2005

1. Altschul SF, Wootton JC, Gertz EM, Agarwala R, Morgulis A, Schäffer AA, Yu YK . Protein database searches using compositionally adjusted substitution matrices.. Federation of European Biochemical Societies Journal. 2005 Oct; 272(20):5101-9. Review. PMID: 16218944.

2. Alves G, Yu YK. Robust Accurate Identification of Peptides (RAId): deciphering MS2 data using a structured library search with de novo based statistics. Bioinformatics. 2005 Oct 1;21(19):3726-32. Epub 2005 Aug 16. PMID: 16105903.

3. Amikam D, Galperin MY. PilZ domain is part of the bacterial c-di-GMP binding protein.. Bioinformatics. 2005 Oct 25; [Epub ahead of print]. PMID: 16249258.

4. Anantharaman V, Aravind L. MEDS and PocR are novel domains with a predicted role in sensing simple hydrocarbon derivatives in prokaryotic signal transduction systems. Bioinformatics. 2005 Jun 15;21(12):2805-11. Epub 2005 Apr 6. PMID: 15814558

5. Anantharaman V, Aravind L. Diversification of Catalytic Activities and Ligand Interactions in the Protein Fold Shared by the Sugar Isomerases, eIF2B, DeoR Transcription Factors, Acyl-CoA Transferases and Methenyltetrahydrofolate Synthetase. Journal of Molecular Biology. 2005 Dec 1. PMID: 16376935.

6. Aravind L, Anantharaman V, Balaji S, Babu MM, Iyer LM. The many faces of the helix-turn-helix domain: transcription regulation and beyond. FEMS Microbiology Review. 2005 Apr;29(2):231-62. Review. PMID: 15808743

7. Aronson AR, Demner D, Humphrey SH, Ide NC, Kim W, Loane RR, Mork JG, Smith LH, Tanabe L, Wilbur WJ, Xie N. Knowledge-Intensive and Statistical Approaches to the Retrieval and Annotation of Genomes MEDLINE Citations, NIST Special Publication 500-261: The Thirteenth Text Retrieval Conference (TREC 2004).

8. Balaji S, Babu MM, Iyer LM, Aravind L. Discovery of the principal specific transcription factors of Apicomplexa and their implication for the evolution of the AP2 integrase DNA binding domains. Nucleic Acids Research. 2005 Jul 21;33(13):3994-4006. Print 2005. PMID: 16040597.

9. Benson DA, Karsch-Mizrachi I, Lipman DJ, Ostell J, Wheeler DL. GenBank. Nucleic Acids Research. 2005 Jan 1;33(Database issue):D34-8. PMID: 15608212.  

10. Brinkmeyer-Langford C, Raudsepp T, Lee EJ, Goh G, Schäffer AA, Agarwala R, Wagner ML, T, Skow LC, Womack JE, Mickelson JR, Chowdhary BP. A high resolution physical map of equine homologs of HSA19 shows divergent evolution compared with other mammals. Mammalian Genome 2005 Aug;16(8):631-49. Epub 2005 Sep 14. PMID: 16180145.

11. Churbanov A, Rogozin IB, Babenko VN, Ali H, Koonin EV. Evolutionary conservation suggests a regulatory function of AUG triplets in 5'-UTRs of eukaryotic genes. Nucleic Acids Research. 2005 Sep 26;33(17):5512-20. Print 2005. PMID: 16186132.

12. Desper R, Difilippantonio MJ, Ried T, Schäffer AA. A comprehensive continuous-time model for the appearance of CGH signal due to chromosomal missegregations during mitosis. Mathematical Biosciences. 2005 Sep;197(1):67-87. PMID: 16043196.

13. Eriksson PR, Mendiratta G, McLaughlin NB, Wolfsberg TG, Marino-Ramirez L, Pompa TA, Jainerin M, Landsman D, Shen CH, Clark DJ. Global regulation by the yeast Spt10 protein is mediated through chromatin structure and the histone upstream activating sequence elements. Molecular and Cellular Biology. 2005 Oct;25(20):9127-37. PMID: 16199888.

