Publications of Nicolas Buchler    :chronological  alphabetical  combined  bibtex listing:


Papers Published

  1. Hendler, A; Medina, EM; Buchler, NE; de Bruin, RAM; Aharoni, A, The evolution of a G1/S transcriptional network in yeasts., Current Genetics, vol. 64 no. 1 (February, 2018), pp. 81-86 [doi]  [abs].
  2. Lin, YT; Buchler, NE, Efficient analysis of stochastic gene dynamics in the non-adiabatic regime using piecewise deterministic Markov processes., Journal of the Royal Society Interface, vol. 15 no. 138 (January, 2018) [doi]  [abs].
  3. Gómez-Schiavon, M; Chen, L-F; West, AE; Buchler, NE, BayFish: Bayesian inference of transcription dynamics from population snapshots of single-molecule RNA FISH in single cells., Genome Biology: biology for the post-genomic era, vol. 18 no. 1 (September, 2017), pp. 164 [doi]  [abs].
  4. Hendler, A; Medina, EM; Kishkevich, A; Abu-Qarn, M; Klier, S; Buchler, NE; de Bruin, RAM; Aharoni, A, Gene duplication and co-evolution of G1/S transcription factor specificity in fungi are essential for optimizing cell fitness., PLoS genetics, vol. 13 no. 5 (May, 2017), pp. e1006778 [doi]  [abs].
  5. Liban, TJ; Medina, EM; Tripathi, S; Sengupta, S; Henry, RW; Buchler, NE; Rubin, SM, Conservation and divergence of C-terminal domain structure in the retinoblastoma protein family., Proceedings of the National Academy of Sciences of USA, vol. 114 no. 19 (May, 2017), pp. 4942-4947 [doi]  [abs].
  6. Tanouchi, Y; Pai, A; Park, H; Huang, S; Buchler, NE; You, L, Long-term growth data of Escherichia coli at a single-cell level., Scientific Data, vol. 4 (March, 2017), pp. 170036 [doi]  [abs].
  7. Medina, EM; Turner, JJ; Gordân, R; Skotheim, JM; Buchler, NE, Punctuated evolution and transitional hybrid network in an ancestral cell cycle of fungi., eLife, vol. 5 no. MAY2016 (May, 2016) [repository], [doi]  [abs].
  8. Burnetti, AJ; Aydin, M; Buchler, NE, Cell cycle Start is coupled to entry into the yeast metabolic cycle across diverse strains and growth rates., Molecular Biology of the Cell, vol. 27 no. 1 (January, 2016), pp. 64-74 [repository], [doi]  [abs].
  9. Karapetyan, S; Buchler, NE, Role of DNA binding sites and slow unbinding kinetics in titration-based oscillators., Physical Review E - Statistical, Nonlinear, and Soft Matter Physics, vol. 92 no. 6 (December, 2015), pp. 062712 [repository], [doi]  [abs].
  10. Schaap, P; Barrantes, I; Minx, P; Sasaki, N; Anderson, RW; Bénard, M; Biggar, KK; Buchler, NE; Bundschuh, R; Chen, X; Fronick, C; Fulton, L; Golderer, G; Jahn, N; Knoop, V; Landweber, LF; Maric, C; Miller, D; Noegel, AA; Peace, R; Pierron, G; Sasaki, T; Schallenberg-Rüdinger, M; Schleicher, M; Singh, R; Spaller, T; Storey, KB; Suzuki, T; Tomlinson, C; Tyson, JJ; Warren, WC; Werner, ER; Werner-Felmayer, G; Wilson, RK; Winckler, T; Gott, JM; Glöckner, G; Marwan, W, The Physarum polycephalum Genome Reveals Extensive Use of Prokaryotic Two-Component and Metazoan-Type Tyrosine Kinase Signaling., Genome Biology and Evolution, vol. 8 no. 1 (November, 2015), pp. 109-125 [repository], [doi]  [abs].
  11. Rienzo, A; Poveda-Huertes, D; Aydin, S; Buchler, NE; Pascual-Ahuir, A; Proft, M, Different Mechanisms Confer Gradual Control and Memory at Nutrient- and Stress-Regulated Genes in Yeast., Molecular and Cellular Biology, vol. 35 no. 21 (November, 2015), pp. 3669-3683 [repository], [doi]  [abs].
  12. Zhou, M; Wang, W; Karapetyan, S; Mwimba, M; Marqués, J; Buchler, NE; Dong, X, Redox rhythm reinforces the circadian clock to gate immune response., Nature, vol. 523 no. 7561 (July, 2015), pp. 472-476 [repository], [doi]  [abs].
