| Year |
Citation |
Score |
| 2024 |
Klein J, Lam H, Mak TD, Bittremieux W, Perez-Riverol Y, Gabriels R, Shofstahl J, Hecht H, Binz PA, Kawano S, Van Den Bossche T, Carver J, Neely BA, Mendoza L, Suomi T, ... ... Bandeira N, et al. The Proteomics Standards Initiative Standardized Formats for Spectral Libraries and Fragment Ion Peak Annotations: mzSpecLib and mzPAF. Analytical Chemistry. 96: 18491-18501. PMID 39514576 DOI: 10.1021/acs.analchem.4c04091 |
0.411 |
|
| 2024 |
Gomes PWP, Mannochio-Russo H, Schmid R, Zuffa S, Damiani T, Quiros-Guerrero LM, Caraballo-Rodríguez AM, Zhao HN, Yang H, Xing S, Charron-Lamoureux V, Chigumba DN, Sedio BE, Myers JA, Allard PM, ... ... Bandeira N, et al. plantMASST - Community-driven chemotaxonomic digitization of plants. Biorxiv : the Preprint Server For Biology. PMID 38798440 DOI: 10.1101/2024.05.13.593988 |
0.34 |
|
| 2024 |
Zuffa S, Schmid R, Bauermeister A, P Gomes PW, Caraballo-Rodriguez AM, El Abiead Y, Aron AT, Gentry EC, Zemlin J, Meehan MJ, Avalon NE, Cichewicz RH, Buzun E, Terrazas MC, Hsu CY, ... ... Bandeira N, et al. microbeMASST: a taxonomically informed mass spectrometry search tool for microbial metabolomics data. Nature Microbiology. PMID 38316926 DOI: 10.1038/s41564-023-01575-9 |
0.472 |
|
| 2024 |
Omenn GS, Lane L, Overall CM, Lindskog C, Pineau C, Packer NH, Cristea IM, Weintraub ST, Orchard S, Roehrl MHA, Nice E, Guo T, Van Eyk JE, Liu S, Bandeira N, et al. The 2023 Report on the Proteome from the HUPO Human Proteome Project. Journal of Proteome Research. PMID 38232391 DOI: 10.1021/acs.jproteome.3c00591 |
0.327 |
|
| 2023 |
Dorrestein P, Zuffa S, Schmid R, Bauermeister A, Gomes PWP, Caraballo-Rodriguez A, Abiead YE, Aron A, Gentry E, Zemlin J, Meehan M, Avalon N, Cichewicz R, Buzun E, Carrillo-Terrazas M, ... ... Bandeira N, et al. A Taxonomically-informed Mass Spectrometry Search Tool for Microbial Metabolomics Data. Research Square. PMID 37577622 DOI: 10.21203/rs.3.rs-3189768/v1 |
0.471 |
|
| 2022 |
Leão TF, Wang M, da Silva R, Gurevich A, Bauermeister A, Gomes PWP, Brejnrod A, Glukhov E, Aron AT, Louwen JJR, Kim HW, Reher R, Fiore MF, van der Hooft JJJ, Gerwick L, ... ... Bandeira N, et al. NPOmix: A machine learning classifier to connect mass spectrometry fragmentation data to biosynthetic gene clusters. Pnas Nexus. 1: pgac257. PMID 36712343 DOI: 10.1093/pnasnexus/pgac257 |
0.331 |
|
| 2022 |
Deutsch EW, Bandeira N, Perez-Riverol Y, Sharma V, Carver JJ, Mendoza L, Kundu DJ, Wang S, Bandla C, Kamatchinathan S, Hewapathirana S, Pullman BS, Wertz J, Sun Z, Kawano S, et al. The ProteomeXchange consortium at 10 years: 2023 update. Nucleic Acids Research. PMID 36370099 DOI: 10.1093/nar/gkac1040 |
0.325 |
|
| 2022 |
LeDuc RD, Deutsch EW, Binz PA, Fellers RT, Cesnik AJ, Klein JA, Van Den Bossche T, Gabriels R, Yalavarthi A, Perez-Riverol Y, Carver J, Bittremieux W, Kawano S, Pullman B, Bandeira N, et al. Proteomics Standards Initiative's ProForma 2.0: Unifying the Encoding of Proteoforms and Peptidoforms. Journal of Proteome Research. PMID 35290070 DOI: 10.1021/acs.jproteome.1c00771 |
0.382 |
|
| 2021 |