14. Galperin MY. The Molecular Biology Database Collection: 2005 update. Nucleic Acids Research. 2005 Jan 1;33(Database issue):D5-D24. PMID: 15608247.  

15. Galperin MY. Life is not defined just in base pairs. Environmental Microbiology. 2005 Feb;7(2):149-52. PMID: 15658982.  

16. Galperin MY. To finish or not to finish? Evironmental Microbiology. 2005 Aug;7(8):1061-4. No abstract available. PMID: 16011744.

17. Galperin MY, Gomelsky M. Bacterial signal transduction modules: from genomics to biology. American Society for Microbiology News. 2005 Jul;71(7):326-33. Not in PubMed.

18. Galperin MY. A census of membrane-bound and intracellular signal transduction proteins in bacteria: Bacterial IQ, extroverts and introverts. BMC Microbiology. 2005 Jun 14;5(1):35. PMID: 15955239

19. Galperin MY. The vibrio that sheds light. Evironmental Microbiology. 2005 Jun;7(6):757-60. No abstract available. PMID: 15892694

20. Galperin MY. On the bottom of the deep blue sea. Evironmental Microbiology. 2005 Apr;7(4):453-8. No abstract available. PMID: 15816911

21. Galperin MY, Rigden DJ. OMICS-Related Research in South America. OMICS. 2005 Spring;9(1):1. No abstract available. PMID: 15805774

22. Galperin MY. The secret of being cool. Evironmental Microbiology. 2005,7(10): 1499-1504. No abstract available. PMID: 16156723.

23. Galperin MY. More cool news from marine bacteria. Environmental Microbiology. 2005, 7(12):1864-7. Review. PMID: 16309385.

24. Ghedin E, Sengamalay NA, Shumway M, Zaborsky J, Feldblyum T, Subbu V, Spiro DJ, Sitz J, Koo H, Bolotov P, Dernovoy D, Tatusova T, Bao Y, St George K, Taylor J, Lipman DJ, Fraser CM, Taubenberger JK, Salzberg SL. Large-scale sequencing of human influenza reveals the dynamic nature of viral genome evolution. Nature. 2005 Oct 20;437(7062):1162-6. Epub 2005 Oct 5. PMID: 16208317.

25. Glazko GV, Koonin EV, Rogozin IB. Molecular dating: ape bones agree with chicken entrails. Trends in Genetics. 2005 Feb;21(2):89-92. PMID: 15661354.  

26. Habibian R, Dzioba J, Barrett J, Galperin MY, Loewen PC, Dibrov P. Functional Analysis of Conserved Polar Residues in Vc-NhaD, Na+/H+ Antiporter of Vibrio cholerae. Journal of Biological Chemistry. 2005 Nov 25;280(47):39637-43. Epub 2005 Sep 26. PMID: 16186100.

27. He Q, Madsen M, Kilkenney A, Gregory B, Christensen EI, Vorum H, Hojrup P, Schäffer AA, Kirkness EF, Tanner SM, de la Chapelle A, Giger U, Moestrup SK, Fyfe JC. Amnionless function is required for cubilin brush-border expression and intrinsic factor-cobalamin (vitamin B12) absorption in vivo. Blood. 2005 Aug 15;106(4):1447-53; Epub 2005 Apr 21. PMID: 15845892

28. Hernandez DG, Paisan-Ruiz C, McInerney-Leo A, Jain S, Meyer-Lindenberg A, Evans EW, Berman KF, Johnson J, Auburger G, Schäffer AA, Lopez GJ, Nussbaum RL, Singleton AB. Clinical and positron emission tomography of Parkinson's disease caused by LRRK2. Annals of Neurology. 2005 Mar;57(3):453-6. PMID: 15732108.  

29. Holmes EC, Ghedin E, Miller N, Taylor J, Bao Y, St George K, Grenfell BT, Salzberg SL, Fraser CM, Lipman DJ, Taubenberger JK. Whole-genome analysis of human influenza A virus reveals multiple persistent lineages and reassortment among recent H3N2 viruses. Public Library of Science Biology. 2005 Sep;3(9):e300. Epub 2005 Jul 26. PMID: 16023181.

