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Publications

1. R. Tharakan, N. Edwards, and D. Graham. "Data Maximization by Multipass Analysis of Protein Mass Spectra." Proteomics (2010).
2. C. Wynne, C. Fenselau, P. Demirev, and N. Edwards. "Top-down identification of protein biomarkers in bacteria with unsequenced genomes." Analytical Chemistry (2009): Article ASAP.
3. A. Phillippy, K. Ayanbule, N. Edwards, and S. Salzberg. "Insignia: a DNA signature search web server for diagnostic assay development." Nucleic Acids Research 37.S2 (2009): W229-W234.
4. N. Edwards, X. Wu, and C.-W. Tseng. "An Unsupervised, Model-Free, Machine-Learning Combiner for Peptide Identifications from Tandem Mass Spectra." Clinical Proteomics 5.1 (2009): 23-36.
5. 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 Enviromental Microbiology 74.3 (2008): 904-906.
6. S. Swatkoski, P. Gutierrez, C. Wynne, A. Petrov, J. D. Dinman, N. Edwards, and C. Fenselau. "Evaluation of microwave-accelerated residue-specific acid cleavage for proteomic applications." Journal of Proteome Research 7.2 (2008): 579–586.
7. 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 6.12 (2007): 4601-4607.
8. 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 66.3 (2007): 787-800.
9. 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 6.11 (2007): 4525-4527.
10. 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 (2007): 1025-1043.
11. S. Russell, N. Edwards, and C. Fenselau. "Detection of Plasmid Insertion in Escherichia coli by MALDI-TOF Mass Spectrometry." Analytical Chemistry 79.14 (2007): 5399-5409.
12. N.J. Edwards. "Novel Peptide Identification using Expressed Sequence Tags and Sequence Database Compression." Molecular Systems Biology 3.102 (2007).
13. 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 (2007): 654-658.
14. C. Fenselau, S. Russell, S. Swatkoski, and N. Edwards. "Proteomic Strategies for Rapid Analysis of Microorganisms." European Journal of Mass Spectrometry 13.1 (2007): 35-39.
15. 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 (2006): 181-188.
16. S. Istrail, et al. "Whole-genome shotgun assembly and comparison of human genome assemblies." Proceedings of the National Academy of Sciences 101.7 (2004): 1916-1921.

1. 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, 2007.
2. N. Edwards and R. Lippert. "Sequence database compression for peptide identification." 4th Workshop on Algorithms in Bioinformatics (WABI). : Lecture Notes in Computer Science, 2004.
3. 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. : Lecture Notes in Computer Science, 2004.
4. V. Bafna and N. Edwards. "On de novo interpretation of peptide spectra." 7th Annual International Conference on Research in Computational Molecular Biology (RECOMB). : ACM Press, 2003.
5. B.V. Halldorsson, V. Bafna, N. Edwards, R. Lippert, S. Yooseph, and S. Istrail. "Combinatorial problems arising in SNP and haplotype analysis." 4th International Conference on Discrete Mathematics and Theoretical Computer Science. : Lecture Notes in Computer Science (vol. 2731), 2003.
6. N. Edwards and R. Lippert. "Generating peptide candidates from amino-acid sequence databases for protein identification via mass spectrometry." 2nd Workshop on Algorithms in Bioinformatics (WABI). : Lecture Notes in Computer Science, 2002.
7. 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). : Bioinformatics, 2001.

