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Jacob R. Waldbauer

TitleAssociate Professor
InstitutionUniversity of Chicago
DepartmentGeophysical Sciences
AddressChicago IL 60637
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    Molecules record the history of coevolution between life and earth environments. Our group develops and applies cutting-edge analytical techniques to explore the relationships between cellular processes and global biogeochemical cycles. A major focus is proteomics, which probes the molecules directly responsible for biochemical activity.

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    Collapse selected publications
    Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Faculty can login to make corrections and additions.
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    PMC Citations indicate the number of times the publication was cited by articles in PubMed Central, and the Altmetric score represents citations in news articles and social media. (Note that publications are often cited in additional ways that are not shown here.) Fields are based on how the National Library of Medicine (NLM) classifies the publication's journal and might not represent the specific topic of the publication. Translation tags are based on the publication type and the MeSH terms NLM assigns to the publication. Some publications (especially newer ones and publications not in PubMed) might not yet be assigned Field or Translation tags.) Click a Field or Translation tag to filter the publications.
    1. Wilkes RA, Waldbauer J, Carroll A, Nieto-Domínguez M, Parker DJ, Zhang L, Guss AM, Aristilde L. Author Correction: Complex regulation in a Comamonas platform for diverse aromatic carbon metabolism. Nat Chem Biol. 2024 Mar; 20(3):392. PMID: 38316916; PMCID: PMC10907295.
      Citations:    Fields:    
    2. Wilkes RA, Waldbauer J, Aristilde L. Erratum for Wilkes et al., "Analogous Metabolic Decoupling in Pseudomonas putida and Comamonas testosteroni Implies Energetic Bypass to Facilitate Gluconeogenic Growth". mBio. 2024 Mar 13; 15(3):e0335223. PMID: 38315009; PMCID: PMC10936209.
      Citations:    Fields:    
    3. Grim SL, Stuart DG, Aron P, Levin NE, Kinsman-Costello L, Waldbauer JR, Dick GJ. Seasonal shifts in community composition and proteome expression in a sulphur-cycling cyanobacterial mat. Environ Microbiol. 2023 11; 25(11):2516-2533. PMID: 37596970.
      Citations: 1     Fields:    Translation:Cells
    4. Chiu BK, Waldbauer J, Elling FJ, Mete ÖZ, Zhang L, Pearson A, Eggleston EM, Leavitt WD. Membrane lipid and expression responses of Saccharolobus islandicus REY15A to acid and cold stress. Front Microbiol. 2023; 14:1219779. PMID: 37649629; PMCID: PMC10465181.
    5. Miller SE, Colman AS, Waldbauer JR. Metaproteomics reveals functional partitioning and vegetational variation among permafrost-affected Arctic soil bacterial communities. mSystems. 2023 Jun 29; 8(3):e0123822. PMID: 37272710; PMCID: PMC10308928.
      Citations:    Fields:    Translation:AnimalsCells
    6. Capovilla G, Braakman R, Fournier GP, Hackl T, Schwartzman J, Lu X, Yelton A, Longnecker K, Soule MCK, Thomas E, Swarr G, Mongera A, Payette JG, Castro KG, Waldbauer JR, Kujawinski EB, Cordero OX, Chisholm SW. Chitin utilization by marine picocyanobacteria and the evolution of a planktonic lifestyle. Proc Natl Acad Sci U S A. 2023 05 16; 120(20):e2213271120. PMID: 37159478; PMCID: PMC10194020.
      Citations: 1     Fields:    Translation:Cells
    7. Gonzalez-Nayeck AC, Grim SL, Waldbauer J, Dick GJ, Pearson A. Isotopic Signatures of Carbon Transfer in a Proterozoic Analogue Microbial Mat. Appl Environ Microbiol. 2023 05 31; 89(5):e0187022. PMID: 37093010; PMCID: PMC10231192.
      Citations:    Fields:    Translation:Cells
    8. Wilkes RA, Waldbauer J, Parker DJ, Zhang L, Guss AM, Aristilde L, Nieto-Domínguez M, Carroll A. Complex regulation in a Comamonas platform for diverse aromatic carbon metabolism. Nat Chem Biol. 2023 05; 19(5):651-662. PMID: 36747056; PMCID: PMC10154247.
