proteome

Summary

Summary: The protein complement of an organism coded for by its genome.

Top Publications

  1. ncbi MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification
    Jürgen Cox
    Department for Proteomics and Signal Transduction, Max Planck Institute for Biochemistry, Am Klopferspitz 18, D 82152 Martinsried, Germany
    Nat Biotechnol 26:1367-72. 2008
  2. ncbi Initial sequencing and analysis of the human genome
    E S Lander
    Whitehead Institute for Biomedical Research, Center for Genome Research, Cambridge, Massachusetts 02142, USA
    Nature 409:860-921. 2001
  3. ncbi Lysine acetylation targets protein complexes and co-regulates major cellular functions
    Chunaram Choudhary
    Proteomics and Signal Transduction, Max Planck Institute for Biochemistry, Martinsried, Germany
    Science 325:834-40. 2009
  4. ncbi Universal sample preparation method for proteome analysis
    Jacek R Wisniewski
    Department of Proteomics and Signal Transduction, Max Planck Institute for Biochemistry, Martinsried, Germany
    Nat Methods 6:359-62. 2009
  5. pmc Expansion of the eukaryotic proteome by alternative splicing
    Timothy W Nilsen
    Center for RNA Molecular Biology, Department of Biochemistry, Case Western Reserve University, School of Medicine, 10900 Euclid Avenue, Cleveland, Ohio 44106, USA
    Nature 463:457-63. 2010
  6. pmc Quantifying E. coli proteome and transcriptome with single-molecule sensitivity in single cells
    Yuichi Taniguchi
    Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA
    Science 329:533-8. 2010
  7. ncbi Target-decoy search strategy for increased confidence in large-scale protein identifications by mass spectrometry
    Joshua E Elias
    Department of Cell Biology, 240 Longwood Avenue, Harvard Medical School, Boston, Massachusetts 02115, USA
    Nat Methods 4:207-14. 2007
  8. pmc A mitochondrial protein compendium elucidates complex I disease biology
    David J Pagliarini
    Center for Human Genetic Research, Massachusetts General Hospital, Boston, MA 02114, USA
    Cell 134:112-23. 2008
  9. pmc Systematic and quantitative assessment of the ubiquitin-modified proteome
    Woong Kim
    Department of Cell Biology, Harvard Medical School, Boston, MA, USA
    Mol Cell 44:325-40. 2011
  10. ncbi Functional profiling of the Saccharomyces cerevisiae genome
    Guri Giaever
    Stanford Genome Technology Center, Stanford University, Palo Alto, California 94304, USA
    Nature 418:387-91. 2002

Detail Information

Publications386 found, 100 shown here

  1. ncbi MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification
    Jürgen Cox
    Department for Proteomics and Signal Transduction, Max Planck Institute for Biochemistry, Am Klopferspitz 18, D 82152 Martinsried, Germany
    Nat Biotechnol 26:1367-72. 2008
    ..MaxQuant automatically quantifies several hundred thousand peptides per SILAC-proteome experiment and allows statistically robust identification and quantification of >4,000 proteins in mammalian ..
  2. ncbi Initial sequencing and analysis of the human genome
    E S Lander
    Whitehead Institute for Biomedical Research, Center for Genome Research, Cambridge, Massachusetts 02142, USA
    Nature 409:860-921. 2001
    ..We also present an initial analysis of the data, describing some of the insights that can be gleaned from the sequence...
  3. ncbi Lysine acetylation targets protein complexes and co-regulates major cellular functions
    Chunaram Choudhary
    Proteomics and Signal Transduction, Max Planck Institute for Biochemistry, Martinsried, Germany
    Science 325:834-40. 2009
    ..Our data demonstrate that the regulatory scope of lysine acetylation is broad and comparable with that of other major posttranslational modifications...
  4. ncbi Universal sample preparation method for proteome analysis
    Jacek R Wisniewski
    Department of Proteomics and Signal Transduction, Max Planck Institute for Biochemistry, Martinsried, Germany
    Nat Methods 6:359-62. 2009
    ..We completely solubilized the proteome in sodium dodecyl sulfate, which we then exchanged by urea on a standard filtration device...
  5. pmc Expansion of the eukaryotic proteome by alternative splicing
    Timothy W Nilsen
    Center for RNA Molecular Biology, Department of Biochemistry, Case Western Reserve University, School of Medicine, 10900 Euclid Avenue, Cleveland, Ohio 44106, USA
    Nature 463:457-63. 2010
    ..It is now clear that the 'missing' information is in large part provided by alternative splicing, the process by which multiple different functional messenger RNAs, and therefore proteins, can be synthesized from a single gene...
  6. pmc Quantifying E. coli proteome and transcriptome with single-molecule sensitivity in single cells
    Yuichi Taniguchi
    Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA
    Science 329:533-8. 2010
    ..At high expression levels, the distributions are dominated by extrinsic noise. We found that a single cell's protein and mRNA copy numbers for any given gene are uncorrelated...
  7. ncbi Target-decoy search strategy for increased confidence in large-scale protein identifications by mass spectrometry
    Joshua E Elias
    Department of Cell Biology, 240 Longwood Avenue, Harvard Medical School, Boston, Massachusetts 02115, USA
    Nat Methods 4:207-14. 2007
    ..As most sequence search engines return results even for 'unmatchable' spectra, proteome researchers must devise ways to distinguish correct from incorrect peptide identifications...
  8. pmc A mitochondrial protein compendium elucidates complex I disease biology
    David J Pagliarini
    Center for Human Genetic Research, Massachusetts General Hospital, Boston, MA 02114, USA
    Cell 134:112-23. 2008
    ..Our results have important implications for understanding CI function and pathogenesis and, more generally, illustrate how our compendium can serve as a foundation for systematic investigations of mitochondria...
  9. pmc Systematic and quantitative assessment of the ubiquitin-modified proteome
    Woong Kim
    Department of Cell Biology, Harvard Medical School, Boston, MA, USA
    Mol Cell 44:325-40. 2011
    ..To globally characterize the human ubiquitin-modified proteome (ubiquitinome), we utilized a monoclonal antibody that recognizes diglycine (diGly)-containing isopeptides ..
  10. ncbi Functional profiling of the Saccharomyces cerevisiae genome
    Guri Giaever
    Stanford Genome Technology Center, Stanford University, Palo Alto, California 94304, USA
    Nature 418:387-91. 2002
    ..Our results validate the yeast gene-deletion collection as a valuable resource for functional genomics...
  11. ncbi Global analysis of protein expression in yeast
    Sina Ghaemmaghami
    Howard Hughes Medical Institute, University of California San Francisco, San Francisco, California 94143 2240, USA
    Nature 425:737-41. 2003
    ..We find that about 80% of the proteome is expressed during normal growth conditions, and, using additional sequence information, we systematically ..
  12. pmc Deep proteome and transcriptome mapping of a human cancer cell line
    Nagarjuna Nagaraj
    Department for Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany
    Mol Syst Biol 7:548. 2011
    ..peptides identified 10 255 different human proteins encoded by 9207 human genes, providing a lower limit on the proteome in this cancer cell line. Deep transcriptome sequencing revealed transcripts for nearly all detected proteins...
  13. ncbi Global analysis of protein localization in budding yeast
    Won Ki Huh
    Howard Hughes Medical Institute, University of California San Francisco, Department of Biochemistry and Biophysics, 600 16th Street, San Francisco, California 94143 2240, USA
    Nature 425:686-91. 2003
    ..We classify these proteins, representing 75% of the yeast proteome, into 22 distinct subcellular localization categories, and provide localization information for 70% of previously ..
  14. pmc The FunCat, a functional annotation scheme for systematic classification of proteins from whole genomes
    Andreas Ruepp
    Institute for Bioinformatics MIPS, GSF National Research Center for Environment and Health, Ingolstaedter Landstrasse 1, D 85764 Neuherberg, Germany
    Nucleic Acids Res 32:5539-45. 2004
    ..Over the last decade, the FunCat has been established as a robust and stable annotation scheme that offers both, meaningful and manageable functional classification as well as ease of perception...
