During my career I have worked on several projects creating software (FASTLINK, CASPAR, rhtspmap,? PedHunter, etc.) and a database (Anabaptist Genealogy database) for genetic studies.? My association with this software and a past track record of effective collaboration? with wet lab scientists leads to more and more such collaborations.? Two highlights from the past year are:? -- publication in the January 2007 issue of Nature Medicine of the characterization of? a new hypopigmentationneutropenia syndrome and identification of its molecular? cause as a mutation in the 3 untranslated region of the gene encoding p14.? -- the completion of major improvements to our software rhtspmap for constructing radiation? hybrid maps; the new version 3.0 was released and accompanied by a short paper in? Bioinformatics describing the improvements.? ? The immunodeficiency work is part of a longstanding collaboration with Dr. Bodo Grimbacher? (formerly U. Freiburg, GERMANY, now University College London, UK) on genetics of? human immunodeficiencies. Our work on neutropenia is led by Prof. Christoph Klein (Hannover ? Medical School, GERMANY). We are actively hunting genes for other human immunodeficiencies? and also hunting more neutropenia genes.? ? The work on rhtspmap is done in collaboration with Dr. Richa Agarwala (NCBI) and summer intern Edward Stallknecht Rice. We try to make the software general and robust enough that users can? use it themselves, and some published maps have been constructed with rhtspmap, without our? intervention. We have been collaborating with William Murphy (Texas A M) University on maps of the cat (Felis catus) and with Bhanu Chowhowdhary and Terje Raudsepp (also Texas A M) on maps of the horse (Equus caballus). During this past year we started collaborating with M. Elisabete J. Amaral (Sao Paulo University) and James Womack on maps of river buffalo (Bubalus bubalis). Several publications resulted from these collaborations including a paper in the February 2007 issue of Genomics presenting a new. denser map of the cat. This map was used by LGDNCI Frederick and their? collaborators as a guide to making the first genome assembly of parts of the cat genome, which? will be published in a future issue of Genome Research.
| Chattaraj, Parna; Munjal, Tina; Honda, Keiji et al. (2017) A common SLC26A4-linked haplotype underlying non-syndromic hearing loss with enlargement of the vestibular aqueduct. J Med Genet 54:665-673 |
| Altschul, Stephen F; Gertz, E Michael; Agarwala, Richa et al. (2009) PSI-BLAST pseudocounts and the minimum description length principle. Nucleic Acids Res 37:815-24 |
| Pollin, Toni I; McBride, Daniel J; Agarwala, Richa et al. (2008) Investigations of the Y chromosome, male founder structure and YSTR mutation rates in the Old Order Amish. Hum Hered 65:91-104 |
| Ianella, P; Venancio, L P R; Stafuzza, N B et al. (2008) First radiation hybrid map of the river buffalo X chromosome (BBUX) and comparison with BTAX. Anim Genet 39:196-200 |
| Salzer, Ulrich; Neumann, Carla; Thiel, Jens et al. (2008) Screening of functional and positional candidate genes in families with common variable immunodeficiency. BMC Immunol 9:3 |
| Morgulis, Aleksandr; Coulouris, George; Raytselis, Yan et al. (2008) Database indexing for production MegaBLAST searches. Bioinformatics 24:1757-64 |
| Menotti-Raymond, Marilyn; David, Victor A; Schaffer, Alejandro A et al. (2007) Mutation in CEP290 discovered for cat model of human retinal degeneration. J Hered 98:211-20 |
| Schaffer, Alejandro A; Salzer, Ulrich; Hammarstrom, Lennart et al. (2007) Deconstructing common variable immunodeficiency by genetic analysis. Curr Opin Genet Dev 17:201-12 |
| Amaral, M E J; Owens, K E; Elliott, J S et al. (2007) Construction of a river buffalo (Bubalus bubalis) whole-genome radiation hybrid panel and preliminary RH mapping of chromosomes 3 and 10. Anim Genet 38:311-4 |
| Woellner, Cristina; Schaffer, Alejandro A; Puck, Jennifer M et al. (2007) The hyper IgE syndrome and mutations in TYK2. Immunity 26:535;author reply 536 |
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