The Bioinformatics Shared Resource (BISR) collaborates with clinical, cancer control, and basic science investigators to use genomics and informatics approaches in cancer research.
We help researchers:
- Better understand the complex processes involved in the development and progression of various types of cancer, especially tobacco-related cancers
- Use this knowledge to predict cancer recurrence, metastasis and response to therapies
- Assign patients to specific targeted therapies, such as immunotherapies, to improve survival and quality-of-life
Our objectives for improving patient outcomes include:
- Identifying germline and somatic genetic and epigenetic alterations that are associated with the development and progression of cancer
- Identifying genetic and epigenetic events and mutation signatures in cancers caused by environmental factors, such as tobacco
- Identifying ethnicity-related genetic and epigenetic alterations that may be underlying factors in health disparities
- Utilizing genetic and epigenetic information for early detection of cancer (personalized risk prediction) and prediction of cancer recurrence and progression (personalized monitoring)
- Promoting precision medicine (personalized intervention)
- Understanding the functional mechanisms by which genetic and epigenetic findings have a direct effect on cancer
The primary goal of the BISR is to facilitate the peer-reviewed research and extramural grant application of Wake Forest Baptist Comprehensive Cancer Center members. We collaborate with members from all scientific programs throughout all phases of cancer-related research projects.
Major responsibilities are assumed for methodological-, computational-, and bioinformatics-related issues, including study design (including sample size, platform and sequencing depth), sampling, interim reviews, and final analysis and result delivery.
We focus on:
- Bioinformatics-based design and data analysis in support of grant development and publications
- Informatics services to Comprehensive Cancer Center investigators from all programs, including genomics data processing, bioinformatics analyses, data annotation and visualization/sharing to support basic, translational and clinical cancer research by leveraging the institutionally maintained Translational Data Warehouse
- Leadership, education, and training, including participating in graduate-level courses and T32 training grants
- Mentoring teams for K awardees and other young investigators
- Facilitating membership and leadership on committees responsible for scientific and administrative decisions for the Comprehensive Cancer Center
- Providing short courses on statistical or bioinformatics methods for Comprehensive Cancer Center members
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Bach, D. H., W. Zhang and A. K. Sood (2019). "Chromosomal Instability in Tumor Initiation and Development." Cancer Res 79(16): 3995-4002.
Bolivar, A. M., R. Luthra, M. Mehrotra, W. Chen, B. A. Barkoh, P. Hu, W. Zhang and R. R. Broaddus (2019). "Targeted next-generation sequencing of endometrial cancer and matched circulating tumor DNA: identification of plasma-based, tumor-associated mutations in early stage patients." Mod Pathol 32(3): 405-414.
Dohm, A., J. Su, E. R. McTyre, J. M. Taylor, L. D. Miller, W. J. Petty, F. Xing, H. W. Lo, L. J. Metheny-Barlow, S. O'Neill, C. Bellinger, T. Dotson, B. Pasche, K. Watabe, M. D. Chan and J. Ruiz (2019). "Identification of CD37, cystatin A, and IL-23A gene expression in association with brain metastasis: analysis of a prospective trial." Int J Biol Markers 34(1): 90-97.
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Dotson, T., C. Bellinger, J. Su (BISR), K. Hansen, G. E. Parks, J. O. Cappellari, L. Craddock, H. Clark, C. Howard, W. J. Petty, B. Prakash, K. Watabe, M. Chan, J. Hovda, L. D. Miller and J. Ruiz (2019). "Feasibility of lung cancer RNA acquisition from a single transbronchial or transthoracic needle pass (FASTT trial)." Lung Cancer 127: 6-11.
Gao, C., Y. Wang, R. Broaddus, L. Sun, F. Xue and W. Zhang (2018). "Exon 3 mutations of CTNNB1 drive tumorigenesis: a review." Oncotarget 9(4): 5492-5508.
