C. KENNETH AND DIANNE WRIGHT CENTER
FOR CLINICAL AND TRANSLATIONAL RESEARCH

Bioinformatics

Our mission is to remove barriers in the analysis of genomic data by providing bioinformatics support to the VCU community. We help researchers focus on biological interpretation without worrying about the technical expertise needed to process and store genomic data. Whether you are considering a new project and need some advice, or you already have a pile of data you need to make sense of, Wright Center bioinformatics experts are here to assist you at every stage of the process, from experimental design through publication and beyond, with extended participation in funded research grants.

Bioinformatics Services

The Wright Center offers a range of bioinformatics services for genomic data, including:

• Free consultations
• Data analysis, visualization and interpretation
• Access to protected and public genomic data from online databases
• Grant/proposal and manuscript writing
• Long-term research support for funded grants

See our Bioinformatics Services.pdf (pdf) for more details.

Bioinformatics Education and Resources

The Wright Center offers complementary short courses on a variety of bioinformatics and translational informatics topics. Some courses offer a Certificate of Completion. VCU employees can access seminar and course recordings through our Kaltura channel. For more information about past offerings, visit the Wright Center Bioinformatics RAMPage. For advanced notification of new course offerings, subscribe to the bioinformatics mailing list by sending an email to cctrbioinfo@vcu.edu that includes your name and the email address you would like on the list.

Authorship

The Wright Center bioinformatics staff requests co-authorship, and will assist with manuscript preparation, if staff members have developed tools, algorithms, pipelines, participated in experiment design planning, or have contributed substantially to a biological question addressed in a manuscript. We ask that, at minimum, you acknowledge us in publications to which we have contributed routine analysis, data management or conversion, or data submission services and that you cite the CTSA grant number (UL1TR002649) accordingly.

Publications

2021

• Dozmorov MG, Tyc KM, Sheffield NC, Boyd DC, Olex AL, Reed J, Harrell JC. (2021). Chromatin conformation capture (Hi-C) sequencing of patient-derived xenografts: analysis guidelines. Gigascience 10, giab022.
• Grible JM, Zot P, Olex AL, Hedrick SE, Harrell JC, Woock AE, Idowu MO, Clevenger CV. (2021). The human intermediate prolactin receptor is a mammary proto-oncogene. npj Breast Cancer 7, 1–11.

2020

• Clark NM, Martinez LM, Murdock S, deLigio JT, Olex AL, Effi C, Dozmorov MG, Bos PD. (2020). Regulatory T Cells Support Breast Cancer Progression by Opposing IFN-γ-Dependent Functional Reprogramming of Myeloid Cells. Cell Reports 33.
• Turner T. (2020). From bedside to bench: Use of patient-derived xenograft models to develop novel therapeutic strategies for triple-negative breast cancer. Theses and Dissertations.
• Wahl S, Olex AL. (2020). Using Active Learning To Build A Foundation For Bioinformatics Training. Transforming Libraries for Graduate Students.

2019

• Alzubi MA, Turner TH, Olex AL, Sohal SS, Tobin NP, Recio SG, Bergh J, Hatschek T, Parker JS, Sartorius CA, Perou CM, Dozmorov MG, Harrell JC. (2019). Separation of breast cancer and organ microenvironment transcriptomes in metastases. Breast Cancer Res 2019;21:36.
• Mignogna, K. (2019). Genome-Wide Systems Genetics of Alcohol Consumption and Dependence. Theses and Dissertations.