  15. ncbi The human plasma proteome: history, character, and diagnostic prospects
    N Leigh Anderson
    Plasma Proteome Institute, Washington, DC 20009 3450, USA
    Mol Cell Proteomics 1:845-67. 2002
    The human plasma proteome holds the promise of a revolution in disease diagnosis and therapeutic monitoring provided that major challenges in proteomics and related disciplines can be addressed...
  16. ncbi Quantitative phosphoproteomics reveals widespread full phosphorylation site occupancy during mitosis
    Jesper V Olsen
    Department of Proteomics and Signal Transduction, Max Planck Institute for Biochemistry, Am Klopferspitz 18, D 82152 Martinsried near Munich, Germany
    Sci Signal 3:ra3. 2010
    ..We applied high-resolution mass spectrometry-based proteomics to investigate the proteome and phosphoproteome of the human cell cycle on a global scale and quantified 6027 proteins and 20,443 unique ..
  17. ncbi Discovering regulatory and signalling circuits in molecular interaction networks
    Trey Ideker
    Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA Institute for Systems Biology, Seattle, WA 98103, USA
    Bioinformatics 18:S233-40. 2002
    ..The method we present here combines a rigorous statistical measure for scoring subnetworks with a search algorithm for identifying subnetworks with high score...
  18. pmc The quantitative proteome of a human cell line
    Martin Beck
    European Molecular Biology Laboratory, Heidelberg, Germany
    Mol Syst Biol 7:549. 2011
    ..Here, we provide a quantitative description of the proteome of a commonly used human cell line in two functional states, interphase and mitosis...
  19. pmc Regulation of cellular metabolism by protein lysine acetylation
    Shimin Zhao
    School of Life Sciences, Fudan University, Shanghai 20032, China
    Science 327:1000-4. 2010
    ..Our study reveals that acetylation plays a major role in metabolic regulation...
  20. pmc Genome sequence of the human malaria parasite Plasmodium falciparum
    Malcolm J Gardner
    The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, Maryland 20850, USA
    Nature 419:498-511. 2002
    ..The genome sequence provides the foundation for future studies of this organism, and is being exploited in the search for new drugs and vaccines to fight malaria...
  21. ncbi Next-generation proteomics: towards an integrative view of proteome dynamics
    A F Maarten Altelaar
    Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
    Nat Rev Genet 14:35-48. 2013
    ..The proteome is extremely multifaceted owing to splicing and protein modifications, and this is further amplified by the ..
  22. ncbi Characterization of mammalian selenoproteomes
    Gregory V Kryukov
    Department of Biochemistry, University of Nebraska, Lincoln, NE 68588 0664, USA
    Science 300:1439-43. 2003
    ..The human selenoproteome consists of 25 selenoproteins...
  23. ncbi Global, in vivo, and site-specific phosphorylation dynamics in signaling networks
    Jesper V Olsen
    Center for Experimental Bioinformatics, Department of Biochemistry and Molecular Biology, University of Southern Denmark, DK 5230 Odense, Denmark
    Cell 127:635-48. 2006
    ..The dynamic phosphoproteome provides a missing link in a global, integrative view of cellular regulation...
  24. ncbi A human protein atlas for normal and cancer tissues based on antibody proteomics
    Mathias Uhlen
    Department of Biotechnology, AlbaNova University Center, Royal Institute of Technology KTH, SE 106 91 Stockholm, Sweden
    Mol Cell Proteomics 4:1920-32. 2005
    Antibody-based proteomics provides a powerful approach for the functional study of the human proteome involving the systematic generation of protein-specific affinity reagents...
  25. pmc The Chlamydomonas genome reveals the evolution of key animal and plant functions
    Sabeeha S Merchant
    Department of Chemistry and Biochemistry, University of California at Los Angeles, Los Angeles, CA 90095, USA
    Science 318:245-50. 2007
    ....
  26. pmc Analysis of the myosin-II-responsive focal adhesion proteome reveals a role for β-Pix in negative regulation of focal adhesion maturation
    Jean Cheng Kuo
    Cell Biology and Physiology Centre, National Heart, Lung, and Blood Institute, NIH, Bethesda, Maryland 20892, USA
    Nat Cell Biol 13:383-93. 2011
    ..459 of which changed in abundance with myosin II inhibition, defining the myosin-II-responsive focal adhesion proteome. The abundance of 73% of the proteins in the myosin-II-responsive focal adhesion proteome was enhanced by ..
  27. pmc AT_CHLORO, a comprehensive chloroplast proteome database with subplastidial localization and curated information on envelope proteins
    Myriam Ferro
    INSERM, Laboratoire d Etude de Dynamique des Protéomes, U880, France
    Mol Cell Proteomics 9:1063-84. 2010
    ..This is especially true for envelope proteins. We went a step further into the knowledge of the chloroplast proteome by focusing, in the same set of experiments, on the localization of proteins in the stroma, the thylakoids, and ..
  28. 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...
  29. pmc The importance of intrinsic disorder for protein phosphorylation
    Lilia M Iakoucheva
    School of Molecular Biosciences, Washington State University, Pullman, WA 99164, USA
    Nucleic Acids Res 32:1037-49. 2004
    ....
  30. pmc Comparative analysis of proteome and transcriptome variation in mouse
    Anatole Ghazalpour
    Department of Medicine Division of Cardiology, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California, United States of America
    PLoS Genet 7:e1001393. 2011
    ..In light of the widespread use of high-throughput technologies in both clinical and basic research, the results presented have practical as well as basic implications...
  31. pmc UniProt: the Universal Protein knowledgebase
    Rolf Apweiler
    The EMBL Outstation European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
    Nucleic Acids Res 32:D115-9. 2004
    ..The UniProt databases can be accessed online (http://www.uniprot.org) or downloaded in several formats (ftp://ftp.uniprot.org/pub). The scientific community is encouraged to submit data for inclusion in UniProt...
  32. ncbi Proteome analysis of erythrocytes lacking AMP-activated protein kinase reveals a role of PAK2 kinase in eryptosis
    Christine Zelenak
    Department of Physiology, University of Tübingen, Germany
    J Proteome Res 10:1690-7. 2011
    ..To determine the link between AMPK and the eryptotic phenotype, we performed a global proteome analysis of erythrocytes from ampk(-/-) mice and wild-type mice using high-accuracy mass spectrometry and label-..
  33. ncbi Feature-based prediction of non-classical and leaderless protein secretion
    Jannick Dyrløv Bendtsen
    Center for Biological Sequence Analysis BioCentrum DTU, Building 208, Technical University of Denmark, DK 2800 Lyngby, Denmark
    Protein Eng Des Sel 17:349-56. 2004
    ..By scanning the entire human proteome we identified new proteins potentially undergoing non-classical secretion. Predictions can be made at http://www...
  34. pmc HAMAP: a database of completely sequenced microbial proteome sets and manually curated microbial protein families in UniProtKB/Swiss-Prot
    Tania Lima
    Swiss Prot group, Swiss Institute of Bioinformatics, 1 rue Michel Servet, 1211 Geneva 4, Switzerland
    Nucleic Acids Res 37:D471-8. 2009
    ..The HAMAP system is composed of two databases, the proteome database and the family database, and of an automatic annotation pipeline...
  35. pmc De novo assembly and validation of planaria transcriptome by massive parallel sequencing and shotgun proteomics
    Catherine Adamidi
    Max Delbruck Center for Molecular Medicine, Berlin Institute for Medical Systems Biology, Robert Rossle Strasse 10, Berlin, Germany
    Genome Res 21:1193-200. 2011
    ..However, the characterization of its transcriptome is far from complete. Furthermore, not a single proteome of the entire phylum has been assayed on a genome-wide level...
  36. ncbi Plant proteome changes under abiotic stress--contribution of proteomics studies to understanding plant stress response
    Klára Kosová
    Department of Genetics and Plant Breeding, Crop Research Institute, Drnovská Street 507, 161 06 Prague 6 Ruzyne, The Czech Republic
    J Proteomics 74:1301-22. 2011
    Plant acclimation to stress is associated with profound changes in proteome composition...
