Publications

List of my publications

54. Current-density relation in the exclusion process with dynamic obstacles, J Szavits-Nossan, B Waclaw, Physical Review E 102, 042117 (2020).

53. A roadblock-and-kill model explains the dynamical response to the DNA-targeting antibiotic ciprofloxacin, N. Ojkic, E. Lilja, S. Direito, A. Dawson, R. J. Allen, B. Waclaw, Antimicrobial Agents and Chemotherapy 64, e02487-19 (2020).

52. Phenotypic delay in the evolution of bacterial antibiotic resistance: mechanistic models and their implications, M Carballo-Pacheco, MD Nicholson, EE Lilja, RJ Allen, B Waclaw, PLOS Computational Biology 16 (5), e1007930 (2020).

51. Absence of MeCP2 binding to non-methylated GT-rich sequences in vivo, J. C. Connelly, J. Cholewa-Waclaw, S. Webb, V. Steccanella, B. Waclaw, A. Bird, Nucleic Acids Research 48 (7), 3542-3552 (2020).

50. Predictable Properties of Fitness Landscapes Induced by Adaptational Tradeoffs, SG Das, SOL Direito, B Waclaw, RJ Allen, J Krug, eLife 9:e55155 (2020).

49. On measuring selection in cancer from subclonal mutation frequencies I. Bozic, C. Paterson, B. Waclaw, PLoS Comput Biol 15(9): e1007368 (2019).

48. Quantitative modelling predicts the impact of DNA methylation on RNA polymerase II traffic, J. Cholewa-Waclaw, R. Shah, S. Webb, K. Chhatbar, B. Ramsahoye, O. Pusch, M. Yu, P. Greulich, B. Waclaw, and A. Bird, bioRxiv:391904,

47. Spatiotemporal regulation of clonogenicity in colorectal cancer xenografts, M. van der Heijden, D. M. Miedema, B. Waclaw, V. L. Veenstra, M. C. Lecca, L. E. Nijman, E. van Dijk, S. M. van Neerven, S. C. Lodestijn, K. J. Lenos, N. E. de Groot, P. R. Prasetyanti, A. Arricibita Varea, D. J. Winton, J. P. Medema, E. Morrissey, B. Ylstra, M. A. Nowak, M. F. Bijlsma, and L. Vermeulen, PNAS (2019).

46. Totally asymmetric exclusion process with site-wise dynamic disorder, B. Waclaw, J. Cholewa-Waclaw, P. Greulich, J. Phys. A: Math. Theor 52, 065002 (2019).

45. Bacterial growth: a statistical physicist’s guide, Rosalind J Allen and Bartlomiej Waclaw, Reports on Progress in Physics 82, 016601 (2018).

44. Reduced adhesion between cells and substrate confers selective advantage in bacterial colonies, C. Watson, P. Hush, J. Williams, A. Dawson, N. Ojkic, S. Titmuss, and B. Waclaw, Europhysics Letters 123, 68001 (2018).

43. Phenotypic switching can speed up biological evolution of microbes, A.C Tadrowski, M.R Evans, and B. Waclaw, Scientific Reports 8, Article number: 8941 (2018).

42. A physics-explicit model of bacterial conjugation shows the stabilizing role of the conjugative junction, J Pastuszak, B Waclaw, arXiv preprint arXiv:1712.01956 (2017).

41. Genes, environment, and “bad luck”, M A Nowak, B Waclaw, Science 355 (6331), 1266-1267 (2017).

40. Mechanical interactions in bacterial colonies and the surfing probability of beneficial mutations, FF Farrell, M Gralka, O Hallatschek, B Waclaw, Journal of The Royal Society Interface 14, 20170073 (2017).

39. An exactly solvable, spatial model of mutation accumulation in cancer, Chay Paterson, Martin A Nowak, Bartlomiej Waclaw, Scientific Reports 6, 39511 (2016).

38. Beyond the Hypercube: Evolutionary Accessibility of Fitness Landscapes with Realistic Mutational Networks, M Zagorski, Z Burda, B Waclaw, PLOS Comp. Biol. 12, e1005218 (2016).

37. Evolution of Drug Resistance in Bacteria, B Waclaw, Biophysics of Infection, 49-67 (2016).

36. Antibiotic resistance: a physicist’s view, R Allen, B Waclaw, Physical Biology 13 (4), 045001 (2016).

35. Allele Surfing Promotes Microbial Adaptation from Standing Variation, M Gralka, F Stiewe, F Farrell, W Moebius, B Waclaw, O Hallatschek, Ecology Letters, doi:10.1111/ele.12625 (2016).

34. A simple non-equilibrium, statistical-physics toy model of thin-film growth, J. K. Ochab, H. Nagel, W. Janke, and B. Waclaw, J. Stat. Mech. (2015) P09013.

33. Condensation in models with factorized and pair-factorized stationary states, M. R. Evans, B. Waclaw, J. Stat. Mech. P09005 (2015).

32. Spatial model predicts dispersal and cell turnover cause reduced intra-tumor heterogeneity
B. Waclaw , I. Bozic , M. E Pittman , R. H Hruban , B. Vogelstein , M. A. Nowak, Nature 525, 261-264 (2015). See also here for a very nice News & Views article by N. Komarova.

31. Lower glycolysis carries a higher flux than any biochemically possible alternative, S. J. Court, B. Waclaw, R. J. Allen, Nature Communications 6 (2015),8427, doi:10.1038/ncomms9427.

30. Condensation in stochastic mass transport models: beyond the zero-range process, M.R. Evans, B Waclaw, Journal of Physics A: Mathematical and Theoretical 47, 095001 (2014).

