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Publications

Articles in Journals
  1. M. Sanda, L. Zhang, N. Edwards, and R. Goldman. "Site specific analysis of changes in the glycosylation of proteins in liver cirrhosis using data independent workflow with soft fragmentation." Analytical and Bioanalytical Chemistry, 409, 2 (2017): 619-627.
  2. S. Chauhan, S. Danielson, V. Clements, N. Edwards, S. Ostrand-Rosenberg, and C. Fenselau. "Surface glycoproteins of exosomes shed by myeloid-derived suppressor cells contribute to function." Journal of Proteome Research, 16, 1 (2017): 238-246.
  3. K. Adams, S. Chauhan, D. Patel, V. Clements, Y. Wang, S. Jay, N. Edwards, S. Ostrand-Rosenberg, and C. Fenselau. "Ubiquitin conjugation probed by inflammation in MDSC extracellular vesicles." Journal of Proteome Research (2017): Available online.
  4. L. Geis-Asteggiante, S. Ostrand-Rosenberg, C. Fenselau, N. Edwards. "Evaluation of spectral counting for relative quantitation of proteoforms in top-down proteomics." Analytical Chemistry, 88, 22 (October 2016): 10900-10907.
  5. P. Rudnick, S. Markey, J. Roth, Y. Mirokhin, X. Yan, D. Tchekhovskoi, N. Edwards, R. Thangudu, K. Ketchum, C. Kinsinger, M. Mesri, H. Rodriguez, and S. Stein. "A Description of the Clinical Proteomic Tumor Analysis Consortium (CPTAC) Common Data Analysis Pipeline." Journal of Proteome Research, 15, 3 (2016): 1023-1032.
  6. Y. Kim, N. Edwards, and C. Fenselau. "Extracellular vesicle proteomes reflect developmental phases of Bacillus subtilis." Clinical Proteomics, 13, 6 (2016)
  7. W. Choksawangkarn, L. M. Graham, M. Burke, S. B. Lee, S. Ostrand-Rosenberg, C. Fenselau, and N. J. Edwards. "Peptide-based systems analysis of inflammation induced myeloid-derived suppressor cells reveals diverse signaling pathways." Proteomics, 16, 13 (2016): 1881-1888.
  8. M. Movassagh, N. Alomran, P. Mudvari, M. Dede, C. Dede, K. Kowsari, P. Restrepo, E. Cauley, S. Bahl, M. Li, W. Waterhouse, K. Tsaneva-Atanasova, N. Edwards, and A. Horvath. "RNA2DNAlign: Nucleotide resolution allele asymmetries through quantitative assessment of paired sequencing data." Nucleic Acids Research (2016): Available online.
  9. P. Mudvari, M. Movassagh, K. Kowsari, A. Seyfi, M. Kokkinaki, N. J. Edwards, N. Golestaneh, and A. Horvath. "SNPlice: Variants that Modulate Intron-retention from RNA-sequencing Data." Bioinformatics, 31, 8 (2015): 1191-1198.
  10. N. J. Edwards, M. Oberti, R. R. Thangudu, S. Cai, P. B. McGarvey, S. Jacob, S. Madhavan, K. A. Ketchum. "The CPTAC Data Portal: A Resource for Cancer Proteomics Research." Journal of Proteome Research, 14, 6 (2015): 2707-2713.
  11. L. Geis-Asteggiante, A. Dhabaria, N. Edwards, S. Ostrand-Rosenberg, and C. Fenselau. "Top-down analysis of low mass proteins in exosomes shed by murine myeloid-derived suppressor cells." International Journal of Mass Spectrometry, 378 (2015): 264-269.
  12. M. Movassagh, P. Mudvari, M, Kokkinaki, N. J. Edwards, N. Golestaneh, and A. Horvath. "Analysis for co-occurring sequence features identifies link between common synonymous variant and an early-terminated NPC1 isoform." Journal of Clinical Bioinformatics, 4, 14 (2014)
  13. M. Burke, W. Choksawangkarn, N. Edwards, S. Ostrand-Rosenberg, and C. Fenselau. "Exosomes from myeloid derived suppressor cells carry biologically active proteins." Journal of Proteome Research, 13, 2 (2014): 836-843.
