☰

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
Tree Info Similar researchers PubMed Report error

40/125 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
Low-probability matches (unlikely to be authored by this person)
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  0.297
2018 Zhu J, Chen Z, Zhang J, An M, Wu J, Yu Q, Skilton SJ, Bern M, Ilker Sen K, Li L, Lubman DM. Differential Quantitative Determination of Site-Specific Intact N-Glycopeptides in Serum Haptoglobin between Hepatocellular Carcinoma and Cirrhosis Using LC-EThcD-MS/MS. Journal of Proteome Research. PMID 30370771 DOI: 10.1021/Acs.Jproteome.8B00654  0.294
1992 Bern M, R. Gilbert J. Drawing the planar dual Information Processing Letters. 43: 7-13. DOI: 10.1016/0020-0190(92)90022-N  0.292
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  0.291
2016 Bogdanoff WA, Morgenstern D, Bern M, Ueberheide BM, Sanchez-Fauquier A, DuBois RM. De Novo Sequencing and Resurrection of a Human Astrovirus-Neutralizing Antibody. Acs Infectious Diseases. 2: 313-321. PMID 27213181 DOI: 10.1021/Acsinfecdis.6B00026  0.29
1990 Bern M. Hidden surface removal for rectangles Journal of Computer and System Sciences. 40: 49-69. DOI: 10.1016/0022-0000(90)90018-G  0.287
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  0.286
1993 Bern M, Edelsbrunner H, Eppstein D, Mitchell S, Tan TS. Edge insertion for optimal triangulations Discrete & Computational Geometry. 10: 47-65. DOI: 10.1007/Bf02573962  0.285
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  0.283
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  0.282
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  0.282
2010 Bern M, Saladino J, Sharp JS. Conversion of methionine into homocysteic acid in heavily oxidized proteomics samples. Rapid Communications in Mass Spectrometry : Rcm. 24: 768-72. PMID 20169556 DOI: 10.1002/Rcm.4447  0.276
2016 Bern M, Beniston R, Mesnage S. Towards an automated analysis of bacterial peptidoglycan structure. Analytical and Bioanalytical Chemistry. PMID 27520322 DOI: 10.1007/s00216-016-9857-5  0.275
1989 Bern M, Plassmann P. The Steiner problem with edge lengths 1 and 2 Information Processing Letters. 32: 171-176. DOI: 10.1016/0020-0190(89)90039-2  0.273
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  0.273
2004 Bern M, Goldberg D, Stevens RC, Kuhn P. Automatic classification of protein crystallization images using a curve-tracking algorithm Journal of Applied Crystallography. 37: 279-287. DOI: 10.1107/S0021889804001761  0.272
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  0.268
2020 Roushan A, Wilson GM, Kletter D, Sen KI, Tang W, Kil YJ, Carlson E, Bern M. Peak Filtering, Peak Annotation, and Wildcard Search for Glycoproteomics. Molecular & Cellular Proteomics : McP. 20: 100011. PMID 33578083 DOI: 10.1074/mcp.RA120.002260  0.267
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  0.263
1999 Amenta N, Bern M, Eppstein D. Optimal Point Placement for Mesh Smoothing Journal of Algorithms. 30: 302-322. DOI: 10.1006/Jagm.1998.0984  0.261
2006 Bern M, Gilbert JR, Hendrickson B, Nguyen N, Toledo S. Support-graph preconditioners Siam Journal On Matrix Analysis and Applications. 27: 930-951. DOI: 10.1137/S0895479801384019  0.259
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  0.259
1998 Amenta N, Bern M, Eppstein D. The Crust and the β-Skeleton: Combinatorial Curve Reconstruction Graphical Models and Image Processing. 60: 125-135. DOI: 10.1006/Gmip.1998.0465  0.258
1994 Aronov B, Bern M, Eppstein D. On the number of minimal 1-Steiner trees Discrete &Amp; Computational Geometry. 12: 29-34. DOI: 10.1007/Bf02574363  0.257
