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Fundamental and Computational Sciences Directorate

Staff information

Alex Beliaev

Biological Systems Science
Biologist, Team Lead
Pacific Northwest National Laboratory
PO Box 999
MSIN: J4-18
Richland, WA 99352

PNNL Publications

2018

  • Bohutskyi P., L.A. Kucek, E.A. Hill, G.E. Pinchuk, S.G. Mundree, and A.S. Beliaev. 2018. "Conversion of stranded waste-stream carbon and nutrients into value-added products via metabolically coupled binary heterotroph-photoautotroph system." Bioresource Technology 260. PNNL-SA-126703. doi:10.1016/j.biortech.2018.02.080
  • Song H., W.C. Nelson, J. Lee, R.C. Taylor, C.S. Henry, A.S. Beliaev, and D. Ramkrishna, et al. 2018. "Metabolic Network Modeling for Computer-Aided Design of Microbial Interactions." In Emerging Areas in Bioengineering, edited by HN Chang, et al. 793-801. Weinheim:Wiley-VCH Verlag GmbH & Co. PNNL-SA-115176. doi:10.1002/9783527803293.ch45

2017

  • Bernstein H.C., R.S. McClure, V. Thiel, N.C. Sadler, Y. Kim, W.B. Chrisler, and E.A. Hill, et al. 2017. "Indirect interspecies regulation; transcriptional and physiological responses of a cyanobacterium to heterotrophic partnership." mSystems 2, no. 2:Article No. e00181-16. PNNL-SA-113682. doi:10.1128/mSystems.00181-16
  • Hill E.A., W.B. Chrisler, A.S. Beliaev, and H.C. Bernstein. 2017. "A flexible microbial co-culture platform for simultaneous utilization of methane and carbon dioxide from gas feedstocks." Bioresource Technology 228. PNNL-SA-122746. doi:10.1016/j.biortech.2016.12.111

2016

  • Bernstein H.C., R.S. McClure, E.A. Hill, L.M. Markillie, W.B. Chrisler, M.F. Romine, and J.E. McDermott, et al. 2016. "Unlocking the Constraints of Cyanobacterial Productivity: Acclimations Enabling Ultrafast Growth." mBio 7, no. 4:Article No. e00949-16. PNNL-SA-112394. doi:10.1128/mBio.00949-16
  • Lindemann S.R., H.C. Bernstein, H. Song, J.K. Fredrickson, M.W. Fields, W. Shou, and D. Johnson, et al. 2016. "ENGINEERING MICROBIAL CONSORTIA FOR CONTROLLABLE OUTPUTS." The ISME Journal 10, no. 2016:2077-2084. PNNL-SA-110327. doi:10.1038/ismej.2016.26
  • McClure R.S., C.C. Overall, J.E. McDermott, E.A. Hill, L.M. Markillie, L.A. McCue, and R.C. Taylor, et al. 2016. "Network Analysis of Transcriptomics Expands Regulatory Landscapes in Synechococcus sp. PCC 7002." Nucleic Acids Research 44, no. 18:8810-8825. PNNL-SA-113421. doi:10.1093/nar/gkw737
  • Sadler N.C., H.C. Bernstein, M.R. Melnicki, M.A. Charania, E.A. Hill, L.N. Anderson, and M.E. Monroe, et al. 2016. "Dinitrogenase Driven Photobiological Hydrogen Production Combats Oxidative Stress in Cyanothece sp. ATCC 51142." Applied Environmental Microbiology 82, no. 24:7227-7235. PNNL-SA-113160. doi:10.1128/AEM.02098-16
  • Wei H., J. Dai, M. Xia, M.F. Romine, L. Shi, A.S. Beliaev, and J.M. Tiedje, et al. 2016. "Functional roles of CymA and NapC in reduction of nitrate and nitrite by Shewanella putrefaciens W3-18-1." Microbiology 162, no. 6:930-941. PNNL-SA-121585. doi:10.1099/mic.0.000285

