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. 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; : . PubMed PMID:32590607 .
  2. Qiu, Z, Fa, P, Liu, T, Prasad, CB, Ma, S, Hong, Z, Chan, ER, Wang, H, Li, Z, He, K et al.. A Genome-Wide Pooled shRNA Screen Identifies PPP2R2A as a Predictive Biomarker for the Response to ATR and CHK1 Inhibitors. Cancer Res. 2020; : . PubMed PMID:32522823 .
  3. Purkayastha, BPD, Chan, ER, Ravillah, D, Ravi, L, Gupta, R, Canto, MI, Wang, JS, Shaheen, NJ, Willis, JE, Chak, A et al.. Genome-Scale Analysis Identifies Novel Transcript-Variants in Esophageal Adenocarcinoma. Cell Mol Gastroenterol Hepatol 2020; : . PubMed PMID:32344180 .
  4. Kim, GD, Ng, HP, Chan, ER, Mahabeleshwar, GH. Kruppel-like factor 6 promotes macrophage inflammatory and hypoxia response. FASEB J. 2020; 34 (2): 3209-3223. PubMed PMID:31908054 .
  5. Sergeeva, O, Kepe, V, Zhang, Y, Miller-Atkins, GA, Keynon, JD, Iyer, R, Sexton, S, Awadallah, A, Xin, W, Saunthararajah, Y et al.. [18F] Clofarabine for PET Imaging of Hepatocellular Carcinoma. Cancers (Basel) 2019; 11 (11): . PubMed PMID:31703407 PubMed Central PMC6896045.
  6. Sergeeva, O, Zhang, Y, Kenyon, JD, Miller-Atkins, GA, Wu, C, Iyer, R, Sexton, S, Wojtylak, P, Awadallah, A, Xin, W et al.. PET imaging of hepatocellular carcinoma with anti-1-amino-3-[18F]fluorocyclobutanecarboxylic acid in comparison with L-[S-methyl-11C]methionine. EJNMMI Res 2019; 9 (1): 47. PubMed PMID:31119488 PubMed Central PMC6531569.
  7. Han, S, Ray, JW, Pathak, P, Sweet, DR, Zhang, R, Gao, H, Jain, N, Koritzinsky, EH, Matoba, K, Xu, W et al.. KLF15 regulates endobiotic and xenobiotic metabolism. Nat Metab 2019; 1 (4): 422-430. PubMed PMID:32694878 .
  8. Sarvestani, SK, Signs, SA, Lefebvre, V, Mack, S, Ni, Y, Morton, A, Chan, ER, Li, X, Fox, P, Ting, A et al.. Cancer-predicting transcriptomic and epigenetic signatures revealed for ulcerative colitis in patient-derived epithelial organoids. Oncotarget 2018; 9 (47): 28717-28730. PubMed PMID:29983891 PubMed Central PMC6033374.
  9. Cannon, MV, Craine, J, Hester, J, Shalkhauser, A, Chan, ER, Logue, K, Small, S, Serre, D. Dynamic microbial populations along the Cuyahoga River. PLoS ONE 2017; 12 (10): e0186290. PubMed PMID:29049324 PubMed Central PMC5648161.
  10. Howes, RE, Chan, ER, Rakotomanga, TA, Schulte, S, Gibson, J, Zikursh, M, Franchard, T, Ramiranirina, B, Ratsimbasoa, A, Zimmerman, PA et al.. Prevalence and genetic variants of G6PD deficiency among two Malagasy populations living in Plasmodium vivax-endemic areas. Malar. J. 2017; 16 (1): 139. PubMed PMID:28376871 PubMed Central PMC5381087.
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