Alejandro A. Schaffer

Personal Home Page

http://www.ncbi.nlm.nih.gov/CBBresearch/Schaffer/

Articles in Scholarly Journals [Incomplete List]

  1. Investigations of the Y Chromosome, Male Founder Structure and YSTR Mutation Rates in the Old Order Amish
    Human Heredity, vol. 65, no. 2, pp. 91–104, 2008
  2. Initial sequence and comparative analysis of the cat genome
    Genome Research, vol. 17, no. 11, pp. 1675–1689, 2007
  3. A radiation hybrid map of river buffalo (Bubalus bubalis) chromosome 1 (BBU1)
    Cytogenetic and Genome Research, vol. 119, no. 1-2, pp. 100–104, 2007
  4. Deconstructing common variable immunodeficiency by genetic analysis
    Current Opinion in Genetics & Development, vol. 17, no. 3, pp. 201–212, 2007
  5. A 1.5-Mb-resolution radiation hybrid map of the cat genome and comparative analysis with the canine and human genomes
    Genomics, vol. 89, no. 2, pp. 189–196, 2007
  6. The Hyper IgE Syndrome and Mutations in TYK2
    Immunity, vol. 26, no. 5, pp. 535–535, 2007
  7. High-resolution gene maps of horse chromosomes 14 and 21: Additional insights into evolution and rearrangements of HSA5 homologs in mammals
    Genomics, vol. 89, no. 1, pp. 89–112, 2007
  8. rh_tsp_map 3.0: end-to-end radiation hybrid mapping with improved speed and quality control
    Bioinformatics, vol. 23, no. 9, pp. 1156–1158, 2007
  9. Improved BLAST searches using longer words for protein seeding
    Bioinformatics, vol. 23, no. 21, pp. 2949–2951, 2007
  10. Four Independent Mutations in the Feline Fibroblast Growth Factor 5 Gene Determine the Long-Haired Phenotype in Domestic Cats
    Journal of Heredity, vol. 98, no. 6, pp. 555–566, 2007
  11. Construction of a river buffalo (Bubalus bubalis) whole-genome radiation hybrid panel and preliminary RH mapping of chromosomes 3 and 10
    Animal Genetics, vol. 38, no. 3, pp. 311–314, 2007
  12. Preliminary radiation hybrid map for river buffalo chromosome 6 and comparison to bovine chromosome 3
    Animal Genetics, vol. 38, no. 4, pp. 406–409, 2007
  13. Mutation in CEP290 Discovered for Cat Model of Human Retinal Degeneration
    Journal of Heredity, vol. 98, no. 3, pp. 211–220, 2007
  14. STAT3 Mutations in the Hyper-IgE Syndrome
    New England Journal of Medicine, vol. 357, no. 16, pp. 1608–1619, 2007
  15. A novel human primary immunodeficiency syndrome caused by deficiency of the endosomal adaptor protein p14
    Nature Medicine, vol. 13, no. 1, Article ID nm1528, 7 pages, 2006
  16. HAX1 deficiency causes autosomal recessive severe congenital neutropenia (Kostmann disease)
    Nature Genetics, vol. 39, no. 1, Article ID ng1940, 6 pages, 2006
  17. Linkage of autosomal-dominant common variable immunodeficiency to chromosome 4q
    European Journal of Human Genetics, vol. 14, no. 7, Article ID 5201634, 8 pages, 2006
  18. A homozygous single-base deletion in MLPH causes the dilute coat color phenotype in the domestic cat
    Genomics, vol. 88, no. 6, pp. 698–705, 2006
  19. A Fast and Symmetric DUST Implementation to Mask Low-Complexity DNA Sequences
    Journal of Computational Biology, vol. 13, no. 5, pp. 1028–1040, 2006
  20. HLA B44 is associated with decreased severity of autoimmune lymphoproliferative syndrome in patients with CD95 defects (ALPS type Ia)
    Clinical Immunology, vol. 118, no. 1, pp. 59–65, 2006
  21. Genetic alterations in caspase-10 may be causative or protective in autoimmune lymphoproliferative syndrome
    Human Genetics, vol. 119, no. 3, pp. 284–294, 2006
  22. Identification of a homozygous deletion in the AP3B1 gene causing Hermansky-Pudlak syndrome, type 2
    Blood, vol. 108, no. 1, pp. 362–369, 2006
