential targets for antithrombotic intervention that may yield new treatments for patients at risk of cardiovascular and cerebrovascular events. ..
  58. Molecular Crosstalk in Intracellular Signaling Netoworks
    JASON HAUGH; Fiscal Year: 2006
    ..Finally, for conditions found to perturb the signaling network, the corresponding effects on cell proliferation and survival will be assessed. ..
  59. A PROGRAM FOR RAT GENE DISCOVERY AND MAPPING
    Val Sheffield; Fiscal Year: 2001
    ..Progress during the initial phase of this project resulted in unprecedented efficiency in gene discovery. ..
  60. Automated Literature Mining for Validation of High-Throughput Function Prediction
    KARIN MARIA VERSPOOR; Fiscal Year: 2010
    ..It is time to truly integrate the biological literature into the protein function prediction problem. By doing so, we will enable a critical advance in high-throughput protein function prediction ..
  61. Molecular Genetics of Glaucoma
    Val C Sheffield; Fiscal Year: 2010
    ..Candidate genes for mutations screening will be identified using a combination of expression, functional and positional information. ..
  62. CHARACTERIZATION OF B ANTHRACIS EXOSPORIUM PROTEINS
    CHARLES TURNBOUGH; Fiscal Year: 2004
    ..anthracis spore surface (i.e., exosporium) to create affinity-matured single chain antibodies that neutralize exosporium protein activity, then test the effects of these reagents on spore properties. ..
  63. A Staged Strategy for Virus Identification and Discovery
    WALTER LIPKIN; Fiscal Year: 2004
    ..Consistent with aims proposed in AI51292, our initial clinical application will be to analyze enteroviral serotypes implicated in human disease in North America. ..
  64. A DEVELOPMENTAL MODEL FOR AUTISM BASED ON CNS INFECTION
    WALTER LIPKIN; Fiscal Year: 2004
    ..4) Determine how opoptosis contributes to the neuropathology observed after neonatal infection. (5) Analyze regional changes in neurotransmitter systems following neonatal infection. ..
  65. Inhibitors of Yersinia Yop Type III Secretion(RMI)
    Joan Mecsas; Fiscal Year: 2005
    ..In addition, these inhibitors will be valuable tools to probe the structure and function of type III secretion systems encoded by Yersinia species and other Gram-negative bacterial pathogens. ..
  66. BORNA DISEASE VIRUS AND NEUROPSYCHIATRIC DISEASE
    WALTER LIPKIN; Fiscal Year: 2002
    ..This study will be the first to collect and process human sera and PBMC samples in clinical laboratories with no history of BDV research and dispense aliquots to a central laboratory for randomized, blinded analysis. ..