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Ting Wang, PhD

Research Associate
Fred Hutchinson Cancer Research Center
Clinical Research Division, Tomas Building D4-255
1100 Fairview Ave. N., Seattle, WA 98109

Email:

• wang9ting AT gmail.com
• twang23 AT fredhutch.org

Education  Top

• 2018.8 - 2021.2:
  Research Associate,
  Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
  Supervisor: Dr. William Grady
• 2014.8 - 2018.7:
  Postdoctoral Associate,
  Dept of Pediatrics, University of Pittsburgh, Children’s Hospital of Pittsburgh of UPMC, Pittsburgh, USA
  Supervisor: Dr. Wei Chen
• 2009.9 - 2014.7:
  Ph.D. in Control Science and Engineering, major in Bioinformatics,
  Bioinformatics Division, Center for Synthetic & Systems Biology, TNLIST, Dept. of Automation, Tsinghua University, Beijing, China
  Supervisor: Prof. Yanda Li
• 2005.7 - 2009.9:
  B.E. in Automatic Control,
  Dept. of Automation, Tianjin University, Tianjin, China

Experiences  Top

• 2014.8 - 2018.7: Management of computing servers in Biostatistics Lab at CHP of UPMC
• 2009.9 - 2014.7: Secretary for the member of Chinese Academy of Sciences (Prof. Yanda Li) at THU
• 2011.9 - 2012.1: Teaching assistant of "Probabilistic Graphical Models" course at THU

Research Interests  Top

Interested in many topics on Bioinformatics, Biostatistics, Genetics, Network and Systems Biology, especially:

• Integrative analysis of high-throughput and multi-omics biological data to interpret the development and progression of complex diseases, and to identify molecular biomarkers or therapeutic targets for disease diagnosis or treatment.
• Next generation sequencing (RNA-seq, Chip-seq, ATAC-seq, bisulfite sequencing, small-RNA sequencing, single cell sequencing) and microarray (gene expression, DNA methylation) data analysis.
• Systems and network analysis, pathway analysis.
• Design and application of algorithms in Bioinformatics.
• Machine learning, deep learning and application.

Skills  Top

• Theories of biostatistics, machine learning, automatic control
• Computing server management, pipeline design and implementation
• Computer languages: R, Perl, Shell, Python, C++, Matlab

Awards  Top

• Comprehensive first-class scholarship for graduate students, 2013, Tsinghua University
• Outstanding graduate, 2009, Tianjin University
• National Scholarship, 2008, Tianjin University