  23. BMC Biology, vol. 4, no. 1, p. 41, 2006
  24. Retrieval accuracy, statistical significance and compositional similarity in protein sequence database searches
    Nucleic Acids Research, vol. 34, no. 20, pp. 5966–5973, 2006
  25. An  140-kb deletion associated with feline spinal muscular atrophy implies an essential LIX1 function for motor neuron survival
    Genome Research, vol. 16, no. 9, pp. 1084–1090, 2006
  26. A 1.3-Mb interval map of equine homologs of HSA2
    Cytogenetic and Genome Research, vol. 112, no. 3-4, pp. 227–234, 2006
  27. Novel Gene Acquisition on Carnivore Y Chromosomes
    PLoS Genetics, vol. 2, no. 3, p. e43, 2006
  28. Amnionless function is required for cubilin brush-border expression and intrinsic factor-cobalamin (vitamin B12) absorption in vivo
    Blood, vol. 106, no. 4, pp. 1447–1453, 2005
  29. Protein database searches using compositionally adjusted substitution matrices
    FEBS Journal, vol. 272, no. 20, pp. 5101–5109, 2005
  30. Clinical and positron emission tomography of Parkinson's disease caused byLRRK2
    Annals of Neurology, vol. 57, no. 3, pp. 453–456, 2005
  31. Analysis of families with common variable immunodeficiency (CVID) and IgA deficiency suggests linkage of CVID to chromosome 16q
    Human Genetics, vol. 118, no. 6, pp. 725–729, 2005
  32. A high-resolution physical map of equine homologs of HSA19 shows divergent evolution compared with other mammals
    Mammalian Genome, vol. 16, no. 8, pp. 631–649, 2005
  33. A comprehensive continuous-time model for the appearance of CGH signal due to chromosomal missegregations during mitosis
    Mathematical Biosciences, vol. 197, no. 1, pp. 67–87, 2005
  34. A rhesus macaque radiation hybrid map and comparative analysis with the human genome
    Genomics, vol. 86, no. 4, pp. 383–395, 2005
  35. WindowMasker: window-based masker for sequenced genomes
    Bioinformatics, vol. 22, no. 2, pp. 134–141, 2005
  36. Mutations in TNFRSF13B encoding TACI are associated with common variable immunodeficiency in humans
    Nature Genetics, vol. 37, no. 8, Article ID ng1600, 8 pages, 2005
  37. A structure-based method for protein sequence alignment
    Bioinformatics, vol. 21, no. 8, pp. 1451–1456, 2004
  38. Tumor classification using phylogenetic methods on expression data
    Journal of Theoretical Biology, vol. 228, no. 4, pp. 477–496, 2004
  39. A microsatellite polymorphism in intron 2 of human Toll-like receptor 2 gene: functional implications and racial differences
    FEMS Immunology and Medical Microbiology, vol. 40, no. 2, pp. 163–169, 2004
  40. Interferon-? receptor 1 promoter polymorphisms: population distribution and functional implications
    Clinical Immunology, vol. 112, no. 1, pp. 113–119, 2004
  41. The Genetics of Hypogammaglobulinemia
    Current Allergy and Asthma Reports, vol. 4, no. 5, pp. 349–358, 2004
  42. Construction of tree models for pathogenesis of nasopharyngeal carcinoma
    Genes, Chromosomes and Cancer, vol. 40, no. 4, pp. 307–315, 2004
  43. Reduced Incidence of Hip Fracture in the Old Order Amish
    Journal of Bone and Mineral Research, vol. 19, no. 2, pp. 308–313, 2004
  44. Radiation hybrid mapping of 304 novel microsatellites in the domestic cat genome
    Cytogenetic and Genome Research, vol. 102, no. 1-4, pp. 272–276, 2003
  45. Second-Generation Integrated Genetic Linkage/Radiation Hybrid Maps of the Domestic Cat (Felis catus)
    Journal of Heredity, vol. 94, no. 1, pp. 95–106, 2003
  46. Canine Imerslund-Gr?sbeck syndrome maps to a region orthologous to HSA14q
    Mammalian Genome, vol. 14, no. 11, pp. 758–764, 2003
  47. Homozygous loss of ICOS is associated with adult-onset common variable immunodeficiency