30. Imanishi T, Itoh T, Suzuki Y, O'Donovan C, Fukuchi S, Koyanagi KO, Barrero RA, Tamura T, Yamaguchi-Kabata Y, Tanino M, Yura K, Miyazaki S, Ikeo K, Homma K, Kasprzyk A, Nishikawa T, Hirakawa M, Thierry-Mieg J, Thierry-Mieg D, Ashurst J, Jia L, Nakao M, Thomas MA, Mulder N, Karavidopoulou Y, Jin L, Kim S, Yasuda T, Lenhard B, Eveno E, Suzuki Y, Yamasaki C, Takeda J, Gough C, Hilton P, Fujii Y, Sakai H, Tanaka S, Amid C, Bellgard M, Bonaldo Mde F, Bono H, Bromberg SK, Brookes AJ, Bruford E, Carninci P, Chelala C, Couillault C, de Souza SJ, Debily MA, Devignes MD, Dubchak I, Endo T, Estreicher A, Eyras E, Fukami-Kobayashi K, Gopinath GR, Graudens E, Hahn Y, Han M, Han ZG, Hanada K, Hanaoka H, Harada E, Hashimoto K, Hinz U, Hirai M, Hishiki T, Hopkinson I, Imbeaud S, Inoko H, Kanapin A, Kaneko Y, Kasukawa T, Kelso J, Kersey P, Kikuno R, Kimura K, Korn B, Kuryshev V, Makalowska I, Makino T, Mano S, Mariage-Samson R, Mashima J, Matsuda H, Mewes HW, Minoshima S, Nagai K, Nagasaki H, Nagata N, Nigam R, Ogasawara O, Ohara O, Ohtsubo M, Okada N, Okido T, Oota S, Ota M, Ota T, Otsuki T, Piatier-Tonneau D, Poustka A, Ren SX, Saitou N, Sakai K, Sakamoto S, Sakate R, Schupp I, Servant F, Sherry S, Shiba R, Shimizu N, Shimoyama M, Simpson AJ, Soares B, Steward C, Suwa M, Suzuki M, Takahashi A, Tamiya G, Tanaka H, Taylor T, Terwilliger JD, Unneberg P, Veeramachaneni V, Watanabe S, Wilming L, Yasuda N, Yoo HS, Stodolsky M, Makalowski W, Go M, Nakai K, Takagi T, Kanehisa M, Sakaki Y, Quackenbush J, Okazaki Y, Hayashizaki Y, Hide W, Chakraborty R, Nishikawa K, Sugawara H, Tateno Y, Chen Z, Oishi M, Tonellato P, Apweiler R, Okubo K, Wagner L, Wiemann S, Strausberg RL, Isogai T, Auffray C, Nomura N, Gojobori T, Sugano S. Integrative annotation of 21,037 human genes validated by full-length cDNA clones. PLoS Biology. 2004 Jun;2(6):e162. Epub 2004 Apr 20. PMID: 15103394.

31. Iyer LM, Koonin EV, Leipe DD, Aravind L. Origin and evolution of the archaeo-eukaryotic primase superfamily and related palm-domain proteins: structural insights and new members.. Nucleic Acids Research. 2005 Jul 15;33(12):3875-96. Print 2005. PMID: 16027112.

32. Jordan IK, Kondrashov FA, Adzhubei IA, Wolf YI, Koonin EV, Kondrashov AS, Sunyaev S. A universal trend of amino acid gain and loss in protein evolution. Nature. 2005 Feb 10;433(7026):633-8. Epub 2005 Jan 19. PMID: 15660107.  

