Research

1.    Azukas J, Krzysztoń R, Helenek C, Carter S, Li XS, Balázsi G, Strey HH, Single-Cell Parameter Inference Reveals Kinetic Heterogeneity in Synthetic Mammalian Gene Expression. Biophys. J. 125(12):3166-3181 (2026).

1.    Panagoda NT, Balázsi G, Sampson NS. Mycobacterium tuberculosis Mce3R TetR-like Repressor Forms an Asymmetric Four-Helix Bundle and Binds a Nonpalindrome Sequence. ACS Chem. Biol. 19(12):2580-2592 (2024).

2.    Wan Y, Helenek C, Coraci D, Balázsi G. Optimizing a CRISPR-Cas13d Gene Circuit for Tunable Target RNA Downregulation with Minimal Collateral RNA Cutting. ACS Synth. Biol. 13 (10), 3212-3230 (2024).

3.    Matsuzaki T, Weistuch C, de GraffA, Dill KA, Balázsi G. Transcriptional drift in aging cells: A global de-controller. Proc. Natl. Acad. Sci. USA 121(30):e2401830121 (2024).

4.    Helenek C, Krzysztoń R, Petreczky J, Wan Y, Cohen J, Cabral M, Coraci D, Balázsi G. Synthetic gene circuit evolution: Insights and opportunities at the mid-scale. Cell Chem. Biol. 31(8):1447-1459 (2024).

5.    Wan Y, Mu Q, Krzysztoń R, Cohen J, Coraci D, Helenek C, Tompkins C, Lin A, Farquhar K, Cross E, Wang J, Balázsi G. Adaptive DNA amplification of synthetic gene circuit opens a way to overcome cancer chemoresistance. Proc. Natl. Acad. Sci. USA 120(49):e2303114120 (2023).

6.    Delamonica B, Balázsi G, Shub M. Cusp bifurcation in a metastatic regulatory network. J. Theor. Biol. 575:111630 (2023).

7.    Wan Y, Cohen J, Szenk M, Farquhar KS, Coraci D, Krzysztoń R, Azukas J, Van Nest N, Smashnov A, Chern Y-J, De Martino D, Nguyen LC, Bien H, Bravo-Cordero JJ, Chan C-H, Rosner MR, Balázsi G. Nonmonotone invasion landscape by noise-aware control of metastasis activator levels. Nature Chem. Biol. 19(7):887-899 (2023).

8.    Torres A, Cockerell S, Phillips M, Balázsi G, Ghosh K. Maximum Caliber can infer quantitative models from coupled stochastic trajectories of gene expression and cell division. Biophys J. 122(13):2623-2635 (2023).

9.    Tshering LF, Luo F, Russ S, Szenk M, Rubel D, Tutuska K, Rail JG, Balázsi G, Shen MM, Talos F. Immune mechanisms shape the clonal landscape during early progression of prostate cancer. Dev. Cell S1534-5807(23)00180-6 (2023).

10.  Balázsi G. New antivirals exploit viral feedback tricks for a cure without resistance. Cell 185(13):2210-2212 (2022).

11.  Guinn L, Lo E, Balázsi G. Drug-dependent growth curve reshaping reveals mechanisms of antifungal resistance in Saccharomyces cerevisiae. Communications Biol. 5(1): 1–13 (2022).

12.  Vogel C, Balázsi G, Löwer A, Jiang C, Schmid AK, Sommer M, Yang L, Münch C, Wang A, Israni-Winger K, Mühlhaus T, Des Marais DL, Oster H, Socolovsky M. What differentiates a stress response from responsiveness in general? Cell Systems 13(3): 195–200 (2022).

13.  Krzysztoń R, Wan Y, Petreczky J, Balázsi G. Gene-circuit therapy on the horizon: Synthetic biology tools for engineered therapeutics. Acta Biochim Pol. 68(3): 377–383 (2021).

14.  Guinn MT, Coraci D, Guinn L, Balázsi G. Reliably Engineering and Controlling Stable Optogenetic Gene Circuits in Mammalian Cells. J Vis Exp. 6(173) (2021).

