A A Schaffer

Summary

Affiliation: National Institutes of Health
Country: USA

Publications

  1. pmc Domain enhanced lookup time accelerated BLAST
    Grzegorz M Boratyn
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, 8600 Rockville Pike, Bethesda, MD 20894, USA
    Biol Direct 7:12. 2012
  2. pmc Animal models of human granulocyte diseases
    Alejandro A Schäffer
    Computational Biology Branch, National Center for Biotechnology Information, National Institutes of Health, Department of Health and Human Services, 8600 Rockville Pike, Bethesda, MD 20894, USA
    Hematol Oncol Clin North Am 27:129-48, ix. 2013
  3. pmc PedHunter 2.0 and its usage to characterize the founder structure of the Old Order Amish of Lancaster County
    Woei Jyh Lee
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894, USA
    BMC Med Genet 11:68. 2010
  4. pmc Screening of functional and positional candidate genes in families with common variable immunodeficiency
    Ulrich Salzer
    Division of Rheumatology and Clinical Immunology, Medical School, University Hospital Freiburg, Hugstetterstr, 55, 79106 Freiburg, Germany
    BMC Immunol 9:3. 2008
  5. pmc Application of dissociation curve analysis to radiation hybrid panel marker scoring: generation of a map of river buffalo (B. bubalis) chromosome 20
    Kelli J Kochan
    Department of Animal Science, Texas A and M University, College Station, Texas, USA
    BMC Genomics 9:544. 2008
  6. pmc Composition-based statistics and translated nucleotide searches: improving the TBLASTN module of BLAST
    E Michael Gertz
    National Center for Biotechnology Information, National Institutes of Health, Department of Health and Human Services, Bethesda, MD, USA
    BMC Biol 4:41. 2006
  7. pmc Analysis of families with common variable immunodeficiency (CVID) and IgA deficiency suggests linkage of CVID to chromosome 16q
    Alejandro A Schäffer
    Department of Health and Human Services, National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bldg 38A Rm 6S608 8600 Rockville Pike, Bethesda, MD 20894, USA
    Hum Genet 118:725-9. 2006
  8. pmc Improving the accuracy of PSI-BLAST protein database searches with composition-based statistics and other refinements
    A A Schaffer
    National Center for Biotechnology Information, National Institutes of Health, 8600 Rockville Pike, Bethesda, MD 20894, USA
    Nucleic Acids Res 29:2994-3005. 2001
  9. ncbi request reprint Tree models for dependent copy number changes in bladder cancer
    A A Schaffer
    NCBI NIH, Bldg 38A, Room 8N805, 8600 Rockville Pike, Bethesda, MD 20894, USA
    Int J Oncol 18:349-54. 2001
  10. ncbi request reprint Coping with complexity: lessons from the mathematical sciences
    A A Schaffer
    National Human Genome Research Institute, National Institutes of Health, Baltimore, MD 21224, USA
    Hum Genet 103:5-10. 1998

