2024

Tsai K, Zhou Z, Yang J, Xu Z, Xu S, Zandi R, Hao N, Chen W, Alber M. Study of Impacts of Two Types of Cellular Aging on the Yeast Bud Morphogenesis. bioRxiv 2024. (full text)

Naigles B, Soroczynski J, Hao N. Genetic Knock-Ins of Endogenous Fluorescent Tags in RAW 264.7 Murine Macrophages Using CRISPR/Cas9 Genome Editing. Bio Protoc. 2024 Mar 20; 14(6):e4960. (pdf)

O'Laughlin R, Tran Q, Lezia A, Ngamkanjanarat W, Emmanuele P, Hao N, Hasty J. A Standardized Set of MoClo-Compatible Inducible Promoter Systems for Tunable Gene Expression in Yeast. ACS Synth Biol. 2024 Jan 19;13(1):85-102. (pdf)

SarSam RD, Xu J, Lahiri I, Gong W, Li Q, Oh J, Zhou Z, Hou P, Chong J, Hao N, Li S, Wang D, and Leschziner AE. Elf1 promotes Rad26's interaction with lesion-arrested Pol II for transcription-coupled repair. Proc Natl Acad Sci U S A. 2024 Jan 16;121(3):e2314245121. (pdf)

2023

Nevarez AJ, Mudla A, Diaz SA, Hao N. Using Deep Learning to Decipher the Impact of Telomerase Promoter Mutations on the Morpholome. bioRxiv 2023. (full text)

Liu Y, Zhou Z, Wu S, Ni G, Zhang A, Tsimring LS, Hasty J, Hao N. Enhanced cellular longevity arising from environmental fluctuations. bioRxiv 2023. (full text)

Naigles B, Narla AV, Soroczynski J, Tsimring LS, Hao N. Quantifying dynamic pro-inflammatory gene expression and heterogeneity in single macrophage cells. J Biol Chem. 2023 Oct; 299(10):105230. (pdf)

Stasiowski E*, O'Laughlin R*, Holness S, Csicsery N, Hasty J, Hao N. A Microfluidic Platform for Screening Gene Expression Dynamics across Yeast Strain Libraries. Bio Protoc. 2023 Nov 20; 13(22):e4883. (pdf) (* contributed equally)

O'Laughlin R, Forrest E, Hasty J, Hao N. Fabrication of microfluidic devices for continuously monitoring yeast aging. Bio Protoc. 2023 Aug 5; 13(15):e4782. (pdf)

Zhou Z, Liu Y, Feng Y, Klepin S, Tsimring LS, Pillus L, Hasty J, and Hao N. Engineering longevity - design of a synthetic gene oscillator to slow cellular aging. Science 2023 April 28; 380:376-381. (full text) (UCSD News, EurekAlert, KPBS, Yahoo, VICE, Longevity by Design, BioWorld, Interesting Engineering, GEN, WorldHealth.Net, Inverse, REVYUH, labroots, HealthNews, Tech Times, StudyFinds.org, Science Alert, Askby Geeks, Medical News Today, New York Post, GenomeWeb, Daily Mail UK, METRO UK, Sciences et Avenir.fr, Nouvelles du monde, EL PAIS, laSexta, Metropoles, LA NACION, China Science Daily, TimePie, Sina, WuXi AppTec, Express Informer, MIRAGE, PHYS.ORG, Bioengineer.org, 100.3 The Peak)

Commentary: Salis HM. Genetic circuitry boosts cell longevity. Science 2023 April 28; 380:343. (pdf)

Research highlights: Minton K. Engineering an oscillating gene circuit to delay cellular aging. Nature Reviews Genetics 2023 May 16. (pdf)

2022

Kiratitanaporn W, Berry DB, Mudla A, Fried T, Lao A, Yu C, Hao N, Ward SR, Chen S. 3D printing a biocompatible elastomer for modeling muscle regeneration after volumetric muscle loss. Biomater Adv. 2022 Nov;142:213171. (pdf)

Nevarez AJ, Hao N. Quantitative cell imaging approaches to metastatic state profiling. Front Cell Dev Biol. 2022 Oct 25;10:1048630. (pdf)