15.  Cortes MG, Lin Y, Zeng L, Balázsi G. From Bench to Keyboard and Back Again: A Brief History of Lambda Phage Modeling. Annu. Rev. Biophys. 50:117-134 (2021).

16.  Balázsi G. Discovering evolutionary hidden treasures. Nature Comp. Sci. 1:18-19 (2021).

17.  Guinn MT, Wan Y, Levovitz S, Yang D, Rosner MR, Balázsi G. Observation and Control of Gene Expression Noise: Barrier Crossing Analogies Between Drug Resistance and Metastasis. Front. Genet. 11:586726 (2020).

18.  Agozzino L, Balázsi G, Wang J, Dill KA. How Do Cells Adapt? Stories Told in Landscapes. Annu. Rev. Chem. Biomol. Eng. 11:155-182 (2020).

19.  Gama LR, Giovanini G, Balázsi G, Ramos AF. Binary Expression Enhances Reliability of Messaging in Gene Networks. Entropy 22(4):479 (2020).

20.  Szenk M, Yim T, Balázsi G. Multiplexed Gene Expression Tuning with Orthogonal Synthetic Gene Circuits. ACS Synth Biol. 9(4):930-939 (2020). Article Link.

1.    Kheir Gouda M, Manhart M, Balázsi G, Evolutionary regain of lost gene circuit function. Proc. Natl. Acad. Sci. USA 116(50):25162-25171 (2019).

2.    Phillips KN, Widmann S, Lai HY, Nguyen J, Ray JCJ, Balázsi G, Cooper TF, Diversity in lac Operon Regulation among Diverse Escherichia coli Isolates Depends on the Broader Genetic Background but Is Not Explained by Genetic Relatedness. mBio 10(6).pii: e02232-19 (2019).

3.    Cortes MG, Krog J, Balázsi G, Optimality of the spontaneous prophage induction rate. J Theor Biol. 483:110005. (2019).

4.    Kuzdzal-Fick JJ, Chen L, Balázsi G, Disadvantages and benefits of evolved unicellularity versus multicellularity in budding yeast. Ecol Evol. 9(15):8509-8523 (2019).

5.    Guinn MT, Balázsi G, Noise-reducing optogenetic negative-feedback gene circuits in human cells. Nucleic Acids Res. pii: gkz556 (2019).

6.    Farquhar KS, Charlebois DA, Szenk M, Cohen J, Nevozhay D, Balázsi G, Role of network-mediated stochasticity in mammalian drug resistance. Nat Commun. 10(1):2766 (2019).

7.    Zañudo JTG, Guinn MT, Farquhar K, Szenk M, Steinway SN, Balázsi G*, Albert R*, Towards control of cellular decision-making networks in the epithelial-to-mesenchymal transition. Phys Biol. 16(3):031002 (2019). *Co-corr. authors.

8.    Charlebois DA, Balázsi G, Modeling cell population dynamics. In Silico Biol. 13(1-2):21-39 (2019).

9.    Andrews SS, Brent R, Balázsi G, Transferring information without distortion. eLife 7.pii: e41894 (2018).

10.  Charlebois DA, Hauser K, Marshall S, Balázsi G, Multiscale effects of heating and cooling on genes and gene networks. Proc. Natl. Acad. Sci. USA 115(45):E10797-E10806 (2018).

11.  Shao Q, Cortes MG, Trinh JT, Guan J, Balázsi G, Zeng L, Coupling of DNA Replication and Negative Feedback Controls Gene Expression for Cell-Fate Decisions. iScience 6:1-12 (2018).

12.  Li C, Balazsi G, A landscape view on the interplay between EMT and cancer metastasis. npj Syst Biol Appl. 4:34 (2018).

13.  Székely T Jr, Balázsi G, Beyond Promoters: How Genes Tweak Their Own Expression. Trends Genet. 34(10):733-735 (2018).

14.  Charlebois DA, Diao J, Nevozhay D, Balázsi G, Negative Regulation Gene Circuits for Efflux Pump Control. Methods Mol Biol. 1772:25-43 (2018).

15.  Firman T, Balázsi G, Ghosh K, Building Predictive Models of Genetic Circuits Using the Principle of Maximum Caliber. Biophys. J. 113(9):2121-2130 (2017).

