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.
- 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 .
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.