| Year |
Citation |
Score |
| 2020 |
Chaput G, Billings AF, DeDiego L, Orellana R, Adkins JN, Nicora CD, Kim YM, Chu R, Simmons B, DeAngelis KM. Lignin induced iron reduction by novel sp., Tolumonas lignolytic BRL6-1. Plos One. 15: e0233823. PMID 32941430 DOI: 10.1371/Journal.Pone.0233823 |
0.321 |
|
| 2020 |
Negretti NM, Ye Y, Malavasi LM, Pokharel SM, Huynh S, Noh S, Klima CL, Gourley CR, Ragle CA, Bose S, Looft T, Parker CT, Clair G, Adkins JN, Konkel ME. A porcine ligated loop model reveals new insight into the host immune response against . Gut Microbes. 12: 1-25. PMID 32887530 DOI: 10.1080/19490976.2020.1814121 |
0.319 |
|
| 2020 |
Ogden AJ, Bhatt JJ, Brewer HM, Kintigh J, Kariuki SM, Rudrabhatla S, Adkins JN, Curtis WR. Phloem Exudate Protein Profiles during Drought and Recovery Reveal Abiotic Stress Responses in Tomato Vasculature. International Journal of Molecular Sciences. 21. PMID 32586033 DOI: 10.3390/Ijms21124461 |
0.365 |
|
| 2020 |
Howard-Varona C, Lindback MM, Bastien GE, Solonenko N, Zayed AA, Jang H, Andreopoulos B, Brewer HM, Glavina Del Rio T, Adkins JN, Paul S, Sullivan MB, Duhaime MB. Phage-specific metabolic reprogramming of virocells. The Isme Journal. PMID 31896786 DOI: 10.1038/S41396-019-0580-Z |
0.309 |
|
| 2019 |
Dou M, Clair G, Tsai CF, Xu K, Chrisler WB, Sontag RL, Zhao R, Moore RJ, Liu T, Paša-Tolić L, Smith RD, Shi T, Adkins JN, Qian WJ, Kelly RT, et al. High-Throughput Single Cell Proteomics Enabled by Multiplex Isobaric Labelling in a Nanodroplet Sample Preparation Platform. Analytical Chemistry. PMID 31509397 DOI: 10.1021/Acs.Analchem.9B03349 |
0.37 |
|
| 2019 |
McDermott JE, Cort JR, Nakayasu ES, Pruneda JN, Overall C, Adkins JN. Prediction of bacterial E3 ubiquitin ligase effectors using reduced amino acid peptide fingerprinting. Peerj. 7: e7055. PMID 31211016 DOI: 10.7287/Peerj.Preprints.27292V1 |
0.326 |
|
| 2019 |
Negretti NM, Clair G, Talukdar PK, Gourley CR, Huynh S, Adkins JN, Parker CT, Corneau CM, Konkel ME. Demonstrates Conserved Proteomic and Transcriptomic Responses When Co-cultured With Human INT 407 and Caco-2 Epithelial Cells. Frontiers in Microbiology. 10: 755. PMID 31031730 DOI: 10.3389/Fmicb.2019.00755 |
0.37 |
|
| 2018 |
Akberdin IR, Collins DA, Hamilton R, Oshchepkov DY, Shukla AK, Nicora CD, Nakayasu ES, Adkins JN, Kalyuzhnaya MG. Rare Earth Elements Alter Redox Balance in 20Z. Frontiers in Microbiology. 9: 2735. PMID 30542328 DOI: 10.3389/Fmicb.2018.02735 |
0.325 |
|
| 2018 |
Couvillion SP, Zhu Y, Nagy G, Adkins JN, Ansong C, Renslow RS, Piehowski PD, Ibrahim YM, Kelly RT, Metz TO. New mass spectrometry technologies contributing towards comprehensive and high throughput omics analyses of single cells. The Analyst. PMID 30507980 DOI: 10.1039/C8An01574K |
0.351 |
|
| 2018 |
Kushner IK, Clair G, Purvine SO, Lee JY, Adkins JN, Payne SH. Individual variability of protein expression in human tissues. Journal of Proteome Research. PMID 30300549 DOI: 10.1021/Acs.Jproteome.8B00580 |
0.315 |
|
| 2018 |
Howard-Varona C, Hargreaves KR, Solonenko NE, Markillie LM, White RA, Brewer HM, Ansong C, Orr G, Adkins JN, Sullivan MB. Multiple mechanisms drive phage infection efficiency in nearly identical hosts. The Isme Journal. PMID 29568113 DOI: 10.1038/S41396-018-0099-8 |
0.327 |
|
| 2016 |
Oxford KL, Wendler JP, McDermott JE, White Iii RA, Powell JD, Jacobs JM, Adkins JN, Waters KM. The landscape of viral proteomics and its potential to impact human health. Expert Review of Proteomics. PMID 27133506 DOI: 10.1080/14789450.2016.1184091 |
0.361 |
|
| 2015 |
Li J, Overall CC, Johnson RC, Jones MB, McDermott JE, Heffron F, Adkins JN, Cambronne ED. ChIP-Seq Analysis of the σE Regulon of Salmonella enterica Serovar Typhimurium Reveals New Genes Implicated in Heat Shock and Oxidative Stress Response. Plos One. 10: e0138466. PMID 26389830 DOI: 10.1371/Journal.Pone.0138466 |
0.324 |
|
| 2015 |
Elfenbein JR, Knodler LA, Nakayasu ES, Ansong C, Brewer HM, Bogomolnaya L, Adams LG, McClelland M, Adkins JN, Andrews-Polymenis HL. Multicopy Single-Stranded DNA Directs Intestinal Colonization of Enteric Pathogens. Plos Genetics. 11: e1005472. PMID 26367458 DOI: 10.1371/Journal.Pgen.1005472 |
0.318 |
|
| 2015 |
Payne SH, Monroe ME, Overall CC, Kiebel GR, Degan M, Gibbons BC, Fujimoto GM, Purvine SO, Adkins JN, Lipton MS, Smith RD. The Pacific Northwest National Laboratory library of bacterial and archaeal proteomic biodiversity. Scientific Data. 2: 150041. PMID 26306205 DOI: 10.1038/Sdata.2015.41 |
0.355 |
|
| 2015 |
