A Pandey

Summary

Country: Denmark

Publications

  1. ncbi request reprint Computational and experimental analysis reveals a novel Src family kinase in the C. elegans genome
    Akhilesh Pandey
    Center for Experimental Bioinformatics, University of Southern Denmark, Odense M, DK 5230, Denmark
    Bioinformatics 19:169-72. 2003
  2. ncbi request reprint Use of mass spectrometry to study signaling pathways
    A Pandey
    Whitehead Institute for Biomedical Research, Cambridge MA 02142, USA
    Sci STKE 2000:pl1. 2000
  3. ncbi request reprint Cloning of a novel phosphotyrosine binding domain containing molecule, Odin, involved in signaling by receptor tyrosine kinases
    Akhilesh Pandey
    Whitehead Institute for Biomedical Research, Cambridge, Massachusetts 02142, USA
    Oncogene 21:8029-36. 2002
  4. ncbi request reprint Cloning and characterization of PAK5, a novel member of mammalian p21-activated kinase-II subfamily that is predominantly expressed in brain
    Akhilesh Pandey
    Center for Experimental Bioinformatics, University of Southern Denmark, Campusvej 55, DK 5230 Odense M, Denmark
    Oncogene 21:3939-48. 2002
  5. ncbi request reprint Identification of a novel immunoreceptor tyrosine-based activation motif-containing molecule, STAM2, by mass spectrometry and its involvement in growth factor and cytokine receptor signaling pathways
    A Pandey
    Whitehead Institute for Biomedical Research, Cambridge, Massachusetts 02142, USA
    J Biol Chem 275:38633-9. 2000
  6. ncbi request reprint Detection of tyrosine phosphorylated peptides by precursor ion scanning quadrupole TOF mass spectrometry in positive ion mode
    H Steen
    Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense M
    Anal Chem 73:1440-8. 2001
  7. ncbi request reprint Use of mass spectrometry-derived data to annotate nucleotide and protein sequence databases
    M Mann
    Protein Interaction Laboratory PIL, Center for Experimental Bioinformatics, University of Southern Denmark, Campusvej 55, DK 5230, and MDS Protana, Staermosegaardsvej 6, DK 5230, Odense M, Denmark
    Trends Biochem Sci 26:54-61. 2001
  8. pmc Analysis of receptor signaling pathways by mass spectrometry: identification of vav-2 as a substrate of the epidermal and platelet-derived growth factor receptors
    A Pandey
    Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
    Proc Natl Acad Sci U S A 97:179-84. 2000
  9. ncbi request reprint GPMAW--a software tool for analyzing proteins and peptides
    S Peri
    Protein Interaction Laboratory, Center for Experimental Bioinformatics, University of Southern Denmark, Odense, Denmark
    Trends Biochem Sci 26:687-9. 2001
  10. ncbi request reprint Cloning of rat thymic stromal lymphopoietin receptor (TSLPR) and characterization of genomic structure of murine Tslpr gene
    Blagoy Blagoev
    Protein Interaction Laboratory, Center for Experimental Bioinformatics, University of Southern Denmark, Campusvej 55, M, DK 5230, Odense, Denmark
    Gene 284:161-8. 2002

Collaborators

Detail Information

Publications65

  1. ncbi request reprint Computational and experimental analysis reveals a novel Src family kinase in the C. elegans genome
    Akhilesh Pandey
    Center for Experimental Bioinformatics, University of Southern Denmark, Odense M, DK 5230, Denmark
    Bioinformatics 19:169-72. 2003
    ..However, the vast majority of annotated genes are derived by gene prediction methods. It is important to not only validate the predicted coding regions but also to identify genes that may have been missed by these programs...
  2. ncbi request reprint Use of mass spectrometry to study signaling pathways
    A Pandey
    Whitehead Institute for Biomedical Research, Cambridge MA 02142, USA
    Sci STKE 2000:pl1. 2000
    ..Our goal is to provide detailed methods in use today for proteomic applications in general and for receptor-mediated signaling pathways in particular...
  3. ncbi request reprint Cloning of a novel phosphotyrosine binding domain containing molecule, Odin, involved in signaling by receptor tyrosine kinases
    Akhilesh Pandey
    Whitehead Institute for Biomedical Research, Cambridge, Massachusetts 02142, USA
    Oncogene 21:8029-36. 2002
    ..Taken together, our results indicate that Odin may play a negative role in growth factor receptor signaling pathways...
