U.S. Department of Energy

Pacific Northwest National Laboratory

Alex Beliaev

Alex Believe
Professional Title: 
Scientist & Team Lead


  • Bernstein HC, RS McClure, V Thiel, NC Sadler, YM Kim, WB Chrisler, EA Hill, DA Bryant, MF Romine, JK Jansson, JK Fredrickson, and AS Beliaev. 2017. "Indirect interspecies regulation; transcriptional and physiological responses of a cyanobacterium to heterotrophic partnership." mSystems 2(2):Article No. e00181-16.  doi:10.1128/mSystems.00181-16
  • Hill EA, WB Chrisler, AS Beliaev, and HC Bernstein. 2017. "A flexible microbial co-culture platform for simultaneous utilization of methane and carbon dioxide from gas feedstocks." Bioresource Technology 228:250-256.  doi:10.1016/j.biortech.2016.12.111


  • Lindemann SR, HC Bernstein, HS Song, JK Fredrickson, MW Fields, W Shou, D Johnson, and AS Beliaev. 2016. "ENGINEERING MICROBIAL CONSORTIA FOR CONTROLLABLE OUTPUTS." The ISME Journal 10(2016):2077-2084.  doi:10.1038/ismej.2016.26
  • 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
  • Sadler NC, HC Bernstein, MR Melnicki, MA Charania, EA Hill, LN Anderson, ME Monroe, RD Smith, AS Beliaev, and AT Wright. 2016. "Dinitrogenase Driven Photobiological Hydrogen Production Combats Oxidative Stress in Cyanothece sp. ATCC 51142." Applied Environmental Microbiology 82(24):7227-7235.  doi:10.1128/AEM.02098-16
  • Wei H, J Dai, M Xia, MF Romine, L Shi, AS Beliaev, JM Tiedje, KH Nealson, JK Fredrickson, J Zhou, and D Qiu. 2016. "Functional roles of CymA and NapC in reduction of nitrate and nitrite by Shewanella putrefaciens W3-18-1." Microbiology 162(6):930-941. doi:10.1099/mic.0.000285


  • 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
  • Hwang C, A Copeland, S Lucas, A Lapidus, KW Barry, T Glavina del Rio, E Dalin, H Tice, S Pitluck, DR Sims, T Brettin, D Bruce, JC Detter, CF Han, J Schmutz, F Larimer, M Land, L Hauser, NC Kyrpides, A Lykidis, PM Richardson, AS Beliaev, RA Sanford, FE Loeffler, and MW Fields. 2015. "Complete genome sequence of Anaeromyxobacter sp. Fw109-5, an Anaerobic, Metal-Reducing Bacterium Isolated from a Contaminated Subsurface Environment." Journal of Bacteriology 3(1):Article No. e01449-14. doi:10.1128/genomeA.01449-14
  • Song HS, RS McClure, HC Bernstein, CC Overall, EA Hill, and AS Beliaev. 2015. "Integrated in silico analyses of regulatory and metabolic networks of Synechococcus sp. PCC 7002 reveal relationships between gene centrality and essentiality." Life 5(2):1127-1140. doi:10.3390/life5021127


  • Ansong C, NC Sadler, EA Hill, MP Lewis, EM Zink, RD Smith, AS Beliaev, A Konopka, and AT Wright. 2014. "Characterization of protein redox dynamics induced during light-to-dark transitions and nutrient limitation in cyanobacteria." Frontiers in Microbiology 5:Article No. 325.  doi:10.3389/fmicb.2014.00325
  • 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
  • Bernstein HC, A Konopka, MR Melnicki, EA Hill, LA Kucek, S Zhang, G Shen, DA Bryant, and AS Beliaev. 2014. "Effect of mono- and dichromatic light quality on growth rates and photosynthetic performance of Synechococcus sp. PCC 7002." Frontiers in Microbiology 5:Article No. 488.  doi:10.3389/fmicb.2014.00488 
  • Davies FK, VH Work, AS Beliaev, and MC Posewitz. 2014. "Engineering limonene and bisabolene production in wild type and a glycogen-deficient mutant of Synechococcus sp. PCC 7002." Frontiers in Bioengineering and Biotechnology 2:Artcle No. 21. doi:10.3389/fbioe.2014.00021 
  • Sadler NC, MR Melnicki, MH Serres, ED Merkley, WB Chrisler, EA Hill, MF Romine, S Kim, EM Zink, S Datta, RD Smith, AS Beliaev, A Konopka, and AT Wright. 2014. "Live Cell Chemical Profiling of Temporal Redox Dynamics in a Photoautotrophic Cyanobacterium." ACS Chemical Biology 9(1):291-300.  doi:10.1021/cb400769v
  • Song HS, WR Cannon, AS Beliaev, and A Konopka. 2014. "Mathematical Modeling of Microbial Community Dynamics: A Methodological Review." Processes 2(4):711-752. doi:10.3390/pr2040711


