This page contains references for papers published related to FASTLINK, MSA, CASPAR, PedHunter, CGH analysis (oncotrees), mapping, and microarray analysis (METREX) software.

• Cottingham RW Jr, Idury RM, Schäffer AA. Faster sequential genetic linkage computations. Am J Hum Genet. 1993; 53:252-263. [PubMed] [paper1.ps]
  
  
• Schäffer AA, Gupta SK, Shriram K, Cottingham RW Jr. Avoiding recomputation in linkage analysis. Hum Hered. 1994; 44:225-237. [PubMed] [paper2.ps]
  
  
• Dwarkadas S, Schäffer AA, Cottingham RW Jr, Cox AL, Keleher P, Zwaenepoel W. Parallelization of general linkage analysis problems. Hum Hered. 1994; 44:127-141. [PubMed] [paper3.ps]
  
  
• Gupta SK, Schäffer AA, Cox AL, Dwarkadas S, Zwaenepoel W. Integrating parallelization strategies for linkage analysis. Comput Biomed Res. 1995; 28:116-139. [PubMed] [paper4.ps]
  
  
• Schäffer AA. Faster linkage analysis computations for pedigrees with loops or unused alleles. Hum Hered. 1996; 46:226-235. [PubMed] [paper5.ps]
  
  
• Becker A, Geiger D, Schäffer AA. Automatic selection of loop breakers for genetic linkage analysis. Hum Hered. 1998; 48:49-60. [PubMed] [paper6.ps]

• Lipman, DJ, Altschul SF, Kececioglu JD. A tool for multiple sequence alignment. Proc Natl Acad Sci USA. 1989; 86:4412-4415. [PubMed]
  
  
• 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]
  
  
• Carrillo H., Lipman DJ. The multiple sequence alignment problem in biology. SIAM J Appl Math. 1988; 48:1073-1082.
  
  
• Altschul SF, Lipman DJ. Trees, stars, and multiple biological sequence alignment. SIAM J Appl Math. 1989; 49:197-209.
  
  
• Altschul SF. Gap costs for multiple sequence alignment. J Theor Biol. 1989; 138:297-309. [PubMed]
  
  
• Altschul SF, Carroll RJ, Lipman DJ. Weights for data related by a tree. J Mol Biol. 1989; 207:647-653. [PubMed]
  
  
• Altschul SF. Leaf pairs and tree dissections. SIAM J Discrete Math. 1989; 2:293-299.

• Buhler J, Owerbach D, Schäffer AA, Kimmel M, Gabbay KH. Linkage analyses in type I diabetes using CASPAR, a software and statistical program for conditional analysis of polygenic diseases. Hum Hered 1997; 47:211-222. [PubMed]

• 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]
  
  
• Agarwala R, Biesecker LG, Tomlin JF, Schäffer AA. Towards a complete North American Anabaptist genealogy: A systematic approach to merging partially overlapping genealogy resources. Am J Med Genet. 1999; 86:156-161. [PubMed]
  
  
• Agarwala R, Tomlin JF, Schäffer AA. Towards a complete North American Anabaptist genealogy II: Analysis of inbreeding. Hum Biol. 2001; 73:533-545. [PubMed]

• 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]
  
  
• 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]
  
  
• Kainu T, et al. Somatic deletions in hereditary breast cancers implicate 13q21 as a putative novel breast cancer susceptibility locus. Proc Natl Acad Sci USA. 2000; 97: 9603-9608. [PubMed]
  
  
• 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]
  
  
• Radmacher MD, Simon R, Desper R, Taetle R, Schäffer AA, Nelson MA. Graph models of oncogenesis with an application to melanoma. J Theor Biol. 2001;212:535-548. [PubMed]
  
  
• Brodeur GM, Tsiatis AA, Williams DL, Luthardt FW, Green AA. Statistical analysis of cytogenetic abnormalities in human cancer cells. Cancer Genet Cytogenet. 1982; 7:137-152. [PubMed]

• 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]
  
  
• 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]
  
  
• Hitte C, Lorentzen TD, Guyon R, Kim L, Cadieu E, Parker HG, Quignon P, Lowe JK, Gelfenbeyn B, André C, Ostrander EA, Galibert F. Comparison of MultiMap and TSP/CONCORDE for constructing radiation hybrid maps. J Hered. 2003; 94:9-13. [PubMed]
  
  
• Guyon R, Lorentzen TD, Hitte C, Kim L, Cadieu E, Parker HG, Quignon P, Lowe JK, Renier C, Gelfenbeyn B, Vignaux F, DeFrance HB, Gloux S, Mahairas GG, André C, Galibert F, Ostrander EA. A 1-Mb resolution radiation hybrid map of the canine genome. Proc. Natl. Acad. Sci. U S A. 2003; 100:5296-5301. [PubMed]
  
  
• 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]
  

• Desper R, Gascuel O Fast and accurate phylogeny reconstruction algorithms based on the minimum-evolution principle. J. Comp. Biol. 2002; 9:687-705. [PubMed]
  
  
• Desper R, Khan J, and Schäffer AA. Tumor classification using phylogenetic methods on expression data. J. Theor. Biol. 2004; 228:477-496 [PubMed] [PTC.pdf]
  
  
• Felsenstein J. PHYLIP - Phylogeny Inference Package (Version 3.2). Cladistics. 1989; 5:164-166.
  
  
• Swofford D. PAUP - Phylogenetic Analysis Using Parsimony (and other methods), Version 4.0.