Publications

O Aydin, AP Passaro, R Raman, SE Spellicy, RP Weinberg, RD Kamm, M Sample, GA Truskey, J Zartman, RD Dar, S Palacios, J Wang, J Tordoff, N Montserrat, R Bashir, MTA Saif, and R Weiss (2022) Principles for the design of multicellular engineered living systems. APL Bioengineering 6, 010903. https://doi.org/10.1063/5.0076635

T Mahajan, A Singh, and RD Dar (2021) Topological Constraints on Noise Propagation in Gene Regulatory Networks. bioRxiv 2021.10.11.463999. https://doi.org/10.1101/2021.10.11.463999

N Goswami, Y Lu, ME Kandel, MJ Fanous, K Bohn-Wippert, EN Tevonian, RD Dar, and G Popescu (2021) Monitoring Reactivation of Latent HIV by Label-Free Gradient Light Interference Microscopy. iScience 24(8), 102940. https://doi.org/10.1016/j.isci.2021.102940

A Blanco, T Mahajan, RA Coronado, K Ma, DR Demma, and RD Dar (2021) Synergistic Chromatin-Modifying Treatments Reactivate Latent HIV and Decrease Migration of Multiple Host-Cell Types. Viruses 13(6), 1097. https://doi.org/10.3390/v13061097

Y Lu, K Bohn-Wippert, PJ Pazerunas, JM Moy, H Singh, and RD Dar (2021) Screening for gene expression fluctuations reveals latency promoting agents of HIV. Proc Na. Acad Sc. USA 118 (11) e2012191118. https://doi.org/10.1073/pnas.2012191118

--> UIUC Data Bank File Deposit for this Lu et al., PNAS (2021) is found at: https://doi.org/10.13012/B2IDB-8103861_V1 *Includes all image and signal datasets.

--> Noise Analysis Tutorial and Breakdown for Lu et al., PNAS (2021) is found at: link

T Mahajan and RD Dar (2021) Internetwork connectivity of molecular networks across species of life. Scientific Reports 11:1168. https://doi.org/10.1038/s41598-020-80745-9

Y Lu, H Singh, A Singh, and RD Dar (2021) A transient heritable memory regulates HIV reactivation from latency. iScience https://doi.org/10.1016/j.isci.2021.102291

N Goswami, MJ Fanous, K Bohn-Wippert, EN Tevonian, Y Lu, RD Dar, and G Popescu (2020) Detection of HIV reactivation using Spatial Light Interference Microscopy (Conference Presentation). Proc. SPIE 11249, Quantitative Phase Imaging VI, 1124910 (11 March 2020) https://doi.org/10.1117/12.2550061 *(Conference Presentation)

K Bohn-Wippert and RD Dar (2020) Cell size dependent migration of T-cells latently infected with HIV. Journal of Life Sciences 2:1 --> See Mentor-Postdoc Spotlight

K Bohn-Wippert*, EN Tevonian*, Y Lu, M-Y Huang, MR Megaridis, and RD Dar (2018) Cell size-based decision-making of a viral gene circuit. Cell Reports 25:3844-3857. doi.org/10.1016/j.celrep.2018.12.009

RD Kamm, R Bashir, N Arora, RD Dar, LG Griffith, ML Kemp, K Kinlaw, M Levin, AC Martin, TC McDevitt, RM Nerem, M Powers, TA. Saif, J Sharpe, S Takayama, S Takeuchi, R Weiss, K Ye, HG Yevick, and M Zaman (2018) The promise of multi-cellular engineered living systems. APL Bioengineering 2:040901. doi.org/10.1063/1.5038337

MMK Hansen*, WY Wen*, E Ingerman*, BS Razooky, CE Thompson, RD Dar, CW Chin, ML Simpson, and LS Weinberger (2018) A Post-Transcriptional Feedback Mechanism for Noise Suppression and Fate Stabilization. Cell 173:1–13. doi.org/10.1016/j.cell.2018.04.005

RD Dar and R Weiss (2018) Engineering noise in biological systems towards predictive stochastic design. APL Bioengineering 2:020901. doi:10.1063/1.5025033.

