LONGO: Gene Length-Dependent Expression Analysis Tool in Neuronal CellsPI (R package, R Shiny)
Scalable Overlap-Graph Reduction Algorithms for Genome Assembly using Apache Spark on CloudPI (Spark, GraphX, Amazon Cloud, Scala, Python, Shell)
An overlap-graph de novo metagenome assemblerCo-developer (C++, Python)- 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.
Strain-level genome identification algorithm for biosurveillance using high-performance computing.
Main developer (C++, Python, MPI, OpenMP, Supercomputer)
- 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.
Sipros is a database searching program for shotgun proteomics.Co-developer (C++, Python, MPI, OpenMP, Supercomputer)- 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.
Improving the efficiency of the stochastic simulation algorithm (SSA) for chemical kinetics using numerical implicit methods.
Presenting a new probabilistic framework to analyze the performance of dynamic load balancing algorithms for ensembles of simulations.Main-developer (Fortran 90, Matlab)- T.-H. Ahn, A. Sandu, and X. Han, "Implicit Simulation Methods for Stochastic Chemical Kinetics", In press, Journal of Applied Analysis and Computation, 2015.- 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.- 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, 2011.- 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.- 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.
My role for the project was developing algorithms and simulating cell cycle model with stochastic methods.
Co-developer (Java, Matlab)
- 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.- 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.- 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.
Finding missing genes (new and mis-annotated genes) of dangerous mosquito species with mosquitoes' deep sequencing NGS transriptome data using bioinformatics software tools.
- RNA-Seq, PERL, R, GBrowse, My-SQL