**[18] **Q. Yao, JJ Crosskey, **T.-H. Ahn**, Z. Li, S. Tringe, M. Mayes and C. Pan, "STORM: A Scalable Tool for Merging Pair-end Reads with Variable Insert Sizes", *Bioinformatics*, 2016, (Under Review).

**[17] **M. Land, L. Hauser, S. Jun, I. Nookaew, M. Leuze, **T.-H. Ahn**, T. Karpinets, O. Lund, G. Kora, T. Wassenaar, S. Poudel1, and D. Ussery, "Insights from twenty years of bacterial genome sequencing", *Functional & Integrative Genomics*, 15 (2), pp141-161, 2015, (SCIE, IF=2.69).

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

**[15] **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 Biology, *14(1):207, 2014, (SCI, IF=3.41).

**[14] ****T.-H. Ahn**, J. Chai, and C. Pan, "Sigma:Strain-level Inference of Genomes from Metagenomic Analysis for Biosurveillance",*Bioinformatics*, vol. 31, issue 2, pp. 170-177, 2014, (SCI,IF=5.3).

**[13] **B. Haider, **T.-H. Ahn**, B. Bushnell, J. Chai, A. Copeland, and C. Pan, "Omega: an Overlap-graph *de novo* Assembler for Metagenomics", *Bioinformatics*, vol. 30, issue 19, pp. 2717-2722, 2014, (SCI, IF=5.3).

**[12] **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*, 5, article number 4405, 2014, (SCI, IF=10.015).

**[11] 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*, 2014, (SCIE).

**[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*, 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*, vol. 29, no. 16, pp. 2064-2065, 2013, (SCI, IF=5.3).

**[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* 2011, (Acceptance rate = 24%).

**[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*, vol. 10, issue 6, pp. 1-11, 2011, (SCIE, IF=5.2).

**[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, 2011, (Acceptance rate: 25/141=17.7%).

**[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, 2010, (Acceptance rate: 76/307=25%).

**[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*, vol. 51, no. 1, pp. 27-52, 2009, (SCIE).

**[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.