Selected Publications:

1. Bohn G, Allroth A, Brandes G, Thiel J, Glocker E, Schäffer AA, Rathinam C, Taub N, Teis D, Zeidler C, Dewey RA, Geffers R, Buer J, Huber LA, Welte K, Grimbacher B, Klein C. A novel human primary immunodeficiency syndrome caused by deficiency of the endosomal adaptor protein p14. Nat Med. 2007; 13:38-45. [PubMed] [PDF]
   
2. Klein C, Grudzien M, Appaswamy G, Germeshausen M, Sandrock I, Schäffer AA, Rathinam C, Boztug K, Zeidler C, Schwinzer B, Rezaei N, Bohn G, Melin M, Carlsson G, Fadeel B, Dahl N, Palmblad J, Henter J-I, Grimbacher B, Welte K. Deficiency of HAX1 causes autosomal recessive severe congenital neutropenia (Kostmann disease). Nat. Genet. 2007; 39:86-92. [PubMed] [PDF]
   
3. Fyfe JC, Menotti-Raymond M, David VA, Brichta L, Schäffer AA, Agarwala R, Murphy WJ, Wedemeyer WJ, Gregory BL, Buzzell BG, Drummond MC, Wirth B, O'Brien SJ. An ~140kb deletion associated with feline spinal muscular atrophy implies an essential LIX1 function for motor neuron survival. Genome Res. 2006; 16:1084-1090. [PubMed] [PDF]
   
4. Schäffer AA, Pfannsteil J, Webster ADB, Plebani A, Hammarström L, Grimbacher B. Analysis of familiies with common variable immunodeficiency (CVID) and IgA deficiency suggests linkage of CVID to chromosome 16q. Hum Genet. 2006; 118:725-729. [PubMed] [PDF]
   
5. Murphy WJ, Agarwala R, and Schäffer AA, Stephens R, Smith C Jr., Crumpler NJ, David VA, O'Brien SJ. A rhesus macaque radiation hybrid map and comparative analysis with the human genome. Genomics 2005; 86:383-395. [PubMed] [PDF]
   
6. Salzer U, Chapel HM, Webster ADB, Pan-Hammarström Q, Schmitt-Graeff A, Schlesier M, Peter HH, Rockstroh JK, Schneider P, Schäffer AA, Hammarström L, Grimbacher B Mutations in TNFRSF13B encoding TACI are associated with common variable immunodeficiency in humans. Nat Genet. 2005; 37:820-828. [PubMed] [PDF]
   
7. Desper R, Khan J, and Schäffer AA. Tumor classification using phylogenetic methods on expression data. J. Theor. Biol. 2004; 228:477-496. [PubMed] [PDF]
   
8. Nemesure B, Jiao X, He Q, Leske MC, Wu S-Y, Hennis A, Mendell N, Redman J, Garchon H-J, Agarwala R, Schäffer AA, Hejtmancik F, for the Barbados Family Study Group: A genome-wide scan for open-angle glaucoma (POAG): The Barbados Family Study of Open-Angle Glaucoma. Hum Genet. 2003; 112: 600-609. [PubMed] [PDF]
   
9. Menotti-Raymond M, David VA, Chen ZQ, Menotti KA, Sun S, Schäffer AA, Agarwala R, Tomlin JF, O'Brien SJ, Murphy WJ Second-Generation Integrated Genetic Linkage/Radiation Hybrid Maps of the Domestic Cat (Felis catus). J Hered. 2003; 94: 95-106. [PubMed] [PDF]
   
10. Rosenberg MJ, Agarwala R, Bouffard G, Davis J, Fiermonte G, Hilliard MS, Koch T, Kalikin LM, Makalowska I, Morton DH, Petty EM, Weber JL, Palmieri F, Kelley RI, Schäffer AA, Biesecker LG: Mutant deoxynucleotide carrier is associated with congenital microcephaly. Nat Genet. 2002; 32: 175-179. [PubMed] [PDF]
    
11. Schäffer AA, Aravind L, Madden TL, Shavirin S, Spouge JL, Wolf YI, Koonin EV, Altschul SF. Improving the accuracy of PSI-BLAST protein database searches with composition-based statistics and other refinements. Nucleic Acids Res. 2001; 2994-3005. [PubMed] [PS]
    
12. Johnston JJ, Kelley RI, Crawford TO, Morton DH, Agarwala R, Koch T, Schäffer AA, Francomano CA, Biesecker LG: A novel nemaline myopathy in the Amish caused by a mutation in troponin T1. Am J Hum Genet. 2000; 67: 814-821. [PubMed] [PDF]
13. Agarwala R, Applegate DL, Maglott D, Schuler GD, Schäffer AA. A Fast and scalable radiation hybrid map construction and integration strategy. Genome Res. 2000; 10:350-364. [PubMed]
    
14. Simon R, Desper R, Papadimitriou, CH, Peng A, Taetle R, Alberts DS, Trent JM, Schäffer AA. Chromosome abnormalities in ovarian adenocarcinoma III: Using breakpoint data to infer and test mathematical models for oncogenesis. Genes Chromosomes Cancer. 2000; 28: 106-120. [PubMed] [ovar1026.ps]
    
15. Desper R, Jiang F, Kallioniemi O-P, Moch H, Papadimitriou CH, Schäffer AA. Distance-based reconstruction of tree models for oncogenesis. J Comput Biol. 2000; 7: 789-803. [PubMed] [PDF]
    
16. Schäffer AA, Wolf YI, Ponting CP, , Koonin EV, Aravind L, Altschul SF. IMPALA: Matchning a protein sequence against a collection of PSI-BLAST-constructed position-specific score matrices. Bioinformatics 1999; 15:1000-1011. [PubMed] [PDF]
    
17. Desper R, Jiang F, Kallioniemi O-P, Moch H, Papadimitriou CH, Schäffer AA. Inferring tree models for oncogenesis from comparative genome hybridization data. J Comput Biol. 1999; 6: 37-51. [PubMed]
    
18. Agarwala R, Biesecker LG, Hopkins KA, Francomano CA, Schäffer AA. Software for constructing and verifying pedigrees within large genealogies and an application to the Old Order Amish of Lancaster County. Genome Res. 1998; 8:211-221. [PubMed] [pedhunter.ps]
    
19. Becker A, Geiger D, Schäffer AA. Automatic selection of loop breakers for genetic linkage analysis. Hum Hered. 1998; 48:49-60. [PubMed] [paper6.ps]
    
20. Altschul SF, Madden TL, Schäffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 1997; 25: 3389-3402. [PubMed] [PDF]
    
21. Schäffer AA. Faster linkage analysis computations for pedigrees with loops or unused alleles. Hum Hered. 1996; 46:226-235. [PubMed] [paper5.ps]
    
22. Gupta SK, Kececioglu J, Schäffer AA. Improving the practical space and time efficiency of the shortest-paths approach to sum-of-pairs multiple sequence alignment. J Comput Biol. 1995; 2:459-472. [PubMed] [paper.ps]
    
23. Schäffer AA, Gupta SK, Shriram K, Cottingham RW Jr. Avoiding recomputation in linkage analysis. Hum Hered. 1994; 44:225-237. [PubMed] [paper2.ps]
    
24. Cottingham RW Jr, Idury RM, Schäffer AA. Faster sequential genetic linkage computations. Am J Hum Genet. 1993; 53:252-263. [PubMed] [paper1.ps]
    
    

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Revised: 11 December 2007.