Paxman J*, Zhou Z*, O'Laughlin R, Liu Y, Li Y, Tian W, Su H, Jiang Y, Holness SE, Stasiowski E, Tsimring LS, Pillus L, Hasty J, Hao N. Age-dependent aggregation of ribosomal RNA-binding proteins links deterioration in chromatin stability with challenges to proteostasis. eLife 2022 Oct 4;11:e75978. (pdf) (* contributed equally)

Cohen AA, Ferrucci L, Fülöp T, Gravel D, Hao N, Kriete A, Levine ME, Lipsitz LA, Olde Rikkert MGM, Rutenberg A, Stroustrup N, Varadhan R. A complex systems approach to aging biology. Nat Aging 2022 July; 2:580-591. (pdf)

2021

Choi J, Wang S, Li Y, Hao N, Zid BM. Age-induced P-bodies become detrimental and shorten the lifespan of yeast. bioRxiv 2021. (full text)

Jiang Y, Hao N. Memorizing environmental signals through feedback and feedforward loops. Curr Opin Cell Biol. 2021 April; 69:96-102. (pdf)

2020

Mudla A, Jiang Y, Arimoto K, Xu B, Rajesh A, Ryan AP, Wang W, Daugherty MD, Zhang DE, Hao N. Cell-cycle-gated feedback control mediates desensitization to interferon stimulation. eLife 2020 Sep 18;9:e58825. (pdf) (UCSD News, ScienceDaily, Agile Capital Markets, The Diet World)

Li Y, Jiang Y, Paxman J, O'Laughlin R, Klepin S, Zhu Y, Pillus L, Tsimring LS, Hasty J, Hao N. A programmable fate decision landscape underlies single-cell aging in yeast. Science 2020 July 17; 369(6501):325-329. (pdf) (CNN, Daily Mail UK, Fox 5, UCSD News, KPBS News, Metro World News, GEN, Inverse, PHYS.ORG, Medical News, ScienceDaily, Patch,Technology Networks, Sky tg24 Italy, Sputnik News France, Express Informer)

Jiang Y, AkhavanAghdam Z, Li Y, Zid BM, Hao N. A protein kinase A-regulated network encodes short- and long-lived cellular memories. Sci Signal. 2020 May 19;13(632):eaay3585. (pdf)

O'Laughlin R, Jin M, Li Y, Pillus L, Tsimring LS, Hasty J, Hao N. Advances in quantitative biology methods for studying replicative aging in Saccharomyces cerevisiae. Transl Med Aging. 2020; 4:151-160. (pdf)

2019

Shellhammer JP, Pomeroy AE, Li Y, Dujmusic L, Elston TC, Hao N, Dohlman HG. Quantitative analysis of the yeast pheromone pathway. Yeast. 2019 Apr 25. (pdf)

Jin M, Li Y, O'Laughlin R, Bittihn P, Pillus L, Tsimring LS*, Hasty J*, Hao N*. Divergent aging of isogenic yeast cells revealed through single-cell phenotypic dynamics. Cell Syst. 2019 Mar;8,1-12. (pdf) (* co-correspondence)

2018

Baumgartner B, O'Laughlin R, Jin M, Tsimring LS, Hao N, Hasty J. Flavin-based metabolic cycles are integral features of growth and division in single yeast cells. Sci Rep. 2018 Dec;8:18045. (pdf)

2017

Li Y, Roberts J, AkhavanAghdam Z, Hao N. Mitogen-activated protein kinase (MAPK) dynamics determine cell fate in the yeast mating response. J Biol Chem. 2017 Dec; 292(50):20354-20361. (pdf)

Li Y, Jin M, O'Laughlin R, Bittihn P, Tsimring LS, Pillus L, Hasty J, Hao N. Multigenerational silencing dynamics control cell aging. Proc Natl Acad Sci U S A. 2017 Oct; 114 (42): 11253-11258. (pdf) (UCSD News, KUSI News, abc 10 News, PHYS.ORG, ScienceDaily, Medindia, Kurzweilai, UCSD Guardian)

Shao B, Yuan H, Zhang R, Wang X, Zhang S, Ouyang Q, Hao N*, Luo C*. Reconstructing the regulatory circuit of cell fate determination in yeast mating response. PLoS Comput Biol. 2017 Jul; 13(7):e1005671. (pdf) (* co-correspondence)