Collaborators

Detail Information

Publications25

  1. pmc Domain enhanced lookup time accelerated BLAST
    Grzegorz M Boratyn
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, 8600 Rockville Pike, Bethesda, MD 20894, USA
    Biol Direct 7:12. 2012
    ....
  2. pmc Animal models of human granulocyte diseases
    Alejandro A Schäffer
    Computational Biology Branch, National Center for Biotechnology Information, National Institutes of Health, Department of Health and Human Services, 8600 Rockville Pike, Bethesda, MD 20894, USA
    Hematol Oncol Clin North Am 27:129-48, ix. 2013
    ..Strengths and weaknesses of each system are summarized, and clinical investigators may thus be inspired to develop further lines of research to improve diagnosis and therapy by use of the appropriate animal model system...
  3. pmc PedHunter 2.0 and its usage to characterize the founder structure of the Old Order Amish of Lancaster County
    Woei Jyh Lee
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894, USA
    BMC Med Genet 11:68. 2010
    ..In addition, we developed PedHunter, a suite of query software that can solve pedigree-related problems automatically and systematically...
  4. pmc Screening of functional and positional candidate genes in families with common variable immunodeficiency
    Ulrich Salzer
    Division of Rheumatology and Clinical Immunology, Medical School, University Hospital Freiburg, Hugstetterstr, 55, 79106 Freiburg, Germany
    BMC Immunol 9:3. 2008
    ..The recent discovery that some CVID patients show monogenic defects in the genes encoding ICOS, TACI or CD19 prompted us to investigate several functional candidate genes in individuals with CVID...
  5. pmc Application of dissociation curve analysis to radiation hybrid panel marker scoring: generation of a map of river buffalo (B. bubalis) chromosome 20
    Kelli J Kochan
    Department of Animal Science, Texas A and M University, College Station, Texas, USA
    BMC Genomics 9:544. 2008
    ..To improve sensitivity and efficiency of radiation hybrid panel analysis in comparison to gel-based methods, we adapted fluorescence-based real-time PCR and dissociation curve analysis for use as a novel scoring method...
  6. pmc Composition-based statistics and translated nucleotide searches: improving the TBLASTN module of BLAST
    E Michael Gertz
    National Center for Biotechnology Information, National Institutes of Health, Department of Health and Human Services, Bethesda, MD, USA
    BMC Biol 4:41. 2006
    ..Until recently, composition-based statistics were available only for protein-protein searches. They are now available as a command line option for recent versions of TBLASTN and as an option for TBLASTN on the NCBI BLAST web server...
  7. pmc Analysis of families with common variable immunodeficiency (CVID) and IgA deficiency suggests linkage of CVID to chromosome 16q
    Alejandro A Schäffer
    Department of Health and Human Services, National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bldg 38A Rm 6S608 8600 Rockville Pike, Bethesda, MD 20894, USA
    Hum Genet 118:725-9. 2006
    ..83 at theta=0.07, and a 4-marker LOD score under heterogeneity peaks at 3.00 with alpha=0.68. The (model-free) NPL score using the same markers peaks at the same location with a value of 3.38 (P=0.0001)...
  8. pmc Improving the accuracy of PSI-BLAST protein database searches with composition-based statistics and other refinements
    A A Schaffer
    National Center for Biotechnology Information, National Institutes of Health, 8600 Rockville Pike, Bethesda, MD 20894, USA
    Nucleic Acids Res 29:2994-3005. 2001
    ..The use of composition-based statistics is particularly beneficial for large-scale automated applications of PSI-BLAST...
  9. ncbi request reprint Tree models for dependent copy number changes in bladder cancer
    A A Schaffer
    NCBI NIH, Bldg 38A, Room 8N805, 8600 Rockville Pike, Bethesda, MD 20894, USA
    Int J Oncol 18:349-54. 2001
    ..We conclude that the combination of large data sets and tree models provide a useful approach to systematically identifying tumor subgroups characterized by more than a single chromosomal aberration...
  10. ncbi request reprint Coping with complexity: lessons from the mathematical sciences
    A A Schaffer
    National Human Genome Research Institute, National Institutes of Health, Baltimore, MD 21224, USA
    Hum Genet 103:5-10. 1998
    ..This essay is intended to provoke discussion and not to resolve any problems. It represents a written version of remarks that I made as "Discussant" at a session at the 1997 National Institutes of Health Research Festival...
  11. ncbi request reprint IMPALA: matching a protein sequence against a collection of PSI-BLAST-constructed position-specific score matrices
    A A Schaffer
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    Bioinformatics 15:1000-11. 1999
    ..One popular program for constructing a PSSM and comparing it with a database of sequences is Position-Specific Iterated BLAST (PSI-BLAST)...
  12. pmc Somatic deletions in hereditary breast cancers implicate 13q21 as a putative novel breast cancer susceptibility locus
    T Kainu
    Cancer Genetics Branch and Inherited Disease Research Branch, National Human Genome Research Institute, Bethesda, MD 20892, USA
    Proc Natl Acad Sci U S A 97:9603-8. 2000
