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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.


pmartR: Quality Control and Statistics for Mass Spectrometry-Based Biological Data.

Stratton KG, Webb-Robertson BM, McCue LA, Stanfill B, Claborne D, Godinez I, Johansen T, Thompson AM, Burnum-Johnson KE, Waters KM, Bramer LM.

J Proteome Res. 2019 Mar 1;18(3):1418-1425. doi: 10.1021/acs.jproteome.8b00760. Epub 2019 Jan 28.


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.


Factors affecting the bacterial community composition and heterotrophic production of Columbia River estuarine turbidity maxima.

Herfort L, Crump BC, Fortunato CS, McCue LA, Campbell V, Simon HM, Baptista AM, Zuber P.

Microbiologyopen. 2017 Dec;6(6). doi: 10.1002/mbo3.522. Epub 2017 Aug 6.


FQC Dashboard: integrates FastQC results into a web-based, interactive, and extensible FASTQ quality control tool.

Brown J, Pirrung M, McCue LA.

Bioinformatics. 2017 Jun 9. doi: 10.1093/bioinformatics/btx373. [Epub ahead of print]


Network analysis of transcriptomics expands regulatory landscapes in Synechococcus sp. PCC 7002.

McClure RS, Overall CC, McDermott JE, Hill EA, Markillie LM, McCue LA, Taylor RC, Ludwig M, Bryant DA, Beliaev AS.

Nucleic Acids Res. 2016 Oct 14;44(18):8810-8825. Epub 2016 Aug 27.


Soil Respiration and Bacterial Structure and Function after 17 Years of a Reciprocal Soil Transplant Experiment.

Bond-Lamberty B, Bolton H, Fansler S, Heredia-Langner A, Liu C, McCue LA, Smith J, Bailey V.

PLoS One. 2016 Mar 2;11(3):e0150599. doi: 10.1371/journal.pone.0150599. eCollection 2016.


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.


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.


Linking microbial community structure to β-glucosidic function in soil aggregates.

Bailey VL, Fansler SJ, Stegen JC, McCue LA.

ISME J. 2013 Oct;7(10):2044-53. doi: 10.1038/ismej.2013.87. Epub 2013 May 30.


Fluctuations in species-level protein expression occur during element and nutrient cycling in the subsurface.

Wilkins MJ, Wrighton KC, Nicora CD, Williams KH, McCue LA, Handley KM, Miller CS, Giloteaux L, Montgomery AP, Lovley DR, Banfield JF, Long PE, Lipton MS.

PLoS One. 2013;8(3):e57819. doi: 10.1371/journal.pone.0057819. Epub 2013 Mar 5.


Fusion of laboratory and textual data for investigative bioforensics.

Webb-Robertson BJ, Corley C, McCue LA, Wahl K, Kreuzer H.

Forensic Sci Int. 2013 Mar 10;226(1-3):118-24. doi: 10.1016/j.forsciint.2012.12.016. Epub 2013 Jan 10.


Geoarchaeota: a new candidate phylum in the Archaea from high-temperature acidic iron mats in Yellowstone National Park.

Kozubal MA, Romine M, Jennings Rd, Jay ZJ, Tringe SG, Rusch DB, Beam JP, McCue LA, Inskeep WP.

ISME J. 2013 Mar;7(3):622-34. doi: 10.1038/ismej.2012.132. Epub 2012 Nov 15.


VESPA: software to facilitate genomic annotation of prokaryotic organisms through integration of proteomic and transcriptomic data.

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.

BMC Genomics. 2012 Apr 5;13:131. doi: 10.1186/1471-2164-13-131.


Modeling microbial dynamics in heterogeneous environments: growth on soil carbon sources.

Resat H, Bailey V, McCue LA, Konopka A.

Microb Ecol. 2012 May;63(4):883-97. doi: 10.1007/s00248-011-9965-x. Epub 2011 Dec 23.


A model of cyclic transcriptomic behavior in the cyanobacterium Cyanothece sp. ATCC 51142.

