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Items: 1 to 50 of 59

1.

Species-specific transcriptomic network inference of interspecies interactions.

McClure RS, Overall CC, Hill EA, Song HS, Charania M, Bernstein HC, McDermott JE, Beliaev AS.

ISME J. 2018 Aug;12(8):2011-2023. doi: 10.1038/s41396-018-0145-6. Epub 2018 May 24.

2.

Conversion of stranded waste-stream carbon and nutrients into value-added products via metabolically coupled binary heterotroph-photoautotroph system.

Bohutskyi P, Kucek LA, Hill E, Pinchuk GE, Mundree SG, Beliaev AS.

Bioresour Technol. 2018 Jul;260:68-75. doi: 10.1016/j.biortech.2018.02.080. Epub 2018 Feb 19.

PMID:
29614453
3.

Indirect Interspecies Regulation: Transcriptional and Physiological Responses of a Cyanobacterium to Heterotrophic Partnership.

Bernstein HC, McClure RS, Thiel V, Sadler NC, Kim YM, Chrisler WB, Hill EA, Bryant DA, Romine MF, Jansson JK, Fredrickson JK, Beliaev AS.

mSystems. 2017 Mar 7;2(2). pii: e00181-16. doi: 10.1128/mSystems.00181-16. eCollection 2017 Mar-Apr.

4.

A flexible microbial co-culture platform for simultaneous utilization of methane and carbon dioxide from gas feedstocks.

Hill EA, Chrisler WB, Beliaev AS, Bernstein HC.

Bioresour Technol. 2017 Mar;228:250-256. doi: 10.1016/j.biortech.2016.12.111. Epub 2017 Jan 3.

5.

Dinitrogenase-Driven Photobiological Hydrogen Production Combats Oxidative Stress in Cyanothece sp. Strain ATCC 51142.

Sadler NC, Bernstein HC, Melnicki MR, Charania MA, Hill EA, Anderson LN, Monroe ME, Smith RD, Beliaev AS, Wright AT.

Appl Environ Microbiol. 2016 Nov 21;82(24):7227-7235. Print 2016 Dec 15.

6.

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.

7.

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.

8.

Engineering microbial consortia for controllable outputs.

Lindemann SR, Bernstein HC, Song HS, Fredrickson JK, Fields MW, Shou W, Johnson DR, Beliaev AS.

ISME J. 2016 Sep;10(9):2077-84. doi: 10.1038/ismej.2016.26. Epub 2016 Mar 11.

9.

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.

10.

Lauric Acid Production in a Glycogen-Less Strain of Synechococcus sp. PCC 7002.

Work VH, Melnicki MR, Hill EA, Davies FK, Kucek LA, Beliaev AS, Posewitz MC.

Front Bioeng Biotechnol. 2015 Apr 24;3:48. doi: 10.3389/fbioe.2015.00048. eCollection 2015.

11.

Integrated in silico Analyses of Regulatory and Metabolic Networks of Synechococcus sp. PCC 7002 Reveal Relationships between Gene Centrality and Essentiality.

Song HS, McClure RS, Bernstein HC, Overall CC, Hill EA, Beliaev AS.

Life (Basel). 2015 Mar 27;5(2):1127-40. doi: 10.3390/life5021127.

12.

Effect of mono- and dichromatic light quality on growth rates and photosynthetic performance of Synechococcus sp. PCC 7002.

Bernstein HC, Konopka A, Melnicki MR, Hill EA, Kucek LA, Zhang S, Shen G, Bryant DA, Beliaev AS.

Front Microbiol. 2014 Sep 19;5:488. doi: 10.3389/fmicb.2014.00488. eCollection 2014.

13.

Engineering Limonene and Bisabolene Production in Wild Type and a Glycogen-Deficient Mutant of Synechococcus sp. PCC 7002.

Davies FK, Work VH, Beliaev AS, Posewitz MC.

Front Bioeng Biotechnol. 2014 Jun 19;2:21. doi: 10.3389/fbioe.2014.00021. eCollection 2014.

14.

Characterization of protein redox dynamics induced during light-to-dark transitions and nutrient limitation in cyanobacteria.

Ansong C, Sadler NC, Hill EA, Lewis MP, Zink EM, Smith RD, Beliaev AS, Konopka AE, Wright AT.

Front Microbiol. 2014 Jul 3;5:325. doi: 10.3389/fmicb.2014.00325. eCollection 2014.

15.

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.

16.

Live cell chemical profiling of temporal redox dynamics in a photoautotrophic cyanobacterium.

