Sean Mooney

Summary

Affiliation: Indiana University
Country: USA

Publications

  1. pmc MutDB services: interactive structural analysis of mutation data
    Jessica Dantzer
    Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, IN 46202, USA
    Nucleic Acids Res 33:W311-4. 2005
  2. pmc Using RNase sequence specificity to refine the identification of RNA-protein binding regions
    Xin Wang
    Division of Biostatistics Department of Medicine, Indiana University School of Medicine, Indianapolis, IN 46202, USA
    BMC Genomics 9:S17. 2008
  3. ncbi request reprint Extensible open source content management systems and frameworks: a solution for many needs of a bioinformatics group
    Sean D Mooney
    Center for Computational Biology and Bioinformatics, Department of Medical and Molecular Genetics, Indiana University School of Medicine, 410 W 10th St, Suite 5000, Indianapolis, IN 46202, USA
    Brief Bioinform 9:69-74. 2008
  4. ncbi request reprint Bioinformatics approaches and resources for single nucleotide polymorphism functional analysis
    Sean Mooney
    Center for Computational Biology and Bioinformatics, Department of Medical and Molecular Genetics, Indiana University School of Medicine, 714 N Senate Ave EF 250, Indianapolis, IN 46202, USA
    Brief Bioinform 6:44-56. 2005
  5. pmc Structural characterization of proteins using residue environments
    Sean D Mooney
    Department of Genetics, Stanford University, Stanford, California, USA
    Proteins 61:741-7. 2005
  6. pmc Identification of similar regions of protein structures using integrated sequence and structure analysis tools
    Brandon Peters
    Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, IN 46202, USA
    BMC Struct Biol 6:4. 2006
  7. pmc Identifying viral integration sites using SeqMap 2.0
    Troy B Hawkins
    Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN 46202, USA
    Bioinformatics 27:720-2. 2011
  8. pmc Evaluation of features for catalytic residue prediction in novel folds
    Eunseog Youn
    Center for Computational Biology and Bioinformatics, Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN 46202, USA
    Protein Sci 16:216-26. 2007
  9. ncbi request reprint MutDB: annotating human variation with functionally relevant data
    Sean D Mooney
    Department of Genetics, Stanford Medical Informatics, Stanford University, 251 Campus Drive, MSOB X 215 Stanford, CA 94305 5479, USA
    Bioinformatics 19:1858-60. 2003
  10. pmc MutDB: update on development of tools for the biochemical analysis of genetic variation
    Arti Singh
    Center for Computational Biology and Bioinfomatics, Department of Medical and Molecular Genetics, Indiana University School of Medicine, 410 W 10th Street, Suite 5000, Indianapolis, IN 46202, USA
    Nucleic Acids Res 36:D815-9. 2008