2018 Busch F, Van Aernum ZL, Ju Y, Yan J, Gilbert JD, Quintyn RS, Bern M, Wysocki VH. Localization of protein complex bound ligands by surface-induced dissociation high-resolution mass spectrometry. Analytical Chemistry. PMID 30299922 DOI: 10.1021/Acs.Analchem.8B03263  0.257
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  0.252
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  0.249
1993 Bern M. Approximate closest-point queries in high dimensions Information Processing Letters. 45: 95-99. DOI: 10.1016/0020-0190(93)90222-U  0.248
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  0.248
2023 Waldenmaier HE, Gorre E, Poltash ML, Gunawardena HP, Zhai XA, Li J, Zhai B, Beil EJ, Terzo JC, Lawler R, English AM, Bern M, Mahan AD, Carlson E, Nanda H. "Lab of the Future"─Today: Fully Automated System for High-Throughput Mass Spectrometry Analysis of Biotherapeutics. Journal of the American Society For Mass Spectrometry. PMID 37186948 DOI: 10.1021/jasms.3c00036  0.246
2017 Schmit PO, Vialaret J, Wessels HJCT, Van Gool A, Hirtz C, Lehmann S, Gabelle A, Wood J, Bern M, Paape R, Suckau D, Kruppa G, Hirtz C. Towards a routine application of Top-Down approaches for label-free discovery workflows. Journal of Proteomics. PMID 28855124 DOI: 10.1016/j.jprot.2017.08.003  0.243
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  0.242
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  0.242
2021 Nichols AC, Kil YJ, Mahan A, Zhai B, Hepler R, Nields K, Nanda H, Carlson E, Bern M. Orthogonal Comparison of Analytical Methods by Theoretical Reconstruction from Bottom-up Assay Data. Journal of the American Society For Mass Spectrometry. PMID 33765378 DOI: 10.1021/jasms.0c00433  0.239
2003 Bern M, Demaine ED, Eppstein D, Kuo E, Mantler A, Snoeyink J. Ununfoldable polyhedra with convex faces Computational Geometry: Theory and Applications. 24: 51-62. DOI: 10.1016/S0925-7721(02)00091-3  0.232
2009 Datta R, Bern M. Spectrum fusion: using multiple mass spectra for de novo Peptide sequencing. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. 16: 1169-82. PMID 19645594 DOI: 10.1089/cmb.2009.0122  0.232
2004 Wong HC, Chen J, Mouche F, Rouiller I, Bern M. Model-based particle picking for cryo-electron microscopy. Journal of Structural Biology. 145: 157-67. PMID 15065683 DOI: 10.1016/J.Jsb.2003.05.001  0.23
2022 Wecksler AT, Veale L, Basanta-Sanchez M, Bern M. Development of Software Workflow for the Rapid Detection of Cross-Linked Dipeptides. Journal of the American Society For Mass Spectrometry. PMID 35157447 DOI: 10.1021/jasms.1c00312  0.23
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  0.225
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  0.214
2022 Santos IC, Lanzillotti M, Shilov I, Basanta-Sanchez M, Roushan A, Lawler R, Tang W, Bern M, Brodbelt JS. Ultraviolet Photodissociation and Activated Electron Photodetachment Mass Spectrometry for Top-Down Sequencing of Modified Oligoribonucleotides. Journal of the American Society For Mass Spectrometry. 33: 510-520. PMID 35157441 DOI: 10.1021/jasms.1c00340  0.203
2021 Čaval T, Hecht ES, Tang W, Uy-Gomez M, Nichols A, Kil YJ, Sandoval W, Bern M, Heck AJR. The lysosomal endopeptidases Cathepsin D and L are selective and effective proteases for the middle-down characterization of antibodies. The Febs Journal. PMID 33713388 DOI: 10.1111/febs.15813  0.196
2021 Patel AV, Turner RD, Rifflet A, Acosta-Martin AE, Nichols A, Awad MM, Lyras D, Gomperts Boneca I, Bern M, Collins MO, Mesnage S. PGFinder, a novel analysis pipeline for the consistent, reproducible, and high-resolution structural analysis of bacterial peptidoglycans. Elife. 10. PMID 34579805 DOI: 10.7554/eLife.70597  0.196
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  0.193
2007 Oliveira LB, Ferreira A, Vilaça MA, Wong HC, Bern M, Dahab R, Loureiro AA. SecLEACH—On the security of clustered sensor networks Signal Processing. 87: 2882-2895. DOI: 10.1016/J.Sigpro.2007.05.016  0.193