  4. ncbi request reprint Cloning and characterization of PAK5, a novel member of mammalian p21-activated kinase-II subfamily that is predominantly expressed in brain
    Akhilesh Pandey
    Center for Experimental Bioinformatics, University of Southern Denmark, Campusvej 55, DK 5230 Odense M, Denmark
    Oncogene 21:3939-48. 2002
    ..The expression pattern of PAK5 is distinct from that of PAK4 and PAK6, suggesting a functional division among PAK-II subfamily kinases based on differential tissue distribution...
  5. ncbi request reprint Identification of a novel immunoreceptor tyrosine-based activation motif-containing molecule, STAM2, by mass spectrometry and its involvement in growth factor and cytokine receptor signaling pathways
    A Pandey
    Whitehead Institute for Biomedical Research, Cambridge, Massachusetts 02142, USA
    J Biol Chem 275:38633-9. 2000
    ..Finally, overexpression of wild type STAM2 led to an increase in IL-2-mediated induction of c-Myc promoter activation indicating that it potentiates cytokine receptor signaling...
  6. ncbi request reprint Detection of tyrosine phosphorylated peptides by precursor ion scanning quadrupole TOF mass spectrometry in positive ion mode
    H Steen
    Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense M
    Anal Chem 73:1440-8. 2001
    ..The new method can be applied to unknown protein samples, because the identification and localization of the modification is performed on the same sample...
  7. ncbi request reprint Use of mass spectrometry-derived data to annotate nucleotide and protein sequence databases
    M Mann
    Protein Interaction Laboratory PIL, Center for Experimental Bioinformatics, University of Southern Denmark, Campusvej 55, DK 5230, and MDS Protana, Staermosegaardsvej 6, DK 5230, Odense M, Denmark
    Trends Biochem Sci 26:54-61. 2001
    ....
  8. pmc Analysis of receptor signaling pathways by mass spectrometry: identification of vav-2 as a substrate of the epidermal and platelet-derived growth factor receptors
    A Pandey
    Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
    Proc Natl Acad Sci U S A 97:179-84. 2000
    ..The strategy suggested here can be used for routine identification of downstream components of cell surface receptors in mammalian cells...
  9. ncbi request reprint GPMAW--a software tool for analyzing proteins and peptides
    S Peri
    Protein Interaction Laboratory, Center for Experimental Bioinformatics, University of Southern Denmark, Odense, Denmark
    Trends Biochem Sci 26:687-9. 2001
    ....
  10. ncbi request reprint Cloning of rat thymic stromal lymphopoietin receptor (TSLPR) and characterization of genomic structure of murine Tslpr gene
    Blagoy Blagoev
    Protein Interaction Laboratory, Center for Experimental Bioinformatics, University of Southern Denmark, Campusvej 55, M, DK 5230, Odense, Denmark
    Gene 284:161-8. 2002
    ..Finally, using linkage analysis, we mapped the murine Tslpr gene to mouse chromosome 5 between the Ecm2 and Pxn genes...
  11. ncbi request reprint Analysis of proteins and proteomes by mass spectrometry
    M Mann
    Protein Interaction Laboratory and Center for Experimental BioInformatics CEBI, Department of Biochemistry and Molecular Biology, University of Southern Denmark, Campusvej 55, 5230 Odense M, Denmark
    Annu Rev Biochem 70:437-73. 2001
    ..By these and similar strategies, entire protein complexes, signaling pathways, and whole organelles are being characterized. Posttranslational modifications remain difficult to analyze but are starting to yield to generic strategies...
  12. ncbi request reprint A novel Src homology 2 domain-containing molecule, Src-like adapter protein-2 (SLAP-2), which negatively regulates T cell receptor signaling
    Akhilesh Pandey
    Whitehead Institute for Biomedical Research, Cambridge, Massachusetts 02142, USA
    J Biol Chem 277:19131-8. 2002
    ..This report therefore implicates SLAP and SLAP-2 as a family of adapter proteins that negatively regulate T cell receptor signaling...
