Introduction to Editorial Board Member: Professor Francis J. Doyle III

by Bagheri, Neda, Gunawan, Rudiyanto
Published in Bioeng Transl Med (2017)

Agent-Based Models Predict Emergent Behavior of Heterogeneous Cell Populations in Dynamic Microenvironments

by Yu, Jessica S., Bagheri, Neda
Published in Front Bioeng Biotechnol (2020)

Hybrid analysis of gene dynamics predicts context-specific expression and offers regulatory insights

by Finkle, Justin D, Bagheri, Neda
Published in Bioinformatics (2019)

Circadian Phase Resetting via Single and Multiple Control Targets

by Bagheri, Neda, Stelling, Jörg, Doyle, Francis J.
Published 2008

Windowed Granger causal inference strategy improves discovery of gene regulatory networks

by Finkle, Justin D., Wu, Jia J., Bagheri, Neda
Published in Proc Natl Acad Sci U S A (2018)

Modeling the Drosophila melanogaster Circadian Oscillator via Phase Optimization

by Bagheri, Neda, Lawson, Michael J., Stelling, Jörg, Doyle, Francis J.
Published 2008

A Dynamical Systems Model for Combinatorial Cancer Therapy Enhances Oncolytic Adenovirus Efficacy by MEK-Inhibition

by Bagheri, Neda, Shiina, Marisa, Lauffenburger, Douglas A., Korn, W. Michael
Published 2011

Machine Learning on Signal-to-Noise Ratios Improves Peptide Array Design in SAMDI Mass Spectrometry

by Xue, Albert Y., Szymczak, Lindsey C., Mrksich, Milan, Bagheri, Neda
Published in Anal Chem (2017)

Network inference performance complexity: a consequence of topological, experimental and algorithmic determinants

by Muldoon, Joseph J, Yu, Jessica S, Fassia, Mohammad-Kasim, Bagheri, Neda
Published in Bioinformatics (2019)

Macrophages employ quorum licensing to regulate collective activation

by Muldoon, Joseph J., Chuang, Yishan, Bagheri, Neda, Leonard, Joshua N.
Published in Nat Commun (2020)

A Systems Approach to Integrative Biology: An Overview of Statistical Methods to Elucidate Association and Architecture

by Ciaccio, Mark F., Finkle, Justin D., Xue, Albert Y., Bagheri, Neda
Published 2014

The DIONESUS algorithm provides scalable and accurate reconstruction of dynamic phosphoproteomic networks to reveal new drug targets

by Ciaccio, Mark F., Chen, Vincent C., Jones, Richard B., Bagheri, Neda
Published in Integr Biol (Camb) (2015)

DUETT quantitatively identifies known and novel events in nascent RNA structural dynamics from chemical probing data

by Xue, Albert Y, Yu, Angela M, Lucks, Julius B, Bagheri, Neda
Published in Bioinformatics (2019)

Synchrony and entrainment properties of robust circadian oscillators

by Bagheri, Neda, Taylor, Stephanie R., Meeker, Kirsten, Petzold, Linda R., Doyle, Francis J.
Published 2008

Multiplexing engineered receptors for multiparametric evaluation of environmental ligands

by Hartfield, Rachel M., Schwarz, Kelly A., Muldoon, Joseph J., Bagheri, Neda, Leonard, Joshua N.
Published in ACS Synth Biol (2017)

Modulating and evaluating receptor promiscuity through directed evolution and modeling

by Stainbrook, Sarah C., Yu, Jessica S., Reddick, Michael P., Bagheri, Neda, Tyo, Keith E. J.
Published in Protein Eng Des Sel (2017)

Fly-QMA: Automated analysis of mosaic imaginal discs in Drosophila

by Bernasek, Sebastian M., Peláez, Nicolás, Carthew, Richard W., Bagheri, Neda, Amaral, Luís A. N.
Published in PLoS Comput Biol (2020)

Problem of Foreign Body in GI Tract

by Daneshbod, Yahya, Talei, Abdolrasoul, Negahban, Shahrzad, Soleimanpour, Hossein, Aledavoud, Azita, Bagheri, Neda, Khanlari, Mahsa, Daneshbod, Khosrow
Published 2011

Polyfunctional responses by human T cells result from sequential release of cytokines

by Han, Qing, Bagheri, Neda, Bradshaw, Elizabeth M., Hafler, David A., Lauffenburger, Douglas A., Love, J. Christopher
Published 2012

Exploration of the nanomedicine-design space with high-throughput screening and machine learning

by Yamankurt, Gokay, Berns, Eric J., Xue, Albert, Lee, Andrew, Bagheri, Neda, Mrksich, Milan, Mirkin, Chad A.
Published in Nat Biomed Eng (2019)