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.

Affiliations

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Recent Publications

  1. 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.
  2. 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 .
  3. 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.
  4. 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.
  5. 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.
  6. 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.
  7. 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 .
  8. 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.
  9. 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.
  10. Verma, S, Shankar, E, Lin, S, Singh, V, Chan, ER, Cao, S, Fu, P, MacLennan, GT, Ponsky, LE, Gupta, S et al.. Identification of Key Genes Associated with Progression and Prognosis of Bladder Cancer through Integrated Bioinformatics Analysis. Cancers (Basel) 2021; 13 (23): . PubMed PMID:34885040 PubMed Central PMC8656554.
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