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Items: 38

1.

Wetland Sediments Host Diverse Microbial Taxa Capable of Cycling Alcohols.

Dalcin Martins P, Frank J, Mitchell H, Markillie LM, Wilkins MJ.

Appl Environ Microbiol. 2019 May 30;85(12). pii: e00189-19. doi: 10.1128/AEM.00189-19. Print 2019 Jun 15.

2.

Reference genes for accurate normalization of gene expression in wood-decomposing fungi.

Zhang J, Mitchell HD, Markillie LM, Gaffrey MJ, Orr G, Schilling J.

Fungal Genet Biol. 2019 Feb;123:33-40. doi: 10.1016/j.fgb.2018.11.005. Epub 2018 Dec 5.

PMID:
30529285
3.

Multiple mechanisms drive phage infection efficiency in nearly identical hosts.

Howard-Varona C, Hargreaves KR, Solonenko NE, Markillie LM, White RA 3rd, Brewer HM, Ansong C, Orr G, Adkins JN, Sullivan MB.

ISME J. 2018 Jun;12(6):1605-1618. doi: 10.1038/s41396-018-0099-8. Epub 2018 Mar 22.

4.

Phenotypic responses to interspecies competition and commensalism in a naturally-derived microbial co-culture.

Khan N, Maezato Y, McClure RS, Brislawn CJ, Mobberley JM, Isern N, Chrisler WB, Markillie LM, Barney BM, Song HS, Nelson WC, Bernstein HC.

Sci Rep. 2018 Jan 10;8(1):297. doi: 10.1038/s41598-017-18630-1.

5.

Multi-time series RNA-seq analysis of Enterobacter lignolyticus SCF1 during growth in lignin-amended medium.

Orellana R, Chaput G, Markillie LM, Mitchell H, Gaffrey M, Orr G, DeAngelis KM.

PLoS One. 2017 Oct 19;12(10):e0186440. doi: 10.1371/journal.pone.0186440. eCollection 2017.

6.

Fluctuation localization imaging-based fluorescence in situ hybridization (fliFISH) for accurate detection and counting of RNA copies in single cells.

Cui Y, Hu D, Markillie LM, Chrisler WB, Gaffrey MJ, Ansong C, Sussel L, Orr G.

Nucleic Acids Res. 2018 Jan 25;46(2):e7. doi: 10.1093/nar/gkx874.

7.

Regulation of infection efficiency in a globally abundant marine Bacteriodetes virus.

Howard-Varona C, Roux S, Dore H, Solonenko NE, Holmfeldt K, Markillie LM, Orr G, Sullivan MB.

ISME J. 2017 Aug;11(8):1942. doi: 10.1038/ismej.2017.92.

8.

Predicting Species-Resolved Macronutrient Acquisition during Succession in a Model Phototrophic Biofilm Using an Integrated 'Omics Approach.

Lindemann SR, Mobberley JM, Cole JK, Markillie LM, Taylor RC, Huang E, Chrisler WB, Wiley HS, Lipton MS, Nelson WC, Fredrickson JK, Romine MF.

Front Microbiol. 2017 Jun 13;8:1020. doi: 10.3389/fmicb.2017.01020. eCollection 2017.

9.

Identification of Differential Gene Expression Patterns after Acute Exposure to High and Low Doses of Low-LET Ionizing Radiation in a Reconstituted Human Skin Tissue.

Tilton SC, Markillie LM, Hays S, Taylor RC, Stenoien DL.

Radiat Res. 2016 Nov;186(5):531-538. Epub 2016 Nov 1.

PMID:
27802111
10.

Cells Respond to Distinct Nanoparticle Properties with Multiple Strategies As Revealed by Single-Cell RNA-Seq.

Mitchell HD, Markillie LM, Chrisler WB, Gaffrey MJ, Hu D, Szymanski CJ, Xie Y, Melby ES, Dohnalkova A, Taylor RC, Grate EK, Cooley SK, McDermott JE, Heredia-Langner A, Orr G.

ACS Nano. 2016 Nov 22;10(11):10173-10185. Epub 2016 Oct 31.

PMID:
27788331
11.

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.

12.

Unlocking the Constraints of Cyanobacterial Productivity: Acclimations Enabling Ultrafast Growth.

Bernstein HC, McClure RS, Hill EA, Markillie LM, Chrisler WB, Romine MF, McDermott JE, Posewitz MC, Bryant DA, Konopka AE, Fredrickson JK, Beliaev AS.

MBio. 2016 Jul 26;7(4). pii: e00949-16. doi: 10.1128/mBio.00949-16.

13.

