Publications

Publications

Modeling aging and its impact on cellular function and organismal behavior 

Emerson Santiago, David F. Moreno, and Murat Acar
Experimental Gerontology (2021)

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A yeast-optimized single-cell transcriptomics platform elucidates how mycophenolic acid and guanine alter global mRNA levels 

Guste Urbonaite, Jimmy T. H. Lee, Ping Liu, Guillermo E. Parada, Martin Hemberg, and Murat Acar
Communications Biology 4, 822  (2021)

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Chromatin regulatory genes differentially interact in networks to facilitate distinct GAL1 activity and noise profiles

David F. Moreno and Murat Acar
Current Genetics 67, 267-281 (2021)

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Epigenetic mechanisms contribute to evolutionary adaptation of gene network activity under environmental selection  

Xinyue Luo, Ruijie Song, David F. Moreno, Hong-Yeoul Ryu, Mark Hochstrasser, and Murat Acar
Cell Reports  33, 108306 (2020)

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Characterization of the impact of GMP/GDP synthesis inhibition on replicative lifespan extension in yeast

Ping Liu, Ethan A. Sarnoski, Tolga T. Olmez, Thomas Z. Young, and Murat Acar
Current Genetics   doi.org/10.1007/s00294-020-01068-w  (2020)

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Quantitative insights into age-associated DNA-repair inefficiency in single cells  

Thomas Z. Young, Ping Liu, Guste Urbonaite, and Murat Acar
Cell Reports  28, 2220-2230 (2019)

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Stochastic modeling of aging cells reveals how damage accumulation, repair, and cell-division asymmetry affect clonal senescence and population fitness  

Ruijie Song and Murat Acar
BMC Bioinformatics  20:391 (2019)

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Insights into bidirectional gene expression control using the canonical GAL1/GAL10 promoter 

Gregory L. Elison, Yuan Xue, Ruijie Song, and Murat Acar
Cell Reports  25, 737-748 (2018)

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The systems biology of single-cell aging 

Ruijie Song, Ethan A. Sarnoski, and Murat Acar
iScience  7, 154-169 (2018)

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Fundamental characteristics of single-cell aging in diploid yeast 

Ethan A. Sarnoski, Ruijie Song, Ege Ertekin, Noelle Koonce, and Murat Acar
iScience  7, 96-109 (2018)

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Multi-component gene network design as a survival strategy in diverse environments 

Xinyue Luo, Ruijie Song, and Murat Acar
BMC Systems Biology 12:85 (2018)

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Live-cell imaging of chromatin condensation dynamics by CRISPR 

Yuan Xue and Murat Acar
iScience 4, 216-235 (2018)

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Scarless genome editing: progress towards understanding genotype-phenotype relationships 

Gregory L. Elison and Murat Acar
Current Genetics (2018)  doi.org/10.1007/s00294-018-0850-8

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Mechanisms for the epigenetic inheritance of stress response in single cells 

Yuan Xue and Murat Acar
Current Genetics (2018)  doi.org/10.1007/s00294-018-0849-1

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Heritable stress response dynamics revealed by single-cell genealogy 

Meenakshi Chatterjee and Murat Acar
Science Advances 4, e1701775 (2018)

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The generational scalability of single-cell replicative aging 

Ping Liu and Murat Acar
Science Advances 4, eaao4666 (2018)

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A high-throughput screen for yeast replicative lifespan identifies lifespan-extending compounds

Ethan A. Sarnoski, Ping Liu, and Murat Acar
Cell Reports 21, 2639-2646 (2017)

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Noise reduction as an emergent property of single-cell aging

Ping Liu, Ruijie Song, Gregory L. Elison, Weilin Peng, and Murat Acar
Nature Communications 8:680 (2017)

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A precise genome editing method reveals insights into the activity of eukaryotic promoters

Gregory L. Elison, Ruijie Song, and Murat Acar
Cell Reports 18, 275-286 (2017)

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Noise reduction facilitated by dosage compensation in gene networks

Weilin Peng, Ruijie Song, and Murat Acar
Nature Communications 7:12959 (2016)

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A cell size- and cell cycle-aware stochastic model for predicting time-dynamic gene network activity in individual cells

Ruijie Song, Weilin Peng, Ping Liu, and Murat Acar
BMC Systems Biology 9:91 (2015)

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Yeast replicator: a high-throughput multiplexed microfluidics platform for automated measurements of single-cell aging

Ping Liu, Thomas Z. Young, and Murat Acar
Cell Reports 13:634-644 (2015)

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Evolution of gene network activity by tuning the strength of negative-feedback regulation

Weilin Peng, Ping Liu, Yuan Xue, and Murat Acar
Nature Communications 6:6226 (2015)

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Network-dosage compensation topologies as recurrent network motifs in natural gene networks

Ruijie Song, Ping Liu, and Murat Acar
BMC Systems Biology 8:69 (2014)

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A general mechanism for network-dosage compensation in gene circuits

Murat Acar, Bernardo F. Pando, Frances H. Arnold, Michael B. Elowitz, and Alexander van Oudenaarden
Science 329, 1656-1660 (2010)

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Stochastic switching as a survival strategy in fluctuating environments

Murat Acar, Jerome T. Mettetal, and Alexander van Oudenaarden
Nature Genetics 40, 471-475 (2008)

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Enhancement of cellular memory by reducing stochastic transitions

Murat Acar, Attila Becskei, and Alexander van Oudenaarden
Nature 435, 228-232 (2005)

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Photodissociation spectroscopy of Al+ -acetaldehyde

Wenyun Lu, Murat Acar, and Paul D. Kleiber
Journal of Chemical Physics 116, 4847-4852 (2002)

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