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Gapped BLAST and PSI-BLAST: a new generation of protein database search programs.
Altschul SF, Madden TL, Schäffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ. Altschul SF, et al. Nucleic Acids Res. 1997 Sep 1;25(17):3389-402. doi: 10.1093/nar/25.17.3389. Nucleic Acids Res. 1997. PMID: 9254694 Free PMC article. Review.
Protein sequence similarity searches using patterns as seeds.
Zhang Z, Schäffer AA, Miller W, Madden TL, Lipman DJ, Koonin EV, Altschul SF. Zhang Z, et al. Nucleic Acids Res. 1998 Sep 1;26(17):3986-90. doi: 10.1093/nar/26.17.3986. Nucleic Acids Res. 1998. PMID: 9705509 Free PMC article.
Computing probabilities of homozygosity by descent.
Schäffer AA. Schäffer AA. Genet Epidemiol. 1999;16(2):135-49. doi: 10.1002/(SICI)1098-2272(1999)16:2<135::AID-GEPI2>3.0.CO;2-W. Genet Epidemiol. 1999. PMID: 10030397
Towards a complete North American Anabaptist genealogy: A systematic approach to merging partially overlapping genealogy resources.
Agarwala R, Biesecker LG, Tomlin JF, Schäffer AA. Agarwala R, et al. Am J Med Genet. 1999 Sep 10;86(2):156-61. doi: 10.1002/(sici)1096-8628(19990910)86:2<156::aid-ajmg13>;2-5. Am J Med Genet. 1999. PMID: 10449652
A fast and scalable radiation hybrid map construction and integration strategy.
Agarwala R, Applegate DL, Maglott D, Schuler GD, Schäffer AA. Agarwala R, et al. Genome Res. 2000 Mar;10(3):350-64. doi: 10.1101/gr.10.3.350. Genome Res. 2000. PMID: 10720576 Free PMC article.
Improving the accuracy of PSI-BLAST protein database searches with composition-based statistics and other refinements.
Schäffer AA, Aravind L, Madden TL, Shavirin S, Spouge JL, Wolf YI, Koonin EV, Altschul SF. Schäffer AA, et al. Nucleic Acids Res. 2001 Jul 15;29(14):2994-3005. doi: 10.1093/nar/29.14.2994. Nucleic Acids Res. 2001. PMID: 11452024 Free PMC article. Review.
Anabaptist genealogy database.
Agarwala R, Biesecker LG, Schäffer AA. Agarwala R, et al. Am J Med Genet C Semin Med Genet. 2003 Aug 15;121C(1):32-7. doi: 10.1002/ajmg.c.20004. Am J Med Genet C Semin Med Genet. 2003. PMID: 12888984
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