Petras D, Phelan VV, Acharya D, Allen AE, Aron AT, Bandeira N, Bowen BP, Belle-Oudry D, Boecker S, Cummings DA, Deutsch JM, Fahy E, Garg N, Gregor R, Handelsman J, et al. GNPS Dashboard: collaborative exploration of mass spectrometry data in the web browser. Nature Methods. PMID 34862502 DOI: 10.1038/s41592-021-01339-5 |
0.308 |
|
| 2021 |
Deutsch EW, Perez-Riverol Y, Carver J, Kawano S, Mendoza L, Van Den Bossche T, Gabriels R, Binz PA, Pullman B, Sun Z, Shofstahl J, Bittremieux W, Mak TD, Klein J, Zhu Y, ... ... Bandeira N, et al. Universal Spectrum Identifier for mass spectra. Nature Methods. PMID 34183830 DOI: 10.1038/s41592-021-01184-6 |
0.37 |
|
| 2021 |
Leão T, Wang M, Moss N, da Silva R, Sanders J, Nurk S, Gurevich A, Humphrey G, Reher R, Zhu Q, Belda-Ferre P, Glukhov E, Whitner S, Alexander KL, Rex R, ... ... Bandeira N, et al. A Multi-Omics Characterization of the Natural Product Potential of Tropical Filamentous Marine Cyanobacteria. Marine Drugs. 19. PMID 33418911 DOI: 10.3390/md19010020 |
0.533 |
|
| 2020 |
Hoopmann MR, Kusebauch U, Palmblad M, Bandeira N, Shteynberg DD, He L, Xia B, Stoychev SH, Omenn GS, Weintraub ST, Moritz RL. Insights from the First Phosphopeptide Challenge of the MS Resource Pillar of the HUPO Human Proteome Project. Journal of Proteome Research. PMID 33166149 DOI: 10.1021/acs.jproteome.0c00648 |
0.413 |
|
| 2020 |
Omenn GS, Lane L, Overall CM, Cristea IM, Corrales FJ, Lindskog C, Paik YK, Van Eyk JE, Liu S, Pennington S, Snyder MP, Baker MS, Bandeira N, Aebersold R, Moritz RL, et al. Research on The Human Proteome Reaches a Major Milestone: >90% of Predicted Human Proteins Now Credibly Detected, according to the HUPO Human Proteome Project. Journal of Proteome Research. PMID 32931287 DOI: 10.1021/Acs.Jproteome.0C00485 |
0.361 |
|
| 2020 |
Choi M, Carver J, Chiva C, Tzouros M, Huang T, Tsai TH, Pullman B, Bernhardt OM, Hüttenhain R, Teo GC, Perez-Riverol Y, Muntel J, Müller M, Goetze S, Pavlou M, ... ... Bandeira N, et al. MassIVE.quant: a community resource of quantitative mass spectrometry-based proteomics datasets. Nature Methods. PMID 32929271 DOI: 10.1038/S41592-020-0955-0 |
0.442 |
|
| 2020 |
Nothias LF, Petras D, Schmid R, Dührkop K, Rainer J, Sarvepalli A, Protsyuk I, Ernst M, Tsugawa H, Fleischauer M, Aicheler F, Aksenov AA, Alka O, Allard PM, Barsch A, ... ... Bandeira N, et al. Feature-based molecular networking in the GNPS analysis environment. Nature Methods. PMID 32839597 DOI: 10.1038/S41592-020-0933-6 |
0.331 |
|
| 2020 |
Jarmusch AK, Wang M, Aceves CM, Advani RS, Aguirre S, Aksenov AA, Aleti G, Aron AT, Bauermeister A, Bolleddu S, Bouslimani A, Caraballo Rodriguez AM, Chaar R, Coras R, Elijah EO, ... ... Bandeira N, et al. ReDU: a framework to find and reanalyze public mass spectrometry data. Nature Methods. PMID 32807955 DOI: 10.1038/S41592-020-0916-7 |
0.405 |
|
| 2020 |
Aron AT, Gentry EC, McPhail KL, Nothias LF, Nothias-Esposito M, Bouslimani A, Petras D, Gauglitz JM, Sikora N, Vargas F, van der Hooft JJJ, Ernst M, Kang KB, Aceves CM, Caraballo-Rodríguez AM, ... ... Bandeira N, et al. Reproducible molecular networking of untargeted mass spectrometry data using GNPS. Nature Protocols. PMID 32405051 DOI: 10.1038/S41596-020-0317-5 |
