Journal Publications

STAT6-targeting Antisense Oligonucleotides against Solitary Fibrous Tumor.
Li, Y., J. Mondaza-Hernandez, D. Moura, A. Revenko, A. Tolentino, J. Nguyen, N. Tran, C. Meyer, J. Merino-Garcia, R. Ramos, D Di Lernia, J. Martin-Broto, H. Hayenga, L. Bleris.
Molecular Therapy-Nucleic Acids, 2024. URL - PDF

RNA "COURIERs": Enabling synthetic cell-to-cell communication in human cells.
Kang, T. and L. Bleris.
Cell, 186(17), 2023. URL - PDF

Impact of Variability in Cell Cycle Periodicity on Cell Population Dynamics.
Nowak, C., T. Quarton, L. Bleris.
PLOS Computational Biology, 19(6), 2023. URL - PDF

Reduction of Tumor Growth with RNA-Targeting Treatment of the NAB2-STAT6 Fusion Transcript in Solitary Fibrous Tumor Models.
Li, Y., J. T. Nguyen, M. Ammanamanchi, Z. Zhou, E. Fletcher Harbut, J. L. Mondaza-Hernandez, C. A. Meyer, D. S. Moura, J. Martin-Broto, H. N. Hayenga*, L. Bleris*.
Cancers, 15(12), 2023. URL - PDF

Non-viral Nitric Oxide-Based Gene Therapy Improves Perfusion and Liposomal Doxorubicin Sonopermeation in Neuroblastoma Models.
Bellary, A., C. Nowak, I. Iwanicki, F. Flores-Guzman, L. Wu, J. J. Kandel, T. W. Laetsch, L. Bleris, S. L. Hernandez*, S. R. Sirsi*.
Theranostics, 13(10), 2023. URL - PDF

Clinical gene therapy development for the central nervous system: Candidates and challenges for AAVs.
Leong, T. W., A. Pal, Q. Cai, Z. Gao, X. Li, L. Bleris, H. N. Hayenga, Z. Qin.
Journal of Controlled Release 357, 511-530, 2023. URL - PDF

Genetic Physical Unclonable Functions in Human Cells.
Li, Y., M. Bidmeshki, T. Kang, C. Nowak, Y. Makris*, L. Bleris*.
Science Advances, 8(18), 2022. URL - PDF

Plasmonic LAMP: Improving the Detection Specificity and Sensitivity for SARS-CoV-2 by Plasmonic Sensing of Isothermally Amplified Nucleic Acids.
Ye, H., C. Nowak, Y. Liu, Y. Li, T. Zhang, L. Bleris*, Z. Qin*.
Small, 18(12), 2022. URL - PDF

Machine learning-based approaches for identifying human blood cells harboring CRISPR-mediated fetal chromatin domain ablations.
Li, Y., S. Zaheri, K. Nguyen, L. Liu, F. Hassanipour, B. Pace, L. Bleris.
Scientific Reports, 12(1481), 2022. URL

Cell Morphology-based Machine Learning Models for Human Cell State Classification.
Li, Y., C. Nowak, U. Pham, K. Nguyen, L. Bleris.
npj Systems Biology and Applications, 7(23), 2021. URL - PDF

Robust filtering and noise suppression in intragenic miRNA-mediated host regulation.
Kang, T., T. Quarton, K. Ehrhardt, C. Nowak, A. Singh, Y. Li, L. Bleris.
iScience, 23(10), 2020. URL - PDF

Transcriptomics and Solid Tumors: The Next Frontier in Precision Cancer Medicine.
Tsimberidou, A., Fountzilas, E., Bleris, L. and R. Kurzrock
Seminars in Cancer Biology, 2020. URL

Uncoupling gene expression noise along the central dogma using genome engineered human cell lines.
Quarton, T., Kang, T., Papakis, V., Nguyen, K., Nowak, C., Li, Y. and L. Bleris
Nucleic Acids Research, 48(16), 2020. URL - PDF
News: UT Dallas - ScienceDaily

Mechanistic insights into host adaptation, virulence and epidemiology of the phytopathogen Xanthomonas.
An, S., Potnis, N., Dow, J., Vorholter, F., He, Y., Becker, A., Teper, D., Li, Y., Wang, N., Bleris, L., Ji-Liang Tang
FEMS Microbiology Reviews, 44(1), 2020. URL

