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Building Predictive Models of Genetic Circuits Using the Principle of Maximum Caliber.

Firman T, Balázsi G, Ghosh K.

Biophys J. 2017 Nov 7;113(9):2121-2130. doi: 10.1016/j.bpj.2017.08.057.


Late-Arriving Signals Contribute Less to Cell-Fate Decisions.

Cortes MG, Trinh JT, Zeng L, Balázsi G.

Biophys J. 2017 Nov 7;113(9):2110-2120. doi: 10.1016/j.bpj.2017.09.012.


Correction: Phenotypic heterogeneity promotes adaptive evolution.

Bódi Z, Farkas Z, Nevozhay D, Kalapis D, Lázár V, Csörgő B, Nyerges Á, Szamecz B, Fekete G, Papp B, Araújo H, Oliveira JL, Moura G, Santos MAS, Székely T Jr, Balázsi G, Pál C.

PLoS Biol. 2017 Jun 20;15(6):e1002607. doi: 10.1371/journal.pbio.1002607. eCollection 2017 Jun.


Generational distribution of a Candida glabrata population: Resilient old cells prevail, while younger cells dominate in the vulnerable host.

Bouklas T, Alonso-Crisóstomo L, Székely T Jr, Diago-Navarro E, Orner EP, Smith K, Munshi MA, Del Poeta M, Balázsi G, Fries BC.

PLoS Pathog. 2017 May 10;13(5):e1006355. doi: 10.1371/journal.ppat.1006355. eCollection 2017 May.


Phenotypic heterogeneity promotes adaptive evolution.

Bódi Z, Farkas Z, Nevozhay D, Kalapis D, Lázár V, Csörgő B, Nyerges Á, Szamecz B, Fekete G, Papp B, Araújo H, Oliveira JL, Moura G, Santos MAS, Székely T Jr, Balázsi G, Pál C.

PLoS Biol. 2017 May 9;15(5):e2000644. doi: 10.1371/journal.pbio.2000644. eCollection 2017 May. Erratum in: PLoS Biol. 2017 Jun 20;15(6):e1002607.


Cell fate decisions emerge as phages cooperate or compete inside their host.

Trinh JT, Székely T, Shao Q, Balázsi G, Zeng L.

Nat Commun. 2017 Feb 6;8:14341. doi: 10.1038/ncomms14341.


Lysis-lysogeny coexistence: prophage integration during lytic development.

Shao Q, Trinh JT, McIntosh CS, Christenson B, Balázsi G, Zeng L.

Microbiologyopen. 2017 Feb;6(1). doi: 10.1002/mbo3.395. Epub 2016 Aug 17.


Frequency-dependent selection: a diversifying force in microbial populations.

Charlebois DA, Balázsi G.

Mol Syst Biol. 2016 Aug 3;12(8):880. doi: 10.15252/msb.20167133. No abstract available.


Efflux Pump Control Alters Synthetic Gene Circuit Function.

Diao J, Charlebois DA, Nevozhay D, Bódi Z, Pál C, Balázsi G.

ACS Synth Biol. 2016 Jul 15;5(7):619-31. doi: 10.1021/acssynbio.5b00154. Epub 2016 May 4.


Reconstruction and topological characterization of the sigma factor regulatory network of Mycobacterium tuberculosis.

Chauhan R, Ravi J, Datta P, Chen T, Schnappinger D, Bassler KE, Balázsi G, Gennaro ML.

Nat Commun. 2016 Mar 31;7:11062. doi: 10.1038/ncomms11062.


Cellular Growth Arrest and Persistence from Enzyme Saturation.

Ray JC, Wickersheim ML, Jalihal AP, Adeshina YO, Cooper TF, Balázsi G.

PLoS Comput Biol. 2016 Mar 24;12(3):e1004825. doi: 10.1371/journal.pcbi.1004825. eCollection 2016 Mar.


Optimality and adaptation of phenotypically switching cells in fluctuating environments.

Belete MK, Balázsi G.

Phys Rev E Stat Nonlin Soft Matter Phys. 2015 Dec;92(6):062716. doi: 10.1103/PhysRevE.92.062716. Epub 2015 Dec 31.


Stress-response balance drives the evolution of a network module and its host genome.

González C, Ray JC, Manhart M, Adams RM, Nevozhay D, Morozov AV, Balázsi G.

Mol Syst Biol. 2015 Aug 31;11(8):827. doi: 10.15252/msb.20156185.


Two-dimensionality of yeast colony expansion accompanied by pattern formation.

Chen L, Noorbakhsh J, Adams RM, Samaniego-Evans J, Agollah G, Nevozhay D, Kuzdzal-Fick J, Mehta P, Balázsi G.

PLoS Comput Biol. 2014 Dec 11;10(12):e1003979. doi: 10.1371/journal.pcbi.1003979. eCollection 2014 Dec.


Coherent feedforward transcriptional regulatory motifs enhance drug resistance.

Charlebois DA, Balázsi G, Kærn M.