33. Jordan IK, Marino-Ramirez L, Koonin EV. Evolutionary significance of gene expression divergence. Gene. 2005 Jan 17;345(1):119-26. Epub 2004 Dec 29. PMID: 15716085

34. Jothi R, Kann MG, Przytycka TM. Predicting protein-protein interaction by searching evolutionary tree automorphism space. Bioinformatics. 2005 Jun 1;21 Suppl 1:i241-i250. PMID: 15961463

35. Kann MG, Thiessen PA, Panchenko AR, Schäffer AA, Altschul SF, Bryant SH. A structure-based method for protein sequence alignment. Bioinformatics. 2005 Apr 15;21(8):1451-6. Epub 2004 Dec 21. PMID: 15613392

36. Karev GP, Berezovskaya FS, Koonin EV. Modeling genome evolution with a diffusion approximation of a birth-and-death process. Bioinformatics. 2005 Nov 1;21 Suppl 3:iii12-iii19. PMID: 16306387.

37. Khan A, Taylor S, Su C, Mackey AJ, Boyle J, Cole R, Glover D, Tang K, Paulsen IT, Berriman M, Boothroyd JC, Pfefferkorn ER, Dubey JP, Ajioka JW, Roos DS, Wootton JC, Sibley LD. Composite genome map and recombination parameters derived from three archetypal lineages of Toxoplasma gondii. Nucleic Acids Research. 2005 May 23;33(9):2980-92. Print 2005. PMID: 15911631

38. Kolker E, Picone AF, Galperin MY, Romine MF, Higdon R, Makarova KS, Kolker N, Anderson GA, Qiu X, Auberry KJ, Babnigg G, Beliaev AS, Edlefsen P, Elias DA, Gorby YA, Holzman T, Klappenbach JA, Konstantinidis KT, Land ML, Lipton MS, McCue LA, Monroe M, Pasa-Tolic L, Pinchuk G, Purvine S, Serres MH, Tsapin S, Zakrajsek BA, Zhu W, Zhou J, Larimer FW, Lawrence CE, Riley M, Collart FR, Yates JR 3rd, Smith RD, Giometti CS, Nealson KH, Fredrickson JK, Tiedje JM. Global profiling of Shewanella oneidensis MR-1: expression of hypothetical genes and improved functional annotations. Proceedings of the National Academy of Sciences U S A. 2005 Feb 8;102(6):2099-104. PMID: 15684069  

39. Kondrashov AS. Evolutionary biology: fruitfly genome is not junk. . Bioessays. 2005 Oct 20;437(7062):1106. No abstract available. PMID: 16237433. [PubMed - indexed for MEDLINE]

40. Kondrashov FA, Ogurtsov AY, Kondrashov AS. Selection in favor of nucleotides G and C diversifies evolution rates and levels of polymorphism at mammalian synonymous sites. Journal of Theoretical Biology. 2005 Dec 9; [Epub ahead of print]. PMID: 16343547.

41. Kondrashov FA, Kondrashov AS. Role of selection in fixation of gene duplications. Journal of Theoretical Biology. 2005 Oct 19; [Epub ahead of print]. PMID: 16242725.

42. Koonin EV. Virology: Gulliver among the Lilliputians. Current Biology. 2005 Mar 8;15(5):R167-9. PMID: 15753027  

43. Koonin EV, Rogozin IB, Glazko GV. p53 gain-of-function: tumor biology and bioinformatics come together. Cell Cycle. 2005 May;4(5):686-8. Epub 2005 May 28. PMID: 15846083

44. Koonin EV. Orthologs, Paralogs, and Evolutionary Genomics. Annual Review of Genetics. 2005 Aug 30; [Epub ahead of print]. PMID: 16131346.

45. Koonin EV. Paralogs and mutational robustness linked through transcriptional reprogramming. Bioessays. 2005 Sep;27(9):865-8. PMID: 16108060.

46. Kravchenko JE, Rogozin IB, Koonin EV, Chumakov PM. Transcription of mammalian messenger RNAs by a nuclear RNA polymerase of mitochondrial origin. Nature. 2005 Aug 4;436(7051):735-9. PMID: 16079853.

47. Kschischo M, Lassig M, Yu YK. Toward an accurate statistics of gapped alignments. Bulletin of Mathematical Biology. 2005 Jan;67(1):169-91. PMID: 15691544  

48. Maglott D, Ostell J, Pruitt KD, Tatusova T. Entrez Gene: gene-centered information at NCBI. Nucleic Acids Research. 2005 Jan 1;33(Database issue):D54-8. PMID: 15608257  

49. Makarova KS, Wolf YI, Mekhedov SL, Mirkin BG, Koonin EV. Ancestral paralogs and pseudoparalogs and their role in the emergence of the eukaryotic cell. Nucleic Acids Research. 2005 Aug 16;33(14):4626-38. Print 2005. PMID: 16106042.