  13. ncbi request reprint A reassessment of the translation initiation codon in vertebrates
    S Peri
    Protein Interaction Laboratory, Center for Experimental Bioinformatics, University of Southern Denmark, Odense M, Denmark
    Trends Genet 17:685-7. 2001
    ....
  14. ncbi request reprint Cloning of a receptor subunit required for signaling by thymic stromal lymphopoietin
    A Pandey
    Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
    Nat Immunol 1:59-64. 2000
    ..Cloning of TSLPR should facilitate an understanding of TSLP function and its signaling mechanism...
  15. ncbi request reprint Characterization of promoter region and genomic structure of the murine and human genes encoding Src like adapter protein
    I Kratchmarova
    Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense University, M, DK 5230, Odense, Denmark
    Gene 262:267-73. 2001
    ..Since SLAP is transcriptionally regulated by retinoic acid and by activation of B cells, the cloning of its promoter region will permit a detailed analysis of the elements required for its transcriptional regulation...
  16. ncbi request reprint Context-specific effects of fibulin-5 (DANCE/EVEC) on cell proliferation, motility, and invasion. Fibulin-5 is induced by transforming growth factor-beta and affects protein kinase cascades
    William P Schiemann
    Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
    J Biol Chem 277:27367-77. 2002
    ..Our findings also indicate that aberrant FBLN-5 expression likely contributes to tumor development in humans...
  17. ncbi request reprint An evaluation of the use of two-dimensional gel electrophoresis in proteomics
    S E Ong
    Protein Interaction Laboratory, Center for Experimental Bioinformatics, University of Southern Denmark, Odense
    Biomol Eng 18:195-205. 2001
    ..In the wake of recent advances in mass spectrometry and related areas, we outline areas where two-dimensional gels can best be utilized as the preferred separation method in proteomic strategies...
  18. ncbi request reprint Phosphotyrosine mapping in Bcr/Abl oncoprotein using phosphotyrosine-specific immonium ion scanning
    Hanno Steen
    Center for Experimental Bioinformatics, Department of Biochemistry and Molecular Biology, University of Southern Denmark, 5230 Odense M, Denmark
    Mol Cell Proteomics 2:138-45. 2003
    ..This study shows the power of phosphotyrosine-specific immonium ion scanning for sensitive phosphotyrosine mapping when limited amounts of samples are available...
  19. ncbi request reprint Tyrosine phosphorylation mapping of the epidermal growth factor receptor signaling pathway
    Hanno Steen
    Protein Interaction Laboratory, Center for Experimental Bioinformatics, Department of Biochemistry and Molecular Biology, University of Southern Denmark, Campusvej 55, 5230 Odense M, Denmark
    J Biol Chem 277:1031-9. 2002
    ..Because of its sensitivity and selectivity, this approach will be useful in proteomic approaches to study tyrosine phosphorylation in a number of signal transduction pathways...
  20. ncbi request reprint A mass spectrometry-based proteomic approach for identification of serine/threonine-phosphorylated proteins by enrichment with phospho-specific antibodies: identification of a novel protein, Frigg, as a protein kinase A substrate
    Mads Grønborg
    Department of Biochemistry and Molecular Biology, Center for Experimental Bioinformatics, University of Southern Denmark, Campusvej 55, 5230 Odense M, Denmark
    Mol Cell Proteomics 1:517-27. 2002
    ..Our method should be applicable as a generic strategy for enrichment and identification of serine/threonine-phosphorylated substrates in signal transduction pathways...
  21. ncbi request reprint Analysis of protein phosphorylation using mass spectrometry: deciphering the phosphoproteome
    Matthias Mann
    Center for Experimental Bioinformatics, University of Southern Denmark, M, DK 5230, Odense, Denmark
    Trends Biotechnol 20:261-8. 2002
    ..In this article, we outline several methods for enrichment of phosphorylated proteins and peptides and discuss various options for their identification and quantitation with special emphasis on mass spectrometry-based techniques...