2018 Vialaret J, Schmit PO, Lehmann S, Gabelle A, Wood J, Bern M, Paape R, Suckau D, Kruppa G, Hirtz C. Identification of multiple proteoforms biomarkers on clinical samples by routine Top-Down approaches. Data in Brief. 18: 1013-1021. PMID 29900270 DOI: 10.1016/j.dib.2018.03.114  0.188
1991 Bern M, Bienstock D. Polynomially solvable special cases of the Steiner problem in planar networks Annals of Operations Research. 33: 403-418. DOI: 10.1007/Bf02071979  0.173
1994 Bern M, Greene DH, Raghunathan A, Sudan M. On-line algorithms for locating checkpoints Algorithmica. 11: 33-52. DOI: 10.1007/Bf01294262  0.17
2021 Kawahara R, Chernykh A, Alagesan K, Bern M, Cao W, Chalkley RJ, Cheng K, Choo MS, Edwards N, Goldman R, Hoffmann M, Hu Y, Huang Y, Kim JY, Kletter D, et al. Community evaluation of glycoproteomics informatics solutions reveals high-performance search strategies for serum glycopeptide analysis. Nature Methods. PMID 34725484 DOI: 10.1038/s41592-021-01309-x  0.165
2001 Bern M, Eppstein D. Optimal möbius transformations for information visualization and meshing Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 2125: 14-25. DOI: 10.1007/3-540-44634-6_3  0.157
1999 BERN M, EPPSTEIN D, Teng S. PARALLEL CONSTRUCTION OF QUADTREES AND QUALITY TRIANGULATIONS International Journal of Computational Geometry & Applications. 9: 517-532. DOI: 10.1142/S0218195999000303  0.138
1999 Amenta N, Bern M. Surface reconstruction by Voronoi filtering Discrete and Computational Geometry. 22: 481-504. DOI: 10.1007/Pl00009475  0.138
1994 Bern M, Eppstein D, Gilbert J. Provably good mesh generation Journal of Computer and System Sciences. 48: 384-409. DOI: 10.1016/S0022-0000(05)80059-5  0.131
2015 Kil YJ, Bern M, Crowell K, Kletter D, Bern N, Tang W, Carlson E, Becker C. Towards a Comprehensive Bioinformatic Analysis of the NIST Reference mAb Acs Symposium Series. 1202: 395-414. DOI: 10.1021/bk-2015-1202.ch014  0.127
1999 Amenta N, Bern M, Eppstein D. Optimal Point Placement for Mesh Smoothing Journal of Algorithms. 30: 302-322.  0.127
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  0.126
1995 BERN M, DOBKIN D, EPPSTEIN D. TRIANGULATING POLYGONS WITHOUT LARGE ANGLES International Journal of Computational Geometry & Applications. 5: 171-192. DOI: 10.1142/S0218195995000106  0.122
1990 Bern M. Faster exact algorithms for steiner trees in planar networks Networks. 20: 109-120. DOI: 10.1002/net.3230200110  0.122
1991 BERN M, EPPSTEIN D, YAO F. THE EXPECTED EXTREMES IN A DELAUNAY TRIANGULATION International Journal of Computational Geometry & Applications. 1: 79-91. DOI: 10.1142/S0218195991000074  0.119
1994 Bern M, Dobkin D, Eppstein D, Grossman R. Visibility with a moving point of view Algorithmica. 11: 360-378. DOI: 10.1007/BF01187019  0.118
2020 Sandoz KM, Moore RA, Beare PA, Patel AV, Smith RE, Bern M, Hwang H, Cooper CJ, Priola SA, Parks JM, Gumbart JC, Mesnage S, Heinzen RA. β-Barrel proteins tether the outer membrane in many Gram-negative bacteria. Nature Microbiology. PMID 33139883 DOI: 10.1038/s41564-020-00798-4  0.118
2000 Amenta N, Bern M, Eppstein D, Teng SH. Regression depth and center points Discrete and Computational Geometry. 23: 305-323.  0.112
1998 Amenta N, Bern M, Kamvysselis M. A new voronoi-based surface reconstruction algorithm Proceedings of the 25th Annual Conference On Computer Graphics and Interactive Techniques, Siggraph 1998. 415-422. DOI: 10.1145/280814.280947  0.109
1992 BERN M, EPPSTEIN D. POLYNOMIAL-SIZE NONOBTUSE TRIANGULATION OF POLYGONS International Journal of Computational Geometry & Applications. 2: 241-255. DOI: 10.1142/S0218195992000159  0.104
2002 Bern M, Eppstein D. Multivariate regression depth Discrete and Computational Geometry. 28: 1-17. DOI: 10.1007/s00454-001-0092-1  0.099