50. Marchler-Bauer A, Anderson JB, Cherukuri PF, DeWeese-Scott C, Geer LY, Gwadz M, He S, Hurwitz DI, Jackson JD, Ke Z, Lanczycki CJ, Liebert CA, Liu C, Lu F, Marchler GH, Mullokandov M, Shoemaker BA, Simonyan V, Song JS, Thiessen PA, Yamashita RA, Yin JJ, Zhang D, Bryant SH. CDD: a Conserved Domain Database for protein classification. Nucleic Acids Research. 2005 Jan 1;33(Database issue):D192-6. PMID: 15608175  

51. Marino-Ramirez L, Hsu B, Baxevanis AD, Landsman D. The histone database: A comprehensive resource for histones and histone fold-containing proteins. Proteins. 2005 Dec 12; [Epub ahead of print] PMID: 16345076.

52. Marino-Ramirez L, Kann MG, Shoemaker BA, Landsman D. Histone structure and nucleosome stability. Expert Review of Proteomics. 2005 Oct;2(5):719-29. PMID: 16209651.

53. Marino-Ramirez L, Lewis KC, Landsman D, Jordan IK. Transposable elements donate lineage-specific regulatory sequences to host genomes. Cytogenetic and Genome Research. 2005;110(1-4):333-41. PMID: 16093685.

54. Moroz OV, Murzin AG, Makarova KS, Koonin EV, Wilson KS, Galperin MY. Dimeric dUTPases, HisE, and MazG belong to a new superfamily of all-alpha NTP pyrophosphohydrolases with potential "house-cleaning" functions. Journal of Molecular Biology. 2005 Mar 25;347(2):243-55. Epub 2005 Jan 27. PMID: 15740738  

55. Ng CL, Waterman D, Koonin EV, Antson AA, Ortiz-Lombardia M. Crystal structure of Mil (Mth680): internal duplication and similarity between the Imp4/Brix domain and the anticodon-binding domain of class IIa aminoacyl-tRNA synthetases. EMBO Reports. 2005 Feb;6(2):140-6. PMID: 15654320  

56. Novozhilov AS, Karev GP, Koonin EV. Mathematical modeling of evolution of horizontally transferred genes. Molecular Biology and Evolution. 2005 Aug;22(8):1721-32. Epub 2005 May 18. PMID: 15901840

57. Park Y, Sheetlin S, Spouge JL. Accelerated Convergence and Robust Asymptotic Regression of the Gumbel Scale Parameter for Gapped Sequence Alignment", 38, (1) 97-108, Journal of Physics A: Mathematical and General, 2005.

58. Pruitt KD, Tatusova T, Maglott DR. NCBI Reference Sequence (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins. Nucleic Acids Research. 2005 Jan 1;33(Database issue):D501-4. PMID: 15608248  

59. Przytycka T, Davis G, Song N, Durand D. Graph Theoretical Insights into Evolution of Multidomain Protein Evolution. Presented at RECOMB 2005 and published in: LNBI 3500, Springer Verlag, 311-325.

60. Rigden DJ, Galperin MY. OMICS-Related Research in Latin America. OMICS. 2005 Summer;9(2):129. No abstract available. PMID: 15969644

61. Robin G, DeBonis S, Dornier A, Cappello G, Ebel C, Wade RH, Thierry-Mieg D, Kozielski F. Essential kinesins: characterization of Caenorhabditis elegans KLP-15. Biochemistry. 2005 May 3;44(17):6526-36. PMID: 15850386.

