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Items: 49

1.

Determining the Reliability of Measuring Mercury Cycling Gene Abundance with Correlations with Mercury and Methylmercury Concentrations.

Christensen GA, Gionfriddo CM, King AJ, Moberly JG, Miller CL, Somenahally AC, Callister SJ, Brewer H, Podar M, Brown SD, Palumbo AV, Brandt CC, Wymore AM, Brooks SC, Hwang C, Fields MW, Wall JD, Gilmour CC, Elias DA.

Environ Sci Technol. 2019 Aug 6;53(15):8649-8663. doi: 10.1021/acs.est.8b06389. Epub 2019 Jul 12.

PMID:
31260289
2.

Metaphenomic Responses of a Native Prairie Soil Microbiome to Moisture Perturbations.

Roy Chowdhury T, Lee JY, Bottos EM, Brislawn CJ, White RA 3rd, Bramer LM, Brown J, Zucker JD, Kim YM, Jumpponen A, Rice CW, Fansler SJ, Metz TO, McCue LA, Callister SJ, Song HS, Jansson JK.

mSystems. 2019 Jun 11;4(4). pii: e00061-19. doi: 10.1128/mSystems.00061-19.

3.

Identification of metabolite and protein explanatory variables governing microbiome establishment and re-establishment within a cellulose-degrading anaerobic bioreactor.

Callister SJ, McCue LA, Boaro AA, LaMarche B, White RA 3rd, Brown JM, Ahring BK.

PLoS One. 2018 Oct 5;13(10):e0204831. doi: 10.1371/journal.pone.0204831. eCollection 2018.

4.

Specialized proteomic responses and an ancient photoprotection mechanism sustain marine green algal growth during phosphate limitation.

Guo J, Wilken S, Jimenez V, Choi CJ, Ansong C, Dannebaum R, Sudek L, Milner DS, Bachy C, Reistetter EN, Elrod VA, Klimov D, Purvine SO, Wei CL, Kunde-Ramamoorthy G, Richards TA, Goodenough U, Smith RD, Callister SJ, Worden AZ.

Nat Microbiol. 2018 Jul;3(7):781-790. doi: 10.1038/s41564-018-0178-7. Epub 2018 Jun 25.

PMID:
29946165
5.

Physiological and proteomic analyses of Fe(III)-reducing co-cultures of Desulfotomaculum reducens MI-1 and Geobacter sulfurreducens PCA.

Otwell AE, Callister SJ, Sherwood RW, Zhang S, Goldman AR, Smith RD, Richardson RE.

Geobiology. 2018 Sep;16(5):522-539. doi: 10.1111/gbi.12295. Epub 2018 Jun 15.

PMID:
29905980
6.

Proteomics Coupled with Metabolite and Cell Wall Profiling Reveal Metabolic Processes of a Developing Rice Stem Internode.

Lin F, Williams BJ, Thangella PAV, Ladak A, Schepmoes AA, Olivos HJ, Zhao K, Callister SJ, Bartley LE.

Front Plant Sci. 2017 Jul 13;8:1134. doi: 10.3389/fpls.2017.01134. eCollection 2017.

7.

Identifying Aspects of the Post-Transcriptional Program Governing the Proteome of the Green Alga Micromonas pusilla.

Waltman PH, Guo J, Reistetter EN, Purvine S, Ansong CK, van Baren MJ, Wong CH, Wei CL, Smith RD, Callister SJ, Stuart JM, Worden AZ.

PLoS One. 2016 Jul 19;11(7):e0155839. doi: 10.1371/journal.pone.0155839. eCollection 2016.

8.

Evidence-based green algal genomics reveals marine diversity and ancestral characteristics of land plants.

van Baren MJ, Bachy C, Reistetter EN, Purvine SO, Grimwood J, Sudek S, Yu H, Poirier C, Deerinck TJ, Kuo A, Grigoriev IV, Wong CH, Smith RD, Callister SJ, Wei CL, Schmutz J, Worden AZ.