  37. ncbi A quantitative analysis of kinase inhibitor selectivity
    Mazen W Karaman
    Ambit Biosciences, 4215 Sorrento Valley Blvd, San Diego, California 92121, USA
    Nat Biotechnol 26:127-32. 2008
    ..We further investigate the impact of panel size and find that small assay panels do not provide a robust measure of selectivity...
  38. pmc Aneuploidy confers quantitative proteome changes and phenotypic variation in budding yeast
    Norman Pavelka
    Stowers Institute for Medical Research, 1000 East 50th Street, Kansas City, Missouri 64110, USA
    Nature 468:321-5. 2010
    ..results provide strong evidence that aneuploidy directly affects gene expression at both the transcriptome and proteome levels and can generate significant phenotypic variation that could bring about fitness gains under diverse ..
  39. pmc PHOSIDA (phosphorylation site database): management, structural and evolutionary investigation, and prediction of phosphosites
    Florian Gnad
    Department for Proteomics and Signal Transduction, Max Planck Institute for Biochemistry, Am Klopferspitz, D 82152 Martinsried, Germany
    Genome Biol 8:R250. 2007
    ..For each phosphosite, PHOSIDA lists matching kinase motifs, predicted secondary structures, conservation patterns, and its dynamic regulation upon stimulus. Using support vector machines, PHOSIDA also predicts phosphosites...
  40. pmc ProteoWizard: open source software for rapid proteomics tools development
    Darren Kessner
    Spielberg Family Center for Applied Proteomics, Cedars Sinai Medical Center, USA
    Bioinformatics 24:2534-6. 2008
    ..In addition to the library, we also introduce a rapidly growing set of companion tools whose implementation helps to illustrate the simplicity of developing applications on top of the ProteoWizard library...
  41. ncbi Decoding signalling networks by mass spectrometry-based proteomics
    Chunaram Choudhary
    The Novo Nordisk Foundation Center for Protein Research, Faculty of Health Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
    Nat Rev Mol Cell Biol 11:427-39. 2010
    ..Large-scale proteomics-based signalling research will fundamentally change our understanding of signalling networks...
  42. ncbi Initial sequencing and comparative analysis of the mouse genome
    Robert H Waterston
    Genome Sequencing Center, Washington University School of Medicine, Campus Box 8501, 4444 Forest Park Avenue, St Louis, Missouri 63108, USA
    Nature 420:520-62. 2002
    ....
  43. ncbi Mass spectrometry in high-throughput proteomics: ready for the big time
    Tommy Nilsson
    Research Institute of the McGill University Health Centre, McGill University, Montreal, Quebec, Canada
    Nat Methods 7:681-5. 2010
    Mass spectrometry has evolved and matured to a level where it is able to assess the complexity of the human proteome. We discuss some of the expected challenges ahead and promising strategies for success.
  44. 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...
  45. pmc Mapping intact protein isoforms in discovery mode using top-down proteomics
    John C Tran
    Department of Chemistry and Biochemistry, and the Institute for Genomic Biology, University of Illinois at Urbana Champaign, Urbana, Illinois 61801, USA
    Nature 480:254-8. 2011
    A full description of the human proteome relies on the challenging task of detecting mature and changing forms of protein molecules in the body...
  46. ncbi Proteomic analysis of proteins associated with lipid droplets of basal and lipolytically stimulated 3T3-L1 adipocytes
    Dawn L Brasaemle
    Department of Nutritional Sciences, Rutgers, The State University of New Jersey, New Brunswick, New Jersey 08901, USA
    J Biol Chem 279:46835-42. 2004
    ....
  47. ncbi The Arabidopsis thaliana chloroplast proteome reveals pathway abundance and novel protein functions
    Torsten Kleffmann
    Institute of Plant Sciences and Functional Genomics Center Zurich, Swiss Federal Institute of Technology, ETH Zentrum, LFW E51 1, Universitatstrasse 2, CH 8092 Zurich, Switzerland
    Curr Biol 14:354-62. 2004
    ..Since protein targeting is difficult to predict, many nuclear-encoded plastid proteins are still to be discovered...
  48. ncbi Quantitative, high-resolution proteomics for data-driven systems biology
    Jürgen Cox
    Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried D 82152, Germany
    Annu Rev Biochem 80:273-99. 2011
    ..It is used to quantify proteins between different proteome states, including the temporal variation of the proteome, to determine the complete primary structure of proteins ..
  49. pmc PeptideAtlas: a resource for target selection for emerging targeted proteomics workflows
    Eric W Deutsch
    Institute for Systems Biology, 1441 N 34th Street, Seattle, Washington 98103, USA
    EMBO Rep 9:429-34. 2008
    ..Here, we describe the PeptideAtlas Project, its contents and components, and show how together they provide a unique platform to select and validate mass spectrometry targets, thereby allowing the next revolution in proteomics...
  50. ncbi Mass spectrometry and protein analysis
    Bruno Domon
    Institute of Molecular Systems Biology, ETH Zurich, CH 8093 Zurich, Switzerland
    Science 312:212-7. 2006
    ..Here we review recent advances in mass spectrometry instrumentation in the context of current and emerging research strategies in protein science...
  51. pmc Scansite 2.0: Proteome-wide prediction of cell signaling interactions using short sequence motifs
    John C Obenauer
    Center for Cancer Research, E18 580, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
    Nucleic Acids Res 31:3635-41. 2003
    ..In addition, a new series of Sequence Match programs for non-quantitative user-defined motifs has been implemented. Scansite is available via the World Wide Web at http://scansite.mit.edu...
  52. pmc Proteome-wide analysis of disease-associated SNPs that show allele-specific transcription factor binding
    Falk Butter
    Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany
    PLoS Genet 8:e1002982. 2012
    ..Here we apply PWAS ("proteome-wide analysis of SNPs"), a methodology based on quantitative mass spectrometry that enables rapid screening of ..
  53. pmc The PRoteomics IDEntification (PRIDE) Converter 2 framework: an improved suite of tools to facilitate data submission to the PRIDE database and the ProteomeXchange consortium
    Richard G Côté
    Proteomics Services Team, EMBL Outstation, European Bioinformatics Institute EBI, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
    Mol Cell Proteomics 11:1682-9. 2012
    ..The PRIDE Converter 2 tool suite will thus become a cornerstone in the submission process to PRIDE and, by extension, to the ProteomeXchange consortium of MS-proteomics data repositories...
  54. ncbi The complete Corynebacterium glutamicum ATCC 13032 genome sequence and its impact on the production of L-aspartate-derived amino acids and vitamins
    Jorn Kalinowski
    Institut für Genomforschung, Universitat Bielefeld, Universitatsstrasse 25, D 33615 Bielefeld, Germany
    J Biotechnol 104:5-25. 2003
    ..As an example for biotechnological application the complete genome sequence was used to reconstruct the metabolic flow of carbon into a number of industrially important products derived from the amino acid L-aspartate...
  55. ncbi A roadmap to generate renewable protein binders to the human proteome
    Karen Colwill
    Samuel Lunenfeld Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada
    Nat Methods 8:551-8. 2011
    ..is often hindered by their inconsistent validation, their poor performance and the inadequate coverage of the proteome. These issues could be addressed by systematic, genome-wide efforts to generate and validate renewable protein ..
  56. ncbi Comprehensive proteomics
    Martin Beck
    European Molecular Biology Laboratory, Meyerhofstrasse 1, Heidelberg, Germany
    Curr Opin Biotechnol 22:3-8. 2011
    Extensive proteome discovery projects using a variety of mass spectrometric techniques have identified proteins matching to 50-70% of the predicted gene models of various species...
  57. pmc Defining the protein complex proteome of plant mitochondria
    Jennifer Klodmann
    Institute for Plant Genetics, Faculty of Natural Sciences, Leibniz Universitat Hannover, D 30419 Hannover, Germany
    Plant Physiol 157:587-98. 2011
    ..tandem mass spectrometry and up-to-date computer technology to characterize the mitochondrial "protein complex proteome" of Arabidopsis (Arabidopsis thaliana) in so far unrivaled depth...
