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

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
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  1
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  1
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  1
2016 Barallobre-Barreiro J, Gupta SK, Zoccarato A, Kitazume-Taneike R, Fava M, Yin X, Werner T, Hirt MN, Zampetaki A, Viviano A, Chong M, Bern M, Kourliouros A, Domenech N, Willeit P, et al. Glycoproteomics Reveals Decorin Peptides With Anti-Myostatin Activity in Human Atrial Fibrillation. Circulation. PMID 27559042 DOI: 10.1161/CIRCULATIONAHA.115.016423  1
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  1
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  1
2015 Haab BB, Huang Y, Balasenthil S, Partyka K, Tang H, Anderson M, Allen P, Sasson A, Zeh H, Kaul K, Kletter D, Ge S, Bern M, Kwon R, Blasutig I, et al. Definitive Characterization of CA 19-9 in Resectable Pancreatic Cancer Using a Reference Set of Serum and Plasma Specimens. Plos One. 10: e0139049. PMID 26431551 DOI: 10.1371/journal.pone.0139049  1
2015 Marino F, Bern M, Mommen GP, Leney AC, van Gaans-van den Brink JA, Bonvin AM, Becker C, van Els CA, Heck AJ. Extended O-GlcNAc on HLA Class-I-Bound Peptides. Journal of the American Chemical Society. 137: 10922-5. PMID 26280087 DOI: 10.1021/jacs.5b06586  1
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  1
2015 Singh S, Pal K, Yadav J, Tang H, Partyka K, Kletter D, Hsueh P, Ensink E, Kc B, Hostetter G, Xu HE, Bern M, Smith DF, Mehta AS, Brand R, et al. Upregulation of glycans containing 3' fucose in a subset of pancreatic cancers uncovered using fusion-tagged lectins. Journal of Proteome Research. 14: 2594-605. PMID 25938165 DOI: 10.1021/acs.jproteome.5b00142  1
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  1
2015 Tang H, Singh S, Partyka K, Kletter D, Hsueh P, Yadav J, Ensink E, Bern M, Hostetter G, Hartman D, Huang Y, Brand RE, Haab BB. Glycan motif profiling reveals plasma sialyl-lewis x elevations in pancreatic cancers that are negative for sialyl-lewis A. Molecular & Cellular Proteomics : McP. 14: 1323-33. PMID 25733690 DOI: 10.1074/mcp.M114.047837  1
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  1
2014 Gajewiak J, Azam L, Imperial J, Walewska A, Green BR, Bandyopadhyay PK, Raghuraman S, Ueberheide B, Bern M, Zhou HM, Minassian NA, Hagan RH, Flinspach M, Liu Y, Bulaj G, et al. A disulfide tether stabilizes the block of sodium channels by the conotoxin μO§-GVIIJ. Proceedings of the National Academy of Sciences of the United States of America. 111: 2758-63. PMID 24497506 DOI: 10.1073/pnas.1324189111  1
2013 Burlak C, Bern M, Brito AE, Isailovic D, Wang ZY, Estrada JL, Li P, Tector AJ. N-linked glycan profiling of GGTA1/CMAH knockout pigs identifies new potential carbohydrate xenoantigens. Xenotransplantation. 20: 277-91. PMID 24033743 DOI: 10.1111/xen.12047  1
2013 McCarter C, Kletter D, Tang H, Partyka K, Ma Y, Singh S, Yadav J, Bern M, Haab BB. Prediction of glycan motifs using quantitative analysis of multi-lectin binding: Motifs on MUC1 produced by cultured pancreatic cancer cells. Proteomics. Clinical Applications. 7: 632-41. PMID 23956151 DOI: 10.1002/prca.201300069  1
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  1
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  1
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  1
2013 Schweitzer MH, Zheng W, Cleland TP, Bern M. Molecular analyses of dinosaur osteocytes support the presence of endogenous molecules. Bone. 52: 414-23. PMID 23085295 DOI: 10.1016/j.bone.2012.10.010  1
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  1
2012 Martini J, Recht MI, Huck M, Bern MW, Johnson NM, Kiesel P. Time encoded multicolor fluorescence detection in a microfluidic flow cytometer. Lab On a Chip. 12: 5057-62. PMID 23044636 DOI: 10.1039/c2lc40515f  1
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  1
2011 Bern MW, Kil YJ. Two-dimensional target decoy strategy for shotgun proteomics. Journal of Proteome Research. 10: 5296-301. PMID 22010998 DOI: 10.1021/pr200780j  1
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  1
2011 Bern M, Kil YJ. Comment on "Unbiased statistical analysis for multi-stage proteomic search strategies". Journal of Proteome Research. 10: 2123-7. PMID 21288048 DOI: 10.1021/pr101143m  1
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  1
2009 Bern M, Phinney BS, Goldberg D. Reanalysis of Tyrannosaurus rex Mass Spectra. Journal of Proteome Research. 8: 4328-32. PMID 19603827 DOI: 10.1021/pr900349r  1
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  1
2008 Charvátová O, Foley BL, Bern MW, Sharp JS, Orlando R, Woods RJ. Quantifying protein interface footprinting by hydroxyl radical oxidation and molecular dynamics simulation: application to galectin-1. Journal of the American Society For Mass Spectrometry. 19: 1692-705. PMID 18707901 DOI: 10.1016/j.jasms.2008.07.013  1
2008 Bern M, Goldberg D. Improved ranking functions for protein and modification-site identifications. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. 15: 705-19. PMID 18651800 DOI: 10.1089/cmb.2007.0119  1
2008 Recht MI, De Bruyker D, Bell AG, Wolkin MV, Peeters E, Anderson GB, Kolatkar AR, Bern MW, Kuhn P, Bruce RH, Torres FE. Enthalpy array analysis of enzymatic and binding reactions. Analytical Biochemistry. 377: 33-9. PMID 18374654 DOI: 10.1016/j.ab.2008.03.007  1
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  1
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  1
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  1
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  1
2006 Bern M, Goldberg D. De novo analysis of peptide tandem mass spectra by spectral graph partitioning. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. 13: 364-78. PMID 16597246 DOI: 10.1089/cmb.2006.13.364  1
2005 Bern M, Goldberg D. Automatic selection of representative proteins for bacterial phylogeny. Bmc Evolutionary Biology. 5: 34. PMID 15927057 DOI: 10.1186/1471-2148-5-34  1
2004 Bern M, Goldberg D, McDonald WH, Yates JR. Automatic quality assessment of peptide tandem mass spectra. Bioinformatics (Oxford, England). 20: i49-54. PMID 15262780 DOI: 10.1093/bioinformatics/bth947  1
2004 Zhu Y, Carragher B, Glaeser RM, Fellmann D, Bajaj C, Bern M, Mouche F, de Haas F, Hall RJ, Kriegman DJ, Ludtke SJ, Mallick SP, Penczek PA, Roseman AM, Sigworth FJ, et al. Automatic particle selection: results of a comparative study. Journal of Structural Biology. 145: 3-14. PMID 15065668 DOI: 10.1016/j.jsb.2003.09.033  1
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