Nakayasu ES, Sydor MA, Brown RN, Sontag RL, Sobreira TJ, Slysz GW, Humphrys DR, Skarina T, Onoprienko O, Di Leo R, Kaiser BL, Li J, Ansong C, Cambronne ED, Smith RD, ... ... Adkins JN, et al. Identification of Salmonella Typhimurium deubiquitinase SseL substrates by immunoaffinity enrichment and quantitative proteomic analysis. Journal of Proteome Research. PMID 26147956 DOI: 10.1021/Acs.Jproteome.5B00574 |
0.368 |
|
| 2015 |
Suh MJ, Tovchigrechko A, Thovarai V, Rolfe MA, Torralba MG, Wang J, Adkins JN, Webb-Robertson BJ, Osborne W, Cogen FR, Kaplowitz PB, Metz TO, Nelson KE, Madupu R, Pieper R. Quantitative Differences in the Urinary Proteome of Siblings Discordant for Type 1 Diabetes Include Lysosomal Enzymes. Journal of Proteome Research. 14: 3123-35. PMID 26143644 DOI: 10.1021/Acs.Jproteome.5B00052 |
0.325 |
|
| 2015 |
Li J, Nakayasu ES, Overall CC, Johnson RC, Kidwai AS, McDermott JE, Ansong C, Heffron F, Cambronne ED, Adkins JN. Global analysis of Salmonella alternative sigma factor E on protein translation. Journal of Proteome Research. 14: 1716-26. PMID 25686268 DOI: 10.1021/Pr5010423 |
0.34 |
|
| 2015 |
Sontag RL, Mihai C, Orr G, Savchenko A, Skarina T, Cui H, Cort JR, Adkins JN, Brown RN. Electroporation of functional bacterial effectors into mammalian cells. Journal of Visualized Experiments : Jove. 52296. PMID 25650771 DOI: 10.3791/52296 |
0.406 |
|
| 2014 |
Lu J, Wu R, Adkins JN, Joachimiak A, Glover JN. Crystal structures of the F and pSLT plasmid TraJ N-terminal regions reveal similar homodimeric PAS folds with functional interchangeability. Biochemistry. 53: 5810-9. PMID 25148268 DOI: 10.1021/Bi500244M |
0.353 |
|
| 2014 |
Nakayasu ES, Wu S, Sydor MA, Shukla AK, Weitz KK, Moore RJ, Hixson KK, Kim JS, Petyuk VA, Monroe ME, Pasa-Tolic L, Qian WJ, Smith RD, Adkins JN, Ansong C. A method to determine lysine acetylation stoichiometries. International Journal of Proteomics. 2014: 730725. PMID 25143833 DOI: 10.1155/2014/730725 |
0.376 |
|
| 2014 |
Eletsky A, Michalska K, Houliston S, Zhang Q, Daily MD, Xu X, Cui H, Yee A, Lemak A, Wu B, Garcia M, Burnet MC, Meyer KM, Aryal UK, Sanchez O, ... ... Adkins JN, et al. Structural and functional characterization of DUF1471 domains of Salmonella proteins SrfN, YdgH/SssB, and YahO. Plos One. 9: e101787. PMID 25010333 DOI: 10.1371/Journal.Pone.0101787 |
0.314 |
|
| 2014 |
Merkley ED, Rysavy S, Kahraman A, Hafen RP, Daggett V, Adkins JN. Distance restraints from crosslinking mass spectrometry: mining a molecular dynamics simulation database to evaluate lysine-lysine distances. Protein Science : a Publication of the Protein Society. 23: 747-59. PMID 24639379 DOI: 10.1002/Pro.2458 |
0.363 |
|
| 2013 |
Nakayasu ES, Tempel R, Cambronne XA, Petyuk VA, Jones MB, Gritsenko MA, Monroe ME, Yang F, Smith RD, Adkins JN, Heffron F. Comparative phosphoproteomics reveals components of host cell invasion and post-transcriptional regulation during Francisella infection. Molecular & Cellular Proteomics : McP. 12: 3297-309. PMID 23970565 DOI: 10.1074/Mcp.M113.029850 |
0.332 |
|
| 2013 |
Kidwai AS, Mushamiri I, Niemann GS, Brown RN, Adkins JN, Heffron F. Diverse secreted effectors are required for Salmonella persistence in a mouse infection model. Plos One. 8: e70753. PMID 23950998 DOI: 10.1371/Journal.Pone.0070753 |
0.314 |
|
| 2013 |
Merkley ED, Cort JR, Adkins JN. Cross-linking and mass spectrometry methodologies to facilitate structural biology: finding a path through the maze. Journal of Structural and Functional Genomics. 14: 77-90. PMID 23917845 DOI: 10.1007/S10969-013-9160-Z |
0.346 |
|
| 2013 |
Deatherage Kaiser BL, Li J, Sanford JA, Kim YM, Kronewitter SR, Jones MB, Peterson CT, Peterson SN, Frank BC, Purvine SO, Brown JN, Metz TO, Smith RD, Heffron F, Adkins JN. A Multi-Omic View of Host-Pathogen-Commensal Interplay in Salmonella-Mediated Intestinal Infection. Plos One. 8: e67155. PMID 23840608 DOI: 10.1371/Journal.Pone.0067155 |
0.317 |
|
| 2013 |
Ansong C, Wu S, Meng D, Liu X, Brewer HM, Deatherage Kaiser BL, Nakayasu ES, Cort JR, Pevzner P, Smith RD, Heffron F, Adkins JN, Pasa-Tolic L. Top-down proteomics reveals a unique protein S-thiolation switch in Salmonella Typhimurium in response to infection-like conditions. Proceedings of the National Academy of Sciences of the United States of America. 110: 10153-8. PMID 23720318 DOI: 10.1073/Pnas.1221210110 |
0.425 |
|
| 2013 |
Nakayasu ES, Ansong C, Brown JN, Yang F, Lopez-Ferrer D, Qian WJ, Smith RD, Adkins JN. Evaluation of selected binding domains for the analysis of ubiquitinated proteomes. Journal of the American Society For Mass Spectrometry. 24: 1214-23. PMID 23649778 DOI: 10.1007/S13361-013-0619-8 |
0.34 |
|
| 2013 |
Nakayasu ES, Brown RN, Ansong C, Sydor MA, Imtiaz S, Mihai C, Sontag R, Hixson KK, Monroe ME, Sobreira TJ, Orr G, Petyuk VA, Yang F, Smith RD, Adkins JN. Multi-omic data integration links deleted in breast cancer 1 (DBC1) degradation to chromatin remodeling in inflammatory response. Molecular & Cellular Proteomics : McP. 12: 2136-47. PMID 23639857 DOI: 10.1074/Mcp.M112.026138 |