  58. 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...
  59. ncbi Quantitative mass spectrometry in proteomics: a critical review
    Marcus Bantscheff
    Cellzome AG, Meyerhofstrasse 1, 69254, Heidelberg, Germany
    Anal Bioanal Chem 389:1017-31. 2007
    ..In this review, we critically examine the more commonly used quantitative mass spectrometry methods for their individual merits and discuss challenges in arriving at meaningful interpretations of quantitative proteomic data...
  60. pmc Temporal proteome and lipidome profiles reveal hepatitis C virus-associated reprogramming of hepatocellular metabolism and bioenergetics
    Deborah L Diamond
    Department of Microbiology, School of Medicine, University of Washington, Seattle, Washington, USA
    PLoS Pathog 6:e1000719. 2010
    ....
  61. pmc A dynamic model of proteome changes reveals new roles for transcript alteration in yeast
    M Violet Lee
    Department of Chemistry, University of Wisconsin Madison, Madison, WI, USA
    Mol Syst Biol 7:514. 2011
    The transcriptome and proteome change dynamically as cells respond to environmental stress; however, prior proteomic studies reported poor correlation between mRNA and protein, rendering their relationships unclear...
  62. ncbi The genome sequence of the malaria mosquito Anopheles gambiae
    Robert A Holt
    Celera Genomics, 45 West Gude Drive, Rockville, MD 20850, USA
    Science 298:129-49. 2002
    ..An expressed sequence tag analysis of genes regulated by blood feeding provided insights into the physiological adaptations of a hematophagous insect...
  63. ncbi A proteomics approach to understanding protein ubiquitination
    Junmin Peng
    Department of Cell Biology, 240 Longwood Avenue, Harvard Medical School, Boston, Massachusetts 02115, USA
    Nat Biotechnol 21:921-6. 2003
    ..The methodology described here provides a general tool for the large-scale analysis and characterization of protein ubiquitination...
  64. 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...
  65. ncbi Single-cell proteomic analysis of S. cerevisiae reveals the architecture of biological noise
    John R S Newman
    Howard Hughes Medical Institute, San Francisco, California, USA
    Nature 441:840-6. 2006
    ..Thus, these studies reveal a remarkable structure to biological noise and suggest that protein noise levels have been selected to reflect the costs and potential benefits of this variation...
  66. ncbi The ciliary proteome database: an integrated community resource for the genetic and functional dissection of cilia
    Adrian Gherman
    Nat Genet 38:961-2. 2006
  67. pmc Defining the transcriptome and proteome in three functionally different human cell lines
    Emma Lundberg
    Science for Life Laboratory, Royal Institute of Technology, Stockholm, Sweden
    Mol Syst Biol 6:450. 2010
    ..Thus, this study shows a path to characterize the transcriptome and proteome in human cells from different origins.
  68. ncbi Cerebral: a Cytoscape plugin for layout of and interaction with biological networks using subcellular localization annotation
    Aaron Barsky
    Department of Computer Science, University of British Columbia, Vancouver, British Columbia, Canada
    Bioinformatics 23:1040-2. 2007
    ..Cerebral scales well to networks containing thousands of nodes. AVAILABILITY: http://www.pathogenomics.ca/cerebral..
  69. 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...
  70. pmc OrthoMCL-DB: querying a comprehensive multi-species collection of ortholog groups
    Feng Chen
    Department of Chemistry, Center for Bioinformatics, Penn Genomics Institute, University of Pennsylvania, Philadelphia, PA 19104 6018, USA
    Nucleic Acids Res 34:D363-8. 2006
    ..was used to cluster proteins based on sequence similarity, using an all-against-all BLAST search of each species' proteome, followed by normalization of inter-species differences, and Markov clustering. A total of 511,797 proteins (81...
  71. pmc Quantification of mRNA and protein and integration with protein turnover in a bacterium
    Tobias Maier
    EMBL CRG Systems Biology Research Unit, Centre for Genomic Regulation and UPF, Dr Aiguader 88, Barcelona, Spain
    Mol Syst Biol 7:511. 2011
    ..b>Proteome composition changes in response to cellular perturbations reveal specific stress response strategies...
  72. 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.
  73. pmc Expanding the proteome: disordered and alternatively folded proteins
    H Jane Dyson
    Department of Molecular Biology MB2, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
    Q Rev Biophys 44:467-518. 2011
    ....
  74. ncbi Comprehensive mass-spectrometry-based proteome quantification of haploid versus diploid yeast
    Lyris M F de Godoy
    Proteomics and Signal Transduction, Max Planck Institute for Biochemistry, Am Klopferspitz 18, D 82152 Martinsried, Germany
    Nature 455:1251-4. 2008
    ..Stable-isotope labelling by amino acids in cell culture (SILAC) quantification was very accurate across the proteome, as demonstrated by one-to-one ratios of most yeast proteins...
  75. ncbi A Proteome-wide screen for mammalian SxIP motif-containing microtubule plus-end tracking proteins
    Kai Jiang
    Cell Biology, Department of Biology, Faculty of Science, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
    Curr Biol 22:1800-7. 2012
    ..Here, we performed a proteome-wide search for mammalian SxIP-containing +TIPs by combining biochemical and bioinformatics approaches...
  76. pmc Characterization of the rapamycin-sensitive phosphoproteome reveals that Sch9 is a central coordinator of protein synthesis
    Alexandre Huber
    Department of Molecular Biology, University of Geneva, Geneva, Switzerland
    Genes Dev 23:1929-43. 2009
    ..This demonstrates that Sch9 is a master regulator of protein synthesis...
  77. pmc Structural disorder in eukaryotes
    Rita Pancsa
    VIB Department of Structural Biology, Vrije Universiteit Brussel, Brussels, Belgium
    PLoS ONE 7:e34687. 2012
    ..We conclude that protists have been the evolutionary hot-bed of experimentation with structural disorder, in a period when structural disorder was actively invented and the major functional classes of disordered proteins established...
  78. ncbi Proteome-wide identification of poly(ADP-Ribosyl)ation targets in different genotoxic stress responses
    Stephanie Jungmichel
    Department of Proteomics, The Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, 2200 Copenhagen, Denmark
    Mol Cell 52:272-85. 2013
    ....
  79. ncbi The effects of alternate optimal solutions in constraint-based genome-scale metabolic models
    R Mahadevan
    Genomatica, Inc, Bioprocessing Division, 5405 Morehouse Drive, Suite 210, San Diego, CA 92121, USA
    Metab Eng 5:264-76. 2003
    ..These methods also provide an efficient and robust method to calculate the range of flux distributions that can be derived from quantitative fermentation data...
  80. pmc Characterization of the proteome, diseases and evolution of the human postsynaptic density
    Alex Bayes
    Genes to Cognition Programme, Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridgeshire, UK
    Nat Neurosci 14:19-21. 2011
    ..The hPSD is an important structure for nervous system disease and behavior...
  81. pmc Large-scale Arabidopsis phosphoproteome profiling reveals novel chloroplast kinase substrates and phosphorylation networks
    Sonja Reiland
    Department of Biology, Eidgenossische Technische Hochschule Zurich, 8092 Zurich, Switzerland
    Plant Physiol 150:889-903. 2009
    ..We propose that ATP synthase is regulated in cooperation with 14-3-3 proteins by CKII-mediated phosphorylation of ATP synthase beta-subunit in the dark...
  82. pmc Analysis of the Aspergillus fumigatus proteome reveals metabolic changes and the activation of the pseurotin A biosynthesis gene cluster in response to hypoxia
    Martin Vödisch
    Department of Molecular and Applied Microbiology, Leibniz Institute for Natural Product Research and Infection Biology Hans Knöll Institute and Friedrich Schiller University, Jena, Germany
    J Proteome Res 10:2508-24. 2011
    ..fumigatus. Therefore, we aimed at obtaining a comprehensive overview about this process on the proteome level...
