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The following is a list of grants, papers, and MS theses that have been computationally supported by, or based on computation that occurred on Beocat.

Grants

2010

  • NSF EPSCoR 1006860 (PI: Andresen) “Prairie Light: Next Generation Networking for Midcontinent Science,” $1,176M August, 2010
  • NIH R01 GM074096 (PI: Tomich) “Model Synthetic Channel Assemblies”, 05/01/10 – 04/30/15
  • NSF MCB 0952514 (PI: Chen) “CAREER: Implicit Modeling of Nonpolar Solvation: Towards Reliable Atomistic Simulation of Intrinsically Disordered Proteins”, 02/01/10 – 01/30/15
  • CAREER: Reasoning under Uncertainty in Cybersecurity (PI). National Science Foundation (Award #0954138). $429,661, 3/1/2010 - 2/28/2015.

2009

  • NSF CPS (Award no. 0932289), “CPS:Medium:Collaborative Research:Infrastructure and Technology Innovations for Medical Device Coordination,” $839,548 September, 2009.
  • NSF CNH (Award no. 0909515), “Hyper-extractive Economies and Sustainability: Policy Scenarios for Sustainable Water Use in the High Plains Aquifer,” $1.5M September, 2009.
  • NSF EPSCoR RII Track II (Award no. 0919443), “Oklahoma and Kansas: A cyberCommons for Ecological Forecasting,” $3M ($1.5M to K-State, $6M between KS and OK) September, 2009.
  • Xia, J., Caragea, D. and Brown, S.J. (2009). Prediction of alternatively spliced exons using support vector machines. In: International Journal on Data Mining and Bioinformatics (IJDMB). To appear.
  • Caragea, C., Silvescu, A., Caragea, D. and Honavar, V. (2009). Abstraction Augmented Markov Models. In: Proceedings of the NIPS Workshop on Machine Learning in Computational Biology (MLCB).
  • Xia, J., Caragea, D. and Hsu, W. (2009). Multi Relational Network Analysis Using a Fast Random Walk with Restart. In: Proceedings of the IEEE International Conference on Data Mining (ICDM 2009), Miami, FL.
  • Haridas, M. and Caragea, D. (2009) Exploring Wikipedia and DMoz as Knowledge Bases for Engineering a User Interests Hierarchy for Social Network Applications. In: Proceedings of the 8th International Conference on Ontologies, DataBases, and Applications of Semantics (ODBASE 2009), Algarve, Portugal.
  • Caragea, D., Bahirwani V., Aljandal, W. and Hsu, W. (2009). Ontology-Based Link Prediction in the LiveJournal Social Network. In: Proceedings of the Eight Symposium on Abstraction, Reformulation and Approximation (SARA'09), Lake Arrowhead, CA.

2008

  • Pilot Grant, KSU COBRE on Epithelial Function (NIH P20 RR017686, PI: Marcus) “Simulation of Spontaneous Peptide Insertion and Assembly in Epithelial Membranes, July”, 07/01/08 – 06/30/10
  • Computational Methods to Characterize Regulatory Networks Involved in Plant Response to Abiotic Stresses. KSU Ecological Genomics Seed Grant (2008-2009). Haiyan Wang (PI), Doina Caragea (co-PI) and Susan J. Brown (co-PI), $35,589.
  • Xia, J., Caragea, D. and Brown, S.J. (2008). Exploring Alternative Splicing Features using Support Vector Machines. In: Proceedings of the IEEE International Conference on Bioinformatics and Biomedicine (BIBM’08), Philadelphia, PA.
  • Bahirwani, V., Caragea, D., Aljandal, W. and Hsu, H.W. (2008). Ontology Engineering and Feature Construction for Predicting Friendship Links in the Live Journal Social Network. In: Proceedings of the KDD 2008 Second Workshop on Social Network Mining and Analysis (SNA-KDD). Las Vegas, NV, August 2008. ACM Digital Library.

