Cleveland Institute for Computational Biology

We lead and collaborate on big data research requiring sophisticated data management and computation. Our work encompasses bench, clinical, translational, and population health inquiries, with consideration for the intersection with demographics, socioeconomics, and geography.

We provide expertise in study design, data harmonization and management, complex analytics, and visualization, as well as grant and manuscript development.

In our work with health systems, we adhere to protocols that protect patient privacy and proprietary enterprise information. Along with our Case Western Reserve University Technology team (UTech), we partner in maintaining a secure research environment for housing human study data. Our team supports state-of-the-art data management and analytics software, and trains our partners in the use of various tools.

Our work is organized around three integrated cores:

• Bioinformatics Core: Original and collaborative research related to next-generation sequencing
• Data Management Core: Consultation, data management and analysis to support laboratory and clinical research
• Computational Phenotyping Core: Original and collaborative research based in Electronic Health Records and other observational data sets

Learn more about the Cleveland Institute for Computational Biology

Recent publications from the core: 

    Chernosky, NM, Tamagno, I, Polak, KL, Chan, ER, Yuan, X, Jackson, MW. Toll-Like receptor 3-mediated interferon-β production is suppressed by oncostatin m and a broader epithelial-mesenchymal transition program. Breast Cancer Res 2024; 26 (1): 167. PubMed PMID:39593161 PubMed Central PMC11590466.
    Druschel, LN, Kasthuri, NM, Song, SS, Wang, JJ, Hess-Dunning, A, Chan, ER, Capadona, JR. Cell-specific spatial profiling of targeted protein expression to characterize the impact of intracortical microelectrode implantation on neuronal health. J Mater Chem B 2024; 12 (47): 12307-12319. PubMed PMID:39479901 PubMed Central PMC11525954.
    Chang, TY, Yan, Y, Yu, ZY, Rathore, M, Lee, NZ, Tseng, HJ, Cheng, LH, Huang, WJ, Zhang, W, Chan, ER et al.. Combined HDAC8 and checkpoint kinase inhibition induces tumor-selective synthetic lethality in preclinical models. J Clin Invest 2024; 134 (23): . PubMed PMID:39436709 PubMed Central PMC11601943.
    Chan, ER, Benchek, P, Miller, G, Brustoski, K, Schaffer, A, Truitt, B, Tag, J, Freebairn, L, Lewis, BA, Stein, CM et al.. Importance of copy number variants in childhood apraxia of speech and other speech sound disorders. Commun Biol 2024; 7 (1): 1273. PubMed PMID:39369109 PubMed Central PMC11455877.
    Song, SS, Druschel, LN, Kasthuri, NM, Wang, JJ, Conard, JH, Chan, ER, Acharya, AP, Capadona, JR. Comprehensive proteomic analysis of the differential expression of 62 proteins following intracortical microelectrode implantation. Sci Rep 2024; 14 (1): 17596. PubMed PMID:39080300 PubMed Central PMC11289480.
    Luo, G, Kumar, H, Aldridge, K, Rieger, S, Han, E, Jiang, E, Chan, ER, Soliman, A, Mahdi, H, Letterio, JJ et al.. A Core NRF2 Gene Set Defined Through Comprehensive Transcriptomic Analysis Predicts Selective Drug Resistance and Poor Multicancer Prognosis. Antioxid Redox Signal 2024; 41 (16-18): 1031-1050. PubMed PMID:39028025.
    Jinadatha, C, Jones, LD, Hailes, JM, Marshall, EK, Hwang, M, Cadnum, JL, Choi, H, Chatterjee, P, Chan, ER, Zimmerman, PA et al.. Transmission of Severe Acute Respiratory Syndrome Coronavirus 2 Among Residents and Employees in a Veterans Affairs Community Living Center: A 42-Month Prospective Cohort Study. Pathog Immun 2024; 9 (1): 91-107. PubMed PMID:38690562 PubMed Central PMC11060326.
    Lee, CM, Chan, ER, Schueller, D, Breitman, M, Haghiac, M, Magrey, M. IL-17-producing cells in ankylosing spondylitis patients show gender-based differences in gene expression. Clin Exp Rheumatol 2024; 42 (5): 1057-1066. PubMed PMID:38436300 .
    Graves, LY, Schwartz, KR, Shiff, J, Chan, ER, Galea, M, Henzel, MK, Olney, C, Bogie, KM. Genomic Biomarkers Can Provide a Deeper Understanding of Recurrent Pressure Injuries. Adv Skin Wound Care 2023; 36 (10): 534-539. PubMed PMID:37729163 PubMed Central PMC10545060.
    Zafar, A, Ng, HP, Chan, ER, Dunwoodie, SL, Mahabeleshwar, GH. Myeloid-CITED2 Deficiency Exacerbates Diet-Induced Obesity and Pro-Inflammatory Macrophage Response. Cells 2023; 12 (17): . PubMed PMID:37681868 PubMed Central PMC10486650.

Recognition, diagnostic practices, and cancer outcomes among patients with unintentional weight loss (UWL) in primary care.
Rao G, Ufholz K, Saroufim P, Menegay H, Beno M. Diagnosis (Berl). 2023 Apr 21;10(3):267-274. doi: 10.1515/dx-2023-0002. eCollection 2023 Aug 1. PMID: 37080911

An informatics infrastructure to catalyze cancer control research and practice.
Rose J, Dong W, Kim U, Hnath J, Statler A, Saroufim P, Song S, Ascha M, Menegay H, Tian Y, Beno M, Koroukian SM. Cancer Causes Control. 2022 Jun;33(6):899-911. doi: 10.1007/s10552-022-01571-0. Epub 2022 Apr 5. PMID: 35380304

Electronic Medical Record Search Engine (EMERSE): An Information Retrieval Tool for Supporting Cancer Research.
Hanauer DA, Barnholtz-Sloan JS, Beno MF, Del Fiol G, Durbin EB, Gologorskaya O, Harris D, Harnett B, Kawamoto K, May B, Meeks E, Pfaff E, Weiss J, Zheng K. JCO Clin Cancer Inform. 2020 May;4:454-463. doi: 10.1200/CCI.19.00134. PMID: 32412846

Facilitating Cancer Epidemiologic Efforts in Cleveland via Creation of Longitudinal De-Duplicated Patient Data Sets.
Tian YD, Menegay H, Waite KA, Saroufim PG, Beno MF, Barnholtz-Sloan JS. Cancer Epidemiol Biomarkers Prev. 2020 Apr;29(4):787-795. doi: 10.1158/1055-9965.EPI-19-0815. Epub 2020 Jan 27. PMID: 31988074 

Bridging the Gaps in Personalized Medicine Value Assessment: A Review of the Need for Outcome Metrics across Stakeholders and Scientific Disciplines.
Bush WS, Cooke Bailey JN, Beno MF, Crawford DC. Public Health Genomics. 2019;22(1-2):16-24. doi: 10.1159/000501974. Epub 2019 Aug 27. PMID: 31454805