Peer-reviewed Publications  Top

1. Willis, Owen P., Ming Yu, Kelly Carter, Ting Wang, Mukta K. Krane, Stacey A. Cohen, Deepti Reddi, Christopher I. Li, Cornelia Ulrich, and William M. Grady. Mo1077 EPIGENETIC AGE ACCELERATION AND COLORECTAL SURGERY OUTCOMES. Gastroenterology 158, no. 6 (2020): S-781.
2. Ting Wang, Sean K. Maden, Georg E. Luebeck, Christopher I. Li, Polly A. Newcomb, Cornelia M. Ulrich, Ji-Hoon E. Joo, Daniel D. Buchanan, Roger L. Milne, Melissa C. Southey, Kelly T. Carter, Amber R. Willbanks, Yanxin Luo, Ming Yu and William M. Grady. Dysfunctional epigenetic aging of the normal colon and colorectal cancer risk. Clinical Epigenetics 12.1 (2020): 1-9. PMID: 31900199.
3. Cancan Qi, Yale Jiang, Ivana V. Yang, Erick Forno, Ting Wang, Judith M. Vonk, Ulrike Gehring, Henriëtte A. Smit, Edith B. Milanzi, Orestes A Carpaij, Marijn Berg, Laura Hesse, Sharon Brouwer, Jonathan Cardwell, Cornelis J. Vermeulen, Edna Acosta-Pérez, Glorisa Canino, Nadia Boutaoui, Maarten van den Berge, Sarah A. Teichmann, Martijn C. Nawijn, Wei Chen, Juan C. Celedón, Cheng-Jian Xu and Gerard H. Koppelman. Nasal DNA methylation profiling of asthma and rhinitis. Journal of Allergy and Clinical Immunology 145.6 (2020): 1655-1663. PMID: 31953105.
4. Anthony R Cillo, Cornelius HL Kürten, Tracy Tabib, Zengbiao Qi, Sayali Onkar, Ting Wang, Angen Liu, Umamaheswar Duvvuri, Seungwon Kim, Ryan J Soose, Steffi Oesterreich, Wei Chen, Robert Lafyatis, Tullia C Bruno, Robert L Ferris, Dario AA Vignali. Immune landscape of viral- and carcinogen-driven head and neck cancer. Immunity 52.1 (2020): 183-199. PMID: 31924475.
5. Guo Y, Ayers JL, Carter KT, Wang T, Maden SK, Edmonds D, Newcomb P, Li C, Ulrich C, Yu M, Grady WM. Senescence-associated tissue microenvironment promotes colon cancer formation through the secretory factor GDF15. Aging Cell (2019): e13013. PMID: 31389184.
6. Chang Liu, Maria Chikina, Rahul Deshpande, Ashley V. Menk, Ting Wang, Tracy Tabib, Erin A. Brunazzi, Kate M. Vignali, Ming Sun, Donna B. Stolz, Robert A. Lafyatis, Wei Chen, Greg M. Delgoffe, Creg J. Workman, Stacy G. Wendell, and Dario A. A. Vignali. Treg Cells Promote the SREBP1-Dependent Metabolic Fitness of Tumor-Promoting Macrophages via Repression of CD8+ T Cell-Derived Interferon-γ. Immunity 51.2 (2019): 381-397. PMID: 31350177.
7. Nadia Boutaoui, Sandeep Puranik, Rong Zhang, Ting Wang, Daniel H. Hui, John Brehm, Erick Forno, Wei Chen, Juan C. Celedón. Epigenome-wide effects of vitamin D on asthma bronchial epithelial cells. Epigenetics 14.9 (2019): 844-849. PMID: 31122150.
8. Micol Falabella, Jill Kolesar, Callen Wallace, Daniel de Jesus, Linqing Sun, Yumiko Taguchi, Catherine Wang, Ting Wang, Irene Xiang, Jonathan Alder, Rathena Maheshan, William Horne, Joshua Turek-Herman, Patrick Pagano, Claudette St. Croix, Neal Sondheimer, Liliya Yatsunyk, F. Brad Johnson, Brett Kaufman. G-quadruplex dynamics contribute to regulation of mitochondrial gene expression. Scientific Reports 9.1 (2019): 5605. PMID: 30944353.
9. Yale Jiang, Olena Gruzieva, Ting Wang, Erick Forno, Nadia Boutaoui, Tao Sun, Simon K. Merid, Edna Acosta- Pérez, Inger Kull, Glorisa Canino, Josep M. Antó, Jean Bousquet, Erik Melén, Wei Chen, Juan C. Celedó. Transcriptomics of atopy and atopic asthma in white blood cells from children and adolescents. European Respiratory Journal 9.1 (2019): 2045-2322. PMID: 30923181.
10. Erick Forno, Ting Wang (co-first author), Cancan Qi, Qi Yan, Cheng-Jian Xu, Nadia Boutaoui, Yueh-Ying Han, Daniel E Weeks, Yale Jiang, Franziska Rosser, Judith M Vonk, Sharon Brouwer, Edna Acosta-Perez, Angel Colón-Semidey, María Alvarez, Glorisa Canino, Gerard H. Koppelman, Wei Chen, Juan C. Celedón. DNA methylation in nasal epithelium, atopy, and atopic asthma in children: a genome-wide study. The Lancet Respiratory Medicine 7, no. 4 (2019): 336-346. PMID: 30584054.
11. Zhou Fang, Tianzhou Ma, Gong Tang, Li Zhu, Qi Yan, Ting Wang, Juan C. Celedón, Wei Chen and George C. Tseng. Bayesian integrative model for multi-omics data with missingness. Bioinformatics 1 (2018): 8. PMID: 30184058.
12. Kristy Boggs, Ting Wang (co-first author), Abrahim I. Orabi, Tanveer A. Javed, Tao Sun, John F. Eisses, Farzad Esni, Wei Chen, Sohail Z. Husain. Pancreatic gene expression during recovery after pancreatitis reveals unique transcriptome profiles. Scientific Reports 8.1 (2018): 1406, DOI: http://doi.org/10.1038/s41598-018-19392-0. PMID: 29362419.
13. Tracy Tabib, Christina Morse, Ting Wang, Wei Chen, Robert Lafyatis. SFRP2/DPP4 and FMO1/LSP1 define major fibroblast populations in human skin. Journal of Investigative Dermatology (2017). DOI: https://doi.org/10.1016/j.jid.2017.09.045. PMID: 29080679.
14. Zhe Sun, Ting Wang, Ke Deng, Xiao-Feng Wang, Robert Lafyatis, Ying Ding, Ming Hu, and Wei Chen. DIMM-SC: A Dirichlet mixture model for clustering droplet-based single cell transcriptomic data. Bioinformatics.(2017), btx490, https://doi.org/10.1093/bioinformatics/btx490. PMID: 29036318.