Guan, M., S. Cho, R. Petro, W. Zhang, B. Pasche and U. Topaloglu (2019). "Natural language processing and recurrent network models for identifying genomic mutation-associated cancer treatment change from patient progress notes." JAMIA Open 2(1): 139-149.
Hu, J. J., J. J. Urbanic, L. D. Case, C. Takita, J. L. Wright, D. R. Brown, C. D. Langefeld, M. O. Lively, S. E. Mitchell, A. Thakrar, D. Bryant, K. Baglan, J. Strasser, L. Baez-Diaz, G. J. Lesser and E. G. Shaw (2018). "Association Between Inflammatory Biomarker C-Reactive Protein and Radiotherapy-Induced Early Adverse Skin Reactions in a Multiracial/Ethnic Breast Cancer Population." J Clin Oncol 36(24): 2473-2482.
Huang, K. L., R. J. Mashl, Y. Wu, D. I. Ritter, J. Wang, C. Oh, M. Paczkowska, S. Reynolds, M. A. Wyczalkowski, N. Oak, A. D. Scott, M. Krassowski, A. D. Cherniack, K. E. Houlahan, R. Jayasinghe, L. B. Wang, D. C. Zhou, D. Liu, S. Cao, Y. W. Kim, A. Koire, J. F. McMichael, V. Hucthagowder, T. B. Kim, A. Hahn, C. Wang, M. D. McLellan, F. Al-Mulla, K. J. Johnson, N. Cancer Genome Atlas Research, O. Lichtarge, P. C. Boutros, B. Raphael, A. J. Lazar, W. Zhang, M. C. Wendl, R. Govindan, S. Jain, D. Wheeler, S. Kulkarni, J. F. Dipersio, J. Reimand, F. Meric-Bernstam, K. Chen, I. Shmulevich, S. E. Plon, F. Chen and L. Ding (2018). "Pathogenic Germline Variants in 10,389 Adult Cancers." Cell 173(2): 355-370 e314.
Hughes, R. T., A. H. Masters, E. R. McTyre, M. K. Farris, C. Chung, B. R. Page, L. R. Kleinberg, J. Hepel, J. N. Contessa, V. Chiang, J. Ruiz, K. Watabe, J. Su, J. B. Fiveash, S. Braunstein, S. Chao, A. Attia, D. N. Ayala-Peacock and M. D. Chan (2019). "Initial SRS for Patients With 5 to 15 Brain Metastases: Results of a Multi-Institutional Experience." Int J Radiat Oncol Biol Phys 104(5): 1091-1098.
Jimenez, H., M. Wang, J. W. Zimmerman, M. J. Pennison, S. Sharma, T. Surratt, Z. X. Xu, I. Brezovich, D. Absher, R. M. Myers, B. DeYoung, D. L. Caudell, D. Chen, H. W. Lo, H. K. Lin, D. W. Godwin, M. Olivier, A. Ghanekar, K. Chen, L. D. Miller, Y. Gong, M. Capstick, R. B. D'Agostino, Jr., R. Munden, P. Merle, A. Barbault, A. W. Blackstock, H. L. Bonkovsky, G. Y. Yang, G. Jin, L. Liu, W. Zhang, K. Watabe, C. F. Blackman and B. C. Pasche (2019). "Tumour-specific amplitude-modulated radiofrequency electromagnetic fields induce differentiation of hepatocellular carcinoma via targeting Cav3.2T-type voltage-gated calcium channels and Ca(2+) influx." EBioMedicine 44: 209-224.
Kim, G., K. C. Kurnit, B. Djordjevic, C. Singh, M. F. Munsell, W. L. Wang, A. J. Lazar, W. Zhang and R. Broaddus (2018). "Nuclear beta-catenin localization and mutation of the CTNNB1 gene: a context-dependent association." Mod Pathol 31(10): 1553-1559.
