Sequence Informatics Publications
Sequence Informatics Publications

  1. Mukherji M, Bell R, Supekova L, Wang Y, Orth AP, Batalov S, Miraglia L, Huesken D, Lange J, Martin C, et al. Genome-wide functional analysis of human cell-cycle regulators. Proc Natl Acad Sci U S A 2006;103(40):14819-24.
  2. Maeda N, Kasukawa T, Oyama R, Gough J, Frith M, Engstrom PG, Lenhard B, Aturaliya RN, Batalov S, Beisel KW, et al. Transcript annotation in FANTOM3: mouse gene catalog based on physical cDNAs. PLoS Genet 2006;2(4):e62.
  3. Kidgell C, Volkman SK, Daily J, Borevitz JO, Plouffe D, Zhou Y, Johnson JR, Le Roch K, Sarr O, Ndir O, et al. A systematic map of genetic variation in Plasmodium falciparum. PLoS Pathog 2006;2(6):e57.
  4. Engstrom PG, Suzuki H, Ninomiya N, Akalin A, Sessa L, Lavorgna G, Brozzi A, Luzi L, Tan SL, Yang L, et al. Complex Loci in human and mouse genomes. PLoS Genet 2006;2(4):e47.
  5. Willingham AT, Orth AP, Batalov S, Peters EC, Wen BG, Aza-Blanc P, Hogenesch JB, Schultz PG. A strategy for probing the function of noncoding RNAs finds a repressor of NFAT. Science 2005;309(5740):1570-3.
  6. Soares ML, Coelho T, Sousa A, Batalov S, Conceicao I, Sales-Luis ML, Ritchie MD, Williams SM, Nievergelt CM, Schork NJ, et al. Susceptibility and modifier genes in Portuguese transthyretin V30M amyloid polyneuropathy: complexity in a single-gene disease. Hum Mol Genet 2005;14(4):543-53.
  7. Katayama S, Tomaru Y, Kasukawa T, Waki K, Nakanishi M, Nakamura M, Nishida H, Yap CC, Suzuki M, Kawai J, et al. Antisense transcription in the mammalian transcriptome. Science 2005;309(5740):1564-6.
  8. Carninci P, Kasukawa T, Katayama S, Gough J, Frith MC, Maeda N, Oyama R, Ravasi T, Lenhard B, Wells C, et al. The transcriptional landscape of the mammalian genome. Science 2005;309(5740):1559-63.
  9. Zheng L, Liu J, Batalov S, Zhou D, Orth A, Ding S, Schultz PG. An approach to genomewide screens of expressed small interfering RNAs in mammalian cells. Proc Natl Acad Sci U S A 2004;101(1):135-40.
  10. 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.
  11. Sam-Yellowe TY, Florens L, Johnson JR, Wang T, Drazba JA, Le Roch KG, Zhou Y, Batalov S, Carucci DJ, Winzeler EA, et al. A Plasmodium gene family encoding Maurer's cleft membrane proteins: structural properties and expression profiling. Genome Res 2004;14(6):1052-9.
  12. 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 Biol 2004;2(12):e393.
  13. Orth AP, Batalov S, Perrone M, Chanda SK. The promise of genomics to identify novel therapeutic targets. Expert Opin Ther Targets 2004;8(6):587-96.
  14. Wiltshire T, Pletcher MT, Batalov S, Barnes SW, Tarantino LM, Cooke MP, Wu H, Smylie K, Santrosyan A, Copeland NG, et al. Genome-wide single-nucleotide polymorphism analysis defines haplotype patterns in mouse. Proc Natl Acad Sci U S A 2003;100(6):3380-5.
  15. Le Roch KG, Zhou Y, Blair PL, Grainger M, Moch JK, Haynes JD, De La Vega P, Holder AA, Batalov S, Carucci DJ, et al. Discovery of gene function by expression profiling of the malaria parasite life cycle. Science 2003;301(5639):1503-8.
  16. Kanapin A, Batalov S, Davis MJ, Gough J, Grimmond S, Kawaji H, Magrane M, Matsuda H, Schonbach C, Teasdale RD, et al. Mouse proteome analysis. Genome Res 2003;13(6B):1335-44.
  17. Gustincich S, Batalov S, Beisel KW, Bono H, Carninci P, Fletcher CF, Grimmond S, Hirokawa N, Jarvis ED, Jegla T, et al. Analysis of the mouse transcriptome for genes involved in the function of the nervous system. Genome Res 2003;13(6B):1395-401.
  18. Donaldson KM, Li W, Ching KA, Batalov S, Tsai CC, Joazeiro CA. Ubiquitin-mediated sequestration of normal cellular proteins into polyglutamine aggregates. Proc Natl Acad Sci U S A 2003;100(15):8892-7.
  19. Aza-Blanc P, Cooper CL, Wagner K, Batalov S, Deveraux QL, Cooke MP. Identification of modulators of TRAIL-induced apoptosis via RNAi-based phenotypic screening. Mol Cell 2003;12(3):627-37.
  20. Volkman SK, Hartl DL, Wirth DF, Nielsen KM, Choi M, Batalov S, Zhou Y, Plouffe D, Le Roch KG, Abagyan R, et al. Excess polymorphisms in genes for membrane proteins in Plasmodium falciparum. Science 2002;298(5591):216-8.
  21. Okazaki Y, Furuno M, Kasukawa T, Adachi J, Bono H, Kondo S, Nikaido I, Osato N, Saito R, Suzuki H, et al. Analysis of the mouse transcriptome based on functional annotation of 60,770 full-length cDNAs. Nature 2002;420(6915):563-73.
  22. Le Roch KG, Zhou Y, Batalov S, Winzeler EA. Monitoring the chromosome 2 intraerythrocytic transcriptome of Plasmodium falciparum using oligonucleotide arrays. Am J Trop Med Hyg 2002;67(3):233-43.
  23. Kawai J, Shinagawa A, Shibata K, Yoshino M, Itoh M, Ishii Y, Arakawa T, Hara A, Fukunishi Y, Konno H, et al. Functional annotation of a full-length mouse cDNA collection. Nature 2001;409(6821):685-90.
  24. 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.