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Peer Reviewed Journals and Proceedings

[27] K. Bockerstett, S. Lewis, K. Wolf, C. Noto, N. Jackson, E. Ford, T.-H. Ahn, R. DiPaolo "Single Cell Transcriptional Analyses of Spasmolytic Polypeptide Expressing Metaplasia Arising from Acute Drug Injury and Chronic Inflammation in the Stomach", Gut, (IF=17.016), 2019. (In print)

[26] A. Paul, D. Lawrence, M. Song, S.-H. Lim, C. Pan, and T.-H. Ahn*, "Using Apache Spark on Genome Assembly for Scalable Overlap-graph Reduction", BMC Human Genomics, (IF=2.942), 2019. (In print)

[25] V. K. Epuri, S. Sakala, T.-H. Ahn, and M. Song, "Tool Support for Managing RepetitiveProgram Changes in Evolving Software", IET Software, (IF=1.07), 2019.

[24] Z. Harris, E. Dhungel, M. Mosior, and T.-H. Ahn*, "Massive Metagenomic Data Analysis using Abundance-Based Machine Learning", Biology Direct, (IF=2.649), 2019.

[23] J. McMillan, Z. Lu, J. Rodriguez, T.-H. Ahn*, and Z. Lin*, "YeasTSS: An Integrative Web Database of Yeast Transcription Start Sites", Database (Oxford), (IF=3.987), Volume 2019, baz048 (*: co-corresponding authors), 2019.

[22] W. Feng, Z. Yu, M. Kang, H. Gong*, and T.-H. Ahn*, "Practical Evaluation of Different Omics Data Integration Methods", in Precision Health and Medicine. W3PHAI 2019. Studies in Computational Intelligence, vol 843. Springer, Cham, 2019.

[21] A. Paul, D. Lawrence, M. Song, S.-H. Lim, C. Pan, and T.-H. Ahn*, "SORA: Scalable Overlap-graph Reduction Algorithms for Genome Assembly using Apache Spark in the Cloud", in proceedings of the 2018 IEEE International Conference on Bioinformatics and Biomedicine (BIBM), 2018.

[20] K. Wolf, T. Hether, P. Gilchuk, A. Kumar, A. Rajeh, C. Schiebout, J. Maybruck, R. M. Buller, T.-H. Ahn, S. Joyce, R. DiPaolo, "Identifying and Tracking Low Frequency Virus-Specific TCR Clonotypes Using High-Throughput Sequencing", Cell Reports (IF=8.032), VOLUME 25, ISSUE 9, P2369-2378.E4, 2018

[19] M. McCoy, A. Paul, M. Victor, M. Richner, H. Gabel, H. Gong, A. Yoo*, and T.-H. Ahn*, "LONGO: An R Package for Interactive Gene Length Dependent Analysis for Neuronal Identity" , Bioinformatics (IF=5.481), vol. 34, issue 13, pp. i422-428, ISMB-2018, 2018.

[18] Paul, A.J., D. Lawrence, and T.-H. Ahn*, "Overlap Graph Reduction for Genome Assembly using Apache Spark", in Proceedings of the 8th ACM International Conference on Bioinformatics, Computational Biology,and Health Informatics. ACM-BCB 2017, ACM: Boston, Massachusetts, USA. poster, p. 613-613, 2017.

[17] T.-H. Ahn, X. Han, and A. Sandu, Implicit Simulation Methods for Stochastic Chemical Kinetics", Journal of Applied Analysis and Computation (IF=1.063), 5 (3), pp. 420-452, 2015.

[16] M. Land, L. Hauser, S. Jun, I. Nookaew, M. Leuze, T.-H. Ahn, T. Karpinets, O. Lund, G. Kora, T. Wassenaar, S. Poudel, and D. Ussery, "Insights from 20 years of bacterial genome sequencing", Functional & Integrative Genomics (IF=3.889), 15 (2), pp141-161, 2015.

[15] T.-H. Ahn, J. Chai, and C. Pan, "Sigma:Strain-level Inference of Genomes from Metagenomic Analysis for Biosurveillance", Bioinformatics (IF=5.481), vol. 31, issue 2, pp. 170-177, 2015.

[14] T.-H. Ahn, A. Sandu, L.T. Watson, C.A. Shaffer, Y. Cao, and W.T. Baumann, "A Framework to Analyze the Performance of Load Balancing Schemes for Ensembles of Stochastic Simulations", International Journal of Parallel Programming (IF=0.897), Vol. 43 Issue 4, pp 597-630, 2015.

