Kurt Zhang, PhD

Biography

Education and Training

• 1996 B.S., Biochemistry, Wuhan University, China
• 2004 M.S., Computer Science (Computational Biology), Kansas State University
• 2008 Ph.D., Statistics (Bioinformatics), Kansas State University

Research Interests

Dr. Zhang's long-term goal is to decode genetic events and molecular interactions of biological processes, and rigorously represent the complex molecular behaviors with mathematical models. We use advanced high-throughput technology and robust stochastic models to obtain the systematic picture of a biological process. Multiple types of omics data, such as microarray, RNA-seq, ChIP-seq, lipidomics and proteomics are collected through innovative study designs in animals and humans, and are modeled for integrative analysis. Using embryonic mouse as a model system, one of our current focuses is to untangle the spatial and dynamic gene-gene interaction networks during heart development, and illustrate how environmental factors introduce adverse molecular changes and morphological defects. We are also investigating the transgenerational epigenetic variations carried from overweight mother to the offspring, and how the change of lifestyles would prevent childhood obesity.

Selected Publications

1. H. Xu, M. Xiang, Y. Qin, H. Cheng, D. Chen, Q. Fu, K.K. Zhang, L. Xie. Tbx5 inhibits hedgehog signaling in determination of digit identity. Hum Mol Genet. 2019. PMID: 31373354
2. J. Liu, H. Cheng, M. Xiang, L. Zhou, B. Wu, I.P. Moskowitz, K.K. Zhang, L. Xie. Gata4 regulates hedgehog signaling and Gata6 expression for outflow tract development. PLoS Genet. 15(5):e1007711, 2019. PMID: 31120883.
3. Wang L, Sens DA, Garrett SH, Zhang K, Somji S, Voels B (2017) The unique C- and N-terminal sequences of metallothionein isoform 3 (MT3) mediate growth inhibition and vectorial active transport in MCF-7 cells transfected to express MT3. BMC Cancer, 17(1):369. PMID: 28545470
4. Zhou L, Liu J, Xiang M, Olson P, Guzetta A, Zhang K, Moskowitz I, Xie L (2017) Gata4 potenitates second heart field proliferation and Hedgehog signaling for cardiac septation. PNAS 114(8):1422-E1431. PMID: 28167794
5. Xie L, Zhang K, Rasmussen D, Wang J, Wu D, Roemmich NJ, Bundy A, Johnson WT, Claycombe K (2017) Effects of prenatal low protein and postnatal high fat diets on visceral adipose tissue macrophage phenotypes and IL-6 expression in Sparague Dawley rat offspring. PLoS One, 12(1):e0169581. PMID: 28141871
6. Rousova J, Kusler K, Liyanage D, Leadbetter M, dongari N, Zhang KK, Novikov A, Sauter ER, Kubatova A (2016) Determination of trans-resveratrol and its metabolites in rat serum using liquid chromatography with high-resolution time of flight mass spectrometry. J Chromatogr B Analyt Technol Biomed Life Sci, 1039:35-43.
7. Zhang KK, Xiang M, Zhou L, Liu J, Curry N, Suñer DH, Garcia-Pavia P, Zhang X, Wang Q, Xie L. (2016) Gene-network and familial analyses uncover a gene network involving Tbx5/Osr1/Pcsk6 interaction in the second heart field for atrial septation. Human Molecular Genetics, 25(6):1140-1151.
8. Fu Q, Olson P, Rasmussen D, Keith B, Williamson M, Zhang K, Xie L. (2016) A Short-Term Transition from a High-Fat Diet to a Normal-Fat Diet Before Pregnancy Exacerbates Female Mouse Offspring Obesity. International Journal of Obesity, 40(4):564-572.
9. Zhang W, et al. (2015) Comparison of RNA-Seq and microarray-based models for clinical endpoint prediction. Genome Biol 16:133.
10. Zhou L, Liu J, Olson P, Zhang K, Wynne J, Xie L (2015) Tbx5 and Osr1 interact to regulate posterior second heart field cell cycle progression for cardiac septation. J Mol Cell Cardiol (85):1-12.
11. Fu Q, Zhang KK*, Xie L*. (2014) A meta-analysis of case-control studies of high-fat diet and colorectal cancer. Am J Digest Dis. (2):127-135.
12. SEQC Consortium, et al. (2014) A comprehensive assessment of RNA-seq accuracy, reproducibility and information content by the Sequencing Quality Control Consortium, Nat Biotech, 32, 903-914.
13. Wang C et al. (2014) The concordance between RNA-seq and microarray data depends on chemical treatment and transcript abundance, Nat Biotech, 32, 926-932.
14. Qin W, Raatz S, Zhang K, Rosenberger T, Sauter ER. (2014) Polyunsaturated fatty acid content may be increased in the milk of women with pregnancy associated breast cancer.  Journal of Human Lactation, 30(4):420-424.
