Bioinformatics; genetic factors in human diseases; gene expression analysis; methylation; non-coding RNA; metagenomics; medical, environmental and marine genomics; pharmacogenomics and computational drug discovery; machine learning and deep learning
My research involves computational methods to analyze, integrate, and interpret the various sources of biological data for the study of medical, marine, and environmental applications of genomics. I have been involved in a wide range of projects using next generation sequencing, de novo assembly, read mapping, functional annotation, common/rare variants, differential gene expression, and methylation. These bioinformatics analyses have been applied to many human diseases, including addiction, alcohol-induced liver diseases, obesity, longevity, and cancer.
Trina Norden-Krichmar is an Assistant Professor in the Department of Epidemiology at the University of California, Irvine. The goal of her research is to investigate the genomic factors influencing human health and disease. She has a B.S. in Biochemistry from University of Maryland, M.S. in Computer Science from George Washington University, and a Ph.D. in Marine Biology from the Scripps Institution of Oceanography at the University of California, San Diego. In addition to the laboratory skills acquired by her biological research, she also has over 15 years of experience working as a computer programmer at IBM, the National Institutes of Health, and the Salk Institute. She has experience performing bioinformatics analyses applied to projects involving RNA sequencing and gene expression microarrays, DNA sequencing and genotyping arrays, microRNAs, methylomics, proteomics, metagenomics, and metatranscriptomics. She teaches a Bioinformatics course at UC Irvine at both the graduate (EPIDEM 275) and undergraduate (PUBHLTH 119) levels.
Listopad, S., Magnan, C., Asghar, A., Stolz, A., Tayek, J.A., Liu, Z.X., Morgan, T.R., Norden-Krichmar, T.M. (2022) “Differentiating between liver diseases by applying multiclass machine learning approaches to transcriptomics of liver tissue or blood-based samples”, JHEP Reports, doi:10.1016/j.jhepr.2022.100560.
Lucia, R.M., Huang, W., Pathak, K.V., McGilvrey, M., David-Dirgo, V., Alvarez, A., Goodman, D., Masunaka, I., Odegaard, A. O., Ziogas, A., Pirrotte, P., Norden-Krichmar, T.M., and Park, H.L. (2022) “Association of glyphosate exposure with blood DNA methylation”, Environmental Health Perspectives, doi.org/10.1289/EHP10174.
Kakati, T., Bhattacharyya, D.K., Kalita, J.K., and Norden-Krichmar, T.M. (2022) “DEGNext: Classification of Differentially Expressed Genes from RNA-seq data using a Convolutional Neural Network with Transfer Learning”, BMC Bioinformatics, 23:17, doi:10.1186/s12859-021-04527-4.
Lucia, R.M., Huang, W., Alvarez, A., Masunaka, I., Ziogas, A., Goodman, D., Odegaard, A. O., Norden-Krichmar, T.M., and Park, H.L. (2021) “Association of mammographic density with blood DNA methylation”, Epigenetics, doi: 10.1080/15592294.2021.1928994.
Wan, J.Y., Goodman, D.L., Willems, E.L., Freedland, A.R., Norden-Krichmar, T.M. Santorico, S.A., and Edwards, K.L. (2021) “Genome-wide association analysis of metabolic syndrome quantitative traits in the GENNID multiethnic family study”, Diabetology & Metabolic Syndrome, https://doi.org/10.1186/s13098-021-00670-3.
Ryu, S., Han, J., Norden-Krichmar, T., Zhang, Q., Lee, S., Zhang, Z., Atzmon, G., Niedernhofer, L.J., Robbins, P.D., Barzilai, N., Schork, N.J., and Suh, Y. (2021) “Genetic signature of human longevity in PKC and NF-kappa B signaling”, Aging Cell, doi: 10.1111/acel.13362.
Widyastuti, H.P., Norden-Krichmar, T.M., Grosberg, A., and Zaragoza, M.V. (2020) “Gene expression profiling of fibroblasts in a family with LMNA-related cardiomyopathy reveals molecular pathways implicated in disease pathogenesis”, BMC Medical Genetics, 21, 152, doi.org/10.1186/s12881-020-01088-w.
Lucia, R.M., Huang, W., Alvarez, A., Thampy, D. , Elyasian, M., Hidajat, A., Yang, K., Forman, D., Pebdani, A., Masunaka, I., Brain, S., Heditsian, D., Lee, V., Goodman, D., Norden-Krichmar, T.M., Odegaard, A., Ziogas, A., and Park, H.L (2020) “Rationale, Study Design, and Cohort Characteristics for the Markers for Environmental Exposures (MEE) Study”, International Journal of Environmental Research and Public Health, 17, 1174, doi:10.3390/ijerph17051774.
Wan, J.Y., Catabay, C., Liem, A., Jeffrey, E., Norden-Krichmar, T.M., Goodman, D., Santorico, S.A., Edwards, K.L., and American Diabetes Association GENNID Study Group (2019) “Evidence for gene-smoking interactions for hearing loss and deafness in Japanese American families”, Hearing Research, 387, doi:10.1016/j.heares.2019.107875.