2007

  • NSF SIR, “Development of an Open Test-Bed for Application of Formal Methods to Plugand-Play Medical Devices,” $55,000 September, 2007.
  • CT-ISG: Model-Based, Automatic Network Security Management (PI). National Science Foundation (Award #0716665). $258,500, 8/1/2007 - 7/31/2010.
  • IIS 0711356 - Collaborative Research: Learning Classifiers from Autonomous, Semantically Heterogeneous, Distributed Data, National Science Foundation (2007-2010). Vasant Honavar (PI-ISU) and Doina Caragea (PI-ISU), $449,999.

2006

  • NSF CI-TEAM, ”CI-TEAM Demonstration Project: Cyberinfrastructure Education for Bioinformatics and Beyond,” $249,974 December, 2006.
  • NSF EPSCOR, “Ecoforcasting Kansas,” funded at $6,750,000 April, 2006

2004

  • NSF DURIP ”Parallel Analysis of Models or Distributed Real-Time Embedded Systems”, $394,991, May, 2004

Papers

2015

  • J. Comer, R. Chen, H. Poblete, A. Vergara-Jaque, and J. E. Riviere. Predicting Adsorption Affinities of Small Molecules on Carbon Nanotubes Using Molecular Dynamics Simulation. ACS Nano (2015)

2010

  • A. I. Herrera, G. A. Cook, A. Al-Rawi, J. Gao, T. Iwamoto, O. Prakash. J. M. Tomich and J. Chen. Structural Characterization of Two Channel-Forming Peptides: Consequences of Introducing a C-Terminal Tryptophan. Proteins (2010).
  • M. Minchino, J. Chen, R. C. Stevens and C. L. Brooks III. FoldGPCR: structure prediction protocol for the transmembrane domain of G protein-coupled receptors from class A. Proteins (2010).
  • Wang, H. and Akritas, M. (2010a). Asymptotically Distribution Free Tests in Heteroscedastic Unbalanced High Dimensional ANOVA. To appear in Statistica Sinica.
  • Wang, H., Tolos, S. and Wang, S. (2010). A Distribution Free Nonparametric Test to Detect Dependence Between a Response Variable and Covariate in Presence of Heteroscedastic Treatment Effects. To appear in Canadian Journal of Statistics.
  • Wang, H., Higgins, J., and Blasi, D., (2010). Distribution-Free Tests For No Effect of Treatment In Heteroscedastic Functional Data Under Both Weak And Long Range Dependence, Statistics and Probability Letters. 80: 390-402.
  • Wang, H. and Akritas, M.G. (2010b). Inference from heteroscedastic functional data. Journal of Nonparametric Statistics. 22(2):149-168.
  • Bulatewicz, T., Yang, X., Peterson, J. M., Staggenborg, S., Welch, S. M., and Steward, D. R.: Accessible integration of agriculture, groundwater, and economic models using the Open Modeling Interface (OpenMI): methodology and initial results, Hydrol. Earth Syst. Sci., 14, 521-534, 2010.

2009

  • Anderson, M. P., and Dubnicka, S.R. (2009). Sequential Bayesian Classification: DNA Barcodes. Proceedings of Conference on Applied Statistics in Agriculture held in Manhattan, KS April 2009.
  • R. S. Armen, J. Chen and C. L. Brooks III. An Evaluation of Explicit Receptor Flexibility in Molecular Docking Using Molecular Dynamics and Torsion Angle Molecular Dynamics. J. Chem. Theory Comput. 5, 2909-2923 (2009).
  • D. Ganguly and J. Chen. Structural interpretation of paramagnetic relaxation enhancement-derived distances for disordered protein states. J. Mol. Biol. 390, 467-477 (2009).
  • D. Ganguly and J. Chen. Atomic details of the disordered states of KID and pKID. Implications in coupled binding and folding, J. Am. Chem. Soc. 131, 5214–5223 (2009).
  • J. Chen. Intrinsically Disordered p53 Extreme C-Terminus Binds to S100B(bb) through “Fly-Casting”. J. Am. Chem. Soc. 131, 2088-2089 (2009).
  • Wang, H. and Akritas, M.G. (2009). Rank Tests in Heteroscedastic Multi-Way HANOVA. Journal of Nonparametric Statistics. 21(6):663-681.
  • Bulatewicz, T., Jin, W., Staggenborg, S., Lauwo, S., Miller, M., Das, S., Andresen, D., Peterson, J., Steward, D. R., and Welch, S. M.: Calibration of a crop model to irrigated water use using a genetic algorithm, Hydrol. Earth Syst. Sci., 13, 1467-1483, 2009.