Coevolutionary couplings unravel PAM proximal constraints of CRISPR-SpCas9.
Li, Y., Paz, J., Jiang, X., Liu, R., Pokkulandra, A., Bleris, L.*, F. Morcos*
Biophysical Journal, 117(9), 2019. URL

p63 and SOX2 dictate glucose reliance and metabolic vulnerabilities in squamous cell carcinoma.
Hsieh MH, Choe JH, Gadhvi J, Kim YJ, Arguez MA, Palmer M, Gerold H, Nowak C, Do H, Mazambani S, Knighton JK, Cha M, Goodwin J, Kang MK, Jeong JY, Lee SY, Faubert B, Xuan Z, Abel ED, Scafoglio C, Shackelford DB, Minna JD, Singh PK, Shulaev V, Bleris L, Hoyt K, Kim J, Inoue M, DeBarardinis RJ, Kim TH, Kim JW.
Cell Reports, 28(7), 2019. URL - PDF

CRISPR-based editing reveals edge-specific effects in biological networks.
Li, Y., Nowak, C., Withers, D., Pertsemlidis, A., L. Bleris
The CRISPR Journal, 2018. URL - PDF
bioRxiv, 2018. URL

Regulating the Uptake of Viral Nanoparticles in Macrophage and Cancer Cells by via a pH Switch.
Lee, H., Benjamin, C.E., Nowak, C.M., Tuong, L.H., Welch, R.P., Chen, Z., Dharmarwardana, M., Murray, K.W., Bleris, L., D'Arcy, S., Gassensmith, J.J.
Molecular Pharmaceutics, 2018. URL - PDF

Nitroxyl Modified Tobacco Mosaic Virus as a Metal-Free High-Relaxivity MRI and EPR Active Superoxide Sensor.
Dharmarwardana, M., Martins, A.F., Chen, Z., Palacios, P.M., Nowak, C.M., Welch, R.P., Li, S., Luzuriaga, M.A., Bleris, L., Pierce, B.S., Sherry, A.D., Gassensmith, J.J.
Molecular Pharmaceutics, 2018. URL - PDF

Mapping the operational landscape of microRNAs in synthetic gene circuits.
Quarton, T., K. Ehrhardt, J. Lee, S. Kannan, Y. Li, L. Ma, L. Bleris
npj Systems Biology and Applications, 2018. URL - PDF
News: UT Dallas

Techniques and strategies employing engineered transcription factors.
Lawson, S. and L. Bleris
Current Opinion in Biomedical Engineering, 4:152-162, 2017. URL - PDF

Guide RNA engineering for versatile Cas9 functionality.
Nowak, C. S. Lawson, M. Zerez, L. Bleris
Nucleic Acids Research, 2016. URL - PDF

Exploiting the CRISPR/Cas9 PAM constraint for single-nucleotide resolution interventions
Li, Y., Mendiratta, S., Ehrhardt, K., Kashyap, N., White, M. A. and L. Bleris
PLoS ONE, 11(1), 2016. URL - PDF
Editor�s Picks

MiR-192-mediated positive feedback loop controls the robustness of stress-induced p53 oscillations in breast cancer cells.
Moore, R., H. K. Ooi, T. Kang, L. Bleris and L. Ma
PLoS Computational Biology, 11(12), 2015. URL - PDF

Discriminating direct and indirect connectivities in biological networks.
Kang, T., R. Moore, Y. Li, E. Sontag, L. Bleris
Proceedings of the National Academy of Sciences (PNAS), 112, 41, 2015. URL - PDF
News: UT Dallas

Reconfigurable hybrid interface for molecular marker diagnostics and in-situ reporting.
Ehrhardt, K. Guinn, M., Quarton, T., Zhang, M. Q., L. Bleris
Biosensors and Bioelectronics, 2015. URL

CRISPR-based self-cleaving mechanism for controllable gene delivery in human cells.
Moore, R., A. Spinhirne, M. Lai, S. Preisser, Y. Li, T. Kang, L. Bleris
Nucleic Acids Research, 2015. URL
News: BioTechniques - UT Dallas - Bionews Texas- ScienceDaily
Plasmids: Addgene

