JOINSOLVER® Bibliography


  1. Kabat, Elvin A. and National Institutes of Health. 1991. Sequences of proteins of immunological interest. 5th Ed., Public Health Service, National Institutes of Health, Washington, DC.
  2. Chothia, C., A. M. Lesk, A. Tramontano, M. Levitt, S. J. Smith-Gill, G. Air, S. Sheriff, E. A. Padlan, D. Davies, and W. R. Tulip. 1989. Conformations of immunoglobulin hypervariable regions. Nature 342:877-883. Link to PubMed
  3. Morea, V., A. Tramontano, M. Rustici, C. Chothia, and A. M. Lesk. 1997. Antibody structure, prediction and redesign. Biophys.Chem. 68:9-16. Link to PubMed
  4. Morea, V., A. Tramontano, M. Rustici, C. Chothia, and A. M. Lesk. 1998. Conformations of the third hypervariable region in the VH domain of immunoglobulins. J.Mol.Biol. 275:269-294. Link to PubMed
  5. Knappik, A., L. Ge, A. Honegger, P. Pack, M. Fischer, G. Wellnhofer, A. Hoess, J. Wolle, A. Pluckthun, and B. Virnekas. 2000. Fully synthetic human combinatorial antibody libraries (HuCAL) based on modular consensus frameworks and CDRs randomized with trinucleotides. J.Mol.Biol. 296:57-86. Link to PubMed
  6. Lefranc, M. P. 2001. IMGT, the international ImMunoGeneTics database. Nucleic Acids Res. 29:207-209. Link to PubMed
  7. Altschul, S. F., W. Gish, W. Miller, E. W. Myers, and D. J. Lipman. 1990. Basic local alignment search tool. J.Mol.Biol. 215:403-410. Link to PubMed
  8. Brezinschek, H. P., S. J. Foster, R. I. Brezinschek, T. Dorner, R. Domiati-Saad, and P. E. Lipsky. 1997. Analysis of the human VH gene repertoire. Differential effects of selection and somatic hypermutation on human peripheral CD5(+)/IgM+ and CD5(-)/IgM+ B cells. J.Clin.Invest 99:2488-2501. Link to PubMed
  9. Monestier, M. and M. Zouali. 2002. Receptor revision and systemic lupus. Scand.J.Immunol. 55:425-431. Link to PubMed
  10. Raaphorst, F. M., E. Timmers, M. J. Kenter, M. J. Van Tol, J. M. Vossen, and R. K. Schuurman. 1992. Restricted utilization of germ-line VH3 genes and short diverse third complementarity-determining regions (CDR3) in human fetal B lymphocyte immunoglobulin heavy chain rearrangements. Eur.J.Immunol. 22:247-251. Link to PubMed
  11. Meffre, E., E. Davis, C. Schiff, C. Cunningham-Rundles, L. B. Ivashkiv, L. M. Staudt, J. W. Young, and M. C. Nussenzweig. 2000. Circulating human B cells that express surrogate light chains and edited receptors. Nat.Immunol. 1:207-213. Link to PubMed
  12. Klonowski, K. D. and M. Monestier. 2000. Heavy chain revision in MRL mice: a potential mechanism for the development of autoreactive B cell precursors. J.Immunol. 165:4487-4493. Link to PubMed
  13. Klonowski, K. D., L. L. Primiano, and M. Monestier. 1999. Atypical VH-D-JH rearrangements in newborn autoimmune MRL mice. J.Immunol. 162:1566-1572. Link to PubMed
  14. Meek, K. D., C. A. Hasemann, and J. D. Capra. 1989. Novel rearrangements at the immunoglobulin D locus. Inversions and fusions add to IgH somatic diversity. J.Exp.Med. 170:39-57. Link to PubMed
  15. Sanz, I., S. S. Wang, G. Meneses, and M. Fischbach. 1994. Molecular characterization of human Ig heavy chain DIR genes. J.Immunol. 152:3958-3969. Link to PubMed
  16. Tuaillon, N. and J. D. Capra. 1998. Use of D gene segments with irregular spacers in terminal deoxynucleotidyltransferase (TdT)+/+ and TdT-/- mice carrying a human Ig heavy chain transgenic minilocus. Proc.Natl.Acad.Sci.U.S.A 95:1703-1708. Link to PubMed
  17. Ichihara, Y., M. Abe, H. Yasui, H. Matsuoka, and Y. Kurosawa. 1988. At least five DH genes of human immunoglobulin heavy chains are encoded in 9-kilobase DNA fragments. Eur.J.Immunol. 18:649-652. Link to PubMed
  18. Gellert, M. 1992. Molecular analysis of V(D)J recombination. Annu.Rev.Genet. 26:425-446. Link to PubMed
  19. Tuaillon, N., A. B. Miller, P. W. Tucker, and J. D. Capra. 1995. Analysis of direct and inverted DJH rearrangements in a human Ig heavy chain transgenic minilocus. J.Immunol. 154:6453-6465. Link to PubMed