BMC Genomics. 2016 Mar 31;17:267. doi: 10.1186/s12864-016-2585-6.

9.

Comparative Proteomic Analysis of Desulfotomaculum reducens MI-1: Insights into the Metabolic Versatility of a Gram-Positive Sulfate- and Metal-Reducing Bacterium.

Otwell AE, Callister SJ, Zink EM, Smith RD, Richardson RE.

Front Microbiol. 2016 Feb 19;7:191. doi: 10.3389/fmicb.2016.00191. eCollection 2016.

10.

Evaluating Models of Cellulose Degradation by Fibrobacter succinogenes S85.

Burnet MC, Dohnalkova AC, Neumann AP, Lipton MS, Smith RD, Suen G, Callister SJ.

PLoS One. 2015 Dec 2;10(12):e0143809. doi: 10.1371/journal.pone.0143809. eCollection 2015.

11.

Molecular dissection of a putative iron reductase from Desulfotomaculum reducens MI-1.

Li Z, Kim DD, Nelson OD, Otwell AE, Richardson RE, Callister SJ, Lin H.

Biochem Biophys Res Commun. 2015 Nov 20;467(3):503-8. doi: 10.1016/j.bbrc.2015.10.016. Epub 2015 Oct 8.

12.

Indexing Permafrost Soil Organic Matter Degradation Using High-Resolution Mass Spectrometry.

Mann BF, Chen H, Herndon EM, Chu RK, Tolic N, Portier EF, Roy Chowdhury T, Robinson EW, Callister SJ, Wullschleger SD, Graham DE, Liang L, Gu B.

PLoS One. 2015 Jun 12;10(6):e0130557. doi: 10.1371/journal.pone.0130557. eCollection 2015.

13.

Identification of proteins capable of metal reduction from the proteome of the Gram-positive bacterium Desulfotomaculum reducens MI-1 using an NADH-based activity assay.

Otwell AE, Sherwood RW, Zhang S, Nelson OD, Li Z, Lin H, Callister SJ, Richardson RE.

Environ Microbiol. 2015 Jun;17(6):1977-90. doi: 10.1111/1462-2920.12673. Epub 2015 Jan 27.

14.

Integrated 'omics analysis for studying the microbial community response to a pH perturbation of a cellulose-degrading bioreactor culture.

Boaro AA, Kim YM, Konopka AE, Callister SJ, Ahring BK.

FEMS Microbiol Ecol. 2014 Dec;90(3):802-15. doi: 10.1111/1574-6941.12435. Epub 2014 Oct 31.

15.

Gene co-expression network analysis in Rhodobacter capsulatus and application to comparative expression analysis of Rhodobacter sphaeroides.

Peña-Castillo L, Mercer RG, Gurinovich A, Callister SJ, Wright AT, Westbye AB, Beatty JT, Lang AS.

BMC Genomics. 2014 Aug 28;15:730. doi: 10.1186/1471-2164-15-730.

16.

Proteomic profiles of five strains of oxygenic photosynthetic cyanobacteria of the genus Cyanothece.

Aryal UK, Callister SJ, McMahon BH, McCue LA, Brown J, Stöckel J, Liberton M, Mishra S, Zhang X, Nicora CD, Angel TE, Koppenaal DW, Smith RD, Pakrasi HB, Sherman LA.

J Proteome Res. 2014 Jul 3;13(7):3262-76. doi: 10.1021/pr5000889. Epub 2014 Jun 4.

PMID:
24846609
17.

Activity-based protein profiling of secreted cellulolytic enzyme activity dynamics in Trichoderma reesei QM6a, NG14, and RUT-C30.

Anderson LN, Culley DE, Hofstad BA, Chauvigné-Hines LM, Zink EM, Purvine SO, Smith RD, Callister SJ, Magnuson JM, Wright AT.

Mol Biosyst. 2013 Dec;9(12):2992-3000. doi: 10.1039/c3mb70333a. Epub 2013 Oct 14.

