Nick Buchler

Amses, K. R., Simmons, D. R., Longcore, J. E., Mondo, S. J., Seto, K., Jeronimo, G. H., … James, T. Y. (2022). Diploid-dominant life cycles characterize the early evolution of Fungi. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 119(36). https://doi.org/10.1073/pnas.2116841119

Lin, Y. T., & Buchler, N. E. (2022, March 23). Gene expression noise accelerates the evolution of a biological oscillator (Vol. 3). Vol. 3. https://doi.org/10.1101/2022.03.21.485207

Zhang, Y., Ho, T. D., Buchler, N. E., & Gordan, R. (2021). Competition for DNA binding between paralogous transcription factors determines their genomic occupancy and regulatory functions. GENOME RESEARCH, 31(7), 1216-+. https://doi.org/10.1101/gr.275145.120

Medina, E. M., & Buchler, N. E. (2020). Chytrid fungi. Current Biology : CB, 5. https://doi.org/10.1016/j.cub.2020.02.076

Medina, E. M., Robinson, K. A., Bellingham-Johnstun, K., Ianiri, G., Laplante, C., Fritz-Laylin, L. K., & Buchler, N. E. (2020). Genetic transformation of Spizellomyces punctatus, a resource for studying chytrid biology and evolutionary cell biology. ELife. https://doi.org/10.7554/eLife.52741

Chen, L.-F., Lin, Y. T., Gallegos, D. A., Hazlett, M. F., Gomez-Schiavon, M., Yang, M. G., … West, A. E. (2019). Enhancer Histone Acetylation Modulates Transcriptional Bursting Dynamics of Neuronal Activity-Inducible Genes. CELL REPORTS, 26(5), 1174-+. https://doi.org/10.1016/j.celrep.2019.01.032

Gomez-Schiavon, M., & Buchler, N. E. (2019). Epigenetic switching as a strategy for quick adaptation while attenuating biochemical noise. PLOS COMPUTATIONAL BIOLOGY, 15(10). https://doi.org/10.1371/journal.pcbi.1007364

Medina, E. M., Walsh, E., & Buchler, N. E. (2019). [Review of Evolutionary innovation, fungal cell biology, and the lateral gene transfer of a viral KilA-N domain]. CURRENT OPINION IN GENETICS & DEVELOPMENT, 58-59, 103–110. https://doi.org/10.1016/j.gde.2019.08.004

Lin, Y. T., & Buchler, N. E. (2019). Exact and efficient hybrid Monte Carlo algorithm for accelerated Bayesian inference of gene expression models from snapshots of single-cell transcripts. The Journal of Chemical Physics. https://doi.org/10.1063/1.5110503

Gowans, G. J., Bridgers, J. B., Zhang, J., Dronamraju, R., Burnetti, A., King, D. A., … Morrison, A. J. (2019). Recognition of Histone Crotonylation by Taf14 Links Metabolic State to Gene Expression. MOLECULAR CELL, 76(6), 909-+. https://doi.org/10.1016/j.molcel.2019.09.029

Mwimba, M., Karapetyan, S., Liu, L., Marques, J., McGinnis, E. M., Buchler, N. E., & Dong, X. (2018). Daily humidity oscillation regulates the circadian clock to influence plant physiology. NATURE COMMUNICATIONS, 9. https://doi.org/10.1038/s41467-018-06692-2

Lin, Y. T., & Buchler, N. E. (2018). Efficient analysis of stochastic gene dynamics in the non-adiabatic regime using piecewise deterministic Markov processes. Journal of The Royal Society Interface, 15(138), 20170804. https://doi.org/10.1098/rsif.2017.0804

Hendler, A., Medina, E. M., Buchler, N. E., Bruin, R. A. M., & Aharoni, A. (2018). The evolution of a G1/S transcriptional network in yeasts. Current Genetics, 64(1), 81–86. https://doi.org/10.1007/S00294-017-0726-3

Gómez-Schiavon, M., Chen, L.-F., West, A. E., & Buchler, N. E. (2017). BayFish: Bayesian inference of transcription dynamics from population snapshots of single-molecule RNA FISH in single cells. Genome Biology, 18(1). https://doi.org/10.1186/s13059-017-1297-9

