Select Publications

Evarts JI, Cain JY, Chiu PH, Jan I, Allbritton N, Bagheri N. Inductive bias influences the spatial scale of biological features learned from images. Bioinformatics Advances. 2026. DOI: 10.1093/bioadv/vbag238

Chiu PH*, Evarts JI*, Feng P*, Bagheri N. Variable deep learning training horizons reveal the temporal complexity of biological systems. microPublication Biology. 2026. DOI: 10.17912/micropub.biology.001926

Jung JK, Dreyer KS, Dray KE, Muldoon JJ, George J, Shirman S, Cabezas MD, d'Aquino AE, Verosloff MS, Seki K, Rybnicky GA, Alam KK, Bagheri N, Jewett MC, Leonard JN^, Mangan NM^, Lucks JB^. Developing, Characterizing, and Modeling CRISPR-Based Point-of-Use Pathogen Diagnostics. ACS Syn Bio. 14, 1, 129–14, 2024. DOI: 10.1021/acssynbio.4c00469

Yu JS, Bagheri N. Model design choices impact biological insight: Unpacking the broad landscape of spatial-temporal model development decisions. PLoS Comp Biol. 20(3): e1011917, 2024. DOI: 10.1371/journal.pcbi.1011917

Cain JY*, Evarts JI*, Yu JS, Bagheri N. Incorporating temporal information during feature engineering bolsters emulation of spatio-temporal emergence. Bioinform. 40(3), 2024. DOI: 10.1093/bioinformatics/btae131

Qiao S, Bernasek S, Gallagher KD, O'Connell J, Yamada S, Bagheri N, Amaral LAN, Carthew RW. Energy metabolism modulates the regulatory impact of activators on gene expression. Development. 151 (1): dev201986, 2024. DOI: 10.1242/dev.201986

Bernasek SM, Hur SSJ, Peláez-Restrepo N, Lachance JFB, Bakker R, Navarro HT, Sanchez-Luege N, Amaral LAN, Bagheri N, Rebay I^, Carthew RW^. Ratiometric sensing of Pnt and Yan transcription factor levels confers ultrasensitivity to photoreceptor fate transitions in Drosophila. Development. 150 (8): dev201467, 2023. DOI: 10.1242/dev.201467

Cain JY, Yu JS, Bagheri N. The in silico lab: Improving academic code using lessons from biology. Cell Syst. 14(1):1-6, 2023. DOI: 10.1016/j.cels.2022.11.006

Prybutok AN*, Cain JY*, Leonard JN^, Bagheri N^. Fighting fire with fire: deploying complexity in computational modeling to effectively characterize complex biological systems. Curr Opin Biotechnol. 75(102704), 2022. DOI: 10.1016/j.copbio.2022.102704.

Prybutok AN, Yu JS, Leonard JN^, Bagheri N^. Mapping CAR T-cell design space using agent-based models. Front Mol Biosci. 9(849363), 2022. DOI: 10.3389/fmolb.2022.849363

Dray KE, Muldoon JJ, Mangan NM, Bagheri N^, Leonard JN^. GAMES: A dynamic model development workflow for rigorous characterization of synthetic genetic systems. ACS Synth Biol. 11(2):1009–1029, 2022. DOI: 10.1021/acssynbio.1c00528.

Bagheri N, Carpenter AE, Lundberg E, Plant AL, Horwitz R. The new era of quantitative cell imaging—challenges and opportunities. Mol Cell. 82(2), 2022. DOI: 10.1016/j.molcel.2021.12.024

Mousavikhamene Z, Sykora DJ, Mrksich M^, Bagheri N^. Morphological features of single cells enable accurate automated classification of cancer from non-cancer cell lines. Sci Rep. 11, 24375, 2021. DOI: 10.1038/s41598-021-03813-8

Yu JS, Bagheri N. Modular microenvironment components reproduce vascular dynamics de novo in a multi-scale agent-based model. Cell Syst. 12(8):795–809, 2021. DOI: 10.1016/j.cels.2021.05.007.

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

Yu JS, 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 LAN^. Fly-QMA: Automated analysis of mosaic imaginal discs in Drosophila. PLoS Comp Biol. 16, 2020.

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

Donahue PS, Draut JW, Muldoon JJ, Edelstein HI, Bagheri N, Leonard JN. The COMET toolkit for composing customizable genetic programs in mammalian cells. Nat Commun. 11, 2020.

Yamankurt G*, Berns EJ*, Xue AY, Lee A, Bagheri N, Mrksich M, Mirkin CA. 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

Xue AY*, Yu AM*, Lucks JB^, 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.

Muldoon JJ*, Yu JS*, Fassia MK, Bagheri N. Network inference performance complexity: a consequence of topological, experimental, and algorithmic determinants. Bioinform. 2019. DOI: 10.1093/bioinformatics/btz105.

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

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

Bucior BJ, Bobbitt NS, Islamoglu T, Goswami S, Gopalan A, Yildirim T, Farha OK, Bagheri N^, Snurr RQ^. 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 JM*, Ren Z*, Yacoub T, ..., Bagheri N, Hauser AR, Budinger GRS^, Wunderink RG^. Multidimensional assessment of the host response in mechanically ventilated patients with suspected pneumonia. Am J Respir Crit Care Med. 2018. PMID: 30398927.

Finkle JD*, Wu JJ*, 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.

Xue AY, Szymczak LC, 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.

Stainbrook SC*, Yu JS*, Reddick MP, Bagheri N^, Tyo KEJ^. Modulating and evaluating receptor promiscuity through directed evolution and modeling. Protein Eng Des Se. 30(6):455–465, 2017. PMID: 28453776.

Misharin A, ..., Yacoub TJ, ..., Bagheri N, Shilatifard A, Budinger GR, 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.

Hartfield RM*, Schwarz KA*, Muldoon JJ*, Bagheri N, Leonard JN. Multiplexing engineered receptors for multiparametric evaluation of environmental ligands. ACS Synth Biol. 6(11):2042–2055, 2017. PMID: 28771312.

Yu JS, Xue AY, Redei EE, 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 JS, Bagheri N. Multi-class and multi-scale models of complex biological phenomena. Curr Opin Biotechnol. 39:167–173, 2016. PMID: 27779627.

Hill SM, 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 MF, Chen VC, Jones RB, 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 MT*, Shin S*, Wu JJ*, Mays Z, Weng S, Bagheri N^, Miller WM^, Shea LD^. Dynamic transcription factor activity profiles reveal key regulatory interactions during megakaryocytic and erythroid differentiation. Biotechnol Bioeng. 111(10):2082–2094, 2014. PMID: 24853077.

Ciaccio MF, Finkle JD, Xue AY, 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 EM, Hafler DA, Lauffenburger DA, Love JC. 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.

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

Bagheri N*, Shiina M*, Lauffenburger DA, Korn WM. 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*, Taylor SR*, Meeker K, Petzold LR, Doyle III FJ. Synchrony and entrainment properties of robust circadian oscillators. R Soc Interface. 5:S17–S28, 2008. PMID: 18426774.

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

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

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