0.354 |
|
| 2013 |
Latif H, Lerman JA, Portnoy VA, Tarasova Y, Nagarajan H, Schrimpe-Rutledge AC, Smith RD, Adkins JN, Lee DH, Qiu Y, Zengler K. The genome organization of Thermotoga maritima reflects its lifestyle. Plos Genetics. 9: e1003485. PMID 23637642 DOI: 10.1371/Journal.Pgen.1003485 |
0.309 |
|
| 2013 |
Michalska K, Brown RN, Li H, Jedrzejczak R, Niemann GS, Heffron F, Cort JR, Adkins JN, Babnigg G, Joachimiak A. New sub-family of lysozyme-like proteins shows no catalytic activity: crystallographic and biochemical study of STM3605 protein from Salmonella Typhimurium. Journal of Structural and Functional Genomics. 14: 1-10. PMID 23572252 DOI: 10.1007/S10969-013-9151-0 |
0.374 |
|
| 2013 |
Kim YM, Schmidt BJ, Kidwai AS, Jones MB, Deatherage Kaiser BL, Brewer HM, Mitchell HD, Palsson BO, McDermott JE, Heffron F, Smith RD, Peterson SN, Ansong C, Hyduke DR, Metz TO, ... Adkins JN, et al. Salmonella modulates metabolism during growth under conditions that induce expression of virulence genes. Molecular Biosystems. 9: 1522-34. PMID 23559334 DOI: 10.1039/C3Mb25598K |
0.335 |
|
| 2013 |
Merkley ED, Baker ES, Crowell KL, Orton DJ, Taverner T, Ansong C, Ibrahim YM, Burnet MC, Cort JR, Anderson GA, Smith RD, Adkins JN. Mixed-isotope labeling with LC-IMS-MS for characterization of protein-protein interactions by chemical cross-linking. Journal of the American Society For Mass Spectrometry. 24: 444-9. PMID 23423792 DOI: 10.1007/S13361-012-0565-X |
0.351 |
|
| 2013 |
Niemann GS, Brown RN, Mushamiri IT, Nguyen NT, Taiwo R, Stufkens A, Smith RD, Adkins JN, McDermott JE, Heffron F. RNA type III secretion signals that require Hfq. Journal of Bacteriology. 195: 2119-25. PMID 23396917 DOI: 10.1128/Jb.00024-13 |
0.337 |
|
| 2013 |
Ansong C, Ortega C, Payne SH, Haft DH, Chauvignè-Hines LM, Lewis MP, Ollodart AR, Purvine SO, Shukla AK, Fortuin S, Smith RD, Adkins JN, Grundner C, Wright AT. Identification of widespread adenosine nucleotide binding in Mycobacterium tuberculosis. Chemistry & Biology. 20: 123-33. PMID 23352146 DOI: 10.1016/J.Chembiol.2012.11.008 |
0.365 |
|
| 2013 |
Ansong C, Schrimpe-Rutledge AC, Mitchell HD, Chauhan S, Jones MB, Kim YM, McAteer K, Deatherage Kaiser BL, Dubois JL, Brewer HM, Frank BC, McDermott JE, Metz TO, Peterson SN, Smith RD, ... ... Adkins JN, et al. A multi-omic systems approach to elucidating Yersinia virulence mechanisms. Molecular Biosystems. 9: 44-54. PMID 23147219 DOI: 10.1039/C2Mb25287B |
0.375 |
|
| 2012 |
Brown RN, Sanford JA, Park JH, Deatherage BL, Champion BL, Smith RD, Heffron F, Adkins JN. A Comprehensive Subcellular Proteomic Survey of Salmonella Grown under Phagosome-Mimicking versus Standard Laboratory Conditions. International Journal of Proteomics. 2012: 123076. PMID 22900174 DOI: 10.1155/2012/123076 |
0.389 |
|
| 2012 |
Ansong C, Deatherage BL, Hyduke D, Schmidt B, McDermott JE, Jones MB, Chauhan S, Charusanti P, Kim YM, Nakayasu ES, Li J, Kidwai A, Niemann G, Brown RN, Metz TO, ... ... Adkins JN, et al. Studying Salmonellae and Yersiniae Host–Pathogen Interactions Using Integrated ‘Omics and Modeling Current Topics in Microbiology and Immunology. 363: 21-41. PMID 22886542 DOI: 10.1007/82-2012-247 |
0.329 |
|
| 2012 |
Lerman JA, Hyduke DR, Latif H, Portnoy VA, Lewis NE, Orth JD, Schrimpe-Rutledge AC, Smith RD, Adkins JN, Zengler K, Palsson BO. In silico method for modelling metabolism and gene product expression at genome scale. Nature Communications. 3: 929. PMID 22760628 DOI: 10.1038/Ncomms1928 |
0.303 |
|
| 2012 |
Schrimpe-Rutledge AC, Fontès G, Gritsenko MA, Norbeck AD, Anderson DJ, Waters KM, Adkins JN, Smith RD, Poitout V, Metz TO. Discovery of novel glucose-regulated proteins in isolated human pancreatic islets using LC-MS/MS-based proteomics. Journal of Proteome Research. 11: 3520-32. PMID 22578083 DOI: 10.1021/Pr3002996 |
0.32 |
|
| 2012 |
Peterson ES, McCue LA, Schrimpe-Rutledge AC, Jensen JL, Walker H, Kobold MA, Webb SR, Payne SH, Ansong C, Adkins JN, Cannon WR, Webb-Robertson BJ. VESPA: software to facilitate genomic annotation of prokaryotic organisms through integration of proteomic and transcriptomic data. Bmc Genomics. 13: 131. PMID 22480257 DOI: 10.1186/1471-2164-13-131 |
0.319 |
|
| 2012 |
Schrimpe-Rutledge AC, Jones MB, Chauhan S, Purvine SO, Sanford JA, Monroe ME, Brewer HM, Payne SH, Ansong C, Frank BC, Smith RD, Peterson SN, Motin VL, Adkins JN. Comparative omics-driven genome annotation refinement: application across Yersiniae. Plos One. 7: e33903. PMID 22479471 DOI: 10.1371/Journal.Pone.0033903 |
0.363 |
|
| 2011 |
