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Tzu-Ming Chu, Ph.D. - Publications

Affiliations: 
2002 North Carolina State University, Raleigh, NC 
Area:
Biostatistics Biology, Genetics
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23 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2015 Zhang W, Yu Y, Hertwig F, Thierry-Mieg J, Zhang W, Thierry-Mieg D, Wang J, Furlanello C, Devanarayan V, Cheng J, Deng Y, Hero B, Hong H, Jia M, Li L, ... ... Chu TM, et al. Comparison of RNA-seq and microarray-based models for clinical endpoint prediction. Genome Biology. 16: 133. PMID 26109056 DOI: 10.1186/S13059-015-0694-1  0.365
2014 Black MB, Parks BB, Pluta L, Chu TM, Allen BC, Wolfinger RD, Thomas RS. Comparison of microarrays and RNA-seq for gene expression analyses of dose-response experiments. Toxicological Sciences : An Official Journal of the Society of Toxicology. 137: 385-403. PMID 24194394 DOI: 10.1093/Toxsci/Kft249  0.407
2013 Wetmore BA, Wambaugh JF, Ferguson SS, Li L, Clewell HJ, Judson RS, Freeman K, Bao W, Sochaski MA, Chu TM, Black MB, Healy E, Allen B, Andersen ME, Wolfinger RD, et al. Relative impact of incorporating pharmacokinetics on predicting in vivo hazard and mode of action from high-throughput in vitro toxicity assays. Toxicological Sciences : An Official Journal of the Society of Toxicology. 132: 327-46. PMID 23358191 DOI: 10.1093/Toxsci/Kft012  0.302
2012 Thomas RS, Black MB, Li L, Healy E, Chu TM, Bao W, Andersen ME, Wolfinger RD. A comprehensive statistical analysis of predicting in vivo hazard using high-throughput in vitro screening. Toxicological Sciences : An Official Journal of the Society of Toxicology. 128: 398-417. PMID 22543276 DOI: 10.1093/Toxsci/Kfs159  0.437
2012 Thomas RS, Black MB, Li L, Healy E, Chu T, Bao W, Andersen ME, Wolfinger RD. Response to “Incorporating Biological, Chemical, and Toxicological Knowledge Into Predictive Models of Toxicity” Toxicological Sciences. 130: 442-443. DOI: 10.1093/Toxsci/Kfs284  0.39
2011 Hsieh WP, Chu TM, Lin YM, Wolfinger RD. Kernel density weighted loess normalization improves the performance of detection within asymmetrical data. Bmc Bioinformatics. 12: 222. PMID 21631915 DOI: 10.1186/1471-2105-12-222  0.421
2010 Shi L, Campbell G, Jones WD, Campagne F, Wen Z, Walker SJ, Su Z, Chu TM, Goodsaid FM, Pusztai L, Shaughnessy JD, Oberthuer A, Thomas RS, Paules RS, Fielden M, et al. The MicroArray Quality Control (MAQC)-II study of common practices for the development and validation of microarray-based predictive models. Nature Biotechnology. 28: 827-38. PMID 20676074 DOI: 10.1038/Nbt.1665  0.529
2009 Thomas RS, Bao W, Chu TM, Bessarabova M, Nikolskaya T, Nikolsky Y, Andersen ME, Wolfinger RD. Use of short-term transcriptional profiles to assess the long-term cancer-related safety of environmental and industrial chemicals. Toxicological Sciences : An Official Journal of the Society of Toxicology. 112: 311-21. PMID 19776212 DOI: 10.1093/Toxsci/Kfp233  0.476
2008 Shi L, Jones WD, Jensen RV, Harris SC, Perkins RG, Goodsaid FM, Guo L, Croner LJ, Boysen C, Fang H, Qian F, Amur S, Bao W, Barbacioru CC, Bertholet V, ... ... Chu TM, et al. The balance of reproducibility, sensitivity, and specificity of lists of differentially expressed genes in microarray studies. Bmc Bioinformatics. 9: S10. PMID 18793455 DOI: 10.1186/1471-2105-9-S9-S10  0.324
2008 Ascencio-Ibáñez JT, Sozzani R, Lee TJ, Chu TM, Wolfinger RD, Cella R, Hanley-Bowdoin L. Global analysis of Arabidopsis gene expression uncovers a complex array of changes impacting pathogen response and cell cycle during geminivirus infection. Plant Physiology. 148: 436-54. PMID 18650403 DOI: 10.1104/Pp.108.121038  0.343
