Journals

  1. Skol AD., Jung SC, Sokovic AM, Chen S, Fazal S, Sosina O, Borkar PP, Lin A, Sverdlov M, Cao D, Swaroop A, Bebu I, DCCT/ EDIC Study group, Stranger BE, Grassi MA. Integration of genomics and transcriptomics predicts diabetic retinopathy susceptibility genes. . Elife. 9:e59980, 2020.doi:10.7554/eLife.59980.
  2. Funk CC, Casella AM, Jung S, Richards MA, Rodriguez A, Shannon P, Donovan R, Heavner B, Chard K, Xiao Y, Glusman G, Erteskin-Taner N, Golde T, Toga A, Hood L, Van Horn JD, Kesselman C, Foster I, Madduri R, Price ND, Ament S. Atlas of Transcription Factor Binding Sites from ENCODE DNase Hypersensitivity Data Across 27 Tissue Types . Cell Reports. 32(7):108029, 2020. doi:10.1016/j.celrep.2020.108029.
  3. Ebenezer DL, Fu P, Krishnan Y, Maienschein-Cline M, Hu H, Jung SC, Madduri R, Arbieva Z, Harijith A, Natarajan V. Genetic deletion of Sphk2 confers protection against Pseudomonas aeruginosa mediated differential expression of genes related to virulent infection and inflammation in mouse lung . BMC Genomics. (2019) 20:984 doi:10.1186/s12864-019-6367-9.
  4. Madduri R, Chard K, D’Arcy M, Jung SC, Rodriguez A, Sulakhe D, Deutsch E, Funk C, Heavner B, Richards M, Shannon P, Glusman G, Price N, Kesselman C, Foster I. Reproducible big data science: A case study in continuous FAIRness . PloS one. (14)4:e0213013, 2019. doi.org/10.1371/journal.pone.0213013. PMID:30973881.
  5. Al-Khersan H, Shah KP, Jung SC, Rodriguez A, Madduri RK, Grassi MA. A novel MERTK mutation causing retinitis pigmentosa . Graefe's Archive for Clinical and Experimental Ophthalmology. pp 1–7, 2017. doi:10.1007/s00417-017-3679-9. PMID:28462455.
  6. Mulder NJ, Adebiyi E, Adebiyi M, Adeyemi S, Ahmed A, Ahmed R, Akanle B, Alibi M, Armstrong DL, Aron S, Ashano E, Baichoo S, Benkahla A, Brown DK, Chimusa ER, Fadlelmola FM, Falola D, Fatumo S, Ghedira K, Ghouila A, Hazelhurst S, Isewon I, Jung S, Kassim SK, Kayondo JK, Mbiyavanga M, Meintjes A, Mohammed S, Mosaku A, Moussa A, Muhammd M, Mungloo-Dilmohamud Z, Nashiru O, Odia T, Okafor A, Oladipo O, Osamor V, Oyelade J, Sadki K, Salifu SP, Soyemi J, Panji S, Radouani F, Souiai O, Tastan Bishop Ö; H3ABioNet Consortium, as members of the H3Africa Consortium.. Development of Bioinformatics Infrastructure for Genomics Research in H3Africa . Global Heart. pii: S2211-8160(17)30005-4, 2017. doi:10.1016/j.gheart.2017.01.005. PMID:28302555.
  7. Shilpi A, Bi Y , Jung S, Patra SK, Davuluri RV. Identification of Genetic and Epigenetic Variants Associated with Breast Cancer Prognosis by Integrative Bioinformatics Analysis . Cancer Informatics. 16:1-13, 2017. doi:10.4137/CIN.S39783. PMID:28096648.
  8. Jin H, Jung S, DebRoy AR, and Davuluri RV. Identification and validation of regulatory SNPs that modulate transcription factor chromatin binding and gene expression in prostate cancer. Oncotarget, 2016. doi:10.18632/oncotarget.10520. PMID:27409348.
  9. Jung S, Jin H, and Davuluri RV. Identification of candidate regulatory SNPs by integrative analysis for prostate cancer genome data. Proceedings of the 6th ACM Conference on Bioinformatics, Computational Biology, and Health Informatics, ACM, 278–285, 2015. doi:10.1145/2808719.2808748.
  10. Jung S, Bi Y, and Davuluri RV. Evaluation of data discretization methods to derive platform independent gene expression signatures for multi-class tumor subtyping. BMC genomics. 16 (Suppl 11), S3, 2015. doi:10.1186/1471-2164-16-S11-S3. PMID:26576613.
  11. Kim N, Laing C, Elmetwaly S, Jung S, Curuksu J, and Schlick T. Graph-based Sampling Approach for Approximating Global Helical Topologies of RNA. Proc. Natl. Acad. Sci. U.S.A. 111(11):4079–4084, 2014. doi:10.1073/pnas.1318893111. PMID:24591615.
  12. Jung S and Schlick. Interconversion between Parallel and Antiparallel Conformations of a 4H RNA junction in Domain 3 of Foot-and-Mouth-Disease Virus IRES Captured by Dynamics Simulations. Biophysical J. 106(2): 447–458, 2014. doi:10.1016/j.bpj.2013.12.008. PMID:24461020.
  13. Laing C*, Jung S*, Kim N, Elmetwaly S, Zahran M, and Schlick T (*equal contribution). Predicting Helical Topologies in RNA Junctions as Tree Graphs. PLoS One. 8(8):e71947, 2013. doi:10.1371/journal.pone.0071947. PMID:23991010.
  14. Jung S and Schlick T. Candidate RNA Structures for Domain 3 of the Foot-and-Mouth-Disease Virus Internal Ribosome Entry Site. Nucleic Acids Res. 41(3):1483–1495, 2012. 10.1093/nar/gks1302. PMID:23275533.
  15. Schlick T, Collepardo-Guevara R, Halvorsen LA, Jung S and Xiao X. Biomolecular Modeling and Simulation: A Field Coming of Age. Q. Rev. Biophys. 44(2):191–228, 2011. doi:10.1017/S0033583510000284 .PMID:21226976.
  16. Laing C, Jung S, Iqbal A, and Schlick T. Tertiary motifs revealed in analyses of higher order RNA junctions. J. Mol. Biol. 393(1):67–82, 2009. doi:10.1016/j.jmb.2009.07.089. PMID:19660472.
  17. Yousef M, Jung S, Showe LC and Showe MK. Learning from Positive Examples when the Negative Class is Undetermined-microRNA gene identification. Algorithms Mol Biol. 3:2, 2008. doi:10.1186/1748-7188-3-2. PMID:18226233.
  18. Yousef M, Jung S, Kossenkov AV, Showe LC and Showe MK. Naive Bayes classifier for microRNA target gene identification. Bioinformatics. 23(22):2987–92, 2007. doi:10.1093/bioinformatics/btm484. PMID:17925304.
  19. Yousef M, Jung S, Showe LC and Showe MK. Recursive Cluster Elimination (RCE) for Classification and Feature Selection from Gene Expression Data. BMC Bioinformatics. 8:144, 2007. doi:10.1186/1471-2105-8-144. PMID:19077196.

