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.
- 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; : . PubMed PMID:33441309 .
- Yu, WY, Hill, ST, Chan, ER, Pink, JJ, Cooper, K, Leachman, S, Lund, AW, Kulkarni, R, Bordeaux, JS. Computational drug repositioning identifies statins as a modifier of prognostic genetic expression signatures and metastatic behavior in melanoma. J Invest Dermatol 2021; : . PubMed PMID:33417917 .
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.