2007 Adomas A, Heller G, Li G, Olson A, Chu TM, Osborne J, Craig D, van Zyl L, Wolfinger R, Sederoff R, Dean RA, Stenlid J, Finlay R, Asiegbu FO. Transcript profiling of a conifer pathosystem: response of Pinus sylvestris root tissues to pathogen (Heterobasidion annosum) invasion. Tree Physiology. 27: 1441-58. PMID 17669735 DOI: 10.1093/Treephys/27.10.1441  0.377
2007 Hsieh W, Chu T, Wolfinger R. Comparison of statistical performance of univariate and bivariate mixed models for Affymetrix® probe level data Journal of Statistical Computation and Simulation. 77: 251-264. DOI: 10.1080/10629360600826398  0.445
2007 Shi L, Jones WD, Jensen RV, Harris SC, Perkins RG, Goodsaid FM, Guo L, Croner LJ, Boysen C, Fang H, Amur S, Bao W, Barbacioru CC, Bertholet V, Cao XM, ... Chu T, et al. The Reproducibility of Lists of Differentially Expressed Genes in Microarray Studies Nature Precedings. 2: 1-1. DOI: 10.1038/Npre.2007.306.1  0.396
2006 Shi L, Reid LH, Jones WD, Shippy R, Warrington JA, Baker SC, Collins PJ, de Longueville F, Kawasaki ES, Lee KY, Luo Y, Sun YA, Willey JC, Setterquist RA, ... ... Chu TM, et al. The MicroArray Quality Control (MAQC) project shows inter- and intraplatform reproducibility of gene expression measurements. Nature Biotechnology. 24: 1151-61. PMID 16964229 DOI: 10.1038/Nbt1239  0.363
2006 Patterson TA, Lobenhofer EK, Fulmer-Smentek SB, Collins PJ, Chu TM, Bao W, Fang H, Kawasaki ES, Hager J, Tikhonova IR, Walker SJ, Zhang L, Hurban P, de Longueville F, Fuscoe JC, et al. Performance comparison of one-color and two-color platforms within the MicroArray Quality Control (MAQC) project. Nature Biotechnology. 24: 1140-50. PMID 16964228 DOI: 10.1038/Nbt1242  0.419
2006 Tong W, Lucas AB, Shippy R, Fan X, Fang H, Hong H, Orr MS, Chu TM, Guo X, Collins PJ, Sun YA, Wang SJ, Bao W, Wolfinger RD, Shchegrova S, et al. Evaluation of external RNA controls for the assessment of microarray performance. Nature Biotechnology. 24: 1132-9. PMID 16964227 DOI: 10.1038/Nbt1237  0.318
2006 Kazmin D, Prytkova T, Cook CE, Wolfinger R, Chu TM, Beratan D, Norris JD, Chang CY, McDonnell DP. Linking ligand-induced alterations in androgen receptor structure to differential gene expression: A first step in the rational design of selective androgen receptor modulators Molecular Endocrinology. 20: 1201-1217. PMID 16574741 DOI: 10.1210/Me.2005-0309  0.357
2004 Yu X, Chu TM, Gibson G, Wolfinger RD. A mixed model approach to identify yeast transcriptional regulatory motifs via microarray experiments. Statistical Applications in Genetics and Molecular Biology. 3: Article22. PMID 16646801 DOI: 10.2202/1544-6115.1045  0.434
2004 Stasolla C, Bozhkov PV, Chu TM, Van Zyl L, Egertsdotter U, Suarez MF, Craig D, Wolfinger RD, Von Arnold S, Sederoff RR. Variation in transcript abundance during somatic embryogenesis in gymnosperms. Tree Physiology. 24: 1073-85. PMID 15294754 DOI: 10.1093/Treephys/24.10.1073  0.326
2004 Chu TM, Deng S, Wolfinger R, Paules RS, Hamadeh HK. Cross-site comparison of gene expression data reveals high similarity. Environmental Health Perspectives. 112: 449-55. PMID 15033594 DOI: 10.1289/Ehp.6787  0.447
2004 Chu TM, Weir BS, Wolfinger RD. Comparison of Li-Wong and loglinear mixed models for the statistical analysis of oligonucleotide arrays. Bioinformatics (Oxford, England). 20: 500-6. PMID 14990445 DOI: 10.1093/Bioinformatics/Btg435  0.596
2003 Hsieh WP, Chu TM, Wolfinger RD, Gibson G. Mixed-model reanalysis of primate data suggests tissue and species biases in oligonucleotide-based gene expression profiles. Genetics. 165: 747-57. PMID 14573485  0.309
2002 Chu TM, Weir B, Wolfinger R. A systematic statistical linear modeling approach to oligonucleotide array experiments Mathematical Biosciences. 176: 35-51. PMID 11867082 DOI: 10.1016/S0025-5564(01)00107-9  0.549
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