Publications – Chapkin Lab Home

Roitershtein, A, Rastegar, R, Chapkin, RS, Ivanov, I. Extinction scenarios in evolutionary processes: a multinomial Wright-Fisher approach. J Math Biol. 2023;87 (4):63. doi: 10.1007/s00285-023-01993-7. PubMed PMID:37751048 .
Erazo-Oliveras, A, Muñoz-Vega, M, Mlih, M, Thiriveedi, V, Salinas, ML, Rivera-Rodríguez, JM et al.. Mutant APC reshapes Wnt signaling plasma membrane nanodomains by altering cholesterol levels via oncogenic β-catenin. Nat Commun. 2023;14 (1):4342. doi: 10.1038/s41467-023-39640-w. PubMed PMID:37468468 PubMed Central PMC10356786.
Yang, Y, Li, G, Zhong, Y, Xu, Q, Chen, BJ, Lin, YT et al.. Gene knockout inference with variational graph autoencoder learning single-cell gene regulatory networks. Nucleic Acids Res. 2023;51 (13):6578-6592. doi: 10.1093/nar/gkad450. PubMed PMID:37246643 PubMed Central PMC10359630.
Lee, M, Upadhyay, S, Mariyam, F, Martin, G, Hailemariam, A, Lee, K et al.. Flavone and Hydroxyflavones Are Ligands That Bind the Orphan Nuclear Receptor 4A1 (NR4A1). Int J Mol Sci. 2023;24 (9):. doi: 10.3390/ijms24098152. PubMed PMID:37175855 PubMed Central PMC10179475.
Debler, RA, Madison, CA, Hillbrick, L, Gallegos, P, Safe, S, Chapkin, RS et al.. Selective aryl hydrocarbon receptor modulators can act as antidepressants in obese female mice. J Affect Disord. 2023;333 :409-419. doi: 10.1016/j.jad.2023.04.044. PubMed PMID:37084978 .
Turner, ND, Chapkin, RS. Biography of Joanne R Lupton (1944-2020). J Nutr. 2022;152 (4):914-916. doi: 10.1093/jn/nxac022. PubMed PMID:36967178 .
McLeod, A, Wolf, P, Chapkin, RS, Davidson, LA, Ivanov, I, Berbaum, M et al.. Design of the Building Research in CRC prevention (BRIDGE-CRC) trial: a 6-month, parallel group Mediterranean diet and weight loss randomized controlled lifestyle intervention targeting the bile acid-gut microbiome axis to reduce colorectal cancer risk among African American/Black adults with obesity. Trials. 2023;24 (1):113. doi: 10.1186/s13063-023-07115-4. PubMed PMID:36793105 PubMed Central PMC9930092.
Yang, Y, Li, G, Zhong, Y, Xu, Q, Lin, YT, Roman-Vicharra, C et al.. scTenifoldXct: A semi-supervised method for predicting cell-cell interactions and mapping cellular communication graphs. Cell Syst. 2023;14 (4):302-311.e4. doi: 10.1016/j.cels.2023.01.004. PubMed PMID:36787742 PubMed Central PMC10121998.
Safe, S, Kothari, J, Hailemariam, A, Upadhyay, S, Davidson, LA, Chapkin, RS et al.. Health Benefits of Coffee Consumption for Cancer and Other Diseases and Mechanisms of Action. Int J Mol Sci. 2023;24 (3):. doi: 10.3390/ijms24032706. PubMed PMID:36769029 PubMed Central PMC9916720.
Muthyala, S, Chapkin, RS, Wu, C, Wu, CS. Ghrelin Alleviates Experimental Ulcerative Colitis in Old Mice and Modulates Colonocyte Metabolism via PPARγ Pathway. Int J Mol Sci. 2022;24 (1):. doi: 10.3390/ijms24010565. PubMed PMID:36614012 PubMed Central PMC9820475.
Madison, CA, Hillbrick, L, Kuempel, J, Albrecht, GL, Landrock, KK, Safe, S et al.. Intestinal epithelium aryl hydrocarbon receptor is involved in stress sensitivity and maintaining depressive symptoms. Behav Brain Res. 2023;440 :114256. doi: 10.1016/j.bbr.2022.114256. PubMed PMID:36528169 PubMed Central PMC9839636.
Sveeggen, TM, Abbey, CA, Smith, RL, Salinas, ML, Chapkin, RS, Bayless, KJ et al.. Annexin A2 modulates phospholipid membrane composition upstream of Arp2 to control angiogenic sprout initiation. FASEB J. 2023;37 (1):e22715. doi: 10.1096/fj.202201088R. PubMed PMID:36527391 .
Erazo-Oliveras, A, Muñoz-Vega, M, Salinas, ML, Wang, X, Chapkin, RS. Dysregulation of cellular membrane homeostasis as a crucial modulator of cancer risk. FEBS J. 2022; :. doi: 10.1111/febs.16665. PubMed PMID:36282100 PubMed Central PMC10126207.
Madison, CA, Debler, RA, Vardeleon, NI, Hillbrick, L, Jayaraman, A, Safe, S et al.. Sex-dependent differences in the stress mitigating and antidepressant effects of selective aryl hydrocarbon receptor modulators. J Affect Disord. 2022;319 :213-220. doi: 10.1016/j.jad.2022.09.155. PubMed PMID:36206882 PubMed Central PMC10391660.
Schoeller, A, Karki, K, Jayaraman, A, Chapkin, RS, Safe, S. Short chain fatty acids exhibit selective estrogen receptor downregulator (SERD) activity in breast cancer. Am J Cancer Res. 2022;12 (7):3422-3436. . PubMed PMID:35968335 PubMed Central PMC9360213.
Park, H, Jin, UH, Martin, G, Chapkin, RS, Davidson, LA, Lee, K et al.. Structure-activity relationships among mono- and dihydroxy flavones as aryl hydrocarbon receptor (AhR) agonists or antagonists in CACO2 cells. Chem Biol Interact. 2022;365 :110067. doi: 10.1016/j.cbi.2022.110067. PubMed PMID:35917944 PubMed Central PMC9667734.
Mullens, DA, Ivanov, I, Hullar, MAJ, Randolph, TW, Lampe, JW, Chapkin, RS et al.. Personalized Nutrition Using Microbial Metabolite Phenotype to Stratify Participants and Non-Invasive Host Exfoliomics Reveal the Effects of Flaxseed Lignan Supplementation in a Placebo-Controlled Crossover Trial. Nutrients. 2022;14 (12):. doi: 10.3390/nu14122377. PubMed PMID:35745107 PubMed Central PMC9230005.
Osorio, D, Zhong, Y, Li, G, Xu, Q, Yang, Y, Tian, Y et al.. scTenifoldKnk: An efficient virtual knockout tool for gene function predictions via single-cell gene regulatory network perturbation. Patterns (N Y). 2022;3 (3):100434. doi: 10.1016/j.patter.2022.100434. PubMed PMID:35510185 PubMed Central PMC9058914.
Madison, CA, Kuempel, J, Albrecht, GL, Hillbrick, L, Jayaraman, A, Safe, S et al.. 3,3'-Diindolylmethane and 1,4-dihydroxy-2-naphthoic acid prevent chronic mild stress induced depressive-like behaviors in female mice. J Affect Disord. 2022;309 :201-210. doi: 10.1016/j.jad.2022.04.106. PubMed PMID:35461819 PubMed Central PMC9153281.
Turner, ND, Chapkin, RS. Biography of Joanne R Lupton (1944-2020). J Nutr. 2022;152 (4):914-916. doi: 10.1093/jn/nxac022. PubMed PMID:35091750 .

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