2006

1. Aronson AR, Demner-Fushman D, Humphrey SM, Lin J, Liu H, Ruch P, Ruiz MD, Smith, LH, Tanabe L, Wilbur WJ. Fusion of knowledge-intensive and statistical approaches for retrieving and annotating textual genomics documents. The Fourteenth Text Retrieval Conference Proceedings. TREC 2005.

2. Finck A, van der Meer JW, Schäffer AA, Pfannstiel J, Fieschi C, Plebani A, Webster ADB, Hammarstr\"om L, Grimbacher B. Linkage of autosomal dominant common variable immunodeficiency to chromosome 4q. European Journal of Human Genetics. 2006 Apr 26; [Epub ahead of print]. PMID: 16639407.

3. Iyer LM, Balaji S, Koonin EV, Aravind L. Evolutionary genomics of nucleo-cytoplasmic large DNA viruses. Virus Research. 2006 Apr;117(1):156-84. Epub 2006 Feb 21. PMID: 16494962.

4. Iyer LM, Burroughs AM, Aravind L. The ASCH superfamily: novel domains with a fold related to the PUA domain and a potential role in RNA metabolism. Bioinformatics. 2006 Feb 1;22(3):257-63. Epub 2005 Dec 1. PMID: 16322048.

5. Galperin MY. Protecting sausages with bacteria instead of salt. Environmental Microbiology. 2006 Feb;8(2):185-92. PMID: 16423007.

6. Galperin MY. The Molecular Biology Database Collection: 2006 update. Nucleic Acids Research. 2006 Jan 1;34(Database issue):D3-5. PMID: 16381871.

7. Galperin MY, Moroz OV, Wilson KS, Murzin AG. House cleaning, a part of good housekeeping. Molecular Microbiology. 2006 Jan;59(1):5-19. PMID: 16359314.

8. Jeong J, Berman P, Przytycka T. Fold classification based on secondary structure-how much is gained by including loop topology?. BMC Structural Biology. 2006 Mar 8;6:3. PMID: 16524467.

9. Jothi R, Zotenko E, Tasneem A, Przytycka TM. COCO-CL: hierarchical clustering of homology relations based on evolutionary correlations. Bioinformatics. 2006 Apr 1;22(7):779-88. Epub 2006 Jan 24. PMID: 16434444.

10. Jung J, Bohn G, Allroth A, Boztug K, Brandes G, Sandrock I, Schäffer AA, Rathiman C, Köllner I, Berger C, Schilke R, Welte K, Grimbacher B, Klein C . Identification of a homozygous deletion in the AP3B1 gene causing Hermansky-Pudlak syndrome, type 2. Blood. 2006 Mar 14; [Epub ahead of print]. PMID: 16537806.

11. Makarova KS, Koonin EV, Haselkorn R, Galperin MY. Cyanobacterial response regulator PatA contains a conserved N-terminal domain (PATAN) with an alpha-helical insertion.. Bioinformatics. 2006 Mar 16; [Epub ahead of print]. PMID: 16543275.

12. Marino-Ramirez L, Hsu B, Baxevanis AD, Landsman D. The Histone Database: a comprehensive resource for histones and histone fold-containing proteins. Proteins. 2006 Mar 1;62(4):838-42. PMID: 16345076.

13. McArdle PF, Pollin TI, O'Connell JR, Sorkin JD, Agarwala R, Schäffer AA, Streeten EA, King TM, Shuldiner AR, Mitchell BD. Does Having Cildren Extend Lifespan? A Genealogical Study of Parity and Longevity in the Amish. Journal of Gerontology. Series A: Biological and Medical Sciences 61A:190--195, 2006.

14. Morgulis A, Gertz EM, Schäffer AA, Agarwala R. WindowMasker: window-based masker for sequenced genomes. Bioinformatics. 2006 Jan 15;22(2):134-41. Epub 2005 Nov 15. PMID: 16287941.

15. Murphy WJ, Pearks Wilkerson AJ, Raudsepp T, Agarwala R, Schäffer AA, Stanyon R, Chowdhary BP. . Novel gene acquisition on carnivore Y chromosomes. PLoS Genetics. 2006 Mar;2(3):e43. Epub 2006 Mar 31. PMID: 16596168.

16. Przytycka T, Davis G, Song N, Durand D. . Graph theoretical insights into evolution of multidomain proteins.. Journal of Computational Biology. 2006 Mar;13(2):351-63. PMID: 16597245.

17. Schäffer AA, Pfannstiel J, Webster ADB, Plebani A, Hammarström L, Grimbacher B. Analysis of families with common variable immunodeficiency (CVID) and IgA deficiency suggests linkage of CVID to chromosome 16q. Human Genetics. 2006 Feb;118(6):725-9. Epub 2005 Nov 22. PMID: 16287941.

18. 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 defects (ALPS type Ia). Clinical Immunology. 2006 Jan;118(1):59-65. Epub 2005 Oct 27. PMID: 16257267.

19. Wagner ML, Raudsepp T, Goh G, Schäffer AA, Agarwala R, Dranchak PK, Brinkmeyer C, Skow LC, Chowdhary BP, Mickelson JR. A 1.3-Mb interval map of equine homologs of HSA2. . Cytogenetic and Genome Research. 2006;112(3-4):227-34. PMID: 16484777.

20. Zhu S, Hsu AP, Vacek MM, Zheng L, Schäffer AA, Dale JK, Davis J, Fischer RE, Straus SE, Boruchov D, Saulsbury FT, Lenardo MJ, Puck JM. Genetic alterations in caspase-10 may be causative or protective in autoimmune lymphoproliferative syndrome.. Human Genetics. 2006 Apr;119(3):284-94. Epub 2006 Jan 31. PMID: 16446975.

Revised: August 8, 2006.