University of Maryland Nathan Edwards
Center for Bioinformatics and Computational Biology
Home Research Teaching Publications

Publications
Papers
Talks
Posters
Other


Home » Publications
Publications

Papers
  1. S. Swatkoski, P. Gutierrez, C. Wynne, A. Petrov, J.D. Dinman, N. Edwards, and C. Fenselau. Microwave accelerated residue-specific acid cleavage for proteomic applications. Journal of Proteome Research. Under review.

  2. S. Swatkoski, P. Gutierrez, J. Ginter, A. Petrov, J.D. Dinman, N. Edwards, and C. Fenselau. Integration of residue-specific acid cleavage into proteomic workflows. Journal of Proteome Research. ASAP Article; DOI: 10.1021/pr0704682. 2007.

  3. J. Wang, P. Gutierrez, N. Edwards, and C. Fenselau. Integration of 18O Labeling and Solution Isoelectric Focusing in a Shotgun Analysis of Mitochondrial Proteins. Journal of Proteome Research. In Press.

  4. X. Wu, C.-W. Tseng, and N. Edwards. HMMatch: Peptide Identification by Spectral Matching of Tandem Mass Spectra using Hidden Markov Models. Journal of Computational Biology. 14(8):1025-1043, 2007. (Preprint)

  5. J. Xu, O. Laine, M. Masciocchi, J. Manoranjan, J. Smith, S. Du, J. Shao, N. Edwards, X. Zhu, C. Fenselau, and L.-Y. Gao. A unique Mycobacterium ESX-1 protein co-secretes with CFP-10/ESAT-6 and is necessary for inhibiting phagosome maturation. Molecular Microbiology. (OnlineEarly Articles). doi:10.1111/j.1365-2958.2007.05959.x. 2007.

  6. C. Fenselau, C. Havey, N. Teerakulkittipong, S. Swatkoski, O. Laine, and N. Edwards. Identification of Beta-Lactamase in Antibiotic-resistant Bacillus cereus spores. Applied and Environmental Microbiology. Under review.

  7. S. Russell, N. Edwards, and C. Fenselau. Detection of Plasmid Insertion in Escherichia coli by MALDI-TOF Mass Spectrometry. Analytical Chemistry 79:5399-5409, 2007.

  8. N.J. Edwards. Novel Peptide Identification using Expressed Sequence Tags and Sequence Database Compression. Molecular Systems Biology. 3:102, 2007.

  9. D. Fasulo, A.-K. Emde, L.-Y. Wang, K. Noy, and N.J. Edwards. Alignment of Mass Spectrometry Data by Clique Finding and Optimization. Proceedings of the RECOMB Satellite Workshop on Computational Proteomics: Systems Biology and Computational Proteomics, Lecture Notes in Computer Science 4532:119-129, 2007.

  10. S. Swatkoski, S. Russell, N. Edwards, and C. Fenselau. Analysis of a Model Virus Using Residue-Specific Chemical Cleavage and MALDI-TOF Mass Spectrometry. Analytical Chemistry, 79(2):654-658, 2007.

  11. C. Fenselau, S. Russell, S. Swatkoski, and N. Edwards. Proteomic Strategies for Rapid Analysis of Microorganisms. European Journal of Mass Spectrometry. 13(1):35-39, 2007.

  12. S. Swatkoski, S.C. Russell, N. Edwards and C. Fenselau. Rapid chemical digestion of small acid-soluble spore proteins for analysis of Bacillus spores. Analytical Chemistry 78(1):181-188, 2006.

  13. N. Edwards and R. Lippert. Sequence database compression for peptide identification from tandem mass spectra. 4th Workshop on Algorithms in Bioinformatics (WABI 2004), Bergen, Norway, 2004.

  14. S. Istrail, G.G. Sutton, L. Florea, A.L. Halpern, C.M. Mobarry, R. Lippert, B. Walenz, H. Shatkay, I. Dew, J.R. Miller, M. J. Flanigan, N.J. Edwards, R. Bolanos, D. Fasulo, B.V. Halldorsson, S. Hannenhalli, R. Turner, S. Yooseph, F. Lu, D.R. Nusskern, B.C. Shue, X.H. Zheng, F. Zhong, A.L. Delcher, D.H. Huson, S.A. Kravitz, L. Mouchard, K. Reinert, K.A. Remington, A.G. Clark, M.S. Waterman, E.E. Eichler, M.D. Adams, M.W. Hunkapiller, E.W. Myers, and J.C. Venter. Whole-genome shotgun assembly and comparison of human genome assemblies. PNAS 101(7):1916-1921, 2004.

  15. B. V. Halldorsson, V. Bafna, N. Edwards, R. Lippert, S. Yooseph, and S. Istrail. A Survey of Computational Methods for Determining Haplotypes. Computational Methods for SNPs and Haplotype Inference: DIMACS/RECOMB Satellite Workshop, LNCS 2983:26-47, 2004.