      Citations: 1     Fields:    Translation:Cells
    9. Zhang L, Waldbauer JR, Leavitt WD, Ferreira D, Venceslau SS, Bernardino R, Preto A, Pereira IAC. DsrC is involved in fermentative growth and interacts directly with the FlxABCD-HdrABC complex in Desulfovibrio vulgaris Hildenborough. Environ Microbiol. 2023 05; 25(5):962-976. PMID: 36602077.
      Citations: 2     Fields:    Translation:Cells
    10. Zimmerman AE, Podowski JC, Gallagher GE, Coleman ML, Waldbauer JR. Tracking nitrogen allocation to proteome biosynthesis in a marine microbial community. Nat Microbiol. 2023 03; 8(3):498-509. PMID: 36635571.
      Citations: 1     Fields:    Translation:Cells
    11. Gallagher GE, Waldbauer JR. Proteome Expression and Survival Strategies of a Proteorhodopsin-Containing Vibrio Strain under Carbon and Nitrogen Limitation. mSystems. 2022 Apr 26; 7(2):e0126321. PMID: 35384695; PMCID: PMC9040609.
      Citations: 2     Fields:    
    12. Luxem KE, Kraepiel AML, Zhang L, Waldbauer JR, Zhang X. Carbon substrate re-orders relative growth of a bacterium using Mo-, V-, or Fe-nitrogenase for nitrogen fixation. Environ Microbiol. 2022 Apr; 24(4):2170-2176. PMID: 35478483; PMCID: PMC9175542.
      Citations: 1     Fields:    
    13. Wilkes RA, Waldbauer J, Aristilde L. Analogous Metabolic Decoupling in Pseudomonas putida and Comamonas testosteroni Implies Energetic Bypass to Facilitate Gluconeogenic Growth. mBio. 2021 12 21; 12(6):e0325921. PMID: 34903058; PMCID: PMC8669468.
      Citations: 4     Fields:    Translation:Cells
    14. Luxem KE, Kraepiel AML, Zhang L, Waldbauer JR, Zhang X. Carbon substrate re-orders relative growth of a bacterium using Mo-, V-, or Fe-nitrogenase for nitrogen fixation. Environ Microbiol. 2020 04; 22(4):1397-1408. PMID: 32090445; PMCID: PMC7187303.
      Citations: 10     Fields:    Translation:Cells
    15. Zimmerman AE, Howard-Varona C, Needham DM, John SG, Worden AZ, Sullivan MB, Waldbauer JR, Coleman ML. Metabolic and biogeochemical consequences of viral infection in aquatic ecosystems. Nat Rev Microbiol. 2020 01; 18(1):21-34. PMID: 31690825.
      Citations: 106     Fields:    Translation:Cells
    16. Waldbauer JR, Coleman ML, Rizzo AI, Campbell KL, Lotus J, Zhang L. Nitrogen sourcing during viral infection of marine cyanobacteria. Proc Natl Acad Sci U S A. 2019 07 30; 116(31):15590-15595. PMID: 31308237; PMCID: PMC6681717.
      Citations: 23     Fields:    Translation:Cells
    17. Zimmerman AE, Bachy C, Ma X, Roux S, Jang HB, Sullivan MB, Waldbauer JR, Worden AZ. Closely related viruses of the marine picoeukaryotic alga Ostreococcus lucimarinus exhibit different ecological strategies. Environ Microbiol. 2019 06; 21(6):2148-2170. PMID: 30924271; PMCID: PMC6851583.
      Citations: 5     Fields:    Translation:AnimalsCells
    18. Leavitt WD, Waldbauer J, Smith DA, Bradley AS, Venceslau SS, Pereira IAC. Proteomic and Isotopic Response of Desulfovibrio vulgaris to DsrC Perturbation. Front Microbiol. 2019; 10:658. PMID: 31031715; PMCID: PMC6470260.
      Citations: 2     
    19. Miller SE, Rizzo AI, Waldbauer JR. Postnovo: Postprocessing Enables Accurate and FDR-Controlled de Novo Peptide Sequencing. J Proteome Res. 2018 11 02; 17(11):3671-3680. PMID: 30277077.
      Citations: 4     Fields:    Translation:HumansAnimalsCells
    20. Ma X, Coleman ML, Waldbauer JR. Distinct molecular signatures in dissolved organic matter produced by viral lysis of marine cyanobacteria. Environ Microbiol. 2018 08; 20(8):3001-3011. PMID: 30047191.