  20. Corbett, S. J., I. M. Tomlinson, E. L. Sonnhammer, D. Buck, and G. Winter. 1997. Sequence of the human immunoglobulin diversity (D) segment locus: a systematic analysis provides no evidence for the use of DIR segments, inverted D segments, "minor" D segments or D-D recombination. J.Mol.Biol. 270:587-597. Link to PubMed
  21. Kompfner, E., P. Oliveira, A. Montalbano, and A. J. Feeney. 2001. Unusual germline DSP2 gene accounts for all apparent V-D-D-J rearrangements in newborn, but not adult, MRL mice. J.Immunol. 167:6933-6938. Link to PubMed
  22. Brezinschek, H. P., R. I. Brezinschek, and P. E. Lipsky. 1995. Analysis of the heavy chain repertoire of human peripheral B cells using single-cell polymerase chain reaction. J.Immunol. 155:190-202. Link to PubMed
  23. Brezinschek, H. P., R. I. Brezinschek, T. Dorner, and P. E. Lipsky. 1998. Similar characteristics of the CDR3 of V(H)1-69/DP-10 rearrangements in normal human peripheral blood and chronic lymphocytic leukaemia B cells. Br.J.Haematol. 102:516-521. Link to PubMed
  24. Yavuz, S., A. C. Grammer, A. S. Yavuz, T. Nanki, and P. E. Lipsky. 2001. Comparative characteristics of mu chain and alpha chain transcripts expressed by individual tonsil plasma cells. Mol.Immunol. 38:19-34. Link to PubMed
  25. Bauer, K., M. Zemlin, M. Hummel, S. Pfeiffer, J. Karstaedt, G. Steinhauser, X. Xiao, H. Versmold, and C. Berek. 2002. Diversification of Ig heavy chain genes in human preterm neonates prematurely exposed to environmental antigens. J.Immunol. 169:1349-1356. Link to PubMed
  26. Rosner, K., D. B. Winter, R. E. Tarone, G. L. Skovgaard, V. A. Bohr, and P. J. Gearhart. 2001. Third complementarity-determining region of mutated VH immunoglobulin genes contains shorter V, D, J, P, and N components than non-mutated genes. Immunology 103:179-187. Link to PubMed
  27. Chothia, C. and A. M. Lesk. 1987. Canonical structures for the hypervariable regions of immunoglobulins. J.Mol.Biol. 196:901-917. Link to PubMed
  28. Satow, Y., G. H. Cohen, E. A. Padlan, and D. R. Davies. 1986. Phosphocholine binding immunoglobulin Fab McPC603. An X-ray diffraction study at 2.7 A. J.Mol.Biol. 190:593-604. Link to PubMed
  29. Matsuda, F., E. K. Shin, Y. Hirabayashi, H. Nagaoka, M. C. Yoshida, S. Q. Zong, and T. Honjo. 1990. Organization of variable region segments of the human immunoglobulin heavy chain: duplication of the D5 cluster within the locus and interchromosomal translocation of variable region segments. EMBO J. 9:2501-2506. Link to PubMed
  30. Matsuda, F., K. H. Lee, S. Nakai, T. Sato, M. Kodaira, S. Q. Zong, H. Ohno, S. Fukuhara, and T. Honjo. 1988. Dispersed localization of D segments in the human immunoglobulin heavy-chain locus. EMBO J. 7:1047-1051. Link to PubMed
  31. Zong, S. Q., S. Nakai, F. Matsuda, K. H. Lee, and T. Honjo. 1988. Human immunoglobulin D segments: isolation of a new D segment and polymorphic deletion of the D1 segment. Immunol.Lett. 17:329-333. Link to PubMed
  32. Buluwela, L., D. G. Albertson, P. Sherrington, P. H. Rabbitts, N. Spurr, and T. H. Rabbitts. 1988. The use of chromosomal translocations to study human immunoglobulin gene organization: mapping DH segments within 35 kb of the C mu gene and identification of a new DH locus. EMBO J. 7:2003-2010. Link to PubMed
  33. Shiokawa, S., F. Mortari, J. O. Lima, C. Nunez, F. E. Bertrand, III, P. M. Kirkham, S. Zhu, A. P. Dasanayake, and H. W. Schroeder, Jr. 1999. IgM heavy chain complementarity-determining region 3 diversity is constrained by genetic and somatic mechanisms until two months after birth. J.Immunol. 162:6060-6070. Link to PubMed
  34. Girschick, H. J. and P. E. Lipsky. 2002. The kappa gene repertoire of human neonatal B cells. Mol.Immunol. 38:1113-1127. Link to PubMed
  35. Gauss, G. H. and M. R. Lieber. 1996. Mechanistic constraints on diversity in human V(D)J recombination. Mol.Cell Biol. 16:258-269. Link to PubMed