McDermott JE, Oehmen CS, McCue LA, Hill E, Choi DM, Stöckel J, Liberton M, Pakrasi HB, Sherman LA.

Mol Biosyst. 2011 Aug;7(8):2407-18. doi: 10.1039/c1mb05006k. Epub 2011 Jun 23.


Fnr (EtrA) acts as a fine-tuning regulator of anaerobic metabolism in Shewanella oneidensis MR-1.

Cruz-García C, Murray AE, Rodrigues JL, Gralnick JA, McCue LA, Romine MF, Löffler FE, Tiedje JM.

BMC Microbiol. 2011 Mar 30;11:64. doi: 10.1186/1471-2180-11-64.


The tricarboxylic acid cycle in Shewanella oneidensis is independent of Fur and RyhB control.

Yang Y, McCue LA, Parsons AB, Feng S, Zhou J.

BMC Microbiol. 2010 Oct 16;10:264. doi: 10.1186/1471-2180-10-264.


Combined statistical analyses of peptide intensities and peptide occurrences improves identification of significant peptides from MS-based proteomics data.

Webb-Robertson BJ, McCue LA, Waters KM, Matzke MM, Jacobs JM, Metz TO, Varnum SM, Pounds JG.

J Proteome Res. 2010 Nov 5;9(11):5748-56. doi: 10.1021/pr1005247. Epub 2010 Oct 8.


Comparative systems biology across an evolutionary gradient within the Shewanella genus.

Konstantinidis KT, Serres MH, Romine MF, Rodrigues JL, Auchtung J, McCue LA, Lipton MS, Obraztsova A, Giometti CS, Nealson KH, Fredrickson JK, Tiedje JM.

Proc Natl Acad Sci U S A. 2009 Sep 15;106(37):15909-14. doi: 10.1073/pnas.0902000106. Epub 2009 Sep 1.


A Bayesian integration model of high-throughput proteomics and metabolomics data for improved early detection of microbial infections.

Webb-Robertson BJ, McCue LA, Beagley N, McDermott JE, Wunschel DS, Varnum SM, Hu JZ, Isern NG, Buchko GW, Mcateer K, Pounds JG, Skerrett SJ, Liggitt D, Frevert CW.

Pac Symp Biocomput. 2009:451-63.


Identification of diverse carbon utilization pathways in Shewanella oneidensis MR-1 via expression profiling.

Driscoll ME, Romine MF, Juhn FS, Serres MH, McCue LA, Beliaev AS, Fredrickson JK, Gardner TS.

Genome Inform. 2007;18:287-98.


Measuring global credibility with application to local sequence alignment.

Webb-Robertson BJ, McCue LA, Lawrence CE.

PLoS Comput Biol. 2008 May 16;4(5):e1000077. doi: 10.1371/journal.pcbi.1000077.


Using the Gibbs motif sampler to find conserved domains in DNA and protein sequences.

Thompson W, McCue LA, Lawrence CE.

Curr Protoc Bioinformatics. 2005 Jul;Chapter 2:Unit 2.8. doi: 10.1002/0471250953.bi0208s10.


Identification of mobile elements and pseudogenes in the Shewanella oneidensis MR-1 genome.

Romine MF, Carlson TS, Norbeck AD, McCue LA, Lipton MS.

Appl Environ Microbiol. 2008 May;74(10):3257-65. doi: 10.1128/AEM.02720-07. Epub 2008 Mar 31.


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.


Using the Gibbs Motif Sampler for phylogenetic footprinting.

Thompson W, Conlan S, McCue LA, Lawrence CE.

Methods Mol Biol. 2007;395:403-24.


A phylogenetic Gibbs sampler that yields centroid solutions for cis-regulatory site prediction.

Newberg LA, Thompson WA, Conlan S, Smith TM, McCue LA, Lawrence CE.

Bioinformatics. 2007 Jul 15;23(14):1718-27. Epub 2007 May 8.