18.

SPOCS: software for predicting and visualizing orthology/paralogy relationships among genomes.

Curtis DS, Phillips AR, Callister SJ, Conlan S, McCue LA.

Bioinformatics. 2013 Oct 15;29(20):2641-2. doi: 10.1093/bioinformatics/btt454. Epub 2013 Aug 16.

19.

Amino acid treatment enhances protein recovery from sediment and soils for metaproteomic studies.

Nicora CD, Anderson BJ, Callister SJ, Norbeck AD, Purvine SO, Jansson JK, Mason OU, David MM, Jurelevicius D, Smith RD, Lipton MS.

Proteomics. 2013 Oct;13(18-19):2776-85. doi: 10.1002/pmic.201300003. Epub 2013 Aug 16.

PMID:
23776032
20.

Development of an ecophysiological model for Diplosphaera colotermitum TAV2, a termite hindgut Verrucomicrobium.

Isanapong J, Sealy Hambright W, Willis AG, Boonmee A, Callister SJ, Burnum KE, Paša-Tolić L, Nicora CD, Wertz JT, Schmidt TM, Rodrigues JL.

ISME J. 2013 Sep;7(9):1803-13. doi: 10.1038/ismej.2013.74. Epub 2013 May 9.

21.

Characterizing microbial community and geochemical dynamics at hydrothermal vents using osmotically driven continuous fluid samplers.

Robidart J, Callister SJ, Song P, Nicora CD, Wheat CG, Girguis PR.

Environ Sci Technol. 2013 May 7;47(9):4399-407. doi: 10.1021/es3037302. Epub 2013 Apr 5.

PMID:
23495803
22.

MultiAlign: a multiple LC-MS analysis tool for targeted omics analysis.

LaMarche BL, Crowell KL, Jaitly N, Petyuk VA, Shah AR, Polpitiya AD, Sandoval JD, Kiebel GR, Monroe ME, Callister SJ, Metz TO, Anderson GA, Smith RD.

BMC Bioinformatics. 2013 Feb 12;14:49. doi: 10.1186/1471-2105-14-49.

23.

Proteome analyses of strains ATCC 51142 and PCC 7822 of the diazotrophic cyanobacterium Cyanothece sp. under culture conditions resulting in enhanced H₂ production.

Aryal UK, Callister SJ, Mishra S, Zhang X, Shutthanandan JI, Angel TE, Shukla AK, Monroe ME, Moore RJ, Koppenaal DW, Smith RD, Sherman L.

Appl Environ Microbiol. 2013 Feb;79(4):1070-7. doi: 10.1128/AEM.02864-12. Epub 2012 Nov 30.

24.

Suite of activity-based probes for cellulose-degrading enzymes.

Chauvigné-Hines LM, Anderson LN, Weaver HM, Brown JN, Koech PK, Nicora CD, Hofstad BA, Smith RD, Wilkins MJ, Callister SJ, Wright AT.

J Am Chem Soc. 2012 Dec 19;134(50):20521-32. doi: 10.1021/ja309790w. Epub 2012 Dec 6.

25.

Time-course analysis of the Shewanella amazonensis SB2B proteome in response to sodium chloride shock.

Parnell JJ, Callister SJ, Rompato G, Nicora CD, Paša-Tolić L, Williamson A, Pfrender ME.

Sci Rep. 2011;1:25. doi: 10.1038/srep00025. Epub 2011 Jun 29.

26.

Comparison of Chloroflexus aurantiacus strain J-10-fl proteomes of cells grown chemoheterotrophically and photoheterotrophically.

Cao L, Bryant DA, Schepmoes AA, Vogl K, Smith RD, Lipton MS, Callister SJ.

Photosynth Res. 2012 Feb;110(3):153-68. doi: 10.1007/s11120-011-9711-8. Epub 2012 Jan 17.

PMID:
22249883
27.

