| Year |
Citation |
Score |
| 2024 |
Tavis S, Hettich RL. Multi-Omics integration can be used to rescue metabolic information for some of the dark region of the Pseudomonas putida proteome. Bmc Genomics. 25: 267. PMID 38468234 DOI: 10.1186/s12864-024-10082-y |
0.344 |
|
| 2021 |
Poudel S, Cope AL, O'Dell KB, Guss AM, Seo H, Trinh CT, Hettich RL. Identification and characterization of proteins of unknown function (PUFs) in Clostridium thermocellum DSM 1313 strains as potential genetic engineering targets. Biotechnology For Biofuels. 14: 116. PMID 33971924 DOI: 10.1186/s13068-021-01964-4 |
0.69 |
|
| 2020 |
Abraham PE, Matthiadis A, Hettich RL, Kalluri UC. Molecular remodeling in Populus PdKOR RNAi roots profiled using LC-MS/MS proteomics. Proteomics. e2000067. PMID 32846035 DOI: 10.1002/pmic.202000067 |
0.346 |
|
| 2020 |
Abraham PE, Hettich RL. Characterizing Intracellular Proteomes for Microbes: An Experimental Approach Using Label-Free Protein Quantitation. Methods in Molecular Biology (Clifton, N.J.). 2096: 81-87. PMID 32720148 DOI: 10.1007/978-1-0716-0195-2_7 |
0.342 |
|
| 2020 |
Villalobos Solis MI, Poudel S, Bonnot C, Shrestha HK, Hettich RL, Veneault-Fourrey C, Martin F, Abraham PE. Integrating state-of-the-art tandem mass spectrometry with -assisted database peptide sequencing as a viable strategy for the discovery of peptide proteolytic cleavage products (PCPs) in plant-microbe interactions. Molecular Plant-Microbe Interactions : Mpmi. PMID 32597696 DOI: 10.1094/MPMI-04-20-0082-TA |
0.372 |
|
| 2019 |
Solis MIV, Abraham PE, Chourey K, Swift CM, Löffler FE, Hettich RL. Targeted detection of Dehalococcoides mccartyi microbial protein biomarkers as indicators of reductive dechlorination activity in contaminated groundwater. Scientific Reports. 9: 10604. PMID 31332202 DOI: 10.1038/S41598-019-46901-6 |
0.358 |
|
| 2019 |
Villalobos Solis MI, Giannone RJ, Hettich RL, Abraham PE. Exploiting the dynamic relationship between peptide separation quality and peptide co-isolation in a mPSM approach offers a new strategy to optimize bottom-up proteomics throughput and depth. Analytical Chemistry. PMID 31075198 DOI: 10.1021/acs.analchem.9b00819 |
0.306 |
|
| 2018 |
Cope AL, Hettich RL, Gilchrist MA. Quantifying codon usage in signal peptides: Gene expression and amino acid usage explain apparent selection for inefficient codons. Biochimica Et Biophysica Acta. Biomembranes. 1860: 2479-2485. PMID 30279149 DOI: 10.1016/J.Bbamem.2018.09.010 |
0.641 |
|
| 2018 |
Qian C, Chen H, Johs A, Lu X, An J, Pierce EM, Parks JM, Elias DA, Hettich RL, Gu B. Quantitative Proteomic Analysis of Biological Processes and Responses of the Bacterium Desulfovibrio desulfuricans ND132 upon Deletion of its Mercury Methylation Genes. Proteomics. e1700479. PMID 30009483 DOI: 10.1002/Pmic.201700479 |
0.353 |
|
| 2016 |
Bryson S, Li Z, Pett-Ridge J, Hettich RL, Mayali X, Pan C, Mueller RS. Proteomic Stable Isotope Probing Reveals Taxonomically Distinct Patterns in Amino Acid Assimilation by Coastal Marine Bacterioplankton. Msystems. 1. PMID 27822523 DOI: 10.1128/mSystems.00027-15 |
0.345 |
|
| 2016 |
North JA, Sriram J, Chourey K, Ecker CD, Sharma R, Wildenthal JA, Hettich RL, Tabita FR. Metabolic Regulation as a Consequence of Anaerobic 5-Methylthioadenosine Recycling in Rhodospirillum rubrum. Mbio. 7. PMID 27406564 DOI: 10.1128/Mbio.00855-16 |
0.314 |
|
| 2016 |