  14. B. Zhang, J. Wang, X. Wang, J. Zhu, Q. Liu, Z. Shi, M. C. Chambers, L. J. Zimmerman, K. F. Shaddox, S. Kim, S. R. Davies, S. Wang, P. Wang, C. R. Kinsinger, R. C. Rivers, ..., R. R. Townsend. "Proteogenomic characterization of human colon and rectal cancer." Nature, 513, 7518 (2014): 382-387.
  15. K.B. Chandler, Z. Brnakova, M. Sanda, S. Wang, S. H. Stalnaker, R. Bridger, P. Zhao, R. L. Wells, N. J. Edwards, and R. Goldman. "Site-Specific Glycan Microheterogeneity of Inter-alpha-Trypsin Inhibitor Heavy Chain H4." Journal of Proteome Research, 13, 7 (2014): 3314-3329.
  16. M. C. Burke, M. S. Oei, N. J. Edwards, S. Ostrand-Rosenberg, and C. Fenselau. "Ubiquitinated Proteins in Exosomes Secreted by Myeloid-derived Suppressor Cells." Journal of Proteome Research, 13, 12 (2014): 5965-5972.
  17. C. Ubaida Mohien, D.R. Colquhoun, D.K. Mathias, J.G. Gibbons, J.S. Armistead, M. del Carmen-Rodriguez, M.H. Rodriguez, N.J. Edwards, J. Hartler, G.G. Thallinger, D. Graham, ..., R.R. Dinglasan. "A Bioinformatics Approach for Integrated Transcriptomic and Proteomic Comparative Analyses of Model and Non-sequenced Anopheline Vectors of Human Malaria Parasites." Molecular & Cellular Proteomics, 12, 1 (2013): 120-131.
  18. B. Risk, N. Edwards, and M. Giddings. "A peptide-spectrum scoring system based on ion alignment, intensity and pair probabilities." Journal of Proteome Research, 12, 9 (2013): 4240-4247.
  19. W. Choksawangkarn, S.-K. Kim, J. Cannon, N. Edwards, S. B. Lee, and C. Fenselau. "Enrichment of plasma membrane proteins using nanoparticle pellicles: comparison between silica and higher density nanoparticles." Journal of Proteome Research, 12, 3 (2013): 1134-1141.
  20. K. Chandler, P. Pompach, R. Goldman, and N. Edwards. "Exploring Site-Specific N-Glycosylation Microheterogeneity of Haptoglobin using Glycopeptide CID Tandem Mass Spectra and Glycan Database Search." Journal of Proteome Research, 12, 8 (2013): 3652-3666.
  21. N. J. Edwards and V. M. Bierbaum. "Focus in Honor of Catherine Fenselau, Recipient of Recipient of the 2012 Award for Distinguished Contribution in Mass Spectrometry." Journal of the American Society of Mass Spectrometry, 24, 8 (2013): 1157-1160.
  22. J. Cannon, N. Edwards, and C. Fenselau. "Mass biased partitioning to enhance middle down proteomics analysis." Journal of Mass Spectrometry, 48, 3 (2013): 340-343.
  23. N. Edwards. "PepArML: A meta-search peptide identification platform." Current Protocols in Bioinformatics, 44 (2013): 13.23.1-13.23.23.
  24. P. Pompach, Z. Brnakova, M. Sanda, J. Wu, N. Edwards, and R. Goldman. "Site Specific Glycoforms of Haptoglobin in Liver Cirrhosis and Hepatocellular Carcinoma." Molecular & Cellular Proteomics, 12, 5 (2013): 1281-1293.
  25. M. Linde, D. Colquhoun, C. Ubaida Mohien, T. Kole, V. Aquino, R. Cotter, N. Edwards, J. Hildreth, and D. Graham. "The conserved set of host proteins incorporated into HIV-1 virions suggests a common egress pathway in multiple cell types." Journal of Proteome Research, 12, 5 (2013): 2045-2054.
  26. K.J. Brown, H. Seol, D. K. Pillai, B.-J. Sankoorikal, C. A. Formolo, J. Mac, N. J. Edwards, and Y. Hathout. "The human secretome atlas initiative: Implications in health and disease conditions." BBA - Proteins and Proteomics, 1834, 11 (2013): 2454-2461.
