Publications

Amses KR, Simmons DR, Longcore JE, Mondo SJ, Seto K, Jeronimo-Alves GH, Bonds AE, Quandt CA, Davis WJ, Chang Y, Letcher PM, Powell MJ, Kuo A, LaButti K, Pangilinan J, Andreopoulos W, Tritt A, Riley R, Hundley H, Johnson J, Lipzen A, Barry K, Lang BF, Cuomo CA, Berbee ML, Buchler NE, Grigoriev IV, Spatafora JW, Stajich JE, James TY. Diploid-dominant life cycles characterize the early evolution of Fungi. Proc. Natl. Acad. Sci. USA 19: e2116841119 (2022)
Zhang Y, Ho TD, Buchler NE, Gordan R. Competition for DNA binding sites between paralogous transcription factors determines their genomic occupancy and regulatory interactions. Genome Research 31: 1216 (2021)
Medina EM, Buchler NE. Primer: Chytrid fungi. Current Biology 30: R516 (2020) [PDF]
Medina EM, Robinson KA, Bellingham-Johnstun K, Ianiri G, Laplante C, Fritz-Laylin LK, Buchler NE. Genetic transformation of Spizellomyces punctatus, a resource for studying chytrid biology and evolutionary cell biology. eLife 9: e52741 (2020).
Gowans GJ, Bridgers JB, Zhang J, Dronamraju R, Burnetti A, King DA, Thiengmany AV, Shinsky SA, Bhanu NV, Garcia BA, Buchler NE, Strahl BA, Morrison AJ. Recognition of histone crotonylation by Taf14 links metabolic state to gene expression. Molecular Cell 76: 909 (2019).
Gomez-Schiavon M, Buchler NE. Epigenetic switching as a strategy for quick adaptation while attenuating biochemical noise. PLoS Computational Biology 15: e1007364 (2019).
Medina EM, Walsh E, Buchler NE. Evolutionary innovation, fungal cell biology, and the lateral gene transfer of a viral KilA-N domain. Curr. Opin. Genet. Dev. 59: 103 (2019).
Lin YT, Buchler NE. Exact and efficient hybrid Monte Carlo algorithm for accelerated Bayesian inference of gene expression models from snapshots of single-cell transcripts. J. Chem. Physics 151: 024106 (2019) [PDF]
Chen LF, Lin YT, Gallegos DA, Hazlett MF, Gomez-Schiavon M, Yang MG, Kalmeta B, Zhou AS, Holtzman L, Gersbach CA, Grandl J, Buchler NE, West AE. Enhancer histone acetylation modulates transcriptional bursting dynamics of neuronal activity-inducible genes. Cell Reports 26: 1174 (2019) [PDF]
Mwimba M, Karapeytan S, Liu L, Maruqes J, McGinnis EM, Buchler NE, Dong X. Daily humidity oscillation regulates the circadian clock to influence plant physiology. Nature Communications 9: 4290 (2018) [PDF]
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) [PDF]
Hendler A, Medina EM, Buchler NE, de Bruin RAM, Aharoni A. The evolution of a G1/S transcriptional network in yeasts. Current Genetics 64: 81 (2018) [PDF]
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]
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]
Schaap P, Barrantes I, Minx P, Sasaki N, Anderson RW, Bénard M, Biggar KK, Buchler NE, et al. The Physarum polycephalum genome reveals extensive use of prokaryotic two-component and metazoan-type tyrosine kinase signaling. Genome Biol. Evol. 8: 109-125 (2016)
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]
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]