  83. pmc Origin and evolution of the mitochondrial proteome
    C G Kurland
    Department of Molecular Evolution, Evolutionary Biology Centre, University of Uppsala, Uppsala SE 752 36, Lund University, Lund SE 223 62, Sweden
    Microbiol Mol Biol Rev 64:786-820. 2000
    ..The three identifiable ancestral sources to the proteome of mitochondria are proteins descended from the ancestral alpha-proteobacteria symbiont, proteins with no ..
  84. pmc Mass spectrometry-based proteomics in cell biology
    Tobias C Walther
    Organelle Architecture and Dynamics and 2 Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany
    J Cell Biol 190:491-500. 2010
    ....
  85. ncbi A sensitive predictor for potential GPI lipid modification sites in fungal protein sequences and its application to genome-wide studies for Aspergillus nidulans, Candida albicans, Neurospora crassa, Saccharomyces cerevisiae and Schizosaccharomyces pombe
    Birgit Eisenhaber
    Research Institute of Molecular Pathology IMP, Dr Bohr Gasse 7, A 1030 Vienna, Austria
    J Mol Biol 337:243-53. 2004
    ..Lists of potentially GPI lipid anchored proteins for five fungal proteomes have been generated and the hits have been functionally classified. The fungal big-Pi prediction WWW server as well as precursor lists are available at..
  86. pmc Proteome-wide identification of poly(ADP-ribose) binding proteins and poly(ADP-ribose)-associated protein complexes
    Jean Philippe Gagné
    Laval University Medical Research Center, CHUQ, Faculty of Medicine, Laval University, Quebec, Canada
    Nucleic Acids Res 36:6959-76. 2008
    ..In this study, refined in silico prediction of pADPr binding proteins and large-scale mass spectrometry-based proteome analysis of pADPr binding proteins were used to establish a comprehensive repertoire of pADPr-associated proteins...
  87. ncbi A universal molecular clock of protein folds and its power in tracing the early history of aerobic metabolism and planet oxygenation
    Minglei Wang
    Evolutionary Bioinformatics Laboratory, Department of Crop Sciences, University of Illinois, Urbana Champaign, USA
    Mol Biol Evol 28:567-82. 2011
    ..The clock also extends the standard concept that was specific to molecules and their timescales and turns it into a universal timescale-generating tool...
  88. pmc Multi-site assessment of the precision and reproducibility of multiple reaction monitoring-based measurements of proteins in plasma
    Terri A Addona
    Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
    Nat Biotechnol 27:633-41. 2009
    ..We provide data and benchmarks against which individual laboratories can compare their performance and evaluate new technologies for biomarker verification in plasma...
  89. pmc Large-scale proteomics analysis of the human kinome
    Felix S Oppermann
    Department of Molecular Biology, Max Planck Institute of Biochemistry, Martinsried, Germany
    Mol Cell Proteomics 8:1751-64. 2009
    ..However, in global proteome studies, low cellular abundance of protein kinases often results in rather minor peptide species that are ..
  90. ncbi High-throughput generation of selected reaction-monitoring assays for proteins and proteomes
    Paola Picotti
    Institute of Molecular Systems Biology, Swiss Federal Institute of Technology, Zurich, Switzerland
    Nat Methods 7:43-6. 2010
    ..We illustrate the power of the approach by generating and applying validated SRM assays for all Saccharomyces cerevisiae kinases and phosphatases...
  91. ncbi Combination of FASP and StageTip-based fractionation allows in-depth analysis of the hippocampal membrane proteome
    Jacek R Wisniewski
    Department of Proteomics and Signal Transduction, Max Planck Institute for Biochemistry, Am Klopferspitz 18, D 82152 Martinsried, Germany
    J Proteome Res 8:5674-8. 2009
    ..To extend proteome coverage, we developed a simple anion exchange fractionation method in a StageTip format...
  92. ncbi Functional and topological characterization of protein interaction networks
    Soon Hyung Yook
    Department of Physics, University of Notre Dame, Notre Dame, IN 46556, USA
    Proteomics 4:928-42. 2004
    ....
  93. ncbi A genecentric Human Protein Atlas for expression profiles based on antibodies
    Lisa Berglund
    Department of Proteomics, School of Biotechnology, AlbaNova University Center, Royal Institute of Technology, Stockholm, Sweden
    Mol Cell Proteomics 7:2019-27. 2008
    ..The new version of the protein atlas thus is a resource for many areas of biomedical research, including protein science and biomarker discovery...
  94. ncbi The International Protein Index: an integrated database for proteomics experiments
    Paul J Kersey
    EMBL Outstation, The European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
    Proteomics 4:1985-8. 2004
    ..IPI (the International Protein Index) has been developed to address these issues and offers complete nonredundant data sets representing the human, mouse and rat proteomes, built from the Swiss-Prot, TrEMBL, Ensembl and RefSeq databases...
  95. pmc PrediSi: prediction of signal peptides and their cleavage positions
    Karsten Hiller
    Institut fur Mikrobiologie, Technische Universitat Braunschweig, Spielmannstrasse 7, D 38106 Braunschweig, Germany
    Nucleic Acids Res 32:W375-9. 2004
    ..PrediSi allows the evaluation of whole proteome datasets, which are currently accumulating as a result of numerous genome projects and proteomics experiments...
  96. pmc iProphet: multi-level integrative analysis of shotgun proteomic data improves peptide and protein identification rates and error estimates
    David Shteynberg
    Institute for Systems Biology, Seattle, WA, USA
    Mol Cell Proteomics 10:M111.007690. 2011
    ..performance of iProphet is demonstrated on two publicly available data sets: data from a human whole cell lysate proteome profiling experiment representative of typical proteomic data sets, and from a set of Streptococcus pyogenes ..
  97. pmc Mapping the Arabidopsis organelle proteome
    Tom P J Dunkley
    Department of Biochemistry, University of Cambridge, Downing Site, Cambridge CB2 1QW, United Kingdom
    Proc Natl Acad Sci U S A 103:6518-23. 2006
    ..Consequently, genuine organelle residents have been distinguished from contaminating proteins and proteins in transit through the secretory pathway...
  98. ncbi Discovery of a cytokine and its receptor by functional screening of the extracellular proteome
    Haishan Lin
    Five Prime Therapeutics, Inc, 1650 Owens Street, Suite 200, San Francisco, CA 94158, USA
    Science 320:807-11. 2008
    ..This systematic approach is thus useful for discovering new ligands and receptors and assessing the functional selectivity of extracellular regulatory proteins...
  99. ncbi Rapid transcriptome and proteome profiling of a non-model marine invertebrate, Bugula neritina
    Hao Wang
    Department of Biology, Hong Kong University of Science and Technology, Hong Kong SAR, P R China
    Proteomics 10:2972-81. 2010
    ..In this study, we applied a tandem transcriptome and proteome profiling on a non-model marine fouling organism, Bugula neritina...
  100. ncbi Large-scale analysis of the yeast proteome by multidimensional protein identification technology
    M P Washburn
    Syngenta Agricultural Discovery Institute, 3115 Merryfield Row, Suite 100, San Diego, CA 92121, USA
    Nat Biotechnol 19:242-7. 2001
    We describe a largely unbiased method for rapid and large-scale proteome analysis by multidimensional liquid chromatography, tandem mass spectrometry, and database searching by the SEQUEST algorithm, named multidimensional protein ..
  101. ncbi System-wide temporal characterization of the proteome and phosphoproteome of human embryonic stem cell differentiation
    Kristoffer T G Rigbolt
    Center for Experimental Bioinformatics, Department of Biochemistry and Molecular Biology, University of Southern Denmark, Campusvej 55, DK 5230 Odense M, Denmark
    Sci Signal 4:rs3. 2011
    ....

Research Grants82

  1. STATISITICAL DESIGN, MONITORING &COORD. OF VISION CLINICAL TRIALS &EPIDEMIOLOGY
    Keri Hammel; Fiscal Year: 2012
    ..Title: The Vitreous Proteome and Inflammatory Mediators in Ocular Inflammatory Disease Number: 06-EI-0068 Summary: This study will examine the ..
