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.



Recent Publications

  1. Jinadatha, C, Jones, LD, Hailes, JM, Marshall, EK, Hwang, M, Cadnum, JL, Choi, H, Chatterjee, P, Chan, ER, Zimmerman, PA et al.. Transmission of Severe Acute Respiratory Syndrome Coronavirus 2 Among Residents and Employees in a Veterans Affairs Community Living Center: A 42-Month Prospective Cohort Study. Pathog Immun 2024; 9 (1): 91-107. PubMed PMID:38690562 PubMed Central PMC11060326.
  2. Lee, CM, Chan, ER, Schueller, D, Breitman, M, Haghiac, M, Magrey, M. IL-17-producing cells in ankylosing spondylitis patients show gender-based differences in gene expression. Clin Exp Rheumatol 2024; 42 (5): 1057-1066. PubMed PMID:38436300 .
  3. Graves, LY, Schwartz, KR, Shiff, J, Chan, ER, Galea, M, Henzel, MK, Olney, C, Bogie, KM. Genomic Biomarkers Can Provide a Deeper Understanding of Recurrent Pressure Injuries. Adv Skin Wound Care 2023; 36 (10): 534-539. PubMed PMID:37729163 PubMed Central PMC10545060.
  4. Zafar, A, Ng, HP, Chan, ER, Dunwoodie, SL, Mahabeleshwar, GH. Myeloid-CITED2 Deficiency Exacerbates Diet-Induced Obesity and Pro-Inflammatory Macrophage Response. Cells 2023; 12 (17): . PubMed PMID:37681868 PubMed Central PMC10486650.
  5. Cramer, EY, Bartlett, J, Chan, ER, Gaedigk, A, Ratsimbasoa, AC, Mehlotra, RK, Williams, SM, Zimmerman, PA. Pharmacogenomic variation in the Malagasy population: implications for the antimalarial drug primaquine metabolism. Pharmacogenomics 2023; 24 (11): 583-597. PubMed PMID:37551613 PubMed Central PMC10621762.
  6. Song, S, Druschel, LN, Chan, ER, Capadona, JR. Differential expression of genes involved in the chronic response to intracortical microelectrodes. Acta Biomater 2023; 169 : 348-362. PubMed PMID:37507031 PubMed Central PMC10528922.
  7. Wang, M, Osborn, LJ, Jain, S, Meng, X, Weakley, A, Yan, J, Massey, WJ, Varadharajan, V, Horak, A, Banerjee, R et al.. Strain dropouts reveal interactions that govern the metabolic output of the gut microbiome. Cell 2023; 186 (13): 2839-2852.e21. PubMed PMID:37352836 PubMed Central PMC10299816.
  8. Polak, KL, Tamagno, I, Parameswaran, N, Smigiel, J, Chan, ER, Yuan, X, Rios, B, Jackson, MW. Oncostatin-M and OSM-Receptor Feed-Forward Activation of MAPK Induces Separable Stem-like and Mesenchymal Programs. Mol Cancer Res 2023; 21 (9): 975-990. PubMed PMID:37310811 PubMed Central PMC10527478.
  9. Rana, PS, Wang, W, Markovic, V, Szpendyk, J, Chan, ER, Sossey-Alaoui, K. The WAVE2/miR-29/Integrin-β1 Oncogenic Signaling Axis Promotes Tumor Growth and Metastasis in Triple-negative Breast Cancer. Cancer Res Commun 2023; 3 (1): 160-174. PubMed PMID:36968231 PubMed Central PMC10035451.
  10. Sergeeva, O, Zhang, Y, Gao, S, Chan, ER, Sergeev, M, Iyer, R, Sexton, S, Avril, N, Lu, ZR, Lee, Z et al.. PET Imaging of Hepatocellular Carcinoma Using ZD2-(68Ga-NOTA). J Hepatocell Carcinoma 2023; 10 : 291-301. PubMed PMID:36860804 PubMed Central PMC9968869.
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