0.518 |
|
| 2020 |
Wang M, Jarmusch AK, Vargas F, Aksenov AA, Gauglitz JM, Weldon K, Petras D, da Silva R, Quinn R, Melnik AV, van der Hooft JJJ, Caraballo-Rodríguez AM, Nothias LF, Aceves CM, Panitchpakdi M, ... ... Bandeira N, et al. Mass spectrometry searches using MASST. Nature Biotechnology. PMID 31894142 DOI: 10.1038/S41587-019-0375-9 |
0.44 |
|
| 2019 |
Deutsch EW, Bandeira N, Sharma V, Perez-Riverol Y, Carver JJ, Kundu DJ, García-Seisdedos D, Jarnuczak AF, Hewapathirana S, Pullman BS, Wertz J, Sun Z, Kawano S, Okuda S, Watanabe Y, et al. The ProteomeXchange consortium in 2020: enabling 'big data' approaches in proteomics. Nucleic Acids Research. PMID 31686107 DOI: 10.1093/Nar/Gkz984 |
0.351 |
|
| 2019 |
Deutsch EW, Lane L, Overall CM, Bandeira N, Baker MS, Pineau C, Moritz RL, Corrales F, Orchard S, Van Eyk JE, Paik YK, Weintraub ST, Vandenbrouck Y, Omenn GS. Human Proteome Project Mass Spectrometry Data Interpretation Guidelines 3.0. Journal of Proteome Research. PMID 31599596 DOI: 10.1021/Acs.Jproteome.9B00542 |
0.52 |
|
| 2019 |
Gauglitz JM, Aceves CM, Aksenov AA, Aleti G, Almaliti J, Bouslimani A, Brown EA, Campeau A, Caraballo-Rodríguez AM, Chaar R, da Silva RR, Demko AM, Di Ottavio F, Elijah E, Ernst M, ... ... Bandeira N, et al. Untargeted mass spectrometry-based metabolomics approach unveils molecular changes in raw and processed foods and beverages. Food Chemistry. 302: 125290. PMID 31404873 DOI: 10.1016/J.Foodchem.2019.125290 |
0.33 |
|
| 2018 |
Pullman BS, Wertz J, Carver J, Bandeira N. ProteinExplorer: A Repository-Scale Resource for Exploration of Protein Detection in Public Mass Spectrometry Data Sets. Journal of Proteome Research. 17: 4227-4234. PMID 30985146 DOI: 10.1021/Acs.Jproteome.8B00496 |
0.547 |
|
| 2018 |
Deutsch EW, Perez-Riverol Y, Chalkley RJ, Wilhelm M, Tate S, Sachsenberg T, Walzer M, Käll L, Delanghe B, Böcker S, Schymanski EL, Wilmes P, Dorfer V, Kuster B, Volders PJ, ... ... Bandeira N, et al. Expanding the use of spectral libraries in proteomics. Journal of Proteome Research. PMID 30270626 DOI: 10.1021/Acs.Jproteome.8B00485 |
0.474 |
|
| 2018 |
Wang M, Wang J, Carver J, Pullman BS, Cha SW, Bandeira N. Assembling the Community-Scale Discoverable Human Proteome. Cell Systems. PMID 30172843 DOI: 10.1016/J.Cels.2018.08.004 |
0.441 |
|
| 2017 |
Scheubert K, Hufsky F, Petras D, Wang M, Nothias LF, Dührkop K, Bandeira N, Dorrestein PC, Böcker S. Significance estimation for large scale metabolomics annotations by spectral matching. Nature Communications. 8: 1494. PMID 29133785 DOI: 10.1038/S41467-017-01318-5 |
0.411 |
|
| 2017 |
Trevisan-Silva D, Bednaski AV, Fischer JSG, Veiga SS, Bandeira N, Guthals A, Marchini FK, Leprevost FV, Barbosa VC, Senff-Ribeiro A, Carvalho PC. A multi-protease, multi-dissociation, bottom-up-to-top-down proteomic view of the Loxosceles intermedia venom. Scientific Data. 4: 170090. PMID 28696408 DOI: 10.1038/Sdata.2017.90 |
0.413 |
|
| 2017 |
Luzzatto Knaan T, Garg N, Wang M, Glukhov E, Peng Y, Ackermann G, Amir A, Duggan BM, Ryazanov S, Gerwick L, Knight R, Alexandrov T, Bandeira N, Gerwick WH, Dorrestein PC. Digitizing mass spectrometry data to explore the chemical diversity and distribution of marine cyanobacteria and algae. Elife. 6. PMID 28492366 DOI: 10.7554/Elife.24214 |
