Publications in the Genomes to Life Project

• Carbon Sequestration in Synechococcus Sp.: From Molecular Machines to Hierarchical Modeling,
  by Heffelfinger, et al., OMICS Journal of Integrative Biology. No. 6, pp 305-329, 2002

• Characterization of protein structure and funtion at genome scale using a computational predictiton pipeline,
  Dong Xu, Dongsup Kim, Phuongan Dam, Manesh Shah, Ed Uberbacher, and Ying Xu. Genetic Engineering: Methods and Principles, ed. J. Setlow. Kluwer Academic/Plenum Publishers, NY. pp 269-293. 2003

• A Computational Pipeline for Protein Structure Prediction and Analysis at Genome Scale,
  Manesh Shah, Sergei Passovets, Dongsup Kim, Kyle Ellrott, Li Wang, Inna Volkler, Philip LoCascio, Dong Xu, and Ying Xu. Bioinformatics 19: pp 1985-1996, 2003.

• Multivariate Curve Resolution for Hyperspectral Image Analysis: Applications to Microarray Technolgy,
  Haaland, D. M., Timlin, J. A., Sinclair, M. B., Van Benthem, M. H., Martinez, M. J., Aragon, A. D. & Werner-Washburne, M. (2003) in Spectral Imaging: Instrumentation, Applications, and Analysis, (Publisher: International Society for Optical Engineering, San Jose, CA), Vol. 4959, paper 06.

• Identification and removal of contaminating fluorescence from comercial and in-house printed DNA microarrays,
  Martinez, M. J., Aragon, A. D. & Werner-Washburne, M., Rodriguez, A. L, Weber, J. M., Timlin, J. A., Sinclair, M. B., Haaland, D. M., (2003) Nucleic Acids Research, Vol.31, Issue 4, E18.

• PICUPP: Protein Interaction Classification by Unlikely Profile Pair,
  Byung-Hoon Park , George Ostrouchov, Gong-Xin Yu, Al Geist, Andrey Gorin, and Nagiza F. Samatova (2003) IEEE Bioinformatics Conference (submitted)

• An SVM-based algorithm for identification of photosynthesis-specific genome features,
  Gong-Xin Yu , Al Geist, George Ostrouchov, and Nagiza F. Samatova (2003) IEEE Bioinformatics Conference (submitted)

• A New Informatics Method for Measuring Synonymous Codon Usage Bias,
  Xiufeng Wan, Dong Xu, and Jizhong Zhou (2003) ASME ANNIE 2003 Conference (submitted)

• EXCAVATOR: A Computer Program for Efficiently Mining Gene-Expression Data,
  Dong Xu, Victor Olman, Li Wang, and Ying Xu Nucleic Acids Research. No. 31, pp 5582-5589. 2003

• Probability Profiles - Novel Approach in Tandem Mass Spectrometry De Novo Sequencing,
  Tema Fridman, Robert Day, Jane Razumovskaya, Dong Xu, Andrey Gorin. Computational Systems Bioinformatics (CSB2003). IEEE Computer Society, pp. 415-418. 2003

• A new informatics method measuring synonymous codon usage bias,
  Xiufeng Wan, Dong Xu, and Jizhong Zhou. Intelligent engineering systems through artificial neural networks, vol 13, eds. Dagli et al., NY: ASME Press. pp 1101-1018, 2003

• Connecting metabolic rate and temperature to population growth rates in marine autotrophs,
  Andrea Belgrano, Peter Steadman, and Damian Gessler. 2004

• Design, Construction, Characterization, and Application of a Hyperspectral Microarray Scanner,
  Michael B. Sinclair, Jerilyn A. Timlin, David M. Haaland, and Margaret Werner-Washburne, Applied Optics, Vol. 43 Issue 10 Page 2079-2088 (April 2004).

