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Marshall Bern - Publications

Affiliations: 
1987-2014 Palo Alto Research Center (Xerox PARC), Palo Alto, CA, United States 
 2011- Protein Metrics Inc., San Carlos, CA 
Area:
Algorithms, Bioinformatics, Computational Geometry, Combinatorial Optimization
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40 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 Pegg CL, Phung TK, Caboche CH, Niamsuphap S, Bern M, Howell K, Schulz BL. Quantitative data independent acquisition glycoproteomics of sparkling wine. Molecular & Cellular Proteomics : McP. PMID 32938748 DOI: 10.1074/Mcp.Ra120.002181  0.346
2020 Roushan A, Wilson GM, Kletter D, Sen KI, Tang WH, Kil YJ, Carlson E, Bern M. Peak Filtering, Peak Annotation, and Wildcard Search for Glycoproteomics. Molecular & Cellular Proteomics : McP. PMID 32883802 DOI: 10.1074/Mcp.Ra120.002260  0.384
2019 van der Laarse SAM, van Gelder CAGH, Bern M, Akeroyd M, Olsthoorn MMA, Heck AJR. Targeting Proline in (Phospho)Proteomics. The Febs Journal. PMID 31863553 DOI: 10.1111/Febs.15190  0.369
2019 Kretizberg PA, Bern M, Shu Q, Yang F, Serang O. The alphabet projection of spectra. Journal of Proteome Research. PMID 31318211 DOI: 10.1021/Acs.Jproteome.9B00216  0.359
2019 Campuzano IDG, Robinson JH, Hui JO, Shi SD, Netirojjanakul C, Nshanian M, Lippens JL, Bagal D, Egea PF, Loo JA, Bern M. Native and Denaturing MS Protein Deconvolution for Biopharma: Monoclonal Antibodies and Antibody-Drug-Conjugates to Polydisperse Membrane Proteins and Beyond. Analytical Chemistry. PMID 31194911 DOI: 10.1021/Acs.Analchem.9B00062  0.379
2018 Yang S, Wu WW, Shen RF, Bern M, Cipollo J. Identification of Sialic Acid Linkages on Intact Glycopeptides via Differential Chemical Modification Using IntactGIG-HILIC. Journal of the American Society For Mass Spectrometry. PMID 29651731 DOI: 10.1007/S13361-018-1931-0  0.331
2018 Greer SM, Bern M, Becker C, Brodbelt JS. Extending Proteome Coverage by Combining MS/MS Methods and a Modified Bioinformatics Platform Adapted for Database Searching of Positive and Negative Polarity 193 nm Ultraviolet Photodissociation Mass Spectra. Journal of Proteome Research. PMID 29480007 DOI: 10.1021/Acs.Jproteome.7B00673  0.419
2018 Bern M, Caval T, Kil YJ, Tang W, Becker C, Carlson E, Kletter D, Sen KI, Galy N, Hagemans D, Franc V, Heck AJR. Parsimonious Charge Deconvolution for Native Mass Spectrometry. Journal of Proteome Research. PMID 29376659 DOI: 10.1021/Acs.Jproteome.7B00839  0.354
2017 Belov AM, Viner R, Santos MR, Horn DM, Bern M, Karger BL, Ivanov AR. Analysis of Proteins, Protein Complexes, and Organellar Proteomes Using Sheathless Capillary Zone Electrophoresis - Native Mass Spectrometry. Journal of the American Society For Mass Spectrometry. PMID 28875426 DOI: 10.1007/S13361-017-1781-1  0.36
2017 Schroeter ER, DeHart CJ, Cleland TP, Zheng W, Thomas PM, Kelleher NL, Bern M, Schweitzer MH. Expansion for the Brachylophosaurus canadensis Collagen I Sequence and Additional Evidence of the Preservation of Cretaceous Protein. Journal of Proteome Research. PMID 28111950 DOI: 10.1021/Acs.Jproteome.6B00873  0.365
2017 Sen KI, Tang WH, Nayak S, Kil YJ, Bern M, Ozoglu B, Ueberheide B, Davis D, Becker C. Automated Antibody De Novo Sequencing and Its Utility in Biopharmaceutical Discovery. Journal of the American Society For Mass Spectrometry. PMID 28105549 DOI: 10.1007/S13361-016-1580-0  0.318