  13. Tanouchi, Y; Pai, A; Park, H; Huang, S; Stamatov, R; Buchler, NE; You, L, A noisy linear map underlies oscillations in cell size and gene expression in bacteria., Nature, vol. 523 no. 7560 (July, 2015), pp. 357-360 [repository], [doi]  [abs].
  14. Mazo-Vargas, A; Park, H; Aydin, M; Buchler, NE, Measuring fast gene dynamics in single cells with time-lapse luminescence microscopy., Molecular Biology of the Cell, vol. 25 no. 22 (November, 2014), pp. 3699-3708 [repository], [doi]  [abs].
  15. Tanouchi, Y; Pai, A; Buchler, NE; You, L, Programming stress-induced altruistic death in engineered bacteria., Molecular systems biology, vol. 8 (2012), pp. 626 [23169002], [doi]  [abs].
  16. Cross, FR; Buchler, NE; Skotheim, JM, Evolution of networks and sequences in eukaryotic cell cycle control, Philosophical Transactions B, vol. 366 no. 1584 (2011), pp. 3532-3544 [repository], [doi]  [abs].
  17. Buchler, NE; Bai, L, Chromatin: Bind at your own RSC, Current Biology, vol. 21 no. 6 (2011), pp. R223-R225 [repository], [doi]  [abs].
  18. Buchler, NE; Cross, FR, Protein sequestration generates a flexible ultrasensitive response in a genetic network, Molecular systems biology, vol. 5 (2009), pp. 272 [doi]  [abs].
  19. Buchler, NE; Louis, M, Molecular Titration and Ultrasensitivity in Regulatory Networks, Journal of Molecular Biology, vol. 384 no. 5 (2008), pp. 1106-1119 [doi]  [abs].
  20. Fritz, G; Buchler, NE; Hwa, T; Gerland, U, Designing sequential transcription logic: A simple genetic circuit for conditional memory, Systems and Synthetic Biology, vol. 1 no. 2 (2007), pp. 89-98 [doi]  [abs].
  21. Bintu, L; Buchler, NE; Garcia, HG; Gerland, U; Hwa, T; Kondev, J; Kuhlman, T; Phillips, R, Transcriptional regulation by the numbers: Applications, Current Opinion in Genetics and Development, vol. 15 no. 2 (2005), pp. 125-135 [doi]  [abs].
  22. Buchler, NE; Gerland, U; Hwa, T, Nonlinear protein degradation and the function of genetic circuits, Proceedings of the National Academy of Sciences of the United States of America, vol. 102 no. 27 (2005), pp. 9559-9564 [doi]  [abs].
  23. Archambault, V; Buchler, NE; Wilmes, GM; Jacobson, MD; Cross, FR, Two-faced cyclins with eyes on the targets, Cell Cycle, vol. 4 no. 1 (2005), pp. 125-130  [abs].
  24. Bintu, L; Buchler, NE; Garcia, HG; Gerland, U; Hwa, T; Kondev, J; Phillips, R, Transcriptional regulation by the numbers: Models, Current Opinion in Genetics and Development, vol. 15 no. 2 (2005), pp. 116-124 [doi]  [abs].
  25. Buchler, NE; Gerland, U; Hwa, T, On schemes of combinatorial transcription logic, Proceedings of the National Academy of Sciences of the United States of America, vol. 100 no. 9 (2003), pp. 5136-5141 [doi]  [abs].
  26. Buchler, NEG; Goldstein, RA, Surveying determinants of protein structure designability across different energy models and amino-acid alphabets: A consensus, Journal of Chemical Physics, vol. 112 no. 5 (2000), pp. 2533-2547  [abs].
  27. Buchler, NEG; Goldstein, RA, Effect of alphabet size and foldability requirements on protein structure designability, Proteins: Structure, Function and Bioinformatics, vol. 34 no. 1 (1999), pp. 113-124 [doi]  [abs].
  28. Buchler, NEG; Goldstein, RA, Universal correlation between energy gap and foldability for the random energy model and lattice proteins, Journal of Chemical Physics, vol. 111 no. 14 (October, 1999), pp. 6599-6609  [abs].
  29. Buchler, NEG; Zuiderweg, ERP; Wang, H; Goldstein, RA, Protein Heteronuclear NMR Assignments Using Mean-Field Simulated Annealing, Journal of Magnetic Resonance, vol. 125 no. 1 (1997), pp. 34-42  [abs].
  30. J. R. Buchler and N. E. Buchler, BL Herculis model pulsations; III. Livermore opacities, vol. 285 (1994), pp. 213-219 .