  27. W. Choksawangkarn, N. Edwards, Y. Wang, P. Gutierrez, and C. Fenselau. "A Comparative Study of Workflows Optimized for In-gel, In-solution and On-filter Proteolysis in the Analysis of Plasma membrane Proteins." Journal of Proteome Research, 11, 5 (2012): 3030-3034.
  28. J. Lenco, R. Lan, N. Edwards and R. Goldman. "MS/MS library facilitated MRM quantification of native peptides prepared by denaturing ultrafiltration." Proteome Science, 10, 7 (2012)
  29. P. Pompach, K. B. Chandler, R. Lan, N. Edwards, and R. Goldman. "Semi-Automated Identification of N-Glycopeptides by Hydrophilic Interaction Chromatography, nano-Reverse-Phase LC-MS/MS, and Glycan Database Search." Journal of Proteome Research, 11, 3 (2012): 1728-1740.
  30. R. Tharakan, N. Edwards, and D. Graham. "Data Maximization by Multipass Analysis of Protein Mass Spectra." Proteomics, 10, 6 (2010): 1160-1171.
  31. X. Liu, Y. Inbar, P. Dorrestein, C. Wynne, N. Edwards, P. Souda, J. Whitelegge, V. Bafna, and P. Pevzner. "Deconvolution and Database Search of Complex Tandem Mass Spectra of Intact Proteins." Molecular & Cellular Proteomics, 9, 11 (2010): 2772-2782.
  32. J. Cannon, K. Lohnes, C. Wynne, Y. Wang, N. Edwards, and C. Fenselau. "High-Throughput Middle-Down Analysis Using an Orbitrap." Journal of Proteomics, 9, 8 (2010): 3886-3890.
  33. Y. An, S. Bekesova, N. Edwards, and R. Goldman. "Peptides in low molecular weight fraction of serum associated with hepatocellular carcinoma." Disease Markers, 29, 1 (2010): 11-20.
  34. C. Wynne, N. Edwards, and C. Fenselau. "Phyloproteomic classification of unsequenced organisms by top-down identification of bacterial proteins using capLC-MS/MS on an Orbitrap." Proteomics, 10, 20 (2010): 3631-3643.
  35. 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.
  36. 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.
  37. C. Wynne, C. Fenselau, P. Demirev, and N. Edwards. "Top-down identification of protein biomarkers in bacteria with unsequenced genomes." Analytical Chemistry, 81, 23 (2009): 9633-9642.
  38. 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.
  39. 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.
  40. 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.
  41. 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.
  42. 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.
  43. 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.
  44. 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.
  45. 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.
  46. N.J. Edwards. "Novel Peptide Identification using Expressed Sequence Tags and Sequence Database Compression." Molecular Systems Biology, 3, 102 (2007)
  47. 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.
  48. 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.
  49. Sorin Istrail, Granger G. Sutton, Liliana Florea, Aaron L. Halpern, Clark M. Mobarry, Ross Lippert, Brian Walenz, Hagit Shatkay, Ian Dew, Jason R. Miller, Michael J. Flanigan, Nathan J. Edwards, Randall Bolanos, Daniel Fasulo, Bjarni V. Halldorsson, Sridhar Hannenhalli, Russell Turner, Shibu Yooseph, Fu Lu, Deborah R. Nusskern, Bixiong Chris Shue, Xiangqun Holly Zheng, Fei Zhong, Arthur L. Delcher, Daniel H. Huson, Saul A. Kravitz, Laurent Mouchard, Knut Reinert, Karin A. Remington, Andrew G. Clark, Michael S. Waterman, Evan E. Eichler, Mark D. Adams, Michael W. Hunkapiller, Eugene W. Myers And J. Craig Venter. "Whole-genome Shotgun Assembly And Comparison Of Human Genome Assemblies." Proceedings Of The National Academy Of Sciences, 101, 7 (February 17, 2004): 1916-1921.
  50. C.J. Goh and N.J. Edwards. "Approximate output feedback optimal control of higher-order dynamical systems." Optimal Control Applications & Methods, 18, 2 (1997): 123-137.
  51. N.J. Edwards and C.J. Goh. "Direct training method for a continuous-time nonlinear optimal feedback controller." Journal of Optimization Theory and Applications, 84, 3 (1995): 509-528.
  52. C.J. Goh and N.J. Edwards. "Synthesis of optimal feedback controller by neural networks." International Journal of Systems Science, 25, 8 (1994): 1235-1248.
