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Boolean modeling: a logic-based dynamic approach for understanding signaling and regulatory networks and for making useful predictions

Wiley interdisciplinary reviews. Mechanisms of disease, 2014-09, Vol.6 (5), p.353-369

2014

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Executable pathway analysis using ensemble discrete-state modeling for large-scale data

PLoS computational biology, 2019-09, Vol.15 (9), p.e1007317-e1007317

2019

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Pillars of biology: Boolean modeling of gene-regulatory networks

Journal of theoretical biology, 2024-02, Vol.578, p.111682-111682, Article 111682

Thakar, Juilee

2024

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Molecular characterization of atherosclerosis in HIV positive persons

Scientific reports, 2021-02, Vol.11 (1), p.3232-3232, Article 3232

2021

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Meta-analysis of cell- specific transcriptomic data using fuzzy c-means clustering discovers versatile viral responsive genes

BMC bioinformatics, 2017-06, Vol.18 (1), p.295-295, Article 295

2017

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Homeodomain-interacting protein kinase maintains neuronal homeostasis during normal Caenorhabditis elegans aging and systemically regulates longevity from serotonergic and GABAergic neurons

eLife, 2023-06, Vol.12

2023

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IL-1β-driven amyloid plaque clearance is associated with an expansion of transcriptionally reprogrammed microglia

Journal of neuroinflammation, 2019-12, Vol.16 (1), p.261-261, Article 261

2019

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Preparation of noninfectious scRNAseq samples from SARS-CoV-2-infected epithelial cells

PloS one, 2023-02, Vol.18 (2), p.e0281898-e0281898

2023

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Frontline Science: c‐Myc regulates P‐selectin glycoprotein ligand‐1 expression in monocytes during HIV‐1 infection

Journal of leukocyte biology, 2017-10, Vol.102 (4), p.953-964

2017

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Generation and Functional Analysis of Defective Viral Genomes during SARS-CoV-2 Infection

mBio, 2023-06, Vol.14 (3), p.e0025023-e0025023

2023

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Editorial: User-Friendly Tools Applied to Genetics or Systems Biology

Frontiers in genetics, 2020-09, Vol.11, p.985-985

2020

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Boolean network simulations for life scientists

Source code for biology and medicine, 2008-11, Vol.3 (1), p.16-16, Article 16

2008

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Impact of vaccine type on HIV-1 vaccine elicited antibody durability and B cell gene signature

Scientific reports, 2020-08, Vol.10 (1), p.13031-13031, Article 13031

2020

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A systems genomics approach uncovers molecular associates of RSV severity

PLoS computational biology, 2021-12, Vol.17 (12), p.e1009617-e1009617

2021

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Editorial: Innovative Strategies From Synthetic Biology and Bacterial Pathways to Master Biochemical Environmental Challenges

Frontiers in bioengineering and biotechnology, 2022-01, Vol.9, p.828632-828632

2022

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Diversity in Compartmental Dynamics of Gene Regulatory Networks: The Immune Response in Primary Influenza A Infection in Mice

PloS one, 2015-09, Vol.10 (9), p.e0138110-e0138110

2015

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Traditional Farming Lifestyle in Old Older Mennonites Modulates Human Milk Composition

Frontiers in immunology, 2021-10, Vol.12, p.741513

2021

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Network model of immune responses reveals key effectors to single and co-infection dynamics by a respiratory bacterium and a gastrointestinal helminth

PLoS computational biology, 2012-01, Vol.8 (1), p.e1002345-e1002345

2012

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Humoral Dysregulation Associated with Increased Systemic Inflammation among Injection Heroin Users

PloS one, 2016-07, Vol.11 (7), p.e0158641

2016

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Computational and experimental analysis reveals a requirement for eosinophil-derived IL-13 for the development of allergic airway responses in C57BL/6 mice

The Journal of immunology (1950), 2011-03, Vol.186 (5), p.2936-2949

2011

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Cyclosporine a directly affects human and mouse b cell migration in vitro by disrupting a hIF-1 αdependent, o2 sensing, molecular switch

BMC immunology, 2020-03, Vol.21 (1), p.1-18, Article 13

2020

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Cyclosporine A Modulates LSP1 Protein Levels in Human B Cells to Attenuate B Cell Migration at Low O2 Levels

Life (Basel, Switzerland), 2022-08, Vol.12 (8), p.1284

2022

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Executable models of immune signaling pathways in HIV-associated atherosclerosis

NPJ systems biology and applications, 2022-09, Vol.8 (1), p.35-35, Article 35

2022

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Novel Sequence-Based Mapping of Recently Emerging H5NX Influenza Viruses Reveals Pandemic Vaccine Candidates

PloS one, 2016-08, Vol.11 (8), p.e0160510

2016

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Modeling systems-level regulation of host immune responses

PLoS computational biology, 2007-06, Vol.3 (6), p.e109-e109

2007

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Boolean modeling: a logic-based dynamic approach for understanding signaling and regulatory networks and for making useful predictions

Executable pathway analysis using ensemble discrete-state modeling for large-scale data

Pillars of biology: Boolean modeling of gene-regulatory networks

Molecular characterization of atherosclerosis in HIV positive persons

Meta-analysis of cell- specific transcriptomic data using fuzzy c-means clustering discovers versatile viral responsive genes

Homeodomain-interacting protein kinase maintains neuronal homeostasis during normal Caenorhabditis elegans aging and systemically regulates longevity from serotonergic and GABAergic neurons

IL-1β-driven amyloid plaque clearance is associated with an expansion of transcriptionally reprogrammed microglia

Preparation of noninfectious scRNAseq samples from SARS-CoV-2-infected epithelial cells

Frontline Science: c‐Myc regulates P‐selectin glycoprotein ligand‐1 expression in monocytes during HIV‐1 infection

Generation and Functional Analysis of Defective Viral Genomes during SARS-CoV-2 Infection

Editorial: User-Friendly Tools Applied to Genetics or Systems Biology

Boolean network simulations for life scientists

Impact of vaccine type on HIV-1 vaccine elicited antibody durability and B cell gene signature

A systems genomics approach uncovers molecular associates of RSV severity

Editorial: Innovative Strategies From Synthetic Biology and Bacterial Pathways to Master Biochemical Environmental Challenges

Diversity in Compartmental Dynamics of Gene Regulatory Networks: The Immune Response in Primary Influenza A Infection in Mice

Traditional Farming Lifestyle in Old Older Mennonites Modulates Human Milk Composition

Network model of immune responses reveals key effectors to single and co-infection dynamics by a respiratory bacterium and a gastrointestinal helminth

Humoral Dysregulation Associated with Increased Systemic Inflammation among Injection Heroin Users

Computational and experimental analysis reveals a requirement for eosinophil-derived IL-13 for the development of allergic airway responses in C57BL/6 mice

Cyclosporine a directly affects human and mouse b cell migration in vitro by disrupting a hIF-1 αdependent, o2 sensing, molecular switch

Cyclosporine A Modulates LSP1 Protein Levels in Human B Cells to Attenuate B Cell Migration at Low O2 Levels

Executable models of immune signaling pathways in HIV-associated atherosclerosis

Novel Sequence-Based Mapping of Recently Emerging H5NX Influenza Viruses Reveals Pandemic Vaccine Candidates

Modeling systems-level regulation of host immune responses

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