Liban, T. J., Medina, E. M., Tripathi, S., Sengupta, S., Henry, R. W., Buchler, N. E., & Rubin, S. M. (2017). Conservation and divergence of C-terminal domain structure in the retinoblastoma protein family. Proceedings of the National Academy of Sciences, 114(19), 4942–4947. https://doi.org/10.1073/pnas.1619170114

Hendler, A., Medina, E. M., Kishkevich, A., Abu-Qarn, M., Klier, S., Buchler, N. E., … Aharoni, A. (2017). Gene duplication and co-evolution of G1/S transcription factor specificity in fungi are essential for optimizing cell fitness. PLOS Genetics, 13(5), e1006778. https://doi.org/10.1371/journal.pgen.1006778

Tanouchi, Y., Pai, A., Park, H., Huang, S., Buchler, N. E., & You, L. (2017). Long-term growth data of Escherichia coli at a single-cell level. Scientific Data. https://doi.org/10.1038/sdata.2017.36

Burnetti, A. J., Aydin, M., & Buchler, N. E. (2016). Cell cycle Start is coupled to entry into the yeast metabolic cycle across diverse strains and growth rates. Molecular Biology of the Cell, 27(1), 64–74, https://doi.org/10.1091/mbc.e15-07-0454

Medina, E. M., Turner, J. J., Gordân, R., Skotheim, J. M., & Buchler, N. E. (2016). Punctuated evolution and transitional hybrid network in an ancestral cell cycle of fungi. ELife, 5. https://doi.org/10.7554/eLife.09492

Schaap, P., Barrantes, I., Minx, P., Sasaki, N., Anderson, R. W., Bénard, M., … Peace, R. (2016). The Physarum polycephalum Genome Reveals Extensive Use of Prokaryotic Two-Component and Metazoan-Type Tyrosine Kinase Signaling. Genome Biology and Evolution, 8(1), 109–125, https://doi.org/10.1093/GBE/EVV237

Tanouchi, Y., Pai, A., Park, H., Huang, S., Stamatov, R., Buchler, N. E., & You, L. (2015). A noisy linear map underlies oscillations in cell size and gene expression in bacteria. Nature, 523(7560), 357–360. https://doi.org/10.1038/nature14562

Rienzo, A., Poveda-Huertes, D., Aydin, S., Buchler, N. E., Pascual-Ahuir, A., & Proft, M. (2015). Different mechanisms confer gradual control and memory at nutrient- and stress-regulated genes in yeast. Molecular and Cellular Biology, 35(21), 3669–3683. https://doi.org/10.1128/MCB.00729-15

Zhou, M., Wang, W., Karapetyan, S., Mwimba, M., Marqués, J., Buchler, N. E., & Dong, X. (2015). Redox rhythm reinforces the circadian clock to gate immune response. Nature, 523(7561), 472–476. https://doi.org/10.1038/nature14449

Karapetyan, S., Buchler, N. E., & E, P. (2015). Role of DNA binding sites and slow unbinding kinetics in titration-based oscillators. Physical Review E, 92(6), 062712, https://doi.org/10.1103/physreve.92.062712

Mazo-Vargas, A., Park, H., Aydin, M., & Buchler, N. E. (2014). Measuring fast gene dynamics in single cells with time-lapse luminescence microscopy. Molecular Biology of the Cell, 25(22), 3699–3708. https://doi.org/10.1091/mbc.E14-07-1187

Archambault, V., Buchler, N. E., Wilmes, G. M., Jacobson, M. D., & Cross, F. R. (2014). Two-Faced Cyclins with Eyes on the Targets. Cell Cycle, 4(1), 125–130. https://doi.org/10.4161/CC.4.1.1402

Tanouchi, Y., Pai, A., Buchler, N. E., & You, L. (2012). Programming stress-induced altruistic death in engineered bacteria. Molecular Systems Biology, 8. https://doi.org/10.1038/msb.2012.57

Buchler, N. E., & Bai, L. (2011). Chromatin: Bind at your own RSC. Current Biology, 21(6). https://doi.org/10.1016/j.cub.2011.01.060

