Computational Biology Publications
Computational Biology Publications

  1. McClurg P, Janes J, Wu C, Delano DL, Walker JR, Batalov S, Takahashi JS, Shimomura K, Kohsaka A, Bass J, et al. Genomewide association analysis in diverse inbred mice: power and population structure. Genetics 2007;176(1):675-83.
  2. Su AI, Hogenesch JB. Power-law-like distributions in biomedical publications and research funding. Genome Biol 2007;8(4):404.
  3. Sagan SM, Rouleau Y, Leggiadro C, Supekova L, Schultz PG, Su AI, Pezacki JP. The influence of cholesterol and lipid metabolism on host cell structure and hepatitis C virus replication. Biochem Cell Biol 2006;84(1):67-79.
  4. Melnick JS, Janes J, Kim S, Chang JY, Sipes DG, Gunderson D, Jarnes L, Matzen JT, Garcia ME, Hood TL, et al. An efficient rapid system for profiling the cellular activities of molecular libraries. Proc Natl Acad Sci U S A 2006;103(9):3153-8.
  5. McClurg P, Pletcher MT, Wiltshire T, Su AI. Comparative analysis of haplotype association mapping algorithms. BMC bioinformatics [electronic resource] 2006;7:61.
  6. Lee JW, Lee JS, Kang M, Su AI, Chang YT. Visual artificial tongue for quantitative metal-cation analysis by an off-the-shelf dye array. Chemistry 2006;12(22):5691-6.
  7. Zhong JF, Zhao Y, Sutton S, Su A, Zhan Y, Zhu L, Yan C, Gallaher T, Johnston PB, Anderson WF, et al. Gene expression profile of murine long-term reconstituting vs. short-term reconstituting hematopoietic stem cells. Proc Natl Acad Sci U S A 2005;102(7):2448-53.
  8. Yang J, Su AI, Li WH. Gene expression evolves faster in narrowly than in broadly expressed mammalian genes. Mol Biol Evol 2005;22(10):2113-8.
  9. Wilkens SJ, Janes J, Su AI. HierS: hierarchical scaffold clustering using topological chemical graphs. J Med Chem 2005;48(9):3182-93.
  10. Gurkan C, Lapp H, Alory C, Su AI, Hogenesch JB, Balch WE. Large-scale profiling of Rab GTPase trafficking networks: the membrome. Mol Biol Cell 2005;16(8):3847-64.
  11. Bystrykh L, Weersing E, Dontje B, Sutton S, Pletcher MT, Wiltshire T, Su AI, Vellenga E, Wang J, Manly KF, et al. Uncovering regulatory pathways that affect hematopoietic stem cell function using 'genetical genomics'. Nat Genet 2005;37(3):225-32.
  12. Walker JR, Su AI, Self DW, Hogenesch JB, Lapp H, Maier R, Hoyer D, Bilbe G. Applications of a rat multiple tissue gene expression data set. Genome Res 2004;14(4):742-9.
  13. Su AI, Wiltshire T, Batalov S, Lapp H, Ching KA, Block D, Zhang J, Soden R, Hayakawa M, Kreiman G, et al. A gene atlas of the mouse and human protein-encoding transcriptomes. Proc Natl Acad Sci U S A 2004;101(16):6062-7.
  14. Pletcher MT, McClurg P, Batalov S, Su AI, Barnes SW, Lagler E, Korstanje R, Wang X, Nusskern D, Bogue MA, et al. Use of a dense single nucleotide polymorphism map for in silico mapping in the mouse. PLoS biology 2004;2(12):e393.
  15. Conkright MD, Guzman E, Flechner L, Su AI, Hogenesch JB, Montminy M. Genome-wide analysis of CREB target genes reveals a core promoter requirement for cAMP responsiveness. Mol Cell 2003;11(4):1101-8.
  16. Batalov S, Su AI, Ching KA, Fletcher CF. Functional annotation of RIKEN mouse cDNA clones using GNF expression atlas. Genome Res 2003;13(6B):1556-1557.
  17. Supekova L, Pezacki JP, Su AI, Loweth CJ, Riedl R, Geierstanger B, Schultz PG, Wemmer DE. Genomic effects of polyamide/DNA interactions on mRNA expression. Chem Biol 2002;9(7):821-7.
  18. Su AI, Pezacki JP, Wodicka L, Brideau AD, Supekova L, Thimme R, Wieland S, Bukh J, Purcell RH, Schultz PG, et al. Genomic analysis of the host response to hepatitis C virus infection. Proc Natl Acad Sci U S A 2002;99(24):15669-74.
  19. Su AI, Guidotti LG, Pezacki JP, Chisari FV, Schultz PG. Gene expression during the priming phase of liver regeneration after partial hepatectomy in mice. Proc Natl Acad Sci U S A 2002;99(17):11181-6.
  20. Su AI, Cooke MP, Ching KA, Hakak Y, Walker JR, Wiltshire T, Orth AP, Vega RG, Sapinoso LM, Moqrich A, et al. Large-scale analysis of the human and mouse transcriptomes. Proc Natl Acad Sci U S A 2002;99(7):4465-70.
  21. Panda S, Antoch MP, Miller BH, Su AI, Schook AB, Straume M, Schultz PG, Kay SA, Takahashi JS, Hogenesch JB. Coordinated transcription of key pathways in the mouse by the circadian clock. Cell 2002;109(3):307-20.
  22. Frierson HF, Jr., El-Naggar AK, Welsh JB, Sapinoso LM, Su AI, Cheng J, Saku T, Moskaluk CA, Hampton GM. Large scale molecular analysis identifies genes with altered expression in salivary adenoid cystic carcinoma. Am J Pathol 2002;161(4):1315-23.
  23. Wolkenberg SE, Su AI. Combinatorial synthesis and discovery of an antibiotic compound - An experiment suitable for high school and undergraduate laboratories. J Chem Educ 2001;78(6):784-785.
  24. Welsh JB, Sapinoso LM, Su AI, Kern SG, Wang-Rodriguez J, Moskaluk CA, Frierson HF, Jr., Hampton GM. Analysis of gene expression identifies candidate markers and pharmacological targets in prostate cancer. Cancer Res 2001;61(16):5974-8.
  25. Su AI, Welsh JB, Sapinoso LM, Kern SG, Dimitrov P, Lapp H, Schultz PG, Powell SM, Moskaluk CA, Frierson HF, Jr., et al. Molecular classification of human carcinomas by use of gene expression signatures. Cancer Res 2001;61(20):7388-93.
  26. Su AI, Lorber DM, Weston GS, Baase WA, Matthews BW, Shoichet BK. Docking molecules by families to increase the diversity of hits in database screens: computational strategy and experimental evaluation. Proteins 2001;42(2):279-93.
  27. Ratnaswamy G, Huff ME, Su AI, Rion S, Kelly JW. Destabilization of Ca2+-free gelsolin may not be responsible for proteolysis in Familial Amyloidosis of Finnish Type. Proc Natl Acad Sci U S A 2001;98(5):2334-9.
  28. Hogenesch JB, Ching KA, Batalov S, Su AI, Walker JR, Zhou Y, Kay SA, Schultz PG, Cooke MP. A comparison of the Celera and Ensembl predicted gene sets reveals little overlap in novel genes. Cell 2001;106(4):413-5.
  29. Chang YT, Wignall SM, Rosania GR, Gray NS, Hanson SR, Su AI, Merlie J, Jr., Moon HS, Sangankar SB, Perez O, et al. Synthesis and biological evaluation of myoseverin derivatives: microtubule assembly inhibitors. J Med Chem 2001;44(26):4497-500.