• Software: DIMMSC, an R package for clustering the droplet-based single cell RNA-seq data.
15. Erick Forno, Ting Wang (co-first author), Qi Yan, John Brehm, Edna Acosta-Perez, Angel Colon-Semidey, Maria Alvarez, Nadia Boutaoui, Michelle M. Cloutier, John F. Alcorn, Glorisa Canino, Wei Chen, Juan C. Celedón. A multi-omics approach to identify genes associated with childhood asthma risk and morbidity. American Journal of Respiratory Cell and Molecular Biology (2017). DOI: 10.1165/rcmb.2017-0002OC. PMID: 28574721.
16. Wei Chen, Ting Wang (co-first author), Maria Pino-Yanez, Erick Forno, Liming Liang, Qi Yan, Donglei Hu, Daniel E. Weeks, Andrea Baccarelli, Edna Acosta-Perez, Celeste Eng, Yueh-Ying Han, Nadia Boutaoui, Catherine Laprise, Gwyneth A. Davies, Julian M. Hopkin, Miriam F. Moffatt, William O.C.M. Cookson, Glorisa Canino, Esteban G. Burchard, Juan C. Celedón. An epigenome-wide association study of total serum IgE in Hispanic children. Journal of Allergy and Clinical Immunology (2017). DOI: 10.1016/j.jaci.2016.11.030. PMID: 28069425.
17. Sandeep Puranik, Ting Wang (co-first author), John M. Brehm, Daniel Hui, Nadia Boutaoui, Wei Chen, Erick Forno, and Juan C Celedón. Assay For Transposase-Accessible Chromatin Sequencing (ATAC-Seq) To Study The Effects Of Vitamin D On Bronchial Epithelial Cells. In A66. THE MANY FACES OF ASTHMA IN CHILDHOOD, pp. A2226-A2226. American Thoracic Society, 2017.
18. Kong Chen, Zhe Sun, Ting Wang, Wei Chen, and Jay Kolls. Epigenetic Regulation Of Proinflammatory Chemokines In Cystic Fibrosis Lung Epithelium. In A31. MECHANISMS IN CYSTIC FIBROSIS AND OTHER BRONCHIECTATIC DISEASES, pp. A1267-A1267. American Thoracic Society, 2017.
19. Ting Wang, Richard H. Duerr, and Wei Chen. An integrative analysis of ATAC-seq and RNA-seq data in activated, CD4+ CD45RO+ CD196+ human T cells treated with IL-1B and IL-23 with or without PGE2. Proceedings of the 7th ACM International Conference on Bioinformatics, Computational Biology, and Health Informatics. ACM, 2016.
20. Kong Chen, Taylor Eddens, Giraldina Trevejo-Nunez, Emily E. Way, Waleed Elsegeiny, David M. Ricks, Abhishek V. Garg, Carla J. Erb, Meihua Bo, Ting Wang, Wei Chen, Janet S. Lee, Sarah L. Gaffen, Jay Kolls. IL-17 Receptor Signaling in the Lung Epithelium Is Required for Mucosal Chemokine Gradients and Pulmonary Host Defense against K. pneumoniae. Cell Host & Microbe 20.5 (2016):596-605. PMID: 27923703.
21. Kong Chen, Brian T. Campfield, Sally E. Wenzel, Jeremy P. McAleer, James L. Kreindler, Geoffrey Kurland, Radha Gopal, Ting Wang, Wei Chen, Taylor Eddens, Kathleen M. Quinn, Mike M. Myerburg, William T. Horne, Jose M. Lora, Brian K. Albrecht, Joseph M. Pilewski, Jay K. Kolls. Antiinflammatory effects of bromodomain and extraterminal domain inhibition in cystic fibrosis lung inflammation. JCI Insight 1.11 (2016): e87168. doi:10.1172/jci.insight.87168.
22. Ting Wang, Zhao Ren, Ying Ding, Zhou Fang, Matthew L. MacDonald, Robert A. Sweet, Wei Chen. FastGGM: An efficient algorithm for the inference of Gaussian graphical model in biological networks. PloS Computational Bioloy 12.2 (2016): e1004755. PMID: 26872036.
• Software: FastGGM, an efficient R package for inferring Gaussian graphical model.
23. Ting Wang, Weihua Guan, Jerome Lin, Nadia Boutaoui, Glorisa Canino, Jianhua Luo, Juan Carlos Celedón, and Wei Chen. A systematic study of normalization methods for Infinium 450K methylation data using whole-genome bisulfite sequencing data. Epigenetics 10.7 (2015): 662-669. PMID: 26036609.
24. Chen, Wei, John M. Brehm, Jerome Lin, Ting Wang, Erick Forno, Edna Acosta-Pérez, Nadia Boutaoui, Glorisa Canino, and Juan C. Celedón. Expression Quantitative Trait Loci (eQTL) Mapping in Puerto Rican Children. PloS one 10, no. 3 (2015). PMID: 25816334.
25. Ting Wang, Jin Gu, Yanda Li. Inferring the perturbed microRNA regulatory networks from gene expression data using a network propagation based method. BMC bioinformatics 15.1 (2014): 255. PMID: 25069957.
• Software: NP-miRNA, a network propagation based method for inferring perturbed miRNA regulatory networks.
26. Dongfang Wang, Jin Gu, Ting Wang and Zijian Ding. OncomiRDB: a database for the experimentally verified oncogenic and tumor-suppressive microRNAs. Bioinformatics 30.15 (2014): 2237-2238. PMID: 24651967.
• Database: OncomiRDB, a database for the experimentally verified oncogenic and tumor-suppressive microRNAs.
27. Ting Wang, Jin Gu, Jun Yuan, Ran Tao, Yanda Li and Shao Li. Inferring pathway crosstalk networks using gene set co-expression signatures. Mol. BioSyst., 2013, 9(7):1822-1888. PMID: 23591523.
• Software: sGSCA, signature-based gene set co-expression analysis using sparse canonical correlation analysis.