    Nature Immunology, vol. 4, no. 3, Article ID ni902, 7 pages, 2003
  48. Mutant deoxynucleotide carrier is associated with congenital microcephaly
    Nature Genetics, vol. 32, no. 1, Article ID ng948, 4 pages, 2002
  49. Genetic differences detected by comparative genomic hybridization in head and neck squamous cell carcinomas from different tumor sites: construction of oncogenetic trees for tumor progression
    Genes, Chromosomes and Cancer, vol. 34, no. 2, pp. 224–233, 2002
  50. Heritability of life span in the Old Order Amish
    American Journal of Medical Genetics, vol. 102, no. 4, pp. 346–352, 2001
  51. Genomic imbalances in the progression of endocrine pancreatic tumors
    Genes, Chromosomes and Cancer, vol. 32, no. 4, pp. 364–372, 2001
  52. Graph Models of Oncogenesis with an Application to Melanoma
    Journal of Theoretical Biology, vol. 212, no. 4, pp. 535–548, 2001
  53. An Immune Defect Causing Dominant Chronic Mucocutaneous Candidiasis and Thyroid Disease Maps to Chromosome 2p in a Single Family
    The American Journal of Human Genetics, vol. 69, no. 4, pp. 791–803, 2001
  54. Improving the accuracy of PSI-BLAST protein database searches with composition-based statistics and other refinements
    Nucleic Acids Research, vol. 29, no. 14, pp. 2994–3005, 2001
  55. Genetic modifiers of the insulin resistance phenotype in mice
    Diabetes, vol. 49, no. 4, pp. 589–596, 2000
  56. A Novel Nemaline Myopathy in the Amish Caused by a Mutation in Troponin T1
    The American Journal of Human Genetics, vol. 67, no. 4, pp. 814–821, 2000
  57. A Fast and Scalable Radiation Hybrid Map Construction and Integration Strategy
    Genome Research, vol. 10, no. 3, pp. 350–364, 2000
  58. Somatic deletions in hereditary breast cancers implicate 13q21 as a putative novel breast cancer susceptibility locus
    Proceedings of the National Academy of Sciences, vol. 97, no. 17, pp. 9603–9608, 2000
  59. Distance-Based Reconstruction of Tree Models for Oncogenesis
    Journal of Computational Biology, vol. 7, no. 6, pp. 789–803, 2000
  60. Chromosome abnormalities in ovarian adenocarcinoma: III. Using breakpoint data to infer and test mathematical models for oncogenesis
    Genes, Chromosomes and Cancer, vol. 28, no. 1, pp. 106–120, 2000
  61. Inverse inbreeding coefficient problems with an application to linkage analysis of recessive diseases in inbred populations
    Discrete Applied Mathematics, vol. 104, no. 1-3, pp. 3–44, 2000
  62. A Genetic Linkage Map of Microsatellites in the Domestic Cat (Felis catus),
    Genomics, vol. 57, no. 1, pp. 9–23, 1999
  63. Towards a complete North American Anabaptist genealogy: A systematic approach to merging partially overlapping genealogy resources
    American Journal of Medical Genetics, vol. 86, no. 2, pp. 156–161, 1999
  64. Computing probabilities of homozygosity by descent
    Genetic Epidemiology, vol. 16, no. 2, pp. 135–149, 1999
  65. Genetic Linkage of Hyper-IgE Syndrome to Chromosome 4
    The American Journal of Human Genetics, vol. 65, no. 3, pp. 735–744, 1999
  66. Nature Genetics, vol. 21, no. 4, pp. 359–360, 1999
  67. IMPALA: matching a protein sequence against a collection of PSI-BLAST-constructed position-specific score matrices
    Bioinformatics, vol. 15, no. 12, pp. 1000–1011, 1999
  68. Protein sequence similarity searches using patterns as seeds
    Nucleic Acids Research, vol. 26, no. 17, pp. 3986–3990, 1998
  69. Automatic Selection ofLoop Breakers for GeneticLinkage Analysis
    Human Heredity, vol. 48, no. 1, pp. 49–60, 1998
  70. Genetic and physical mapping of the McKusick-Kaufman syndrome
