Pedro A Reche

Summary

Affiliation: Harvard University
Country: USA

Publications

  1. ncbi In silico characterization of the family of PARP-like poly(ADP-ribosyl)transferases (pARTs)
    Helge Otto
    Institute of Immunology, University Hospital Hamburg Eppendorf, Germany
    BMC Genomics 6:139. 2005
  2. ncbi PEPVAC: a web server for multi-epitope vaccine development based on the prediction of supertypic MHC ligands
    Pedro A Reche
    Laboratory of Immunobiology and Department of Medical Oncology, Dana Farber Cancer Institute, Harvard Medical School, 44 Binney Street, Boston, MA 02115, USA
    Nucleic Acids Res 33:W138-42. 2005
  3. ncbi EPIMHC: a curated database of MHC-binding peptides for customized computational vaccinology
    Pedro A Reche
    Laboratory of Immunobiology and Department of Medical Oncology, Dana Farber Cancer Institute, Boston, MA 02115, USA
    Bioinformatics 21:2140-1. 2005
  4. ncbi Enhancement to the RANKPEP resource for the prediction of peptide binding to MHC molecules using profiles
    Pedro A Reche
    Laboratory of Immunobiology and Department of Medical Oncology, Dana Farber Cancer Institute, 44 Binney Street, Boston, MA 02115, USA
    Immunogenetics 56:405-19. 2004
  5. ncbi Antiviral chemotherapy facilitates control of poxvirus infections through inhibition of cellular signal transduction
    Hailin Yang
    Laboratory of Immunobiology, Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts 02115, USA
    J Clin Invest 115:379-87. 2005
  6. ncbi Prediction of MHC class I binding peptides using profile motifs
    Pedro A Reche
    Laboratory of Immunobiology, Dana-Farber Cancer Institute, Boston, MA, USA
    Hum Immunol 63:701-9. 2002
  7. ncbi Genome-wide characterization of a viral cytotoxic T lymphocyte epitope repertoire
    Weimin Zhong
    Laboratory of Immunobiology and Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts 02115, USA
    J Biol Chem 278:45135-44. 2003
  8. ncbi Peptide variants of viral CTL epitopes mediate positive selection and emigration of Ag-specific thymocytes in vivo
    Masha Fridkis-Hareli
    Laboratory of Immunobiology, Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02115, USA
    J Immunol 173:1140-50. 2004
  9. ncbi Sequence variability analysis of human class I and class II MHC molecules: functional and structural correlates of amino acid polymorphisms
    Pedro A Reche
    Laboratory of Immunobiology, Dana Farber Cancer Institute, Harvard Medical School, 44 Binney Street, Boston, MA 02115, USA
    J Mol Biol 331:623-41. 2003
  10. ncbi Biochemical and functional analysis of smallpox growth factor (SPGF) and anti-SPGF monoclonal antibodies
    Mikyung Kim
    Department of Medical Oncology, Dana-Farber Cancer Institute and Department of Medicine, Harvard Medical School, Boston, Massachusetts 02115, USA
    J Biol Chem 279:25838-48. 2004

Collaborators

  • Hong Zhang
  • Raymond M Welsh
  • Mikyung Kim
  • A Razzaque Ahmed
  • Tetsuro Sasada
  • Weimin Zhong
  • Ellis L Reinherz
  • Labib R Zakka
  • Maria Garcia-Boronat
  • Manoj Bhasin
  • Helge Otto
  • Hailin Yang
  • Masha Fridkis-Hareli
  • Emma Fiorini
  • Carmen M Diez-Rivero
  • Fernando Bazan
  • Sung-Kwon Kim
  • Friedrich Koch-Nolte
  • Inger K Damon
  • Tiara J Morehead
  • Friedrich Haag
  • Katharina Dittmar
  • Elena V Tibaldi
  • Ada M Kruisbeek
  • Stephanie L Osborn
  • Rebecca E Hussey
  • Linda K Clayton
  • Maki Touma
  • Ingo Schmitz
  • Wilfred E Marissen