Sadler NC, Melnicki MR, Serres MH, Merkley ED, Chrisler WB, Hill EA, Romine MF, Kim S, Zink EM, Datta S, Smith RD, Beliaev AS, Konopka A, Wright AT.

ACS Chem Biol. 2014 Jan 17;9(1):291-300. doi: 10.1021/cb400769v. Epub 2013 Nov 6.

PMID:
24168666
17.

Computational evaluation of Synechococcus sp. PCC 7002 metabolism for chemical production.

Vu TT, Hill EA, Kucek LA, Konopka AE, Beliaev AS, Reed JL.

Biotechnol J. 2013 May;8(5):619-30. doi: 10.1002/biot.201200315. Epub 2013 Apr 24.

PMID:
23613453
18.

Feedback-controlled LED photobioreactor for photophysiological studies of cyanobacteria.

Melnicki MR, Pinchuk GE, Hill EA, Kucek LA, Stolyar SM, Fredrickson JK, Konopka AE, Beliaev AS.

Bioresour Technol. 2013 Apr;134:127-33. doi: 10.1016/j.biortech.2013.01.079. Epub 2013 Feb 10.

PMID:
23500569
19.

Dynamic modeling of aerobic growth of Shewanella oneidensis. Predicting triauxic growth, flux distributions, and energy requirement for growth.

Song HS, Ramkrishna D, Pinchuk GE, Beliaev AS, Konopka AE, Fredrickson JK.

Metab Eng. 2013 Jan;15:25-33. doi: 10.1016/j.ymben.2012.08.004. Epub 2012 Sep 26.

PMID:
23022551
20.

Sustained H(2) production driven by photosynthetic water splitting in a unicellular cyanobacterium.

Melnicki MR, Pinchuk GE, Hill EA, Kucek LA, Fredrickson JK, Konopka A, Beliaev AS.

MBio. 2012 Aug 7;3(4):e00197-12. doi: 10.1128/mBio.00197-12. Print 2012.

21.

Binding Motifs in Bacterial Gene Promoters Modulate Transcriptional Effects of Global Regulators CRP and ArcA.

Leuze MR, Karpinets TV, Syed MH, Beliaev AS, Uberbacher EC.

Gene Regul Syst Bio. 2012;6:93-107. doi: 10.4137/GRSB.S9357. Epub 2012 May 30.

22.

Genome-scale modeling of light-driven reductant partitioning and carbon fluxes in diazotrophic unicellular cyanobacterium Cyanothece sp. ATCC 51142.

Vu TT, Stolyar SM, Pinchuk GE, Hill EA, Kucek LA, Brown RN, Lipton MS, Osterman A, Fredrickson JK, Konopka AE, Beliaev AS, Reed JL.

PLoS Comput Biol. 2012;8(4):e1002460. doi: 10.1371/journal.pcbi.1002460. Epub 2012 Apr 5.

23.

Pyruvate and lactate metabolism by Shewanella oneidensis MR-1 under fermentation, oxygen limitation, and fumarate respiration conditions.

Pinchuk GE, Geydebrekht OV, Hill EA, Reed JL, Konopka AE, Beliaev AS, Fredrickson JK.

Appl Environ Microbiol. 2011 Dec;77(23):8234-40. doi: 10.1128/AEM.05382-11. Epub 2011 Sep 30.

24.

Structure of a bacterial cell surface decaheme electron conduit.

Clarke TA, Edwards MJ, Gates AJ, Hall A, White GF, Bradley J, Reardon CL, Shi L, Beliaev AS, Marshall MJ, Wang Z, Watmough NJ, Fredrickson JK, Zachara JM, Butt JN, Richardson DJ.

Proc Natl Acad Sci U S A. 2011 Jun 7;108(23):9384-9. doi: 10.1073/pnas.1017200108. Epub 2011 May 23.

25.

Constraint-based model of Shewanella oneidensis MR-1 metabolism: a tool for data analysis and hypothesis generation.

Pinchuk GE, Hill EA, Geydebrekht OV, De Ingeniis J, Zhang X, Osterman A, Scott JH, Reed SB, Romine MF, Konopka AE, Beliaev AS, Fredrickson JK, Reed JL.

PLoS Comput Biol. 2010 Jun 24;6(6):e1000822. doi: 10.1371/journal.pcbi.1000822.

26.

Characterization of an electron conduit between bacteria and the extracellular environment.

Hartshorne RS, Reardon CL, Ross D, Nuester J, Clarke TA, Gates AJ, Mills PC, Fredrickson JK, Zachara JM, Shi L, Beliaev AS, Marshall MJ, Tien M, Brantley S, Butt JN, Richardson DJ.

