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. Kim, GD, Ng, HP, Chan, ER, Mahabeleshwar, GH. Macrophage-Hypoxia-Inducible Factor-1α Signaling in Carotid Artery Stenosis. Am J Pathol 2021; : . PubMed PMID:33753024 .
  2. 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.
  3. 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.
  4. 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; : . PubMed PMID:33417917 .
  5. 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.
  6. 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.
  7. Verma, S, Shankar, E, Chan, ER, Gupta, S. Metabolic Reprogramming and Predominance of Solute Carrier Genes during Acquired Enzalutamide Resistance in Prostate Cancer. Cells 2020; 9 (12): . PubMed PMID:33255236 PubMed Central PMC7759897.
  8. Sergeeva, O, Zhang, Y, Kenyon, J, Miller-Atkins, G, Sergeev, M, Verbus, E, Iyer, R, Sexton, S, Kepe, V, Avril, N et al.. Liver background uptake of [18F]FLT in PET imaging. Am J Nucl Med Mol Imaging 2020; 10 (5): 212-225. PubMed PMID:33224617 PubMed Central PMC7675117.
  9. Sweet, DR, Vasudevan, NT, Fan, L, Booth, CE, Keerthy, KS, Liao, X, Vinayachandran, V, Takami, Y, Tugal, D, Sharma, N et al.. Myeloid Krüppel-like factor 2 is a critical regulator of metabolic inflammation. Nat Commun 2020; 11 (1): 5872. PubMed PMID:33208733 PubMed Central PMC7674440.
  10. Elgharably, H, Okamoto, T, Ayyat, KS, Niikawa, H, Meade, S, Farver, C, Chan, ER, Aldred, MA, McCurry, KR. Human Lungs Airway Epithelium Upregulate MicroRNA-17 and MicroRNA-548b in Response to Cold Ischemia and Ex Vivo Reperfusion. Transplantation 2020; 104 (9): 1842-1852. PubMed PMID:32590607 .
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