Detail Information

Publications16

  1. ncbi In silico characterization of the family of PARP-like poly(ADP-ribosyl)transferases (pARTs)
    Helge Otto
    Institute of Immunology, University Hospital Hamburg Eppendorf, Germany
    BMC Genomics 6:139. 2005
    ....
  2. ncbi PEPVAC: a web server for multi-epitope vaccine development based on the prediction of supertypic MHC ligands
    Pedro A Reche
    Laboratory of Immunobiology and Department of Medical Oncology, Dana Farber Cancer Institute, Harvard Medical School, 44 Binney Street, Boston, MA 02115, USA
    Nucleic Acids Res 33:W138-42. 2005
    ..The PEPVAC server is hosted by the Dana-Farber Cancer Institute at the site http://immunax.dfci.harvard.edu/PEPVAC/...
  3. ncbi EPIMHC: a curated database of MHC-binding peptides for customized computational vaccinology
    Pedro A Reche
    Laboratory of Immunobiology and Department of Medical Oncology, Dana Farber Cancer Institute, Boston, MA 02115, USA
    Bioinformatics 21:2140-1. 2005
    ..AVAILABILITY: The EPIMHC database server is hosted by the Dana-Farber Cancer Institute at the site http://immunax.dfci.harvard.edu/bioinformatics/epimhc/..
  4. ncbi Enhancement to the RANKPEP resource for the prediction of peptide binding to MHC molecules using profiles
    Pedro A Reche
    Laboratory of Immunobiology and Department of Medical Oncology, Dana Farber Cancer Institute, 44 Binney Street, Boston, MA 02115, USA
    Immunogenetics 56:405-19. 2004
    ..This feature focuses prediction on conserved rather than highly variable protein segments encoded by infectious genomes, thereby offering identification of invariant T-cell epitopes to thwart mutation as an immune evasion mechanism...
  5. ncbi Antiviral chemotherapy facilitates control of poxvirus infections through inhibition of cellular signal transduction
    Hailin Yang
    Laboratory of Immunobiology, Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts 02115, USA
    J Clin Invest 115:379-87. 2005
    ..Collectively, these findings show that chemical inhibitors of host-signaling pathways exploited by viral pathogens may represent potent antiviral therapies...
  6. ncbi Prediction of MHC class I binding peptides using profile motifs
    Pedro A Reche
    Laboratory of Immunobiology, Dana-Farber Cancer Institute, Boston, MA, USA
    Hum Immunol 63:701-9. 2002
    ..mifoundation.org/Tools/rankpep.html). In addition, the RANKPEP server also allows the user to enter additional profiles, making the server a powerful and versatile computational biology benchmark for the prediction of peptide-MHC binding...
  7. ncbi Genome-wide characterization of a viral cytotoxic T lymphocyte epitope repertoire
    Weimin Zhong
    Laboratory of Immunobiology and Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts 02115, USA
    J Biol Chem 278:45135-44. 2003
    ..These results have important implications for rationale design of CD8+ T cell vaccines...
  8. ncbi Peptide variants of viral CTL epitopes mediate positive selection and emigration of Ag-specific thymocytes in vivo
    Masha Fridkis-Hareli
    Laboratory of Immunobiology, Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02115, USA
    J Immunol 173:1140-50. 2004
    ..These findings show that the mature T cell repertoire can be altered by in vivo peptide administration through manipulation of thymic selection...
  9. ncbi Sequence variability analysis of human class I and class II MHC molecules: functional and structural correlates of amino acid polymorphisms
    Pedro A Reche
    Laboratory of Immunobiology, Dana Farber Cancer Institute, Harvard Medical School, 44 Binney Street, Boston, MA 02115, USA
    J Mol Biol 331:623-41. 2003
    ..In addition, specific class II (HLA-DP, -DQ, -DR) and class I (HLA-A, -B, -C) contacts for TCR binding are revealed. We discuss these findings in the context of TCR restriction and alloreactivity...
  10. ncbi Biochemical and functional analysis of smallpox growth factor (SPGF) and anti-SPGF monoclonal antibodies
    Mikyung Kim
    Department of Medical Oncology, Dana-Farber Cancer Institute and Department of Medicine, Harvard Medical School, Boston, Massachusetts 02115, USA
    J Biol Chem 279:25838-48. 2004
    ..These findings suggest that blockade of pathogenic factor actions, in general, may be advantageous to the infected host...
  11. ncbi Prediction of methylated CpGs in DNA sequences using a support vector machine
    Manoj Bhasin
    Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115, USA
    FEBS Lett 579:4302-8. 2005
    ..This method is available on line for public use under the name of Methylator at http://bio.dfci.harvard.edu/Methylator/...
  12. ncbi The molecular basis for the presence of two autoimmune diseases occurring simultaneously--preliminary observations based on computer analysis
    Labib R Zakka
    Center for Blistering Diseases, Boston, Massachusetts 02120, USA
    Autoimmunity 45:253-63. 2012
    ..While other explanations and mechanisms exist, the authors suggest that epitope spreading may be one possible mechanism, amongst others, that may result in the simultaneous presence of two separate pathogenic autoantibodies...
  13. ncbi Peptide-induced negative selection of thymocytes activates transcription of an NF-kappa B inhibitor
    Emma Fiorini
    Laboratory of Immunobiology, Dana Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, USA
    Mol Cell 9:637-48. 2002
    ..Retroviral transduction of I kappa BNS in fetal thymic organ culture enhances TCR-triggered cell death consistent with its function in selection...
  14. ncbi PVS: a web server for protein sequence variability analysis tuned to facilitate conserved epitope discovery
    Maria Garcia-Boronat
    Immunomedicine Group, Department of Microbiology I, Division of Immunology, Facultad de Medicina, Universidad Complutense de Madrid, Ave Complutense s n, Madrid 28040, Spain
    Nucleic Acids Res 36:W35-41. 2008
    ..Furthermore, PVS can return a variability-masked sequence, which can be directly submitted to the RANKPEP server for the prediction of conserved T-cell epitopes. PVS is freely available at: http://imed.med.ucm.es/PVS/...
  15. ncbi Definition of MHC supertypes through clustering of MHC peptide-binding repertoires
    Pedro A Reche
    Department of Immunology, Faculated de Medicina, Universidad Complutense de Madrid, Madrid, Spain
    Methods Mol Biol 409:163-73. 2007
    ..In this chapter, we detail a method for defining MHC supertypes based on the analysis and subsequent clustering of their peptide-binding repertoires...
  16. ncbi Prediction of peptide-MHC binding using profiles
    Pedro A Reche
    Department of Immunology, Faculated de Medicina, Universidad Complutense de Madrid, Madrid, 28040, Spain
    Methods Mol Biol 409:185-200. 2007
    ..Following structural considerations of the peptide-MHC interaction, we will describe here how to derive alignments and PSSMs that are suitable for the prediction of peptide-MHC binding...