  36. Mortari, F., J. Y. Wang, and H. W. Schroeder, Jr. 1993. Human cord blood antibody repertoire. Mixed population of VH gene segments and CDR3 distribution in the expressed C alpha and C gamma repertoires. J.Immunol. 150:1348-1357. Link to PubMed
  37. Moore, B. B. and K. Meek. 1995. Recombination potential of the human DIR elements. J.Immunol. 154:2175-2187. Link to PubMed
  38. Gellert, M. 2002. V(D)J recombination: RAG proteins, repair factors, and regulation. Annu.Rev.Biochem. 71:101-132. Link to PubMed
  39. Kurosawa, Y. and S. Tonegawa. 1982. Organization, structure, and assembly of immunoglobulin heavy chain diversity DNA segments. J.Exp.Med. 155:201-218. Link to PubMed
  40. Yamada, M., R. Wasserman, B. A. Reichard, S. Shane, A. J. Caton, and G. Rovera. 1991. Preferential utilization of specific immunoglobulin heavy chain diversity and joining segments in adult human peripheral blood B lymphocytes. J.Exp.Med. 173:395-407. Link to PubMed
  41. Clausen, B. E., S. L. Bridges, Jr., J. C. Lavelle, P. G. Fowler, S. Gay, W. J. Koopman, and H. W. Schroeder, Jr. 1998. Clonally-related immunoglobulin VH domains and nonrandom use of DH gene segments in rheumatoid arthritis synovium. Mol.Med. 4:240-257. Link to PubMed
  42. Collins, A. M., M. Ikutani, D. Puiu, G. A. Buck, A. Nadkarni, and B. Gaeta. 2004. Partitioning of rearranged Ig genes by mutation analysis demonstrates D-D fusion and V gene replacement in the expressed human repertoire. J.Immunol. 172:340-348. Link to PubMed
  43. Ichihara, Y., H. Matsuoka, and Y. Kurosawa. 1988. Organization of human immunoglobulin heavy chain diversity gene loci. EMBO J. 7:4141-4150. Link to PubMed
  44. Black, S. D. and D. R. Mould. 1991. Development of hydrophobicity parameters to analyze proteins which bear post- or cotranslational modifications. Anal.Biochem. 193:72-82. Link to PubMed
  45. Kyte, J. and R. F. Doolittle. 1982. A simple method for displaying the hydropathic character of a protein. J.Mol.Biol. 157:105-132. Link to PubMed
  46. Hopp, T. P. and Woods, K. R. 1983. A computer program for predicting protein antigenic determinants. Mol. Immunol., 20:483-489. Link to PubMed
  47. Betts, M. J. and Russell, R. B. 2003. Amino acid properties and consequences of subsitutions. In Bioinformatics for Geneticists 1st Ed. M. R. Barnes and I. C. Gray, eds. Wiley, Hoboken, NJ.
  48. Feeney, A. J., B. R. Lawson, D. H. Kono, and A. N. Theofilopoulos. 2001. Terminal deoxynucleotidyl transferase deficiency decreases autoimmune disease in MRL-Fas(lpr) mice. J.Immunol. 167:3486-3493. Link to PubMed
  49. Lee, J., N. L. Monson, and P. E. Lipsky. 2000. The V lambda J lambda repertoire in human fetal spleen: evidence for positive selection and extensive receptor editing. J.Immunol. 165:6322-6333. Link to PubMed
  50. Nadel, B., S. Tehranchi, and A. J. Feeney. 1995. Coding end processing is similar throughout ontogeny. J.Immunol. 154:6430-6436. Link to PubMed
  51. Boubnov, N. V., Z. P. Wills, and D. T. Weaver. 1995. Coding sequence composition flanking either signal element alters V(D)J recombination efficiency. Nucleic Acids Res. 23:1060-1067. Link to PubMed
  52. Ma, Y., U. Pannicke, K. Schwarz, and M. R. Lieber. 2002. Hairpin opening and overhang processing by an Artemis/DNA-dependent protein kinase complex in nonhomologous end joining and V(D)J recombination. Cell 108:781-794. Link to PubMed
  53. Paull, T. T. and M. Gellert. 2000. A mechanistic basis for Mre11-directed DNA joining at microhomologies. Proc.Natl.Acad.Sci.U.S.A 97:6409-6414. Link to PubMed
  54. Gauss, G. H., I. Domain, C. L. Hsieh, and M. R. Lieber. 1998. V(D)J recombination activity in human hematopoietic cells: correlation with developmental stage and genome stability. Eur.J.Immunol. 28:351-358. Link to PubMed
  55. Klonowski, K. D. and M. Monestier. 2001. Ig heavy-chain gene revision: leaping towards autoimmunity. Trends Immunol. 22:400-405. Link to PubMed



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