2015

  • Bernstein H.C., M.A. Charania, R.S. McClure, N.C. Sadler, M.R. Melnicki, E.A. Hill, and L.M. Markillie, et al. 2015. "Multi-omic Dynamics Associate Oxygenic Photosynthesis with Nitrogenase-mediated H2 production in Cyanothece sp. ATCC 51142." Scientific Reports 5. PNNL-SA-111925. doi:10.1038/srep16004
  • Hwang C., A. Copeland, S. Lucas, A. Lapidus, K.W. Barry, T. Glavina del Rio, and E. Dalin, et al. 2015. "Complete genome sequence of Anaeromyxobacter sp. Fw109-5, an Anaerobic, Metal-Reducing Bacterium Isolated from a Contaminated Subsurface Environment." Journal of Bacteriology 3, no. 1:Article No. e01449-14. PNNL-SA-107352. doi:10.1128/genomeA.01449-14
  • Song H., R.S. McClure, H.C. Bernstein, C.C. Overall, E.A. Hill, and A.S. 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, no. 2:1127-1140. PNNL-SA-109173. doi:10.3390/life5021127

2014

  • Ansong C., N.C. Sadler, E.A. Hill, M.P. Lewis, E.M. Zink, R.D. Smith, and A.S. Beliaev, et al. 2014. "Characterization of protein redox dynamics induced during light-to-dark transitions and nutrient limitation in cyanobacteria." Frontiers in Microbiology 5. PNNL-SA-101966. doi:10.3389/fmicb.2014.00325
  • Beliaev A.S., M.F. Romine, M. Serres, H.C. Bernstein, B.E. Linggi, L.M. Markillie, and N.G. Isern, et al. 2014. "Inference of Interactions in Cyanobacterial-Heterotrophic Co-Cultures via Transcriptome Sequencing." The ISME Journal 8, no. 11:2243-2255. PNNL-SA-98626. doi:10.1038/ismej.2014.69
  • Bernstein H.C., A. Konopka, M.R. Melnicki, E.A. Hill, L.A. Kucek, S. Zhang, and G. Shen, et al. 2014. "Effect of mono- and dichromatic light quality on growth rates and photosynthetic performance of Synechococcus sp. PCC 7002." Frontiers in Microbiology 5. PNNL-SA-101364. doi:10.3389/fmicb.2014.00488
  • Davies F.K., V.H. Work, A.S. Beliaev, and M.C. 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. PNNL-SA-103690. doi:10.3389/fbioe.2014.00021
  • Sadler N.C., M.R. Melnicki, M.H. Serres, E.D. Merkley, W.B. Chrisler, E.A. Hill, and M.F. Romine, et al. 2014. "Live Cell Chemical Profiling of Temporal Redox Dynamics in a Photoautotrophic Cyanobacterium." ACS Chemical Biology 9, no. 1:291-300. PNNL-SA-93812. doi:10.1021/cb400769v
  • Song H., W.R. Cannon, A.S. Beliaev, and A. Konopka. 2014. "Mathematical Modeling of Microbial Community Dynamics: A Methodological Review." Processes 2, no. 4:711-752. PNNL-SA-104609. doi:10.3390/pr2040711

2013

  • Melnicki M.R., G.E. Pinchuk, E.A. Hill, L.A. Kucek, S. Stolyar, J.K. Fredrickson, and A. Konopka, et al. 2013. "Feedback-Controlled LED Photobioreactor for Photophysiological Studies of Cyanobacteria." Bioresource Technology 134. PNNL-SA-91362. doi:10.1016/j.biortech.2013.01.079
  • Song H., D. Ramkrishna, G.E. Pinchuk, A.S. Beliaev, A. Konopka, and J.K. Fredrickson. 2013. "Dynamic Modeling of Aerobic Growth of Shewanella oneidensis. Predicting Triauxic Growth, Flux Distributions and Energy Requirement for Growth." Metabolic Engineering 15. PNNL-SA-90270. doi:10.1016/j.ymben.2012.08.004
  • Vu T., E.A. Hill, L.A. Kucek, A. Konopka, A.S. Beliaev, and J.L. Reed. 2013. "Computational evaluation of Synechococcus sp. PCC 7002 metabolism for chemical production." Biotechnology Journal 8, no. 5:619-630. PNNL-SA-95015. doi:10.1002/biot.201200315

