RICKY CHAN, PH.D.

Director of the Computational Biology Core

E. Ricky Chan, Ph.D. 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. Miskimen, KL, Chan, ER, Haines, JL. Assay for Transposase-Accessible Chromatin Using Sequencing (ATAC-seq) Data Analysis. Curr Protoc Hum Genet 2017; 92 : 20.4.1-20.4.13. PubMed PMID:28075484 .
  2. Hoppe, G, Yoon, S, Gopalan, B, Savage, AR, Brown, R, Case, K, Vasanji, A, Chan, ER, Silver, RB, Sears, JE et al.. Comparative systems pharmacology of HIF stabilization in the prevention of retinopathy of prematurity. Proc. Natl. Acad. Sci. U.S.A. 2016; 113 (18): E2516-25. PubMed PMID:27091985 PubMed Central PMC4983815.
  3. Cannon, MV, Hester, J, Shalkhauser, A, Chan, ER, Logue, K, Small, ST, Serre, D. In silico assessment of primers for eDNA studies using PrimerTree and application to characterize the biodiversity surrounding the Cuyahoga River. Sci Rep 2016; 6 : 22908. PubMed PMID:26965911 PubMed Central PMC4786790.
  4. Chan, ER, Barnwell, JW, Zimmerman, PA, Serre, D. Comparative analysis of field-isolate and monkey-adapted Plasmodium vivax genomes. PLoS Negl Trop Dis 2015; 9 (3): e0003566. PubMed PMID:25768941 PubMed Central PMC4358935.
  5. Logue, K, Small, ST, Chan, ER, Reimer, L, Siba, PM, Zimmerman, PA, Serre, D. Whole-genome sequencing reveals absence of recent gene flow and separate demographic histories for Anopheles punctulatus mosquitoes in Papua New Guinea. Mol. Ecol. 2015; 24 (6): 1263-74. PubMed PMID:25677924 PubMed Central PMC4504211.
  6. Hester, J, Chan, ER, Menard, D, Mercereau-Puijalon, O, Barnwell, J, Zimmerman, PA, Serre, D. De novo assembly of a field isolate genome reveals novel Plasmodium vivax erythrocyte invasion genes. PLoS Negl Trop Dis 2013; 7 (12): e2569. PubMed PMID:24340114 PubMed Central PMC3854868.
  7. Logue, K, Chan, ER, Phipps, T, Small, ST, Reimer, L, Henry-Halldin, C, Sattabongkot, J, Siba, PM, Zimmerman, PA, Serre, D et al.. Mitochondrial genome sequences reveal deep divergences among Anopheles punctulatus sibling species in Papua New Guinea. Malar. J. 2013; 12 : 64. PubMed PMID:23405960 PubMed Central PMC3577438.
  8. Wong, WP, Altemus, JB, Hester, JF, Chan, ER, Côté, JF, Serre, D, Sehayek, E. Cathepsin B is a novel gender-dependent determinant of cholesterol absorption from the intestine. J. Lipid Res. 2013; 54 (3): 816-22. PubMed PMID:23248330 PubMed Central PMC3617955.
  9. Chan, ER, Menard, D, David, PH, Ratsimbasoa, A, Kim, S, Chim, P, Do, C, Witkowski, B, Mercereau-Puijalon, O, Zimmerman, PA et al.. Whole genome sequencing of field isolates provides robust characterization of genetic diversity in Plasmodium vivax. PLoS Negl Trop Dis 2012; 6 (9): e1811. PubMed PMID:22970335 PubMed Central PMC3435244.
  10. Chan, ER, Hester, J, Kalady, M, Xiao, H, Li, X, Serre, D. A novel method for determining microflora composition using dynamic phylogenetic analysis of 16S ribosomal RNA deep sequencing data. Genomics 2011; 98 (4): 253-9. PubMed PMID:21515358 PubMed Central PMC3168955.

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