TY - JOUR AU - Ingolia, N. T. AU - Weissman, J. S. PY - 2008 DA - 2008// TI - Systems biology: reverse engineering the cell JO - Nature VL - 454 UR - https://doi.org/10.1038/4541059a DO - 10.1038/4541059a ID - Ingolia2008 ER - TY - JOUR AU - Lee, W. -. P. AU - Tzou, W. -. S. PY - 2009 DA - 2009// TI - Computational methods for discovering gene networks from expression data JO - Brief Bioinform VL - 10 ID - Lee2009 ER - TY - JOUR AU - Ay, A. AU - Arnosti, D. N. PY - 2011 DA - 2011// TI - Mathematical modeling of gene expression: a guide for the perplexed biologist JO - Crit Rev Biochem Mol Biol VL - 46 UR - https://doi.org/10.3109/10409238.2011.556597 DO - 10.3109/10409238.2011.556597 ID - Ay2011 ER - TY - JOUR AU - Maki, Y. AU - Ueda, T. AU - Okamoto, M. AU - Uematsu, N. AU - Inamura, K. AU - Uchida, K. AU - Takahashi, Y. AU - Eguchi, Y. PY - 2002 DA - 2002// TI - Inference of genetic network using the expression profile time course data of mouse P19 cells JO - Genome Inform VL - 13 ID - Maki2002 ER - TY - JOUR AU - Kikuchi, S. AU - Tominaga, D. AU - Arita, M. AU - Tomita, M. PY - 2003 DA - 2003// TI - Dynamic modeling of genetic networks using genetic algorithm and S-system JO - Bioinformatics VL - 19 UR - https://doi.org/10.1093/bioinformatics/btg027 DO - 10.1093/bioinformatics/btg027 ID - Kikuchi2003 ER - TY - JOUR AU - Noman, N. AU - Iba, H. PY - 2007 DA - 2007// TI - Inferring gene regulatory networks using differential evolution with local search JO - IEEE/ACM Trans Comput Biol Bioinform VL - 4 UR - https://doi.org/10.1109/TCBB.2007.1058 DO - 10.1109/TCBB.2007.1058 ID - Noman2007 ER - TY - JOUR AU - Ho, S. -. Y. AU - Ho, S. -. Y. AU - Hsieh, C. -. H. AU - Huang, H. L. PY - 2007 DA - 2007// TI - "An intelligent two-stage evolutionary algorithm for dynamic pathway identification from gene expression profiles" JO - IEEE/ACM Trans Comput Biol Bioinform VL - 4 UR - https://doi.org/10.1109/tcbb.2007.1051 DO - 10.1109/tcbb.2007.1051 ID - Ho2007 ER - TY - JOUR AU - Kabir, M. AU - Noman, N. AU - Iba, H. PY - 2010 DA - 2010// TI - Reversely engineering gene regulatory network from microarray data using linear time-variant model JO - BMC Bioinform VL - 11 UR - https://doi.org/10.1186/1471-2105-11-S1-S56 DO - 10.1186/1471-2105-11-S1-S56 ID - Kabir2010 ER - TY - JOUR AU - Lee, W. -. P. AU - Hsiao, Y. -. T. PY - 2012 DA - 2012// TI - Inferring gene regulatory networks using a hybrid GA-PSO approach with numerical constraints and network decomposition JO - Inform Sci VL - 188 UR - https://doi.org/10.1016/j.ins.2011.11.020 DO - 10.1016/j.ins.2011.11.020 ID - Lee2012 ER - TY - STD TI - Germany: it-weise.de (self-published). 2009, Available online:http://www.it-weise.de/, UR - http://www.it-weise.de/ ID - ref10 ER - TY - JOUR AU - Bazil, J. N. AU - Qi, F. AU - Beard, D. A. PY - 2011 DA - 2011// TI - A parallel algorithm for reverse engineering of biological networks JO - Integr Biol VL - 3 UR - https://doi.org/10.1039/c1ib00117e DO - 10.1039/c1ib00117e ID - Bazil2011 ER - TY - JOUR AU - Sirbu, A. AU - Ruskin, H. J. AU - Crane, M. PY - 2010 DA - 2010// TI - Comparison of evolutionary algorithms in gene regulatory network model inference JO - BMC Bioinform VL - 11 UR - https://doi.org/10.1186/1471-2105-11-59 DO - 10.1186/1471-2105-11-59 ID - Sirbu2010 ER - TY - JOUR AU - Jostins, L. AU - Jaeger, J. PY - 2010 DA - 2010// TI - Reverse engineering a gene network using an asynchronous parallel evolution strategy JO - BMC Syst Biol VL - 4 UR - https://doi.org/10.1186/1752-0509-4-17 DO - 10.1186/1752-0509-4-17 ID - Jostins2010 ER - TY - CHAP AU - Tominaga, D. AU - Koga, N. AU - Okamoto, M. PY - 2000 DA - 2000// TI - Efficient numerical optimization algorithm based on genetic algorithm for inverse problem BT - Proc Genet Evol Comput Conf ID - Tominaga2000 ER - TY - JOUR AU - Moles, C. G. AU - Mendes, P. AU - Banga, J. PY - 2003 DA - 2003// TI - Parameter estimation in biochemical pathways: a comparison of global optimization methods JO - Genome Res VL - 13 UR - https://doi.org/10.1101/gr.1262503 DO - 10.1101/gr.1262503 ID - Moles2003 ER - TY - JOUR AU - Lee, W. -. P. AU - Hsiao, Y. -. T. PY - 2011 DA - 2011// TI - An adaptive GA-PSO approach with gene clustering to infer S-system models of gene regulatory networks JO - Comput J VL - 54 UR - https://doi.org/10.1093/comjnl/bxr038 DO - 10.1093/comjnl/bxr038 ID - Lee2011 ER - TY - JOUR AU - Kimura, S. AU - Ide, K. AU - Kashihara, A. AU - Kano, M. AU - Hatakeyama, M. AU - Masui, R. AU - Nakagawa, N. AU - Yokoyama, S. AU - Kuramitsu, S. AU - Konagaya, A. PY - 2005 DA - 2005// TI - Inference of S-system models of genetic networks using a cooperative coevolutionary algorithm JO - Bioinformatics VL - 21 UR - https://doi.org/10.1093/bioinformatics/bti071 DO - 10.1093/bioinformatics/bti071 ID - Kimura2005 ER - TY - CHAP AU - Spieth, C. AU - Streichert, F. AU - Speer, N. AU - Zell, A. PY - 2004 DA - 2004// TI - A memetic inference method for gene regulatory networks based on S-Systems BT - Proc Congress Evol Comput ID - Spieth2004 ER - TY - JOUR AU - Alba, E. AU - Tomassini, M. PY - 2002 DA - 2002// TI - Parallelism and evolutionary algorithms JO - IEEE Trans Evol Comput VL - 6 UR - https://doi.org/10.1109/TEVC.2002.800880 DO - 10.1109/TEVC.2002.800880 ID - Alba2002 ER - TY - BOOK AU - Cantú-Paz, E. PY - 2000 DA - 2000// TI - Efficient and accurate parallel genetic algorithms PB - Springer CY - New York ID - Cantú-Paz2000 ER - TY - JOUR AU - Armbrust, M. AU - Fox, A. AU - Griffith, R. AU - Joseph, A. D. AU - Katz, R. AU - Lee, A. G. AU - Patterson, D. AU - Zaharia, M. PY - 2010 DA - 2010// TI - A view of cloud computing JO - Commun ACM VL - 53 UR - https://doi.org/10.1145/1721654.1721672 DO - 10.1145/1721654.1721672 ID - Armbrust2010 ER - TY - JOUR AU - Dean, J. AU - Ghemawat, S. PY - 2008 DA - 2008// TI - MapReduce: simplified data processing on large clusters JO - Commun ACM VL - 51 UR - https://doi.org/10.1145/1327452.1327492 DO - 10.1145/1327452.1327492 ID - Dean2008 ER - TY - JOUR AU - K–H, L. AU - Lee, Y. -. J. AU - Choi, H. AU - Chung, Y. D. AU - Moon, B. PY - 2011 DA - 2011// TI - Parallel data processing with MapReduce: A survey JO - ACM SIGMOD Record VL - 40 ID - K–H2011 ER - TY - JOUR AU - Qiu, J. AU - Ekanayake, J. AU - Gunarathne, T. AU - Choi, J. Y. AU - S–H, B. AU - Li, H. AU - Zhang, B. AU - Wu, T. -. L. AU - Ruan, Y. AU - Ekanayake, S. AU - Hughes, A. AU - Fox, G. PY - 2010 DA - 2010// TI - Hybrid cloud and cluster computing paradigms for life science applications JO - BMC Bioinform VL - 11 UR - https://doi.org/10.1186/1471-2105-11-S12-S3 DO - 10.1186/1471-2105-11-S12-S3 ID - Qiu2010 ER - TY - JOUR AU - Krampis, K. AU - Booth, T. AU - Chapman, B. AU - Tiwari, B. AU - Bicak, M. AU - Field, D. AU - Nelson, K. PY - 2012 DA - 2012// TI - Cloud BioLinux: pre-configured and on-demand bioinformatics computing for the genomics community JO - BMC Bioinform VL - 13 UR - https://doi.org/10.1186/1471-2105-13-42 DO - 10.1186/1471-2105-13-42 ID - Krampis2012 ER - TY - JOUR AU - Schatz, M. C. AU - Labgmead, B. AU - Salzberg, S. L. PY - 2010 DA - 2010// TI - Cloud computing and the DNA data race JO - Nat Biotechnol VL - 28 UR - https://doi.org/10.1038/nbt0710-691 DO - 10.1038/nbt0710-691 ID - Schatz2010 ER - TY - JOUR AU - Pratt, B. AU - Howbert, J. J. AU - Tasman, N. I. AU - Nilsson, E. J. PY - 2012 DA - 2012// TI - MR-Tandem: parallel X! Tandem using Hadoop MapReduce on Amazon Web Services JO - Bioinformatics VL - 28 UR - https://doi.org/10.1093/bioinformatics/btr615 DO - 10.1093/bioinformatics/btr615 ID - Pratt2012 ER - TY - JOUR AU - Taylor, R. C. PY - 2010 DA - 2010// TI - An overview of the Hadoop/MapReduce/HBase framework and its current applications in bioinformatics JO - BMC Bioinform VL - 11 UR - https://doi.org/10.1186/1471-2105-11-S12-S1 DO - 10.1186/1471-2105-11-S12-S1 ID - Taylor2010 ER - TY - JOUR AU - Schatz, M. PY - 2009 DA - 2009// TI - Cloudburst: highly sensitive read mapping with MapReduce JO - Bioinformatics VL - 25 UR - https://doi.org/10.1093/bioinformatics/btp236 DO - 10.1093/bioinformatics/btp236 ID - Schatz2009 ER - TY - JOUR AU - Langmead, B. AU - Hansen, K. D. AU - Leek, J. T. PY - 2010 DA - 2010// TI - Cloud-scale RNA-sequencing differential expression analysis with Myrna JO - Genome Biol VL - 11 UR - https://doi.org/10.1186/gb-2010-11-8-r83 DO - 10.1186/gb-2010-11-8-r83 ID - Langmead2010 ER - TY - CHAP AU - Sadasivam, G. S. AU - Baktavatchalam, G. PY - 2010 DA - 2010// TI - A novel approach to multiple sequence alignment using hadoop data grids BT - Proc Int Workshop Massive Data Anal Cloud ID - Sadasivam2010 ER - TY - JOUR AU - Lewis, S. AU - Csordas, A. AU - Killcoyne, S. AU - Hermjakob, H. AU - Hoopmann, M. R. AU - Moritz, R. L. AU - Deutsch, E. W. AU - Boyle, J. PY - 2012 DA - 2012// TI - Hydra: a scale proteomic search engine which utilizes the Hadoop distributed computing framework JO - BMC Bioinform VL - 13 UR - https://doi.org/10.1186/1471-2105-13-324 DO - 10.1186/1471-2105-13-324 ID - Lewis2012 ER - TY - JOUR AU - Srirama, S. N. AU - Jakovits, P. AU - Vainikko, E. PY - 2012 DA - 2012// TI - Adapting scientific computing problems to clouds using MapReduce JO - Futur Gener Comput Syst VL - 28 UR - https://doi.org/10.1016/j.future.2011.05.025 DO - 10.1016/j.future.2011.05.025 ID - Srirama2012 ER - TY - CHAP AU - Ekanayake, J. AU - Li, H. AU - Zhang, B. AU - Gunarathne, T. AU - S–H, B. AU - Qiu, J. AU - Fox, G. PY - 2010 DA - 2010// TI - Twister: A runtime for iterative MapReduce BT - Proc Nineteenth ACM Int Symp High Perform Distributed Comput ID - Ekanayake2010 ER - TY - BOOK AU - Kennedy, J. AU - Eberhart, R. PY - 2001 DA - 2001// TI - Swarm intelligence PB - Morgan Kaufman Publishers CY - San Francisco, CA ID - Kennedy2001 ER - TY - BOOK AU - Michalewicz, Z. PY - 1999 DA - 1999// TI - Genetic algorithms + data structures = evolution programs PB - Springer CY - Berlin, Germeny ID - Michalewicz1999 ER - TY - JOUR AU - Schaffter, T. AU - Marbach, D. AU - Floreano, D. PY - 2011 DA - 2011// TI - GeneNetWeaver: in silico benchmark generation and performance profiling of network inference methods JO - Bioinformatics VL - 27 UR - https://doi.org/10.1093/bioinformatics/btr373 DO - 10.1093/bioinformatics/btr373 ID - Schaffter2011 ER - TY - JOUR AU - Kim, S. Y. AU - Imoto, S. AU - Miyano, S. PY - 2003 DA - 2003// TI - Inferring gene networks from time series microarray data using dynamic Bayesian networks JO - Brief Bioinform VL - 4 UR - https://doi.org/10.1093/bib/4.3.228 DO - 10.1093/bib/4.3.228 ID - Kim2003 ER - TY - JOUR AU - Balaji, S. AU - Babu, M. M. AU - Iyer, L. M. AU - Luscombe, N. M. AU - Aravind, L. PY - 2006 DA - 2006// TI - Comprehensive analysis of combinatorial regulation using the transcriptional regulatory network of yeast JO - J Mol Biol VL - 360 UR - https://doi.org/10.1016/j.jmb.2006.04.029 DO - 10.1016/j.jmb.2006.04.029 ID - Balaji2006 ER - TY - JOUR AU - Greenfield, A. AU - Madar, A. AU - Ostrer, H. AU - Bonneau, R. PY - 2010 DA - 2010// TI - DREAM4: Combining genetic and dynamic information to identify biological networks and dynamical models JO - PLoS One VL - 5 UR - https://doi.org/10.1371/journal.pone.0013397 DO - 10.1371/journal.pone.0013397 ID - Greenfield2010 ER - TY - BOOK AU - Gradshtenyn, I. S. AU - Ryzhik, I. M. PY - 1980 DA - 1980// TI - Table of integrals, series, and products PB - Academic Press CY - New York ID - Gradshtenyn1980 ER - TY - JOUR AU - Fusaro, V. A. AU - Patil, P. AU - Gafni, E. AU - Wall, D. AU - Tonellato, P. PY - 2011 DA - 2011// TI - Biomedical cloud computing with Amazon web servers JO - PLoS Comput Biol VL - 7 UR - https://doi.org/10.1371/journal.pcbi.1002147 DO - 10.1371/journal.pcbi.1002147 ID - Fusaro2011 ER - TY - JOUR AU - Hill, M. D. AU - Marty, M. R. PY - 2008 DA - 2008// TI - Amdahl's law in the multicore era JO - IEEE Comput VL - 41 UR - https://doi.org/10.1109/MC.2008.209 DO - 10.1109/MC.2008.209 ID - Hill2008 ER - TY - BOOK AU - Amdahl, G. M. PY - 1967 DA - 1967// TI - Validity of the single processor approach to achieving large scale computing capabilities, Proceedings of Amer Federation of Information Processing Societies Conference PB - AFIPS Press CY - USA ID - Amdahl1967 ER - TY - JOUR AU - Chou, I. C. AU - Voit, E. O. PY - 2009 DA - 2009// TI - Recent developments in parameter estimation and structure identification of biochemical and genomic systems JO - Math Biosci VL - 219 UR - https://doi.org/10.1016/j.mbs.2009.03.002 DO - 10.1016/j.mbs.2009.03.002 ID - Chou2009 ER - TY - JOUR AU - Huynh-Thu, V. A. AU - Irrthum, A. AU - Wehenkel, L. AU - Geurts, P. PY - 2010 DA - 2010// TI - Inferring regulatory networks from expression data using tree-based methods JO - PLoS One VL - 5 UR - https://doi.org/10.1371/journal.pone.0012776 DO - 10.1371/journal.pone.0012776 ID - Huynh-Thu2010 ER - TY - JOUR AU - Haury, A. C. AU - Mordelet, F. AU - Vera-Licona, P. AU - Vert, J. -. P. PY - 2012 DA - 2012// TI - TIGRESS: trustful inference of gene regulation using stability selection JO - BMC Syst Biol VL - 6 UR - https://doi.org/10.1186/1752-0509-6-145 DO - 10.1186/1752-0509-6-145 ID - Haury2012 ER - TY - JOUR AU - Bornholdt, S. PY - 2005 DA - 2005// TI - Systems biology: less is more in modeling large genetic networks JO - Sci Signal VL - 310 ID - Bornholdt2005 ER -