  53. C.J. Goh, N.J. Edwards, and A.Y. Zomaya. "Feedback-control of minimum-time optimal-control problems using neural networks." Optimal Control Applications & Methods, 14, 1 (1993): 1-16.
Book Chapters
  1. Nathan J. Edwards. "Protein Identification From Tandem Mass Spectra By Database Searching." Protein Bioinformatics, Methods In Molecular Biology, edited by Cathy H. Wu, 357-380. New York: Humana Press, 2017.
  2. C. Fenselau, C. Wynne, and N. Edwards. "Broadband Analysis of Bioagents by Mass Spectrometry." Detection of Biological Agents For the Prevention of Bioterrorism, edited by J. Banoub and M. El Essassi, 1-12. Berlin: Springer Press, 2011.
  3. Nathan J. Edwards. "Protein Identification From Tandem Mass Spectra By Database Searching." Methods In Molecular Biology, Bioinformatics For Comparative Proteomics, edited by Cathy H. Wu, 119-138. New York: Humana Press, 2011.
  4. N. Edwards, C. Wynne, A. Dhabaria, and C. Fenselau. "Top-down protein analysis and phylogenetic characterization of unsequenced bacteria." Rapid Characterization of Microorganisms by Mass Spectrometry, edited by C. Fenselau, P. Demirev, 121-142. American Chemical Society, 2011.
  5. X. Wu, N. Edwards, and C.-W. Tseng. "Peptide Identification via Tandem Mass Spectrometry." Advances in Computers: Computational Biology and Bioinformatics, edited by C.W. Tseng, M. Zelkowitz, 256-280. Elsevier, 2006.
Articles in Conference Proceedings
  1. N. Goodacre, N. Edwards, M. Danielsen, P. Uetz, and C. Wu. "Docking Features for Predicting Binding Loss due to Protein Mutation." Proceedings of the 5th ACM Conference on Bioinformatics, Computational Biology, and Health Informatics, 23-32. Association of Computing Machinery, 2014.
  2. 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 Protoeconomics: Systems Biology and Computational Protoeconomics, 119-129. Lecture Notes in Computer Science, 2007.
  3. B.V. Halldorsson, V. Bafna, N. Edwards, R. Lippert, S. Yooseph, and S. Istrail. "A survey of computational methods for determining haplotypes." RSNPsH: RECOMB Workshop on Computational Methods for SNPs and Haplotype Inference, 26-47. Lecture Notes in Computer Science, 2004.
  4. N. Edwards and R. Lippert. "Sequence database compression for peptide identification." 4th International Workshop, 230-241. Lecture Notes in Computer Science, 2004.
  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, 26-47. Lecture Notes in Computer Science (vol. 2731), 2003.
  6. V. Bafna and N. Edwards. "On de novo interpretation of peptide spectra." 7th Annual International Conference on Research in Computational Molecular Biology (RECOMB), 9-18. ACM Press, 2003.
  7. N. Edwards and R. Lippert. "Generating peptide candidates from amino-acid sequence databases for protein identification via mass spectrometry." Algorithms in Bioinformatics, 68-81. Lecture Notes in Computer Science, 2002.
  8. 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), 17:S13-S21. Bioinformatics, 2001.
Talks
  1. "The Clinical Proteomics Tumor Analysis Consortium: Connecting the Genomics and Proteomics of Cancer" 5th Annual Innovation Center for Biomedical Informatics Symposium, Georgetown University (2016).
  2. "Algorithms and Computation: Bottom-Up Data Analysis Workflows", Panel presentation at NSF Workshop: Mass Spectrometry Informatics Big Data to Knowledge (2015).
  3. "Big Data and the CPTAC Data Portal" Big-Data Workshop, US Human Proteome Organiziation Annual Meeting (2014).
  4. "Proteomics and Glycoproteomics (Bio-)Informatics of Protein Isoforms" Seminar, Department of Biology, Howard University (2014).
  5. "Gene Set Enrichment and Splicing Detecting using Spectral Counting" Brown Bag seminar series, Georgetown Center for Cancer Systems Biology (2013).