  22. ncbi request reprint Resources for full-length cDNAs
    Troels Z Kristiansen
    Center for Experimental Bioinformatics, University of Southern Denmark, Odense, Denmark
    Trends Biochem Sci 27:266-7. 2002
  23. ncbi request reprint Inhibition of adipocyte differentiation by resistin-like molecule alpha. Biochemical characterization of its oligomeric nature
    Blagoy Blagoev
    Center for Experimental Bioinformatics, University of Southern Denmark, Odense M DK 5230, Denmark
    J Biol Chem 277:42011-6. 2002
    ..Since RELMalpha is expressed by adipose tissue and it is a secreted factor, our findings suggest that RELMalpha may be involved in the control of the adipogenesis as well as in the process of muscle differentiation...
  24. pmc Cloning of a novel signaling molecule, AMSH-2, that potentiates transforming growth factor beta signaling
    Nieves Ibarrola
    McKusick Nathans Institute of Genetic Medicine and Department of Biological Chemistry, Johns Hopkins University, Baltimore, MD 21205, USA
    BMC Cell Biol 5:2. 2004
    ..Signaling by these factors is mediated chiefly by the Smad family of latent transcription factors...
  25. ncbi request reprint Systematic interactome mapping and genetic perturbation analysis of a C. elegans TGF-beta signaling network
    Muneesh Tewari
    Center for Cancer Systems Biology, Dana Farber Cancer Institute, Boston, Massachusetts 02115, USA
    Mol Cell 13:469-82. 2004
    ..Integrating interactome maps with systematic genetic perturbations may be useful for developing a systems biology approach to this and other signaling modules...
  26. ncbi request reprint Comprehensive proteomic analysis of human pancreatic juice
    Mads Grønborg
    McKusick Nathans Institute of Genetic Medicine and Department of Biological Chemistry, Johns Hopkins University, Baltimore, Maryland 21205, USA
    J Proteome Res 3:1042-55. 2004
    ..The proteins identified in this study could be directly assessed for their potential as biomarkers for pancreatic cancer by quantitative proteomics methods or immunoassays...
  27. ncbi request reprint A manually curated functional annotation of the human X chromosome
    H C Harsha
    Nat Genet 37:331-2. 2005
  28. pmc Genome annotation of Anopheles gambiae using mass spectrometry-derived data
    Dario E Kalume
    McKusick Nathans Institute of Genetic Medicine, Department of Biological Chemistry and Oncology, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA
    BMC Genomics 6:128. 2005
    ..This approach generally does not allow identification of proteins that have not yet been predicted or whose transcripts have not been identified...
  29. ncbi request reprint Phosphoproteome analysis of HeLa cells using stable isotope labeling with amino acids in cell culture (SILAC)
    Ramars Amanchy
    McKusick Nathans Institute for Genetic Medicine and the Department of Biological Chemistry and Oncology, Johns Hopkins University, 733 N Broadway, Baltimore, MD 21205, USA
    J Proteome Res 4:1661-71. 2005
    ..Because of its sensitivity and general applicability, our approach will be useful for investigating signaling pathways in a global fashion and for using phosphoproteomics for functional annotation of genomes...
  30. ncbi request reprint Chemical rescue of a mutant enzyme in living cells
    Yingfeng Qiao
    Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
    Science 311:1293-7. 2006
    ..Rescue of R388A cellular Src provided insights into the mitogen-activated protein kinase pathway. This chemical rescue approach will likely have many applications in cell signaling...
  31. ncbi request reprint Mouse embryonic fibroblasts derived from Odin deficient mice display a hyperproliiferative phenotype
    Troels Zakarias Kristiansen
    McKusick Nathans Institute of Genetic Medicine and Department of Biological Chemistry, Johns Hopkins University, Baltimore, MD 21205, USA
    DNA Res 11:285-92. 2004
    ..Our results confirm that although Odin expression in mice is not essential for any major developmental pathway, it could play a significant functional role to negatively regulate growth factor receptor signaling pathways...
  32. pmc Overlapping of MINK and CHRNE gene loci in the course of mammalian evolution
    Ippeita Dan
    Division of Food Engineering, National Food Research Institute, 2 1 12, Kannondai, Tsukuba, Ibaraki 305 8642, Japan
    Nucleic Acids Res 30:2906-10. 2002
    ..Because CHRNE and MINK are differentially expressed, the potentially hazardous mutations responsible for the exon overlap seem to have escaped evolutionary pressures by differential temporo-spatial expression of the two genes...