  • Melnicki MR, GE Pinchuk, EA Hill, LA Kucek, S Stolyar, JK Fredrickson, A Konopka, and AS Beliaev. 2013. "Feedback-Controlled LED Photobioreactor for Photophysiological Studies of Cyanobacteria." Bioresource Technology 134:127-133.  doi:10.1016/j.biortech.2013.01.079
  • Song HS, D Ramkrishna, GE Pinchuk, AS Beliaev, A Konopka, and JK Fredrickson. 2013. "Dynamic Modeling of Aerobic Growth of Shewanella oneidensis. Predicting Triauxic Growth, Flux Distributions and Energy Requirement for Growth." Metabolic Engineering 15:25-33.  doi:10.1016/j.ymben.2012.08.004
  • Vu T, EA Hill, LA Kucek, A Konopka, AS Beliaev, and JL Reed. 2013. "Computational evaluation of Synechococcus sp. PCC 7002 metabolism for chemical production." Biotechnology Journal 8(5):619-630.  doi:10.1002/biot.201200315


  • Leuze M, TV Karpinets, MH Syed, AS Beliaev, and E Uberbacher. 2012. "Binding motifs in bacterial gene promoters modulate transcriptional effects of global regulators CRP and ArcA." Gene Regulation and Systems Biology 6:93-107.  doi:10.4137/GRSB.S9357
  • Melnicki MR, GE Pinchuk, EA Hill, LA Kucek, JK Fredrickson, A Konopka, and AS Beliaev. 2012. "Sustained H2 Production Driven by Photosynthetic Water Splitting in a Unicellular Cyanobacterium." mBio 3(4):Article No. e00197-12.  doi:10.1128/mBio.00197-12
  • Vu T, S Stolyar, GE Pinchuk, EA Hill, LA Kucek, RN Brown, MS Lipton, AL Osterman, JK Fredrickson, A Konopka, AS Beliaev, and JL Reed. 2012. "Genome-Scale Modeling of Light-Driven Reductant Partitioning and Carbon Fluxes in Diazotrophic Unicellular Cyanobacterium Cyanothece sp. ATCC 51142." PLoS Computational Biology 8(4):E1002460. doi:10.1371/journal.pcbi.1002460
  • Vu T, S Stolyar, GE Pinchuk, EA Hill, LA Kucek, RN Brown, MS Lipton, AL Osterman, JK Fredrickson, A Konopka, AS Beliaev, and JL Reed. 2012. "Genome-scale modeling of light-driven reductant partitioning and carbon fluxes in diazotrophic unicellular cyanobacterium Cyanothece sp. ATCC 51142." PLoS Computational Biology 8(4):e1002460. doi:10.1371/journal.pcbi.1002460
  • Work VH, AS Beliaev, A Konopka, and MC Posewitz. 2012. "Microbial hydrocarbons: back to the future." Biofuels 3(2):103-105.  doi:10.4155/bfs.12.3