    Human Molecular Genetics, vol. 7, no. 3, pp. 475–481, 1998
  71. Coping with complexity: lessons from the mathematical sciences
    Human Genetics, vol. 103, no. 1, pp. 5–10, 1998
  72. Refinement of the gene locus for autosomal recessive juvenile parkinsonism (AR-JP) on chromosome 6q25.2-27 and identification of markers exhibiting linkage disequilibrium
    Journal of Human Genetics, vol. 43, no. 1, pp. 22–31, 1998
  73. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs
    Nucleic Acids Research, vol. 25, no. 17, pp. 3389–3402, 1997
  74. Multiple matching of parameterized patterns
    Theoretical Computer Science, vol. 154, no. 2, pp. 203–224, 1996
  75. Mapping of a Gene for Parkinson's Disease to Chromosome 4q21-q23
    Science, vol. 274, no. 5290, pp. 1197–1199, 1996
  76. Optimal edge ranking of trees in polynomial time
    Algorithmica, vol. 13, no. 6, pp. 592–618, 1995
  77. Improved Dynamic Dictionary Matching
    Information and Computation, vol. 119, no. 2, pp. 258–282, 1995
  78. Multiple Matching of Rectangular Patterns
    Information and Computation, vol. 117, no. 1, pp. 78–90, 1995
  79. Integrating Parallelization Strategies for Linkage Analysis
    Computers and Biomedical Research, vol. 28, no. 2, pp. 116–139, 1995
  80. Markov analysis of multiple-disk prefetching strategies for external merging
    Theoretical Computer Science, vol. 128, no. 1-2, pp. 211–239, 1994
  81. Dynamic dictionary matching with failure functions
    Theoretical Computer Science, vol. 131, no. 2, pp. 295–310, 1994
  82. Faster isometric embedding in products of complete graphs
    Discrete Applied Mathematics, vol. 52, no. 1, pp. 17–28, 1994
  83. A faster algorithm to recognize undirected path graphs
    Discrete Applied Mathematics, vol. 43, no. 3, pp. 261–295, 1993
  84. Triangulating Three-Colored Graphs in Linear Time and Linear Space
    SIAM Journal on Discrete Mathematics, vol. 6, no. 2, p. 289, 1993
  85. Finding the prime factors of strong direct product graphs in polynomial time
    Discrete Mathematics, vol. 109, no. 1-3, pp. 77–102, 1992
  86. An implicit data structure for searching a multikey table in logarithmic time
    Journal of Computer and System Sciences, vol. 43, no. 3, pp. 406–424, 1991
  87. Recognizing brittle graphs: remarks on a paper of Hoàng and Khouzam
    Discrete Applied Mathematics, vol. 31, no. 1, pp. 29–35, 1991
  88. A Note on Finding a Strict Saddlepoint
    The American Mathematical Monthly, vol. 98, no. 5, p. 418, 1991
  89. Simple Local Search Problems that are Hard to Solve
    SIAM Journal on Computing, vol. 20, no. 1, p. 56, 1991
  90. Graph spanners
    Journal of Graph Theory, vol. 13, no. 1, pp. 99–116, 1989
  91. Time bounds on fault-tolerant broadcasting
    Networks, vol. 19, no. 7, pp. 803–822, 1989
  92. Optimal node ranking of trees in linear time
    Information Processing Letters, vol. 33, no. 2, pp. 91–96, 1989
  93. Fast Parallel Algorithms for Chordal Graphs
    SIAM Journal on Computing, vol. 18, no. 2, p. 327, 1989
  94. Recognizing Bellman–Ford-Orderable Graphs
    SIAM Journal on Discrete Mathematics, vol. 1, no. 4, p. 447, 1988
  95. Computing the bump number with techniques from two-processor scheduling
    Order, vol. 5, no. 2, pp. 131–141, 1988
  96. Shortest prefix strings containing all subset permutations
    Discrete Mathematics, vol. 64, no. 2-3, pp. 239–252, 1987
  97. Recognizing Composite Graphs is Equivalent to Testing Graph Isomorphism
    SIAM Journal on Computing, vol. 15, no. 2, p. 619, 1986
  98. A polynomial time algorithm for finding the prime factors of cartesian-product graphs
    Discrete Applied Mathematics, vol. 12, no. 2, pp. 123–138, 1985