  6. "Application of Generalized Protein Parsimony and Spectral Counting to Functional Enrichment Analysis and Protein Isoform Detection" Workshop in Bioinformatics and Statistics, Department of Biostatistics, Bioinformatics and Biomathematics, Georgetown University. (2013)
  7. "Application of Generalized Protein Parsimony and Spectral Counting to Functional Enrichment Analysis and Protein Isoform Detection" Accepted talk at US Human Proteome Organization Annual Meeting. (2013)
  8. "Top-down Characterization of Proteins in Bacteria with Unsequenced Genomes" Invited talk at ASMS Sanibel Conference on Mass Spectrometry, Top Down Mass Spectrometry (2013).
  9. "Protein Bioinformatics and Systems Biology" Omics session, George Washington University and Georgetown University Departments of Biochemistry Retreat (2013).
  10. "Reference Databases" Panel presentation at NSF Workshop: Strengthening Forensic Science through Connections with the Analytical Sciences (2012).
  11. "Generalized Protein Parsimony and Spectral Counting for Functional Enrichment Analysis" NIH Proteomics Interest Group Seminar (2012).
  12. "False-Discovery-Rate Aware Protein Inference by Generalized Protein Parsimony" HUPO World Congress (2012).
  13. "Reference Databases" Panel discussion, FDA public meeting, Highly Multiplexed Microbiology/MCM Devices (2012).
  14. "Glycoprotein Microheterogeneity via N-Glycopeptide Identification" Warren Workshop on Glycoconjugate Analysis (2012).
  15. "Gene Set Enrichment and Splicing Detecting using Spectral Counting" Brown Bag seminar series, Georgetown Center for Cancer Systems Biology (2012).
  16. "Generalized Protein Parsimony" Poster-Flash oral presentation, RECOMB Satellite Conference on Computational Proteomics. (2012)
  17. "Novel empirical FDR estimation techniques in the PepArML meta-search peptide identification platform" US Human Proteome Organization Annual Meeting. (2011)
  18. "Top-down characterization of proteins in bacteria with unsequenced genomes" US Human Proteome Organization Annual Meeting. (2010)
  19. "Improving the Sensitivity of Peptide Identification for Genome Annotation" Imaging Science and Information Systems (ISIS) Center, Georgetown University. (2010)
  20. "Improving the Sensitivity of Peptide Identification for Genome Annotation" Molecular and Cell Biology Seminar Series, University of Maryland, College Park. (2010)
  21. "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)
  22. "Improved Peptide Identification Sensitivity using Meta-Search, Grid-Computing, and Machine-Learning, with Application to Genome Annotation" NIH Proteomics Interest Group Seminar. (2009)
  23. "Improving the Sensitivity of Peptide Identification" NCI Clinical Proteomic Technologies for Cancer Annual Meeting. (2008)
  24. "Improving the Reliability of Peptide Identifications using Machine Learning." US Human Proteome Organization Annual Meeting. (2008)
  25. "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)
  26. "Proteomic Characterization of Alternative Splicing and Coding Polymorphism." NCI Clinical Proteomic Technologies for Cancer Annual Meeting. (2007)
  27. "Proteomic Characterization of Alternative Splicing and Coding Polymophism." Informatics Seminar, Department of Biomedical Informatics, Vanderbilt University School of Medicine (2007)
  28. "Direct Experimental Observation of Functional Protein Isoforms by Tandem Mass Spectrometry." Department of Biochemistry and Molecular and Cellular Biology, Georgetown University Medical Center (2007)
  29. "Improving Genome Annotation using Proteomics" J. Craig Venter Institute (2007)
  30. "Proteomic Characterization of Alternative Splicing and Coding Polymophism." Department of Biochemistry and Molecular and Cellular Biology, Georgetown University Medical Center (2007)
  31. "Optimal k-mer Superstrings for Protein Identification and DNA Assay Design." Department of Computer Science, George Mason University (2007)
  32. "Large Scale Combinatorial Optimization Problems in Bioinformatics." Industrial and Systems Engineering, Lehigh University (2007)
  33. "Proteomic Characterization of Alternative Splicing and Coding Polymophism." Department of Bioinformatics, George Mason University (2007)
  34. "Novel Peptide Identification using ESTs and Genomic Sequence." J. Craig Venter Institute (2007)
  35. "Statistical Significance for Peptide Identification from Tandem Mass Spectra." Statistical Analysis of Metabonomic and Proteomic Data, MolPAGE Training Workpackage (2007)
