Toxicogenomics – A Drug Development Perspective - Genomic Biomarkers for Pharmaceutical Development - page 145

[50] Tanase CP, Albulescu R, Neagu M. Application of 3D hydrogel microarrays in molecular diagnostics: advan-
tages and limitations. Expert Rev Mol Diagn 2011;11(5):461-4.
[51] Weisenberg JLZ, et al. Diagnostic yield and limitations of chromosomal microarray: a retrospective chart
review. Ann Neurol 2008;64:S101.
[52] Lin LL, Huang HC, Juan HF. Revealing the molecular mechanism of gastric cancer marker Annexin A4 in
cancer cell proliferation using exon arrays. Plos One 2012;7(9):e44615.
[53] Raghavachari N, et al. A systematic comparison and evaluation of high density exon arrays and RNA-Seq
technology used to unravel the peripheral blood transcriptome of sickle cell disease. BMC Med Genomics
2012;5:28.
[54] Mockler TC, et al. Applications of DNA tiling arrays for whole-genome analysis. Genomics 2005;85(5):655.
[55] Fiesel FC, et al. TDP-43 regulates global translational yield by splicing of exon junction complex component
SKAR. Nucleic Acids Res 2012;40(6):2668-82.
[56] Liu S, et al. A comparison of RNA-Seq and high-density exon array for detecting differential gene expression
between closely related species. Nucleic Acids Res 2011;39(2):578-88.
[57] Sakarya O, et al. RNA-Seq mapping and detection of gene fusions with a sufix array algorithm. PLoS
Comput Biol 2012;8(4):e1002464.
[58] Seok J, et al. JETTA: junction and exon toolkits for transcriptome analysis. Bioinformatics 2012;28(9):1274-5.
[59] Bi K, Vanderpool D, Singhal S, Linderoth T, Moritz C, Good JM. Transcriptome-based exon capture enables
highly cost-effective comparative genomic data collection at moderate evolutionary scales. BMC Genomics
2012;13:403 (17 August 2012).
[60] Kapetis D, et al. AMDA 2.13: a major update for automated cross-platform microarray data analysis.
Biotechniques 2012;53(1):33.
[61] Gellert P, Ponomareva Y, Braun T, Uchida S. Noncoder: a web interface for exon array-based detection of long
non-coding RNAs. Nucleic Acids Res 2013;41(1):e20.
[62] David L, et al. A high-resolution map of transcription in the yeast genome. Proc Natl Acad Sci USA
2006;103(14):5320-5.
[63] Cheng J, et al. Transcriptional maps of 10 human chromosomes at 5-nucleotide resolution. Science
2005;308(5725):1149-54.
[64] Clark TA, Sugnet CW, Ares M. Genomewide analysis of mRNA processing in yeast using splicing-speciic
microarrays. Science 2002;296(5569):907-10.
[65] Morra L, et al. Characterization of periostin isoform pattern in non-small cell lung cancer. Lung Cancer
2012;76(2):183-90.
[66] Yeo GWM. Splicing regulators: targets and drugs. Genome Biol 2005;6:12.
[67] Farber CR. Systems-level analysis of genome-wide association data. G3 Genes Genomes Genet
2013;3(1):119-29.
[68] Leveque N, Renois F, Andreoletti L. The microarray technology: facts and controversies. Clin Microbiol Infect
2013;19(1):10-14.
[69] Licatalosi DD, Darnell RB. Applications of next-generation sequencing RNA processing and its regulation:
global insights into biological networks. Nat Rev Genet 2010;11(1):75-87.
[70] Lister R, Gregory BD, Ecker JR. Next is now: new technologies for sequencing of genomes, transcriptomes,
and beyond. Curr Opin Plant Biol 2009;12(2):107-18.
[71] Morozova O, Hirst M, Marra MA. Applications of new sequencing technologies for transcriptome analysis.
Annu Rev Genomics Hum Genet 2009:135-51.
[72] Smith AM, et al. Quantitative phenotyping via deep barcode sequencing. Genome Res 2009;19(10):1836-42.
[73] Krupp M, et al. RNA-Seq Atlas - a reference database for gene expression proiling in normal tissue by next-
generation sequencing. Bioinformatics 2012;28(8):1184-5.
[74] Li JJ, et al. Sparse linear modeling of next-generation mRNA sequencing (RNA-Seq) data for isoform discov-
ery and abundance estimation. Proc Natl Acad Sci USA 2011;108(50):19867-72.
[75] Bentley DR, et al. Accurate whole human genome sequencing using reversible terminator chemistry. Nature
2008;456(7218):53-9.
[76] Ardlie K, et al. Analysis of RNAStable treated samples by the illumina DASL assay and illumina RNA
sequencing. J Mol Diagn 2012;14(6):637.
[77] Chelliserry M, et al. Can next generation sequencing replace sanger sequencing? - A review of the Illumina
cystic ibrosis diagnostic test on the MiSeqDx instrument. J Mol Diagn 2012;14(6):651.