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Fundamental and Computational Sciences Directorate

Staff information

Lye Meng Markillie

Biosystms Dynamics & Simula
Pacific Northwest National Laboratory
PO Box 999
MSIN: J4-02
Richland, WA 99352

PNNL Publications


  • Howard-Varona C, S Roux, H Dore, NE Solonenko, KM Holmfeldt, LM Markillie, G Orr, and MB Sullivan. 2017. "Regulation of infection efficiency in a globally abundant marine Bacteriodetes virus." The ISME Journal 11(1):284-295.  doi:10.1038/ismej.2016.81


  • Bernstein HC, RS McClure, EA Hill, LM Markillie, WB Chrisler, MF Romine, JE McDermott, MC Posewitz, DA Bryant, A Konopka, JK Fredrickson, and AS Beliaev. 2016. "Unlocking the Constraints of Cyanobacterial Productivity: Acclimations Enabling Ultrafast Growth." mBio 7(4):Article No. e00949-16.  doi:10.1128/mBio.00949-16
  • McClure RS, CC Overall, JE McDermott, EA Hill, LM Markillie, LA McCue, RC Taylor, M Ludwig, DA Bryant, and AS Beliaev. 2016. "Network Analysis of Transcriptomics Expands Regulatory Landscapes in Synechococcus sp. PCC 7002." Nucleic Acids Research 44(18):8810-8825.  doi:10.1093/nar/gkw737
  • Mitchell HD, LM Markillie, WB Chrisler, MJ Gaffrey, D Hu, CJ Szymanski, Y Xie, ES Melby, A Dohnalkova, RC Taylor, EK Grate, SK Cooley, JE McDermott, A Heredia-Langner, and G Orr. 2016. "Cells Respond to Distinct Nanoparticle Properties with Multiple Strategies as Revealed by Single-Cell RNA-Seq." ACS Nano 10(11):10173-10185.  doi:10.1021/acsnano.6b05452
  • Shi T, M Niepel, JE McDermott, Y Gao, CD Nicora, WB Chrisler, LM Markillie, VA Petyuk, RD Smith, KD Rodland, P Sorger, W Qian, and HS Wiley. 2016. "Conservation of Protein Abundance Patterns Reveals the Regulatory Architecture of the of the EGFR-MAPK Pathway." Science Signaling 9(436):rs6.  doi:10.1126/scisignal.aaf0891
  • Tilton SC, LM Markillie, S Hays, RC Taylor, and DL Stenoien. 2016. "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." Radiation Research 186(5):531-538.  doi:10.1667/RR14471.1


  • Bernstein HC, MA Charania, RS McClure, NC Sadler, MR Melnicki, EA Hill, LM Markillie, CD Nicora, AT Wright, MF Romine, and AS Beliaev. 2015. "Multi-omic Dynamics Associate Oxygenic Photosynthesis with Nitrogenase-mediated H2 production in Cyanothece sp. ATCC 51142." Scientific Reports 5:Article No. 16004.  doi:10.1038/srep16004
  • Castelle C, KC Wrighton, BC Thomas, LA Hug, CT Brown, MJ Wilkins, KR Frischkorn, SG Tringe, A Singh, LM Markillie, RC Taylor, KH Williams, and JF Banfield. 2015. "Genomic expansion of Domain Archaea highlights roles for organisms from new phyla in anaerobic carbon cycling." Current Biology 25(6):690-701.  doi:10.1016/j.cub.2015.01.014


  • Beliaev AS, MF Romine, M Serres, HC Bernstein, BE Linggi, LM Markillie, NG Isern, WB Chrisler, LA Kucek, EA Hill, G Pinchuk, DA Bryant, HS Wiley, JK Fredrickson, and A Konopka. 2014. "Inference of Interactions in Cyanobacterial-Heterotrophic Co-Cultures via Transcriptome Sequencing." The ISME Journal 8(11):2243-2255.  doi:10.1038/ismej.2014.69
  • Croken M, YF Ma, LM Markillie, RC Taylor, G Orr, LM Weiss, and K Kim. 2014. "Distinct Strains of Toxoplasma gondii Feature Divergent Transcriptomes Regardless of Developmental Stage." PLoS One 9(11):Article No. e111297.  doi:10.1371/journal.pone.0111297
  • Eraso JM, LM Markillie, HD Mitchell, RC Taylor, G Orr, and W Margolin. 2014. "The highly conserved MraZ protein is a transcriptional regulator in Escherichia coli." Journal of Bacteriology 196(11):2053-2066.  doi:10.1128/JB.01370-13
  • Welkie DG, X Zhang, LM Markillie, RC Taylor, G Orr, JM Jacobs, K Bhide, J Thimmapuram, MA Gritsenko, HD Mitchell, RD Smith, and LA Sherman. 2014. "Transcriptomic and proteomic dynamics in the metabolism of a diazotrophic cyanobacterium, Cyanothece sp. PCC 7822 during a diurnal light-dark cycle." BMC Genomics 15:Article No. 1185. 
  • Wilkins MJ, DW Hoyt, MJ Marshall, PA Alderson, AE Plymale, LM Markillie, AE Tucker, ED Walter, BE Linggi, A Dohnalkova, and RC Taylor. 2014. "CO2 exposure at pressure impacts metabolism and stress responses in the model sulfate-reducing bacterium Desulfovibrio vulgaris strain Hildenborough." Frontiers in Microbiology 5:Article No. 507.  doi:10.3389/fmicb.2014.00507


