Biosciences Working Group Publications

2018

Suhartanto H, Yanuar A, Wibisono A, Hermawan D, Bustamam A. The Performance of a Molecular Dynamics Simulation for the Plasmodium falciparum Enoyl-acyl carrier-protein Reductase Enzyme using Amber and GTX 780 and 970 Double Graphical Processing Units. International Journal of Technology. 2018 Jan 1;9(1):150-8. http://ijtech.eng.ui.ac.id/article/view/1186

Juanillas VM, Dereeper A, Beaume N, Droc G, Dizon J, Mendoza JR, Perdon JP, Mansueto L, Triplett L, Lang J, Zhou G, Ratharanjan K, Plale B, Haga J, Leach JE, Ruiz M, Thomson M, Alexandrov N, Larmande P, Kretzschmar T, Mauleon RP. Rice Galaxy: an open resource for plant science. bioRxiv. 2018 Jan 1:358754. https://doi.org/10.1101/358754

Huang PC, Huang CH, Yu HE, Huang WC, Chen CT, Chen JH, Chou CY, Hsu CH. A Flexible and Precise Batch-mode Technique for Multi-threaded GATE Simulation. InProceedings of the International Conference on Parallel and Distributed Processing Techniques and Applications (PDPTA) 2017 (pp. 123-126). The Steering Committee of The World Congress in Computer Science, Computer Engineering and Applied Computing (WorldComp).

2016

Sera C, Matlock S, Watashiba Y, Ichikawa K, Haga JH. 2016. Hydra: A High-throughput Virtual Screening Data Visualization and Analysis Tool. Procedia Computer Science. 80: 2312-16. https://doi.org/10.1016/j.procs.2016.05.427

Haga JH, Ichikawa K, S Date. 2016. Virtual screening techniques and current computational infrastructures. Current Pharmaceutical Design. 22(23): 3576-84. [DOI: 10.2174/1381612822666160414142530]

2015

Suhartanto H, Yanuar A, Bustamam A, Basaruddin T, Yasmin Azizah A, Wibisono A, Hilman MH, Hermawan D. 2015. Using Dedicated and Non Dedicated HPC Cluster and GPU NVIDIA Tesla C2070 Cloud computing environment to simulate Molecular Dynamics of PfENR Enzyme with AMBER. International Journal of Advancements in Computing Technology (IJACT). Vol. 7, No. 2. pp. 30-39.

Nguyen A, Matsunaga A, Tsugawa M, Date S, Ichikawa K, Haga JH.2015. Deployment of a Multi-Site Cloud Environment for Molecular Virtual Screenings. 11th IEEE Int Conf on eScience, Munich, Germany, Oct. 2015. DOI: 10.1109/eScience.2015.49

2014

Luo Y, Plale B, Guo Z, Li WW, Qiu J, Sun Y. 2014. Hierarchical MapReduce: Towards Simplified Cross-Domain Processing, Concurrency and Computation: Practice and Experience, on-line publication 24 Sep 2012 10.1002/cpe.2929. Issue publication Vol 26(4), pp. 878-893, 25 Mar 2014.

Suhartanto H, Yanuar A, Bustamam A, Yasmin Azizah A, Ari Wibisono A, Hilman MH. 2014. Performance Analysis of Molecular Dynamics Simulation of PfENR Enzyme using AMBER on
Cluster and GPU computing environment. International Journal of Advancements in Computing Technology (IJACT). Vol. 6, No. 1. pp. 68-78.

2013

Li D, Tsui B, Xue C, Ichikawa K, Date S, Haga JH. 2013. Protein structure modeling in a grid computing environment. 9th IEEE Int Conf on eScience, Beijing, China. DOI: 10.1109/eScience.2013.15

2012

Syahdi RR, Munim A, Suhartanto H, Yanuar A,. 2012. Virtual screening of Indonesian herbal database as HIV-1 reverse transcriptase inhibitor. Bioinformation. 2012;8(24):1206-10. doi: 10.6026/97320630081206. Epub 2012 Dec 8, http://www.ncbi.nlm.nih.gov/pubmed/23275721

Biosciences Patent

Haga, JH, Chien S, Mui M, Pham PD, Levesque MJ. 2012. SSH-2 (SlingSHot-2) Inhibitors and Methods for Making and Using Them (Patent, PCT/US12/29267).