Koerner, S. E., M. D. Smith, D. E. Burkepile, N. P. Hanan, M. L. Avolio, S. L. Collins, A. K. Knapp, N. P. Lemoine, E. J. Forrestel, S. Eby, D. I. Thompson, G. A. Aguado-Santacruz, J. P. Anderson, T. M. Anderson, A. Angassa, S. Bagchi, E. S. Bakker, G. Bastin, L. E. Baur, K. H. Beard, E. A. Beever, P. J. Bohlen, E. H. Boughton, D. Canestro, A. Cesa, E. Chaneton, J. Cheng, C. M. D'Antonio, C. Deleglise, F. Dembele, J. Dorrough, D. J. Eldridge, B. Fernandez-Going, S. Fernandez-Lugo, L. H. Fraser, B. Freedman, G. Garcia-Salgado, J. R. Goheen, L. Guo, S. Husheer, M. Karembe, J. M. H. Knops, T. Kraaij, A. Kulmatiski, M. M. Kytoviita, F. Lezama, G. Loucougaray, A. Loydi, D. G. Milchunas, S. J. Milton, J. W. Morgan, C. Moxham, K. C. Nehring, H. Olff, T. M. Palmer, S. Rebollo, C. Riginos, A. C. Risch, M. Rueda, M. Sankaran, T. Sasaki, K. A. Schoenecker, N. L. Schultz, M. Schutz, A. Schwabe, F. Siebert, C. Smit, K. A. Stahlheber, C. Storm, D. J. Strong, J. Su, Y. V. Tiruvaimozhi, C. Tyler, J. Val, M. L. Vandegehuchte, K. E. Veblen, L. T. Vermeire, D. Ward, J. Wu, T. P. Young, Q. Yu and T. J. Zelikova (2018). "Change in dominance determines herbivore effects on plant biodiversity." Nat Ecol Evol 2(12): 1925-1932.
Kytola, V., U. Topaloglu, L. D. Miller, R. L. Bitting, M. M. Goodman, R. B. D Agostino, R. J. Desnoyers, C. Albright, G. Yacoub, S. A. Qasem, B. DeYoung, V. Thorsson, I. Shmulevich, M. Yang, A. Shcherban, M. Pagni, L. Liu, M. Nykter, K. Chen, G. A. Hawkins, S. C. Grant, W. J. Petty, A. T. Alistar, E. A. Levine, E. D. Staren, C. D. Langefeld, V. Miller, G. Singal, R. M. Petro, M. Robinson, W. Blackstock, B. L. Powell, L. I. Wagner, K. L. Foley, E. Abraham, B. Pasche and W. Zhang (2017). "Mutational Landscapes of Smoking-Related Cancers in Caucasians and African Americans: Precision Oncology Perspectives at Wake Forest Baptist Comprehensive Cancer Center." Theranostics 7(11): 2914-2923.
Lee, E., C. Takita, J. L. Wright, S. H. Slifer, E. R. Martin, J. J. Urbanic, C. D. Langefeld, G. J. Lesser, E. G. Shaw and J. J. Hu (2019). "Genome-wide enriched pathway analysis of acute post-radiotherapy pain in breast cancer patients: a prospective cohort study." Hum Genomics 13(1): 28.
Li, T., C. Zhang, S. Hassan, X. Liu, F. Song, K. Chen, W. Zhang and J. Yang (2018). "Histone deacetylase 6 in cancer." J Hematol Oncol 11(1): 111.
Li, X., B. Pasche, W. Zhang and K. Chen (2018). "Association of MUC16 Mutation With Tumor Mutation Load and Outcomes in Patients With Gastric Cancer." JAMA Oncol 4(12): 1691-1698.
Li, X., S. Zhang, Q. Zhang, X. Wei, M. Gao, W. Zhang and K. Chen (2019). "Deep convolutional neural network models for the diagnosis of thyroid cancer - Authors' reply." Lancet Oncol 20(3): e131.