Proc Natl Acad Sci U S A. 2009 Dec 29;106(52):22169-74. doi: 10.1073/pnas.0900086106. Epub 2009 Dec 17.

27.

Role of outer-membrane cytochromes MtrC and OmcA in the biomineralization of ferrihydrite by Shewanella oneidensis MR-1.

Reardon CL, Dohnalkova AC, Nachimuthu P, Kennedy DW, Saffarini DA, Arey BW, Shi L, Wang Z, Moore D, McLean JS, Moyles D, Marshall MJ, Zachara JM, Fredrickson JK, Beliaev AS.

Geobiology. 2010 Jan;8(1):56-68. doi: 10.1111/j.1472-4669.2009.00226.x. Epub 2009 Nov 25.

PMID:
20002197
28.

The role of 4-hydroxyphenylpyruvate dioxygenase in enhancement of solid-phase electron transfer by Shewanella oneidensis MR-1.

Turick CE, Beliaev AS, Zakrajsek BA, Reardon CL, Lowy DA, Poppy TE, Maloney A, Ekechukwu AA.

FEMS Microbiol Ecol. 2009 May;68(2):223-5. doi: 10.1111/j.1574-6941.2009.00670.x.

29.

Involvement of a membrane-bound class III adenylate cyclase in regulation of anaerobic respiration in Shewanella oneidensis MR-1.

Charania MA, Brockman KL, Zhang Y, Banerjee A, Pinchuk GE, Fredrickson JK, Beliaev AS, Saffarini DA.

J Bacteriol. 2009 Jul;191(13):4298-306. doi: 10.1128/JB.01829-08. Epub 2009 Apr 24.

30.

Genomic reconstruction of Shewanella oneidensis MR-1 metabolism reveals a previously uncharacterized machinery for lactate utilization.

Pinchuk GE, Rodionov DA, Yang C, Li X, Osterman AL, Dervyn E, Geydebrekht OV, Reed SB, Romine MF, Collart FR, Scott JH, Fredrickson JK, Beliaev AS.

Proc Natl Acad Sci U S A. 2009 Feb 24;106(8):2874-9. doi: 10.1073/pnas.0806798106. Epub 2009 Feb 5.

31.

Electron donor-dependent radionuclide reduction and nanoparticle formation by Anaeromyxobacter dehalogenans strain 2CP-C.

Marshall MJ, Dohnalkova AC, Kennedy DW, Plymale AE, Thomas SH, Löffler FE, Sanford RA, Zachara JM, Fredrickson JK, Beliaev AS.

Environ Microbiol. 2009 Feb;11(2):534-43. doi: 10.1111/j.1462-2920.2008.01795.x.

PMID:
19196283
32.

Towards environmental systems biology of Shewanella.

Fredrickson JK, Romine MF, Beliaev AS, Auchtung JM, Driscoll ME, Gardner TS, Nealson KH, Osterman AL, Pinchuk G, Reed JL, Rodionov DA, Rodrigues JL, Saffarini DA, Serres MH, Spormann AM, Zhulin IB, Tiedje JM.

Nat Rev Microbiol. 2008 Aug;6(8):592-603. doi: 10.1038/nrmicro1947. Epub 2008 Jul 7. Review.

PMID:
18604222
33.

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.

PMID:
18546496
34.

Direct involvement of type II secretion system in extracellular translocation of Shewanella oneidensis outer membrane cytochromes MtrC and OmcA.

Shi L, Deng S, Marshall MJ, Wang Z, Kennedy DW, Dohnalkova AC, Mottaz HM, Hill EA, Gorby YA, Beliaev AS, Richardson DJ, Zachara JM, Fredrickson JK.

J Bacteriol. 2008 Aug;190(15):5512-6. doi: 10.1128/JB.00514-08. Epub 2008 May 23.

35.

Oxygen-dependent autoaggregation in Shewanella oneidensis MR-1.

McLean JS, Pinchuk GE, Geydebrekht OV, Bilskis CL, Zakrajsek BA, Hill EA, Saffarini DA, Romine MF, Gorby YA, Fredrickson JK, Beliaev AS.

Environ Microbiol. 2008 Jul;10(7):1861-76. doi: 10.1111/j.1462-2920.2008.01608.x. Epub 2008 Apr 10.

PMID:
18412550
36.

Utilization of DNA as a sole source of phosphorus, carbon, and energy by Shewanella spp.: ecological and physiological implications for dissimilatory metal reduction.

Pinchuk GE, Ammons C, Culley DE, Li SM, McLean JS, Romine MF, Nealson KH, Fredrickson JK, Beliaev AS.