0.397 |
|
| 2017 |
Luzzatto-Knaan T, Garg N, Wang M, Glukhov E, Peng Y, Ackermann G, Amir A, Duggan BM, Ryazanov S, Gerwick L, Knight R, Alexandrov T, Bandeira N, Gerwick WH, Dorrestein PC. Author response: Digitizing mass spectrometry data to explore the chemical diversity and distribution of marine cyanobacteria and algae Elife. DOI: 10.7554/Elife.24214.027 |
0.374 |
|
| 2016 |
Deutsch EW, Csordas A, Sun Z, Jarnuczak A, Perez-Riverol Y, Ternent T, Campbell DS, Bernal-Llinares M, Okuda S, Kawano S, Moritz RL, Carver JJ, Wang M, Ishihama Y, Bandeira N, et al. The ProteomeXchange consortium in 2017: supporting the cultural change in proteomics public data deposition. Nucleic Acids Research. PMID 27924013 DOI: 10.1093/Nar/Gkw936 |
0.333 |
|
| 2016 |
Wohlgemuth G, Mehta SS, Mejia RF, Neumann S, Pedrosa D, Pluskal T, Schymanski EL, Willighagen EL, Wilson M, Wishart DS, Arita M, Dorrestein PC, Bandeira N, Wang M, Schulze T, et al. SPLASH, a hashed identifier for mass spectra. Nature Biotechnology. 34: 1099-1101. PMID 27824832 DOI: 10.1038/Nbt.3689 |
0.439 |
|
| 2016 |
Guthals A, Gan Y, Murray L, Chen Y, Stinson J, Nakamura GR, Lill JR, Sandoval W, Bandeira N. De Novo MS/MS Sequencing of Native Human Antibodies. Journal of Proteome Research. PMID 27779884 DOI: 10.1021/Acs.Jproteome.6B00608 |
0.489 |
|
| 2016 |
Petras D, Nothias LF, Quinn RA, Alexandrov T, Bandeira N, Bouslimani A, Castro-Falcón G, Chen L, Dang T, Floros DJ, Hook VY, Garg N, Hoffner N, Jiang Y, Kapono CA, et al. Mass Spectrometry-Based Visualization of Molecules Associated with Human Habitats. Analytical Chemistry. PMID 27732780 DOI: 10.1021/Acs.Analchem.6B03456 |
0.431 |
|
| 2016 |
Na S, Payne SH, Bandeira N. Multi-species identification of polymorphic peptide variants via propagation in spectral networks. Molecular & Cellular Proteomics : McP. PMID 27609420 DOI: 10.1074/Mcp.O116.060913 |
0.582 |
|
| 2016 |
Li S, Bandeira N, Wang X, Tang H. On the privacy risks of sharing clinical proteomics data. Amia Joint Summits On Translational Science Proceedings. Amia Joint Summits On Translational Science. 2016: 122-31. PMID 27595046 |
0.387 |
|
| 2016 |
Wang M, Carver JJ, Phelan VV, Sanchez LM, Garg N, Peng Y, Nguyen DD, Watrous J, Kapono CA, Luzzatto-Knaan T, Porto C, Bouslimani A, Melnik AV, Meehan MJ, Liu WT, ... ... Bandeira N, et al. Sharing and community curation of mass spectrometry data with Global Natural Products Social Molecular Networking. Nature Biotechnology. 34: 828-837. PMID 27504778 DOI: 10.1038/Nbt.3597 |
0.626 |
|
| 2016 |
Nasir W, Toledo AG, Noborn F, Nilsson J, Wang M, Bandeira N, Larson G. SweetNET: A bioinformatics workflow for glycopeptide MS/MS spectral analysis. Journal of Proteome Research. PMID 27399812 DOI: 10.1021/Acs.Jproteome.6B00417 |
0.561 |
|
| 2016 |
Liu G, Knight JD, Zhang JP, Tsou CC, Wang J, Lambert JP, Larsen B, Tyers M, Raught B, Bandeira N, Nesvizhskii AI, Choi H, Gingras AC. Data Independent Acquisition analysis in ProHits 4.0. Journal of Proteomics. PMID 27132685 DOI: 10.1016/J.Jprot.2016.04.042 |