  • Clarke TA, M Edwards, AJ Gates, A Hall, G White, J Bradley, CL Reardon, L Shi, AS Beliaev, MJ Marshall, Z Wang, N Watmough, JK Fredrickson, JM Zachara, JN Butt, and DJ Richardson. 2011. "Structure of a Bacterial Cell Surface Decaheme Electron Conduit." Proceedings of the National Academy of Sciences of the United States of America 108(23):9384-9389.  doi:10.1073/pnas.1017200108
  • Pinchuk GE, OV Geydebrekht, EA Hill, JL Reed, A Konopka, AS Beliaev, and JK Fredrickson. 2011. "Pyruvate and Lactate Metabolism by Shewanella oneidensis MR-1 under Fermentation, Oxygen Limitation, and Fumarate Respiration Conditions." Applied and Environmental Microbiology 77(23):8234-8240.  doi:10.1128/AEM.05382-11
  • Pinchuk GE, OV Geydebrekht, EA Hill, JL Reed, A Konopka, AS Beliaev, and JK Fredrickson. 2011. "Pyruvate and Lactate Metabolism by Shewanella oneidensis MR-1 under Fermentation, Oxygen Limitation, and Fumarate Respiration Conditions." Applied and Environmental Microbiology 77(23):8234-8240.  doi:10.1128/AEM.05382-11


  • Marshall MJ, AS Beliaev, and JK Fredrickson. 2010. "Microbiological Transformations of Radionuclides in the Subsurface." Chapter 4 in Environmental Microbiology, Second Edition, ed. R. Mitchell; J.-D. Gu, pp. 96-114.  Wiley-Blackwell, Hoboken, NJ. 
  • Bouhenni R, GJ Vora, JC Biffinger, S Shirodkar, KL Brockman, R Ray, P Wu, BJ Johnson, EM Biddle, MJ Marshall, LA Fitzgerald, B Little, JK Fredrickson, AS Beliaev, BR Ringeisen, and D Saffarini. 2010. "The role of Shewanella oneidensis MR-1 outer surface structures in extracellular electron transfer." Electroanalysis 22(7-8):856-864. 
  • Pinchuk GE, EA Hill, OV Geydebrekht, J De Ingeniis, X Zhang, A Osterman, JH Scott, SB Reed, MF Romine, A Konopka, AS Beliaev, JK Fredrickson, and JL Reed. 2010. "Constraint-Based Model of Shewanella oneidensis MR-1 Metabolism: a Tool for Data Analysis and Hypothesis Generation." PLoS Computational Biology 6(6):Art. No. e1000822. doi:10.1371/journal.pcbi.1000822
  • Reardon CL, A Dohnalkova, P Nachimuthu, DW Kennedy, D Saffarini, BW Arey, L Shi, Z Wang, DA Moore, JS Mclean, DM Moyles, MJ Marshall, JM Zachara, JK Fredrickson, and AS Beliaev. 2010. "Role of Outer-Membrane Cytochromes MtrC and OmcA in the Biomineralization of Ferrihydrite by Shewanella oneidensis MR-1." Geobiology 8(1):56-68. doi:10.1111/j.1472-4669.2009.00226.x


  • Marshall MJ, A Dohnalkova, DW Kennedy, AE Plymale, SH Thomas, FE Loffler, R Sanford, JM Zachara, JK Fredrickson, and AS Beliaev. 2009. "Electron donor-dependent radionuclide reduction and nanoparticle formation by Anaeromyxobacter dehalogenans strain 2CP-C." Environmental Microbiology 11(2):534-543. 
  • Pinchuk GE, DA Rodionov, C Yang, X Li, AL Osterman, E Dervyn, OV Geydebrekht, SB Reed, MF Romine, FR Collart, J Scott, JK Fredrickson, and AS Beliaev. 2009. "Genomic reconstruction of Shewanella oneidensis MR-1 metabolism reveals previously uncharacterized machinery for lactate utilization." Proceedings of the National Academy of Sciences of the United States of America 106(8):2874-2879. 
  • Charania M, K Brockman, Y Zhang, A Banerjee, G Pinchuk, JK Fredrickson, AS Beliaev, and D Saffarini. 2009. "Involvement of a Membrane-Bound Class III Adenylate Cyclase in Regulation of Anaerobic Respiration in Shewanella oneidensis MR-1 ." Journal of Bacteriology 191(13):4298-4306.  doi:10.1128/JB.01829-08
  • Charania M, KL Brockman, Y Zhang, A Banerjee, GE Pinchuk, JK Fredrickson, AS Beliaev, and D Saffarini. 2009. "Involvement of a Membrane-Bound Class III Adenylate Cyclase in Regulation of Anaerobic Respiration in Shewanella oneidensis MR-1." Journal of Bacteriology 191(13):4298-4306. 
  • Hartshorne RS, CL Reardon, DE Ross, J Nuester, TA Clarke, AJ Gates, PC Mills, JK Fredrickson, JM Zachara, L Shi, AS Beliaev, MJ Marshall, M Tien, SL Brantley, JN Butt, and D Richardson. 2009. "Characterization of an electron conduit between bacteria and the extracellular environment." Proceedings of the National Academy of Sciences of the United States of America 106(52):22169-22174.  doi:10.1073/pnas.0900086106
  • Turick CE, AS Beliaev, BA Zakrajsek, CL Reardon, DA Lowy, TE Poppy, A Maloney, and AA Ekechukwu. 2009. "The Role of 4-Hydroxyphenylpyruvate Dioxygenase in Enhancement of Solid-Phase Electron Transfer by Shewanella oneidensis MR-1." FEMS Microbiology Ecology 68(2):223-225. 