2012

  • Leuze M., M. Leuze, T.V. Karpinets, M.H. Syed, A.S. 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. PNNL-SA-86561. doi:10.4137/GRSB.S9357
  • Melnicki M.R., G.E. Pinchuk, E.A. Hill, L.A. Kucek, J.K. Fredrickson, A. Konopka, and A.S. Beliaev. 2012. "Sustained H2 Production Driven by Photosynthetic Water Splitting in a Unicellular Cyanobacterium." mBio 3, no. 4:Article No. e00197-12. PNNL-SA-85855. doi:10.1128/mBio.00197-12
  • Vu T., S. Stolyar, G.E. Pinchuk, E.A. Hill, L.A. Kucek, R.N. Brown, and M.S. Lipton, et al. 2012. "Genome-Scale Modeling of Light-Driven Reductant Partitioning and Carbon Fluxes in Diazotrophic Unicellular Cyanobacterium Cyanothece sp. ATCC 51142." PLoS Computational Biology 8, no. 4:E1002460. PNNL-SA-83135. doi:10.1371/journal.pcbi.1002460
  • Vu T., S. Stolyar, G.E. Pinchuk, E.A. Hill, L.A. Kucek, R.N. Brown, and M.S. Lipton, et al. 2012. "Genome-scale modeling of light-driven reductant partitioning and carbon fluxes in diazotrophic unicellular cyanobacterium Cyanothece sp. ATCC 51142." PLoS Computational Biology 8, no. 4:e1002460. PNNL-SA-83348. doi:10.1371/journal.pcbi.1002460
  • Work V.H., A.S. Beliaev, A. Konopka, and M.C. Posewitz. 2012. "Microbial hydrocarbons: back to the future." Biofuels 3, no. 2:103-105. PNNL-SA-86542. doi:10.4155/bfs.12.3

2011

  • Clarke T.A., M. Edwards, A.J. Gates, A.J. Gates, A. Hall, G. White, and J. Bradley, et al. 2011. "Structure of a Bacterial Cell Surface Decaheme Electron Conduit." Proceedings of the National Academy of Sciences of the United States of America 108, no. 23:9384-9389. PNNL-SA-79964. doi:10.1073/pnas.1017200108
  • Pinchuk G.E., O.V. Geydebrekht, E.A. Hill, J.L. Reed, A. Konopka, A.S. Beliaev, and J.K. Fredrickson. 2011. "Pyruvate and Lactate Metabolism by Shewanella oneidensis MR-1 under Fermentation, Oxygen Limitation, and Fumarate Respiration Conditions." Applied and Environmental Microbiology 77, no. 23:8234-8240. PNNL-SA-79834. doi:10.1128/AEM.05382-11
  • Pinchuk G.E., O.V. Geydebrekht, E.A. Hill, J.L. Reed, A. Konopka, A.S. Beliaev, and J.K. Fredrickson. 2011. "Pyruvate and Lactate Metabolism by Shewanella oneidensis MR-1 under Fermentation, Oxygen Limitation, and Fumarate Respiration Conditions." Applied and Environmental Microbiology 77, no. 23:8234-8240. PNNL-SA-83134. doi:10.1128/AEM.05382-11

2010

  • Bouhenni R., G.J. Vora, J.C. Biffinger, S. Shirodkar, K.L. Brockman, R. Ray, and P. Wu, et al. 2010. "The role of Shewanella oneidensis MR-1 outer surface structures in extracellular electron transfer." Electroanalysis 22, no. 7-8:856-864. PNNL-SA-52140.
  • Marshall M.J., A.S. Beliaev, and J.K. Fredrickson. 2010. "Microbiological Transformations of Radionuclides in the Subsurface." In Environmental Microbiology, Second Edition, edited by R. Mitchell; J.-D. Gu. 96-114. Hoboken, New Jersey:Wiley-Blackwell. PNNL-SA-62329.
  • Pinchuk G.E., E.A. Hill, O.V. Geydebrekht, J. De Ingeniis, X. Zhang, A. Osterman, and J.H. Scott, et al. 2010. "Constraint-Based Model of Shewanella oneidensis MR-1 Metabolism: a Tool for Data Analysis and Hypothesis Generation." PLoS Computational Biology 6, no. 6:Art. No. e1000822. PNNL-SA-68769. doi:10.1371/journal.pcbi.1000822
  • Reardon C.L., A. Dohnalkova, P. Nachimuthu, D.W. Kennedy, D. Saffarini, B.W. Arey, and L. Shi, et al. 2010. "Role of Outer-Membrane Cytochromes MtrC and OmcA in the Biomineralization of Ferrihydrite by Shewanella oneidensis MR-1." Geobiology 8, no. 1:56-68. PNNL-SA-57383. doi:10.1111/j.1472-4669.2009.00226.x