Appl Environ Microbiol. 2008 Feb;74(4):1198-208. Epub 2007 Dec 21.

37.

Hydrogenase- and outer membrane c-type cytochrome-facilitated reduction of technetium(VII) by Shewanella oneidensis MR-1.

Marshall MJ, Plymale AE, Kennedy DW, Shi L, Wang Z, Reed SB, Dohnalkova AC, Simonson CJ, Liu C, Saffarini DA, Romine MF, Zachara JM, Beliaev AS, Fredrickson JK.

Environ Microbiol. 2008 Jan;10(1):125-36. Epub 2007 Sep 18.

PMID:
17888007
38.

Current production and metal oxide reduction by Shewanella oneidensis MR-1 wild type and mutants.

Bretschger O, Obraztsova A, Sturm CA, Chang IS, Gorby YA, Reed SB, Culley DE, Reardon CL, Barua S, Romine MF, Zhou J, Beliaev AS, Bouhenni R, Saffarini D, Mansfeld F, Kim BH, Fredrickson JK, Nealson KH.

Appl Environ Microbiol. 2007 Nov;73(21):7003-12. Epub 2007 Jul 20. Erratum in: Appl Environ Microbiol. 2008 Jan;74(2):553.

39.
40.

c-Type cytochrome-dependent formation of U(IV) nanoparticles by Shewanella oneidensis.

Marshall MJ, Beliaev AS, Dohnalkova AC, Kennedy DW, Shi L, Wang Z, Boyanov MI, Lai B, Kemner KM, McLean JS, Reed SB, Culley DE, Bailey VL, Simonson CJ, Saffarini DA, Romine MF, Zachara JM, Fredrickson JK.

PLoS Biol. 2006 Sep;4(9):e268.

41.

Isolation of a high-affinity functional protein complex between OmcA and MtrC: Two outer membrane decaheme c-type cytochromes of Shewanella oneidensis MR-1.

Shi L, Chen B, Wang Z, Elias DA, Mayer MU, Gorby YA, Ni S, Lower BH, Kennedy DW, Wunschel DS, Mottaz HM, Marshall MJ, Hill EA, Beliaev AS, Zachara JM, Fredrickson JK, Squier TC.

J Bacteriol. 2006 Jul;188(13):4705-14.

42.

Global transcriptome analysis of Shewanella oneidensis MR-1 exposed to different terminal electron acceptors.

Beliaev AS, Klingeman DM, Klappenbach JA, Wu L, Romine MF, Tiedje JM, Nealson KH, Fredrickson JK, Zhou J.

J Bacteriol. 2005 Oct;187(20):7138-45.

43.

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.

44.

Transcriptome dynamics of Deinococcus radiodurans recovering from ionizing radiation.

Liu Y, Zhou J, Omelchenko MV, Beliaev AS, Venkateswaran A, Stair J, Wu L, Thompson DK, Xu D, Rogozin IB, Gaidamakova EK, Zhai M, Makarova KS, Koonin EV, Daly MJ.

Proc Natl Acad Sci U S A. 2003 Apr 1;100(7):4191-6. Epub 2003 Mar 21.

45.

Microarray transcription profiling of a Shewanella oneidensis etrA mutant.

Beliaev AS, Thompson DK, Fields MW, Wu L, Lies DP, Nealson KH, Zhou J.

J Bacteriol. 2002 Aug;184(16):4612-6.

46.

Gene and protein expression profiles of Shewanella oneidensis during anaerobic growth with different electron acceptors.

Beliaev AS, Thompson DK, Khare T, Lim H, Brandt CC, Li G, Murray AE, Heidelberg JF, Giometti CS, Yates J 3rd, Nealson KH, Tiedje JM, Zhoui J.

OMICS. 2002;6(1):39-60. Erratum in: OMICS. 2003 Spring;7(1):138-9.

PMID:
11881834
47.
48.

Transcriptional and proteomic analysis of a ferric uptake regulator (fur) mutant of Shewanella oneidensis: possible involvement of fur in energy metabolism, transcriptional regulation, and oxidative stress.

Thompson DK, Beliaev AS, Giometti CS, Tollaksen SL, Khare T, Lies DP, Nealson KH, Lim H, Yates J 3rd, Brandt CC, Tiedje JM, Zhou J.

Appl Environ Microbiol. 2002 Feb;68(2):881-92.

49.

MtrC, an outer membrane decahaem c cytochrome required for metal reduction in Shewanella putrefaciens MR-1.

Beliaev AS, Saffarini DA, McLaughlin JL, Hunnicutt D.

Mol Microbiol. 2001 Feb;39(3):722-30.

50.

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