Collaborators

Detail Information

Publications20

  1. pmc MutDB services: interactive structural analysis of mutation data
    Jessica Dantzer
    Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, IN 46202, USA
    Nucleic Acids Res 33:W311-4. 2005
    ..The web services portal and plugins can be downloaded from http://www.lifescienceweb.org/ and the web interface is at http://www.mutdb.org/...
  2. pmc Using RNase sequence specificity to refine the identification of RNA-protein binding regions
    Xin Wang
    Division of Biostatistics Department of Medicine, Indiana University School of Medicine, Indianapolis, IN 46202, USA
    BMC Genomics 9:S17. 2008
    ..We present two regions to which multiple amplicons map as examples to demonstrate this approach...
  3. ncbi request reprint Extensible open source content management systems and frameworks: a solution for many needs of a bioinformatics group
    Sean D Mooney
    Center for Computational Biology and Bioinformatics, Department of Medical and Molecular Genetics, Indiana University School of Medicine, 410 W 10th St, Suite 5000, Indianapolis, IN 46202, USA
    Brief Bioinform 9:69-74. 2008
    ..Additionally, some examples of their use in biomedical research are given...
  4. ncbi request reprint Bioinformatics approaches and resources for single nucleotide polymorphism functional analysis
    Sean Mooney
    Center for Computational Biology and Bioinformatics, Department of Medical and Molecular Genetics, Indiana University School of Medicine, 714 N Senate Ave EF 250, Indianapolis, IN 46202, USA
    Brief Bioinform 6:44-56. 2005
    ..Additionally, public resources available for SNP identification and characterisation are summarised...
  5. pmc Structural characterization of proteins using residue environments
    Sean D Mooney
    Department of Genetics, Stanford University, Stanford, California, USA
    Proteins 61:741-7. 2005
    ..S-BLEST was able to associate 20 proteins with at least one local structural neighbor and identify the amino acid environments that are most similar between those neighbors...
  6. pmc Identification of similar regions of protein structures using integrated sequence and structure analysis tools
    Brandon Peters
    Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, IN 46202, USA
    BMC Struct Biol 6:4. 2006
    ..Additionally, we have extended UCSF Chimera and PyMOL to support our web services, so that users can characterize their own proteins of interest...
  7. pmc Identifying viral integration sites using SeqMap 2.0
    Troy B Hawkins
    Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN 46202, USA
    Bioinformatics 27:720-2. 2011
    ..Individual sequence reads are masked to remove non-genomic sequence, aligned to the host genome and assembled into contiguous fragments used to pinpoint the position of integration...
  8. pmc Evaluation of features for catalytic residue prediction in novel folds
    Eunseog Youn
    Center for Computational Biology and Bioinformatics, Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN 46202, USA
    Protein Sci 16:216-26. 2007
    ..We then applied the method to 2781 coordinate files from the structural genomics target pipeline and identified both highly ranked and highly clustered groups of predicted catalytic residues...
  9. ncbi request reprint MutDB: annotating human variation with functionally relevant data
    Sean D Mooney
    Department of Genetics, Stanford Medical Informatics, Stanford University, 251 Campus Drive, MSOB X 215 Stanford, CA 94305 5479, USA
    Bioinformatics 19:1858-60. 2003
    ..MutDB provides interactive mutation maps at the gene and protein levels, and allows for ranking of their predicted functional consequences based on conservation in multiple sequence alignments...
  10. pmc MutDB: update on development of tools for the biochemical analysis of genetic variation
    Arti Singh
    Center for Computational Biology and Bioinfomatics, Department of Medical and Molecular Genetics, Indiana University School of Medicine, 410 W 10th Street, Suite 5000, Indianapolis, IN 46202, USA
    Nucleic Acids Res 36:D815-9. 2008
    ....
  11. pmc Connecting protein interaction data, mutations, and disease using bioinformatics
    Jake Y Chen
    Informatics and Technology Complex IT, Indiana University School of Informatics, IUPUI, Indianapolis, IN, USA
    Methods Mol Biol 541:449-61. 2009
    ..As the molecular causes of disease become more understood, models such as these will be useful for identifying candidate variants most likely to be causative...
  12. ncbi request reprint Genetic nondiscrimination legislation: a critical prerequisite for pharmacogenomics data sharing
    Russ B Altman
    Stanford University, Department of Genetics and Bioengineering, Clark S172, Stanford, CA 94305 5444, USA
    Pharmacogenomics 8:519. 2007
  13. pmc A functional analysis of disease-associated mutations in the androgen receptor gene
    Sean D Mooney
    Stanford Medical Informatics, Department of Genetics, Stanford University, MSOB X 215, 251 Campus Drive, Stanford, CA 94305 5479, USA
    Nucleic Acids Res 31:e42. 2003
    ..Our method provides a means for assessing the significance of single nucleotide polymorphisms (SNPs) and cancer-associated mutations...
  14. ncbi request reprint Conformational preferences of substituted prolines in the collagen triple helix
    Sean D Mooney
    Stanford Medical Informatics, 251 Campus Drive, MSOB X 215, Stanford University, Stanford, CA 94305 5479, USA
    Biopolymers 64:63-71. 2002
    ..The results of our simulations suggest that pyrrolidine ring conformation is mediated by the strength of the gauche effect and classical electrostatic interactions...
  15. ncbi request reprint Fibroblast growth factor-23 mutants causing familial tumoral calcinosis are differentially processed
    Tobias Larsson
    Department of Medical and Molecular Genetics, 975 West Walnut Street, IB130, Indiana University School of Medicine, Indianapolis, Indiana 46202, USA
    Endocrinology 146:3883-91. 2005
    ..The destabilizing nature of these mutations provides new insight into the pathophysiology of TC and exemplifies the physiological importance of FGF23 in phosphate and vitamin D metabolism...
  16. doi request reprint Bioinformatic tools for identifying disease gene and SNP candidates
    Sean D Mooney
    Department of Medical and Molecular Genetics, Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, IN, USA
    Methods Mol Biol 628:307-19. 2010
    ..The intent of this chapter is to provide an introduction to the online tools that are both easy to use and useful...
  17. pmc The functional importance of disease-associated mutation
    Sean D Mooney
    Department of Genetics and Stanford Medical Informatics Division, Stanford University, Stanford, California, 94305, USA
    BMC Bioinformatics 3:24. 2002
    ..Here we show that disease-associated mutations occur in regions of genes that are conserved, and can identify likely disease-causing mutations...
  18. pmc Gain and loss of phosphorylation sites in human cancer
    Predrag Radivojac
    School of Informatics, Indiana University, 901 East Tenth Street, Bloomington, IN 47408, USA
    Bioinformatics 24:i241-7. 2008
    ..Understanding the mechanism and contribution these variants make to a clinical phenotype is a formidable problem...
  19. pmc An integrated approach to inferring gene-disease associations in humans
    Predrag Radivojac
    School of Informatics, Indiana University, Bloomington, Indiana 47408, USA
    Proteins 72:1030-7. 2008
    ..Availability: www.phenopred.org...
  20. ncbi request reprint Extended mutational analyses of FGFR1 in osteoglophonic dysplasia
    Emily G Farrow
    Am J Med Genet A 140:537-9. 2006