Selected Genomics Related Publications

  1. Zhang, Chenyu, Pujan Joshi, Honglin Wang, Seung-Hyun Hong, Riqiang Yan, and Dong-Guk Shin. Pola Viz Reveals Microglia Polarization at Single Cell Level in Alzheimer’s Disease. 2022 IEEE International Conference on Bioinformatics and Biomedicine (BIBM). IEEE, 2022. PDF
  2. Wang, Honglin, Pujan Joshi, Seung-Hyun Hong, Peter F. Maye, David W. Rowe, and Dong-Guk Shin. Predicting the targets of IRF8 and NFATc1 during osteoclast differentiation using the machine learning method framework cTAP. BMC genomics 23, no. 1 (2022): 1-18. PMID:34991467
  3. Joshi P, Basso B, Wang H, Hong SH, Giardina C, Shin DG. rPAC: Route based pathway analysis for cohorts of gene expression data sets. Methods. 2022 Feb;198:76-87. doi: 10.1016/j.ymeth.2021.10.002. Epub 2021 Oct 7. PMID: 34628030; PMCID: PMC8792230.
  4. Wang, Honglin, Pujan Joshi, Seung-Hyun Hong, Peter F. Maye, David W. Rowe, and Dong-Guk Shin. cTAP: A Machine Learning Framework for Predicting Target Genes of a Transcription Factor using a Cohort of Gene Expression Data Sets. In 2020 IEEE International Conference on Bioinformatics and Biomedicine (BIBM), pp. 164-167. IEEE, 2020. PDF
  5. Hoang TH, Zhao Y, Lam Y, Piekos S, Han YC, Reilly C, Joshi P, Hong SH, Sung CO, Giardina C, Shin DG. BioTarget: A Computational Framework Identifying Cancer Type Specific Transcriptional Targets of Immune Response Pathways. Sci Rep. 2019 Jun 21;9(1):9029. doi: 10.1038/s41598-019-45304-x. PMID: 31227749.
  6. Zhao Y, Shin DG. Deep Pathway Analysis V2.0: A Pathway Analysis Framework Incorporating Multi-dimensional Omics Data. IEEE/ACM Trans Comput Biol Bioinform 2019 Oct 7. PMID: 31603796 doi: 10.1109/TCBB.2019.2945959.
  7. Zhao Y, Joshi P, Shin DG. Recurrent Neural Network for Gene Regulation Network construction on Time Series Expression Data. IEEE International Conference on Bioinformatics and Biomedicine (IEEE BIBM 2019), Nov. 18-21, San Diego, CA, USA. PDF
  8. Thibodeau A, Shin DG, TriPOINT: a software tool to prioritize important genes in pathways and their non-coding regulators, Bioinformatics 2019 Aug 1; 35(15), Oxford University Press. PMID: 30566622
  9. Zhao Y, Piekos S,  Hoang TH, Shin DG. A Framework using Topological Pathways for Deeper Analysis of Transcriptome Data.  BMC Special Issue of ISBRA. 2019 (To Be Published) PDF
  10. Shin DJ, Joshi P, Shin DG, Wang L. Genome-Wide Analysis for Identifying FOXO Protein-Binding Sites. Methods Mol Biol2019;1890:193-203doi: 10.1007/978-1-4939-8900-3_16. PubMed PMID: 30414155.
  11. Bae M, Lee Y, Park YK, Shin DG, Joshi P, Hong SH, Alder N, Koo SI, Lee JY. Astaxanthin attenuates the increase in mitochondrial respiration during the activation of hepatic stellate cells. J Nutr Biochem. 2019 Sep;71:82-89. doi: 10.1016/j.jnutbio.2019.06.001. Epub 2019 Jun 20. PMID: 31302374
  12. Hong BY, Sobue T, Choquette L, Dupuy AK, Thompson A, Burleson JA, Salner AL, Schauer PK, Joshi P, Fox E, Shin DG, Weinstock GM, Strausbaugh LD, Dongari-Bagtzoglou A, Peterson DE, Diaz PI. Chemotherapy-induced oral mucositis is associated with detrimental bacterial dysbiosis.Microbiome. 2019 Apr 25;7(1):66. doi: 10.1186/s40168-019-0679-5. PubMed PMID: 31018870; PubMed Central PMCID: PMC6482518.
