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. 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.
  2. 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.
  3. 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.
  4. 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.
  5. 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.
  6. 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.
  7. 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.
  8. 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.
  9. Qu, DC, Neu, D, Khawaja, ZQ, Wang, R, Bartels, CF, Lovrenert, K, Chan, ER, Hill-Baskin, AE, Scacheri, PC, Berger, NA et al.. Epigenetic effects of high-fat diet on intestinal tumorigenesis in C57BL/6J-Apc Min/+ mice. J Transl Genet Genom 2023; 7 (1): 3-16. PubMed PMID:36817228 PubMed Central PMC9937564.
  10. Massey, WJ, Varadharajan, V, Banerjee, R, Brown, AL, Horak, AJ, Hohe, RC, Jung, BM, Qiu, Y, Chan, ER, Pan, C et al.. MBOAT7-driven lysophosphatidylinositol acylation in adipocytes contributes to systemic glucose homeostasis. J Lipid Res 2023; 64 (4): 100349. PubMed PMID:36806709 PubMed Central PMC10041558.
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