Charusanti P, Chauhan S, McAteer K, Lerman JA, Hyduke DR, Motin VL, Ansong C, Adkins JN, Palsson BO. An experimentally-supported genome-scale metabolic network reconstruction for Yersinia pestis CO92. Bmc Systems Biology. 5: 163. PMID 21995956 DOI: 10.1186/1752-0509-5-163 |
0.309 |
|
| 2011 |
Ansong C, Tolić N, Purvine SO, Porwollik S, Jones M, Yoon H, Payne SH, Martin JL, Burnet MC, Monroe ME, Venepally P, Smith RD, Peterson SN, Heffron F, McClelland M, ... Adkins JN, et al. Experimental annotation of post-translational features and translated coding regions in the pathogen Salmonella Typhimurium. Bmc Genomics. 12: 433. PMID 21867535 DOI: 10.1186/1471-2164-12-433 |
0.33 |
|
| 2011 |
Stanley JR, Adkins JN, Slysz GW, Monroe ME, Purvine SO, Karpievitch YV, Anderson GA, Smith RD, Dabney AR. A statistical method for assessing peptide identification confidence in accurate mass and time tag proteomics. Analytical Chemistry. 83: 6135-40. PMID 21692516 DOI: 10.1021/Ac2009806 |
0.346 |
|
| 2011 |
McDermott JE, Yoon H, Nakayasu ES, Metz TO, Hyduke DR, Kidwai AS, Palsson BO, Adkins JN, Heffron F. Technologies and approaches to elucidate and model the virulence program of salmonella. Frontiers in Microbiology. 2: 121. PMID 21687430 DOI: 10.3389/Fmicb.2011.00121 |
0.331 |
|
| 2011 |
Yoon H, Ansong C, Adkins JN, Heffron F. Discovery of Salmonella virulence factors translocated via outer membrane vesicles to murine macrophages. Infection and Immunity. 79: 2182-92. PMID 21464085 DOI: 10.1128/Iai.01277-10 |
0.355 |
|
| 2011 |
Schutzer SE, Angel TE, Liu T, Schepmoes AA, Clauss TR, Adkins JN, Camp DG, Holland BK, Bergquist J, Coyle PK, Smith RD, Fallon BA, Natelson BH. Distinct cerebrospinal fluid proteomes differentiate post-treatment lyme disease from chronic fatigue syndrome. Plos One. 6: e17287. PMID 21383843 DOI: 10.1371/Journal.Pone.0017287 |
0.369 |
|
| 2011 |
McDermott JE, Archuleta M, Thrall BD, Adkins JN, Waters KM. Controlling the response: predictive modeling of a highly central, pathogen-targeted core response module in macrophage activation. Plos One. 6: e14673. PMID 21339814 DOI: 10.1371/Journal.Pone.0014673 |
0.315 |
|
| 2011 |
Du X, Chowdhury SM, Manes NP, Wu S, Mayer MU, Adkins JN, Anderson GA, Smith RD. Xlink-identifier: an automated data analysis platform for confident identifications of chemically cross-linked peptides using tandem mass spectrometry. Journal of Proteome Research. 10: 923-31. PMID 21175198 DOI: 10.1021/Pr100848A |
0.412 |
|
| 2011 |
Niemann GS, Brown RN, Gustin JK, Stufkens A, Shaikh-Kidwai AS, Li J, McDermott JE, Brewer HM, Schepmoes A, Smith RD, Adkins JN, Heffron F. Discovery of novel secreted virulence factors from Salmonella enterica serovar Typhimurium by proteomic analysis of culture supernatants. Infection and Immunity. 79: 33-43. PMID 20974834 DOI: 10.1128/Iai.00771-10 |
0.385 |
|
| 2011 |
McDermott JE, Corrigan A, Peterson E, Oehmen C, Niemann G, Cambronne ED, Sharp D, Adkins JN, Samudrala R, Heffron F. Computational prediction of type III and IV secreted effectors in gram-negative bacteria. Infection and Immunity. 79: 23-32. PMID 20974833 DOI: 10.1128/Iai.00537-10 |
0.319 |
|
| 2010 |
Buchko GW, Niemann G, Baker ES, Belov ME, Smith RD, Heffron F, Adkins JN, McDermott JE. A multi-pronged search for a common structural motif in the secretion signal of Salmonella enterica serovar Typhimurium type III effector proteins. Molecular Biosystems. 6: 2448-58. PMID 20877914 DOI: 10.1039/C0Mb00097C |
0.355 |
|
| 2010 |
Jung HJ, Purvine SO, Kim H, Petyuk VA, Hyung SW, Monroe ME, Mun DG, Kim KC, Park JM, Kim SJ, Tolic N, Slysz GW, Moore RJ, Zhao R, Adkins JN, et al. Integrated post-experiment monoisotopic mass refinement: an integrated approach to accurately assign monoisotopic precursor masses to tandem mass spectrometric data. Analytical Chemistry. 82: 8510-8. PMID 20863060 DOI: 10.1021/Ac101388B |
0.33 |
|
| 2010 |
Brown JN, Estep RD, Lopez-Ferrer D, Brewer HM, Clauss TR, Manes NP, O'Connor M, Li H, Adkins JN, Wong SW, Smith RD. Characterization of macaque pulmonary fluid proteome during monkeypox infection: dynamics of host response. Molecular & Cellular Proteomics : McP. 9: 2760-71. PMID 20736407 DOI: 10.1074/Mcp.M110.001875 |
0.337 |
|
| 2010 |
Rana GS, York TP, Edmiston JS, Zedler BK, Pounds JG, Adkins JN, Varnum SM, Smith RD, Liu Z, Li G, Webb BT, Murrelle EL, Flora JW. Proteomic biomarkers in plasma that differentiate rapid and slow decline in lung function in adult cigarette smokers with chronic obstructive pulmonary disease (COPD). Analytical and Bioanalytical Chemistry. 397: 1809-19. PMID 20442989 DOI: 10.1007/S00216-010-3742-4 |
0.334 |
|
| 2010 |
