Nicholas Panchy

Current: Research Consultant, Michigan State University

Previous: Postdoctoral Fellow, Department of Biochemistry and Cellular and Molecular Biology (BCMB)

Education & Training

Postdoctoral Fellow          National Institute for Mathematical and Biological Synthesis (Nick at NIMBioS)

Ph.D.      Genetics, Michigan State University

B.S.   Mathematics, University of North Carolina, Chapel Hill

B.S.   Biology University of North Carolina, Chapel Hill


Research

Nick Panchy is exploring the role and regulation of intermediate epithelial-to-mesenchymal transition (EMT) cell-types by modeling gene regulatory networks controlling expression across EMT.


Publications

Groves SM, Panchy N, Tyson DR, Harris LA, Quaranta V, Hong T. Involvement of epithelial-mesenchymal transition genes in small cell lung cancer phenotypic plasticity. Cancers 2023, 15(5):1477
[Link] [Article]

Willems A, Panchy N, Hong T. Using single-cell RNA sequencing and microRNA targeting data to improve colorectal cancer survival prediction. Cells 2023, 12(2):228
[Link] [Article]

Panchy N, Watanabe K, Takahashi M, Willems A, Hong T. Comparative single-cell transcriptomes of dose and time dependent epithelial–mesenchymal spectrums. NAR Genom Bioinform 2022, 4(3):lqac072 (Editor’s choice)
[Link] [Article]

Panchy N, Watanabe K, Hong T. Interpretable, scalable, and transferrable functional projection of large-scale transcriptome data using constrained matrix decomposition. Front Genet 2021, 12:719099
[Link] [Article]

Panchy N, von Arnim A, Hong T. Early Detection of Daylengths with a Feedforward Circuit Coregulated by Circadian and Diurnal Cycles. Biophys J 2020, 119(9):1878
[Link] [Article]

Panchy N, Azeredo-Tseng C, Luo M, Randall N, Hong T. Integrative transcriptomic analysis reveals a multiphasic epithelial–mesenchymal spectrum in cancer and non-tumorigenic cells. Front Oncol 2020, 9:1479  
[Link] [Article]

Watanabe K*, Panchy N*, Noguchi S, Suzuki H, Hong T. Combinatorial perturbation analysis reveals divergent regulations of mesenchymal genes during epithelial-to-mesenchymal transition. NPJ Syst Biol Appl. 2019 Jun 14; 5:21. (* Co-first author)
[Link] [Article]

Panchy NL, Azodi CB, Winship EF, O’Malley RC, Shiu SH. Expression and regulatory asymmetry of retained Arabidopsis thaliana transcription factor genes derived from whole genome duplication. BMC Evol Biol. 2019 Mar 13; 19(1):77. doi: 10.1186/s12862-019-1398-z.  

Law M, Childs KL, Campbell MS, Stein JC, Olson AJ, Holt C, Panchy N, Lei J, Jiao D, Andorf CM, Lawrence CJ, Ware D, Shiu SH, Sun Y, Jiang N, Yandell M. Automated update, revision, and quality control of the maize genome annotations using MAKER-P improves the B73 RefGen_v3 gene models and identifies new genes. Plant Physiol. 2015 Jan; 167(1):25-39. doi: 10.1104/pp.114.245027.  

Poliner E, Panchy N, Newton L, Wu G, Lapinsky A, Bullard B, Zienkiewicz A, Benning C, Shiu SH, Farré EM. Transcriptional coordination of physiological responses in Nannochloropsis oceanica CCMP1779 under light/dark cycles. Plant J. 2015 Sep; 83(6):1097-113. doi: 10.1111/tpj.12944.  

Panchy N, Wu G, Newton L, Tsai CH, Chen J, Benning C, Farré EM, Shiu SH. Prevalence, evolution, and cis-regulation of diel transcription in Chlamydomonas reinhardtii. G3 (Bethesda). 2014 Oct 28;4(12):2461-71. doi: 10.1534/g3.114.015032.  

Wang P, Moore BM, Panchy NL, Meng F, Lehti-Shiu MD, Shiu SH. Factors Influencing Gene Family Size Variation Among Related Species in a Plant Family, Solanaceae. Genome Biol Evol. 2018 Oct 1; 10(10):2596-2613. doi: 10.1093/gbe/evy193.  

Liu MJ, Sugimoto K, Uygun S, Panchy N, Campbell MS, Yandell M, Howe GA, Shiu SH. Regulatory Divergence in Wound-Responsive Gene Expression between Domesticated and Wild Tomato. Plant Cell. 2018 Jul; 30(7):1445-1460. doi: 10.1105/tpc.18.00194.  

Lloyd JP, Tsai ZT, Sowers RP, Panchy NL, Shiu SH. A Model-Based Approach for Identifying Functional Intergenic Transcribed Regions and Noncoding RNAs. Mol Biol Evol. 2018 Jun 1;35(6):1422-1436. doi: 10.1093/molbev/msy035.  

Lehti-Shiu MD, Panchy N, Wang P, Uygun S, Shiu SH. Diversity, expansion, and evolutionary novelty of plant DNA-binding transcription factor families. Biochim Biophys Acta Gene Regul Mech. 2017 Jan;1860(1):3-20. doi: 10.1016/j.bbagrm.2016.08.005.  

Panchy N, Lehti-Shiu M, Shiu SH. Evolution of Gene Duplication in Plants. Plant Physiol. 2016 Aug; 171(4):2294-316. doi: 10.1104/pp.16.00523.