  33. ncbi request reprint Cloning of MASK, a novel member of the mammalian germinal center kinase III subfamily, with apoptosis-inducing properties
    Ippeita Dan
    Kusumi Membrane Organizer Project, Exploratory Research for Advanced Technology, Japan Science and Technology Corporation, 5 11 33 Chiyoda, Nagoya 460 0012, Japan
    J Biol Chem 277:5929-39. 2002
    ..Finally, wild type and C-terminally truncated forms of MASK can both induce apoptosis upon overexpression in mammalian cells that is abrogated by CrmA, suggesting involvement of MASK in the apoptotic machinery in mammalian cells...
  34. ncbi request reprint Analysis of tyrosine phosphorylation sites in signaling molecules by a phosphotyrosine-specific immonium ion scanning method
    Hanno Steen
    Harvard Medical School, Department of Cell Biology, 240 Longwood Avenue, Boston, MA 02115, USA
    Sci STKE 2002:pl16. 2002
    ..Because of its simplicity and specificity, PSI scanning is likely to become an important tool in proteomic studies of pathways involving tyrosine phosphorylation...
  35. ncbi request reprint A proteomic approach for quantitation of phosphorylation using stable isotope labeling in cell culture
    Nieves Ibarrola
    McKusick Nathans Institute for Genetic Medicine and the Department of Biological Chemistry, Johns Hopkins University, Baltimore, Maryland 21287, USA
    Anal Chem 75:6043-9. 2003
    ..We have used SILAC to quantitate the extent of known phosphorylation sites as well as to identify and quantitate novel phosphorylation sites...
  36. ncbi request reprint Analysis of the human protein interactome and comparison with yeast, worm and fly interaction datasets
    T K B Gandhi
    Institute of Bioinformatics, International Technology Park, Bangalore 560 066, India
    Nat Genet 38:285-93. 2006
    ..The human interaction map constructed from our analysis should facilitate an integrative systems biology approach to elucidating the cellular networks that contribute to health and disease states...
  37. ncbi request reprint Identification of protein ubiquitylation by electrospray ionization tandem mass spectrometric analysis of sulfonated tryptic peptides
    Dongxia Wang
    Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
    Anal Chem 78:3681-7. 2006
    ..The method is demonstrated by the analysis of three ubiquitin-conjugated proteins using LC/MS/MS...
  38. ncbi request reprint GCN5 acetyltransferase complex controls glucose metabolism through transcriptional repression of PGC-1alpha
    Carles Lerin
    Department of Cell Biology, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
    Cell Metab 3:429-38. 2006
    ..GCN5 might be a pharmacological target to regulate the activity of PGC-1alpha, providing a potential treatment for metabolic disorders in which hepatic glucose output is dysregulated...
  39. pmc Phosphoproteomic analysis of Her2/neu signaling and inhibition
    Ron Bose
    Department of Pharmacology, McKusick Nathans Institute for Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
    Proc Natl Acad Sci U S A 103:9773-8. 2006
    ..Network modeling, which combined phosphoproteomic results with literature-curated protein-protein interaction data, was used to suggest roles for some of the previously unidentified Her2 signaling proteins...
  40. ncbi request reprint Upstream stimulatory factors regulate the C/EBP alpha gene during differentiation of 3T3-L1 preadipocytes
    Jae Woo Kim
    Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
    Biochem Biophys Res Commun 354:517-21. 2007
    ..The expression of AP-4 is reciprocally regulated with USF-1 during adipocyte differentiation. These findings suggest that USF-1 and 2 play roles in C/EBPalpha expression, whereas the AP-4 represses it...
  41. pmc Global proteomic profiling of phosphopeptides using electron transfer dissociation tandem mass spectrometry
    Henrik Molina
    McKusick Nathans Institute for Genetic Medicine, The Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
    Proc Natl Acad Sci U S A 104:2199-204. 2007
    ..Overall, ETD is an excellent method for localization of phosphorylation sites and should be an integral component of any strategy for comprehensive phosphorylation analysis...