  • Marshall MJ, AE Plymale, DW Kennedy, L Shi, Z Wang, SB Reed, A Dohnalkova, CJ Simonson, C Liu, D Saffarini, MF Romine, JM Zachara, AS Beliaev, and JK Fredrickson. 2008. "Hydrogenase- and Outer Membrane c-Type Cytochrome-Facilitated Reduction of Technetium(VII) by Shewanella oneidensis MR-1." Environmental Microbiology 10(1):125-136.  doi:10.1111/j.1462-2920.2007.01438.x
  • Pinchuk GE, CG Ammons, DE Culley, SM Li, JS McLean, MF Romine, KH Nealson, JK Fredrickson, and AS Beliaev. 2008. "Utilization of DNA as a Sole Source of Phosphorus, Carbon, and Energy by Shewanella spp.: Ecological and Physiological Implications for Dissimilatory Metal Reduction." Applied and Environmental Microbiology 74(4):1198-1208. doi:10.1128/AEM.02026-07
  • Fredrickson JK, MF Romine, AS Beliaev, JM Auchutung, ME Driscoll, TS Gardner, KH Nealson, AL Osterman, GE Pinchuk, JL Reed, D Rodionov, JLM Rodrigues, D Saffarini, MH Serres, AM Spormann, IB Zhulin, and JM Tiedje. 2008. "Towards Environmental Systems Biology of Shewanella." Nature Reviews. Microbiology 6(8):592-603.  doi:10.1038/nrmicro1947
  • Mclean JS, GE Pinchuk, OV Geydebrekht, CL Bilskis, BA Zakrajsek, EA Hill, D Saffarini, MF Romine, YA Gorby, JK Fredrickson, and AS Beliaev. 2008. "Oxygen-dependent autoaggregation in Shewanella oneidensis MR-1." Environmental Microbiology 10(7):1861-1876.  doi:10.1111/j.1462-2920.2008.01608.x
  • Shi L, S Deng, MJ Marshall, Z Wang, DW Kennedy, A Dohnalkova, HM Mottaz, EA Hill, YA Gorby, AS Beliaev, DJ Richardson, JM Zachara, and JK Fredrickson. 2008. " Direct Involvement of Type II Secretion System in Extracellular Translocation of Shewanella Oneidensis Outer Membrane Cytochromes MtrC and OmcA." Journal of Bacteriology 190(15):5512-5516.  doi:10.1128/JB.00514-08


  • Bretschger O, A Obraztsova, CA Sturm, IS Chang, YA Gorby, SB Reed, DE Culley, CL Reardon, S Barua, MF Romine, J Zhou, AS Beliaev, R Bouhenni, D Saffarini, F Mansfeld, BH Kim, JK Fredrickson, and KH Nealson. 2007. "Current Production and Metal Oxide Reduction by Shewanella Oneidensis MR-1 Wild Type and Mutants." Applied and Environmental Microbiology 73(21):7003-7012.  doi:10.1128/AEM.01087-07
  • Driscoll ME, MF Romine, FS Juhn, MH Serres, LA McCue, AS Beliaev, JK Fredrickson, and TS Gardner. 2007. "Identification of diverse carbon utilization pathways in Shewanella oneidensis MR-1 via expression profiling." Genome Informatics 18:287-298. 
  • Elias DA, F Yang, HM Mottaz, AS Beliaev, and MS Lipton. 2007. "Enrichment of Functional Redox Reactive Proteins and Identification by Mass Spectrometry Results in Several Terminal Fe(III)-reducing Candidate Proteins in Shewanella oneidensis MR-1." Journal of Microbiological Methods 68(2):367-375. 


