Purdue University

Mugler Group




39. S. Fancher and A. Mugler. Diffusion vs. direct transport in the precision of morphogen readout. arXiv:1806.08318. [preprint]

38. A. Erez*, T. A. Byrd*, R. M. Vogel, G. Altan-Bonnet, and A. Mugler (*equal contributors). Universality of biochemical feedback and its application to immune cells. arXiv:1703.04194. [preprint]



37. J. W. Larkin, X. Zhai, K. Kikuchi, S. Redford, A. Prindle, J. Liu, S. Greenfield, A. M. Walczak, J. Garcia-Ojalvo, A. Mugler, and G. M. Süel. Signal percolation within a bacterial community. Cell Systems 7(2):137-145, 2018. [paper] [press release] [journal cover]

36. A. Mugler and S. Fancher. Stochastic modeling of gene expression, protein modification, and polymerization. Quantitative Biology: Theory, Computational Methods, and Models, Ch. 28, p. 563-580, 2018. [book] [preprint]

35. S. GuptaJ. Varennes, H. C. Korswagen, and A. Mugler. Temporal precision of regulated gene expression. PLoS Computational Biology 14(6):e1006201, 2018. [paper] [preprint]

34. A. Erez, R. Vogel, A. Mugler, A. Belmonte, and G. Altan-Bonnet. Modeling of cytometry data in logarithmic space: When is a bimodal distribution not bimodal? Cytometry A 93(6):611-619, 2018. [paper] [preprint]



33. J. VarennesS. Fancher, B. Han, and A. Mugler. Emergent versus individual-based multicellular chemotaxis. Physical Review Letters 119:188101, 2017. [paper] [press release] [preprint]

32. X. Shao, A. Mugler, J. Kim, H. J. Jeong, B. Levin, and I. Nemenman. Growth of bacteria in 3-d colonies. PLoS Computational Biology 13(7):e1005679, 2017. [paper] [preprint]

31. G. D. Potter, T. A. ByrdA. Mugler, and B. Sun. Dynamic sampling and information encoding in biochemical networks. Biophysical Journal 112(4):795–804, 2017. [paper] [preprint]

30. S. Fancher and A. Mugler. Fundamental limits to collective concentration sensing in cell populations. Physical Review Letters (Editor's Suggestion) 118:078101, 2017. [paper] [synopsis] [press release] [preprint]



29. G. D. Potter*, T. A. Byrd*, A. Mugler, and B. Sun (*equal contributors). Communication shapes sensory response in multicellular networks. Proceedings of the National Academy of Sciences, USA, 113(37):10334–10339, 2016. [paper] [preprint]

28. J. Varennes, B. Han, and A. Mugler. Collective chemotaxis through noisy multicellular gradient sensing. Biophysical Journal 111(3):640-649, 2016. [paper] [video] [preprint]

27. T. Smith*, S. Fancher*, A. Levchenko, I. Nemenman, and A. Mugler (*equal contributors). Role of spatial averaging in multicellular gradient sensing. Physical Biology 13(3):035004, 2016. [paper] [preprint]

26. E. Roob III*, N. Trendel*, P. R. ten Wolde, and A. Mugler (*equal contributors). Cooperative clustering digitizes biochemical signaling and enhances its fidelity. Biophysical Journal 110(7):1661-1669, 2016. [paper] [preprint]

25. A. Mugler*, M. Kittisopikul*, L. Hayden, J. Liu, C. H. Wiggins, G. M. Suel, and A. M. Walczak (*equal contributors). Noise expands the response range of the Bacillus subtilis competence circuit. PLoS Computational Biology 12(3):e1004793, 2016. [paper] [preprint]

24. J. Varennes and A. Mugler. Sense and sensitivity: physical limits to multicellular sensing, migration and drug response. Molecular Pharmaceutics 13(7):2224–2232, 2016. [paper] [preprint]

23. A. Mugler, A. Levchenko, and I. Nemenman. Limits to the precision of gradient sensing with spatial communication and temporal integration. Proceedings of the National Academy of Sciences, USA, 13(6):E689-E695, 2016. [paper] [commentary] [press release] [preprint]

22. D. Ellison*, A. Mugler*, M. Brennan*, S. H. Lee, R. Huebner, E. Shamir, L. A. Woo, J. Kim, P. Amar, I. Nemenman, A. J. Ewald, and A. Levchenko (*equal contributors). Cell-cell communication enhances the capacity of cell ensembles to sense shallow gradients during morphogenesis. Proceedings of the National Academy of Sciences, USA, 13(6):E679-E688, 2016. [paper] [commentary] [press release] [preprint]

21. P. R. ten Wolde, N. B. Becker, T. E. Ouldridge, and A. Mugler. Fundamental limits to cellular sensing. Journal of Statistical Physics, 162:1395-1424, 2016. [paper] [preprint]