  2. STATISITICAL DESIGN, MONITORING &COORD. OF VISION CLINICAL TRIALS &EPIDEMIOLOGY
    Keri Hammel; Fiscal Year: 2013
    ..Title: The Vitreous Proteome and Inflammatory Mediators in Ocular Inflammatory Disease Number: 06-EI-0068 Summary: This study will examine the ..
  3. Variation in M. tuberculosis in response to host selection
    Sarah Fortune; Fiscal Year: 2009
    ..In these studies, we expect to provide fundamental insights into the mechanisms and targets of diversifying immune selection in M. tuberculosis. ..
  4. Personalized Clinical Diagnostics and Beyond: Integrated Ring Resonator Arrays
    Ryan Bailey; Fiscal Year: 2009
    ..This technology promises to broadly impact the landscape of the biomedical sciences, both meeting the clinical diagnostic challenges of today and pioneering the paradigm-shifting discoveries of tomorrow. ..
  5. Vaccine Development for Falciparum Malaria in Pregnant Women and Their Offspring
    Ian C Michelow; Fiscal Year: 2013
    ..Based on the successful approach pioneered by Dr. Kurtis, they will perform a differential high throughput whole proteome screen on select groups of pooled plasma from mothers of infants with severe malaria vs...
  6. Prevention of Acute Lung Injury by IL-6 activated STAT3
    Ana Moran; Fiscal Year: 2010
    ..AEC apoptosis can be prevented by blocking critical alterations in the T/HS-induced apoptosis transcriptome and proteome within AECs ("intrinsic" protection) and/or within cells such as neutrophils, macrophages and lymphocytes that ..
  7. Functional Genomics of the Mitochondrial Proteome
    Dennis R Winge; Fiscal Year: 2011
    ..The growing interest in mitochondria has stimulated large-scale proteomics efforts to define the mitochondrial proteome. Mammalian mitochondria harbor ~ 1000 proteins, but of these proteins, the function of ~ 300 remain largely ..
  8. Patient-Derived Stem Cells for Phosphoproteomic Profiling Neuropsychopathology
    Dieter A Wolf; Fiscal Year: 2011
    ..of changes in the expression of key proteins, particularly their phosphorylation state, at the level of the proteome &phosphoproteome...
  9. Identification of Proteins Important for Male Osteoporosis
    Hong Wen Deng; Fiscal Year: 2013
    ..A NOVEL approach to this problem is subcellular proteome extraction to stepwise isolate proteins from membrane, cytosol, nucleus, and cytoskeleton E fractions followed by ..
  10. Functional characters of non-coding RNAs in alcoholic liver injury
    Fanyin Meng; Fiscal Year: 2013
    ..are small ncRNAs that have been recently identified as master regulators of the cellular transcriptome and proteome. miRNAs play a crucial role in shaping the differentiation and function of tissues and organs in both health and ..
  11. Screening Complete TB Proteome for Protective Antigens
    Alan Greener; Fiscal Year: 2010
    ..In our prior SBIR Phase I grant (R43 AI053636-01), we developed a platform technology for high throughput, proteome-based identification of antigens that have a high probability of inducing protective cellular immunity when ..
  12. Delineation of the molecular mechanisms underlying group A Streptococcus virulenc
    Paul Sumby; Fiscal Year: 2013
    ..Public health may be enhanced through the long-term goal of translating knowledge of FASX regulatory pathways into new treatment and/or preventative regimes based upon the inhibition of these pathways by novel antimicrobial agents. ..
  13. Identifying underlying mechanisms of intracellular changes in response to caregiv
    MELANIE SARAH FLINT; Fiscal Year: 2013
    ..proposal will be the first of its kind to molecularly analyze psychological stress effects on the comprehensive proteome of circulating T lymphocytes in humans...
  14. Proteomic signatures of an early life asthma-protective exposure
    Serrine S Lau; Fiscal Year: 2010
    ..The hypotheses we seek to test are: a) specific signatures of early dog exposure are detectable in the proteome of the exposed children;b) these signatures mark molecules targeted by environmental signals and are related to ..
  15. Studies on the virulence of Fillifactor alocis
    Hansel M Fletcher; Fiscal Year: 2013
    ..gingivalis compared to the F. alocis ATCC 35896 strain. In addition, there was variation in the proteome of the clinical isolates compared to the ATCC 35896 strain...
  16. Regulation of Signaling Receptor Activity by LRP-1
    Steven L Gonias; Fiscal Year: 2013
    ..PROTOMAP platform, and available LC-MS technology to assess the ability of LRP-1 to regulate the plasma membrane proteome. Pilot studies applying our proposed methodology have already revealed novel plasma membrane proteins that may be ..
  17. Autoimmunity in the Mediation of Infectious Myocarditis
    Jay Reddy; Fiscal Year: 2013
    ..Panel of mimicry epitopes identified from the CVB proteome are capable of inducing pathogenic cross-reactive T cells for three cardiac antigens as evaluated by T cell ..
  18. Tick Midgut Proteins Critical for Borrelia Transmission
    Sukanya Narasimhan; Fiscal Year: 2010
    ..salivary gland transcriptome and its dynamic influence on pathogen transmission, little is known about the midgut proteome and how Borrelia interacts with the midgut proteins during the critical phase of growth and migration...
  19. Proteome Bead-Display for Discovery of Tumor Antigens
    Mark Lim; Fiscal Year: 2013
    ..One general approach to TAA discovery is screening the sera of patients having particular cancers against proteome-scale libraries of human proteins, to detect autoantibody binding...
  20. Mechanisms of assembly of photoreceptor G protein complexes
    Barry M Willardson; Fiscal Year: 2013
    ..Similar disruptions of proteome homeostasis cause neuronal degeneration of the photoreceptor cells of the retina...
  21. Multiplex Serodiagnostic Protein Microarray
    PHILIP LOUIS FELGNER; Fiscal Year: 2012
    ..Here we will fabricate whole proteome microarrays for Coxiella burnetii, Rickettsia prowazekii, Brucella melitensis, Salmonella typhi, and non-..
  22. Control of Renal Glutaminase Expression during Acidosis
    Norman P Curthoys; Fiscal Year: 2012
    ..the mechanism by which the proximal tubule cell senses slight changes in pH and mediates the remodeling of its proteome in response to acidosis...
  23. Skin Regeneration with Stem Cells and Scaffolds
    SUSAN RENEE OPALENIK; Fiscal Year: 2013
    ..This concept is bolstered by our recently published work and our current findings that the MRL wound proteome has distinct differences from other mouse strains...
  24. Identification of Biomarkers for Early Detection of Renal Cell Carcinoma
    Othon Iliopoulos; Fiscal Year: 2012
    ..selectively the peptidome of urine and to cross-reference these findings with RCC related plasma peptidome and proteome changes. Finally we describe how we will develop a statistical rule for early detection of RCC relapse...
  25. Identification and Validation of Alcohol Biomarker Signatures by Proteomics
    Emanuel Rubin; Fiscal Year: 2010
    ..Early diagnosis of this condition by specific biomarkers will offer the opportunity for treatment and prevention of heart enlargement, congestive heart failure and death. ..
  26. Functional Selection of Novel Ligands from the Neuroendocrine Secretome
    David Larocca; Fiscal Year: 2010
    ..applicant): In the post-genomic era, an estimated 25,000 to 30,000 genes are thought to encode the complex human proteome. However, the challenge remains to understand the multitude of RNAs and proteins derived from this deceptively ..
  27. SPLICING OF MRNA PRECURSORS
    Michael R Green; Fiscal Year: 2013
    ..an important mechanism of gene regulation and is responsible for substantially increasing diversity of the human proteome. However, the mechanisms that regulate alternative splicing remain largely unknown...