Adkins JN, Mottaz H, Metz TO, Ansong C, Manes NP, Smith RD, Heffron F. Performing comparative peptidomics analyses of Salmonella from different growth conditions. Methods in Molecular Biology (Clifton, N.J.). 615: 13-27. PMID 20013197 DOI: 10.1007/978-1-60761-535-4_2 |
0.414 |
|
| 2009 |
Shi L, Ansong C, Smallwood H, Rommereim L, McDermott JE, Brewer HM, Norbeck AD, Taylor RC, Gustin JK, Heffron F, Smith RD, Adkins JN. Proteome of Salmonella Enterica Serotype Typhimurium Grown in a Low Mg/pH Medium. Journal of Proteomics & Bioinformatics. 2: 388-397. PMID 19953200 DOI: 10.4172/Jpb.1000099 |
0.362 |
|
| 2009 |
Karpievitch YV, Taverner T, Adkins JN, Callister SJ, Anderson GA, Smith RD, Dabney AR. Normalization of peak intensities in bottom-up MS-based proteomics using singular value decomposition. Bioinformatics (Oxford, England). 25: 2573-80. PMID 19602524 DOI: 10.1093/Bioinformatics/Btp426 |
0.352 |
|
| 2009 |
Karpievitch Y, Stanley J, Taverner T, Huang J, Adkins JN, Ansong C, Heffron F, Metz TO, Qian WJ, Yoon H, Smith RD, Dabney AR. A statistical framework for protein quantitation in bottom-up MS-based proteomics. Bioinformatics (Oxford, England). 25: 2028-34. PMID 19535538 DOI: 10.1093/Bioinformatics/Btp362 |
0.389 |
|
| 2009 |
Shi L, Chowdhury SM, Smallwood HS, Yoon H, Mottaz-Brewer HM, Norbeck AD, McDermott JE, Clauss TR, Heffron F, Smith RD, Adkins JN. Proteomic investigation of the time course responses of RAW 264.7 macrophages to infection with Salmonella enterica. Infection and Immunity. 77: 3227-33. PMID 19528222 DOI: 10.1128/Iai.00063-09 |
0.349 |
|
| 2009 |
Chowdhury SM, Du X, Toli? N, Wu S, Moore RJ, Mayer MU, Smith RD, Adkins JN. Identification of cross-linked peptides after click-based enrichment using sequential collision-induced dissociation and electron transfer dissociation tandem mass spectrometry. Analytical Chemistry. 81: 5524-32. PMID 19496583 DOI: 10.1021/Ac900853K |
0.367 |
|
| 2009 |
Jaitly N, Mayampurath A, Littlefield K, Adkins JN, Anderson GA, Smith RD. Decon2LS: An open-source software package for automated processing and visualization of high resolution mass spectrometry data. Bmc Bioinformatics. 10: 87. PMID 19292916 DOI: 10.1186/1471-2105-10-87 |
0.344 |
|
| 2009 |
Ansong C, Yoon H, Porwollik S, Mottaz-Brewer H, Petritis BO, Jaitly N, Adkins JN, McClelland M, Heffron F, Smith RD. Global systems-level analysis of Hfq and SmpB deletion mutants in Salmonella: implications for virulence and global protein translation. Plos One. 4: e4809. PMID 19277208 DOI: 10.1371/Journal.Pone.0004809 |
0.409 |
|
| 2009 |
Chowdhury SM, Shi L, Yoon H, Ansong C, Rommereim LM, Norbeck AD, Auberry KJ, Moore RJ, Adkins JN, Heffron F, Smith RD. A method for investigating protein-protein interactions related to salmonella typhimurium pathogenesis. Journal of Proteome Research. 8: 1504-14. PMID 19206470 DOI: 10.1021/Pr800865D |
0.388 |
|
| 2008 |
Rodland KD, Adkins JN, Ansong C, Chowdhury S, Manes NP, Shi L, Yoon H, Smith RD, Heffron F. Use of high-throughput mass spectrometry to elucidate host-pathogen interactions in Salmonella. Future Microbiology. 3: 625-34. PMID 19072180 DOI: 10.2217/17460913.3.6.625 |
0.42 |
|
| 2008 |
Tolmachev AV, Monroe ME, Purvine SO, Moore RJ, Jaitly N, Adkins JN, Anderson GA, Smith RD. Characterization of strategies for obtaining confident identifications in bottom-up proteomics measurements using hybrid FTMS instruments. Analytical Chemistry. 80: 8514-25. PMID 18855412 DOI: 10.1021/Ac801376G |
0.356 |
|
| 2008 |
Ding SJ, Wang Y, Jacobs JM, Qian WJ, Yang F, Tolmachev AV, Du X, Wang W, Moore RJ, Monroe ME, Purvine SO, Waters K, Heibeck TH, Adkins JN, Camp DG, et al. Quantitative phosphoproteome analysis of lysophosphatidic acid induced chemotaxis applying dual-step (18)O labeling coupled with immobilized metal-ion affinity chromatography. Journal of Proteome Research. 7: 4215-24. PMID 18785766 DOI: 10.1021/Pr7007785 |
0.387 |
|
| 2008 |
Polpitiya AD, Qian WJ, Jaitly N, Petyuk VA, Adkins JN, Camp DG, Anderson GA, Smith RD. DAnTE: a statistical tool for quantitative analysis of -omics data. Bioinformatics (Oxford, England). 24: 1556-8. PMID 18453552 DOI: 10.1093/Bioinformatics/Btn217 |
0.301 |
|
| 2008 |
Du X, Callister SJ, Manes NP, Adkins JN, Alexandridis RA, Zeng X, Roh JH, Smith WE, Donohue TJ, Kaplan S, Smith RD, Lipton MS. A computational strategy to analyze label-free temporal bottom-up proteomics data. Journal of Proteome Research. 7: 2595-604. PMID 18442284 DOI: 10.1021/Pr0704837 |
0.355 |
|
| 2008 |
Monroe ME, Shaw JL, Daly DS, Adkins JN, Smith RD. MASIC: a software program for fast quantitation and flexible visualization of chromatographic profiles from detected LC-MS(/MS) features. Computational Biology and Chemistry. 32: 215-7. PMID 18440872 DOI: 10.1016/J.Compbiolchem.2008.02.006 |