      Citations: 17     Fields:    Translation:Cells
    21. Waldbauer J, Zhang L, Rizzo A, Muratore D. diDO-IPTL: A Peptide-Labeling Strategy for Precision Quantitative Proteomics. Anal Chem. 2017 11 07; 89(21):11498-11504. PMID: 29016104.
      Citations: 12     Fields:    Translation:Cells
    22. Schwartz MH, Waldbauer JR, Zhang L, Pan T. Global tRNA misacylation induced by anaerobiosis and antibiotic exposure broadly increases stress resistance in Escherichia coli. Nucleic Acids Res. 2016 Dec 01; 44(21):10292-10303. PMID: 27672035; PMCID: PMC5137444.
      Citations: 23     Fields:    Translation:Cells
    23. Moran MA, Kujawinski EB, Stubbins A, Fatland R, Aluwihare LI, Buchan A, Crump BC, Dorrestein PC, Dyhrman ST, Hess NJ, Howe B, Longnecker K, Medeiros PM, Niggemann J, Repeta DJ, Waldbauer JR, Obernosterer I. Deciphering ocean carbon in a changing world. Proc Natl Acad Sci U S A. 2016 Mar 22; 113(12):3143-51. PMID: 26951682; PMCID: PMC4812754.
      Citations: 63     Fields:    
    24. Waldbauer JR, Coleman ML, Chisholm SW, Rodrigue S. Transcriptome and proteome dynamics of a light-dark synchronized bacterial cell cycle. PLoS One. 2012; 7(8):e43432. PMID: 22952681; PMCID: PMC3430701.
      Citations: 76     Fields:    Translation:Cells
    25. Waldbauer JR, Newman DK, Summons RE. Microaerobic steroid biosynthesis and the molecular fossil record of Archean life. Proc Natl Acad Sci U S A. 2011 Aug 16; 108(33):13409-14. PMID: 21825157; PMCID: PMC3158215.
      Citations: 27     Fields:    Translation:Cells
    26. Frias-Lopez J, Thompson A, Waldbauer J, Chisholm SW. Use of stable isotope-labelled cells to identify active grazers of picocyanobacteria in ocean surface waters. Environ Microbiol. 2009 Feb; 11(2):512-25. PMID: 19196281; PMCID: PMC2702499.
      Citations: 45     Fields:    Translation:AnimalsCells
    27. Martinez A, Bradley AS, Waldbauer JR, Summons RE, DeLong EF. Proteorhodopsin photosystem gene expression enables photophosphorylation in a heterologous host. Proc Natl Acad Sci U S A. 2007 Mar 27; 104(13):5590-5. PMID: 17372221; PMCID: PMC1838496.
      Citations: 72     Fields:    Translation:Cells
    28. Summons RE, Bradley AS, Jahnke LL, Waldbauer JR. Steroids, triterpenoids and molecular oxygen. Philos Trans R Soc Lond B Biol Sci. 2006 Jun 29; 361(1470):951-68. PMID: 16754609; PMCID: PMC1578733.
      Citations: 97     Fields:    Translation:Cells
    29. Hayes JM, Waldbauer JR. The carbon cycle and associated redox processes through time. Philos Trans R Soc Lond B Biol Sci. 2006 Jun 29; 361(1470):931-50. PMID: 16754608; PMCID: PMC1578725.
      Citations: 46     Fields:    Translation:Cells
    30. Chamberlain CP, Waldbauer JR, Fox-Dobbs K, Newsome SD, Koch PL, Smith DR, Church ME, Chamberlain SD, Sorenson KJ, Risebrough R. Pleistocene to recent dietary shifts in California condors. Proc Natl Acad Sci U S A. 2005 Nov 15; 102(46):16707-11. PMID: 16275902; PMCID: PMC1283853.
      Citations: 34     Fields:    Translation:Animals
    31. Rubenstein DR, Chamberlain CP, Holmes RT, Ayres MP, Waldbauer JR, Graves GR, Tuross NC, Rubenstein DR, Chamberlain CP, Holmes RT, Ayres MP, Waldbauer JR, Graves GR, Tuross NC. Linking breeding and wintering ranges of a migratory songbird using stable isotopes. Science. 2002 Feb 08; 295(5557):1062-5. PMID: 11834833.
      Citations: 37     Fields:    Translation:Animals
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