Recent Publications from the BRC

Atchley WR, and Fernandes AD. 2005. Sequence signatures and the probabilistic identification of proteins in the Myc-Max-Mad network. PNAS USA 102: 6401-06.

Atchley WR, Zhao J, Fernandes AD, and Druke T. 2005. Solving the protein sequence metric problem. PNAS USA 102: 6395-6400.

Chou JW, Paules RS, and Bushel PR. 2005. Systematic variation normalization in microarray data to get gene expression comparison unbiased. J Bioinform Comput Biol 3(2): 225-41.

Coffman CJ, Doerge RW, Simonsen KL, Nichols KM, Duarte CK, Wolfinger RD, and McIntyre LM. 2005. Model selection in binary trait locus mapping. Genetics 170: 1281-1297.

Cooper GM, Stone EA, Asimenos G, NISC Comparative Sequencing Program, Green ED, Batzoglou S, and Sidow A. 2005. Distribution and intensity of constraint in mammalian genomic sequence. Genome Research 15: 901-913.

Dworkin I, Palsson A, and Gibson G. 2005. Replication of an Egfr-wing shape association in a wild-caught cohort of Drosophila melanogaster. Genetics 169: 2115-2125.

Gardner RJ, Hobolth A, Jensen EBV, and Sorensen FB. 2005. Shape discrimination by total curvature, with a view to cancer diagnostics. J Microscopy 217: 49-59.

Gibson G. 2005. Q&A: Greg Gibson. Current Biol 15: R531-532.

Gibson G. 2005. The synthesis and evolution of a supermodel. Science 307: 1890-1891.

Gibson G. 2005. Mutational accumulation of the transcriptome. Nature Genetics 37(5): 458-460.

Gibson G, and Weir, BS. 2005. The quantitative genetics of transcription. Trends in Genetics (in press).

Goering LM, and Gibson G. 2005. Genetic variation for dorsal-ventral patterning of the Drosophila melanogaster eggshell. Evol and Devel 7(2): 81-88.

Halverson J, and Basten C. 2005. A PCR multiplex and database for forensic DNA identification of dogs. J Forensic Sci 50(2): 352-363.

Heber S, and Savage CD. 2005. Common intervals of trees. Information Processing Letters 93(2): 69-74.

Hobolth A, and Jensen JL. 2005. Statistical inference in evolutionary models of DNA sequences via the EM algorithm. Statistical Applications in Genetics and Molecular Biology 4(1): Article 18.

Hobolth A, and Jensen JL. 2005. Applications of hidden Markov models for characterization of homologous DNA sequences with a common gene. J Comput Biol 12: 186-203. Maphysto Research Report 2003-35, Dept. of Theoretical Statistics, University of Aarhus.

International HapMap Consortium (B.S. Weir is among the many authors). 2005. A haplotype map of the human genome. Nature 437: 1299-1320.

Johnson MR, Montero CI, Conners SB, Shockley KR, Bridger SL, and Kelly RM. 2005. Population density-dependent regulation of exopolysaccharide formation in the hyperthermophilic bacterium Thermotoga maritima. Molecular Microbiol. 55(3): 664-674.

Jorgensen FG, Hobolth A, Hornshoj H, Bendixen C, Fredholm M, and Schierup MH. 2005. Comparative analysis of protein coding sequences from human, mouse and the domesticated pig. BMC Biol 3: 2.

Kashuk CS, Stone EA, Grice EA, Portnoy ME, Green ED, Sidow A, Chakravarti A, McCallion AS. 2005. Phenotype-genotype correlation in Hirschsprung disease is illuminated by comparative analysis of the RET protein sequence. PNAS USA 102: 8949-54.

Kirst M, Basten CJ, Myburg AA, Zeng Z-B, and Sederoff RR. 2005. Genetic architecture of transcript level variation in differentiating xylem of an Eucalyptus hybrid. Genetics 169 (April).