[13] J. Chai, G. Kora, T.-H. Ahn, D. Hyatt, and C. Pan, "FunctionalPhylogenomics Analysis of Bacteria and Archaea using Consistent GenomeAnnotation with UniFam", BMC Evolutionary Biolog (IF=3.027), 14(1):207, 2014.

[12] B. Haider, T.-H. Ahn, B. Bushnell, J. Chai, A. Copeland, and C. Pan, "Omega: an Overlap-graph de novo Assembler for Metagenomics", Bioinformatics (IF=5.481), vol. 30, issue 19, pp. 2717-2722, 2014.

[11] Z. Li, Y. Wang, Q. Yao, N.B. Justice, T.-H. Ahn, D. Xu, R.L. Hettich, J.F. Banfield, and C. Pan, "Diverse and divergent post-translational modification of proteins of closely related bacteria in two growth stages of a natural microbial community", Nature Communication (IF=12.353), 5, article number 4405, 2014.

[10] D. Dechev and T.-H. Ahn, "Using SST/macro for Effective Analysis of MPI-based Applications: Evaluating Large-Scale Genomic Sequence Search", IEEE Access (IF=3.557), vol. 1, pp. 428-435, 2013.

[9] Y. Wang, T.-H. Ahn, Z. Li, and C. Pan, "Sipros/ProRata: a versatile informatics system for quantitative community proteomics", Bioinformatics (IF=5.481), vol. 29, no. 16, pp. 2064-2065, 2013.

[8] T.-H. Ahn and A. Sandu, "Implicit Second Order Weak Taylor Tau-Leaping Methods for the Stochastic Simulations of Chemical Kinetics", Procedia Computer Science, Volume 4, pp 2297-2306, International Conference on Computational Science, ICCS (Acceptance rate = 24%), 2011.

[7] D.A. Ball, T.-H. Ahn, P. Wang, K.C. Chen, Y. Cao, J.J. Tyson, J. Peccoud, and W.T. Baumann, "Stochastic Exit from Mitosis in Budding Yeast: Model Predictions and Experimental Observations", Cell Cycle (IF=3.952), vol. 10, issue 6, pp. 1-11, 2011.

[6] T.-H. Ahn, D. Dechev, H. Lin, H. Adalsteinsson and C. Janssen, "Evaluating Performance Optimizations of Large-Scale Genomic Sequence Search Applications Using SST/macro", in Proceedings of International Conference on Simulation and Modeling Methodologies, Technologies and Applications (SIMULTECH 2011), Noordwijkerhout, Netherlands, (Acceptance rate: 25/141=17.7%), 2011.

[5] T.-H. Ahn and A. Sandu, "Fully Implicit Tau-Leaping Methods for the Stochastic Simulation of Chemical Kinetics", in Proceedings of the 19th High Performance Computing Symposium (HPC 2011) part of the 2011 Spring Simulation Multiconference, ser. SpringSim '11, Boston, MA, USA: Society for Computer Simulation International, 2011.

[4] T.H. Ahn and A. Sandu, "Parallel Stochastic Simulations of Budding Yeast Cell Cycle: Load Balancing Strategies and Theoretical Analysis", in Proceedings of the First ACM International Conference on Bioinformatics and Computational Biology, ser. BCB '10, New York, NY, USA:ACM, pp. 237-246, (Acceptance rate: 76/307=25%), 2010.

[3] T.-H. Ahn, L. T. Watson, Y. Cao, C. A. Shaffer, and W. T. Baumann, "Cell cycle modeling for budding yeast with stochastic simulation algorithms", Computer Modeling in Engineering and Sciences (IF=0.75), vol. 51, no. 1, pp. 27-52, 2009.

[2] T.-H. Ahn, P. Wang, L.T. Watson, Y. Cao, C.A. Shaffer, and W.T. Baumann, "Stochastic cell cycle modeling for budding yeast", in Proceedings of the 2009 Spring Simulation Multiconference, ser. SpringSim '09, San Diego, CA, USA: Society for Computer Simulation International, pp. 113:1-113:6, 2009.

[1] T.-H. Ahn, Y. Cao, and L.T. Watson, "Stochastic Simulation Algorithms for Chemical Reactions," in Proceedings of the 2008 International Conference on Bioinformatics & Computational Biology, BIOCOMP'08, Las Vegas, Nevada, USA, pp. 431-436, July, 2008.