Jiang Y, AkhavanAghdam Z,Tsimring LS, Hao N. Coupled feedback loops control the stimulus-dependent dynamics of the yeast transcription factor Msn2. J Biol Chem. 2017 Jun; 292(30):12366-12372. (pdf)

Zhang R, Yuan H, Wang S, Ouyang Q, Chen Y, Hao N, Luo C. High-throughput single-cell analysis for the proteomic dynamics study of the yeast osmotic stress response. Sci Rep. 2017 Feb;7:42200. (pdf)

2016

AkhavanAghdam Z, Sinha J, Tabbaa OP, Hao N. Dynamic control of gene regulatory logic by seemingly redundant transcription factors. eLife 2016 Sep;5. (pdf)

Yuan H, Zhang R, Shao B, Wang X, Ouyang Q, Hao N, Luo C. Protein expression patterns of the yeast mating response. Integr Biol. 2016 Jun;8(6):712-9. (pdf)

2015

Hansen AS, Hao N, O’Shea EK. High-throughput microfluidics to control and measure signaling dynamics in single yeast cells. Nat Protoc. 2015 Aug;10(8):1181-97. (pdf)

2013 and before

Hao N, Budnik BA, Gunawardena J, O’Shea EK. Tunable signal processing through modular control of transcription factor translocation. Science 2013 Jan 25; 339(6118):460-4.

Hao N, Yildirim N, Nagiec MJ, Parnell SC, Errede B, Dohlman HG, Elston TC. Combined computational and experimental analysis reveals MAP kinase-mediated feedback phosphorylation as a mechanism for signaling specificity. Mol Biol Cell. 2012 Oct;23(19):3899-910.

Hao N, O'Shea EK. Signal-dependent dynamics of transcription factor translocation controls gene expression. Nat Struct Mol Biol. 2011 Dec 18;19(1):31-9.

Hao N, Zeng Y, Elston TC, Dohlman HG. Control of MAPK specificity by feedback phosphorylation of shared adaptor protein Ste50. J Biol Chem. 2008 Dec 5;283(49):33798-802.

Behar M, Hao N, Dohlman HG, Elston TC. Dose-to-duration encoding and signaling beyond saturation in intracellular signaling networks. PLoS Comput Biol. 2008 Oct;4(10):e1000197.

Hao N, Nayak S, Behar M, Shanks RH, Nagiec MJ, Errede B, Hasty J, Elston TC, Dohlman HG. Regulation of cell signaling dynamics by the protein kinase-scaffold Ste5. Mol Cell. 2008 Jun 6;30(5):649-56.

Behar M, Hao N, Dohlman HG, Elston TC. Mathematical and computational analysis of adaptation via feedback inhibition in signal transduction pathways. Biophys J. 2007 Aug 1;93(3):806-21.

Hao N, Behar M, Elston TC, Dohlman HG. Systems biology analysis of G protein and MAP kinase signaling in yeast. Oncogene 2007 May 14;26(22):3254-66. Review.

Hao N, Behar M, Parnell SC, Torres MP, Borchers CH, Elston TC, Dohlman HG. A systems-biology analysis of feedback inhibition in the Sho1 osmotic-stress-response pathway. Curr Biol. 2007 Apr 17;17(8):659-67.

Chasse SA, Flanary P, Parnell SC, Hao N, Cha JY, Siderovski DP, Dohlman HG. Genome-scale analysis reveals Sst2 as the principal regulator of mating pheromone signaling in the yeast Saccharomyces cerevisiae. Eukaryot Cell 2006 Feb;5(2):330-46.

Wang X, Hao N, Dohlman HG, Elston TC. Bistability, stochasticity, and oscillations in the mitogen-activated protein kinase cascade. Biophys J. 2006 Mar 15;90(6):1961-78.

Yildirim N, Hao N, Dohlman HG, Elston TC. Mathematical modeling of RGS and G-protein regulation in yeast. Methods Enzymol. 2004;389:383-98. Review.

Hao N, Yildirim N, Wang Y, Elston TC, Dohlman HG. Regulators of G protein signaling and transient activation of signaling: experimental and computational analysis reveals negative and positive feedback controls on G protein activity. J Biol Chem. 2003 Nov 21;278(47):46506-15.