20. K. Yehl, A. Mugler, S. Vivek, Y. Liu, Y. Zhang, M. Fan, E. R. Weeks, and K. Salaita. High-speed DNA-based rolling motors powered by RNase H. Nature Nanotechnology, 11:184-190, 2016. [paper] [press release]



19. N. B. Becker, A. Mugler, and P. R. ten Wolde. Optimal prediction by cellular signaling networks. Physical Review Letters, 115:258103, 2015. [paper] [preprint]



18. M. Wehrens, P. R. ten Wolde, and A. Mugler. Positive feedback can lead to dynamic nanometer-scale clustering on cell membranes. Journal of Chemical Physics, 141:205102, 2014. [paper] [preprint]

17. A. Mugler, S. J. Tans, and A. Mashaghi. Circuit topology of self-interacting chains: implications for folding and unfolding dynamics. Physical Chemistry Chemical Physics, 16(41):22537-22544, 2014. [paper]

16. P. R. ten Wolde and A. Mugler. Importance of crowding in signaling, genetic, and metabolic networks. International Review of Cell and Molecular Biology, 307:419-442, 2014. [paper] [preprint]



15. A. Mugler, F. Tostevin, and P. R. ten Wolde. Spatial partitioning enhances the reliability of biochemical signaling. Proceedings of the National Academy of Sciences, USA, 110(15):5927-5932, 2013. [paper] [preprint]

14. A. Mugler and P. R. ten Wolde. The macroscopic effects of microscopic heterogeneity in cell signaling. Advances in Chemical Physics, 153:373-396, 2013. [paper] [preprint]



13. W. de Ronde, P. R. ten Wolde, and A. Mugler. Protein logic: a statistical mechanical study of signal integration at the single-molecule level. Biophysical Journal, 103(5):1097-1107, 2012. [paper] [preprint]

12. A. Mugler, A. G. Bailey, K. Takahashi, and P. R. ten Wolde. Membrane clustering and the role of rebinding in biochemical signaling. Biophysical Journal, 102(5):1069-1078, 2012. [paper] [preprint]

11. A. M. Walczak, A. Mugler, and C. H. Wiggins. Analytic methods for modeling stochastic regulatory networks. Methods in Molecular Biology, 880:273-322, 2012. [paper] [preprint]



10. A. Mugler, B. Grinshpun, R. Franks, and C. H. Wiggins. Statistical method for revealing form-function relations in biological networks. Proceedings of the National Academy of Sciences, USA, 108(2):446-451, 2011. [paper] [preprint]



9. A. Mugler, A. M. Walczak, and C. H. Wiggins. Information-optimal transcriptional response to oscillatory driving. Physical Review Letters, 105:058101, 2010. [paper] [preprint]

8. R. Ginoza and A. Mugler. Network motifs come in sets: correlations in the randomization process. Physical Review E, 82:011921, 2010. [paper] [preprint]



7. A. Mugler, A. M. Walczak, and C. H. Wiggins. Spectral solutions to stochastic models of gene expression with bursts and regulation. Physical Review E, 80:041921, 2009. [paper] [preprint]

6. W. H. de Ronde*, B. C. Daniels*, A. Mugler*, N. A. Sinitsyn, and I. Nemenman (*equal contributors). Mesoscopic statistical properties of multistep enzyme-mediated reactions. IET Systems Biology, 3(5):429-437, 2009. [paper] [preprint]

5. A. Mugler, E. Ziv, I. Nemenman, and C. H. Wiggins. Quantifying evolvability in small biological networks. IET Systems Biology, 3(5):379-387, 2009. [paper] [preprint]

4. A. M. Walczak, A. Mugler, and C. H. Wiggins. A stochastic spectral analysis of transcriptional regulatory cascades. Proceedings of the National Academy of Sciences, USA, 106(16):6529-6534, 2009. [paper] [preprint]



3. A. Mugler, E. Ziv, I. Nemenman, and C. H. Wiggins. Serially-regulated biological networks fully realise a constrained set of functions. IET Systems Biology, 2(5):313-322, 2008. [paper] [preprint]



2. T. D. Donnelly, J. Hogan, A. Mugler, M. Schubmehl, N. Schommer, A. J. Bernoff, S. Dasnurkar, and T. Ditmire. Using ultrasonic atomization to produce an aerosol of micron-scale particles. Review of Scientific Instruments, 76:113301, 2005. [paper]



1. T. D. Donnelly, J. Hogan, A. Mugler, N. Schommer, M. Schubmehl, A. J. Bernoff, and B. Forrest. An experimental study of micron-scale droplet aerosols produced via ultrasonic atomization. Physics of Fluids, 16(8):2843, 2004. [paper]