0.316 |
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| 2008 |
Du X, Yang F, Manes NP, Stenoien DL, Monroe ME, Adkins JN, States DJ, Purvine SO, Camp DG, Smith RD. Linear discriminant analysis-based estimation of the false discovery rate for phosphopeptide identifications. Journal of Proteome Research. 7: 2195-203. PMID 18422353 DOI: 10.1021/Pr070510T |
0.329 |
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| 2008 |
Ham BM, Yang F, Jayachandran H, Jaitly N, Monroe ME, Gritsenko MA, Livesay EA, Zhao R, Purvine SO, Orton D, Adkins JN, Camp DG, Rossie S, Smith RD. The influence of sample preparation and replicate analyses on HeLa Cell phosphoproteome coverage. Journal of Proteome Research. 7: 2215-21. PMID 18412383 DOI: 10.1021/Pr700575M |
0.38 |
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| 2008 |
Ansong C, Purvine SO, Adkins JN, Lipton MS, Smith RD. Proteogenomics: needs and roles to be filled by proteomics in genome annotation. Briefings in Functional Genomics & Proteomics. 7: 50-62. PMID 18334489 DOI: 10.1093/Bfgp/Eln010 |
0.34 |
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| 2008 |
Pounds JG, Flora JW, Adkins JN, Lee KM, Rana GS, Sengupta T, Smith RD, McKinney WJ. Characterization of the mouse bronchoalveolar lavage proteome by micro-capillary LC-FTICR mass spectrometry. Journal of Chromatography. B, Analytical Technologies in the Biomedical and Life Sciences. 864: 95-101. PMID 18313996 DOI: 10.1016/J.Jchromb.2008.01.044 |
0.394 |
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| 2008 |
Shen Y, Tolić N, Hixson KK, Purvine SO, Pasa-Tolić L, Qian WJ, Adkins JN, Moore RJ, Smith RD. Proteome-wide identification of proteins and their modifications with decreased ambiguities and improved false discovery rates using unique sequence tags. Analytical Chemistry. 80: 1871-82. PMID 18271604 DOI: 10.1021/Ac702328X |
0.399 |
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| 2008 |
Callister SJ, McCue LA, Turse JE, Monroe ME, Auberry KJ, Smith RD, Adkins JN, Lipton MS. Comparative bacterial proteomics: analysis of the core genome concept. Plos One. 3: e1542. PMID 18253490 DOI: 10.1371/Journal.Pone.0001542 |
0.34 |
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| 2008 |
Manes NP, Estep RD, Mottaz HM, Moore RJ, Clauss TR, Monroe ME, Du X, Adkins JN, Wong SW, Smith RD. Comparative proteomics of human monkeypox and vaccinia intracellular mature and extracellular enveloped virions. Journal of Proteome Research. 7: 960-8. PMID 18205298 DOI: 10.1021/Pr070432+ |
0.377 |
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| 2008 |
Ansong C, Yoon H, Norbeck AD, Gustin JK, McDermott JE, Mottaz HM, Rue J, Adkins JN, Heffron F, Smith RD. Proteomics analysis of the causative agent of typhoid fever. Journal of Proteome Research. 7: 546-57. PMID 18166006 DOI: 10.1021/Pr070434U |
0.359 |
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| 2008 |
Petyuk VA, Jaitly N, Moore RJ, Ding J, Metz TO, Tang K, Monroe ME, Tolmachev AV, Adkins JN, Belov ME, Dabney AR, Qian WJ, Camp DG, Smith RD. Elimination of systematic mass measurement errors in liquid chromatography-mass spectrometry based proteomics using regression models and a priori partial knowledge of the sample content. Analytical Chemistry. 80: 693-706. PMID 18163597 DOI: 10.1021/Ac701863D |
0.322 |
|
| 2007 |
Yang F, Jaitly N, Jayachandran H, Luo Q, Monroe ME, Du X, Gritsenko MA, Zhang R, Anderson DJ, Purvine SO, Adkins JN, Moore RJ, Mottaz HM, Ding SJ, Lipton MS, et al. Applying a targeted label-free approach using LC-MS AMT tags to evaluate changes in protein phosphorylation following phosphatase inhibition. Journal of Proteome Research. 6: 4489-97. PMID 17929957 DOI: 10.1021/Pr070068E |
0.378 |
|
| 2007 |
Gupta N, Tanner S, Jaitly N, Adkins JN, Lipton M, Edwards R, Romine M, Osterman A, Bafna V, Smith RD, Pevzner PA. Whole proteome analysis of post-translational modifications: applications of mass-spectrometry for proteogenomic annotation. Genome Research. 17: 1362-77. PMID 17690205 DOI: 10.1101/Gr.6427907 |
0.373 |
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| 2007 |
Monroe ME, Tolić N, Jaitly N, Shaw JL, Adkins JN, Smith RD. VIPER: an advanced software package to support high-throughput LC-MS peptide identification. Bioinformatics (Oxford, England). 23: 2021-3. PMID 17545182 DOI: 10.1093/Bioinformatics/Btm281 |
0.333 |
|
| 2007 |
Webb-Robertson BJ, Peterson ES, Singhal M, Klicker KR, Oehmen CS, Adkins JN, Havre SL. PQuad--a visual analysis platform for proteomic data exploration of microbial organisms. Bioinformatics (Oxford, England). 23: 1705-7. PMID 17483503 DOI: 10.1093/Bioinformatics/Btm132 |
0.311 |
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| 2007 |