2016 Reatini BS, Ensink E, Liau B, Sinha JY, Powers TW, Partyka K, Bern M, Brand RE, Rudd PM, Kletter D, Drake RR, Haab BB. Characterizing Protein Glycosylation through On-Chip Glycan Modification and Probing. Analytical Chemistry. PMID 27809484 DOI: 10.1021/Acs.Analchem.6B02998  0.362
2016 Lee LY, Moh ES, Parker BL, Bern M, Packer NH, Thaysen-Andersen M. Towards Automated N-Glycopeptide Identification in Glycoproteomics. Journal of Proteome Research. PMID 27519006 DOI: 10.1021/Acs.Jproteome.6B00438  0.343
2016 Riley NM, Bern M, Westphall MS, Coon JJ. A full-featured search algorithm for negative electron transfer dissociation. Journal of Proteome Research. PMID 27402189 DOI: 10.1021/Acs.Jproteome.6B00319  0.396
2015 Cleland TP, Schroeter ER, Zamdborg L, Zheng W, Lee JE, Tran JC, Bern M, Duncan MB, Lebleu VS, Ahlf DR, Thomas PM, Kalluri R, Kelleher NL, Schweitzer MH. Mass Spectrometry and Antibody-Based Characterization of Blood Vessels from Brachylophosaurus canadensis. Journal of Proteome Research. PMID 26595531 DOI: 10.1021/Acs.Jproteome.5B00675  0.337
2015 Brito AE, Kletter D, Singhal M, Bern M. Benchmark study of automatic annotation of MALDI-TOF N-glycan profiles. Journal of Proteomics. 129: 71-7. PMID 26047718 DOI: 10.1016/J.Jprot.2015.05.028  0.351
2015 Kletter D, Curnutte B, Maupin KA, Bern M, Haab BB. Exploring the specificities of glycan-binding proteins using glycan array data and the GlycoSearch software. Methods in Molecular Biology (Clifton, N.J.). 1273: 203-14. PMID 25753713 DOI: 10.1007/978-1-4939-2343-4_15  0.309
2015 Tang H, Hsueh P, Kletter D, Bern M, Haab B. The detection and discovery of glycan motifs in biological samples using lectins and antibodies: new methods and opportunities. Advances in Cancer Research. 126: 167-202. PMID 25727148 DOI: 10.1016/Bs.Acr.2014.11.003  0.31
2015 Singh S, Pal K, Ensink E, Yadav J, Kletter D, Bern M, Mehta A, Melcher K, Haab BB. Abstract B31: Development of fucose based pancreatic cancer biomarkers using modified lectins Cancer Research. 75. DOI: 10.1158/1538-7445.Panca2014-B31  0.316
2014 Han X, Wang Y, Aslanian A, Bern M, Lavallée-Adam M, Yates JR. Sheathless capillary electrophoresis-tandem mass spectrometry for top-down characterization of Pyrococcus furiosus proteins on a proteome scale. Analytical Chemistry. 86: 11006-12. PMID 25346219 DOI: 10.1021/Ac503439N  0.367
2013 Kletter D, Cao Z, Bern M, Haab B. Determining lectin specificity from glycan array data using motif segregation and GlycoSearch software. Current Protocols in Chemical Biology. 5: 157-69. PMID 23839995 DOI: 10.1002/9780470559277.Ch130028  0.313
2013 McClintock CS, Parks JM, Bern M, Ghattyvenkatakrishna PK, Hettich RL. Comparative informatics analysis to evaluate site-specific protein oxidation in multidimensional LC-MS/MS data. Journal of Proteome Research. 12: 3307-16. PMID 23827042 DOI: 10.1021/Pr400141P  0.343
2013 Kletter D, Singh S, Bern M, Haab BB. Global comparisons of lectin-glycan interactions using a database of analyzed glycan array data. Molecular & Cellular Proteomics : McP. 12: 1026-35. PMID 23399549 DOI: 10.1074/Mcp.M112.026641  0.332
2013 Yin X, Bern M, Xing Q, Ho J, Viner R, Mayr M. Glycoproteomic analysis of the secretome of human endothelial cells. Molecular & Cellular Proteomics : McP. 12: 956-78. PMID 23345538 DOI: 10.1074/Mcp.M112.024018  0.34
2013 Bern M, Brito AE, Pang PC, Rekhi A, Dell A, Haslam SM. Polylactosaminoglycan glycomics: enhancing the detection of high-molecular-weight N-glycans in matrix-assisted laser desorption ionization time-of-flight profiles by matched filtering. Molecular & Cellular Proteomics : McP. 12: 996-1004. PMID 23325768 DOI: 10.1074/Mcp.O112.026377  0.361