  • Marshall MJ, AS Beliaev, A Dohnalkova, DW Kennedy, L Shi, Z Wang, MI Boyanov, B Lai, KM Kemner, JS Mclean, SB Reed, DE Culley, VL Bailey, CJ Simonson, D Saffarini, MF Romine, JM Zachara, and JK Fredrickson. 2006. "c-Type Cytochrome-Dependent Formation of U(IV) Nanoparticles by Shewanella oneidensis ." PloS Biology 4(8):1324-1333. 
  • Shi L, B Chen, Z Wang, DA Elias, MU Mayer, YA Gorby, S Ni, BH Lower, DW Kennedy, DS Wunschel, HM Mottaz, MJ Marshall, EA Hill, AS Beliaev, JM Zachara, JK Fredrickson, and TC Squier. 2006. "Isolation of a High-Affinity Functional Protein Complex between OmcA and MtrC: Two Outer Membrane Decaheme c-type Cytochromes of Shewanella oneidensis MR-1 ." Journal of Bacteriology 188(13):4705-4714.  doi:10.1128/JB.01966-05


  • Beliaev AS, DM Klingeman, J Klappenbach, L Wu, MF Romine, JM Tiedje, KH Nealson, JK Fredrickson, and J Zhou. 2005. "Global Transcriptome Analysis of Shewanella oneidensis MR-1 Exposed to Different Terminal Electron Acceptors." Journal of Bacteriology 187(20):7138-7145.  doi:10.1128/JB.187.20.7138-7145.2005
  • Elias DA, ME Monroe, MJ Marshall, MF Romine, AS Beliaev, JK Fredrickson, GA Anderson, RD Smith, and MS Lipton. 2005. "Global detection and characterization of hypothetical proteins in Shewanella oneidensis MR-1 using LC-MS based proteomics based proteomics." Proteomics 5(12):3120-3130.  doi:10.1002/pmic.200401140
  • Kolker E, AF Picone, MY Galperin, MF Romine, R Higdon, KS Makarova, N Kolker, GA Anderson, X Qiu, KJ Auberry, G Babnigg, AS Beliaev, P Edlefsen, DA Elias, YA Gorby, T Holzman, J Klappenbach, K Konstantinidis, ML Land, MS Lipton, LA McCue, ME Monroe, L Pasa-Tolic, GE Pinchuk, SO Purvine, M Serres, S Tsapin, BA Zakrajsek, W Zhu, J Zhou, F Larimer, C Lawrence, M Riley, FR Collart, JR Yates, III, RD Smith, CS Giometti, K Nealson, JK Fredrickson, and JM Tiedje. 2005. "Global Profiling of Shewanella oneidensis MR-1: Expression of Hypothetical Genes and Improved functional annotations." Proceedings of the National Academy of Sciences of the United States of America 102(6):2099-2104. 


  • Beliaev AS. 2004. "Mutagenesis as a functional genomics tool." In Microbial Functional Genomics, ed. J Zhou, DK Thompson, JM Tiedje, pp. 207-240.  John Wiley & Sons, New York, NY. 


  • Liu Y, J Zhou, MV Omelchenko, AS Beliaev, A Venkateswaran, J Stair, L Wu, DK Thompson, D Xu, IB Rogozin, E Gaidamakova, M Zhai, KS Makarova, EV Koonin, and MJ Daly. 2003. "Transcriptome dynamics of Deinococcus radiodurans recovering from ionizing radiation." Proceedings of the National Academy of Sciences of the United States of America 100(7):4191-4196. 
  • Saffarini D, R Schultz, and AS Beliaev. 2003. "Involvement of cyclic AMP (cAMP) and cAMP receptor protein in anaerobic respiration of Shewanella oneidensis." Journal of Bacteriology 185(12):3668-3671. 
  • Yost C, LJ Hauser, F Larimer, D Thompson, AS Beliaev, J Zhou, Y Xu, and D Xu. 2003. "A computational study of Shewanella oneidensis MR-1: Structural prediction and functional inference of hypothetical proteins." OMICS. A Journal of Integrative Biology 7(2):177-191. 
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