Assembly and validation of versatile transcription activator-like effector libraries.
Li, Y., K. Ehrhardt, M. Q. Zhang, L. Bleris
Scientific Reports 4:4857, 2014. URL

A Biological 2-input decoder circuit in human cells.
Guinn, M. and L. Bleris
ACS Synthetic Biology, 2014. URL

Transcription activator-like effectors: A toolkit for synthetic biology.
Moore, R., A. Chandrahas, L. Bleris
ACS Synthetic Biology, 2014. URL

Synthetic mammalian transgene negative autoregulation.
Shimoga, V.*, J. White*, Y. Li, E. Sontag, L. Bleris
Molecular Systems Biology, 9:670, 2013. URL
(*equal contribution)

Reverse engineering validation using a benchmark synthetic gene circuit in human cells.
Kang, T., J. White, Z. Xie, Y. Benenson, E. Sontag, L. Bleris
ACS Synthetic Biology, 2 (5), 2013. URL

Transcripts for combined synthetic microRNA and gene delivery.
Kashyap, N., B. Pham, Z. Xie, L. Bleris
Molecular BioSystems, 9, 2013. URL

Transcription activator-like effector hybrids for conditional control and rewiring of chromosomal transgene expression.
Li, Y., R. Moore, M. Guinn, L. Bleris
Scientific Reports 2:897, 2012. URL

MicroRNA circuits for transcriptional logic.
Leisner, M., L. Bleris, J. Lohmueller, Z. Xie, Y. Benenson.
Methods in Molecular Biology, Volume 813, Part 2, 2012. URL

Synthetic incoherent feedforward circuits show adaptation to the amount of their genetic template.
Bleris, L., Z. Xie, D. Glass, A. Adadey, E. Sontag, Y. Benenson
Molecular Systems Biology 7, 2011. URL

Linear control theory for gene network modeling.
Shin Y. J. and L. Bleris.
PLoS One, 5(9), 2010. URL

Rationally designed logic integration of regulatory signals in mammalian cells.
Leisner, M., L. Bleris, J. Lohmueller, Z. Xie, Y. Benenson.
Nature Nanotechnology 5, 2010.

Logic integration of mRNA signals by an RNAi-based molecular computer.
Xie, Z., S. J. Liu, L. Bleris, Y. Benenson.
Nucleic Acids Research 38(8):2692-701. 2010.

A System-on-a-Chip Implementation for Embedded Real-Time Model Predictive Control.
Vouzis, P. D., L. Bleris, M. G. Arnold, M. V. Kothare.
IEEE Transactions on Control Systems Technology, 17:5, 1006-1017, 2009.

A universal RNAi-based logic evaluator that operates in mammalian cells.
Rinaudo, K.*, L. Bleris*, R. Maddamsetti, S. Subramanian, R. Weiss, Y. Benenson.
Nature Biotechnology 25, 795-801, 2007
(*equal contribution)

Pathways for Optimization-based Drug Delivery Systems and Devices.
Bleris, L., P. D. Vouzis, J. G. Garcia, M. G. Arnold, M. V. Kothare.
Control Engineering Practice, Volume 15, Issue 10, October 2007, Pages 1280-1291

Model Predictive Hydrodynamic Regulation of Microflows.
Bleris, L., J. G. Garcia, M. G. Arnold., M. V. Kothare.
Journal of Micromechanics and Microengineering, 16, 1792-1799, 2006.

Towards Embedded Model Predictive Control for System-On-a-Chip Applications.
Bleris, L, J. G. Garcia, M. V. Kothare, M. G. Arnold.
Journal of Process Control, 16, 255-264, Mar. 2006.

Reduced Order Distributed Boundary Control of Thermal Transients in Microsystems.
Bleris, L. and M. V. Kothare.
IEEE Transactions on Control Systems Technology, 13:6, 853-867, 2005.

Low-Order Empirical Modeling of Distributed Parameter Systems Using Temporal and Spatial Eigenfunctions.
Bleris, L. and M. V. Kothare.
Computers & Chemical Engineering, 29, 817-827, 2005.