Marlow JJ, Skennerton CT, Li Z, Chourey K, Hettich RL, Pan C, Orphan VJ. Proteomic Stable Isotope Probing Reveals Biosynthesis Dynamics of Slow Growing Methane Based Microbial Communities. Frontiers in Microbiology. 7: 563. PMID 27199908 DOI: 10.3389/Fmicb.2016.00563 |
0.354 |
|
| 2015 |
Abraham PE, Wang X, Ranjan P, Nookaew I, Zhang B, Tuskan GA, Hettich RL. Integrating mRNA and Protein Sequencing Enables the Detection and Quantitative Profiling of Natural Protein Sequence Variants of Populus trichocarpa. Journal of Proteome Research. PMID 26483142 DOI: 10.1021/Acs.Jproteome.5B00823 |
0.316 |
|
| 2015 |
Giannone RJ, Wurch LL, Podar M, Hettich RL. Rescuing Those Left Behind: Recovering and Characterizing Underdigested Membrane and Hydrophobic Proteins To Enhance Proteome Measurement Depth. Analytical Chemistry. 87: 7720-8. PMID 26110888 DOI: 10.1021/Acs.Analchem.5B01187 |
0.365 |
|
| 2015 |
Giannone RJ, Wurch LL, Heimerl T, Martin S, Yang Z, Huber H, Rachel R, Hettich RL, Podar M. Life on the edge: functional genomic response of Ignicoccus hospitalis to the presence of Nanoarchaeum equitans. The Isme Journal. 9: 101-14. PMID 25012904 DOI: 10.1038/Ismej.2014.112 |
0.369 |
|
| 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 |
0.3 |
|
| 2013 |
Abraham P, Adams RM, Tuskan GA, Hettich RL. Moving away from the reference genome: evaluating a peptide sequencing tagging approach for single amino acid polymorphism identifications in the genus Populus. Journal of Proteome Research. 12: 3642-51. PMID 23795892 DOI: 10.1021/pr400192r |
0.317 |
|
| 2013 |
Dykstra AB, Rodriguez M, Raman B, Cook KD, Hettich RL. Characterizing the range of extracellular protein post-translational modifications in a cellulose-degrading bacteria using a multiple proteolyic digestion/peptide fragmentation approach. Analytical Chemistry. 85: 3144-51. PMID 23406086 DOI: 10.1021/Ac3032838 |
0.431 |
|
| 2013 |
Abraham P, Giannone RJ, Adams RM, Kalluri U, Tuskan GA, Hettich RL. Putting the pieces together: high-performance LC-MS/MS provides network-, pathway-, and protein-level perspectives in Populus. Molecular & Cellular Proteomics : McP. 12: 106-19. PMID 23073815 DOI: 10.1074/mcp.M112.022996 |
0.449 |
|
| 2012 |
Sharma R, Dill BD, Chourey K, Shah M, VerBerkmoes NC, Hettich RL. Coupling a detergent lysis/cleanup methodology with intact protein fractionation for enhanced proteome characterization. Journal of Proteome Research. 11: 6008-18. PMID 23126408 DOI: 10.1021/pr300709k |
0.333 |
|
| 2012 |
Huang EL, Orsat V, Shah MB, Hettich RL, VerBerkmoes NC, Lefsrud MG. The temporal analysis of yeast exponential phase using shotgun proteomics as a fermentation monitoring technique. Journal of Proteomics. 75: 5206-14. PMID 22705714 DOI: 10.1016/j.jprot.2012.06.005 |
0.376 |
|
| 2012 |
Wheeler KE, Erickson BK, Mueller R, Singer SW, Verberkmoes NC, Hwang M, Thelen MP, Hettich RL. Metal affinity enrichment increases the range and depth of proteome identification for extracellular microbial proteins. Journal of Proteome Research. 11: 861-70. PMID 22191549 DOI: 10.1021/Pr200693U |
0.414 |
|
| 2012 |
Abraham P, Adams R, Giannone RJ, Kalluri U, Ranjan P, Erickson B, Shah M, Tuskan GA, Hettich RL. Defining the boundaries and characterizing the landscape of functional genome expression in vascular tissues of Populus using shotgun proteomics. Journal of Proteome Research. 11: 449-60. PMID 22003893 DOI: 10.1021/pr200851y |
0.425 |
|
| 2011 |
