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.
- 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 .
- 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; 80 (16): 3305-3318. PubMed PMID:32522823 PubMed Central PMC7518641.
- 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; 10 (3): 652-654.e17. PubMed PMID:32344180 PubMed Central PMC7474160.
- 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 .
- 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.
- 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.
- 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 .
- 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.
- 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.
- 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.