Liu Y, and Zeng Z-B. 2005. Mixture model equations for marker-assisted genetic evaluation. J Anim Breed Genet 122: 229-239.

Martin ER, Bronson P, Li Y-J, Wall N, Chung R-H, Pericak-Vance M, et al. 2005. Interaction between the alpha-T catenin gene (VR22) and APOE in Alzheimer's disease. J Med Genet 42: 787-792.

Moser JM, Freitas T, Arasu P, and Gibson G. 2005. Gene expression profiles associated with the transition to parasitism in Ancylostoma caninum larvae. Mol Biochem Parasitol 143: 39-48.

Mu J, Awadalla P, Duan J, McGee KM, Joy DA, McVean GAT, and Su X. 2005. Recombination hotspots and population structure in Plasmodium falciparum. Plos Biol 3(10): e335.

Palsson A, Dodgson J, Dworkin I, and Gibson G. 2005. Tests for the replication of an association between Egfr and natural variation in Drosophila melanogaster wing morphology. BMC Genet 6: 44.

Psarros M, Heber S, Sick M, Thoppae G, Harshman K, and Sick B. 2005. RACE: Remote analysis computation for gene expression data. Nucl Acids Res 33: W638-W643; doi:10.1093/nar/gki490.

Seo TK, Kishino H, and Thorne JL. 2005. Incorporating gene-specific variation when inferring and evaluating optimal evolutionary tree topologies from multilocus sequence data. PNAS 102(12): 4436-41.

Shockley KR, Scott KL, Pysz MA, Conners SB, Johnson MR, Montero CI, Wolfinger RD, and Kelly RM. 2005. Genome-wide transcriptional variation within and between steady states for continuous growth of the hyperthermophile Thermotoga maritima. Appl Environ Microbiol: 5572-76 (Sept.)

Stafford-Smith M, Podgoreanu M, Swaminathan M, Phillips-Bute B, Mathew JP, Hauser EH, Winn M, Milano C, Nielsen DM, et al. 2005. Association of genetic polymorphisms with risk of renal injury after coronary bypass graft surgery. Am J of Kidney Disease 45(3): 519-531.

Starmer J, Stomp A, Vouk M, and Bitzer D. 2005. Predicting fidelity of protein synthesis in E. coli. Proc. IEEE International Workshop on Genomic Signal Processing and Statistics (GENSIPS 2005), May 22-24, 2005 Newport, Rhode Island.

Stone EA, Cooper GM, and Sidow A. 2005. Trade-offs in detecting evolutionarily constrained sequence by comparative genomics. Annu Rev Genomics Hum Genet 6: 143-164.

Stone EA, and Sidow A. 2005. Physicochemical constraint violation by missense substitutions mediates impairment of protein function and disease severity. Genome Research 15: 978-986.

Strain E, and Muse SV. 2005. Positively selected sites in the Arabidposis receptor-like kinase gene family. J Mol Evol 61: 325-332.

Thomson S, Kennerly E, Olby N, Mickelson J, Hoffmann D, Dickinson P, Gibson G, and Breen M. 2005. Microarray analysis of differentially expressed genes of primary tumors in the canine central nervous system. Veterinary Pathology 42(5): 550-558.

Tzeng, J-Y. 2005. Evolutionary-based grouping of haplotypes in association analysis. Genetic Epidemiology 28: 220-231.

Weir BS, Cardon LR, Anderson AD, Nielsen DM, and Hill WG. 2005. Measures of human population structure show heterogeneity among genomic regions. Genome Research 15: 1468-76.

Welsby IJ, Podgoreanu MV, Phillips-Bute B, White WD, Nielsen DM, et al. 2005. Genetic factors contribute to bleeding after cardiac surgery. J Thromb Haemost 3(6): 1206-12.

Zeng Z-B. 2005. QTL mapping and the genetic basis of adaptation: recent developments. Genetica 123: 25-37.

Zeng Z-B, Wang T, and Zou W. 2005. Modeling quantitative trait loci and interpretation of models. Genetics 169: 1711-25.