Li, X., S. Zhang, Q. Zhang, X. Wei, Y. Pan, J. Zhao, X. Xin, C. Qin, X. Wang, J. Li, F. Yang, Y. Zhao, M. Yang, Q. Wang, Z. Zheng, X. Zheng, X. Yang, C. T. Whitlow, M. N. Gurcan, L. Zhang, X. Wang, B. C. Pasche, M. Gao, W. Zhang and K. Chen (2019). "Diagnosis of thyroid cancer using deep convolutional neural network models applied to sonographic images: a retrospective, multicohort, diagnostic study." Lancet Oncol 20(2): 193-201.
Li, X., W. Zhang and K. Chen (2019). "Tumor Mutation Load and Frequently Mutated Genes in Gastric Cancer-In Reply." JAMA Oncol 5(4): 577-578.
Li, X. C., M. Y. Wang, M. Yang, H. J. Dai, B. F. Zhang, W. Wang, X. L. Chu, X. Wang, H. Zheng, R. F. Niu, W. Zhang and K. X. Chen (2018). "A mutational signature associated with alcohol consumption and prognostically significantly mutated driver genes in esophageal squamous cell carcinoma." Ann Oncol 29(4): 938-944.
Liu, L., J. Ruiz, S. S. O'Neill, S. C. Grant, W. J. Petty, M. Yang, K. Chen, U. Topaloglu, B. Pasche and W. Zhang (2018). "Favorable outcome of patients with lung adenocarcinoma harboring POLE mutations and expressing high PD-L1." Mol Cancer 17(1): 81.
Naczki, C., B. John, C. Patel, A. Lafferty, A. Ghoneum, H. Afify, M. White, A. Davis, G. Jin, S. Kridel and N. Said (2018). "SPARC Inhibits Metabolic Plasticity in Ovarian Cancer." Cancers (Basel) 10(10).
Pardee, T. S., R. G. Anderson, K. M. Pladna, S. Isom, L. P. Ghiraldeli, L. D. Miller, J. A. Chou, G. Jin, W. Zhang, L. R. Ellis, D. Berenzon, D. S. Howard, D. Hurd, M. Manuel, S. Dralle, S. Lyerly and B. L. Powell (2018). "A phase I study of CPI-613 in combination with high dose cytarabine and mitoxantrone for relapsed or refractory acute myeloid leukemia." Clin Cancer Res.
Pardee, T. S., R. G. Anderson, K. M. Pladna, S. Isom, L. P. Ghiraldeli, L. D. Miller, J. W. Chou, G. Jin, W. Zhang, L. R. Ellis, D. Berenzon, D. S. Howard, D. D. Hurd, M. Manuel, S. Dralle, S. Lyerly and B. L. Powell (2018). "A Phase I Study of CPI-613 in Combination with High-Dose Cytarabine and Mitoxantrone for Relapsed or Refractory Acute Myeloid Leukemia." Clin Cancer Res 24(9): 2060-2073.
Salvador Moreno, N., J. Liu, K. M. Haas, L. L. Parker, C. Chakraborty, S. J. Kron, K. Hodges, L. D. Miller, C. Langefeld, P. J. Robinson, S. A. Lelievre and P. A. Vidi (2019). "The nuclear structural protein NuMA is a negative regulator of 53BP1 in DNA double-strand break repair." Nucleic Acids Res 47(6): 2703-2715.
Shenker, R. F., R. T. Hughes, E. R. McTyre, C. Lanier, H. W. Lo , L. Metheny-Barlow, J. Su, A. Thomas, D. R. Brown, T. Avery, B. Pasche , C. K. Cramer, A. W. Laxton, S. B. Tatter, K. Watabe and M. D. Chan (2018). "Potential prognostic markers for survival and neurologic death in patients with breast cancer brain metastases who receive upfront SRS alone." J Radiosurg SBRT 5(4): 277-283.
Sirkisoon, S. R., R. L. Carpenter, T. Rimkus, A. Anderson, A. Harrison, A. M. Lange, G. Jin, K. Watabe and H. W. Lo (2018). "Interaction between STAT3 and GLI1/tGLI1 oncogenic transcription factors promotes the aggressiveness of triple-negative breast cancers and HER2-enriched breast cancer." Oncogene 37(19): 2502-2514.