Phys Rev E Stat Nonlin Soft Matter Phys. 2014 May;89(5):052708. Epub 2014 May 14.


Unraveling the regulatory connections between two controllers of breast cancer cell fate.

Lee J, Tiwari A, Shum V, Mills GB, Mancini MA, Igoshin OA, Balázsi G.

Nucleic Acids Res. 2014 Jun;42(11):6839-49. doi: 10.1093/nar/gku360. Epub 2014 May 3.


Network of mutually repressive metastasis regulators can promote cell heterogeneity and metastatic transitions.

Lee J, Lee J, Farquhar KS, Yun J, Frankenberger CA, Bevilacqua E, Yeung K, Kim EJ, Balázsi G, Rosner MR.

Proc Natl Acad Sci U S A. 2014 Jan 21;111(3):E364-73. doi: 10.1073/pnas.1304840111. Epub 2014 Jan 6.


Transferring a synthetic gene circuit from yeast to mammalian cells.

Nevozhay D, Zal T, Balázsi G.

Nat Commun. 2013;4:1451. doi: 10.1038/ncomms2471.


Genome-wide discovery of small RNAs in Mycobacterium tuberculosis.

Miotto P, Forti F, Ambrosi A, Pellin D, Veiga DF, Balazsi G, Gennaro ML, Di Serio C, Ghisotti D, Cirillo DM.

PLoS One. 2012;7(12):e51950. doi: 10.1371/journal.pone.0051950. Epub 2012 Dec 19.


Abortive autophagy induces endoplasmic reticulum stress and cell death in cancer cells.

Claerhout S, Dutta B, Bossuyt W, Zhang F, Nguyen-Charles C, Dennison JB, Yu Q, Yu S, Balázsi G, Lu Y, Mills GB.

PLoS One. 2012;7(6):e39400. doi: 10.1371/journal.pone.0039400. Epub 2012 Jun 26.


Linking the transcriptional profiles and the physiological states of Mycobacterium tuberculosis during an extended intracellular infection.

Rohde KH, Veiga DF, Caldwell S, Balázsi G, Russell DG.

PLoS Pathog. 2012;8(6):e1002769. doi: 10.1371/journal.ppat.1002769. Epub 2012 Jun 21.


Mapping the environmental fitness landscape of a synthetic gene circuit.

Nevozhay D, Adams RM, Van Itallie E, Bennett MR, Balázsi G.

PLoS Comput Biol. 2012;8(4):e1002480. doi: 10.1371/journal.pcbi.1002480. Epub 2012 Apr 12.


A network-based, integrative study to identify core biological pathways that drive breast cancer clinical subtypes.

Dutta B, Pusztai L, Qi Y, André F, Lazar V, Bianchini G, Ueno N, Agarwal R, Wang B, Shiang CY, Hortobagyi GN, Mills GB, Symmans WF, Balázsi G.

Br J Cancer. 2012 Mar 13;106(6):1107-16. doi: 10.1038/bjc.2011.584. Epub 2012 Feb 16.


Adaptive evolution of the lactose utilization network in experimentally evolved populations of Escherichia coli.

Quan S, Ray JC, Kwota Z, Duong T, Balázsi G, Cooper TF, Monds RD.

PLoS Genet. 2012 Jan;8(1):e1002444. doi: 10.1371/journal.pgen.1002444. Epub 2012 Jan 12.


A common repressor pool results in indeterminacy of extrinsic noise.

Stamatakis M, Adams RM, Balázsi G.

Chaos. 2011 Dec;21(4):047523. doi: 10.1063/1.3658618.


Kinome siRNA-phosphoproteomic screen identifies networks regulating AKT signaling.

Lu Y, Muller M, Smith D, Dutta B, Komurov K, Iadevaia S, Ruths D, Tseng JT, Yu S, Yu Q, Nakhleh L, Balazsi G, Donnelly J, Schurdak M, Morgan-Lappe S, Fesik S, Ram PT, Mills GB.

Oncogene. 2011 Nov 10;30(45):4567-77. doi: 10.1038/onc.2011.164. Epub 2011 Jun 13.


Linearizer gene circuits with negative feedback regulation.

Nevozhay D, Adams RM, Balázsi G.

Methods Mol Biol. 2011;734:81-100. doi: 10.1007/978-1-61779-086-7_5.


Cellular decision making and biological noise: from microbes to mammals.

Balázsi G, van Oudenaarden A, Collins JJ.

Cell. 2011 Mar 18;144(6):910-25. doi: 10.1016/j.cell.2011.01.030. Review.


Regulation of central metabolism genes of Mycobacterium tuberculosis by parallel feed-forward loops controlled by sigma factor E (σ(E)).

Datta P, Shi L, Bibi N, Balázsi G, Gennaro ML.

J Bacteriol. 2011 Mar;193(5):1154-60. doi: 10.1128/JB.00459-10. Epub 2010 Dec 30.


Network reconstruction reveals new links between aging and calorie restriction in yeast.

