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Author Details

Neda Bagheri
University of Washington
2007
41
16
Emma Lundberg (CM4AI)
PMIDPaper TitleJournal TitlePublished Year
36657389The in silico lab: Improving academic code using lessons from biology.Cell Syst2023
36942737Ratiometric sensing of Pnt and Yan transcription factor levels confers ultrasensitivity to photoreceptor fate transitions in Drosophila.Development2023
35231773Fighting fire with fire: deploying complexity in computational modeling to effectively characterize complex biological systems.Curr Opin Biotechnol2022
35903149Mapping CAR T-Cell Design Space Using Agent-Based Models.Front Mol Biosci2022
35291433Effect of Preoperative Administration of Oral Melatonin on Pneumatic Tourniquet-Induced Ischemia-Reperfusion Injury in Orthopedic Surgery of Lower Extremities: A Randomized Clinical Trial.Iran J Med Sci2022
35063094The new era of quantitative cell imaging-challenges and opportunities.Mol Cell2022
35271255Correction to "GAMES: A Dynamic Model Development Workflow for Rigorous Characterization of Synthetic Genetic Systems".ACS Synth Biol2022
35023730GAMES: A Dynamic Model Development Workflow for Rigorous Characterization of Synthetic Genetic Systems.ACS Synth Biol2022
34139155Modular microenvironment components reproduce vascular dynamics de novo in a multi-scale agent-based model.Cell Syst2021
33608279Model-guided design of mammalian genetic programs.Sci Adv2021
34934149Morphological features of single cells enable accurate automated classification of cancer from non-cancer cell lines.Sci Rep2021
32126077Fly-QMA: Automated analysis of mosaic imaginal discs in Drosophila.PLoS Comput Biol2020
32054845Macrophages employ quorum licensing to regulate collective activation.Nat Commun2020
32034124The COMET toolkit for composing customizable genetic programs in mammalian cells.Nat Commun2020
32596213Agent-Based Models Predict Emergent Behavior of Heterogeneous Cell Populations in Dynamic Microenvironments.Front Bioeng Biotechnol2020
30398927Multidimensional Assessment of the Host Response in Mechanically Ventilated Patients with Suspected Pneumonia.Am J Respir Crit Care Med2019
31389563DUETT quantitatively identifies known and novel events in nascent RNA structural dynamics from chemical probing data.Bioinformatics2019
31353220Repressive Gene Regulation Synchronizes Development with Cellular Metabolism.Cell2019
30952978Exploration of the nanomedicine-design space with high-throughput screening and machine learning.Nat Biomed Eng2019
30994899Hybrid analysis of gene dynamics predicts context-specific expression and offers regulatory insights.Bioinformatics2019
30932143Network inference performance complexity: a consequence of topological, experimental and algorithmic determinants.Bioinformatics2019
29440433Windowed Granger causal inference strategy improves discovery of gene regulatory networks.Proc Natl Acad Sci U S A2018
28719743Machine Learning on Signal-to-Noise Ratios Improves Peptide Array Design in SAMDI Mass Spectrometry.Anal Chem2017
28453776Modulating and evaluating receptor promiscuity through directed evolution and modeling.Protein Eng Des Sel2017
28771312Multiplexing Engineered Receptors for Multiparametric Evaluation of Environmental Ligands.ACS Synth Biol2017
28694385Monocyte-derived alveolar macrophages drive lung fibrosis and persist in the lung over the life span.J Exp Med2017
27115496Multi-class and multi-scale models of complex biological phenomena.Curr Opin Biotechnol2016
26531308Osteopetrosis in siblings.Intern Emerg Med2016
27779627A support vector machine model provides an accurate transcript-level-based diagnostic for major depressive disorder.Transl Psychiatry2016
26057728The DIONESUS algorithm provides scalable and accurate reconstruction of dynamic phosphoproteomic networks to reveal new drug targets.Integr Biol (Camb)2015
24853077Dynamic transcription factor activity profiles reveal key regulatory interactions during megakaryocytic and erythroid differentiation.Biotechnol Bioeng2014
24813462A systems approach to integrative biology: an overview of statistical methods to elucidate association and architecture.Integr Comp Biol2014
22160692Polyfunctional responses by human T cells result from sequential release of cytokines.Proc Natl Acad Sci U S A2012
21379332A dynamical systems model for combinatorial cancer therapy enhances oncolytic adenovirus efficacy by MEK-inhibition.PLoS Comput Biol2011
22125463Problem of foreign body in GI tract.ScientificWorldJournal2011
21791911Cytologic, immunocytologic, histopathologic and immunohistologic diagnosis of the poorly differentiated sertoli-leydig cell tumor.Acta Cytol2011
20805448Prenatal presentation of a metastasizing rhabdoid tumor with homozygous deletion of the SMARCB1 gene.J Clin Oncol2010
18426774Synchrony and entrainment properties of robust circadian oscillators.J R Soc Interface2008
18795146Circadian phase resetting via single and multiple control targets.PLoS Comput Biol2008
19060261Modeling the Drosophila melanogaster circadian oscillator via phase optimization.J Biol Rhythms2008
17158515Quantitative performance metrics for robustness in circadian rhythms.Bioinformatics2007
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Collaborators

Milan Mrksich
Northwestern University
Co-authored papers 3
Douglas A Lauffenburger
Massachusetts Institute of Technology
Co-authored papers 2
Reiner Siebert
Co-authored papers 1
Alan Rick Horwitz
Allen Institute for Cell Science
Co-authored papers 1
Richard G Wunderink
Northwestern University Feinberg School of Medicine
Co-authored papers 1
Ali Shilatifard
Northwestern University Feinberg School of Medicine
Co-authored papers 1
David A Hafler
Yale School of Medicine, Yale School of Public Health
Co-authored papers 1
Monique Hinchcliff
Yale School of Medicine
Co-authored papers 1
Linda R Petzold
Co-authored papers 1
Anne E Carpenter
Broad Institute of MIT and Harvard
Co-authored papers 1
Anne L Plant
National Institute of Standards and Technology
Co-authored papers 1
Joseph Paonessa
Northwestern University Feinberg School of Medicine
Co-authored papers 1
Emma Lundberg (CM4AI)
Stanford University
Co-authored papers 1
Release 1.2