2009

  • Charania M., K. Brockman, Y. Zhang, A. Banerjee, G. Pinchuk, J.K. Fredrickson, and A.S. Beliaev, et al. 2009. "Involvement of a Membrane-Bound Class III Adenylate Cyclase in Regulation of Anaerobic Respiration in Shewanella oneidensis MR-1." Journal of Bacteriology 191, no. 13:4298-4306. PNNL-SA-52138. doi:10.1128/JB.01829-08
  • Charania M., K.L. Brockman, Y. Zhang, A. Banerjee, G.E. Pinchuk, J.K. Fredrickson, and A.S. Beliaev, et al. 2009. "Involvement of a Membrane-Bound Class III Adenylate Cyclase in Regulation of Anaerobic Respiration in Shewanella oneidensis MR-1." Journal of Bacteriology 191, no. 13:4298-4306. PNNL-SA-67111.
  • Hartshorne R.S., C.L. Reardon, D.E. Ross, J. Nuester, J. Nuester, T.A. Clarke, and A.J. Gates, et al. 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, no. 52:22169-22174. PNNL-SA-68587. doi:10.1073/pnas.0900086106
  • Marshall M.J., A. Dohnalkova, D.W. Kennedy, A.E. Plymale, S.H. Thomas, F.E. Loffler, and R. Sanford, et al. 2009. "Electron donor-dependent radionuclide reduction and nanoparticle formation by Anaeromyxobacter dehalogenans strain 2CP-C." Environmental Microbiology 11, no. 2:534-543. PNNL-SA-57365.
  • Pinchuk G.E., D.A. Rodionov, C. Yang, X. Li, A.L. Osterman, E. Dervyn, and O.V. Geydebrekht, et al. 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, no. 8:2874-2879. PNNL-SA-52141.
  • Turick C.E., A.S. Beliaev, B.A. Zakrajsek, C.L. Reardon, D.A. Lowy, T.E. Poppy, and A. Maloney, et al. 2009. "The Role of 4-Hydroxyphenylpyruvate Dioxygenase in Enhancement of Solid-Phase Electron Transfer by Shewanella oneidensis MR-1." FEMS Microbiology Ecology 68, no. 2:223-225. PNNL-SA-61518.

2008

  • Fredrickson J.K., M.F. Romine, A.S. Beliaev, J.M. Auchutung, M.E. Driscoll, T.S. Gardner, and K.H. Nealson, et al. 2008. "Towards Environmental Systems Biology of Shewanella." Nature Reviews. Microbiology 6, no. 8:592-603. PNNL-SA-60993. doi:10.1038/nrmicro1947
  • Marshall M.J., A.E. Plymale, D.W. Kennedy, L. Shi, Z. Wang, S.B. Reed, and A. Dohnalkova, et al. 2008. "Hydrogenase- and Outer Membrane c-Type Cytochrome-Facilitated Reduction of Technetium(VII) by Shewanella oneidensis MR-1." Environmental Microbiology 10, no. 1:125-136. PNNL-SA-52126. doi:10.1111/j.1462-2920.2007.01438.x
  • Mclean J.S., G.E. Pinchuk, O.V. Geydebrekht, C.L. Bilskis, B.A. Zakrajsek, E.A. Hill, and D. Saffarini, et al. 2008. "Oxygen-dependent autoaggregation in Shewanella oneidensis MR-1." Environmental Microbiology 10, no. 7:1861-1876. PNNL-SA-47123. doi:10.1111/j.1462-2920.2008.01608.x
  • Pinchuk G.E., C.G. Ammons, D.E. Culley, S. Li, J.S. McLean, M.F. Romine, and K.H. Nealson, et al. 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, no. 4:1198-1208. PNNL-SA-45480. doi:10.1128/AEM.02026-07
  • Shi L., S. Deng, M.J. Marshall, Z. Wang, D.W. Kennedy, A. Dohnalkova, and H.M. Mottaz, et al. 2008. "Direct Involvement of Type II Secretion System in Extracellular Translocation of Shewanella Oneidensis Outer Membrane Cytochromes MtrC and OmcA." Journal of Bacteriology 190, no. 15:5512-5516. PNNL-SA-55117. doi:10.1128/JB.00514-08