Abstracts

  1. Magnan CN, Lau-Rivera S, Diaz FL, Ou C, Thomas B, Nam H, Weiss LM, Jung SC, Funari VA.An efficient probe design algorithm for direct fusion targeting from RNA . Cancer Research (2021). 3:E4(E5), Proceedings: AACR Annual Meeting, 2021.
  2. Jung SC, Thangavelu M, Nam H, Bender R, Agersborg S, Weiss LM, Funari VA.Accessing Genomic Alternations in Chronic Lymphocytic Leukemia Using an NGS-Based Comprehensive Genomic Profiling Assay . Blood (2020). 136 (Supplement 1):8, Proceedings: ASH 2020. doi:10.1182/blood-2020-141690
  3. Yu Y, Alarcon F, Mou Y, Jung SC, Nam H, Thomas B, Keeler L, Shinbrot E, Magnan C, Weiss T, Bender R, Jiang SP, Agersborg S, Weiss LM, Ye F, Funari VA.A Novel Multimodal Next Generation Sequencing Assay with Total Nucleic Acid Input to Provide Comprehensive Genomic Profiling for Hematologic Malignancies . Blood (2020). 136 (Supplement 1):29-30, Proceedings: ASH 2020. doi:10.1182/blood-2020-140460
  4. Jung SC, Yu Y, Mou Y, Nam H, Wong C, Koo S, Thomas B, Blocker F, Lyle D, Bender R, Agersborg S, Weiss LM, Funari VA.A comprehensive genomic profiling approach to interrogate hematologic malignancies using a novel multimodal next generation sequencing assay in a single-tube . Cancer Research. 80 (16 Suppl), Proceedings: AACR Annual Meeting, 2020. doi:10.1158/1538-7445.AM2020-182
  5. Ebenezer DL, Fu P, Krishnan YH, Jung SC, Hu H, Arbieva Z, Madduri R, Harijith AK, and Natarajan V.Expression profiling of genes regulated by Sphingosine kinase 2 in a murine model of Pseudomonas aeruginosa mediated acute lung inflammation. The FASEB Journal. Vol. 32, No. 1_supplement, 2018. doi:10.1096/fasebj.2018.32.1_supplement.540.11.
  6. Funk CC, Richards MA, Shannon P, Donovan-Maiye R, Rappaport N, Robinson M, Allen M, Carrasquillo MM, Chakrabarty P, McFarland K, Jung SC, Rodriguez A, Ertekin-Taner N, Golde TE, Hood L, Foster I, Ament S, Madduri R, Price ND.MECHANISTIC AND DIRECTIONAL TRANSCRIPTIONAL REGULATORY NETWORKS IN ALZHEIMER’S DISEASE. The Journal of the Alzheimer's Association. Volume 14, Issue 7, Supplement, Pages P1014–P1015, 2018. doi:10.1016/j.jalz.2018.06.2782.
  7. Jung S, Bi Y and Davuluri RV. Informatics framework for clustering and deriving gene signatures for prognostic stratification of cancer patients. Cancer Research. 75 (15 Suppl), 2185, Proceedings: AACR 106th Annual Meeting 2015. doi:10.1158/1538-7445.AM2015-2185.
  8. Jung S, Bi Y and Davuluri RV. Comparison of Data Discretization Methods for Cross Platform Transfer of Gene-expression based Tumor Subtyping Classifier. IEEE, 2014. doi:10.1109/ICCABS.2014.6863918.

Theses

  1. Jung S. Modeling RNA junctions with applications to structure predictions of regulatory regions of viral RNA. Ph.D. thesis, New York Univ., 2013.
  2. Jung S. One-Class Machine Learning Approach for MicroRNA Gene Predictions. Master thesis, Drexel Univ., 2007.