RICKY CHAN, PHD
Director of the Computational Biology Core
E. Ricky Chan, PhD, is a Research Scientist and Director of the Computational Biology Core. His focus for the core is to provide a gateway for labs seeking assistance in the field of bioinformatics and computational analysis. This need has grown tremendously as additional research projects are leveraging the use of next-generation sequencing methods but lack the computational expertise to handle large datasets. Dr. Chan received his Ph.D. from Case Western Reserve University under the mentorship of Dr. Mark Adams, mapping ENU-induced mutations in mouse models of blood disorders, uncovering a recessive mutation in the TPO receptor that leads to thrombocytopenia with over-dominance. He continued his training as a post-doctoral fellow with Dr. David Serre at the Cleveland Clinic where his focus was on the genomic characterization of the malarial parasite Plasmodium vivax, revealing a common duplication of the Duffy binding protein in Malagasy individuals which may be involved in the uncanny observation of P. vivax infecting Duffy negative individuals in that region. During his post-doc training Dr. Chan also developed and implemented a novel method and pipeline for the characterization of microbiome data using 16s sequencing in several disease models and studies including colon cancer, metabolic uptake, and restoration of colonization resistance of nosocomial pathogens after antimicrobial treatment. From these highly collaborative experiences Dr. Chan has become an expert in the processing and analysis of next-generation sequencing data. As the director of the Computational Biology core he continues to develop and test new genomic and computational tools to assist in various research studies including but not limited to infectious disease, cancer, metabolism, and the microbiome. Please contact Dr. Chan if you have a project requiring analytical assistance with next-generation sequencing data including whole genome or exome sequencing, RNA-Seq, locus-specific sequencing, SNP and variant detection and comparative genomics.
- Fan, L, Lesser, AF, Sweet, DR, Keerthy, KS, Lu, Y, Chan, ER, Vinayachandran, V, Ilkayeva, O, Das, T, Newgard, CB et al.. KLF15 controls brown adipose tissue transcriptional flexibility and metabolism in response to various energetic demands. iScience 2022; 25 (11): 105292. PubMed PMID:36304102 PubMed Central PMC9593730.
- Chan, ER, Jones, LD, Linger, M, Kovach, JD, Torres-Teran, MM, Wertz, A, Donskey, CJ, Zimmerman, PA. COVID-19 infection and transmission includes complex sequence diversity. PLoS Genet 2022; 18 (9): e1010200. PubMed PMID:36074769 PubMed Central PMC9455841.
- Chan, ER, Lee, J, Meyerson, H, Merkulova, A, Smith, S, Lin, F, Cho, JS, Schmaier, AH. Vascular surgery patients with elevated neutrophil lymphocyte ratios have downregulated neutrophil complement RNA expression. Blood Adv 2022; : . PubMed PMID:36006440 .
- Song, S, Regan, B, Ereifej, ES, Chan, ER, Capadona, JR. Neuroinflammatory Gene Expression Analysis Reveals Pathways of Interest as Potential Targets to Improve the Recording Performance of Intracortical Microelectrodes. Cells 2022; 11 (15): . PubMed PMID:35954192 PubMed Central PMC9367362.
- Sergeeva, O, Zhang, Y, Julian, W, Sasikumar, A, Awadallah, A, Kenyon, J, Shi, W, Sergeev, M, Huang, S, Sexton, S et al.. Imaging of Tumor-Associated Vascular Prostate-Specific Membrane Antigen in Woodchuck Model of Hepatocellular Carcinoma. Gastro Hep Adv 2022; 1 (4): 631-639. PubMed PMID:35844243 PubMed Central PMC9280909.
- Massey, W, Osborn, LJ, Banerjee, R, Horak, A, Fung, KK, Orabi, D, Chan, ER, Sangwan, N, Wang, Z, Brown, JM et al.. Flavin-Containing Monooxygenase 3 (FMO3) Is Critical for Dioxin-Induced Reorganization of the Gut Microbiome and Host Insulin Sensitivity. Metabolites 2022; 12 (4): . PubMed PMID:35448550 PubMed Central PMC9029240.
- Chan, ER, Mehlotra, RK, Pirani, KA, Ratsimbasoa, AC, Williams, SM, Gaedigk, A, Zimmerman, PA. CYP2D6 gene resequencing in the Malagasy, a population at the crossroads between Asia and Africa: a pilot study. Pharmacogenomics 2022; 23 (5): 315-325. PubMed PMID:35230160 PubMed Central PMC8965795.
- Jones, LD, Chan, ER, Cadnum, JL, Redmond, SN, Navas, ME, Zabarsky, TF, Eckstein, EC, Kovach, JD, Linger, M, Zimmerman, PA et al.. Investigation of a cluster of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections in a hospital administration building. Infect Control Hosp Epidemiol 2022; : 1-7. PubMed PMID:35189996 .
- O'Neill, WQ, Xie, X, Gui, S, Yu, H, Davenport, J, Cartwright, T, Storl-Desmond, M, Ryu, E, Chan, ER, Cao, S et al.. Repositioning Fenofibrate to Reactivate p53 and Reprogram the Tumor-Immune Microenvironment in HPV+ Head and Neck Squamous Cell Carcinoma. Cancers (Basel) 2022; 14 (2): . PubMed PMID:35053444 PubMed Central PMC8773501.
- Rana, N, Privitera, G, Kondolf, HC, Bulek, K, Lechuga, S, De Salvo, C, Corridoni, D, Antanaviciute, A, Maywald, RL, Hurtado, AM et al.. GSDMB is increased in IBD and regulates epithelial restitution/repair independent of pyroptosis. Cell 2022; 185 (2): 283-298.e17. PubMed PMID:35021065 PubMed Central PMC8879997.