  42. ncbi request reprint A curated compendium of phosphorylation motifs
    Ramars Amanchy
    Nat Biotechnol 25:285-6. 2007
  43. ncbi request reprint Dynamic interplay between O-linked N-acetylglucosaminylation and glycogen synthase kinase-3-dependent phosphorylation
    Zihao Wang
    Department of Biological Chemistry, The Johns Hopkins University School of Medicine, Baltimore, Maryland 21205 2185, USA
    Mol Cell Proteomics 6:1365-79. 2007
    ..Taken together, these data indicated the complex interplay between phosphorylation and O-GlcNAcylation that occurs within signaling networks...
  44. pmc Disruption of Plasmodium falciparum development by antibodies against a conserved mosquito midgut antigen
    Rhoel R Dinglasan
    Department of Molecular Microbiology and Immunology, Malaria Research Institute, Johns Hopkins Bloomberg School of Public Health, 615 North Wolfe Street, Baltimore, MD 21205, USA
    Proc Natl Acad Sci U S A 104:13461-6. 2007
    ..These results advance our understanding of malaria parasite-mosquito host interactions and guide in the design of transmission-blocking vaccines...
  45. pmc Protein pyrophosphorylation by inositol pyrophosphates is a posttranslational event
    Rashna Bhandari
    The Solomon H Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, 725 North Wolfe Street, Baltimore, MD 21205, USA
    Proc Natl Acad Sci U S A 104:15305-10. 2007
    ..Pyrophosphorylation may represent a novel mode of signaling to proteins...
  46. ncbi request reprint Phosphoproteomics
    Jun Zhong
    Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
    Curr Protoc Protein Sci . 2007
    ....
  47. pmc Global impact of oncogenic Src on a phosphotyrosine proteome
    Weifeng Luo
    Department of Cell and Developmental Biology, Cancer Biology, Biostatistics, and Biochemistry, and The Proteomics Laboratory of the Mass Spectrometry Research Center, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
    J Proteome Res 7:3447-60. 2008
    ..This select group, of particular interest as diagnostic biomarkers, includes well-established Src sites on signaling/adhesion/cytoskeletal proteins, but also uncharacterized sites of potential relevance to the transformed cell phenotype...
  48. pmc Identification of c-Src tyrosine kinase substrates using mass spectrometry and peptide microarrays
    Ramars Amanchy
    McKusick Nathans Institute of Genetic Medicine and the Departments of Biological Chemistry, Pathology and Oncology, Johns Hopkins University, Baltimore, Maryland 21205, USA
    J Proteome Res 7:3900-10. 2008
    ....
  49. pmc Insights into the role of histone H3 and histone H4 core modifiable residues in Saccharomyces cerevisiae
    Edel M Hyland
    High Throughput Biology Center, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
    Mol Cell Biol 25:10060-70. 2005
    ..Finally, we allude to the possible molecular mechanisms underlying the effects of these modifications...
  50. ncbi request reprint A database of transcriptional start sites
    Troels Z Kristiansen
    Trends Biochem Sci 27:174. 2002
  51. pmc Development of human protein reference database as an initial platform for approaching systems biology in humans
    Suraj Peri
    McKusick Nathans Institute of Genetic Medicine, Johns Hopkins University, Baltimore, Maryland 21287, USA
    Genome Res 13:2363-71. 2003
    ..hprd.org to the academic community. This unified bioinformatics platform will be useful in cataloging and mining the large number of proteomic interactions and alterations that will be discovered in the postgenomic era...
  52. ncbi request reprint A roadmap of the mouse genome
    Babylakshmi Muthusamy
    Trends Genet 18:553. 2002
  53. ncbi request reprint The HUPO PSI's molecular interaction format--a community standard for the representation of protein interaction data
    Henning Hermjakob
    European Bioinformatics Institute, EBI Hinxton, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
    Nat Biotechnol 22:177-83. 2004
    ....
  54. pmc A role for thymic stromal lymphopoietin in CD4(+) T cell development
    Amin Al-Shami
    Laboratory of Molecular Immunology, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
    J Exp Med 200:159-68. 2004
    ..Thus, as compared with other known cytokines, TSLP is distinctive in exhibiting a lineage preference for the expansion and survival of CD4(+) T cells...
  55. ncbi request reprint Identification of novel highly expressed genes in pancreatic ductal adenocarcinomas through a bioinformatics analysis of expressed sequence tags
    Dengfeng Cao
    Department of Pathology, The Johns Hopkins Medical Institutions, Baltimore, Maryland 21231, USA
    Cancer Biol Ther 3:1081-9; discussion 1090-1. 2004
    ....