2008

  • S. Warren, D. Andresen, D. Wilson and S. Hoskins, “Embedded Design Considerations for a Wearable Cattle Health Monitoring System,” in the Proceedings of the 2008 International Conference on Embedded Systems and Applications (ESA ’08), pp. 55-62, Las Vegas, NV, July 14-17, 2008.

2007

  • T. Bulatewicz, D. Andresen, S. Welch, W. Jin, S. Das, M. Miller, “A Framework for Scalable Parameter Estimation on Clusters,” in the Proceedings of the 8th LCI International Conference on High-Performance Clustered Computing (LCI-HPCC’07) , Tahoe, CA, May 15-17, 2007.
  • Wang, LJ, S Wang, Y. Li and SJ Brown (2007) Beetlebase: a database for the Tribolium Genome Project NAR (database issue) D476-9.

2006

  • E. Bernard, D. Andresen, J. Hutchinson, “Linking Chemical Information with GeoDatabase Features via Web Services,” in the Proceedings of the Twenty-sixth ESRI International User Conference, San Diego, CA, August 7-11, 2006.
  • V. Ranganath, A. King, D. Andresen, “Automatic code generation for LYE, a high-performance caching SOAP implementation,” in the Proceedings of the 2006 International Conference on Semantic Web and Web Services (SWWS’06) , pp. 73–79, Las Vegas, NV, June 26–29, 2006.
  • Wang, LJ and SJ Brown (2006) BindN: a web-based tool for efficient prediction of DNA and RNA binding sites in amino acid sequences NAR 34 (Web server issue): W243-W248.(cover article)
  • Wang, LJ and SJ Brown (2006) Prediciton of RNA-Binding Residues in Protein Sequences using Support Vector Machines Proc. of the 28th Annual Internat. Conf. of the IEE EMBS. P5830-5833.
  • Wang, LJ and SJ Brown (2006) Prediction of DNA-Binding Residues from Sequence Features. J. Bioinform. and Comp. Biol. 4:1141-1158.
  • The Honeybee Genome Sequencing Consortium (2006) Insights into social insects from the genome of the honeybee Apis mellifera Nature 443: p931-949.

2003

  • D. Andresen, M. Nielsen, G. Singh, and P. Kalita “Dharma: a Grid-enabled Domain-specific Metaware for Hydrology,” in the Proceedings of the IASTED International Conference on Parallel and Distributed Computing and Systems (PDCS 2003), pp. 791–796. Winner of IASTED Best Paper Award in the area of Distributed Computing Applications. Marina Del Rey, CA, November 3-5, 2003.

MS Theses

2010

  • Vishal Bahirwani (2010) Exploring Transcription Patterns and Regulatory Motifs in Arabidopsis thaliana

2009

  • Mandar Haridas (2009) Exploring Knowledge Bases for Engineering a User Interests Hierarchy for Social Network Applications.

2008

  • Jing Xia (2008) Bioinformatics Analyses of Alternative Splicing, EST-based and Machine Learning-Based Prediction
  • Vikas Bahirwani (2008) Ontology Engineering and Feature Construction for Predicting Friendship Links and User Interests in the LiveJournal Social Network.