  13. Becker T, Lee WP, Leone J, Zhu Q, Zhang C, Liu S, Sargent J, Shanker K, Mil-Homens A, Cerveira E, Ryan M, Cha J, Navarro FCP, Galeev T, Gerstein M, Mills RE, Shin DG, Lee C, Malhotra A. FusorSV: an algorithm for optimally combining data from multiple structural variation detection methods. Genome Biol. 2018 Mar 20; 19(1):38. doi: 10.1186/s13059-018-1404-6. PMID: 29559002
  14. Zhao Y, Hoang TH, Joshi P, Hong SH, Giardina C, Shin DG. A route-based pathway analysis framework integrating mutation information and gene expression data. Methods. 2017 Jul 15;124:3-12. PMID: 28647608
  15. Thibodeau A, Márquez EJ, Shin DG, Vera-Licona P, Ucar D. Chromatin interaction networks revealed unique connectivity patterns of broad H3K4me3 domains and super enhancers in 3D chromatin. Sci Rep. 2017 Oct 31;7(1):14466. PMID: 29089515 PMCID: PMC5663946
  16. Thibodeau A, Márquez EJ, Luo O, Ruan Y, Menghi F, Shin DG, Stitzel ML, Vera-Licona P, Ucar D. QuIN: A Web Server for Querying and Visualizing Chromatin Interaction Networks. PLoS Comput Biol. 2016 Jun 23;12(6) PMCID: 27336171 PMCID: PMC491905
  17. Lieberman R, Kranzler HR, Joshi P, Shin DG, Covault J, GABRA2 Alcohol Dependence Risk Allele is Associated with Reduced Expression of Chromosome 4p12 GABAA Subunit Genes in Human Neural Cultures. Alcohol Clin Exp Res. 2015 Sep;39(9):1654-64. doi: 10.1111/acer.12807. Epub 2015 Aug 6 PMID: 26250693 PMCID: PMC4558268
  18. Bayarsaihan D, Shin DG. Epigenetic drug therapy based on bromodomain inhibition. Epigenomics2014;6(5):473-6doi: 10.2217/epi.14.45. PubMed PMID: 25431940.
  19. Zhao Y, Chen MH, Pei B, Rowe D, Shin DG, Xie W, Yu F, Kuo L. A Bayesian Approach to Pathway Analysis by Integrating Gene-Gene Functional Directions and Microarray Data. Stat Biosci 2012;4(1):105-31.PMID: 23482678.
  20. Pei B, Shin DG. Reconstruction of biological networks by incorporating prior knowledge into Bayesian network models. Journal of computational biology: a journal of computational molecular cell biology. 2012; 19(12):1324-34. PMID: 23210479 PMCID: PMC3513982
  21. Shin, DG., Kazmi, S., Baikang, P. Kim, Y-A., Maddox, J., Nori. R. Wong, A., Krueger, W., and Rowe, D. Computing Consistencies between Microarray Data and Known Gene Regulation Relationships”, IEEE Transactions on Information Technology in Biomedicine, 2009; 13(6):1075-82, PMID: 19783507

Selected Skeletal Image Processing Related Publications

  1. Rowe DW, Adams DJ, Hong SH, Zhang C, Shin DG. Renata RC, Chen L, Wu Z, Garland G, Godfrey DA, Sundberg JP, Ackert-Bicknell C, Screening Gene Knockout Mice for Variation in Bone Mass: Analysis by μCT and Histomorphometry, Current Osteoporosis Reports, 2018, 1-18, doi: 10.1007/s11914-018-0421-4. PMID: 29508144    
  2. Dyment NA, Jiang X, Chen L, Hong SH, Adams DJ, Ackert-Bicknell C, Shin DG, Rowe DW. High-Throughput, Multi-Image Cryohistology of Mineralized Tissues. J Vis Exp. 2016 Sep 14;(115). doi: 10.3791/54468. PMID: 27684089 PMCID: PMC5092021
  3. Hong SH, Jiang X, Chen L, Joshi P, Shin DG, Rowe D. Computer-Automated Static, Dynamic and Cellular Bone Histomorphometry. J Tissue Sci Eng. 2012 Dec 24;Suppl 1:004. PMID: 25019033