  16. B. V. Halldorsson, V. Bafna, N. Edwards, R. Lippert, S. Yooseph, and S. Istrail. Combinatorial problems arising in SNP and haplotype analysis. Fourth International Conference on Discrete Mathematics and Theoretical Computer Science (DMTCS 2003), LNCS 2731:26-47, 2003.

  17. V. Bafna and N. Edwards. On de novo interpretation of tandem mass spectra for peptide identification. Seventh Annual International Conference on Research in Computational Molecular Biology (RECOMB 2003), Berlin, Germany, 2003. (Preprint)

  18. N. J. Edwards and R. A. Lippert. Generating peptide candidates from amino-acid sequence databases for protein identification via mass spectrometry. 2nd Workshop on Algorithms in Bioinformatics (WABI 2002), Rome, Italy, 2002. (Preprint)

  19. R. J. Turner, K. Chaturvedi, N. J. Edwards, D. Fasulo, A. L. Halpern, D. H. Huson, O. Kohlbacher, J. R. Miller, K. Reinert, K. A. Remington, R. Schwartz, B. Walenz, S. Yooseph, and S. Istrail. Visualization challenges for a new cyberpharmaceutical computing paradigm. Proceedings of the IEEE 2001 symposium on parallel and large-data visualization and graphics, San Deigo, California, October 2001.

  20. V. Bafna and N. J. Edwards. SCOPE: A probabilistic model for scoring tandem mass spectra against a peptide database. 9th International Conference on Intelligent Systems for Molecular Biology (ISMB 2001), Copenhagen, Denmark, July 2001. (Preprint)

  21. C. J. Goh and N. J. Edwards. Approximate output feedback optimal control of higher-order dynamical systems. Optimal Control Applications and Methods, 18(2):123-137, 1997.

  22. N. J. Edwards and C. J. Goh. A direct method for continuous-time nonlinear optimal feedback controller. Journal of Optimization Theory and Applications, 84(3):509-528, 1995.

  23. C. J. Goh and N. J. Edwards. Synthesis of optimal feedback controller by neural networks. International Journal of Systems Science, 25(8):1235-1248, 1994.

  24. C. J. Goh, N. J. Edwards and A. Y. Zomaya. Feedback control of minimum-time optimal control problems using neural networks. Optimal Control Applications and Methods, 14(1):1-16, 1993.

Talks
  1. Proteomic Characterization of Alternative Splicing and Coding Polymorphism. NCI Clinical Proteomic Technologies for Cancer Annual Meeting. (2007)

  2. "Proteomic Characterization of Alternative Splicing and Coding Polymophism" Informatics Seminar, Department of Biomedical Informatics, Vanderbilt University School of Medicine (2007)

  3. "Direct Experimental Observation of Functional Protein Isoforms by Tandem Mass Spectrometry" Department of Biochemistry and Molecular and Cellular Biology, Georgetown University Medical Center (2007)

  4. "Improving Genome Annotation using Proteomics" J. Craig Venter Institute (2007)

  5. "Proteomic Characterization of Alternative Splicing and Coding Polymophism" Department of Biochemistry and Molecular and Cellular Biology, Georgetown University Medical Center (2007)

  6. "Optimal k-mer Superstrings for Protein Identification and DNA Assay Design" Department of Computer Science, George Mason University (2007)

  7. "Large Scale Combinatorial Optimization Problems in Bioinformatics" Industrial and Systems Engineering, Lehigh University (2007)

  8. "Proteomic Characterization of Alternative Splicing and Coding Polymophism" Department of Bioinformatics, George Mason University (2007)

  9. "Novel Peptide Identification using ESTs and Genomic Sequence" J. Craig Venter Institute (2007)

  10. "Novel Peptide Identification using Expressed Sequence Tags and Sequence Database Compression." RECOMB Satallite Workshop on Computational Proteomics (2006)

  11. "Novel Peptide Identification using ESTs and Genomic Sequence." Computational Genomics (2006)

  12. "Novel Peptide Identification using ESTs and Genomic Sequence." International BCB-Workshop on Computational Proteomics (2006)

  13. "Aggressive Enumeration of Peptide Sequences for MS/MS Peptide Identification." Center for Bioinformatics and Computational Biology Seminar Series (2005)

  14. "Faster, more sensitive peptide identification by sequence database compression." NIH Proteomics and Mass Spectrometry Interest Groups Seminar (2005)

  15. "Optimal k-mer superstrings for peptide identification from tandem mass spectra." Capital Area Theory Seminar (CATS), University of Maryland, College Park (2005)

  16. "Faster, more sensitive peptide identification by sequence database compression." Mathematical Biosciences Institute, Ohio State University. Workshop 3: Biomarker Discovery: Much More than Just a Mass Spectrometry Problem (2005)

  17. "Bioinformatics challenges for protein identification from tandem mass spectra." Colloquium, Department of Biochemistry, Georgetown University Medical Center (2004)