Proteotyping of microbial communities by optimization of tandem mass spectrometry data interpretation.

Hugo A, Baxter DJ, Cannon WR, Kalyanaraman A, Kulkarni G, Callister SJ.

Pac Symp Biocomput. 2012:225-34.

28.

Large improvements in MS/MS-based peptide identification rates using a hybrid analysis.

Cannon WR, Rawlins MM, Baxter DJ, Callister SJ, Lipton MS, Bryant DA.

J Proteome Res. 2011 May 6;10(5):2306-17. doi: 10.1021/pr101130b. Epub 2011 Mar 30.

PMID:
21391700
29.

Development of a biomarker for Geobacter activity and strain composition; proteogenomic analysis of the citrate synthase protein during bioremediation of U(VI).

Wilkins MJ, Callister SJ, Miletto M, Williams KH, Nicora CD, Lovley DR, Long PE, Lipton MS.

Microb Biotechnol. 2011 Jan;4(1):55-63. doi: 10.1111/j.1751-7915.2010.00194.x.

30.

An empirical strategy for characterizing bacterial proteomes across species in the absence of genomic sequences.

Turse JE, Marshall MJ, Fredrickson JK, Lipton MS, Callister SJ.

PLoS One. 2010 Nov 12;5(11):e13968. doi: 10.1371/journal.pone.0013968.

31.

Analysis of biostimulated microbial communities from two field experiments reveals temporal and spatial differences in proteome profiles.

Callister SJ, Wilkins MJ, Nicora CD, Williams KH, Banfield JF, VerBerkmoes NC, Hettich RL, N'Guessan L, Mouser PJ, Elifantz H, Smith RD, Lovley DR, Lipton MS, Long PE.

Environ Sci Technol. 2010 Dec 1;44(23):8897-903. doi: 10.1021/es101029f. Epub 2010 Nov 8.

PMID:
21058662
32.

Proteome insights into the symbiotic relationship between a captive colony of Nasutitermes corniger and its hindgut microbiome.

Burnum KE, Callister SJ, Nicora CD, Purvine SO, Hugenholtz P, Warnecke F, Scheffrahn RH, Smith RD, Lipton MS.

ISME J. 2011 Jan;5(1):161-4. doi: 10.1038/ismej.2010.97. Epub 2010 Jul 8.

33.

Loss of the response regulator CtrA causes pleiotropic effects on gene expression but does not affect growth phase regulation in Rhodobacter capsulatus.

Mercer RG, Callister SJ, Lipton MS, Pasa-Tolic L, Strnad H, Paces V, Beatty JT, Lang AS.

J Bacteriol. 2010 Jun;192(11):2701-10. doi: 10.1128/JB.00160-10. Epub 2010 Apr 2.

34.

Proteogenomic monitoring of Geobacter physiology during stimulated uranium bioremediation.

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, Banfield JF.

Appl Environ Microbiol. 2009 Oct;75(20):6591-9. doi: 10.1128/AEM.01064-09. Epub 2009 Aug 28.

35.

Normalization of peak intensities in bottom-up MS-based proteomics using singular value decomposition.

Karpievitch YV, Taverner T, Adkins JN, Callister SJ, Anderson GA, Smith RD, Dabney AR.

Bioinformatics. 2009 Oct 1;25(19):2573-80. doi: 10.1093/bioinformatics/btp426. Epub 2009 Jul 14.

36.

Relating perturbation magnitude to temporal gene expression in biological systems.

Callister SJ, Parnell JJ, Pfrender ME, Hashsham SA.

BMC Res Notes. 2009 Mar 19;2:43. doi: 10.1186/1756-0500-2-43.

37.

Role of the global transcriptional regulator PrrA in Rhodobacter sphaeroides 2.4.1: combined transcriptome and proteome analysis.

Eraso JM, Roh JH, Zeng X, Callister SJ, Lipton MS, Kaplan S.

J Bacteriol. 2008 Jul;190(14):4831-48. doi: 10.1128/JB.00301-08. Epub 2008 May 16.