    ..25 from the new locus. The simulation substantiated the evidence of linkage at D13S1308 (P < 0.0017). The results warrant studies of this putative breast cancer predisposition locus in other populations...
  13. pmc A novel nemaline myopathy in the Amish caused by a mutation in troponin T1
    J J Johnston
    Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, 20892, USA
    Am J Hum Genet 67:814-21. 2000
    ..We conclude that Amish nemaline myopathy is a distinct, heritable, myopathic disorder caused by a mutation in TNNT1...
  14. ncbi request reprint Towards a complete North American Anabaptist genealogy: A systematic approach to merging partially overlapping genealogy resources
    R Agarwala
    Inherited Diseases Research Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland 20892 4472, USA
    Am J Med Genet 86:156-61. 1999
    ..Am. J. Med. Genet. 86:156-161, 1999. Published 1999 Wiley-Liss, Inc...
  15. pmc Gapped BLAST and PSI-BLAST: a new generation of protein database search programs
    S F Altschul
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    Nucleic Acids Res 25:3389-402. 1997
    ..PSI-BLAST is used to uncover several new and interesting members of the BRCT superfamily...
  16. ncbi request reprint Computing probabilities of homozygosity by descent
    A A Schaffer
    National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, USA
    Genet Epidemiol 16:135-49. 1999
    ..I implemented a program to compute the IPA. The contribution of this work is the application of basic, abstract methods from computer science to address a problem in genetics...
  17. pmc Genetic linkage of hyper-IgE syndrome to chromosome 4
    B Grimbacher
    Genetics and Molecular Biology Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892 4442, USA
    Am J Hum Genet 65:735-44. 1999
    ..Linkage analysis showed a maximum two-point LOD score of 3.61 at recombination fraction of 0 with marker D4S428. Multipoint analysis and simulation testing confirmed that the proximal 4q region contains a disease locus for HIES...
  18. pmc Fine mapping of the nail-patella syndrome locus at 9q34
    I McIntosh
    Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21287 4922, USA
    Am J Hum Genet 60:133-42. 1997
    ..0; theta = .00) and D9S315 (LOD = 22.0; theta = .00). Informative recombination events place the NPS locus within a 1-2-cM interval between D9S60 and the adenylate kinase gene (AK1)...
  19. ncbi request reprint Towards a complete North American Anabaptist Genealogy II: analysis of inbreeding
    R Agarwala
    Information Engineering Branch, National Center for Biotechnology Information, NIH, Bethesda, MD, USA
    Hum Biol 73:533-45. 2001
    ..However, this association reverses dramatically (p < 0.0005 in the opposite direction) for individuals born in 1960-1979. We tested for an association between inbreeding and being the mother of twins, but found none...
  20. ncbi request reprint Graph models of oncogenesis with an application to melanoma
    M D Radmacher
    Biometric Research Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
    J Theor Biol 212:535-48. 2001
    ..This study illustrates that the application of graph models to genetic data from tumor sets provide new information on the interrelationships among genetic changes during tumor progression...
  21. ncbi request reprint Genetic modifiers of the insulin resistance phenotype in mice
    Y Kido
    Developmental Endocrinology Branch, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland, USA
    Diabetes 49:589-96. 2000
    ..These findings indicate that targeted mutations in knockout mice can be used to unravel the complex genetic interactions underlying insulin resistance...
  22. ncbi request reprint Radiation hybrid mapping of 304 novel microsatellites in the domestic cat genome
    M Menotti-Raymond
    Laboratory of Genomic Diversity, National Cancer Institute, Department of Health and Human Services, Frederick, MD 21702, USA
    Cytogenet Genome Res 102:272-6. 2003
    ..These resources can also be extended to the remaining 36 species of the cat family for population genetic and evolutionary genomic analyses...
  23. ncbi request reprint Heritability of life span in the Old Order Amish
    B D Mitchell
    Department of Medicine, Division of Endocrinology, University of Maryland School of Medicine, 660 W Redwood St, Baltimore, MD 21201, USA
    Am J Med Genet 102:346-52. 2001
    ..We conclude that longevity is moderately heritable in the OOA, that the genetic effects are additive, and that genetic influences on longevity are likely to be expressed across a broad range of ages. Published 2001 Wiley-Liss, Inc...
  24. ncbi request reprint Mapping of a gene for Parkinson's disease to chromosome 4q21-q23
    M H Polymeropoulos
    Laboratory of Genetic Disease Research, National Center for Human Genome Research, National Institutes of Health, Bethesda, MD 20892 1430, USA
    Science 274:1197-9. 1996
    ..00 for marker D4S2380. This finding will facilitate identification of the gene and research on the pathogenesis of PD...
  25. ncbi request reprint Genetic and physical mapping of the McKusick-Kaufman syndrome
    D L Stone
    Laboratory of Genetic Disease Research, Laboratory of Gene Transfer and Medical Genetics Branch, National Human Genome Research Institute, NIH, Bethesda, MD 20892, USA
    Hum Mol Genet 7:475-81. 1998
    ..Sequencing of jagged1 in two unrelated individuals affected with McKusick-Kaufman syndrome has not revealed any disease-causing mutations...