Listopad, S.A. and Norden-Krichmar, T.M. (2019) “A-Lister: A tool for analysis of differentially expressed -omics entities across multiple pairwise comparisons”, BMC Bioinformatics, 20, 595, doi:10.1186/s12859-019-3121-x.
Willems, E.L., Wan, J.Y., Norden-Krichmar, T.M., Edwards, K.L., and Santorico, S.A. (2019) “Trans-ethnic meta-analysis of metabolic syndrome in a multi-ethnic study” ”, Genetic Epidemiology, doi:10.1002/gepi.22267.
Ryu, S., Han, J., Norden-Krichmar, T.M., Schork, N.J., and Suh, Y. (2018) “Effective discovery of rare variants by pooled target capture sequencing: A comparative analysis with individually indexed target capture sequencing”, Mutation Research Fundamental and Molecular Mechanisms of Mutagenesis, 809:24-31, doi:10.1016/j.mrfmmm.2018.03.007.
Schomberg, J., Ziogas, A., Anton-Culver, H., and Norden-Krichmar, T. (2018) “Identification of a gene expression signature predicting survival in oral cavity squamous cell carcinoma using Monte Carlo cross validation”, Oral Oncology, 78:72-79, doi:10.1016/j.oraloncology.2018.01.012.
Norden-Krichmar, T.M., Gizer, I.R., Wilhelmsen, K.C., Schork, N.J., and Ehlers, C.L. (2015) “Variants near CCK receptors are associated with electrophysiological responses to pre-pulse startle stimuli in a Mexican American cohort”, Twin Research and Human Genetics, doi:10.1017/thg.2015.77.
Ishii, S., Suzuki, S., Tenney, A., Norden-Krichmar, T.M., Nealson, K.H., and Bretschger, O. (2015) “Microbial metabolic networks in complex electrogenic biofilm recovered from a stimulus-induced metatranscriptomics approach”, Scientific Reports, 5:14840, doi: 10.1038/srep14840.
Norden-Krichmar, T.M., Gizer, I.R., Wilhelmsen, K.C., Schork, N.J., and Ehlers, C.L. (2014) “Protective variant associated with alcohol dependence in a Mexican American cohort”, BMC Medical Genetics, 15:136, doi:10.1186/s12881-014-0136-z.
Norden-Krichmar, T.M., Gizer, I.R., Libiger, O., Wilhelmsen, K.C., Ehlers, C.L., and Schork, N.J. (2014) “Correlation analysis of genetic admixture and social identification with body mass index in a Native American community”, American Journal of Human Biology, doi:10.1002/ajhb.22521.
Ishii, S., Suzuki, S., Norden-Krichmar, T.M., Phan, T., Wanger, G., Nealson, K.H., Sekiguchi, Y., Gorby, Y.A., and Bretschger, O. (2013) “Microbial population and functional dynamics associated with surface potential and carbon metabolism”, International Society of Microbial Ecology (ISME) Journal, doi:10.1038/ismej.2013.217.
Ishii, S., Suzuki, S., Norden-Krichmar, T.M., Wu, A., Yamanaka, Y., Nealson, K.H., and Bretschger, O. (2013) “Identifying the microbial communities and operational conditions for optimized wastewater treatment in microbial fuel cells”, Water Research Journal, 47:7120-7130, doi:10.1016/j.watres.2013.07.048.
Ishii, S., Suzuki, S., Norden-Krichmar, T.M., Tenney, A., Chain P.S.G., Scholz, M., Nealson, K.H., and Bretschger, O. (2013) “A novel metatranscriptomic approach to identify gene expression dynamics during extracellular electron transfer”, Nature Communications 4:1601, doi:10.1038/ncomms2615.
Shrestha, R.P., Tesson, B., Norden-Krichmar, T.M., Federowicz, S., Hildebrand, M. and Allen, A.E. (2012) ”Whole transcriptome analysis of the silicon response of the diatom Thalassiosira pseudonana” BMC Genomics, 13:499, doi:10.1186/1471-2164-13-499.
Bertrand, E.M., Allen, A.E., Dupont, C.L., Norden-Krichmar, T.M., Bai, J., Valas, R.E. and Saito, M.A. (2012) "Influence of cobalamin scarcity on diatom molecular physiology and identification of a cobalamin acquisition protein" PNAS, doi:10.1073/pnas.1201731109.
Ishii, S., Suzuki, S., Norden-Krichmar, T.M., Nealson, K.H., Sekiguchi, Y., Gorby, Y.A., Bretschger, O. (2012) “Functionally stable and phylogenetically diverse microbial enrichments from microbial fuel cells during wastewater treatment” PLoS ONE 7(2): e30495, doi:10.1371/journal.pone.0030495.
Norden-Krichmar, T.M., Allen, A.E., Gaasterland, T., and Hildebrand, M. (2011) “Characterization of the small RNA transcriptome of the diatom, Thalassiosira pseudonana” PLoS ONE 6(8): e22870, doi:10.1371/journal.pone.0022870.
Norden-Krichmar, T.M., Holtz, J., Pasquinelli, A.E., and Gaasterland, T. (2007) “Computational prediction and experimental validation of Ciona intestinalis microRNA genes” BMC Genomics, 8: 445.