☰

Nathan J. Edwards, Ph.D. - Publications

Affiliations: 
2001 Cornell University, Ithaca, NY, United States 
Area:
Operations Research, Industrial Engineering, Computer Science
Tree Info Similar researchers PubMed Report error

42 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2020 Thangudu RR, Rudnick PA, Holck M, Singhal D, MacCoss MJ, Edwards NJ, Ketchum KA, Kinsinger CR, Kim E, Basu A. Abstract LB-242: Proteomic Data Commons: A resource for proteogenomic analysis Cancer Research. 80. DOI: 10.1158/1538-7445.Am2020-Lb-242  0.345
2019 Clark DJ, Dhanasekaran SM, Petralia F, Pan J, Song X, Hu Y, da Veiga Leprevost F, Reva B, Lih TM, Chang HY, Ma W, Huang C, Ricketts CJ, Chen L, Krek A, ... ... Edwards N, et al. Integrated Proteogenomic Characterization of Clear Cell Renal Cell Carcinoma. Cell. 179: 964-983.e31. PMID 31675502 DOI: 10.1016/J.Cell.2019.10.007  0.314
2017 Geis-Asteggiante L, Belew AT, Clements VK, Edwards NJ, Ostrand-Rosenberg S, El-Sayed NM, Fenselau C. Differential content of proteins, mRNAs, and miRNAs suggests that MDSC and their exosomes may mediate distinct immune suppressive functions. Journal of Proteome Research. PMID 29139296 DOI: 10.1021/Acs.Jproteome.7B00646  0.304
2017 Adams KR, Chauhan S, Patel DB, Clements VK, Wang Y, Jay SM, Edwards NJ, Ostrand-Rosenberg S, Fenselau C. Ubiquitin conjugation probed by inflammation in MDSC extracellular vesicles. Journal of Proteome Research. PMID 29061044 DOI: 10.1021/Acs.Jproteome.7B00585  0.348
2017 Edwards NJ. Protein Identification from Tandem Mass Spectra by Database Searching. Methods in Molecular Biology (Clifton, N.J.). 1558: 357-380. PMID 28150247 DOI: 10.1007/978-1-4939-6783-4_17  0.415
2016 Sanda M, Zhang L, Edwards NJ, Goldman R. Site-specific analysis of changes in the glycosylation of proteins in liver cirrhosis using data-independent workflow with soft fragmentation. Analytical and Bioanalytical Chemistry. PMID 27822650 DOI: 10.1007/S00216-016-0041-8  0.398
2016 Geis-Asteggiante L, Ostrand-Rosenberg S, Fenselau C, Edwards NJ. Evaluation of spectral counting for relative quantitation of proteoforms in top-down proteomics. Analytical Chemistry. PMID 27748581 DOI: 10.1021/Acs.Analchem.6B02151  0.335
2016 Movassagh M, Alomran N, Mudvari P, Dede M, Dede C, Kowsari K, Restrepo P, Cauley E, Bahl S, Li M, Waterhouse W, Tsaneva-Atanasova K, Edwards N, Horvath A. RNA2DNAlign: nucleotide resolution allele asymmetries through quantitative assessment of RNA and DNA paired sequencing data. Nucleic Acids Research. PMID 27576531 DOI: 10.1093/Nar/Gkw757  0.301
2016 Choksawangkarn W, Graham LM, Burke M, Lee SB, Ostrand-Rosenberg S, Fenselau C, Edwards NJ. Peptide-based systems analysis of inflammation induced myeloid-derived suppressor cells reveals diverse signaling pathways. Proteomics. PMID 27193397 DOI: 10.1002/Pmic.201500102  0.325
2016 Rudnick PA, Markey SP, Roth J, Mirokhin Y, Yan X, Tchekhovskoi DV, Edwards NJ, Thangudu RR, Ketchum KA, Kinsinger CR, Mesri M, Rodriguez H, Stein SE. A Description of the Clinical Proteomic Tumor Analysis Consortium (CPTAC) Common Data Analysis Pipeline. Journal of Proteome Research. PMID 26860878 DOI: 10.1021/Acs.Jproteome.5B01091  0.395
2016 Goodacre N, Edwards N, Danielsen M, Uetz P, Wu C. Predicting nsSNPs the disrupt protein-protein interactions using docking. Ieee/Acm Transactions On Computational Biology and Bioinformatics. PMID 26812731 DOI: 10.1109/Tcbb.2016.2520931  0.34