62. Rogozin IB, Sverdlov AV, Babenko VN, Koonin EV. Analysis of evolution of exon-intron structure of eukaryotic genes. Briefings in Bioinformatics. 2005 Jun;6(2):118-34. PMID: 15975222

63. Rogozin IB, Basu MK, Jordan IK, Pavlov YI, Koonin EV. APOBEC4, a new member of the AID/APOBEC family of polynucleotide (deoxy)cytidine deaminases predicted by computational analysis. Cell Cycle. 2005 Sep;4(9):1281-5. Epub 2005 Sep 6. PMID: 16082223.

64. Romling U, Gomelsky M, Galperin MY. C-di-GMP: the dawning of a novel bacterial signalling system. Molecular Microbiology. 2005 Aug;57(3):629-39. Review. PMID: 16045609.

65. Sardiu ME, Alves G, Yu YK. . Score statistics of global sequence alignment from the energy distribution of a modified directed polymer and directed percolation problem. Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics. 2005 Dec;72 (6 Pt 1):061917. Epub 2005 Dec 23. PMID: 16485984.

66. Schäffer AA, Kaplan FS, Tracy MR, O'Brien ML, Dormans JP, Shore EM, Harland RM, Kusumi K. Developmental anomalies of the cervical spine in patients with fibrodysplasiaossificans progressiva are distinctly different from those in patients with Klippel-Feil syndrome: clues from the BMP signaling pathway. Spine. 2005 Jun 15;30(12):1379-85. PMID: 15959366

67. Schäffer AA. "Human Genetic Linkage Analysis." Handbook of Computational Molecular Biology. Vol. 9. Chapman & Hall/CRC Computer & Information Science Series. New York: Taylor & Francis CRC Press, 2005.

68. Salzer U, Chapel HM, Webster AD, Pan-Hammarstrom Q, Schmitt-Graeff A, Schlesier M, Peter HH, Rockstroh JK, Schneider P, Schäffer AA, Hammarstrom L, Grimbacher B. Mutations in TNFRSF13B encoding TACI are associated with common variable immunodeficiency in humans. Nature Genetics. 2005 Aug;37(8):820-8. Epub 2005 Jul 10. PMID: 16007087.

69. Seydel KB, Gaur D, Aravind L, Subramanian G, Miller LH. Plasmodium falciparum: characterization of a late asexual stage golgi protein containing both ankyrin and DHHC domains.. Experimental Parasitology. 2005 Aug;110(4):389-93. PMID: 15882865.

70. Sheetlin S, Park Y, Spouge JL. The Gumbel pre-factor k for gapped local alignment can be estimated from simulations of global alignment. Nucleic Acids Research. 2005 Sep 6;33(15):4987-94. Print 2005 PMID: 16147981.

71. Smith LH, Tanabe L, Rindflesch T, Wilbur WJ. MedTag: A Collection of Biomedical Annotations. Proceedings of the ACL-ISMB BioLink Workshop: Mining Biological Semantics. Detroit, MI, June 2005.

72. Sverdlov AV, Rogozin IB, Babenko VN, Koonin EV. Conservation versus parallel gains in intron evolution. Nucleic Acids Research. 2005 Mar 23;33(6):1741-8. Print 2005. PMID: 15788746  

73. Tanabe L, Xie N, Thom LH, Matten W, Wilbur WJ. GENETAG: a tagged corpus for gene/protein named entity recognition. BMC Bioinformatics. 2005;6 Suppl 1:S3. Epub 2005 May 24. PMID: 15960837

74. Tanabe L. "The Genomic Data Mine." Medical Informatics: Knowledge Management and Data Mining in Biomedicine. Ed. Fuller SS, Chen H, Friedman C, Hersh W. New York: Springer, 2005. 547-71.

75. Tasneem A, Iyer LM, Jakobsson E, Aravind L. Identification of the prokaryotic ligand-gated ion channels and their implications for the mechanisms and origins of animal Cys-loop ion channels. Genome Biology. 2005;6(1):R4. Epub 2004 Dec 20. PMID: 15642096

76. Teplyakov A, Obmolova G, Toedt J, Galperin MY, Gilliland GL. Crystal structure of the bacterial YhcH protein indicates a role in sialic acid catabolism.. Journal of Bacteriology. 2005 Aug;187(16):5520-7. PMID: 16077096.