Conference Presentations/Abstracts  Top

1. Ting Wang. Dysfunctional epigenetic aging of the normal colon and colorectal cancer risk. Masoro-Barshop Conference on Aging. Oct. 2020. (Virtual talk)
2. Ting Wang. Epigenome- and transcriptome-wide analyses of atopic asthma in nasal epithelium and white blood cells of Hispanic children. CHP Pulmonary Research Conference, Oct. 2017. Pittsburgh, PA, USA. (Talk)
3. Ting Wang. An epigenome-wide association study of total serum immunoglobulin E in Hispanic children. CHP Pulmonary Research Conference. Nov. 2016. Pittsburgh, PA, USA. (Talk)
4. Ting Wang. FastGGM: An Efficient Algorithm for the Inference of Gaussian Graphical Model in Biological Networks. q-Med, Nov. 2016. Pittsburgh, PA, USA. (Poster)
5. Ting Wang. An integrative analysis of ATAC-seq and RNA-seq data in activated, CD4+CD45RO+CD196+ human T cells treated with IL-1B and IL-23 with or without PGE2. ACM-BCB, Oct. 2016. Seattle, WA, USA. (Poster)
6. Ting Wang. A systematic study of normalization methods for Infinium 450K methylation data using whole-genome bisulfite sequencing data. ASHG, 2015. Baltimore, MD, USA. (Poster)
7. Ting Wang. Construction and inference of large-scale biological networks using Gaussian graphical model. ASHG, 2015. Baltimore, MD, USA. (Poster)
8. Ting Wang. Network-based gene set perturbation analysis to identify causal or therapeutic miRNAs for cancers. RECOMB, 2013. Beijing, China. (Poster)
9. Ting Wang. GS-LMMA—An approach to construct the functional pathway networks for cancers. CSHL Meeting on System Biology: Global Regulation of Gene Expression. Mar. 2012. CSHL, NY, USA. (Poster)
10. Ting Wang. Defining gene expression adaptive responses regulated by microRNAs and transcription factors in human umbilical vein endothelial cells. CSHA Conference on Computational Biology. Oct. 2010. Suzhou, China. (Talk)

Editorial Experiences  Top

1. Editorial Board: Case Reports Journal; Annals of Medical Case Reports; SM Journal of Chronic Diseases; SM Pulmonology & Clinical Research; Immunology & Auto immune Diseases; Chronic Journal of Allergy and Immunology.
2. Invited Reviewer: Bioinformatics; Scientific Reports; PLOS ONE; BMC Bioinformatics; Frontiers of Computer Science; Pediatric Allergy, Immunology, and Pulmonology; SAGE Open Medicine; BioMed Research International; Infectious Diseases; SM Journal of Chronic Diseases; Journal of the Royal Society Interface; Mediators of Inflammation; International Journal of Carcinogenesis and Mutagenesis.