2015 Geis-Asteggiante L, Dhabaria A, Edwards N, Ostrand-Rosenberg S, Fenselau C. Top-down analysis of low mass proteins in exosomes shed by murine myeloid-derived suppressor cells. International Journal of Mass Spectrometry. 378: 264-269. PMID 25937807 DOI: 10.1016/J.Ijms.2014.08.035  0.389
2015 Edwards NJ, Oberti M, Thangudu RR, Cai S, McGarvey PB, Jacob S, Madhavan S, Ketchum KA. The CPTAC Data Portal: A Resource for Cancer Proteomics Research. Journal of Proteome Research. 14: 2707-13. PMID 25873244 DOI: 10.1021/Pr501254J  0.369
2014 Burke MC, Oei MS, Edwards NJ, Ostrand-Rosenberg S, Fenselau C. Ubiquitinated proteins in exosomes secreted by myeloid-derived suppressor cells. Journal of Proteome Research. 13: 5965-72. PMID 25285581 DOI: 10.1021/Pr500854X  0.398
2014 Burke M, Choksawangkarn W, Edwards N, Ostrand-Rosenberg S, Fenselau C. Exosomes from myeloid-derived suppressor cells carry biologically active proteins. Journal of Proteome Research. 13: 836-43. PMID 24295599 DOI: 10.1021/Pr400879C  0.316
2014 Movassagh M, Mudvari P, Kokkinaki M, Edwards NJ, Golestaneh N, Horvath A. Analysis for co-occurring sequence features identifies link between common synonymous variant and an early-terminated NPC1 isoform Journal of Clinical Bioinformatics. 4: 14. DOI: 10.1186/2043-9113-4-14  0.307
2013 Edwards NJ. PepArML: A Meta-Search Peptide Identification Platform. Current Protocols in Bioinformatics / Editoral Board, Andreas D. Baxevanis ... [Et Al.]. 13: 13.23.1-13.23.23. PMID 25663956 DOI: 10.1002/0471250953.Bi1323S44  0.356
2013 Risk BA, Edwards NJ, Giddings MC. A peptide-spectrum scoring system based on ion alignment, intensity, and pair probabilities. Journal of Proteome Research. 12: 4240-7. PMID 23875887 DOI: 10.1021/Pr400286P  0.311
2013 Chandler KB, Pompach P, Goldman R, Edwards N. Exploring site-specific N-glycosylation microheterogeneity of haptoglobin using glycopeptide CID tandem mass spectra and glycan database search. Journal of Proteome Research. 12: 3652-66. PMID 23829323 DOI: 10.1021/Pr400196S  0.409
2013 Cannon JR, Edwards NJ, Fenselau C. Mass-biased partitioning to enhance middle down proteomics analysis. Journal of Mass Spectrometry : Jms. 48: 340-3. PMID 23494789 DOI: 10.1002/Jms.3164  0.381
2013 Linde ME, Colquhoun DR, Ubaida Mohien C, Kole T, Aquino V, Cotter R, Edwards N, Hildreth JE, Graham DR. 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: 2045-54. PMID 23432411 DOI: 10.1021/Pr300918R  0.348
2013 Ubaida Mohien C, Colquhoun DR, Mathias DK, Gibbons JG, Armistead JS, Rodriguez MC, Rodriguez MH, Edwards NJ, Hartler J, Thallinger GG, Graham DR, Martinez-Barnetche J, Rokas A, Dinglasan RR. A bioinformatics approach for integrated transcriptomic and proteomic comparative analyses of model and non-sequenced anopheline vectors of human malaria parasites. Molecular & Cellular Proteomics : McP. 12: 120-31. PMID 23082028 DOI: 10.1074/Mcp.M112.019596  0.32
2012 Choksawangkarn W, Edwards N, Wang Y, Gutierrez P, Fenselau C. 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: 3030-4. PMID 22500775 DOI: 10.1021/Pr300188B  0.343
2012 Lenco J, Lan R, Edwards N, Goldman R. MS/MS library facilitated MRM quantification of native peptides prepared by denaturing ultrafiltration. Proteome Science. 10: 7. PMID 22304756 DOI: 10.1186/1477-5956-10-7  0.35
2012 Pompach P, Chandler KB, Lan R, Edwards N, Goldman R. 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: 1728-40. PMID 22239659 DOI: 10.1021/Pr201183W  0.391
2011 Edwards NJ. Protein identification from tandem mass spectra by database searching. Methods in Molecular Biology (Clifton, N.J.). 694: 119-38. PMID 21082432 DOI: 10.1007/978-1-60761-977-2_9  0.316