• The Signature Molecular Descriptor. 3. Inverse Quantitative Structure-Activity Relationship of ICAM-1 Inhibitory Peptides
  Churchwell, C. J., Rintoul, M. D, Martin, S., Visco D., Kotu, A., Larson, R. S., Sillerud, L. O., Brown, D. C., Faulon, J. L., J. Molec. Graph. and Model, 22, 263-273, 2004.

• Compilation and Review of Data Standards and Application to the Genomes to Life Program
  Arkin, A., Ambrosiano, J., Babnigg, G., Frank, E., Geist, A., Giometti, C., Jacobsen, J., Samatova, N., Slater, N., and Taylor, R., DOE GTL Technical Report, January 31, 2004.

• Inference of Protein-Protein Interactions by Unlikely Profile Pair,
  Park, H., Ostrouchov, G.,Yu, G.X., Geist, A., Gorin, A. and Samatova, N., Proceedings of the Third IEEE International Conference on Data Mining, Melbourne, Florida, USA, November 19-22, 2003.

• "Analysis of Protein Interface Sites through Separated Data Spaces,"
  Park, Byung-Hoon, Munavalli Rajesh, Geist, Al, Samatova, Nagiza F., Proceedings of Bioinformatics Workshop in conjunction with the SIAM International Conference on Data Mining, Florida, April 22-24, 2004.

• ChemCell: A Particle-Based Model of Protein Chemistry and Diffusion in Microbial Cells
  Plimpton, S., Slepoy, A., Sandia Technical Report SAND2003-4509, Dec. 2003.

• Operon prediction by comparative genomics: an application to the Synechococcus sp. WH8102 genome
  Chen, X., Su, Z., Dam, P., Palenik, B., Xu, Y., and Jiang, T., Journal of Nucleic Acids Research (accepted April 2004)

• Computing assignment of orthologous genes via genome rearrangement
  Chen, X., Zheng, J., Fu, Z., Nan, P., Zhong, Y., Lonardi, S., and Jiang, T., Proceedings of Asian Pacific Bioinformatics Conference, Jan 18-20, 2005, Singapore (invited paper)

• In-silico Prediction of Surface Residue Clusters for Enzyme-Substrate Specificity
  Yu, G-X, Park, B-H, Chandramohan, P., Geist, A., Samatova, M., Proceedings of IEEE Bioinformatics Conference, August, 2004.

• Predicting Protein-Protein Interactions Using Signature Product
  Martin, S., Roe, D., Faulon, J.-L., to appear in Bioinformatics 2004.

• Dynamical Robustness in Gene Regulatory Networks
  Faulon, J.-L., Martin, S., Carr, R. D., IEEE Computational Systems Bioinformatics (CSB) 2004.

• Inferring Genetic Networks from Microarray Data
  Martin, S., Davidson, G.S., May, E.E., Faulon, J.-L., Werner-Washburne, M., IEEE Computational Systems Bioinformatics (CSB) 2004.

• Intrinsic terminator prediction and its application in Synechococcus sp. WH8102
  Xiu-Feng Wan and Dong Xu. Journal of Computer and Science Technology (2004).

• Global Protein Function Annotation through Mining Genome-Scale Data in Yeast Saccharomyces cerevisiae
  Yu Chen and Dong Xu. Nucleic Acid Research (In Press 2004).

• Genome-Scale Understanding Protein Dispensability through Machine-Learning Analysis of High-Throughput Data
  Yu Chen and Dong Xu. Bioinformatics. (In Press 2004).

• Profiles and fuzzy k-nearest neighbor algorithm for protein secondary structure prediction
  Rajkumar Bondugula, Ognen Duzlevski, and Dong Xu, Proceeding of the 3rd Asia-Pacific Bioinformatics Conference (APBC 2005)

• Genome-Scale Protein Function Prediction in Yeast Saccharomyces Cerevisiae Through Integrating Multiple Sources Of High-Throughput Data
  Yu Chen and Dong Xu, Proceedings of the 2005 Pacific Symposium on Biocomputing (PSB 2005)

• Application of computational biology in understanding emerging infectious diseases: inferring the biological function for S-M complex of SARS-CoV
  Xiu-Feng Wan, Demet Ataman, and Dong Xu, Bioinformatics. (In Press 2004).