The Gibbs Centroid Sampler.

Thompson WA, Newberg LA, Conlan S, McCue LA, Lawrence CE.

Nucleic Acids Res. 2007 Jul;35(Web Server issue):W232-7. Epub 2007 May 5.


PhyloScan: identification of transcription factor binding sites using cross-species evidence.

Carmack CS, McCue LA, Newberg LA, Lawrence CE.

Algorithms Mol Biol. 2007 Jan 23;2:1.


Software to perform automated comparisons of pair-wise percent identities for microbial species.

Conlan S, McCue LA.

Biotechniques. 2006 May;40(5):578, 580,582. No abstract available.


The relative inefficiency of sequence weights approaches in determining a nucleotide position weight matrix.

Newberg LA, McCue LA, Lawrence CE.

Stat Appl Genet Mol Biol. 2005;4:Article13. Epub 2005 Jun 1.


Rhodopseudomonas palustris regulons detected by cross-species analysis of alphaproteobacterial genomes.

Conlan S, Lawrence C, McCue LA.

Appl Environ Microbiol. 2005 Nov;71(11):7442-52.


Global profiling of Shewanella oneidensis MR-1: expression of hypothetical genes and improved functional annotations.

Kolker E, Picone AF, Galperin MY, Romine MF, Higdon R, Makarova KS, Kolker N, Anderson GA, Qiu X, Auberry KJ, Babnigg G, Beliaev AS, Edlefsen P, Elias DA, Gorby YA, Holzman T, Klappenbach JA, Konstantinidis KT, Land ML, Lipton MS, McCue LA, Monroe M, Pasa-Tolic L, Pinchuk G, Purvine S, Serres MH, Tsapin S, Zakrajsek BA, Zhu W, Zhou J, Larimer FW, Lawrence CE, Riley M, Collart FR, Yates JR 3rd, Smith RD, Giometti CS, Nealson KH, Fredrickson JK, Tiedje JM.

Proc Natl Acad Sci U S A. 2005 Feb 8;102(6):2099-104. Epub 2005 Jan 31.


Making connections between novel transcription factors and their DNA motifs.

Tan K, McCue LA, Stormo GD.

Genome Res. 2005 Feb;15(2):312-20. Epub 2005 Jan 14.


Transcriptomic and proteomic characterization of the Fur modulon in the metal-reducing bacterium Shewanella oneidensis.

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.

J Bacteriol. 2004 Dec;186(24):8385-400.


A family of acr-coregulated Mycobacterium tuberculosis genes shares a common DNA motif and requires Rv3133c (dosR or devR) for expression.

Florczyk MA, McCue LA, Purkayastha A, Currenti E, Wolin MJ, McDonough KA.

Infect Immun. 2003 Sep;71(9):5332-43.


Identification of co-regulated genes through Bayesian clustering of predicted regulatory binding sites.

Qin ZS, McCue LA, Thompson W, Mayerhofer L, Lawrence CE, Liu JS.

Nat Biotechnol. 2003 Apr;21(4):435-9. Epub 2003 Mar 10.


Factors influencing the identification of transcription factor binding sites by cross-species comparison.

McCue LA, Thompson W, Carmack CS, Lawrence CE.

Genome Res. 2002 Oct;12(10):1523-32.


Bayesian protein family classifier.

Qu K, McCue LA, Lawrence CE.

Proc Int Conf Intell Syst Mol Biol. 1998;6:131-9.


Identification of bldA mutants of Streptomyces griseus.

Kwak J, McCue LA, Kendrick KE.

Gene. 1996 May 24;171(1):75-8.


Analysis of a gene that suppresses the morphological defect of bald mutants of Streptomyces griseus.

McCue LA, Kwak J, Wang J, Kendrick KE.

J Bacteriol. 1996 May;178(10):2867-75.


The human cytomegalovirus genes and proteins required for DNA synthesis.

Anders DG, McCue LA.

Intervirology. 1996;39(5-6):378-88. Review.


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