1992 Bern MW, Karloff HJ, Raghavan P, Schieber B. Fast geometric approximation techniques and geometric embedding problems Theoretical Computer Science. 106: 265-281. DOI: 10.1016/0304-3975(92)90252-B  0.098
2000 BERN M, EPPSTEIN D. QUADRILATERAL MESHING BY CIRCLE PACKING International Journal of Computational Geometry & Applications. 10: 347-360. DOI: 10.1142/S0218195900000206  0.085
2004 Zhu X, Sun S, Bern M. Classification of protein crystallization imagery. Conference Proceedings : ... Annual International Conference of the Ieee Engineering in Medicine and Biology Society. Ieee Engineering in Medicine and Biology Society. Annual Conference. 3: 1628-31. PMID 17272013 DOI: 10.1109/IEMBS.2004.1403493  0.082
1988 Bern MW. Two probabilistic results on rectilinear steiner trees Algorithmica. 3: 191-204. DOI: 10.1007/BF01762114  0.076
2021 Kawahara R, Chernykh A, Alagesan K, Bern M, Cao W, Chalkley RJ, Cheng K, Choo MS, Edwards N, Goldman R, Hoffmann M, Hu Y, Huang Y, Kim JY, Kletter D, et al. Author Correction: Community evaluation of glycoproteomics informatics solutions reveals high-performance search strategies for serum glycopeptide analysis. Nature Methods. PMID 34893784 DOI: 10.1038/s41592-021-01368-0  0.075
1998 Bern M, Sahai A. Pushing Disks Together—The Continuous-Motion Case Discrete & Computational Geometry. 20: 499-514. DOI: 10.1007/Pl00009398  0.067
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  0.066
1989 Bern MW, Graham RL. The Shortest-Network Problem Scientific American. 260: 84-89. DOI: 10.1038/SCIENTIFICAMERICAN0189-84  0.059
2001 Bern M, Eppstein D. Optimization over zonotopes and training support vector machines Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 2125: 111-121. DOI: 10.1007/3-540-44634-6_11  0.058
1992 BERN M, EPPSTEIN D. ERRATA: "POLYNOMIAL-SIZE NONOBTUSE TRIANGULATION OF POLYGONS" International Journal of Computational Geometry & Applications. 2: 449-450. DOI: 10.1142/S0218195992000305  0.053
2002 Bern M, Eppstein D, Erickson J. Flipping cubical meshes Engineering With Computers. 18: 173-187. DOI: 10.1007/S003660200016  0.052
2011 Zhang Y, Bern M, Liu J, Partridge K, Begole B, Moore B, Reich J, Kishimoto K. Ubiquitous meeting facilitator with playful real-time user interface Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 6905: 3-11. DOI: 10.1007/978-3-642-23641-9_3  0.045
2010 Bern M, Hayes B. Origami Embedding of Piecewise-Linear Two-Manifolds Algorithmica. 59: 3-15. DOI: 10.1007/s00453-010-9399-8  0.041
2004 Goldberg D, Malon C, Bern M. A global approach to automatic solution of jigsaw puzzles Computational Geometry. 28: 165-174. DOI: 10.1016/j.comgeo.2004.03.007  0.038
2010 Zhang Y, Bern M, Liu J, Partridge K, Begole B, Moore B, Reich J, Kishimoto K. Facilitating meetings with playful feedback Conference On Human Factors in Computing Systems - Proceedings. 4033-4038. DOI: 10.1145/1753846.1754098  0.035
2014 Yin X, Barallobre-Barreiro J, de Waard V, Viner R, Fava M, Skroblin P, Bern M, Mulder B, Mayr M. Glycoproteomic analysis of aortas from patients with Marfan syndrome Atherosclerosis. 237: e16. DOI: 10.1016/j.atherosclerosis.2014.10.082  0.031
2008 Yatani K, Partridge K, Bern M, Newman MW. Escape: A target selection technique using visually-cued gestures Conference On Human Factors in Computing Systems - Proceedings. 285-294. DOI: 10.1145/1357054.1357104  0.027
1995 Bern M. COMPATIBLE TETRAHEDRALIZATIONS Fundamenta Informaticae. 22: 371-384. DOI: 10.3233/FI-1995-2244  0.026
1999 Amenta N, Bern M. Surface Reconstruction by Voronoi Filtering Discrete & Computational Geometry. 22: 481-504. DOI: 10.1007/PL00009475  0.022
2000 Bern M. Guest Editor’s Foreword Discrete & Computational Geometry. 24: 575-576. DOI: 10.1007/s4540010079  0.01
Hide low-probability matches.