• Quantitative relationship between codon usage bias and GC composition across the unicellular genomes
  Xiu-Feng Wan, Dong Xu, Andris Kleinhofs, and Jizhong Zhou, BMC Evolutionary Biology, 4:19, 2004

• Prediction of Protein dispensability through integrated analysis of multi-source high-throughput data
  Yu Chen and Dong Xu. International Conference on Software Engineering, Artificial Intelligence, Networking and Parallel/Distributed Computing (SNPD 2004), pp 158-166. June 2004.

• Function Prediction for Hypothetical Proteins in Yeast Saccharomyces cerevisiae Using Multiple Sources of High-Throughput Data
  Joshi, Trupti; Chen, Yu; Becker, Jeffrey; Alexandrov, Nickolai; Xu, Dong. Proceeding of the 8th World Multi-Conference on Systemics, Cybernetics and Informatics Vol. IX, pp 17-20 (2004).

• PROSPECT-PSPP: An Automatic Computational Pipeline for Protein Structure Prediction
  Guo, J., Ellrott, K., Chung, W. J., Xu, D., Passovets S., and Xu, Y., Nuclear Acids Research. 32: W522-CW525, 2004.

• Aquatic food-webs' ecology: old and new challenges
  Andrea Belgrano In: Aquatic Food Webs an ecosystem approach edited by Andrea Belgrano; Ursula M. Scharler, Jennifer Dunne, and Robert E. Ulanowicz. Oxford University Press (2005).

• Gorin, Andrey and Al-Hashimi, Hashim M., “Combinatorial Assignment Procedure for RNA and Proteins,” Proceedings of Keystone Conference 2003: Frontiers of NMR in Molecular Biology VIII, p 166. (2003).

• Gorin, Andrey and Al-Hashimi, Hashim M. “Computational Challenges in Rapid Characterization of Protein-protein Interactions by NMR Based Methods,” Proceedings of the International Moscow Conference on Computational Biology, Moscow State University pp 86-87, 2003.

• Chivian D, Kim DE, Malmstrom L, Bradley P, Robertson T, Murphy P, Strauss CEM, Bonneau R, Rohl CA, Baker D., “Automated Prediction of CASP-5 Structures Using the Robetta Server,” Proteins, 53, Suppl 6:524-33, 2003.

• Olken, Frank, “Biopathways Graph Data Management,” OMICS, July 2003.

• Nagiza F. Samatova, Gong-Xin Yu, Praveen Chandramohan, Hoony Park, George Ostrouchov, Al Geist, Natalia Maltsev. “Hierarchical feature extraction based approach to functional differentiation of highly homologous protein functional groups” (to be submitted to Bioinformatics journal).

• Rohl, Carol A., Strauss, Charlie E. M., Chivian, Dylan, Baker, David “Modeling Structurally Variable Regions In Homologous Proteins With Rosetta” Proteins, Submitted, August 2003.

• Rohl, Carol A., Strauss, Charlie E. M., Misura, Kira M. S., Baker, David “Protein Structure Prediction Using Rosetta”, Methods Enzymol, Submitted, August 2003.

• Su, Z., Dam, A., Chen, X., Jiang, T., Palenik, B., and Xu, Y., “Computational Inference of Regulatory Pathways in Microbes in Synechococcus sp”, Genome Research, Submitted, 2003.

• Choi, Hyuk S., Lee, Wen H., Abagyan, Ruben A., and Gorin, Andrey, “Exploring DNA Mismatch Repair Machinery by Protein Docking Simulation,” Accepted, Fourth Georgia Tech International Bioinformatics Conference: From Genomics to Epidemiology, Atlanta, GA, November 13-16, 2003.