  28. Role of Tumor and Stromal Cell Metabolism in Stress Adaptation and Progression
    EILEEN contact WHITE; Fiscal Year: 2010
    ..We discovered that tumor cell dormancy dramatically alters the cellular proteome and gene expression with evidence of compensatory nutrient uptake, Foxo and Notch pathway activation, and ..
  29. Photocleavable Bead Technology for Glycomics
    Mark Lim; Fiscal Year: 2013
    ..are already known and are found in an estimated 80% of all proteins, accounting in part for the vastly larger proteome compared to the genome...
  30. Validation and Quantification of FFPE Antigen Retrieval by Proteome Analysis
    XUPEING FANG; Fiscal Year: 2010
    ..In addition to sample amount constraints imposed by current proteome techniques including two-dimensional polyacrylamide gel electrophoresis and multidimensional liquid ..
  31. Seriodiagnostic arrays for biodefense and emerging infectious diseases
    DAVID HUW DAVIES; Fiscal Year: 2010
    ....
  32. Proteome-wide screen for M. tuberculosis antigens
    Robert N Husson; Fiscal Year: 2010
    ..The overall objective of this research is to undertake a proteome-wide search for protein antigens of Mycobacterium tuberculosis (Mtb) that are recognized by the human humoral ..
  33. The Role of Alternative Splicing Factor Sfrs10 in Neural Development
    Rahul N Kanadia; Fiscal Year: 2010
    ..the difference between the relatively few (~24,000) protein coding genes in the human genome to its vast proteome. Interestingly, of all the mammal tissues, the central nervous system (CNS) has the highest degree of AS...
  34. Cerebrospinal fluid proteome mediated signaling in the developing CNS
    Maria Lehtinen; Fiscal Year: 2013
    ..My immediate research goal in this proposal is to investigate the role of embryonic CSF proteome in regulating cortical progenitor proliferation during development...
  35. Cerebrospinal fluid proteome mediated signaling in the developing CNS
    Maria Lehtinen; Fiscal Year: 2011
    ..My immediate research goal in this proposal is to investigate the role of embryonic CSF proteome in regulating cortical progenitor proliferation during development...
  36. Molecular genetics of egg activation and pronuclear function in Drosophila
    MARIANA FEDERICA WOLFNER; Fiscal Year: 2010
    ..We will test this hypothesis by determining how activation changes the phosphorylation state of the proteome. We will identify the functions of selected proteins whose phosphorylation state is regulated by activation...
  37. Global Proteomic Screening by MALDI Spectrometric Imaging of Protein-Bead Arrays
    Mark Lim; Fiscal Year: 2012
    ..Sequencing of the human genome has led to a new and even more ambitious goal - characterization of the human proteome. Such an endeavor involves not only understanding the function of hundreds of thousands of different proteins ..
  38. Naltrexone and AIDS progression
    GREGORY MICHAEL MILLER; Fiscal Year: 2013
    ..measures of viral RNA loads will be collected, and SIV-specific CD4+ and CD8+ T cell responses to the entire SIV proteome will be quantitated by Elispot and intracellular cytokine staining assays using overlapping SIVmac239 peptides...
  39. Affinity Tagging of Adipocyte Nuclei to Examine Epigenetic Controls in Obesity
    Richard Brian Meagher; Fiscal Year: 2013
    ..for any cell type;thu, this proposed work will enable researchers to understand how chromatin structures and the nuclear proteome of cells in the adipocyte lineage in different tissues differ from each other and from adjacent cells.
  40. Immune-based detection of rifampicin-resistance in HIV/TB
    Gregory P Bisson; Fiscal Year: 2013
    ..Our overarching hypothesis challenges this paradigm by hypothesizing that the changes in the proteome of pathogens that specifically occur as a result of genetic mutation(s) conferring drug resistance can be ..
  41. Legionella pneumophila developmental cycle & virulence
    PAUL STOKES HOFFMAN; Fiscal Year: 2011
    ..morphogenesis by light and electron microscopy;(i) by reporter gene fusions;(iii) pulse chase radiolabeling and proteome profiling and (iv)to assess cyst forms for resilience to detergents, biocides, and antibiotics;and infectiousness ..
  42. Adiporedoxin, a Novel Player in Adipokine Secretion
    Paul F Pilch; Fiscal Year: 2013
    ..to determine how this protein functions in its physiological milieu in vitro We will interrogate the entire proteome, the secretome and the plasma membrane proteome of Arx over and under expressing fat cells...
  43. Helicobacter induced hepatitis and tumorigenesis
    James Fox; Fiscal Year: 2009
    ..expression profile analysis, host expression profile analysis (at the cell, tissue, and organ level), and proteome analysis (using immunohistochemistry, western analysis, and analytic biochemistry)...
  44. FUNCTIONAL ANALYSIS OF NUCLEAR RECEPTOR VARIANTS
    Curtis J Omiecinski; Fiscal Year: 2013
    ..regulator, it is imperative to fully characterize the biological processes directed by the human CAR proteome. Progress in the previous research program included the discovery of novel forms of CAR, CAR2 and CAR3;receptors ..
  45. GENETIC ANALYSIS OF BASAL BODY FUNCTION
    Susan K Dutcher; Fiscal Year: 2013
    ..To probe its role, we will find targets of this kinase in the basal body proteome using genetic and biochemical approaches...
  46. RhoA mediated survival signals in cardiomyocytes
    Joan Heller Brown; Fiscal Year: 2013
    ..e. its localization at mitochondria, as demonstrated by its presence in the mitochondrial heart proteome and by subcellular fractionation studies...
  47. The amelioration of peroxisomal disorders due to defects in Pex10
    Lee A Niswander; Fiscal Year: 2013
    ..Aim 2 will provide the first definition of the peroxisomal proteome in the fetus and will determine the changes in the contents of the peroxisome in Pex10 mutants, in particular in ..
  48. SCABIES: BIOLOGY, CULTURE, HOST SPECIFICITY AND ANTIGENS
    Larry G Arlian; Fiscal Year: 2013
    ..comprehensive proteomic analysis (using MALDI- TOF/TOF MS and other appropriate technologies) of the scabies mite proteome;by constructing and screening a scabies cDNA library;and by testing selected scabies mite proteins (both those ..
  49. SMN Control of snRNP Biogenesis: Role in RNA Splicing and Motor Neuron Survival
    Livio Pellizzoni; Fiscal Year: 2013
    ..by applicant): Project Summary Regulation of RNA splicing is the primary mechanism responsible for generating the proteome diversity and phenotypic complexity of humans...
  50. Diagnosis of sub-clinical cryptic group A streptococcal myonecrosis
    Amy Evelyn Bryant; Fiscal Year: 2013
    ..unbiased LC-MS-based systems proteomics approach will be used to screen the murine tibialis anterior (TA) muscle proteome for candidate biomarkers that discriminate between 1) normal muscle, 2) muscle injury alone and 3) injury ..
  51. Forms of HCV NS5A in vivo
    Craig E Cameron; Fiscal Year: 2013
    ..These cleaved and phosphorylated forms may expand the NS5A proteome, creating forms of the protein essential for virus multiplication...
  52. Age-related Response of Hippocampal Neurons to Stress
    Gregory Brewer; Fiscal Year: 2009
    ..Aim 2 will investigate the consequences to the aging oxidizable proteome of this age-related loss of neuronal GSH, NADH and redox potential...
  53. Impact of Pregnancy on Drug Absorption, Disposition and End Organ Response
    Steve N Caritis; Fiscal Year: 2013
    ..biomarkers including cervical length and density, matrix metalloproteinases, cytokines, and the cervicovaginal proteome. These analyses will allow us to compare the PK of these two progestins, identify their targets and evaluate ..
  54. Generation and Evaluation of KSHV VLPs as Vaccines
    GARY S contact HAYWARD; Fiscal Year: 2010
    ..a DNA-free VLP-based preventative vaccine for KSHV/KS, and to develop a revolutionizing high-throughput global proteome approach to measuring viral antibody and neutralization responses in KSHV-positive patients with and without KS, ..