Cross, F. R., Buchler, N. E., & Skotheim, J. M. (2011). Evolution of networks and sequences in eukaryotic cell cycle control. Philosophical Transactions of the Royal Society B: Biological Sciences, 366(1584), 3532–3544. https://doi.org/10.1098/rstb.2011.0078

Buchler, N. E., & Cross, F. R. (2009). Protein sequestration generates a flexible ultrasensitive response in a genetic network. Molecular Systems Biology, 5. https://doi.org/10.1038/msb.2009.30

Buchler, N. E., & Louis, M. (2008). Molecular Titration and Ultrasensitivity in Regulatory Networks. Journal of Molecular Biology, 384(5), 1106–1119. https://doi.org/10.1016/j.jmb.2008.09.079

Fritz, G., Buchler, N. E., Hwa, T., & Gerland, U. (2007). Designing sequential transcription logic: A simple genetic circuit for conditional memory. Systems and Synthetic Biology, 1(2), 89–98. https://doi.org/10.1007/s11693-007-9006-8

Buchler, N. E., Gerland, U., & Hwa, T. (2005). Nonlinear protein degradation and the function of genetic circuits. Proceedings of the National Academy of Sciences of the United States of America, 102(27), 9559–9564. https://doi.org/10.1073/pnas.0409553102

Bintu, L., Buchler, N. E., Garcia, H. G., Gerland, U., Hwa, T., Kondev, J., … Phillips, R. (2005). Transcriptional regulation by the numbers: Applications. Current Opinion in Genetics and Development, 15(2), 125–135. https://doi.org/10.1016/j.gde.2005.02.006

Bintu, L., Buchler, N. E., Garcia, H. G., Gerland, U., Hwa, T., Kondev, J., & Phillips, R. (2005). Transcriptional regulation by the numbers: Models. Current Opinion in Genetics and Development, 15(2), 116–124. https://doi.org/10.1016/j.gde.2005.02.007

Archambault, V., Buchler, N. E., Wilmes, G. M., Jacobson, M. D., & Cross, F. R. (2005). Two-faced cyclins with eyes on the targets. Cell Cycle, 4(1), 125–130. Retrieved from http://www.scopus.com/inward/record.url?eid=2-s2.0-14844287697&partnerID=MN8TOARS

Buchler, N. E., Gerland, U., & Hwa, T. (2003). On schemes of combinatorial transcription logic. Proceedings of the National Academy of Sciences of the United States of America, 100(9), 5136–5141. https://doi.org/10.1073/pnas.0930314100

Surveying determinants of protein structure designability across different energy models and amino-acid alphabets: A consensus. (2000). The Journal of Chemical Physics. https://doi.org/10.1063/1.480893

Buchler, N. E. G., & Goldstein, R. A. (1999). Effect of alphabet size and foldability requirements on protein structure designability. Proteins: Structure, Function and Genetics, 34(1), 113–124. https://doi.org/10.1002/(SICI)1097-0134(19990101)34:1<113::AID-PROT9>3.0.CO;2-J

Universal correlation between energy gap and foldability for the random energy model and lattice proteins. (1999). The Journal of Chemical Physics. https://doi.org/10.1063/1.479951

Buchler, N. E. G., Zuiderweg, E. R. P., Wang, H., & Goldstein, R. A. (1997). Protein Heteronuclear NMR Assignments Using Mean-Field Simulated Annealing. Journal of Magnetic Resonance, 125(1), 34–42. https://doi.org/10.1006/JMRE.1997.1106

Buchler, N. E. G., Zuiderweg, E. R. P., Wang, H., & Goldstein, R. A. (1997). Protein Heteronuclear NMR Assignments Using Mean-Field Simulated Annealing. Journal of Magnetic Resonance, 125(1), 34–42. Retrieved from http://www.scopus.com/inward/record.url?eid=2-s2.0-0031083526&partnerID=MN8TOARS

BL HERCULIS MODEL PULSATIONS .3. LIVERMORE OPACITIES. (1994). Astronomy & Astrophysics. Retrieved from https://publons.com/publon/51431452/