MR Megaridis*, Y Lu*, EN Tevonian, KM Junger, JM Moy, K Bohn-Wippert, and RD Dar (2018) Fine-tuning of noise in gene expression with nucleosome remodeling. APL Bioengineering 2:026106. doi:10.1063/1.5021183.

K Bohn-Wippert, EN Tevonian, MR Megaridis, and RD Dar (2017) Similarity in viral and host promoters couples viral reactivation with host cell migration Nature Communications 8:15006. doi:10.1038/ncomms15006.

RD Dar, SM Shaffer, A Singh, BS Razooky, ML Simpson, A Raj, and LS Weinberger (2016) Transcriptional bursting explains the noise-versus-mean relationship in mRNA and protein levels PLoS ONE 11(7): e0158298. doi:10.1371/journal.pone.0158298.

RD Dar, BS Razooky, LS Weinberger, CD Cox, and ML Simpson (2015) The low noise limit in gene expression. PLoS ONE 10(10): e0140969. doi:10.1371/journal.pone.0140969.

RD Dar, NN Hosmane, MR Arkin, RF Siliciano, and LS Weinberger (2014) Screening for noise in gene expression identifies drug synergies. Science 44:1392–1396.

D Boehm, V Calvanese, RD Dar, S Xing, S Schroeder, L Martins, K Aull, P Li, V Planelles, JE Bradner, M Zhou, RF Siliciano, LS Weinberger, E Verdin, and M Ott (2012) BET bromodomain-targeting compounds reactivate HIV from latency via a Tat-independent mechanism. Cell Cycle 2:452–462.

MW Teng*, C Bolovan-Fritts*, RD Dar, A Womack, T Shenk, ML Simpson, and LS Weinberger (2012) An endogenous accelerator for viral gene expression provides a fitness advantage. Cell 151:1569–1580.

RD Dar*, BS Razooky*, A Singh, TV Trimeloni, JM McCollum, CD Cox, ML Simpson, and LS Weinberger (2012) Transcriptional burst frequency and burst size are equally modulated across the human genome. Proc Na. Acad Sc. USA 109:17454–17459.

A Singh, BS Razooky, RD Dar, and LS Weinberger (2012) Dynamics of protein noise can distinguish between alternative sources of gene-expression variability. Mol Syst Biol 8:607..

DK Karig, P Siuti, RD Dar, ST Retterer, MJ Doktycz, and ML Simpson (2011) Model for biological communication in a nanofabricated cell-mimic driven by stochastic resonance. Nano Comm Net 2:39–49.

RD Dar, DK Karig, JF Cooke, CD Cox, and ML Simpson (2010) Distribution and regulation of stochasticity and plasticity in Saccharomyces cerevisiae. Chaos 20:037106.

ML Simpson, CD Cox, MS Allen, JM McCollum, RD Dar, DK Karig, and JF Cooke (2009) Noise in Biological Circuits. In WIREs Nanomed Nanobiotechnol 1: 214–225.

LS Weinberger*, RD Dar*, and ML Simpson (2008) Transient mediated fate-determination in a transcriptional circuit of HIV. Nature Genetics 40:466–470.

CD Cox, JM McCollum, MS Allen, RD Dar, and ML Simpson (2008) Using noise to probe and characterize gene circuits. Proc Nat Acad Sci USA 105:10809–10814.

DW Austin, MS Allen, JM McCollum, RD Dar, JR Wilgus, GS Sayler, NF Samatova, CD Cox, and ML Simpson (2006) Gene network shaping of inherent noise spectra. Nature 439:608–11.

CD Cox, JM McCollum, DW Austin, MS Allen, RD Dar, and ML Simpson (2006) Frequency domain analysis of noise in simple gene circuits. Chaos 16:026102.

*Denotes equal contribution.