16.  Cortes MG, Trinh JT, Zeng L, Balázsi G, Late-arriving signals contribute less to cell-fate decisions. Biophys. J. 113(9):2110-2120 (2017).

17.  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, Phenotypic heterogeneity promotes adaptive evolution. PLoS Biol. 15(5):e2000644 (2017).

18.  Bouklas T, Alonso-Crisóstomo L, Székely T Jr, Diago-Navarro E, Orner EP, Smith K, Munshi MA, Del Poeta M, Balázsi G, Fries BC, Generational distribution of a Candida glabrata population: Resilient old cells prevail, while younger cells dominate in the vulnerable host. PLoS Pathog. 13(5):e1006355 (2017).

19.  Trinh JT, Székely T, Shao Q, Balázsi G, Zeng L, Cell fate decisions emerge as phages cooperate or compete inside their host. Nat. Commun. 8:14341 (2017).

20.  Shao Q, Trinh JT, McIntosh CS, Christenson B, Balázsi G, Zeng L, Lysis-lysogeny coexistence: prophage integration during lytic development. MicrobiologyOpen. 6(1) (2016).

21.  Charlebois DA, Balázsi G, Frequency-dependent selection: a diversifying force in microbial populations. Mol. Syst. Biol. 12(8):880 (2016).

22.  Diao J, Charlebois DA, Nevozhay D, Bódi Z, Pál C, Balázsi G, Efflux Pump Control Alters Synthetic Gene Circuit Function. ACS Synth. Biol. 5(7):619-31 (2016).

23.  Chauhan R, Ravi J, Datta P, Chen T, Schnappinger D, Bassler KE, Balázsi G, Gennaro ML, Reconstruction and topological characterization of the sigma factor regulatory network of Mycobacterium tuberculosis. Nat Commun. 7:11062 (2016).

24.  Ray JC, Wickersheim ML, Jalihal AP, Adeshina YO, Cooper TF, Balázsi G, Cellular Growth Arrest and Persistence from Enzyme Saturation. PLoS Comput. Biol. 12(3):e1004825 (2016).

25.  Belete MK, Balázsi G, Optimality and adaptation of phenotypically switching cells in fluctuating environments. Phys. Rev. E 92(6):062716 (2015).

26.  González C, Ray JCJ, Manhart M, Adams RM, Nevozhay D, Morozov AV, Balázsi G, Stress-response balance drives the evolution of a network module and its host genome. Mol. Syst. Biol. 11(8):827 (2015). Article Link.

1.    Chen L, Noorbakhsh J, Adams RM, Samaniego-Evans J, Agollah J, Nevozhay D, Kuzdzal-Fick J, Mehta P, Balázsi G, Two Dimensionality of Yeast Colony Expansion Accompanied by Pattern Formation. PLoS Comput. Biol. 10(12):e1003979 (2014).

2.    Charlebois DC, Balázsi G, Kaern M, Coherent feedforward transcriptional regulatory motifs enhance drug resistance. Phys. Rev. E 89:052708 (2014).

3.    Lee J, Tiwari A, Shum V, Mills GB, Mancini MA, Igoshin OA*, Balázsi G*, Unraveling the regulatory connections between two controllers of breast cancer cell fate. Nucleic Acids Res. 42(11), 6839-49 (2014). *Co-corr. authors.

4.    Lee J, Lee J, Farquhar KS, Yun J, Frankenberger CA, Bevilacqua E, Yeung K, Kim EJ, Balázsi G*, Rosner MR*, Network of mutually repressive metastasis regulators can promote cell heterogeneity and metastatic transitions. Proc. Natl. Acad. Sci. USA 111(3), E364-373 (2014). *Co-corr. authors.

5.    Nevozhay D, Zal T, Balázsi G, Transferring a synthetic gene circuit from yeast to mammalian cells. Nature Communications 4, 1451 (2013).

6.    Nevozhay D, Adams RM, Van Itallie E, Bennett MR, Balázsi G. Mapping the environmental fitness landscape of a synthetic gene circuit. PLoS Comput. Biol. 8(4):e1002480 (2012).

7.    Quan S, Ray JC, Kwota Z, Duong T, Balázsi G, Cooper TF, Monds RD. Adaptive evolution of the lactose utilization network in experimentally evolved populations of E. coli. PLoS Genet. 8(1):e1002444 (2012).