Cantarel BL, Erickson AR, VerBerkmoes NC, Erickson BK, Carey PA, Pan C, Shah M, Mongodin EF, Jansson JK, Fraser-Liggett CM, Hettich RL. Strategies for metagenomic-guided whole-community proteomics of complex microbial environments. Plos One. 6: e27173. PMID 22132090 DOI: 10.1371/Journal.Pone.0027173 |
0.379 |
|
| 2011 |
Giannone RJ, Huber H, Karpinets T, Heimerl T, Küper U, Rachel R, Keller M, Hettich RL, Podar M. Proteomic characterization of cellular and molecular processes that enable the Nanoarchaeum equitans--Ignicoccus hospitalis relationship. Plos One. 6: e22942. PMID 21826220 DOI: 10.1371/Journal.Pone.0022942 |
0.319 |
|
| 2011 |
Jiao Y, D'haeseleer P, Dill BD, Shah M, Verberkmoes NC, Hettich RL, Banfield JF, Thelen MP. Identification of biofilm matrix-associated proteins from an acid mine drainage microbial community. Applied and Environmental Microbiology. 77: 5230-7. PMID 21685158 DOI: 10.1128/Aem.03005-10 |
0.347 |
|
| 2011 |
Lochner A, Giannone RJ, Rodriguez M, Shah MB, Mielenz JR, Keller M, Antranikian G, Graham DE, Hettich RL. Use of label-free quantitative proteomics to distinguish the secreted cellulolytic systems of Caldicellulosiruptor bescii and Caldicellulosiruptor obsidiansis. Applied and Environmental Microbiology. 77: 4042-54. PMID 21498747 DOI: 10.1128/Aem.02811-10 |
0.31 |
|
| 2011 |
Yang X, Tschaplinski TJ, Hurst GB, Jawdy S, Abraham PE, Lankford PK, Adams RM, Shah MB, Hettich RL, Lindquist E, Kalluri UC, Gunter LE, Pennacchio C, Tuskan GA. Discovery and annotation of small proteins using genomics, proteomics, and computational approaches. Genome Research. 21: 634-41. PMID 21367939 DOI: 10.1101/Gr.109280.110 |
0.348 |
|
| 2010 |
Erickson BK, Mueller RS, VerBerkmoes NC, Shah M, Singer SW, Thelen MP, Banfield JF, Hettich RL. Computational prediction and experimental validation of signal peptide cleavages in the extracellular proteome of a natural microbial community. Journal of Proteome Research. 9: 2148-59. PMID 20218729 DOI: 10.1021/Pr900877A |
0.425 |
|
| 2009 |
Kertesz V, Connelly HM, Erickson BK, Hettich RL. PTMSearchPlus: software tool for automated protein identification and post-translational modification characterization by integrating accurate intact protein mass and bottom-up mass spectrometric data searches. Analytical Chemistry. 81: 8387-95. PMID 19775152 DOI: 10.1021/ac901163c |
0.424 |
|
| 2009 |
Wilkins MJ, Verberkmoes NC, Williams KH, Callister SJ, Mouser PJ, Elifantz H, N'guessan AL, Thomas BC, Nicora CD, Shah MB, Abraham P, Lipton MS, Lovley DR, Hettich RL, Long PE, et al. Proteogenomic monitoring of Geobacter physiology during stimulated uranium bioremediation. Applied and Environmental Microbiology. 75: 6591-9. PMID 19717633 DOI: 10.1128/AEM.01064-09 |
0.372 |
|
| 2009 |
Goltsman DS, Denef VJ, Singer SW, VerBerkmoes NC, Lefsrud M, Mueller RS, Dick GJ, Sun CL, Wheeler KE, Zemla A, Baker BJ, Hauser L, Land M, Shah MB, Thelen MP, ... Hettich RL, et al. Community genomic and proteomic analyses of chemoautotrophic iron-oxidizing "Leptospirillum rubarum" (Group II) and "Leptospirillum ferrodiazotrophum" (Group III) bacteria in acid mine drainage biofilms. Applied and Environmental Microbiology. 75: 4599-615. PMID 19429552 DOI: 10.1128/Aem.02943-08 |
0.3 |
|
| 2009 |
Chourey K, Thompson MR, Shah M, Zhang B, Verberkmoes NC, Thompson DK, Hettich RL. Comparative temporal proteomics of a response regulator (SO2426)-deficient strain and wild-type Shewanella oneidensis MR-1 during chromate transformation. Journal of Proteome Research. 8: 59-71. PMID 19118451 DOI: 10.1021/Pr800776D |