77. Tharakaraman K, Marino-Ramirez L, Sheetlin S, Landsman D, Spouge JL. Alignments anchored on genomic landmarks can aid in the identification of regulatory elements. Bioinformatics. 2005 Jun 1;21 Suppl 1:i440-i448. PMID: 15961489

78. Thierry-Mieg, Jean. "Su(2/1) Super-Unification of the Standard Model and Non- Commutative Geometry." World Scientific Series in 20th Century Physics. Eds. Remo Ruffini and Yosef Verbin. Vol. 38: World Scientific Press, 2005.

79. Tsang MW, Chu CL, Kam YW, Kwong KH, Lam CK, Ngan SY, Yu YK. Characterising atherothrombosis in Hong Kong: results of the Hong Kong data from a global atherothrombosis epidemiological survey. Hong Kong Medical Journal. 2005 Feb;11(1):36-41. PMID: 15687514  

80. Ulrich LE, Koonin EV, Zhulin IB. One-component systems dominate signal transduction in prokaryotes. Trends in Microbiology. 2005 Feb;13(2):52-6. Review. PMID: 15680762  

81. Vacek MM, Schäffer AA, Davis J, Fischer RE, Dale JK, Adams S, Straus SE, Puck JM. HLA B44 is Associated with Decreased Severity of Autoimmune Lymphoproliferative Syndrome in Patients with CD95 Mutations (ALPS Type Ia). Clinical Immunology. 118:59--65, 2006.

82. Wheeler DL, Barrett T, Benson DA, Bryant SH, Canese K, Church DM, DiCuccio M, Edgar R, Federhen S, Helmberg W, Kenton DL, Khovayko O, Lipman DJ, Madden TL, Maglott DR, Ostell J, Pontius JU, Pruitt KD, Schuler GD, Schriml LM, Sequeira E, Sherry ST, Sirotkin K, Starchenko G, Suzek TO, Tatusov R, Tatusova TA, Wagner L, Yaschenko E. Database resources of the National Center for Biotechnology Information. Nucleic Acids Research. 2005 Jan 1;33(Database issue):D39-45. PMID: 15608222  

83. Wheeler DL, Smith-White B, Chetvernin V, Resenchuk S, Dombrowski SM, Pechous SW, Tatusova T, Ostell J. Plant genome resources at the National Center for Biotechnology Information.. Plant Physiology. 2005 Jul;138(3):1280-8. PMID: 16010002.

84. Xu M, Geer LY, Bryant SH, Roth JS, Kowalak JA, Maynard DM, Markey SP. Assessing data quality of Peptide mass spectra obtained by quadrupole ion trap mass spectrometry. Journal of Proteome Research. 2005 Mar-Apr;4(2):300-5. PMID: 15822904

85. Yampolsky LY, Kondrashov FA, Kondrashov AS. Distribution of the strength of selection against amino acid replacements in human proteins. Human Molecular Genetics. 2005 Sep 20; [Epub ahead of print] PMID: 16174645.

86. Yampolsky L, Allen CD, Shabalina SA, Kondrashov AS. Persistence Time Of Loss-Of Function Mutations At Non-Essential Loci Affecting Eye Color In Drosophila melanogaster. Genetics. 2005 Dec;171(4):2133-8. Epub 2005 Aug 22. PMID: 16118190.

87. Yampolsky LY, Kondrashov FA, Kondrashov AS. Distribution of the strength of selection against amino acid replacements in human proteins. Human Molecular Genetics. 2005 Nov 1;14(21):3191-201. Epub 2005 Sep 20. PMID: 16174645.

88. Yu YK, Altschul SF. The construction of amino acid substitution matrices for the comparison of proteins with non-standard compositions. Bioinformatics. 2005 Apr 1;21(7):902-11. Epub 2004 Oct 27. PMID: 15509610

89. Yu YK, Wong KH, Chang MM. Recursive three-dimensional model reconstruction based on Kalman filtering. IEEE Systems, Man, and Cybernetics Society. 2005 Jun;35(3):587-92. PMID: 15971927

Revised: August 8, 2006.