Conservation of protein abundance patterns reveals the regulatory architecture of the EGFR-MAPK pathway.

Shi T, Niepel M, McDermott JE, Gao Y, Nicora CD, Chrisler WB, Markillie LM, Petyuk VA, Smith RD, Rodland KD, Sorger PK, Qian WJ, Wiley HS.

Sci Signal. 2016 Jul 12;9(436):rs6. doi: 10.1126/scisignal.aaf0891.

14.

Regulation of infection efficiency in a globally abundant marine Bacteriodetes virus.

Howard-Varona C, Roux S, Dore H, Solonenko NE, Holmfeldt K, Markillie LM, Orr G, Sullivan MB.

ISME J. 2017 Jan;11(1):284-295. doi: 10.1038/ismej.2016.81. Epub 2016 May 17. Erratum in: ISME J. 2017 Aug;11(8):1942.

15.

Multi-Omic Dynamics Associate Oxygenic Photosynthesis with Nitrogenase-Mediated H2 Production in Cyanothece sp. ATCC 51142.

Bernstein HC, Charania MA, McClure RS, Sadler NC, Melnicki MR, Hill EA, Markillie LM, Nicora CD, Wright AT, Romine MF, Beliaev AS.

Sci Rep. 2015 Nov 3;5:16004. doi: 10.1038/srep16004.

16.

Genomic expansion of domain archaea highlights roles for organisms from new phyla in anaerobic carbon cycling.

Castelle CJ, Wrighton KC, Thomas BC, Hug LA, Brown CT, Wilkins MJ, Frischkorn KR, Tringe SG, Singh A, Markillie LM, Taylor RC, Williams KH, Banfield JF.

Curr Biol. 2015 Mar 16;25(6):690-701. doi: 10.1016/j.cub.2015.01.014. Epub 2015 Feb 19.

17.

Distinct strains of Toxoplasma gondii feature divergent transcriptomes regardless of developmental stage.

Croken MM, Ma Y, Markillie LM, Taylor RC, Orr G, Weiss LM, Kim K.

PLoS One. 2014 Nov 13;9(11):e111297. doi: 10.1371/journal.pone.0111297. eCollection 2014.

18.

CO2 exposure at pressure impacts metabolism and stress responses in the model sulfate-reducing bacterium Desulfovibrio vulgaris strain Hildenborough.

Wilkins MJ, Hoyt DW, Marshall MJ, Alderson PA, Plymale AE, Markillie LM, Tucker AE, Walter ED, Linggi BE, Dohnalkova AC, Taylor RC.

Front Microbiol. 2014 Sep 25;5:507. doi: 10.3389/fmicb.2014.00507. eCollection 2014.

19.

Inference of interactions in cyanobacterial-heterotrophic co-cultures via transcriptome sequencing.

Beliaev AS, Romine MF, Serres M, Bernstein HC, Linggi BE, Markillie LM, Isern NG, Chrisler WB, Kucek LA, Hill EA, Pinchuk GE, Bryant DA, Wiley HS, Fredrickson JK, Konopka A.

ISME J. 2014 Nov;8(11):2243-55. doi: 10.1038/ismej.2014.69. Epub 2014 Apr 29.

20.

The highly conserved MraZ protein is a transcriptional regulator in Escherichia coli.

Eraso JM, Markillie LM, Mitchell HD, Taylor RC, Orr G, Margolin W.

J Bacteriol. 2014 Jun;196(11):2053-66. doi: 10.1128/JB.01370-13. Epub 2014 Mar 21.

21.

The Toxoplasma gondii cyst wall protein CST1 is critical for cyst wall integrity and promotes bradyzoite persistence.

Tomita T, Bzik DJ, Ma YF, Fox BA, Markillie LM, Taylor RC, Kim K, Weiss LM.

PLoS Pathog. 2013;9(12):e1003823. doi: 10.1371/journal.ppat.1003823. Epub 2013 Dec 26.

22.

Changes in translational efficiency is a dominant regulatory mechanism in the environmental response of bacteria.

Taylor RC, Webb Robertson BJ, Markillie LM, Serres MH, Linggi BE, Aldrich JT, Hill EA, Romine MF, Lipton MS, Wiley HS.

Integr Biol (Camb). 2013 Nov;5(11):1393-406. doi: 10.1039/c3ib40120k. Epub 2013 Sep 30.

23.

Coregulation of Terpenoid Pathway Genes and Prediction of Isoprene Production in Bacillus subtilis Using Transcriptomics.

Hess BM, Xue J, Markillie LM, Taylor RC, Wiley HS, Ahring BK, Linggi B.

PLoS One. 2013 Jun 19;8(6):e66104. doi: 10.1371/journal.pone.0066104. Print 2013.