Petyuk VA, Qian WJ, Chin MH, Wang H, Livesay EA, Monroe ME, Adkins JN, Jaitly N, Anderson DJ, Camp DG, Smith DJ, Smith RD. Spatial mapping of protein abundances in the mouse brain by voxelation integrated with high-throughput liquid chromatography-mass spectrometry. Genome Research. 17: 328-36. PMID 17255552 DOI: 10.1101/Gr.5799207 |
0.356 |
|
| 2007 |
Manes NP, Gustin JK, Rue J, Mottaz HM, Purvine SO, Norbeck AD, Monroe ME, Zimmer JS, Metz TO, Adkins JN, Smith RD, Heffron F. Targeted protein degradation by Salmonella under phagosome-mimicking culture conditions investigated using comparative peptidomics. Molecular & Cellular Proteomics : McP. 6: 717-27. PMID 17228056 DOI: 10.1074/Mcp.M600282-Mcp200 |
0.387 |
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| 2006 |
Tolmachev AV, Monroe ME, Jaitly N, Petyuk VA, Adkins JN, Smith RD. Mass measurement accuracy in analyses of highly complex mixtures based upon multidimensional recalibration. Analytical Chemistry. 78: 8374-85. PMID 17165830 DOI: 10.1021/Ac0606251 |
0.317 |
|
| 2006 |
Hixson KK, Adkins JN, Baker SE, Moore RJ, Chromy BA, Smith RD, McCutchen-Maloney SL, Lipton MS. Biomarker candidate identification in Yersinia pestis using organism-wide semiquantitative proteomics. Journal of Proteome Research. 5: 3008-17. PMID 17081052 DOI: 10.1021/Pr060179Y |
0.363 |
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| 2006 |
Jaitly N, Monroe ME, Petyuk VA, Clauss TR, Adkins JN, Smith RD. Robust algorithm for alignment of liquid chromatography-mass spectrometry analyses in an accurate mass and time tag data analysis pipeline. Analytical Chemistry. 78: 7397-409. PMID 17073405 DOI: 10.1021/Ac052197P |
0.317 |
|
| 2006 |
Shi L, Adkins JN, Coleman JR, Schepmoes AA, Dohnkova A, Mottaz HM, Norbeck AD, Purvine SO, Manes NP, Smallwood HS, Wang H, Forbes J, Gros P, Uzzau S, Rodland KD, et al. Proteomic analysis of Salmonella enterica serovar typhimurium isolated from RAW 264.7 macrophages: identification of a novel protein that contributes to the replication of serovar typhimurium inside macrophages. The Journal of Biological Chemistry. 281: 29131-40. PMID 16893888 DOI: 10.1074/Jbc.M604640200 |
0.408 |
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| 2006 |
Ding YH, Hixson KK, Giometti CS, Stanley A, Esteve-Núñez A, Khare T, Tollaksen SL, Zhu W, Adkins JN, Lipton MS, Smith RD, Mester T, Lovley DR. The proteome of dissimilatory metal-reducing microorganism Geobacter sulfurreducens under various growth conditions. Biochimica Et Biophysica Acta. 1764: 1198-206. PMID 16797259 DOI: 10.1016/J.Bbapap.2006.04.017 |
0.401 |
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| 2006 |
Adkins JN, Mottaz HM, Norbeck AD, Gustin JK, Rue J, Clauss TR, Purvine SO, Rodland KD, Heffron F, Smith RD. Analysis of the Salmonella typhimurium proteome through environmental response toward infectious conditions. Molecular & Cellular Proteomics : McP. 5: 1450-61. PMID 16684765 DOI: 10.1074/Mcp.M600139-Mcp200 |
0.382 |
|
| 2006 |
Yang F, Stenoien DL, Strittmatter EF, Wang J, Ding L, Lipton MS, Monroe ME, Nicora CD, Gristenko MA, Tang K, Fang R, Adkins JN, Camp DG, Chen DJ, Smith RD. Phosphoproteome profiling of human skin fibroblast cells in response to low- and high-dose irradiation. Journal of Proteome Research. 5: 1252-60. PMID 16674116 DOI: 10.1021/Pr060028V |
0.32 |
|
| 2006 |
Callister SJ, Barry RC, Adkins JN, Johnson ET, Qian WJ, Webb-Robertson BJ, Smith RD, Lipton MS. Normalization approaches for removing systematic biases associated with mass spectrometry and label-free proteomics. Journal of Proteome Research. 5: 277-86. PMID 16457593 DOI: 10.1021/Pr050300L |
0.34 |
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| 2006 |
Fang R, Elias DA, Monroe ME, Shen Y, McIntosh M, Wang P, Goddard CD, Callister SJ, Moore RJ, Gorby YA, Adkins JN, Fredrickson JK, Lipton MS, Smith RD. Differential label-free quantitative proteomic analysis of Shewanella oneidensis cultured under aerobic and suboxic conditions by accurate mass and time tag approach. Molecular & Cellular Proteomics : McP. 5: 714-25. PMID 16401633 DOI: 10.1074/Mcp.M500301-Mcp200 |
0.405 |
|
| 2005 |
Springer DL, Ahram M, Adkins JN, Kathmann LE, Miller JH. Characterization of medium conditioned by irradiated cells using proteome-wide, high-throughput mass spectrometry Radiation Research. 164: 651-654. PMID 16238442 DOI: 10.1667/Rr3457.1 |
0.369 |
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| 2005 |
Omenn GS, States DJ, Adamski M, Blackwell TW, Menon R, Hermjakob H, Apweiler R, Haab BB, Simpson RJ, Eddes JS, Kapp EA, Moritz RL, Chan DW, Rai AJ, Admon A, ... ... Adkins J, et al. Overview of the HUPO Plasma Proteome Project: results from the pilot phase with 35 collaborating laboratories and multiple analytical groups, generating a core dataset of 3020 proteins and a publicly-available database. Proteomics. 5: 3226-45. PMID 16104056 DOI: 10.1002/Pmic.200500358 |