  18. "Generating peptide candidates from protein sequence databases for protein identification via mass spectrometry". Institute for Pure and Applied Mathematics, UCLA. Proteomics: Sequence, Structure, Function Workshop I: High Throughput Technologies and Methods of Analysis (2004)

  19. "Adventures in bioinformatics and computational biology". Colloquium, School of Operations Research and Industrial Engineering. Cornell University (2004)

Posters

  1. Nathan J. Edwards Proteomic Characterization of Alternative Splicing and Coding Polymorphism. NCI Clinical Proteomic Technologies for Cancer Annual Meeting. (2007)

  2. X. Wu, N.J. Edwards, and C.-W. Tseng. Peptide Identification by Spectral Matching of Tandem Mass Spectra Using Hidden Markov Models. RECOMB Satallite Workshop on Computational Proteomics, 2006.

  3. X. Wu, N. Edwards, and C.-W. Tseng. Experimental Comparison of Peptide Identification Algorithms, 9th Annual Conference on Computational Genomics, 2006.

  4. Nathan J. Edwards and Fernando Pineda. Rapid Microorganism Identification Database (www.RMIDb.org). American Society of Mass Spectrometry Conference, 2006.

  5. S. Swatkoski, S. Russell, N. Edwards, and C. Fenselau. A new proteomics strategy for the identification of viruses. 54th American Society for Mass Spectrometry Conference (ASMS), 2006.

  6. N.J. Edwards, X. Wu, and C.-W. Tseng. Novel peptide identification using ESTs and genomic sequence. 2nd Annual Symposium, US Human Proteome Organization, 2006.

  7. E. Patton, N. Edwards, B. Oktem, and C. Fenselau. A microwave and detergent procedure to detect high molecular mass proteins from vegetative bacteria by MALDI-TOF MS. American Chemical Society National Meeting, Washington D.C., 2005.

  8. N.J. Edwards. Faster, more sensitive peptide identification from tandem mass spectra by sequence database compression. 1st Annual Symposium, US Human Proteome Organization, 2005.

  9. I.P. Smirnov, K.C. Parker, D. Patterson, A.J. Tomlinson, P.S. Juhasz, T. Taylor, N. Edwards, D. Fasulo, A. Graber, S.A. Martin, J. Ramirez, T. Colpitts, S.D. Stroupe. Development of MALDI based human serum biomarkers workflows. American Society of Mass Spectrometry (ASMS), 2004.

  10. R. Nutter, L. Johnston-Dow, J. Sorenson, H.C. Gire, S. Glanowski, C. Fosler, J. Hoglund, M.A. Rydland, P.-H. Shen, K. Glasser, C. Forbes, I. Singh, V. Sathineni, L. Wu, B. Small, P. Dunn, N. Edwards, C.-C. Chang, J. Ni, B. Jones, K. Woodford, P. Vatta, R. Loboda, G. Wang, B. Murphy, P. St. John, S. Ferreira, A. Parker, E. Gonzalez, C. Kosman, Q. Doan, L.Z. Pham, O. Bell. A resequencing primer set for 3,000 genes implicated in cancer genetics. European Society of Human Genetics (ESHG), 2003.

  11. J. Sorenson, S. Glanowski, N. Edwards, C. Fosler, A. Parker, L. Johnston-Dow, M. Furtado, C. Gire, L.-Z. Pham. Development and validation of a predictive model for robust primer design. American Society of Human Genetics (ASHG), 2003.

  12. R. Nutter, J. Sorenson, C. Gire, P. Shen, M.A. Rydland, S. Glanowski, N. Edwards, M. Furtado, R. Fang and L.-Z. Pham. Development and performance of the VariantSEQr resequencing system in sigh throughput DNA sequence variation studies. Genome Sequencing and Analysis Conference (GSAC), 2003.

Other
  1. X. Wu, N. Edwards, C.-W. Tseng. Peptide Identification via Tandem Mass Spectrometry. Chapter 6 of Advances in Computers, volume 68, ed. Chau-Wen Tseng and Marvin Zelkowitz, 2006.

  2. C. Fenselau, N. Edwards, and S. Russell. Strategy for Rapid Recognition of Bioengineered Bacteria. US Patent Application US60/862,105.

  3. N. J. Edwards. Approximation algorithms for the multi-level facility location problem. Ph.D. Thesis, Field of Operations Research, Cornell University, 2001.

  4. N. J. Edwards. Synthesizing optimal feedback control with neural networks. B.Sc. Honors Thesis, Departments of Mathematics and Computer Science, University of Western Australia, 1991.
.......... .......... .......... .......... .......... .......... .......... .......... .......... .......... .......... .......... .......... .......... .......... .......... .......... .......... .......... .......... .......... .......... .......... .......... .......... .......... .......... .......... .......... .......... .......... .......... .......... .......... .......... ..........

Home | Research | Teaching | Publications

University of Maryland     UM Home | Directories | Search | Admissions | Calendar
Original created by John Fuetsch
Questions and comments to Nathan Edwards