UW Bio UW ChemE eScience AICS
Lab Affiliations: NU CSB NU NICO UW CMB

Select Publications

Google Scholar

* Equal contributions.
^ Co-corresponding authors.


Muldoon J. J., Kandula V., Hong M., Donahue P. S., Boucher J. D., Bagheri N., Leonard J. N. Model-guided design of mammalian genetic programs. Sci Adv. 7(8), 2021. DOI: 10.1126/sciadv.abe9375.


Yu J. S., Bagheri N. Agent-based models predict emergent behavior of heterogeneous cell populations in dynamic microenvironments. Front Bioeng Biotechnol. 8, 2020. DOI: 10.3389/fbioe.2020.00249.

Bernasek S., Peláez N., Carthew R., Bagheri N.^, Amaral L.^ Fly-QMA: Automated analysis of mosaic imaginal discs in Drosophila. PLoS Comp Biol. 16, 2020.

Muldoon J. J., Chuang Y., Bagheri N.^, Leonard J. N.^ Macrophages employ quorum licensing to regulate collective activation. Nat Commun. 11, 2020.

Donahue P. S., Draut J. W., Muldoon J. J., Edelstein H. I., Bagheri N., Leonard J. N. The COMET toolkit for composing customizable genetic programs in mammalian cells. Nat Commun. 11, 2020.


Cassidy J. J.*, Bernasek S.*, Bakker R., Giri R., Peláez N., Eder B., Bobrowska A., Bagheri N., Amaral L. A. N.^, Carthew R. W.^ Repressive gene regulation synchronizes development with cellular metabolism. Cell. 178:980–992, 2019. PMID: 31353220.

Xue A. Y.*, Yu A. M.*, Lucks J. B.^, Bagheri N.^ DUETT quantitatively identifies known and novel events in nascent RNA structural dynamics from chemical probing data. Bioinform. 2019. DOI: 10.1093/bioinformatics/btz449.

Finkle J. D., Bagheri N. Hybrid analysis of gene dynamics predicts context specific expression and offers regulatory insights. Bioinform. 2019. DOI: 10.1093/bioinformatics/btz256.

Muldoon J. J.*, Yu J. S.*, Fassia M.-K., Bagheri N. Network inference performance complexity: a consequence of topological, experimental, and algorithmic determinants. Bioinform. 2019. DOI: 10.1093/bioinformatics/btz105.

Yamankurt G.*, Berns E. J.*, Xue A. Y., Lee A., Bagheri N., Mrksich M., Mirkin C. A. Exploration of the nanomedicine-design space with high-throughput screening and machine learning. Nat Biomed Eng. 3:318–327, 2019. DOI: 10.1038/s41551-019-0351-1

Bucior B. J., Bobbitt N. S., Islamoglu T., Goswami S., Gopalan A., Yildirim T., Farha O. K., Bagheri N.^, Snurr R. Q.^ Energy-based descriptors to rapidly predict hydrogen storage in metal–organic frameworks. Mol Syst Des Eng. 4:162-174, 2019. DOI: 10.1039/C8ME00050F.


Walter J. M.*, Ren Z.*, Yacoub T., ..., Bagheri N., Hauser A. R., Budinger G. R. S.^, Wunderink, R. G.^ Multidimensional assessment of the host response in mechanically ventilated patients with suspected pneumonia. Am J Respir Crit Care Med. 2018. PMID: 30398927.

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 Signal-to-Noise Ratios Improves Peptide Array Design in SAMDI Mass Spectrometry. 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 Se. 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. 39:167–173, 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.

Prior to 2014

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.