24.

Quantitative phosphoproteomics identifies filaggrin and other targets of ionizing radiation in a human skin model.

Yang F, Waters KM, Webb-Robertson BJ, Sowa MB, von Neubeck C, Aldrich JT, Markillie LM, Wirgau RM, Gritsenko MA, Zhao R, Camp DG 2nd, Smith RD, Stenoien DL.

Exp Dermatol. 2012 May;21(5):352-7. doi: 10.1111/j.1600-0625.2012.01470.x.

25.

Reactive oxygen species alter autocrine and paracrine signaling.

Zangar RC, Bollinger N, Weber TJ, Tan RM, Markillie LM, Karin NJ.

Free Radic Biol Med. 2011 Dec 1;51(11):2041-7. doi: 10.1016/j.freeradbiomed.2011.09.001. Epub 2011 Sep 10.

26.

Characterization and improvement of RNA-Seq precision in quantitative transcript expression profiling.

Łabaj PP, Leparc GG, Linggi BE, Markillie LM, Wiley HS, Kreil DP.

Bioinformatics. 2011 Jul 1;27(13):i383-91. doi: 10.1093/bioinformatics/btr247.

27.

Cellular recognition and trafficking of amorphous silica nanoparticles by macrophage scavenger receptor A.

Orr GA, Chrisler WB, Cassens KJ, Tan R, Tarasevich BJ, Markillie LM, Zangar RC, Thrall BD.

Nanotoxicology. 2011 Sep;5(3):296-311. doi: 10.3109/17435390.2010.513836. Epub 2010 Sep 17.

PMID:
20849212
28.

Increased catalytic efficiency following gene fusion of bifunctional methionine sulfoxide reductase enzymes from Shewanella oneidensis.

Chen B, Markillie LM, Xiong Y, Mayer MU, Squier TC.

Biochemistry. 2007 Dec 11;46(49):14153-61. Epub 2007 Nov 13.

29.

Functional link between TNF biosynthesis and CaM-dependent activation of inducible nitric oxide synthase in RAW 264.7 macrophages.

Weber TJ, Smallwood HS, Kathmann LE, Markillie LM, Squier TC, Thrall BD.

Am J Physiol Cell Physiol. 2006 Jun;290(6):C1512-20. Epub 2006 Jan 18.

30.

Simple protein complex purification and identification method for high-throughput mapping of protein interaction networks.

Markillie LM, Lin CT, Adkins JN, Auberry DL, Hill EA, Hooker BS, Moore PA, Moore RJ, Shi L, Wiley HS, Kery V.

J Proteome Res. 2005 Mar-Apr;4(2):268-74.

PMID:
15822902
31.

A paracrine signal mediates the cell transformation response to low dose gamma radiation in JB6 cells.

Weber TJ, Siegel RW, Markillie LM, Chrisler WB, Lei XC, Colburn NH.

Mol Carcinog. 2005 May;43(1):31-7.

PMID:
15800926
32.

Overexpression of multi-heme C-type cytochromes.

Shi L, Lin JT, Markillie LM, Squier TC, Hooker BS.

Biotechniques. 2005 Feb;38(2):297-9. No abstract available.

33.

Dynamic motion of helix A in the amino-terminal domain of calmodulin is stabilized upon calcium activation.

Chen B, Mayer MU, Markillie LM, Stenoien DL, Squier TC.

Biochemistry. 2005 Jan 25;44(3):905-14.

PMID:
15654746
34.
35.

Modulation of JB6 mouse epidermal cell transformation response by the prostaglandin F2alpha receptor.

Weber TJ, Markillie LM, Chrisler WB, Vielhauer GA, Regan JW.

Mol Carcinog. 2002 Dec;35(4):163-72.

PMID:
12489107
36.

Global analysis of the Deinococcus radiodurans proteome by using accurate mass tags.

Lipton MS, Pasa-Tolic' L, Anderson GA, Anderson DJ, Auberry DL, Battista JR, Daly MJ, Fredrickson J, Hixson KK, Kostandarithes H, Masselon C, Markillie LM, Moore RJ, Romine MF, Shen Y, Stritmatter E, Tolic' N, Udseth HR, Venkateswaran A, Wong KK, Zhao R, Smith RD.

Proc Natl Acad Sci U S A. 2002 Aug 20;99(17):11049-54. Epub 2002 Aug 12.

38.

A novel method for producing partial restriction digestion of DNA fragments by PCR with 5-methyl-CTP.

Wong KK, Markillie LM, Saffer JD.

Nucleic Acids Res. 1997 Oct 15;25(20):4169-71.

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