2012 Bern M, Kil YJ, Becker C. Byonic: advanced peptide and protein identification software. Current Protocols in Bioinformatics / Editoral Board, Andreas D. Baxevanis ... [Et Al.]. Unit13.20. PMID 23255153 DOI: 10.1002/0471250953.Bi1320S40  0.346
2012 Bhatia S, Kil YJ, Ueberheide B, Chait BT, Tayo L, Cruz L, Lu B, Yates JR, Bern M. Constrained de novo sequencing of conotoxins. Journal of Proteome Research. 11: 4191-200. PMID 22709442 DOI: 10.1021/Pr300312H  0.592
2011 Kil YJ, Becker C, Sandoval W, Goldberg D, Bern M. Preview: a program for surveying shotgun proteomics tandem mass spectrometry data. Analytical Chemistry. 83: 5259-67. PMID 21619057 DOI: 10.1021/Ac200609A  0.358
2011 Becker CH, Bern M. Recent developments in quantitative proteomics. Mutation Research. 722: 171-82. PMID 20620221 DOI: 10.1016/J.Mrgentox.2010.06.016  0.388
2011 Bhatia S, Kil YJ, Ueberheide B, Chait B, Tayo LL, Cruz LJ, Lu B, Yates JR, Bern M. Constrained de novo sequencing of peptides with application to conotoxins Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 6577: 16-30. DOI: 10.1007/978-3-642-20036-6_2  0.552
2010 Chen X, Drogaris P, Bern M. Identification of tandem mass spectra of mixtures of isomeric peptides. Journal of Proteome Research. 9: 3270-9. PMID 20329787 DOI: 10.1021/Pr100205K  0.374
2010 Bern M, Finney G, Hoopmann MR, Merrihew G, Toth MJ, MacCoss MJ. Deconvolution of mixture spectra from ion-trap data-independent-acquisition tandem mass spectrometry. Analytical Chemistry. 82: 833-41. PMID 20039681 DOI: 10.1021/Ac901801B  0.381
2009 Zhu Y, Guo T, Park JE, Li X, Meng W, Datta A, Bern M, Lim SK, Sze SK. Elucidating in vivo structural dynamics in integral membrane protein by hydroxyl radical footprinting. Molecular & Cellular Proteomics : McP. 8: 1999-2010. PMID 19473960 DOI: 10.1074/Mcp.M900081-Mcp200  0.316
2009 Goldberg D, Bern M, North SJ, Haslam SM, Dell A. Glycan family analysis for deducing N-glycan topology from single MS. Bioinformatics (Oxford, England). 25: 365-71. PMID 19073587 DOI: 10.1093/Bioinformatics/Btn636  0.336
2007 Goldberg D, Bern M, Parry S, Sutton-Smith M, Panico M, Morris HR, Dell A. Automated N-glycopeptide identification using a combination of single- and tandem-MS. Journal of Proteome Research. 6: 3995-4005. PMID 17727280 DOI: 10.1021/Pr070239F  0.353
2007 Bern M, Cai Y, Goldberg D. Lookup peaks: a hybrid of de novo sequencing and database search for protein identification by tandem mass spectrometry. Analytical Chemistry. 79: 1393-400. PMID 17243770 DOI: 10.1021/Ac0617013  0.411
2006 Bern M, Goldberg D, Lyashenko E. Data mining for proteins characteristic of clades. Nucleic Acids Research. 34: 4342-53. PMID 16936320 DOI: 10.1093/Nar/Gkl440  0.306
2006 Goldberg D, Bern M, Li B, Lebrilla CB. Automatic determination of O-glycan structure from fragmentation spectra. Journal of Proteome Research. 5: 1429-34. PMID 16739994 DOI: 10.1021/Pr060035J  0.347
1995 Bern M, Michell S, Ruppert J. Linear-size nonobtuse triangulation of polygons Discrete & Computational Geometry. 14: 411-428. DOI: 10.1007/Bf02570715  0.311
1987 Bern M, Lawler E, Wong A. Linear-time computation of optimal subgraphs of decomposable graphs Journal of Algorithms. 8: 216-235. DOI: 10.1016/0196-6774(87)90039-3  0.606
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