0.501 |
|
| 2015 |
Wang J, Tucholska M, Knight JD, Lambert JP, Tate S, Larsen B, Gingras AC, Bandeira N. MSPLIT-DIA: sensitive peptide identification for data-independent acquisition. Nature Methods. PMID 26550773 DOI: 10.1038/Nmeth.3655 |
0.494 |
|
| 2015 |
Hook V, Bandeira N. Neuropeptidomics Mass Spectrometry Reveals Signaling Networks Generated by Distinct Protease Pathways in Human Systems. Journal of the American Society For Mass Spectrometry. PMID 26483184 DOI: 10.1007/S13361-015-1251-6 |
0.357 |
|
| 2015 |
Duncan KR, Crüsemann M, Lechner A, Sarkar A, Li J, Ziemert N, Wang M, Bandeira N, Moore BS, Dorrestein PC, Jensen PR. Molecular networking and pattern-based genome mining improves discovery of biosynthetic gene clusters and their products from Salinispora species. Chemistry & Biology. 22: 460-71. PMID 25865308 DOI: 10.1016/J.Chembiol.2015.03.010 |
0.315 |
|
| 2015 |
Guthals A, Boucher C, Bandeira N. The generating function approach for Peptide identification in spectral networks. Journal of Computational Biology. 22: 353-366. PMID 25423621 DOI: 10.1089/Cmb.2014.0165 |
0.645 |
|
| 2014 |
Wang J, Bourne PE, Bandeira N. MixGF: spectral probabilities for mixture spectra from more than one peptide. Molecular & Cellular Proteomics : McP. 13: 3688-97. PMID 25225354 DOI: 10.1074/Mcp.O113.037218 |
0.666 |
|
| 2014 |
Griss J, Jones AR, Sachsenberg T, Walzer M, Gatto L, Hartler J, Thallinger GG, Salek RM, Steinbeck C, Neuhauser N, Cox J, Neumann S, Fan J, Reisinger F, Xu QW, ... ... Bandeira N, et al. The mzTab data exchange format: communicating mass-spectrometry-based proteomics and metabolomics experimental results to a wider audience. Molecular & Cellular Proteomics : McP. 13: 2765-75. PMID 24980485 DOI: 10.1074/Mcp.O113.036681 |
0.529 |
|
| 2014 |
Mohimani H, Kersten RD, Liu WT, Wang M, Purvine SO, Wu S, Brewer HM, Pasa-Tolic L, Bandeira N, Moore BS, Pevzner PA, Dorrestein PC. Automated genome mining of ribosomal peptide natural products. Acs Chemical Biology. 9: 1545-51. PMID 24802639 DOI: 10.1021/Cb500199H |
0.701 |
|
| 2014 |
Vizcaíno JA, Deutsch EW, Wang R, Csordas A, Reisinger F, Ríos D, Dianes JA, Sun Z, Farrah T, Bandeira N, Binz PA, Xenarios I, Eisenacher M, Mayer G, Gatto L, et al. ProteomeXchange provides globally coordinated proteomics data submission and dissemination. Nature Biotechnology. 32: 223-6. PMID 24727771 DOI: 10.1038/Nbt.2839 |
0.301 |
|
| 2014 |
Wang J, Anania VG, Knott J, Rush J, Lill JR, Bourne PE, Bandeira N. Combinatorial approach for large-scale identification of linked peptides from tandem mass spectrometry spectra. Molecular & Cellular Proteomics : McP. 13: 1128-36. PMID 24493012 DOI: 10.1074/Mcp.M113.035758 |
0.658 |
|
| 2014 |
Wang J, Anania VG, Knott J, Rush J, Lill JR, Bourne PE, Bandeira N. A turn-key approach for large-scale identification of complex posttranslational modifications. Journal of Proteome Research. 13: 1190-9. PMID 24437954 DOI: 10.1021/Pr400368U |
0.602 |
|
| 2014 |
Meyer JG, Kim S, Maltby DA, Ghassemian M, Bandeira N, Komives EA. Expanding proteome coverage with orthogonal-specificity α-lytic proteases. Molecular & Cellular Proteomics : McP. 13: 823-35. PMID 24425750 DOI: 10.1074/Mcp.M113.034710 |