1. "Improving the Sensitivity of Peptide Identification from Tandem Mass Spectra Using Meta-Search, Grid-Computing, and Machine-Learning" NCI Clinical Proteomic Technologies for Cancer Annual Meeting. (2009)
2. "Improved Peptide Identification Sensitivity using Meta-Search, Grid-Computing, and Machine-Learning, with Application to Genome Annotation" NIH Proteomics Interest Group Seminar. (2009)
3. "Improving the Sensitivity of Peptide Identification" NCI Clinical Proteomic Technologies for Cancer Annual Meeting. (2008)
4. "Improving the Reliability of Peptide Identifications using Machine Learning." US Human Proteome Organization Annual Meeting. (2008)
5. "Improving the Reliability of Peptide Identification by Tandem Mass Spectrometry for Clinical Proteomics and Genome Annotation." CCMB Lecture Series, Center for Computational Molecular Biology, Brown University (2008)
6. "Proteomic Characterization of Alternative Splicing and Coding Polymorphism." NCI Clinical Proteomic Technologies for Cancer Annual Meeting. (2007)
7. "Proteomic Characterization of Alternative Splicing and Coding Polymophism." Informatics Seminar, Department of Biomedical Informatics, Vanderbilt University School of Medicine (2007)
8. "Direct Experimental Observation of Functional Protein Isoforms by Tandem Mass Spectrometry." Department of Biochemistry and Molecular and Cellular Biology, Georgetown University Medical Center (2007)
9. "Improving Genome Annotation using Proteomics" J. Craig Venter Institute (2007)
10. "Proteomic Characterization of Alternative Splicing and Coding Polymophism." Department of Biochemistry and Molecular and Cellular Biology, Georgetown University Medical Center (2007)
11. "Optimal k-mer Superstrings for Protein Identification and DNA Assay Design." Department of Computer Science, George Mason University (2007)
12. "Large Scale Combinatorial Optimization Problems in Bioinformatics." Industrial and Systems Engineering, Lehigh University (2007)
13. "Proteomic Characterization of Alternative Splicing and Coding Polymophism." Department of Bioinformatics, George Mason University (2007)
14. "Novel Peptide Identification using ESTs and Genomic Sequence." J. Craig Venter Institute (2007)
15. "Statistical Significance for Peptide Identification from Tandem Mass Spectra." Statistical Analysis of Metabonomic and Proteomic Data, MolPAGE Training Workpackage (2007)
16. "Novel Peptide Identification using Expressed Sequence Tags and Sequence Database Compression." RECOMB Satallite Workshop on Computational Proteomics (2006)
17. "Novel Peptide Identification using ESTs and Genomic Sequence." Computational Genomics (2006)
18. "Novel Peptide Identification using ESTs and Genomic Sequence." International BCB-Workshop on Computational Proteomics (2006)
19. "Aggressive Enumeration of Peptide Sequences for MS/MS Peptide Identification." Center for Bioinformatics and Computational Biology Seminar Series (2005)
20. "Faster, more sensitive peptide identification by sequence database compression." NIH Proteomics and Mass Spectrometry Interest Groups Seminar (2005)
21. "Optimal k-mer superstrings for peptide identification from tandem mass spectra." Capital Area Theory Seminar (CATS), University of Maryland, College Park (2005)
22. "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)
23. "Bioinformatics challenges for protein identification from tandem mass spectra." Colloquium, Department of Biochemistry, Georgetown University Medical Center (2004)
24. "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)
25. "Adventures in bioinformatics and computational biology." Colloquium, School of Operations Research and Industrial Engineering. Cornell University (2004)

1. "Improving the Sensitivity of Peptide Identification from Tandem Mass Spectra Using Meta-Search, Grid-Computing, and Machine-Learning" NCI Clinical Proteomic Technologies for Cancer Annual Meeting, 2009.
2. N. J. Edwards. "Improving the Sensitivity of Peptide Identification from Tandem Mass Spectra using Meta-Search, Grid-Computing, and Machine-Learning" American Society for Mass Spectrometry Annual Meeting, 2009.
3. C. Fenselau, J. Cannon, N. Edwards, K. Lohnes, and C. Wynne "Production of polypeptides, 3000-10000 Da, and middle-down analysis by LC-MSMS" US Human Proteome Organization Annual Meeting, 2009.
4. N.J. Edwards, X. Wu, and C.-W. Tseng "Improving the Sensitivity of Peptide Identification with Meta-Search and Machine Learning" NCI Clinical Proteomic Technologies for Cancer Annual Meeting, 2008.
5. X. Wu, N.J. Edwards, and C.-W. Tseng. "Peptide Identification by Spectral Matching of Tandem Mass Spectra Using Hidden Markov Models." US Human Proteome Organization Annual Meeting, 2008.
6. 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.
7. X. Wu, N. Edwards, and C.-W. Tseng. "Experimental Comparison of Peptide Identification Algorithms.", 9th Annual Conference on Computational Genomics, 2006.
8. Nathan J. Edwards and Fernando Pineda. "Rapid Microorganism Identification Database (www.RMIDb.org)" American Society of Mass Spectrometry Conference, 2006.
9. 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.
10. 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.
11. 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.
12. N.J. Edwards. "Faster, more sensitive peptide identification from tandem mass spectra by sequence database compression." 1st Annual Symposium, US Human Proteome Organization, 2005.
13. 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.
14. 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.
15. 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.
16. 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.

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.