2007

  • Bretschger O., A. Obraztsova, C.A. Sturm, C.A. Sturm, I.S. Chang, Y.A. Gorby, and S.B. Reed, et al. 2007. "Current Production and Metal Oxide Reduction by Shewanella Oneidensis MR-1 Wild Type and Mutants." Applied and Environmental Microbiology 73, no. 21:7003-7012. PNNL-SA-57449. doi:10.1128/AEM.01087-07
  • Driscoll M.E., M.F. Romine, F.S. Juhn, M.H. Serres, L.A. McCue, A.S. Beliaev, and J.K. Fredrickson, et al. 2007. "Identification of diverse carbon utilization pathways in Shewanella oneidensis MR-1 via expression profiling." Genome Informatics 18. PNNL-SA-52139.
  • Elias D.A., F. Yang, H.M. Mottaz, A.S. Beliaev, and M.S. 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, no. 2:367-375. PNNL-SA-52214.

2006

  • Marshall M.J., A.S. Beliaev, A. Dohnalkova, D.W. Kennedy, L. Shi, Z. Wang, and M.I. Boyanov, et al. 2006. "c-Type Cytochrome-Dependent Formation of U(IV) Nanoparticles by Shewanella oneidensis." PLoS Biology 4, no. 8:1324-1333. PNNL-SA-47126.
  • Shi L., B. Chen, Z. Wang, D.A. Elias, M.U. Mayer, Y.A. Gorby, and S. Ni, et al. 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, no. 13:4705-4714. PNNL-SA-45401. doi:10.1128/JB.01966-05

2005

  • Beliaev A.S., D.M. Klingeman, J. Klappenbach, L. Wu, M.F. Romine, J.M. Tiedje, and K.H. Nealson, et al. 2005. "Global Transcriptome Analysis of Shewanella oneidensis MR-1 Exposed to Different Terminal Electron Acceptors." Journal of Bacteriology 187, no. 20:7138-7145. PNNL-SA-43819. doi:10.1128/JB.187.20.7138-7145.2005
  • Elias D.A., M.E. Monroe, M.J. Marshall, M.F. Romine, A.S. Beliaev, J.K. Fredrickson, and G.A. Anderson, et al. 2005. "Global detection and characterization of hypothetical proteins in Shewanella oneidensis MR-1 using LC-MS based proteomics based proteomics." Proteomics 5, no. 12:3120-3130. PNNL-SA-42041. doi:10.1002/pmic.200401140
  • Kolker E., A.F. Picone, M.Y. Galperin, M.F. Romine, R. Higdon, K.S. Makarova, and N. Kolker, et al. 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, no. 6:2099-2104. PNNL-SA-43139.

2004

  • Beliaev A.S. 2004. "Mutagenesis as a functional genomics tool." In Microbial Functional Genomics, edited by J Zhou, DK Thompson, JM Tiedje. 207-240. New York, New York:John Wiley & Sons. PNNL-SA-43191.

2003

  • Liu Y., J. Zhou, M.V. Omelchenko, A.S. Beliaev, A. Venkateswaran, J. Stair, and L. Wu, et al. 2003. "Transcriptome dynamics of Deinococcus radiodurans recovering from ionizing radiation." Proceedings of the National Academy of Sciences of the United States of America 100, no. 7:4191-4196. PNNL-SA-43195.
  • Saffarini D., R. Schultz, and A.S. Beliaev. 2003. "Involvement of cyclic AMP (cAMP) and cAMP receptor protein in anaerobic respiration of Shewanella oneidensis." Journal of Bacteriology 185, no. 12:3668-3671. PNNL-SA-43164.
  • Yost C., L.J. Hauser, F. Larimer, D. Thompson, A.S. Beliaev, J. Zhou, and Y. Xu, et al. 2003. "A computational study of Shewanella oneidensis MR-1: Structural prediction and functional inference of hypothetical proteins." OMICS. A Journal of Integrative Biology 7, no. 2:177-191. PNNL-SA-43162.

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