0.688 |
|
| 2014 |
Chalkley RJ, Bandeira N, Chambers MC, Clauser KR, Cottrell JS, Deutsch EW, Kapp EA, Lam HH, McDonald WH, Neubert TA, Sun RX. Proteome informatics research group (iPRG)_2012: a study on detecting modified peptides in a complex mixture. Molecular & Cellular Proteomics : McP. 13: 360-71. PMID 24187338 DOI: 10.1074/Mcp.M113.032813 |
0.452 |
|
| 2013 |
Richards AL, Vincent CE, Guthals A, Rose CM, Westphall MS, Bandeira N, Coon JJ. Neutron-encoded signatures enable product ion annotation from tandem mass spectra. Molecular & Cellular Proteomics : McP. 12: 3812-23. PMID 24043425 DOI: 10.1074/Mcp.M113.028951 |
0.461 |
|
| 2013 |
Wang M, Bandeira N. Spectral library generating function for assessing spectrum-spectrum match significance. Journal of Proteome Research. 12: 3944-3951. PMID 23808827 DOI: 10.1021/Pr400230P |
0.589 |
|
| 2013 |
Nguyen DD, Wu CH, Moree WJ, Lamsa A, Medema MH, Zhao X, Gavilan RG, Aparicio M, Atencio L, Jackson C, Ballesteros J, Sanchez J, Watrous JD, Phelan VV, van de Wiel C, ... ... Bandeira N, et al. MS/MS networking guided analysis of molecule and gene cluster families. Proceedings of the National Academy of Sciences of the United States of America. 110: E2611-20. PMID 23798442 DOI: 10.1073/Pnas.1303471110 |
0.497 |
|
| 2013 |
Guthals A, Clauser KR, Frank AM, Bandeira N. Sequencing-grade de novo analysis of MS/MS triplets (CID/HCD/ETD) from overlapping peptides. Journal of Proteome Research. 12: 2846-57. PMID 23679345 DOI: 10.1021/Pr400173D |
0.78 |
|
| 2012 |
Jeong K, Kim S, Bandeira N. False discovery rates in spectral identification. Bmc Bioinformatics. 13: S2. PMID 23176207 DOI: 10.1186/1471-2105-13-S16-S2 |
0.732 |
|
| 2012 |
Moree WJ, Phelan VV, Wu CH, Bandeira N, Cornett DS, Duggan BM, Dorrestein PC. Interkingdom metabolic transformations captured by microbial imaging mass spectrometry. Proceedings of the National Academy of Sciences of the United States of America. 109: 13811-6. PMID 22869730 DOI: 10.1073/Pnas.1206855109 |
0.459 |
|
| 2012 |
Guthals A, Clauser KR, Bandeira N. Shotgun Protein Sequencing with Meta-contig Assembly Molecular & Cellular Proteomics. 11: 1084-1096. PMID 22798278 DOI: 10.1074/Mcp.M111.015768 |
0.572 |
|
| 2012 |
Guthals A, Watrous JD, Dorrestein PC, Bandeira N. The spectral networks paradigm in high throughput mass spectrometry. Molecular Biosystems. 8: 2535-44. PMID 22610447 DOI: 10.1039/C2Mb25085C |
0.641 |
|
| 2012 |
Guthals A, Bandeira N. Peptide Identification by Tandem Mass Spectrometry with Alternate Fragmentation Modes Molecular & Cellular Proteomics. 11: 550-557. PMID 22595789 DOI: 10.1074/Mcp.R112.018556 |
0.653 |
|
| 2012 |
Watrous J, Roach P, Alexandrov T, Heath BS, Yang JY, Kersten RD, van der Voort M, Pogliano K, Gross H, Raaijmakers JM, Moore BS, Laskin J, Bandeira N, Dorrestein PC. Mass spectral molecular networking of living microbial colonies. Proceedings of the National Academy of Sciences of the United States of America. 109: E1743-52. PMID 22586093 DOI: 10.1073/Pnas.1203689109 |
0.498 |
|
| 2012 |