2018

• Turner TH, Alzubi MA, Sohal SS, Olex AL, Dozmorov MG, Harrell JC. (2018). Characterizing the efficacy of cancer therapeutics in patient-derived xenograft models of metastatic breast cancer. Breast Cancer Res Treat 2018:1–14.
• Nulton TJ, Kim N-K, DiNardo LJ, Morgan IM, Windle B. (2018). Patients with integrated HPV16 in head and neck cancer show poor survival. Oral Oncol2018;80:52–5.
• Olex A, Wolen A, Arendt J, Gau KH, Moeller FG. (2018). Short Courses: Flexible Learning Opportunities in Informatics. VCU Libr Fac Staff Present

2017

• Nulton TJ, Olex AL, Dozmorov M, Morgan IM, Windle B. (2017). Analysis of The Cancer Genome Atlas sequencing data reveals novel properties of the human papillomavirus 16 genome in head and neck squamous cell carcinoma. Oncotarget2017;8:17684–99.
• Ramanathan R, Olex AL, Dozmorov M, Bear HD, Fernandez LJ, Takabe K. (2017). Angiopoietin pathway gene expression associated with poor breast cancer survival. Breast Cancer Res Treat; 162:191–8.
• van der Vaart, AD, Wolstenholme, JT, Smith, ML, Harris, GM, Lopez, MF, Wolen, AR, Becker, HC, Williams, RW and Miles, MF. (2017). The allostatic impact of chronic ethanol on gene expression: A genetic analysis of chronic intermittent ethanol treatment in the BXD cohort. Alcohol.
• Edwards, AC, Heron, J, Vladimirov, V, Wolen, AR, Adkins, DE, Aliev, F, Hickman, M and Kendler, KS. (2017). The Rate of Change in Alcohol Misuse Across Adolescence is Heritable. Alcohol Clin Exp Res.
• Webb, BT, Edwards, AC, Wolen, AR, Salvatore, JE, Aliev, F, Riley, BP, Sun, C, Williamson, VS, Kitchens, JN, Pedersen, K, Adkins, A, Cooke, ME,et al.(2017). Molecular Genetic Influences on Normative and Problematic Alcohol Use in a Population-Based Sample of College Students. Front Genet.

2016

• Gau KH, Arendt JA, Olex A, Wolen AR. (2016) Providing Hands-on Training with Bioinformatics Databases: A Collaboration Between VCU Libraries & Wright Center for Clinical and Translational Research. 2016:2.
• Huang, W, Liang, J, Nagahashi, M, Avni, D, Yamada, A, Maceyka, M, Wolen, AR, Kordula, T, Milstien, S, Takabe, K, Oravecz, T and Spiegel, S. (2016). Sphingosine-1-phosphate phosphatase 2 promotes disruption of mucosal integrity, and contributes to ulcerative colitis in mice and humans. FASEB J.
• Putman, AH, Wolen, AR, Harenza, JL, Yordanova, RK, Webb, BT, Chesler, EJ and Miles, MF. (2016). Identification of quantitative trait loci and candidate genes for an anxiolytic-like response to ethanol in BXD recombinant inbred strains. Genes Brain Behav.
• Hettema, J, Otowa, T, Hek, K, Lee, M, Byrne, E, Mirza, S, Nivard, M, Bigdeli, T, Aggen, S, Adkins, D, Wolen, AR, Fanous, A,et al.(2016). Meta-analysis of genome-wide association studies of anxiety disorders. Moleculary Psychiatry.
• Wright, ML, Dozmorov, MG, Wolen, AR, Jackson-Cook, C, Starkweather, AR, Lyon, DE and York, TP. (2016). Establishing an analytic pipeline for genome-wide DNA methylation. Clin Epigenetics.
• Smith, ML, Lopez, MF, Archer, KJ, Wolen, AR, Becker, HC and Miles, MF. (2016). Time-Course Analysis of Brain Regional Expression Network Responses to Chronic Intermittent Ethanol and Withdrawal: Implications for Mechanisms Underlying Excessive Ethanol Consumption. PLoS One.

2014

• Edwards, AC, Aliev, F, Wolen, AR, Salvatore, JE, Gardner, CO, McMahon, G, Evans, DM, Macleod, J, Hickman, M, Dick, DM and Kendler, KS. (2014). Genomic influences on alcohol problems in a population-based sample of young adults. Addiction.
• Schizophrenia Working Group of the Psychiatric Genomics Consortium. (2014). Biological insights from 108 schizophrenia-associated genetic loci. Nature.