Select Publications

Rachel M Hartfield*, Kelly A Schwarz*, Joseph J Muldoon*, Neda Bagheri, and Joshua N Leonard (2017). Multiplexing engineered receptors for multiparametric evaluation of environmental ligands. ACS Synthetic Biology.

Albert Y Xue, Lindsey C Szymczak, Milan Mrksich, and Neda Bagheri (2017). Machine learning on SAMDI mass spectrometry signal to noise ratio improves peptide array designs. ACS Analytical Chemistry.

Alexander Misharin, ..., Tyrone J Yacoub, ..., Neda Bagheri, Ali Shilatifard, GR Budinger, and Harris Perlma. (2017). Monocyte-derived alveolar macrophages drive lung fibrosis and persist in the lung over the lifespan. The Journal of Experimental Medicine.

Sarah C Stainbrook*, Jessica S Yu*, Michael P Reddick, Neda Bagheri^, and Keith EJ Tyo^ (2017). Modulating and evaluating receptor promiscuity through directed evolution and modeling. Protein Engineering Design & Selection.

Jessica S. Yu, Albert Y. Xue, Eva E. Redei, and Neda Bagheri (2016). A support vector machine model provides an accurate transcript-level-based diagnostic for major depressive disorder. Translational Psychiatry.

Jessica S. Yu and Neda Bagheri (2016). Multi-class and multi-scale models of complex biological phenomena. Current Opinion in Biotechnology.

Steven M. Hill, et al. and HPN-DREAM Consortium (2016). Inferring causal molecular networks: empirical assessment through a community-based effort. Nature Methods.

Mark F. Ciaccio, Vincent C. Chen, Richard B. Jones, Neda Bagheri (2015). The DIONESUS algorithm provides scalable and accurate reconstruction of dynamic phosphoproteomic networks to reveal new drug targets. Integrative Biology.

Mark T. Duncan*, Seungjin Shin*, Jia J. Wu*, Zachary Mays, Stanley Weng, Neda Bagheri^, William M. Miller^, Lonnie D. Shea^ (2014). Dynamic transcription factor activity profiles reveal key regulatory interactions during megakaryocytic and erythroid differentiation. Biotechnology and Bioengineering.

Mark F. Ciaccio, Justin D. Finkle, Albert Y. Xue, Neda Bagheri (2014). A systems approach to integrative biology: an overview of statistical methods to elucidate association and architecture. Integrative and Comparative Biology.

Qing Han*, Neda Bagheri*, Elizabeth M. Bradshaw, David A. Hafler, Douglas A. Lauffenburger, J. Christopher Love (2012). Polyfunctional responses by human T cells result from sequential release of cytokines. Proc. Natl. Acad. Sci. U. S. A. 109(5):1607-12. DOI: 10.1073/pnas.1117194109 *Equal contribution

Neda Bagheri, Marisa Shiina, Douglas A. Lauffenburger, W. Michael Korn (2011). A Dynamical Systems Model for Combinatorial Cancer Therapy Enhances Oncolytic Adenovirus Efficacy by MEK-inhibition. PLoS Comput Biol 7(2): e1001085. DOI: 10.1371/journal.pcbi.1001085.

Neda Bagheri, Jörg Stelling, and Francis J. Doyle III (2008). Modeling the Drosophila melanogaster Circadian Oscillator via Phase Optimization. Journal of Biological Rhythms 23(6): 525-537. DOI: 10.1177/0748730408325041.

Neda Bagheri, Jörg Stelling, and Francis J. Doyle III (2008). Circadian phase resetting via Single & Multiple Control Targets. PLoS Comput Biol 4(7): e1000104. DOI: 10.1371/journal.pcbi.1000104.

Neda Bagheri*, Stephanie R. Taylor*, Kirsten Meeker, Linda R. Petzold, and Francis J. Doyle III (2008).Synchrony and Entrainment Properties of Robust Circadian Oscillators. R. Soc. Interface 5: S17–S28. DOI: 10.1098/rsif.2008.0045.focus.

Neda Bagheri, Jörg Stelling, and Francis J. Doyle III (2007). Circadian phase entrainment via nonlinear model predictive control. International Journal of Robust and Nonlinear Control 17: 1555-1571. DOI: 10.1002/rnc.1209.

Neda Bagheri, Jörg Stelling, and Francis J. Doyle III (2007). Quantitative performance metrics for robustness in circadian rhythms. Bioinformatics 23(3): 358-364. DOI: 10.1093/bioinformatics/btl627.

Francis J. Doyle III, Rudiyanto Gunawan, Neda Bagheri, Henry Mirsky, and Tsz Leung To (2006).Circadian rhythm: A natural, robust, multi-scale control system. Computers & Chemical Engineering 30: 1700-1711. DOI:10.1016/j.compchemeng.2006.05.029.

* Equal contributions.
^ Co-corresponding authors.