0.413 |
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| 2005 |
Jacobs JM, Adkins JN, Qian WJ, Liu T, Shen Y, Camp DG, Smith RD. Utilizing human blood plasma for proteomic biomarker discovery. Journal of Proteome Research. 4: 1073-85. PMID 16083256 DOI: 10.1021/Pr0500657 |
0.363 |
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| 2005 |
Adkins JN, Monroe ME, Auberry KJ, Shen Y, Jacobs JM, Camp DG, Vitzthum F, Rodland KD, Zangar RC, Smith RD, Pounds JG. A proteomic study of the HUPO Plasma Proteome Project's pilot samples using an accurate mass and time tag strategy. Proteomics. 5: 3454-66. PMID 16052625 DOI: 10.1002/Pmic.200401333 |
0.36 |
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| 2005 |
Haab BB, Geierstanger BH, Michailidis G, Vitzthum F, Forrester S, Okon R, Saviranta P, Brinker A, Sorette M, Perlee L, Suresh S, Drwal G, Adkins JN, Omenn GS. Immunoassay and antibody microarray analysis of the HUPO Plasma Proteome Project reference specimens: systematic variation between sample types and calibration of mass spectrometry data. Proteomics. 5: 3278-91. PMID 16038022 DOI: 10.1002/Pmic.200401276 |
0.349 |
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| 2005 |
Norbeck AD, Monroe ME, Adkins JN, Anderson KK, Daly DS, Smith RD. The utility of accurate mass and LC elution time information in the analysis of complex proteomes. Journal of the American Society For Mass Spectrometry. 16: 1239-49. PMID 15979333 DOI: 10.1016/J.Jasms.2005.05.009 |
0.372 |
|
| 2005 |
Markillie LM, Lin CT, Adkins JN, Auberry DL, Hill EA, Hooker BS, Moore PA, Moore RJ, Shi L, Wiley HS, Kery V. Simple protein complex purification and identification method for high-throughput mapping of protein interaction networks. Journal of Proteome Research. 4: 268-74. PMID 15822902 DOI: 10.1021/Pr049847A |
0.392 |
|
| 2005 |
Ahram M, Strittmatter EF, Monroe ME, Adkins JN, Hunter JC, Miller JH, Springer DL. Identification of shed proteins from Chinese hamster ovary cells: application of statistical confidence using human and mouse protein databases. Proteomics. 5: 1815-26. PMID 15815987 DOI: 10.1002/Pmic.200401072 |
0.432 |
|
| 2005 |
Ahram M, Adkins JN, Auberry DL, Wunschel DS, Springer DL. A proteomic approach to characterize protein shedding Proteomics. 5: 123-131. PMID 15672459 DOI: 10.1002/Pmic.200400912 |
0.424 |
|
| 2005 |
Edberg DD, Adkins JN, Springer DL, Reeves R. Dynamic and differential in vivo modifications of the isoform HMGA1a and HMGA1b chromatin proteins. The Journal of Biological Chemistry. 280: 8961-73. PMID 15591590 DOI: 10.1074/Jbc.M407348200 |
0.35 |
|
| 2004 |
Anderson NL, Polanski M, Pieper R, Gatlin T, Tirumalai RS, Conrads TP, Veenstra TD, Adkins JN, Pounds JG, Fagan R, Lobley A. The human plasma proteome: a nonredundant list developed by combination of four separate sources. Molecular & Cellular Proteomics : McP. 3: 311-26. PMID 14718574 DOI: 10.1074/Mcp.M300127-Mcp200 |
0.424 |
|
| 2003 |
Springer DL, Auberry DL, Ahram M, Adkins JN, Feldhaus JM, Wahl JH, Wunschel DS, Rodland KD. Characterization of plasma membrane proteins from ovarian cancer cells using mass spectrometry Disease Markers. 19: 219-228. PMID 15258336 DOI: 10.1155/2004/725617 |
0.377 |
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| 2002 |
Adkins JN, Varnum SM, Auberry KJ, Moore RJ, Angell NH, Smith RD, Springer DL, Pounds JG. Toward a human blood serum proteome: analysis by multidimensional separation coupled with mass spectrometry Molecular &Amp; Cellular Proteomics : McP. 1: 947-955. PMID 12543931 DOI: 10.1074/Mcp.M200066-Mcp200 |
0.38 |
|
| 2002 |
Bienkiewicz EA, Adkins JN, Lumb KJ. Functional consequences of preorganized helical structure in the intrinsically disordered cell-cycle inhibitor p27(Kip1). Biochemistry. 41: 752-9. PMID 11790096 DOI: 10.1021/Bi015763T |
0.623 |
|
| 2002 |
Adkins JN, Lumb KJ. Intrinsic structural disorder and sequence features of the cell cycle inhibitor p57Kip2. Proteins. 46: 1-7. PMID 11746698 DOI: 10.1002/Prot.10018 |
0.639 |
|
| 2001 |
Stargell LA, Ogg RC, Adkins JN, Robinson MM, Lumb KJ. Transcriptional activity of the TFIIA four-helix bundle in vivo. Proteins. 43: 227-32. PMID 11276091 DOI: 10.1002/1097-0134(20010501)43:2<227::Aid-Prot1033>3.0.Co;2-C |
0.61 |
|
| 2000 |
Adkins JN, Lumb KJ. Stoichiometry of cyclin A-cyclin-dependent kinase 2 inhibition by p21Cip1/Waf1. Biochemistry. 39: 13925-30. PMID 11076534 DOI: 10.1021/Bi001524E |
0.614 |
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