Lin YT, Buchler NE. Efficient analysis of stochastic gene dynamics in the non-adiabatic regime using piecewise deterministic Markov processes. J. R. Soc. Interface 15: 20170804 (2018)

Hendler A, Medina EM, Buchler NE, de Bruin RAM, Aharoni A.  The evolution of a G1/S transcriptional network in yeastsCurrent Genetics 64: 81 (2018)

Gomez-Schiavon M, Chen LF, West AE, Buchler NE.  BayFish: Bayesian inference of transcription dynamics from population snapshots of single-molecule RNA FISH in single cells.  Genome Biology 18: 164 (2017) [PDF]

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 4: 170036 (2017) [PDF]

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 fitness.  PLoS Genetics 13: e1006778 (2017) [PDF]

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. Proc. Natl. Acad. Sci. USA 114: 4942 (2017) [PDF]

Gomez-Schiavon M, Buchler NE. Evolutionary dynamics of an epigenetic switch in a fluctuating environment. bioRxiv preprint (2017)

Medina EM, Turner JJ, Gordan R, Skotheim JM, Buchler NE. Punctuated evolution and transitional hybrid network in an ancestral cell cycle of fungi. eLife 5:e09492 (2016) [PDF]
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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 Biol. Evol. 8: 109-125 (2016) [PDF]

Burnetti AJ, Aydin M, Buchler NE. Cell cycle Start is coupled to entry into the yeast metabolic cycle across diverse strains and growth rates. Mol. Biol. Cell 27: 64-74 (2016) [PDF]

Karapetyan S, Buchler NE. Role of DNA binding sites and slow unbinding kinetics in titration-based oscillators. Phys. Rev. E 92: 062712 (2015) [PDF]

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. Mol. Cell. Biol. 35: 3669-83 (2015) [PDF]

Zhou M, Wang W, Karapetyan S, Mwimba M, Marques J, Buchler NE, Dong X. Redox rhythm reinforces circadian clock to gate immune response. Nature 523: 472-476 (2015) [PDF]
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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 523: 357-360 (2015).

Mazo-Vargas A, Park H, Aydin M, Buchler NE. Measuring fast gene dynamics in single cells using timelapse luminescence microscopy. Mol. Biol. Cell 25: 3699-3708 (2014) [PDF]

Tanouchi Y, Pai A, Buchler NE, You L. Programming stress-induced altruistic death in engineered bacteria Mol. Syst. Biol. 8: 626 (2012) [PDF]

Cross FR, Buchler NE, Skotheim JM. Evolution of networks and sequences in eukaryotic cell cycle control. Phil. Trans. R. Soc. B 366: 3532-3544 (2011) [PDF]

Buchler NE, Bai L. Chromatin: Bind at your own RSC. Curr. Biol. 21: R223-225 (2011) [PDF]

Buchler NE, Cross FR. Protein sequestration generates a flexible ultrasensitive response in a genetic network. Mol. Syst. Biol. 5: 272 (2009) [PDF]

Buchler NE, Louis M. Molecular titration and ultrasensitivity in regulatory networks. J. Mol. Biol. 384: 1106-1119 (2008) [PDF]

Fritz G, Buchler NE, Hwa T, Gerland U. Designing sequential transcription logic: a simple genetic circuit for conditional memory. Syst. Synth. Biol. 1: 89-98 (2007) [PDF]

Archambault V, Buchler NE, Wilmes GM, Jacobson MD, Cross FR. Two-faced cyclins with eyes on the targets. Cell Cycle 4: 125-130 (2005) [PDF]

Buchler NE, Gerland U, Hwa T. Nonlinear protein degradation and the function of genetic circuits. Proc. Natl. Acad. Sci. U.S.A. 102: 9559-9564 (2005) [Research roundup in JBC] [PDF]

Bintu L, Buchler NE, Garcia HG, Gerland U, Hwa T, Kondev J, Phillips R. Transcriptional regulation by the numbers: models. Curr. Opin. Genet. Dev. 15: 116-124 (2005) Review. [PDF]

Bintu L, Buchler NE, Garcia HG, Gerland U, Hwa T, Kondev J, Kuhlman T, Phillips R. Transcriptional regulation by the numbers: applications. Curr. Opin. Genet. Dev. 15: 125-135 (2005) Review. [PDF]

Buchler NE, Gerland U, Hwa T. On schemes of combinatorial transcription logic. Proc. Natl. Acad. Sci. U.S.A. 100: 5136-5141 (2003) [PDF]