Balázsi G.

HFSP J. 2010 Jun;4(3-4):94-9. doi: 10.2976/1.3366829. Epub 2010 Apr 6.


The interplay of multiple feedback loops with post-translational kinetics results in bistability of mycobacterial stress response.

Tiwari A, Balázsi G, Gennaro ML, Igoshin OA.

Phys Biol. 2010 Aug 23;7(3):036005. doi: 10.1088/1478-3975/7/3/036005.


Tuning and controlling gene expression noise in synthetic gene networks.

Murphy KF, Adams RM, Wang X, Balázsi G, Collins JJ.

Nucleic Acids Res. 2010 May;38(8):2712-26. doi: 10.1093/nar/gkq091. Epub 2010 Mar 8.


Network inference and network response identification: moving genome-scale data to the next level of biological discovery.

Veiga DF, Dutta B, Balázsi G.

Mol Biosyst. 2010 Mar;6(3):469-80. doi: 10.1039/b916989j. Epub 2009 Dec 11. Review.


Adaptive-control model for neutrophil orientation in the direction of chemical gradients.

Irimia D, Balázsi G, Agrawal N, Toner M.

Biophys J. 2009 May 20;96(10):3897-916. doi: 10.1016/j.bpj.2008.12.3967.


Negative autoregulation linearizes the dose-response and suppresses the heterogeneity of gene expression.

Nevozhay D, Adams RM, Murphy KF, Josic K, Balázsi G.

Proc Natl Acad Sci U S A. 2009 Mar 31;106(13):5123-8. doi: 10.1073/pnas.0809901106. Epub 2009 Mar 11.


The temporal response of the Mycobacterium tuberculosis gene regulatory network during growth arrest.

Balázsi G, Heath AP, Shi L, Gennaro ML.

Mol Syst Biol. 2008;4:225. doi: 10.1038/msb.2008.63. Epub 2008 Nov 4.


Statistical evaluation of genetic footprinting data.

Balázsi G.

Methods Mol Biol. 2008;416:355-9. doi: 10.1007/978-1-59745-321-9_23.


A semi-supervised method for predicting transcription factor-gene interactions in Escherichia coli.

Ernst J, Beg QK, Kay KA, Balázsi G, Oltvai ZN, Bar-Joseph Z.

PLoS Comput Biol. 2008 Mar 28;4(3):e1000044. doi: 10.1371/journal.pcbi.1000044.


Combinatorial promoter design for engineering noisy gene expression.

Murphy KF, Balázsi G, Collins JJ.

Proc Natl Acad Sci U S A. 2007 Jul 31;104(31):12726-31. Epub 2007 Jul 24.


Planktonic copepods reacting selectively to hydrodynamic disturbances.

Strickler JR, Balázsi G.

Philos Trans R Soc Lond B Biol Sci. 2007 Nov 29;362(1487):1947-58.


Taking the inventory inside single cells.

Balázsi G, Collins JJ.

Nat Chem Biol. 2007 Mar;3(3):141-2. No abstract available.


Phenotypic consequences of promoter-mediated transcriptional noise.

Blake WJ, Balázsi G, Kohanski MA, Isaacs FJ, Murphy KF, Kuang Y, Cantor CR, Walt DR, Collins JJ.

Mol Cell. 2006 Dec 28;24(6):853-65.


Topological units of environmental signal processing in the transcriptional regulatory network of Escherichia coli.

Balázsi G, Barabási AL, Oltvai ZN.

Proc Natl Acad Sci U S A. 2005 May 31;102(22):7841-6. Epub 2005 May 20.


Sensing your surroundings: how transcription-regulatory networks of the cell discern environmental signals.

Balázsi G, Oltvai ZN.

Sci STKE. 2005 May 3;2005(282):pe20. Review.


Genome-scale identification of conditionally essential genes in E. coli by DNA microarrays.

Tong X, Campbell JW, Balázsi G, Kay KA, Wanner BL, Gerdes SY, Oltvai ZN.

Biochem Biophys Res Commun. 2004 Sep 10;322(1):347-54.


Experimental determination and system level analysis of essential genes in Escherichia coli MG1655.

Gerdes SY, Scholle MD, Campbell JW, Balázsi G, Ravasz E, Daugherty MD, Somera AL, Kyrpides NC, Anderson I, Gelfand MS, Bhattacharya A, Kapatral V, D'Souza M, Baev MV, Grechkin Y, Mseeh F, Fonstein MY, Overbeek R, Barabási AL, Oltvai ZN, Osterman AL.

J Bacteriol. 2003 Oct;185(19):5673-84.


Spurious spatial periodicity of co-expression in microarray data due to printing design.

Balázsi G, Kay KA, Barabási AL, Oltvai ZN.

Nucleic Acids Res. 2003 Aug 1;31(15):4425-33.


Spatiotemporal stochastic resonance and its consequences in neural model systems.

Balazsi G, Kish LB, Moss FE.

Chaos. 2001 Sep;11(3):563-569.


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