Norden-Krichmar Lab

University of California, Irvine

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Publications

  • Kaplan, D.E., Teerlink, C.C., Schwantes-An, T., Norden-Krichmar, T.M., DuVall, S.L., Morgan, T.R., Tsao, P.S., Voight, B.M., Lynch, J.A., Vujkovic, M., and Chang, K,M. (2024) “Clinical and genetic risk factors for progressive fibrosis in metabolic dysfunction–associated steatotic liver disease”, Hepatology Communications, 8(7):e0487, doi.org/10.1097/HC9.0000000000000487.
  • Listopad, S., Magnan, C., Day, L.Z., Asghar, A., Stolz, A., Tayek, J.A., Liu, Z.X., Jacobs, J.M., Morgan, T.R., Norden-Krichmar, T.M.  (2024) “Identification of integrated proteomics and transcriptomics signature of alcohol-associated liver disease using machine learning”, PLOS Digital Health, 3(2), doi.org/10.1371/journal.pdig.0000447.
  • Liu, X., Liu, Z.X., Morgan, T.R., and Norden-Krichmar, T.M.  (2023) Single-cell transcriptomics of peripheral blood mononuclear cells indicates impaired immune and inflammatory responses in alcohol-associated hepatitis. Human Immunology, doi.org/10.1016/j.humimm.2023.110735
  • Thangavelu, C.S. and Norden-Krichmar, T.M. (2023) Integrative Meta-Analysis during Induced Pluripotent Stem Cell Reprogramming Reveals Conserved Networks and Chromatin Accessibility Signatures in Human and Mouse.  BioMedInformatics, 3, 1015-1039, doi.org/10.3390/biomedinformatics3040061
  • Norden-Krichmar, T. M., Rotroff, D., Schwantes-An, T. H., Bataller, R., Goldman, D., Nagy, L. E., and Liangpunsakul, S. (2023) Genomic approaches to explore susceptibility and pathogenesis of alcohol use disorder and alcohol-associated liver disease. Hepatology, 10-1097, doi.org/10.1097/HEP.0000000000000617
  • Wan, J.Y., Goodman, D., Makhnoon, S., Norden-Krichmar, T.M., Wu, B., and Edwards, K.L. (2023) Heterogeneity in familial clustering of metabolic syndrome components in the multiethnic GENNID study. Obesity (Silver Spring), 1-11, doi:10.1002/oby.23914
  • Leaks, K., Norden-Krichmar, T. and Brody, J.P. (2023) Predicting moderate drinking behaviors in National Health and Nutrition Examination Survey participants using biochemical and demographical factors with machine learning. Alcohol, 113, pp.1-10, doi.org/10.1016/j.alcohol.2023.07.005
  • Lucia, R.M., Liao, X., Huang, W.L., Forman, D., Kim, A., Ziogas, A., Norden-Krichmar, T.M., Goodman, D., Alvarez, A., Masunaka, I., Pathak, K.V., McGilvrey, M., Hegde, A.M., Pirrotte, P., and Park, H.L. (2023). Urinary glyphosate and AMPA levels in a cross-sectional study of postmenopausal women: Associations with organic eating behavior and dietary intake. International journal of hygiene and environmental health, 252, 114211, doi.org/10.1016/j.ijheh.2023.114211
  • Argemi, J., Kedia, K., Gritsenko, M.A., Clemente-Sanchez, A., Asghar, A., Herranz, J.M., Liu, Z.X., Atkinson, S.R., Smith, R.D., Norden-Krichmar, T.M., Day, L.Z., Stolz, A., Tayek, J.A., Bataller, R., Morgan, T.R., Jacobs, J.M., the Southern California Alcoholic Hepatitis Consortium and the InTeam Consortium. (2022) “Integrated Transcriptomic and Proteomic Analysis Identifies Plasma Biomarkers of Hepatocellular Failure in Alcohol-Associated Hepatitis”, The American Journal of Pathology, https://doi.org/10.1016/j.ajpath.2022.08.009.
  • 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: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, doi: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-κB 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: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.
  • 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.
  • 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.
  • 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, doi:10.1186/1471-2164-8-445.
  • Degtyarenko, A.M., Simon, E.S., Norden-Krichmar, T., and Burke, R.E. (1998) “Modulation of oligosynaptic cutaneous and muscle afferent reflex pathways during fictive locomotion and scratching in the cat”. Neurophysiology, 79(1), p. 447-463.
  • Ward, K.B., Perozzo, M.A., and Norden, T.M. (1986) “Precession photography of protein single crystals”. National Synchrotron Light Source Annual Report, ed. by S. White-DePace and N. Gmur, BNL 52045 UC-13, Brookhaven National Laboratory, New York, p. 471-2.