• Day, Robert M. and Gorin, Andrey, “High Probability Islands – Novel Approach in Tandem Mass Spectrometry for Peptide Tagging,” Accepted, Fourth Georgia Tech International Bioinformatics Conference: From Genomics to Epidemiology, Atlanta, GA, November 13-16, 2003.

• Razumovskaya, Jane, Fridman, Tema, Day, Robert M., and Gorin, Andrey “Probability Profile Method for Charge Determination in Tandem Mass Spectrometry,” Accepted, Fourth Georgia Tech International Bioinformatics Conference: From Genomics to Epidemiology, Atlanta, GA, November 13-16, 2003.

• Chen X., Su, Z., Dam, P., Palenik, B., Xu, Y., Jiang T., “Operon Prediction by Comparative Genomics: An Application to the Synechococcus sp. WH8102 Genome,” Conditional Acceptance, Nuclear Acids Res., 2003.

• Chen, X., Zheng, J., Fu, Z., Nan, P., Zhong, Y., Lonardi, S., Jiang T, “Assignment of Orthologous Genes Via Genome Rearrangement,” Submitted, ISMB 2004.

• Olman, V., Peng, H., Su, Z., Xu, Y., “Mapping of Microbial Pathways and Regulons Across Multiple Genomes,” Submitted, PNAS, 2004.

• Olman, V., Peng, H., Su, Z., Xu, Y., “Mapping of Microbial Pathways Through Constrained Mapping of Orthologous,” Submitted, ISMB, 2004.

• Su, Z., Dam, A., Chen, X., Olman, V., Jiang, T., Palenik, B., and Xu, Y., “Computational Inference of Regulatory Pathways in Microbes: an Application to the Construction of Phosphorus Assimilation Pathways in Synechococcus WH8102,” Proceedings of the 14th International Conference on Genome Informatics, pp 3- 13, Universal Academy Press Inc. Dec. 2003.

• Su, Z., Dam, A., Chen, X., Jiang, T., Palenik, B., and Xu, Y., “Computational Inference of Regulatory Pathways in Microbes in Synechococcus sp,” Under Review, Genome Research, 2003.

• Su, Z., Dam, A., Chen, X., Olman, V., Jiang, T., Palenik, B., and Xu, Ying, “Computational Inference of Regulatory Pathways in Microbes: an application to the construction of phosphorus assimilation pathways in Synechococcus WH8102,” Bioinformatics, May 2003.

• Su, Z., Dam, P., Chen X., Olman, V., Jiang, T., Palenik, B., Xu, Y., “Computational Inference of Regulatory Pathways in Microbes,” Paper submitted to Fourth Georgia Tech International Conference on Bioinformatics (2003).

• More to come...

  White Papers Developed for this GTL project

• Current state of the data in the cyanobacterium Synechococcus
  Jeff Blanchard, NCGR Santa Fe (2003)

• Physiology and Molecular Ecology of Synechococcus WH8102
  Jeff Blanchard, NCGR Santa Fe (2003)

• Overview of Modeling and Simulation and Object Oriented Software Design Pertinent to Development of a Hierarchical Simulation Platform
  Peter Steadman, NCGR Santa Fe (2003)

• Population Dynamics, Marine Community Ecology, and Oceanography of Marine Microbes
  Damian Gessler, NCGR Santa Fe (2003)

• Steadman, P., Gessler, D., "Design Document: Hierarchical Simulation Platform," National Center for Genome Resources, June 2003b

• Steadman, P., Gessler, D., “Requirements Document: Hierarchical Simulation Platform,” National Center for Genome Resources, June 2003.

• Belgrano, A., Steadman, P., Gessler, D. “Connecting Metabolic Rate and Temperature to Population Growth Rates in Marine Autotrophs,” National Center for Genome Resources, 2003.

• More to come...

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This work sponsored by the US Department of Energy's Office of Science Genomes to Life Program
Last Modified May 20, 2005 by Al Geist