Dost B, Bandeira N, Li X, Shen Z, Briggs SP, Bafna V. Accurate mass spectrometry based protein quantification via shared peptides. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. 19: 337-48. PMID 22414154 DOI: 10.1089/Cmb.2009.0267 |
0.676 |
|
| 2012 |
Na S, Bandeira N, Paek E. Fast multi-blind modification search through tandem mass spectrometry Molecular &Amp; Cellular Proteomics : McP. 11. PMID 22186716 DOI: 10.1074/Mcp.M111.010199 |
0.609 |
|
| 2011 |
Gupta N, Bandeira N, Keich U, Pevzner PA. Target-decoy approach and false discovery rate: when things may go wrong. Journal of the American Society For Mass Spectrometry. 22: 1111-20. PMID 21953092 DOI: 10.1007/S13361-011-0139-3 |
0.707 |
|
| 2011 |
Wang J, Bourne PE, Bandeira N. Peptide identification by database search of mixture tandem mass spectra. Molecular & Cellular Proteomics : McP. 10: M111.010017. PMID 21862760 DOI: 10.1074/Mcp.M111.010017 |
0.591 |
|
| 2011 |
Kim Y, Bark S, Hook V, Bandeira N. NeuroPedia: neuropeptide database and spectral library. Bioinformatics (Oxford, England). 27: 2772-3. PMID 21821666 DOI: 10.1093/Bioinformatics/Btr445 |
0.673 |
|
| 2011 |
Yang YL, Xu Y, Kersten RD, Liu WT, Meehan MJ, Moore BS, Bandeira N, Dorrestein PC. Connecting chemotypes and phenotypes of cultured marine microbial assemblages by imaging mass spectrometry. Angewandte Chemie (International Ed. in English). 50: 5839-42. PMID 21574228 DOI: 10.1002/Anie.201101225 |
0.343 |
|
| 2011 |
Frank AM, Monroe ME, Shah AR, Carver JJ, Bandeira N, Moore RJ, Anderson GA, Smith RD, Pevzner PA. Spectral archives: extending spectral libraries to analyze both identified and unidentified spectra. Nature Methods. 8: 587-91. PMID 21572408 DOI: 10.1038/Nmeth.1609 |
0.783 |
|
| 2011 |
Jeong K, Kim S, Bandeira N, Pevzner PA. Gapped spectral dictionaries and their applications for database searches of tandem mass spectra. Molecular & Cellular Proteomics : McP. 10: M110.002220. PMID 21444829 DOI: 10.1074/Mcp.M110.002220 |
0.821 |
|
| 2011 |
Bandeira N. Protein identification by spectral networks analysis. Methods of Molecular Biology. 694: 151. PMID 21082434 DOI: 10.1007/978-1-60761-977-2_11 |
0.661 |
|
| 2011 |
Yang Y, Xu Y, Kersten RD, Liu W, Meehan MJ, Moore BS, Bandeira N, Dorrestein PC. Cover Picture: Connecting Chemotypes and Phenotypes of Cultured Marine Microbial Assemblages by Imaging Mass Spectrometry (Angew. Chem. Int. Ed. 26/2011) Angewandte Chemie International Edition. 50: 5773-5773. DOI: 10.1002/Anie.201102745 |
0.327 |
|
| 2011 |
Yang Y, Xu Y, Kersten RD, Liu W, Meehan MJ, Moore BS, Bandeira N, Dorrestein PC. Titelbild: Connecting Chemotypes and Phenotypes of Cultured Marine Microbial Assemblages by Imaging Mass Spectrometry (Angew. Chem. 26/2011) Angewandte Chemie. 123: 5893-5893. DOI: 10.1002/Ange.201102745 |
0.33 |
|
| 2010 |
Kim S, Mischerikow N, Bandeira N, Navarro JD, Wich L, Mohammed S, Heck AJ, Pevzner PA. The generating function of CID, ETD, and CID/ETD pairs of tandem mass spectra: applications to database search. Molecular & Cellular Proteomics : McP. 9: 2840-52. PMID 20829449 DOI: 10.1074/Mcp.M110.003731 |
0.797 |
|
| 2010 |