29. The role of mechanical forces in the planar-to-bulk transition in growing Escherichia coli microcolonies, M.A.A. Grant, B. Waclaw, R.J. Allen, P. Cicuta, J. R. Soc. Interface. 11 (97), 20140400 (2014).

28. An exclusion process on a tree with constant aggregate hopping rate, P. Mottishaw, B. Waclaw, M.R. Evans, J. Phys. A: Math. Theor. 46, 405003 (2013)

27. Mechanically driven growth of quasi-two dimensional microbial colonies, F.D.C. Farrell, O. Hallatschek, D. Marenduzzo, B. Waclaw, Phys. Rev. Lett. 111, 168101 (2013); click here for a synopsis in Physics; and here for a news article in Physics World.

26. Quantum widening of CDT universe,  L. Bogacz , Z. Burda , B. Waclaw,  Phys. Rev. D 86, 104015 (2012)

25. Mutational pathway determines whether drug gradients accelerate evolution of drug-resistant cells,  P. Greulich , B. Waclaw , R. J. Allen,  Phys. Rev. Lett. 109, 088101 (2012); see also a viewpoint article: Bacteria Evolve to Go Against the Grain, O. Hallatschek, Physics 5, 93 (2012).

24. Stochastic Description of a Bistable Frustrated Unit,  A. Garai , B. Waclaw , H. Nagel , H. Meyer-Ortmanns,  J. Stat. Mech. P01009 (2012)

23. Explosive condensation in a mass transport model,  B. Waclaw , M. R. Evans,  Phys. Rev. Lett. 108, 070601 (2012)

22. Random matrices and localization in the quasispecies theory,  B. Waclaw,  Acta Physica Polonica B 42, 1141 (2011)

21. Dynamical phase transition in a model for evolution with migration,  B. Waclaw , R. J. Allen , M. R. Evans,  Phys. Rev. Lett. 105, 268101 (2010)

20. The various facets of random walk entropy,  Z. Burda , J. Duda , J.M. Luck , B. Waclaw,  Acta Phys. Polon. B 41, 949 (2010)

19. Spectrum of the Product of Independent Random Gaussian Matrices,  Z. Burda , R. A. Janik , B. Waclaw,  Phys. Rev. E 81, 041132 (2010)

18. Mass condensation in one dimension with pair-factorized steady states,  B. Waclaw , J. Sopik , W. Janke , H. Meyer-Ortmanns,  J. Stat. Mech. P10021 (2009)

17. Pair-factorized steady states on arbitrary graphs,  B. Waclaw , J. Sopik , W. Janke , H. Meyer-Ortmanns,  J. Phys. A: Math. Theor. 42, 315003 (2009)

16. Tuning the shape of the condensate in spontaneous symmetry breaking,  B. Waclaw , J. Sopik , W. Janke , H. Meyer-Ortmanns,  Phys. Rev. Lett. 103, 080602 (2009)

15. Localization of maximal entropy random walk,  Z. Burda , J. Duda , J. M. Luck , B. Waclaw,  Phys. Rev. Lett. 102, 160602 (2009)

14. Approaching the thermodynamic limit in equilibrated scale-free networks,  B. Waclaw , L.Bogacz , W. Janke,  Phys. Rev. E 78, 061125 (2008)

13. Power laws in zero-range processes on random networks,  B. Waclaw , Z. Burda , W. Janke,  Eur. Phys. J. B 65, 565 (2008)

12. Counting metastable states of Ising spin glasses on arbitrary graphs,  B. Waclaw , Z. Burda,  Phys. Rev. E 77, 041114 (2008)

11. Free zero-range processes on networks,  L. Bogacz , Z. Burda , W. Janke , B. Waclaw,  Proceedings of SPIE – Volume 6601, 66010V (2007)

10. Condensation in zero-range processes on inhomogeneous networks,  B. Waclaw, L. Bogacz, Z. Burda, W. Janke,  Phys. Rev. E 76, 046114 (2007)

9. Balls-in-boxes condensation on networks,  L. Bogacz , Z. Burda , W. Janke , B. Waclaw,  Chaos 17, 026112 (2007)

8. Finite size effects in Barabasi-Albert growing networks,  B. Waclaw , I. M. Sokolov,  Phys. Rev. E 75, 056114 (2007)

7. Spectral properties of empirical covariance matrices for data with power-law tails,  Z. Burda , A. Goerlich , B. Waclaw,  Phys. Rev. E 74, 041129 (2006)

6. Eigenvalue density of empirical covariance matrix for correlated samples,  Z. Burda , J. Jurkiewicz , B. Waclaw,  Acta Phys. Pol. B 36, 2641 (2005)

5. Correlated Wishart Matrices and Critical Horizons,  Z. Burda , A. Goerlich , J. Jurkiewicz , B. Waclaw,  Eur. Phys. J. B 49, 319 (2006)

4. A program generating homogeneous random graphs with given weights,  L. Bogacz , Z. Burda , W. Janke , B. Waclaw,  Comp. Phys. Comm. 173, 162-174 (2005)

3. Causal and homogeneous networks,  P. Bialas , Z. Burda , B. Waclaw,  AIP Conf. Proc. 776, 14 (2005)

2. Homogeneous complex networks,  L. Bogacz , Z. Burda , B. Waclaw,  Physica A, 366, 587 (2006).

1. Spectral Moments of Correlated Wishart Matrices,  Z. Burda , J. Jurkiewicz , B. Waclaw,  Phys. Rev. E 71, 026111 (2005)

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