  55. Global Genomic and Proteomic Profiling of African Children with Typhoid Fever
    Stephen Obaro; Fiscal Year: 2013
    ..typhi proteome microarrays and develop prototype serologic assay for acute typhoid (ELISA) 3) Validate classifier genes and ..
  56. Characterization of the Plasma Proteome in Mouse Models of Colon Cancer
    Kenneth E Hung; Fiscal Year: 2010
    ..Relevance: This proposal will lay the foundation for the identification of biomarkers which may be used for the early detection of colorectal cancer through the analysis of perhaps a single drop of blood. ..
  57. Campylobacter jejuni outer membrane protein vaccine
    Stuart Thompson; Fiscal Year: 2009
    ..helpful as a starting point toward understanding its complement of OMPs, only direct identification of OMPs (by proteome analysis) will provide detailed information about the OMPs actually expressed by C. jejuni strains...
  58. A Proteomic Approach to Biomarker Discovery in Prion Disease
    Lingjun Li; Fiscal Year: 2009
    ..with prion infection will result in an altered protein profile of the cerebrospinal fluids (CSF) and/or serum proteome. (2) The combination of accurate mass measurements, isotopic labeling strategy for quantitative analyses, tandem ..
  59. A protein array platform for anti-citrulline antibodies in Rheumatoid Arthritis
    Ji Qiu; Fiscal Year: 2013
    ..We will establish this platform to profile anti-citrullinated protein antibodies in RA at the proteome level and to map immuno-dominant epitopes of citrullinated autoantigens on array with the key advantages being ..
  60. T1D:Investigating the Gut Microbiome, Urinary Proteome and Metabolome
    Ramana Madupu; Fiscal Year: 2011
    ..We propose to study the complex interplay of environmental, immunological and genetic factors to discover molecular signatures with a potential to advance clinical diagnosis and therapy at or before the onset of T1D. ..
  61. Discovery of a urine biomarker of HIV for noninvasive, point-of-care testing use
    Hans P Schlecht; Fiscal Year: 2011
    ..g., those previously vaccinated with candidate HIV vaccines. Upon accomplishment of this project, we will have furthered the development of methods for biomarker discovery in urine, which can then be applied to other infections. ..
  62. Protease regulation of ovarian recrudescence
    KELLY ANSLEY YOUNG; Fiscal Year: 2013
    ..proteomics approach to identify substrates cleaved by MMPs during recrudescence by comparing the proteome of GM6001-treated vs. control ovaries. Examination of both mRNA and protein for key markers of angiogenesis (e.g...
  63. Vaccinia Proteome Affinity Reagents From Phage Display
    Philip Felgner; Fiscal Year: 2005
    ..binding partner, or "Artificial Antibody" (ArtAb), for each protein in the vaccinia virus (smallpox vaccine) proteome. The approach proposed here to accomplish this applies vast libraries of novel protein variants fused to ..
  64. Human serum carbonyl proteome in cardiovascular diseases
    Nisha Jain Garg; Fiscal Year: 2010
    ..In this study, we propose to develop a plasma oxidative proteome in chagasic patients...
  65. Identifying Calpain-10 Substrates from Human Proteome
    Rihe Liu; Fiscal Year: 2005
    ..This proposal is directed at scanning the human proteome to identify the downstream targets of calpain-10 using a novel proteomic technology platform called mRNA display...
  66. Global Analysis of the Rickettsia prowazekii Proteome
    David Wood; Fiscal Year: 2007
    ..prowazekii. Important targets for a proteome approach are the bacterial pathogens of humans, organisms that exhibit unique biologies, and unfortunately, in ..
  67. Normal and Type-2 Diabetic Platelet Proteomics and Storage for Transfusion
    Richard Phipps; Fiscal Year: 2007
    ..Our multidisciplinary team will test the hypothesis that the platelet proteome differs between normal and type-2 diabetics...
  68. A proteomic approach for early diagnosis of diabetes
    Julian Watts; Fiscal Year: 2005
    ..This application is thus based upon the assumption that the composition of the plasma proteome reflects the general physiologic state of the human body, thus quantitative proteomic measurements of the plasma ..
  69. Sensing Protein Folding Capacity in the Cell During Aging
    ROCKLAND L WISEMAN; Fiscal Year: 2010
    ..2008) Science 319: 916), a complex network of molecular interactions that determines the health of the proteome. Proteostasis balances protein biosynthesis, folding, translocation, assembly/disassembly and clearance with the ..
  70. Identification of the Interactome of Methylated Histones from Human Proteome
    Rihe Liu; Fiscal Year: 2009
    ..The protein sequences that bind to distinct methylation states will be isolated from an mRNA-displayed human proteome library. The selections will be performed under very specific conditions...
  71. Proteomics of Cerebrospinal Fluid in Chronic Fatigue Syndrome
    James Baraniuk; Fiscal Year: 2009
    ..Despite the diverse clinical syndromes, the CFS-related proteome is the same, suggesting a unified pathogenesis...
  72. Scanning the Vaccinia Proteome for antiSmallpox Antigens
    David Roth; Fiscal Year: 2002
    ..under a previously funded Phase I SBIR grant will be applied to producing the complete proteome from vaccinia virus and the proteome will be applied to the general problem of identifying potent vaccine ..
  73. Functional Proteomic Analysis of Cardiac Mitochondria
    Peipei Ping; Fiscal Year: 2005
    ..At least two proteomic approaches may be utilized to map the mitochondrial sub-proteome. One focuses on broad-scale annotation of proteins (i.e...
  74. Top-Down Mass Spectrometry of Salivary Fluids for Cancer Assessment
    Joseph Loo; Fiscal Year: 2007
    unreadable] DESCRIPTION (provided by applicant): [unreadable] Top-down proteome profiling and protein characterization to measure reproducibly 1500 protein features in human whole salivary fluids will be performed to assess the ..
  75. Novel Comprehensive Proteome Analyses of Metastasis
    David Speicher; Fiscal Year: 2004
    ..Our global proteome strategy should result in reliable quantitative comparisons of up to 10,000 proteins instead of the 1,500 to 2,..
  76. Proteome of Glomerular Cells in Diabetic Nephropathy
    Paul Voziyan; Fiscal Year: 2007
    ..New proteomic technologies that allow characterizing cellular proteome offer a powerful tool for determining molecular mechanisms of diabetic nephropathy...
  77. Proteostasis sensors to assess the cellular protein folding capacity
    RICHARD I contact MORIMOTO; Fiscal Year: 2010
    ..This is achieved by proteostasis, a complex network of molecular interactions that determines the health of the proteome. Proteostasis balances protein biosynthesis, folding, translocation, assembly/disassembly, and clearance with the ..
  78. Novel Comprehensive Proteome Analyses of Metastasis
    David Speicher; Fiscal Year: 2001
    ..Our global proteome strategy should result in reliable quantitative comparisons of up to 10,000 proteins instead of the 1,500 to 2,..
  79. Proteomic Profiling of the Vocal Fold Extracellular Matrix
    Nathan Welham; Fiscal Year: 2009
    ..Our overarching long- term hypothesis is that disease specific alterations in the VF-ECM are the result of proteome-wide changes involving the cell-mediated coordination of functionally interdependent proteins...
  80. Proteomic Analysis of Persistent Chlamydia pneumoniae
    James Summersgill; Fiscal Year: 2004
    ..pneumoniae can produce under various growth conditions, a process known as proteome analysis...
  81. PKC EPSILON AND SRC PTK SIGNALING IN PRECONDITIONING
    Peipei Ping; Fiscal Year: 2009
    ..Instead, it recruits the participation of other molecules to form a cardioprotective sub-proteome. This knowledge in hand, we are now focusing on the next challenge: to determine the subcellular targets of ..
  82. MASS SPECTROMETRY ANALYSIS OF THE HUMAN CSF PROTEOME
    Dominic Desiderio; Fiscal Year: 2001
    DESCRIPTION: (adapted from applicant's abstract) We hypothesize that the proteome obtained from human cerebrospinal fluid (CSF) differs between controls and those patients who are diagnosed with idiopathic low back pain because our ..