2010 Liu X, Inbar Y, Dorrestein PC, Wynne C, Edwards N, Souda P, Whitelegge JP, Bafna V, Pevzner PA. Deconvolution and database search of complex tandem mass spectra of intact proteins: a combinatorial approach. Molecular & Cellular Proteomics : McP. 9: 2772-82. PMID 20855543 DOI: 10.1074/Mcp.M110.002766  0.396
2010 Wynne C, Edwards NJ, Fenselau C. Phyloproteomic classification of unsequenced organisms by top-down identification of bacterial proteins using capLC-MS/MS on an Orbitrap. Proteomics. 10: 3631-43. PMID 20845332 DOI: 10.1002/Pmic.201000172  0.415
2010 An Y, Bekesova S, Edwards N, Goldman R. Peptides in low molecular weight fraction of serum associated with hepatocellular carcinoma. Disease Markers. 29: 11-20. PMID 20826913 DOI: 10.3233/Dma-2010-0721  0.328
2010 Cannon J, Lohnes K, Wynne C, Wang Y, Edwards N, Fenselau C. High-throughput middle-down analysis using an orbitrap. Journal of Proteome Research. 9: 3886-90. PMID 20557100 DOI: 10.1021/Pr1000994  0.38
2010 Tharakan R, Edwards N, Graham DRM. Data maximization by multipass analysis of protein mass spectra. Proteomics. 10: 1160-1171. PMID 20082346 DOI: 10.1002/Pmic.200900433  0.349
2009 Wynne C, Fenselau C, Demirev PA, Edwards N. Top-down identification of protein biomarkers in bacteria with unsequenced genomes. Analytical Chemistry. 81: 9633-42. PMID 19883058 DOI: 10.1021/Ac9016677  0.42
2009 Edwards N, Wu X, Tseng C. An Unsupervised, Model-Free, Machine-Learning Combiner for Peptide Identifications from Tandem Mass Spectra Clinical Proteomics. 5: 23-36. DOI: 10.1007/S12014-009-9024-5  0.323
2007 Wang J, Gutierrez P, Edwards N, Fenselau C. Integration of 18O labeling and solution isoelectric focusing in a shotgun analysis of mitochondrial proteins. Journal of Proteome Research. 6: 4601-7. PMID 17994687 DOI: 10.1021/Pr070401E  0.338
2007 Wu X, Tseng CW, Edwards N. HMMatch: peptide identification by spectral matching of tandem mass spectra using hidden Markov models. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. 14: 1025-43. PMID 17985986 DOI: 10.1089/Cmb.2007.0071  0.366
2007 Swatkoski S, Gutierrez P, Ginter J, Petrov A, Dinman JD, Edwards N, Fenselau C. Integration of residue-specific acid cleavage into proteomic workflows. Journal of Proteome Research. 6: 4525-7. PMID 17902642 DOI: 10.1021/Pr0704682  0.361
2007 Russell SC, Edwards N, Fenselau C. Detection of plasmid insertion in Escherichia coli by MALDI-TOF mass spectrometry. Analytical Chemistry. 79: 5399-406. PMID 17579482 DOI: 10.1021/Ac0705061  0.367
2007 Edwards NJ. Novel peptide identification from tandem mass spectra using ESTs and sequence database compression. Molecular Systems Biology. 3: 102. PMID 17437027 DOI: 10.1038/Msb4100142  0.416
2007 Swatkoski S, Russell S, Edwards N, Fenselau C. Analysis of a model virus using residue-specific chemical cleavage and MALDI-TOF mass spectrometry. Analytical Chemistry. 79: 654-8. PMID 17222033 DOI: 10.1021/Ac061493E  0.366
2006 Swatkoski S, Russell SC, Edwards N, Fenselau C. Rapid chemical digestion of small acid-soluble spore proteins for analysis of Bacillus spores. Analytical Chemistry. 78: 181-8. PMID 16383326 DOI: 10.1021/Ac051521D  0.365
2006 Wu X, Edwards N, Tseng C. Peptide Identification via Tandem Mass Spectrometry Advances in Computers. 68: 253-278. DOI: 10.1016/S0065-2458(06)68006-6  0.386
2001 Bafna V, Edwards N. SCOPE: A probabilistic model for scoring tandem mass spectra against a peptide database Bioinformatics. 17. PMID 11472988 DOI: 10.1093/Bioinformatics/17.Suppl_1.S13  0.427
Show low-probability matches.