0.664 |
|
| 2009 |
Verberkmoes NC, Russell AL, Shah M, Godzik A, Rosenquist M, Halfvarson J, Lefsrud MG, Apajalahti J, Tysk C, Hettich RL, Jansson JK. Shotgun metaproteomics of the human distal gut microbiota. The Isme Journal. 3: 179-89. PMID 18971961 DOI: 10.1038/Ismej.2008.108 |
0.355 |
|
| 2008 |
Thompson MR, Chourey K, Froelich JM, Erickson BK, VerBerkmoes NC, Hettich RL. Experimental approach for deep proteome measurements from small-scale microbial biomass samples. Analytical Chemistry. 80: 9517-25. PMID 19072265 DOI: 10.1021/ac801707s |
0.618 |
|
| 2008 |
Jeans C, Singer SW, Chan CS, Verberkmoes NC, Shah M, Hettich RL, Banfield JF, Thelen MP. Cytochrome 572 is a conspicuous membrane protein with iron oxidation activity purified directly from a natural acidophilic microbial community. The Isme Journal. 2: 542-50. PMID 18463612 DOI: 10.1038/Ismej.2008.17 |
0.306 |
|
| 2008 |
Wilmes P, Andersson AF, Lefsrud MG, Wexler M, Shah M, Zhang B, Hettich RL, Bond PL, VerBerkmoes NC, Banfield JF. Community proteogenomics highlights microbial strain-variant protein expression within activated sludge performing enhanced biological phosphorus removal. The Isme Journal. 2: 853-64. PMID 18449217 DOI: 10.1038/Ismej.2008.38 |
0.39 |
|
| 2008 |
Thompson MR, Thompson DK, Hettich RL. Systematic assessment of the benefits and caveats in mining microbial post-translational modifications from shotgun proteomic data: the response of Shewanella oneidensis to chromate exposure. Journal of Proteome Research. 7: 648-58. PMID 18171020 DOI: 10.1021/pr070531n |
0.687 |
|
| 2007 |
Denef VJ, Shah MB, Verberkmoes NC, Hettich RL, Banfield JF. Implications of strain- and species-level sequence divergence for community and isolate shotgun proteomic analysis. Journal of Proteome Research. 6: 3152-61. PMID 17602579 DOI: 10.1021/Pr0701005 |
0.341 |
|
| 2007 |
Thompson MR, VerBerkmoes NC, Chourey K, Shah M, Thompson DK, Hettich RL. Dosage-dependent proteome response of Shewanella oneidensis MR-1 to acute chromate challenge. Journal of Proteome Research. 6: 1745-57. PMID 17385904 DOI: 10.1021/pr060502x |
0.678 |
|
| 2007 |
Pan C, Hettich RL. Multipole-storage-assisted dissociation for the characterization of large proteins and simple protein mixtures by ESI-FTICR-MS. Analytical Chemistry. 77: 3072-82. PMID 15889895 DOI: 10.1021/ac048297x |
0.304 |
|
| 2006 |
Zhang B, VerBerkmoes NC, Langston MA, Uberbacher E, Hettich RL, Samatova NF. Detecting differential and correlated protein expression in label-free shotgun proteomics. Journal of Proteome Research. 5: 2909-18. PMID 17081042 DOI: 10.1021/Pr0600273 |
0.385 |
|
| 2006 |
Chourey K, Thompson MR, Morrell-Falvey J, Verberkmoes NC, Brown SD, Shah M, Zhou J, Doktycz M, Hettich RL, Thompson DK. Global molecular and morphological effects of 24-hour chromium(VI) exposure on Shewanella oneidensis MR-1. Applied and Environmental Microbiology. 72: 6331-44. PMID 16957260 DOI: 10.1128/Aem.00813-06 |
0.64 |
|
| 2006 |
Connelly HM, Pelletier DA, Lu TY, Lankford PK, Hettich RL. Characterization of pII family (GlnK1, GlnK2, and GlnB) protein uridylylation in response to nitrogen availability for Rhodopseudomonas palustris. Analytical Biochemistry. 357: 93-104. PMID 16860774 DOI: 10.1016/J.Ab.2006.05.038 |
0.389 |
|
| 2006 |