  • Walker RW, LM Markillie, AHA Colotelo, DR Geist, ME Gay, CM Woodley, MB Eppard, and RS Brown. 2013. "Ultraviolet radiation as disinfection for fish surgical tools." Animal Biotelemetry 1:Article No. 4.  doi:10.1186/2050-3385-1-4
  • Walker RW, LM Markillie, AHA Colotelo, ME Gay, CM Woodley, and RS Brown. 2013. The Efficacy of Ultraviolet Radiation for Sterilizing Tools Used for Surgically Implanting Transmitters into Fish PNNL-21126, Pacific Northwest National Laboratory, Richland, WA. 
  • DeAngelis KM, D Sharma, R Varney, BA Simmons, NG Isern, LM Markillie, CD Nicora, AD Norbeck, RC Taylor, JT Aldrich, and EW Robinson. 2013. "Evidence supporting dissimilatory and assimilatory lignin degradation in Enterobacter lignolyticus SCF1." Frontiers in Microbiology 4:Article No. 280. 
  • Hess BM, J Xue, LM Markillie, RC Taylor, HS Wiley, BK Ahring, and BE Linggi. 2013. "Coregulation of terpenoid pathway genes and prediction of isoprene production in Bacillus subtilis using transcriptomics." PLoS One 8(6):e66104.  doi:10.1371/journal.pone.0066104
  • Piao H, LM Markillie, DE Culley, RI Mackie, and M Hess. 2013. "Improved Method for Isolation of Microbial RNA from Biofuel Feedstock for Metatranscriptomics." Advances in Microbiology 3(1):101-107.  doi:10.4236/aim.2013.31016
  • Suvorova ES, M Croken, S Kratzer, LM Ting, M Conde de Felipe, B Balu, LM Markillie, LM Weiss, K Kim, and MW White. 2013. "Discovery of a Splicing Regulator Required for Cell Cycle Progression." PLoS Genetics 9(2):Article No. e1003305.  doi:10.1371/journal.pgen.1003305
  • Taylor RC, BJM Webb-Robertson, LM Markillie, MH Serres, BE Linggi, JT Aldrich, EA Hill, MF Romine, MS Lipton, and HS Wiley. 2013. "Changes in Translational Efficiency is a Dominant Regulatory Mechanism in the Environmental Response of Bacteria." Integrative Biology 5(11):1393-1406.  doi:10.1039/C3IB40120K
  • Tomita T, DJ Bzik, YF Ma, BA Fox, LM Markillie, RC Taylor, K Kim, and LM Weiss. 2013. "The Toxoplasma gondii cyst wall protein CST1 is critical for cyst wall integrity and promotes bradyzoite persistence." PLoS Pathogens 9(12):e1003823.  doi:10.1371/journal.ppat.1003823


  • Yang F, KM Waters, BJM Webb-Robertson, MB Sowa, CH Freiin von Neubeck, JT Aldrich, LM Markillie, RM Wirgau, MA Gristenko, R Zhao, DG Camp, II, RD Smith, and DL Stenoien. 2012. "Quantitative Phosphoproteomics Identifies Filaggrin and other Targets of Ionizing Radiation in a Human Skin Model." Experimental Dermatology 21(5):352-357.  doi:10.1111/j.1600-0625.2012.01470.x


  • Orr G, WB Chrisler, KJ Cassens, R Tan, BJ Tarasevich, LM Markillie, RC Zangar, and BD Thrall. 2011. "Cellular Recognition and Trafficking of Amorphous Silica Nanoparticles by Macrophage Scavenger Receptor A." Nanotoxicology 5(3):296-311.  doi:10.3109/17435390.2010.513836
  • Labaj PP, GG Leparc, BE Linggi, LM Markillie, HS Wiley, and DP Kreil. 2011. "Characterization and Improvement of RNA-Seq Precision in Quantitative Transcript Expression Profiling." Bioinformatics 27(13):I383-I391.  doi:10.1093/bioinformatics/btr247
  • Zangar RC, N Bollinger, TJ Weber, R Tan, LM Markillie, and NJ Karin. 2011. "Reactive Oxygen Species Alter Autocrine and Paracrine Signaling." Free Radical Biology & Medicine 51(11):2041-2047.  doi:10.1016/j.freeradbiomed.2011.09.001


