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. Zafar, A, Ng, HP, Kim, GD, Chan, ER, Mahabeleshwar, GH. BHLHE40 promotes macrophage pro-inflammatory gene expression and functions. FASEB J 2021; 35 (10): e21940. PubMed PMID:34551158 PubMed Central PMC8607355.
  2. Benchek, P, Igo, RP Jr, Voss-Hoynes, H, Wren, Y, Miller, G, Truitt, B, Zhang, W, Osterman, M, Freebairn, L, Tag, J et al.. Association between genes regulating neural pathways for quantitative traits of speech and language disorders. NPJ Genom Med 2021; 6 (1): 64. PubMed PMID:34315907 PubMed Central PMC8316336.
  3. Chan, ER, Jones, LD, Redmond, SN, Navas, ME, Kachaluba, NM, Zabarsky, TF, Bhullar, D, Cadnum, JL, Zimmerman, PA, Donskey, CJ et al.. Use of whole-genome sequencing to investigate a cluster of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections in emergency department personnel. Infect Control Hosp Epidemiol 2021; : 1-3. PubMed PMID:33941299 PubMed Central PMC8144813.
  4. Jones, LD, Chan, ER, Zabarsky, TF, Cadnum, JL, Navas, ME, Redmond, SN, Kovach, JD, Linger, M, Rutala, WA, Zimmerman, PA et al.. Transmission of SARS-CoV-2 on a Patient Transport Van. Clin Infect Dis 2021; : . PubMed PMID:33893474 PubMed Central PMC8135457.
  5. Kim, GD, Ng, HP, Chan, ER, Mahabeleshwar, GH. Macrophage-Hypoxia-Inducible Factor-1α Signaling in Carotid Artery Stenosis. Am J Pathol 2021; 191 (6): 1118-1134. PubMed PMID:33753024 PubMed Central PMC8176143.
  6. Fan, L, Sweet, DR, Prosdocimo, DA, Vinayachandran, V, Chan, ER, Zhang, R, Ilkayeva, O, Lu, Y, Keerthy, KS, Booth, CE et al.. Muscle Krüppel-like factor 15 regulates lipid flux and systemic metabolic homeostasis. J Clin Invest 2021; 131 (4): . PubMed PMID:33586679 PubMed Central PMC7880311.
  7. Wang, L, Yu, S, Chan, ER, Chen, KY, Liu, C, Che, D, Awadallah, A, Myers, J, Askew, D, Huang, AY et al.. Notch-Regulated Dendritic Cells Restrain Inflammation-Associated Colorectal Carcinogenesis. Cancer Immunol Res 2021; 9 (3): 348-361. PubMed PMID:33441309 PubMed Central PMC7925430.
  8. Yu, WY, Hill, ST, Chan, ER, Pink, JJ, Cooper, K, Leachman, S, Lund, AW, Kulkarni, R, Bordeaux, JS. Computational Drug Repositioning Identifies Statins as Modifiers of Prognostic Genetic Expression Signatures and Metastatic Behavior in Melanoma. J Invest Dermatol 2021; 141 (7): 1802-1809. PubMed PMID:33417917 PubMed Central PMC8238797.
  9. Verma, S, Shankar, E, Kalayci, FNC, Mukunda, A, Alassfar, M, Singh, V, Chan, ER, MacLennan, GT, Gupta, S. Androgen Deprivation Induces Transcriptional Reprogramming in Prostate Cancer Cells to Develop Stem Cell-Like Characteristics. Int J Mol Sci 2020; 21 (24): . PubMed PMID:33339129 PubMed Central PMC7765584.
  10. Zhang, X, Wang, R, Hu, D, Sun, X, Fujioka, H, Lundberg, K, Chan, ER, Wang, Q, Xu, R, Flanagan, ME et al.. Oligodendroglial glycolytic stress triggers inflammasome activation and neuropathology in Alzheimer's disease. Sci Adv 2020; 6 (49): . PubMed PMID:33277246 PubMed Central PMC7717916.
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