Brown SD, Thompson MR, Verberkmoes NC, Chourey K, Shah M, Zhou J, Hettich RL, Thompson DK. Molecular dynamics of the Shewanella oneidensis response to chromate stress. Molecular & Cellular Proteomics : McP. 5: 1054-71. PMID 16524964 DOI: 10.1074/Mcp.M500394-Mcp200 |
0.668 |
|
| 2006 |
VerBerkmoes NC, Shah MB, Lankford PK, Pelletier DA, Strader MB, Tabb DL, McDonald WH, Barton JW, Hurst GB, Hauser L, Davison BH, Beatty JT, Harwood CS, Tabita FR, Hettich RL, et al. Determination and comparison of the baseline proteomes of the versatile microbe Rhodopseudomonas palustris under its major metabolic states. Journal of Proteome Research. 5: 287-98. PMID 16457594 DOI: 10.1021/Pr0503230 |
0.402 |
|
| 2006 |
VerBerkmoes NC, Connelly HM, Pan C, Hettich RL. Mass spectrometric approaches for characterizing bacterial proteomes. Expert Review of Proteomics. 1: 433-47. PMID 15966840 DOI: 10.1586/14789450.1.4.433 |
0.345 |
|
| 2005 |
Banfield JF, Verberkmoes NC, Hettich RL, Thelen MP. Proteogenomic approaches for the molecular characterization of natural microbial communities Omics a Journal of Integrative Biology. 9: 301-333. PMID 16402891 DOI: 10.1089/Omi.2005.9.301 |
0.304 |
|
| 2005 |
Narasimhan C, Tabb DL, Verberkmoes NC, Thompson MR, Hettich RL, Uberbacher EC. MASPIC: intensity-based tandem mass spectrometry scoring scheme that improves peptide identification at high confidence. Analytical Chemistry. 77: 7581-93. PMID 16316165 DOI: 10.1021/ac0501745 |
0.652 |
|
| 2005 |
Ram RJ, Verberkmoes NC, Thelen MP, Tyson GW, Baker BJ, Blake RC, Shah M, Hettich RL, Banfield JF. Community proteomics of a natural microbial biofilm. Science (New York, N.Y.). 308: 1915-20. PMID 15879173 DOI: 10.1126/Science. |
0.378 |
|
| 2004 |
Wan XF, Verberkmoes NC, McCue LA, Stanek D, Connelly H, Hauser LJ, Wu L, Liu X, Yan T, Leaphart A, Hettich RL, Zhou J, Thompson DK. Transcriptomic and proteomic characterization of the Fur modulon in the metal-reducing bacterium Shewanella oneidensis. Journal of Bacteriology. 186: 8385-400. PMID 15576789 DOI: 10.1128/Jb.186.24.8385-8400.2004 |
0.35 |
|
| 2004 |
Strader MB, Verberkmoes NC, Tabb DL, Connelly HM, Barton JW, Bruce BD, Pelletier DA, Davison BH, Hettich RL, Larimer FW, Hurst GB. Characterization of the 70S Ribosome from Rhodopseudomonas palustris using an integrated "top-down" and "bottom-up" mass spectrometric approach. Journal of Proteome Research. 3: 965-78. PMID 15473684 DOI: 10.1021/Pr049940Z |
0.382 |
|
| 2004 |
Razumovskaya J, Olman V, Xu D, Uberbacher EC, VerBerkmoes NC, Hettich RL, Xu Y. A computational method for assessing peptide- identification reliability in tandem mass spectrometry analysis with SEQUEST. Proteomics. 4: 961-9. PMID 15048978 DOI: 10.1002/pmic.200300656 |
0.376 |
|
| 2004 |
Sharp JS, Becker JM, Hettich RL. Analysis of protein solvent accessible surfaces by photochemical oxidation and mass spectrometry. Analytical Chemistry. 76: 672-83. PMID 14750862 DOI: 10.1021/ac0302004 |
0.319 |
|
| 2002 |
VerBerkmoes NC, Bundy JL, Hauser L, Asano KG, Razumovskaya J, Larimer F, Hettich RL, Stephenson JL. Integrating 'top-down" and "bottom-up" mass spectrometric approaches for proteomic analysis of Shewanella oneidensis. Journal of Proteome Research. 1: 239-52. PMID 12645901 DOI: 10.1021/pr025508a |
0.403 |
|
| 2002 |
Uchiki T, Hettich R, Gupta V, Dealwis C. Characterization of monomeric and dimeric forms of recombinant Sml1p-histag protein by electrospray mass spectrometry. Analytical Biochemistry. 301: 35-48. PMID 11811965 DOI: 10.1006/Abio.2001.5492 |
0.369 |
|
| Show low-probability matches. |