38.

Proteomic analysis of stationary phase in the marine bacterium "Candidatus Pelagibacter ubique".

Sowell SM, Norbeck AD, Lipton MS, Nicora CD, Callister SJ, Smith RD, Barofsky DF, Giovannoni SJ.

Appl Environ Microbiol. 2008 Jul;74(13):4091-100. doi: 10.1128/AEM.00599-08. Epub 2008 May 9.

39.

A computational strategy to analyze label-free temporal bottom-up proteomics data.

Du X, Callister SJ, Manes NP, Adkins JN, Alexandridis RA, Zeng X, Roh JH, Smith WE, Donohue TJ, Kaplan S, Smith RD, Lipton MS.

J Proteome Res. 2008 Jul;7(7):2595-604. doi: 10.1021/pr0704837. Epub 2008 Apr 29.

40.

Comparative bacterial proteomics: analysis of the core genome concept.

Callister SJ, McCue LA, Turse JE, Monroe ME, Auberry KJ, Smith RD, Adkins JN, Lipton MS.

PLoS One. 2008 Feb 6;3(2):e1542. doi: 10.1371/journal.pone.0001542.

41.

Proteomic characterization of the Rhodobacter sphaeroides 2.4.1 photosynthetic membrane: identification of new proteins.

Zeng X, Roh JH, Callister SJ, Tavano CL, Donohue TJ, Lipton MS, Kaplan S.

J Bacteriol. 2007 Oct;189(20):7464-74. Epub 2007 Aug 17.

42.

Proteome analysis of Desulfovibrio desulfuricans G20 mutants using the accurate mass and time (AMT) tag approach.

Luo Q, Hixson KK, Callister SJ, Lipton MS, Morris BE, Krumholz LR.

J Proteome Res. 2007 Aug;6(8):3042-53. Epub 2007 Jun 30.

PMID:
17602684
43.

The future of liquid chromatography-mass spectrometry (LC-MS) in metabolic profiling and metabolomic studies for biomarker discovery.

Metz TO, Zhang Q, Page JS, Shen Y, Callister SJ, Jacobs JM, Smith RD.

Biomark Med. 2007 Jun;1(1):159-185.

44.

Proteomic approaches to bacterial differentiation.

Norbeck AD, Callister SJ, Monroe ME, Jaitly N, Elias DA, Lipton MS, Smith RD.

J Microbiol Methods. 2006 Dec;67(3):473-86. Epub 2006 Aug 17.

PMID:
16919344
45.

Application of the accurate mass and time tag approach to the proteome analysis of sub-cellular fractions obtained from Rhodobacter sphaeroides 2.4.1. Aerobic and photosynthetic cell cultures.

Callister SJ, Dominguez MA, Nicora CD, Zeng X, Tavano CL, Kaplan S, Donohue TJ, Smith RD, Lipton MS.

J Proteome Res. 2006 Aug;5(8):1940-7.

46.

Comparison of aerobic and photosynthetic Rhodobacter sphaeroides 2.4.1 proteomes.

Callister SJ, Nicora CD, Zeng X, Roh JH, Dominguez MA, Tavano CL, Monroe ME, Kaplan S, Donohue TJ, Smith RD, Lipton MS.

J Microbiol Methods. 2006 Dec;67(3):424-36. Epub 2006 Jul 7.

47.

Normalization approaches for removing systematic biases associated with mass spectrometry and label-free proteomics.

Callister SJ, Barry RC, Adkins JN, Johnson ET, Qian WJ, Webb-Robertson BJ, Smith RD, Lipton MS.

J Proteome Res. 2006 Feb;5(2):277-86.

48.

Differential label-free quantitative proteomic analysis of Shewanella oneidensis cultured under aerobic and suboxic conditions by accurate mass and time tag approach.

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.

Mol Cell Proteomics. 2006 Apr;5(4):714-25. Epub 2006 Jan 9.

49.

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