Hook V, Bark S, Gupta N, Lortie M, Lu WD, Bandeira N, Funkelstein L, Wegrzyn J, O'Connor DT, Pevzner P. Neuropeptidomic components generated by proteomic functions in secretory vesicles for cell-cell communication. The Aaps Journal. 12: 635-45. PMID 20734175 DOI: 10.1208/S12248-010-9223-Z |
0.713 |
|
| 2010 |
Wang J, Pérez-Santiago J, Katz JE, Mallick P, Bandeira N. Peptide identification from mixture tandem mass spectra. Molecular & Cellular Proteomics : McP. 9: 1476-85. PMID 20348588 DOI: 10.1074/Mcp.M000136-Mcp201 |
0.633 |
|
| 2009 |
Ng J, Bandeira N, Liu WT, Ghassemian M, Simmons TL, Gerwick WH, Linington R, Dorrestein PC, Pevzner PA. Dereplication and de novo sequencing of nonribosomal peptides. Nature Methods. 6: 596-9. PMID 19597502 DOI: 10.1038/Nmeth.1350 |
0.733 |
|
| 2009 |
Liu WT, Ng J, Meluzzi D, Bandeira N, Gutierrez M, Simmons TL, Schultz AW, Linington RG, Moore BS, Gerwick WH, Pevzner PA, Dorrestein PC. Interpretation of tandem mass spectra obtained from cyclic nonribosomal peptides. Analytical Chemistry. 81: 4200-9. PMID 19413302 DOI: 10.1021/Ac900114T |
0.78 |
|
| 2009 |
Kim S, Bandeira N, Pevzner PA. Spectral profiles, a novel representation of tandem mass spectra and their applications for de novo peptide sequencing and identification. Molecular & Cellular Proteomics : McP. 8: 1391-400. PMID 19254948 DOI: 10.1074/Mcp.M800535-Mcp200 |
0.761 |
|
| 2009 |
Kim S, Gupta N, Bandeira N, Pevzner PA. Spectral dictionaries: Integrating de novo peptide sequencing with database search of tandem mass spectra. Molecular & Cellular Proteomics : McP. 8: 53-69. PMID 18703573 DOI: 10.1074/Mcp.M800103-Mcp200 |
0.806 |
|
| 2008 |
Bandeira N, Pham V, Pevzner P, Arnott D, Lill JR. Automated de novo protein sequencing of monoclonal antibodies Nature Biotechnology. 26: 1336-1338. PMID 19060866 DOI: 10.1038/Nbt1208-1336 |
0.549 |
|
| 2008 |
Bandeira N, Olsen JV, Mann JV, Mann M, Pevzner PA. Multi-spectra peptide sequencing and its applications to multistage mass spectrometry. Bioinformatics (Oxford, England). 24: i416-23. PMID 18785330 DOI: 10.1093/bioinformatics/btn184 |
0.718 |
|
| 2008 |
Frank AM, Bandeira N, Shen Z, Tanner S, Briggs SP, Smith RD, Pevzner PA. Clustering millions of tandem mass spectra. Journal of Proteome Research. 7: 113-22. PMID 18067247 DOI: 10.1021/Pr070361E |
0.796 |
|
| 2007 |
Bandeira N. Spectral networks: a new approach to de novo discovery of protein sequences and posttranslational modifications. Biotechniques. 42: 687-697. PMID 17612289 DOI: 10.2144/000112487 |
0.449 |
|
| 2007 |
Bandeira N, Clauser KR, Pevzner PA. Shotgun protein sequencing: assembly of peptide tandem mass spectra from mixtures of modified proteins. Molecular & Cellular Proteomics : McP. 6: 1123-34. PMID 17446555 DOI: 10.1074/Mcp.M700001-Mcp200 |
0.712 |
|
| 2007 |
Bandeira N, Tsur D, Frank A, Pevzner PA. Protein identification by spectral networks analysis. Proceedings of the National Academy of Sciences of the United States of America. 104: 6140-5. PMID 17404225 DOI: 10.1073/Pnas.0701130104 |
0.816 |
|
| 2004 |
Bandeira N, Tang H, Bafna V, Pevzner P. Shotgun protein sequencing by tandem mass spectra assembly. Analytical Chemistry. 76: 7221-33. PMID 15595863 DOI: 10.1021/Ac0489162 |
0.794 |
|
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