15. Garrett S, Somji S, Sens D, Zhang KK*. Prediction of the Number of Activated Genes in Multiple Independent Cd+2- and As+3-Induced Malignant Transformations of Human Urothelial Cells (UROtsa). PLOS ONE, 9(1):e85614.
16. Qin W, Zhang K, Clarke K, Weiland T, Sauter ER. (2014) Methylation and miRNA effects of resveratrol on mammary tumors vs. normal tissue.  Nutrition & Cancer, 66(2):270-277.
17. Xiong XR, Liang F, Li H, Mesik L, Zhang KK, Polley DB, Tao HW, Xiao Z, Zhang LI. (2013) Interaural Level Difference Dependent Gain Control and Synaptic Scaling Underlying Binaural Computation. Neuron, 79(4):738-753.
18. Wang SZ, Lbrahim LA, Kim YJ, Gibson DA, Leung HC, Yuan W, Zhang KK, Tao HW, Ma L, Zhang L. (2013) Slit/Robo Signaling Mediates Spatial Positioning of Spiral Ganglion Neurons during Development of Cochlear Innervation. J Neurosci, 33(30):12242-54.
19. Qin W, Zhang K, Kliethermes B, Amjad R, Clarke K and Sauter ER (2013). Differential expression of cancer-associated proteins in breast milk. Breastfeeding Medicine, 8(1):120-126.
20. Clarke K, Yang Y, Marsh R, Xie L, Zhang KK*. (2013) Comparative analysis of de novo transcriptome assembly. Sci China Life Sci, 56(2):156-62.
21. Garrett SH, Clarke K, Sens DA, Deng Y, Somji S, Zhang KK*. (2013) Short and long term gene expression variation and networking in human proximal tubule cells when exposed to cadmium. BMC Medical Genomics 6(Suppl 1):S2.
22. Arcaro KF, Browne EP, Qin W, Zhang K, Aderton DL, Sauter ER. (2012) Differential expression of cancer-related proteins in paired breast milk samples from women with breast cancer.  Journal of Human Lactation, 28(4), 543-546.
23. Xie L, Hoffmann AD, Durnicka-Turek O, Firedland-Little JM, Zhang K, Moskowitz IP. (2012) Tbx5-Hedgehog Molecular Networks Are Essential in the Second Heart Field for Atrial Septation. Developmental Cell 23, 280-291.
24. Qin W, Zhang K, Kliethermes B, Ruhlen R, Browne E, Arcaro K, and Sauter ER. (2012) Differential expression of cancer associated proteins in breast milk based on age at first full term pregnancy. BMC Cancer, 12:100.
25. Zhu W, Qin W, Zhang K, Rottinghaus GF, Chen Y-C, Kliethermes B, Sauter ER. (2012) Trans-resveratrol alters mammary promoter hypermethylation in women at increased risk for breast cancer. Nutr Cancer, 1-8.
26. Qin W, Gui G, Zhang K, Twelves D, Kliethermes B and Sauter ER. (2012) Proteins and carbohydrates in nipple aspirate fluid predict the presence of atypia and cancer in women requiring diagnoistic breast biopsy. BMC Cancer, 12:52.
27. Xie L, Weichel B, Ohm JE, Zhang K*. (2011) An integrative analysis of DNA methylation and RNA-Seq data for human heart, kidney and liver. BMC Systems Biology 5(Suppl 3):S4.
28. Zhang K*, Yang Y, Devanarayan V, Xie L, Deng Y, Sens D. (2011) A hidden Markov model-based algorithm for identifying tumor subtype using array CGH data. BMC Genomics 12(Suppl 5): S10.
29. Jiang F, Albert DH, Luo Y, Tapang P, Zhang K, Davidsen SK, Fox GB, Lesniewski RR and McKeegan EM. (2011) ABT-869, a multi-targeted receptor tyrosine kinase inhibitor, reduces tumor microvascularity and improves vascular wall integrity in preclinical tumor models. Journal of Pharmacology and Experimental Therapeutics, 338:134-142.
30. Zhang K*, Wang H, Batheke AC, Harrar SW, Piepho HP and Deng YP. (2011) Gene set analysis for longitudinal gene expression data. BMC Bioinformatics, 12:273.
31. Garrett SH, Somji S, Sens MA, Zhang K, and Sens DA. (2011) Microarray analysis of gene expression patterns in human proximal tubule cells over a short and long time course of cadmium exposure. Journal of Toxicology and Environmental Health 74, 24-42.
32. Lu X,  Zhang K, Sant CV, Coon J, and Semizarov D. (2010) An algorithm for classifying tumors based on genomic aberrations and selecting representative tumor models. BMC Medical Genomics 3:23.
33. Zhang K. and Wang H. (2010) Nonparametric tests for longitudinal array comparative genomic hybridization data. Statistics and Its Interface 3, 211-221.
34. Bathke AC, Harrar SW, Wang H, Zhang K, and Piepho HP. (2010) Series of randomized complete block experiments with non-normal data. Computational Statistics and Data Analysis 57(7), 1840-1857.