8.    Miotto P, Forti F, Ambrosi A, Pellin D, Veiga DF, Balázsi G, Gennaro ML, Di Serio C, Ghisotti D, Cirillo DM. Genome-wide discovery of small RNAs in Mycobacterium tuberculosis. PLoS One 7(12):e51950, (2012).

9.    Claerhout S, Dutta B, Bossuyt W, Zhang F, Nguyen-Charles C, Dennison JB, Yu Q, Yu S, Balázsi G, Lu Y, Mills GB. Abortive autophagy induces endoplasmic reticulum stress and cell death in cancer cells. PLoS One 7(6):e39400, (2012).

10.  Rohde KH, Veiga DF, Caldwell S, Balázsi G, Russell DG. Linking the Transcriptional Profiles and the Physiological States of Mycobacterium tuberculosis During an Extended Intracellular Infection”. PLoS Pathogens 8(6):e1002769, (2012).

11.  Quan S, Ray JC, Kwota Z, Duong T, Balázsi G, Cooper TF, Monds RD. Adaptive Evolution of the Lactose Utilization Network in Experimentally Evolved Populations of Escherichia coli. PLoS Genetics 8(1):e1002444, (2012).

12.  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, A network-based, integrative study to identify core biological pathways that drive breast cancer clinical subtypes. Br. J. Cancer 106(6):1107-1116 (2012).

13.  Stamatakis M, Adams RM, Balázsi G. A common repressor pool results in indeterminacy of extrinsic noise. Chaos 21(4):047523 (2011).

14.  Balázsi G, van Oudenaarden A, Collins JJ. Cellular decision making and biological noise: from microbes to mammals. Cell 144(6):910-25 (2011).

15.  Lu Y, Muller M, Smith D, Dutta B, Komurov K, Iadevaia S, Ruths D, Tseng JT, Yu S, Yu Q, Nakhleh L, Balázsi G, Donnelly J, Schurdak M, Morgan-Lappe S, Fesik S, Ram PT, Mills GB. Kinome siRNA-phosphoproteomic screen identifies networks regulating AKT signaling. Oncogene 30(45):4567-77, (2011).

16.  Datta P, Shi L, Bibi N, Balázsi G, Gennaro ML. Regulation of central metabolism genes of Mycobacterium tuberculosis by parallel feed-forward loops controlled by sigma factor E (σE). J. Bacteriology 193(5):1154-60, (2011).

17.  Murphy KF, Adams RM, Wang X, Balázsi G, Collins JJ, Tuning and controlling gene expression noise in synthetic gene networks. Nucleic Acids Res. 38(8), 2712-2726 (2010).

18.  Veiga DF, Dutta B, Balázsi G, Network inference and network response identification: moving genome-scale data to the next level of biological discovery. Mol Biosyst. 6(3) 469-480 (2010).

19.  Tiwari A, Balázsi G, Gennaro ML, Igoshin OA. The interplay of multiple feedback loops with post-translational kinetics results in bistability of mycobacterial stress response. Physical Biology 7(3):036005, (2010).

20.  Balázsi G. Network reconstruction reveals new links between aging and calorie restriction in yeast. Human Frontier Science Program Journal 4(3-4):94-9 (2010). Article Link.

1.    Nevozhay D, Adams R, Murphy KF, Josić K, Balázsi G, Negative autoregulation linearizes the dose-response and suppresses the heterogeneity of gene expression. Proc Natl Acad Sci USA 106(13), 5123-5128 (2009).

2.    Irimia D, Balázsi G, Agrawal N, Toner M. Adaptive-control model for neutrophil orientation in the direction of chemical gradients”. Biophysical Journal 96(10):3897-3916 (2009).

3.    Balázsi G, Heath AP, Shi L, Gennaro ML, The temporal response of the Mycobacterium tuberculosis gene regulatory network during growth arrest. Mol Syst Biol. 4, 225 (2008).

4.    Heath AP, Kavraki LE, Balázsi G, Bipolarity of the Saccharomyces cerevisiae genome. IEEE Proc. 2nd Intl. Conf. Bioinf. Biomed. Eng. (2008).