  • Chen B, LM Markillie, Y Xiong, MU Mayer, and TC Squier. 2007. "Increased Catalytic Efficiency Following Gene Fusion of Bifunctional Methionine Sulfoxide Reductase Enzymes from Shewanella oneidensis." Biochemistry 46(49):14153-14161.  doi:10.1021/bi701151t


  • Xiong Y, B Chen, HS Smallwood, RJ Urbauer, LM Markillie, NA Galeva, TD Williams, and TC Squier. 2006. " High-Affinity and Cooperative Binding of Oxidized Calmodulin by Methionine Sulfoxide Reductase." Biochemistry 45(49):14642-14654.  doi:10.1021/bi0612465
  • Weber TJ, HS Smallwood, LE Kathmann, LM Markillie, TC Squier, and BD Thrall. 2006. "Functional link between TNF biosynthesis and CaM-dependent activation of inducible nitric oxide synthase in RAW 264.7 macrophages ." American Journal of Physiology. Cell Physiology 290(6):C1512-C1520.  doi:10.1152/ajpcell.00527.2005


  • Weber TJ, RW Siegel, LM Markillie, WB Chrisler, XC Lei, and NH Colburn. 2005. "A paracrine signal mediates the cell transformation response to low dose gamma radiation in JB6 cells ." Molecular Carcinogenesis 43(1):31-37. 
  • Chen B, MU Mayer, LM Markillie, DL Stenoien, and TC Squier. 2005. "Dynamic Motion of Helix A in the Amino-terminal Domain of Calmodulin is Stabilized Upon Calcium Activation." Biochemistry 44(3):905-914. 
  • Chen B, MU Mayer, LM Markillie, DL Stenoien, and TC Squier. 2005. "Dynamic Motion of Helix A in the Amino-terminal Domain of Calmodulin is Stabilized Upon Calcium Activation." Biochemistry 44:905-914. 
  • Galeva NA, SW Esch, TD Williams, LM Markillie, and TC Squier. 2005. "Rapid Method for Quantifying the Extent of Methionine Oxidation in Intact Calmodulin." Journal of the American Society for Mass Spectrometry 16(9):1470-80. 
  • Markillie LM, CT Lin, JN Adkins, DL Auberry, EA Hill, BS Hooker, PA Moore, RJ Moore, L Shi, HS Wiley, and V Kery. 2005. "Simple Protein Complex Purification and Identification Method Suitable for High- throughput Mapping of Protein Interaction Networks." Journal of Proteome Research 4(2):268-274.  doi:10.1021/pr049847a
  • Shi L, CT Lin, LM Markillie, TC Squier, and BS Hooker. 2005. "Over-expression of Multi-heme C-type Cytochromes." BioTechniques 38(2):297-299. 


  • Jasionowski M, KJ Krzyminski, WB Chrisler, LM Markillie, JE Morris, and A Gutowska. 2004. "Thermally-reversible gels for 3D cell culture of chondrocytes." Journal of Materials Science. Materials in Medicine 15(5):575-582. 


  • Weber TJ, and LM Markillie. 2003. "Regulation of Activator Protein-1 by 8-iso-Prostaglandin E2 in a Thromboxane A2 Receptor-Dependent and -Independent Manner ." Molecular Pharmacology 63(5):1075-81. 
  • Weber TJ, and LM Markillie. 2003. "Regulation of activator protein-1 by 8-iso-prostaglandin E2 in a thromboxane A2 receptor-dependent and -independent manner." Molecular Pharmacology 63(5):1075-1081. 


  • Weber TJ, LM Markillie, WB Chrisler, GA Vielhauer, and JW Regan. 2002. "Modulation of JB6 Mouse Epidermal Cell Transformation Response by the Prostaglandin F2 alpha Receptor." Molecular Carcinogenesis 35(4):163-172. 
  • Weber TJ, LM Markillie, WB Chrisler, GA Vielhauer, and JW Regan. 2002. "Modulation of JB6 Mouse Epidermal Cell Transformation Response by the Prostaglandin F2 Alpha Receptor." Molecular Carcinogenesis 35(4):163-172. 
  • Lipton MS, L Pasa-Tolic, GA Anderson, DJ Anderson, DL Auberry, JR Battista, MJ Daly, JK Fredrickson, KK Hixson, HM Kostandarithes, CD Masselon, LM Markillie, RJ Moore, MF Romine, Y Shen, EF Strittmatter, N Tolic, HR Udseth, A Venkateswaran, KK Wong, R Zhao, and RD Smith. 2002. "Global Analysis of Deinococcus Radiodurans Proteome by Csing Accurate Mass Tags." Proceedings of the National Academy of Sciences of the United States of America 99(17):11049-11054. 


  • Markillie LM, SM Varnum, PB Hradecky, and KK Wong. 1999. "Targeted mutagenesis by duplication insertion in the radioresistant bacterium Deinococcus radiodurans: radiation sensitivities of catalase (katA) and superoxide dismutase (sodA) mutants." Journal of Bacteriology 181(2):666-669. 

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