Select Publications

Finkle J. D.*, Wu J. J.*, Bagheri N. Windowed Granger causal inference strategy improves discovery of gene regulatory networks. Proc Natl Acad Sci U.S.A. 115(9):2252–2257, 2018. PMID: 29440433.

Hartfield R. M.*, Schwarz K. A.*, Muldoon J. J.*, Bagheri N., Leonard J. N. Multiplexing engineered receptors for multiparametric evaluation of environmental ligands. ACS Synth Biol. 6(11):2042–2055, 2017. PMID: 28771312.

Xue A. Y., Szymczak L. C., Mrksich M., Bagheri N. Machine learning on SAMDI mass spectrometry signal to noise ratio improves peptide array designs. Anal Chem. 89(17):9039–9047, 2017. PMID: 28719743.

Misharin A., ..., Yacoub T. J., ..., Bagheri N., Shilatifard A., Budinger G. R., Perlma H. Monocyte-derived alveolar macrophages drive lung fibrosis and persist in the lung over the lifespan. J Exp Med. 214(8):2387–2404, 2017. PMID: 28694385.

Stainbrook S. C.*, Yu J. S.*, Reddick M. P., Bagheri N.^, Tyo K. E. J.^ Modulating and evaluating receptor promiscuity through directed evolution and modeling. Protein Eng Des Sel. 30(6):455–465, 2017. PMID: 28453776.

Yu J. S., Xue A. Y., Redei E. E., Bagheri N. A support vector machine model provides an accurate transcript-level-based diagnostic for major depressive disorder. Transl Psychiatry. 6(10):e931, 2016. PMID: 27779627.

Yu J. S., Bagheri N. Multi-class and multi-scale models of complex biological phenomena. Curr Opin Biotechnol. 6(10):e931, 2016. PMID: 27779627.

Hill S. M., et al. and HPN-DREAM Consortium. Inferring causal molecular networks: empirical assessment through a community-based effort. Nat Methods. 13(4):310–318, 2016. PMID: 26901648.

Ciaccio M. F., Chen V. C., Jones R. B., Bagheri N. The DIONESUS algorithm provides scalable and accurate reconstruction of dynamic phosphoproteomic networks to reveal new drug targets. Integr Biol. 7(7):776–791, 2015. PMID: 26057728.

Duncan M. T.*, Shin S.*, Wu J. J.*, Mays Z., Weng S., Bagheri N.^, Miller W. M.^, Shea L. D.^ Dynamic transcription factor activity profiles reveal key regulatory interactions during megakaryocytic and erythroid differentiation. Biotechnol Bioeng. 111(10):2082–2094, 2014. PMID: 24853077.

Ciaccio M. F., Finkle J. D., Xue A. Y., Bagheri N. A systems approach to integrative biology: an overview of statistical methods to elucidate association and architecture. Integr Comp Biol. 54(2):296–306, 2014. PMID: 24813462.

Han Q.*, Bagheri N.*, Bradshaw E. M., Hafler D. A., Lauffenburger D. A., Love J. C. Polyfunctional responses by human T cells result from sequential release of cytokines. Proc Natl Acad Sci U.S.A. 109(5):1607–1612, 2012. PMID: 22160692.

Bagheri N., Shiina M., Lauffenburger D. A., Korn W. M. A Dynamical systems model for combinatorial cancer therapy enhances oncolytic adenovirus efficacy by MEK-inhibition. PLoS Comput Biol. 7(2):e1001085, 2011. PMID: 21379332.

Bagheri N., Stelling J., Doyle III F. J. Modeling the Drosophila melanogaster circadian oscillator via phase optimization. J Biol Rhythms. 23(6):525–537, 2008. PMID: 19060261.

Bagheri N., Stelling J., Doyle III F. J. Circadian phase resetting via single & multiple control targets. PLoS Comput Biol. 4(7):e1000104, 2008. PMID: 18795146.

Bagheri N.*, Taylor S. R.*, Meeker K., Petzold L. R., Doyle III F. J. Synchrony and entrainment properties of robust circadian oscillators. R Soc Interface. 5:S17–S28, 2008. PMID: 18426774.

Bagheri N., Stelling J., Doyle III F. J. Circadian phase entrainment via nonlinear model predictive control. Int J Robust Nonlin. 17:1555–1571, 2007.

Bagheri N., Stelling J., Doyle III F. J. Quantitative performance metrics for robustness in circadian rhythms. Bioinform. 23(3):358–364, 2007. PMID: 17158515.

Doyle III F. J., Gunawan R., Bagheri N., Mirsky H., To T. L. Circadian rhythm: A natural, robust, multi-scale control system. Comput Chem Eng. 30:1700–1711, 2006.

* Equal contributions.
^ Co-corresponding authors.