Soike, M. H., E. R. McTyre, R. T. Hughes, M. Farris, C. K. Cramer, M. C. LeCompte, C. M. Lanier, J. Ruiz, J. Su, K. Watabe, J. D. Bourland, M. T. Munley, S. O'Neill, A. W. Laxton, S. B. Tatter and M. D. Chan (2018). "Initial brain metastasis velocity: does the rate at which cancers first seed the brain affect outcomes?" J Neurooncol 139(2): 461-467.
Song, Q., G. A. Hawkins, L. Wudel, P. C. Chou, E. Forbes, A. K. Pullikuth, L. Liu, G. Jin, L. Craddock, U. Topaloglu, G. Kucera, S. O'Neill, E. A. Levine, P. Sun, K. Watabe, Y. Lu, M. A. Alexander-Miller, B. Pasche, L. D. Miller and W. Zhang (2019). "Dissecting intratumoral myeloid cell plasticity by single cell RNA-seq." Cancer Med 8(6): 3072-3085.
Su, W., L. Hong, X. Xu, S. Huang, D. Herpai, L. Li, Y. Xu, L. Truong, W. Y. Hu, X. Wu, C. Xiao, W. Zhang , J. Han, W. Debinski, R. Xiang and P. Sun (2018). "miR-30 disrupts senescence and promotes cancer by targeting both p16(INK4A) and DNA damage pathways." Oncogene 37(42): 5618-5632.
Thomas, A., E. D. Routh, A. Pullikuth, G. Jin, J. Su, J. W. Chou, K. A. Hoadley, C. Print, N. Knowlton, M. A. Black, S. Demaria, E. Wang, D. Bedognetti, W. D. Jones, G. A. Mehta, M. L. Gatza, C. M. Perou, D. B. Page, P. Triozzi and L. D. Miller (2018). "Tumor mutational burden is a determinant of immune-mediated survival in breast cancer." Oncoimmunology 7(10): e1490854.
Tian, W., F. Teng, J. Gao, C. Gao, G. Liu, Y. Zhang, S. Yu, W. Zhang, Y. Wang and F. Xue (2019). "Estrogen and insulin synergistically promote endometrial cancer progression via crosstalk between their receptor signaling pathways." Cancer Biol Med 16(1): 55-70.
Wang, H., X. Sun, S. Ahmad, J. Su, C. M. Ferrario and L. Groban (2019). "Estrogen modulates the differential expression of cardiac myocyte chymase isoforms and diastolic function." Mol Cell Biochem 456(1-2): 85-93.
Xing, F., Y. Liu, S. Y. Wu, K. Wu, S. Sharma, Y. Y. Mo, J. Feng, S. Sanders, G. Jin, R. Singh, P. A. Vidi, A. Tyagi, M. D. Chan, J. Ruiz, W. Debinski, B. C. Pasche, H. W. Lo, L. J. Metheny-Barlow, R. B. D'Agostino, Jr. and K. Watabe (2018). "Loss of XIST in Breast Cancer Activates MSN-c-Met and Reprograms Microglia via Exosomal miRNA to Promote Brain Metastasis." Cancer Res 78(15): 4316-4330.
Xue, G., G. Jin, J. Fang and Y. Lu (2019). "IL-4 together with IL-1beta induces antitumor Th9 cell differentiation in the absence of TGF-beta signaling." Nat Commun 10(1): 1376.
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Yang, M., M. E. Forbes, R. L. Bitting, S. S. O'Neill, P. C. Chou, U. Topaloglu, L. D. Miller, G. A. Hawkins, S. C. Grant, B. R. DeYoung, W. J. Petty, K. Chen, B. C. Pasche and W. Zhang (2018). "Incorporating blood-based liquid biopsy information into cancer staging: time for a TNMB system?" Ann Oncol 29(2): 311-323.