@article{chu_weir_wolfinger_2004, title={Comparison of Li-Wong and loglinear mixed models for the statistical analysis of oligonucleotide arrays}, volume={20}, ISSN={["1460-2059"]}, DOI={10.1093/bioinformatics/btg435}, abstractNote={Abstract}, number={4}, journal={BIOINFORMATICS}, author={Chu, TM and Weir, BS and Wolfinger, RD}, year={2004}, month={Mar}, pages={500–506} }
 @article{stasolla_bozhkov_chu_van zyl_egertsdotter_suarez_craig_wolfinger_von arnold_sederoff_2004, title={Variation an transcript abundance during somatic embryogenesis in gymnosperms}, volume={24}, ISSN={["1758-4469"]}, DOI={10.1093/treephys/24.10.1073}, abstractNote={Somatic embryogenesis of Norway spruce (Picea abies L.) is a versatile model system to study molecular mechanisms regulating embryo development because it proceeds through defined developmental stages corresponding to specific culture treatments. Normal embryonic development involves early differentiation of proembryogenic masses (PEMs) into somatic embryos, followed by early and late embryogeny leading to the formation of mature cotyledonary embryos. In some cell lines there is a developmental arrest at the PEM-somatic embryo transition. To learn more about the molecular mechanisms regulating embryogenesis, we compared the transcript profiles of two normal lines and one developmentally arrested line. Ribonucleic acid, extracted from these cell lines at successive developmental stages, was analyzed on DNA microarrays containing 2178 expressed sequence tags (ESTs) (corresponding to 2110 unique cDNAs) from loblolly pine (Pinus taeda L.). Hybridization between spruce and pine species on microarrays has been shown to be effective (van Zyl et al. 2002, Stasolla et al. 2003). In contrast to the developmentally arrested line, the early phases of normal embryo development are characterized by a precise pattern of gene expression, i.e., repression followed by induction. Comparison of transcript levels between successive stages of embryogenesis allowed us to identify several genes that showed unique expression responses during normal development. Several of these genes encode proteins involved in detoxification processes, methionine synthesis and utilization, and carbohydrate metabolism. The potential role of these genes in embryo development is discussed.}, number={10}, journal={TREE PHYSIOLOGY}, author={Stasolla, C and Bozhkov, PV and Chu, TM and Van Zyl, L and Egertsdotter, U and Suarez, MF and Craig, D and Wolfinger, RD and Von Arnold, S and Sederoff, RR}, year={2004}, month={Oct}, pages={1073–1085} }
 @article{chu_weir_wolfinger_2002, title={A systematic statistical linear modeling approach to oligonucleotide array experiments}, volume={176}, ISSN={["0025-5564"]}, DOI={10.1016/S0025-5564(01)00107-9}, abstractNote={We outline and describe steps for a statistically rigorous approach to analyzing probe-level Affymetrix GeneChip data. The approach employs classical linear mixed models and operates on a gene-by-gene basis. Forgoing any attempts at gene presence or absence calls, the method simultaneously considers the data across all chips in an experiment. Primary output includes precise estimates of fold change (some as low as 1.1), their statistical significance, and measures of array and probe variability. The method can accommodate complex experiments involving many kinds of treatments and can test for their effects at the probe level. Furthermore, mismatch probe data can be incorporated in different ways or ignored altogether. Data from an ionizing radiation experiment on human cell lines illustrate the key concepts.}, number={1}, journal={MATHEMATICAL BIOSCIENCES}, author={Chu, TM and Weir, B and Wolfinger, R}, year={2002}, month={Mar}, pages={35–51} }