  36. "Novel Peptide Identification using Expressed Sequence Tags and Sequence Database Compression." RECOMB Satallite Workshop on Computational Proteomics (2006)
  37. "Novel Peptide Identification using ESTs and Genomic Sequence." Computational Genomics (2006)
  38. "Novel Peptide Identification using ESTs and Genomic Sequence." International BCB-Workshop on Computational Proteomics (2006)
  39. "Aggressive Enumeration of Peptide Sequences for MS/MS Peptide Identification." Center for Bioinformatics and Computational Biology Seminar Series (2005)
  40. "Faster, more sensitive peptide identification by sequence database compression." NIH Proteomics and Mass Spectrometry Interest Groups Seminar (2005)
  41. "Optimal k-mer superstrings for peptide identification from tandem mass spectra." Capital Area Theory Seminar (CATS), University of Maryland, College Park (2005)
  42. "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)
  43. "Bioinformatics challenges for protein identification from tandem mass spectra." Colloquium, Department of Biochemistry, Georgetown University Medical Center (2004)
  44. "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)
  45. "Adventures in bioinformatics and computational biology." Colloquium, School of Operations Research and Industrial Engineering. Cornell University (2004)
Posters
  1. G. Berry, S. Leviyang, R. Goldman, and N. Edwards"Characterization of N-glycan Microheterogeneity from CID Glycopeptide Fragmentation Mass-Spectra using Spectral Similarity Networks" US Human Proteome Organization Annual Meeting, 2014.
  2. K.B. Chandler, P. Pompach, R. Goldman, and N. Edwards "N-Glycopeptide Identification from CID Tandem Mass Spectra using Glycan Databases and False Discovery Rate Estimation" Warren Workshop on Glycoconjugate Analysis, 2012.
  3. N. Edwards "Protein Inference by Generalized Protein Parsimony reduces False Positive Proteins in Bottom-Up Workflows" RECOMB Satellite Conference on Computational Proteomics, 2012.
  4. N. Edwards "Protein Inference by Generalized Protein Parsimony reduces False Positive Proteins in Bottom-Up Workflows" US Human Proteome Organization Annual Meeting, 2012.
  5. K.B. Chandler, P. Pompach, M. Bern, R. Goldman, and N. Edwards "Automated N-Glycopeptide Lookup from Glycan Databases using Tandem Mass Spectra." ASMS Conference on Mass Spectrometry, 2011.
  6. K.B. Chandler, P. Pompach, M. Bern, R. Goldman, and N. Edwards "Automated N-Glycopeptide Lookup using Tandem Mass Spectra and Glycan Databases." RECOMB Satellite Conference on Computational Proteomics, 2011.
  7. D. Retz and N. Edwards "Novel FDR Estimation for PepArML - A Meta-Search Peptide Identification Platform." RECOMB Satellite Conference on Computational Proteomics, 2011.
  8. P. Gubbala and N. Edwards "Boosting Peptide Identification Performance by Combining Many Search Engines, Spectral Matching, and Proteotypic and Physicochemical Peptide Properties." US Human Proteome Organization Annual Meeting, 2010.
  9. N.J. Edwards "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.
  10. 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.
  11. 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.
  12. 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.
  13. 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.
  14. 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.
  15. X. Wu, N. Edwards, and C.-W. Tseng. "Experimental Comparison of Peptide Identification Algorithms.", 9th Annual Conference on Computational Genomics, 2006.
  16. Nathan J. Edwards and Fernando Pineda. "Rapid Microorganism Identification Database (www.RMIDb.org)" American Society of Mass Spectrometry Conference, 2006.
  17. 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.
  18. 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.
  19. 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.
  20. N.J. Edwards. "Faster, more sensitive peptide identification from tandem mass spectra by sequence database compression." 1st Annual Symposium, US Human Proteome Organization, 2005.
  21. 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.
  22. 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.
  23. 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.
  24. 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. C. Fenselau, N. Edwards, and S. Russell. "Strategy for Rapid Recognition of Bioengineered Bacteria." US Patent Application US60/862,105.
  2. N. J. Edwards. "Approximation algorithms for the multi-level facility location problem." Ph.D. Thesis, Field of Operations Research, Cornell University, 2001.
  3. 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.