5.    Balázsi G, Statistical evaluation of genetic footprinting data. Methods Mol Biol. 416, 355-359 (2008).

6.    Ernst J, Beg QK, Kay KA, Balázsi G, Oltvai ZN, Bar-Joseph Z, A semi-supervised method for predicting transcription factor-gene interactions in Escherichia coli. PLoS Comput Biol. 4(3), e1000044 (2008).

7.    Strickler JR, Balázsi G, Planktonic copepods reacting selectively to disturbances. Phil. Trans. R. Soc. B 362(1487), 1947-1958 (2007).

8.    Balázsi G, Oltvai ZN, A pitfall in series of microarrays: the position of probes affects the cross-correlation of gene expression profiles. Methods Mol Biol. 377, 153-162 (2007).

9.    Murphy KF*, Balázsi G*, and Collins JJ, Combinatorial promoter design for engineering noisy gene expression. Proc Natl Acad Sci USA 104(31), 12726-12731 (2007). *equal contribution

10.  Balázsi G, Collins JJ, Taking the inventory inside single cells. Nature Chem. Biol. 3(3), 141‑142 (2007).

11.  Blake WJ, Balázsi G, Kohanski MA, Isaacs FJ, Murphy KF, Kuang Y, Cantor CR, Walt DR, Collins JJ, Phenotypic consequences of promoter-mediated transcriptional noise. Mol. Cell 24(6), 853-865 (2006).

12.  Balázsi G, Barabási AL, Oltvai ZN, Topological units of environmental signal processing in the transcriptional-regulatory network of E. coli, Proc. Nat. Acad. Sci. USA 102(22), 7841‑7846 (2005).

13.  Balázsi G, Oltvai ZN, Sensing Your Surroundings: How Transcription‑Regulatory Networks of the Cell Discern Environmental Signals, Invited Perspective, Sci STKE 2005(282), pe20 (2005). Article Link.

1.    Tong X, Campbell JW, Balázsi G, Kay KA, Wanner BL, Gerdes SY, Oltvai ZN, Genome-scale identification of conditionally essential genes in E. coli by DNA microarrays, Biochem. Biophys. Res. Commun. 322(1), 347‑354 (2004).

2.    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, Mseeh F, Fonstein MY, Overbeek R, Barabási AL, Oltvai ZN, Osterman AL, Experimental Determination and System-Level Analysis of Essential Genes in Escherichia coli MG1655, J. Bacteriology 185(19), 5673-5684 (2003).

3.    Ordemann A, Balázsi G, Moss F, Pattern formation and stochastic motion of the zooplankton Daphnia in a light field, Physica A 325, 260-266 (2003).

4.    Balázsi G, Kay KA, Barabási AL, Oltvai ZN, Spurious spatial periodicity of co-expression in microarray data due to printing design, Nucl. Acids Res. 31(15), 4425‑4433 (2003).

5.    Balázsi G, Cornell-Bell AH, Neiman A, Moss F, Increased phase synchronization of spontaneous calcium oscillations in epileptic human versus normal rat astrocyte cultures, Chaos 13(2), 515-518 (2003).

6.    Ordemann A, Balazsi G, Caspari E, Moss F, Daphnia swarms: from single agent dynamics to collective vortex formation. SPIE's First International Symposium on Fluctuations and Noise, 172-179 (2003).

7.    Karsai I, Balázsi G, Regulation of Construction Behavior of Social Wasps. J. Theor. Biol. 218, 549 (2002).

8.    Balázsi G, Cornell-Bell AH, Neiman A, Moss F, Synchronization of Hyperexcitable Systems with Phase-Repulsive Coupling. Phys. Rev. E 64, 041912 (2001).

9.    Balázsi G, Kish LB, Moss F, Spatiotemporal Stochastic Resonance and its consequences in neural model systems. Chaos 11(3), 563-569 (2001).

10.  Balázsi G, Kish LB, From Stochastic Resonance to Brain Waves. Physics Letters A 265, 304-316 (2000). Article Link.

1.    Dill K, Bromberg S, Kocher CD, Balázsi G, Molecular Driving Forces. Third Edition, MIT Press (2026).