  56. ncbi request reprint Toll and interleukin-1 receptor (TIR) domain-containing proteins in plants: a genomic perspective
    Judith A Jebanathirajah
    Dept of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
    Trends Plant Sci 7:388-91. 2002
    ..Several novel types of TIR-domain-containing proteins are found in Arabidopsis that are not found in other genomes. Here, we discuss the roles of TIR-domain-containing proteins in pathogen resistance and as candidate signaling modules...
  57. ncbi request reprint Differentially expressed genes in pancreatic ductal adenocarcinomas identified through serial analysis of gene expression
    Steven R Hustinx
    Department of Pathology, The Johns Hopkins Medical Institutions, Baltimore, Maryland 21231, USA
    Cancer Biol Ther 3:1254-61. 2004
    ..TAGmapper should prove to be a powerful tool for the discovery of novel tumor markers through assignment of uncharacterized SAGE tags...
  58. pmc Human protein reference database as a discovery resource for proteomics
    Suraj Peri
    McKusick Nathans Institute of Genetic Medicine and Department of Biological Chemistry, Johns Hopkins University, Baltimore, MD 21287, USA
    Nucleic Acids Res 32:D497-501. 2004
    ..This database will assist in biomedical discoveries by serving as a resource of genomic and proteomic information and providing an integrated view of sequence, structure, function and protein networks in health and disease...
  59. ncbi request reprint Proteomics goes quantitative: measuring protein abundance
    Hanno Steen
    Department Cell Biology, Harvard Medical School, Boston, MA 02115, USA
    Trends Biotechnol 20:361-4. 2002
    ..Furthermore, methods for the quantitation of relative protein abundance at the protein level are getting more advanced, which should complement gene expression monitoring at the mRNA level...
  60. pmc Sequential phosphorylation of CCAAT enhancer-binding protein beta by MAPK and glycogen synthase kinase 3beta is required for adipogenesis
    Qi Qun Tang
    Departments of Pediatrics Division of Endocrinology, McKusick Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
    Proc Natl Acad Sci U S A 102:9766-71. 2005
    ..The delayed transactivation of the C/EBPalpha and PPARgamma genes by C/EBPbeta appears necessary to allow mitotic clonal expansion, which would otherwise be prevented, because C/EBPalpha and PPARgamma are antimitotic...
  61. ncbi request reprint Plasma Proteome Database as a resource for proteomics research
    Babylakshmi Muthusamy
    Institute of Bioinformatics, Bangalore, India
    Proteomics 5:3531-6. 2005
    ..This database is an attempt at comprehensive annotation of a complex subproteome and is available on the web at http://www.plasmaproteomedatabase.org...
  62. ncbi request reprint Probabilistic model of the human protein-protein interaction network
    Daniel R Rhodes
    Bioinformatics Program, Department of Pathology, University of Michigan Medical School, Ann Arbor, Michigan 48109, USA
    Nat Biotechnol 23:951-9. 2005
    ..This integrative analysis provides a comprehensive framework for exploring the human protein interaction network...
  63. ncbi request reprint A functional annotation of subproteomes in human plasma
    Peipei Ping
    Department of Physiology and Medicine, Division of Cardiology, Cardiovascular Research Laboratories, University of California, Los Angeles, CA, USA
    Proteomics 5:3506-19. 2005
    ..The HPPP-organized, multi-laboratory effort, as described herein, resulted in much synergy and was essential to the success of this project...
  64. ncbi request reprint TAGmapper: a web-based tool for mapping SAGE tags
    P Bala
    Institute of Bioinformatics, International Tech Park, Whitefield Road, Bangalore 560 066, India
    Gene 364:123-9. 2005
    ..We anticipate that TAGmapper will be a useful tool in functional genomic approaches by providing accurate identification of genes in SAGE experiments...
  65. pmc Comparisons of tyrosine phosphorylated proteins in cells expressing lung cancer-specific alleles of EGFR and KRAS
    Udayan Guha
    Program in Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
    Proc Natl Acad Sci U S A 105:14112-7. 2008
    ..Bayesian network analysis of these and other datasets revealed that PTRF might be a potentially important component of the ERBB signaling network...