Julia Hoeng

Verification of systems biology research in the age of collaborative competition.

Identification of new human cadherin genes using a combination of protein motif search and gene finding methods.

An ATP gate controls tubulin binding by the tethered head of kinesin-1.

Construction of a computable cell proliferation network focused on non-diseased lung cells.

A computable cellular stress network model for non-diseased pulmonary and cardiovascular tissue.

A network-based approach to quantifying the impact of biologically active substances.

Industrial methodology for process verification in research (IMPROVER): toward systems biology verification.

Assessment of network perturbation amplitudes by applying high-throughput data to causal biological networks.

Modulation of atherogenic lipidome by cigarette smoke in apolipoprotein E-deficient mice.

Human bronchial epithelial cells exposed in vitro to cigarette smoke at the air-liquid interface resemble bronchial epithelium from human smokers.

Construction of a computable network model for DNA damage, autophagy, cell death, and senescence.

Cigarette-smoke-induced atherogenic lipid profiles in plasma and vascular tissue of apolipoprotein E-deficient mice are attenuated by smoking cessation.

A modular cell-type focused inflammatory process network model for non-diseased pulmonary tissue.

Systems approaches to computational modeling of the oral microbiome.

Confero: an integrated contrast data and gene set platform for computational analysis and biological interpretation of omics data.

Systematic verification of upstream regulators of a computable cellular proliferation network model on non-diseased lung cells using a dedicated dataset.

Quantitative assessment of biological impact using transcriptomic data and mechanistic network models.

Case study: the role of mechanistic network models in systems toxicology.

Strengths and limitations of microarray-based phenotype prediction: lessons learned from the IMPROVER Diagnostic Signature Challenge.

Cigarette smoke induces molecular responses in respiratory tissues of ApoE(-/-) mice that are progressively deactivated upon cessation.

On Crowd-verification of Biological Networks.

Systems approaches evaluating the perturbation of xenobiotic metabolism in response to cigarette smoke exposure in nasal and bronchial tissues.

Systems biology approach for evaluating the biological impact of environmental toxicants in vitro.

Systems toxicology: from basic research to risk assessment.

Discovery of Emphysema Relevant Molecular Networks from an A/J Mouse Inhalation Study Using Reverse Engineering and Forward Simulation (REFS™).

A 28-day rat inhalation study with an integrated molecular toxicology endpoint demonstrates reduced exposure effects for a prototypic modified risk tobacco product compared with conventional cigarettes.

Mechanism of an indirect effect of aqueous cigarette smoke extract on the adhesion of monocytic cells to endothelial cells in an in vitro assay revealed by transcriptomics analysis.

Assessment of a novel multi-array normalization method based on spike-in control probes suitable for microRNA datasets with global decreases in expression.

A vascular biology network model focused on inflammatory processes to investigate atherogenesis and plaque instability.

Quantification of biological network perturbations for mechanistic insight and diagnostics using two-layer causal models.

In vitro systems toxicology approach to investigate the effects of repeated cigarette smoke exposure on human buccal and gingival organotypic epithelial tissue cultures.

CSEO - the Cigarette Smoke Exposure Ontology.

Understanding the limits of animal models as predictors of human biology: lessons learned from the sbv IMPROVER Species Translation Challenge.

A crowd-sourcing approach for the construction of species-specific cell signaling networks.

The response of human nasal and bronchial organotypic tissue cultures to repeated whole cigarette smoke exposure.

Proteomics for systems toxicology.

Characterization of the Vitrocell® 24/48 in vitro aerosol exposure system using mainstream cigarette smoke.

Reputation-based collaborative network biology.

Enhancement of COPD biological networks using a web-based collaboration interface.

A systems biology approach reveals the dose- and time-dependent effect of primary human airway epithelium tissue culture after exposure to cigarette smoke in vitro.

Systems Toxicology: The Future of Risk Assessment.

A prototypic modified risk tobacco product exhibits reduced effects on chemotaxis and transendothelial migration of monocytes compared with a reference cigarette.

A 7-month cigarette smoke inhalation study in C57BL/6 mice demonstrates reduced lung inflammation and emphysema following smoking cessation or aerosol exposure from a prototypic modified risk tobacco product.

Causal biological network database: a comprehensive platform of causal biological network models focused on the pulmonary and vascular systems.

Transcriptional profiling and targeted proteomics reveals common molecular changes associated with cigarette smoke-induced lung emphysema development in five susceptible mouse strains.

The species translation challenge-a systems biology perspective on human and rat bronchial epithelial cells.

Impact Assessment of Cigarette Smoke Exposure on Organotypic Bronchial Epithelial Tissue Cultures: A Comparison of Mono-Culture and Coculture Model Containing Fibroblasts.

Systems toxicology approaches enable mechanistic comparison of spontaneous and cigarette smoke-related lung tumor development in the A/J mouse model.

Systems Biology Research into Cardiovascular Disease: Contributions of Lipidomics-based Approaches to Biomarker Discovery.

Systems Biology Reveals Cigarette Smoke-Induced Concentration-Dependent Direct and Indirect Mechanisms That Promote Monocyte-Endothelial Cell Adhesion.

Construction of biological networks from unstructured information based on a semi-automated curation workflow.

Toxicity of aerosols of nicotine and pyruvic acid (separate and combined) in Sprague-Dawley rats in a 28-day OECD 412 inhalation study and assessment of systems toxicology.

Alterations in the sputum proteome and transcriptome in smokers and early-stage COPD subjects.

Aerosol from a candidate modified risk tobacco product has reduced effects on chemotaxis and transendothelial migration compared to combustion of conventional cigarettes.

Effects of Cigarette Smoke, Cessation, and Switching to Two Heat-Not-Burn Tobacco Products on Lung Lipid Metabolism in C57BL/6 and Apoe-/- Mice-An Integrative Systems Toxicology Analysis.

An 8-Month Systems Toxicology Inhalation/Cessation Study in Apoe-/- Mice to Investigate Cardiovascular and Respiratory Exposure Effects of a Candidate Modified Risk Tobacco Product, THS 2.2, Compared With Conventional Cigarettes.

In Vitro Systems Toxicology Assessment of a Candidate Modified Risk Tobacco Product Shows Reduced Toxicity Compared to That of a Conventional Cigarette.

Systems toxicology-based assessment of the candidate modified risk tobacco product THS2.2 for the adhesion of monocytic cells to human coronary arterial endothelial cells.

Comprehensive systems biology analysis of a 7-month cigarette smoke inhalation study in C57BL/6 mice.

Effects of cigarette smoke, cessation and switching to a candidate modified risk tobacco product on the liver in Apoe(-/-) mice - a systems toxicology analysis.

A framework for in vitro systems toxicology assessment of e-liquids.

The Apoe(-/-) mouse model: a suitable model to study cardiovascular and respiratory diseases in the context of cigarette smoke exposure and harm reduction.

3-D nasal cultures: Systems toxicological assessment of a candidate modified-risk tobacco product.

Community-Reviewed Biological Network Models for Toxicology and Drug Discovery Applications.

Evaluation of the Tobacco Heating System 2.2. Part 1: Description of the system and the scientific assessment program.

Training and evaluation corpora for the extraction of causal relationships encoded in biological expression language (BEL).

Alterations in Serum Polyunsaturated Fatty Acids and Eicosanoids in Patients with Mild to Moderate Chronic Obstructive Pulmonary Disease (COPD).

A new fluorescence-based method for characterizing in vitro aerosol exposure systems.

The BEL information extraction workflow (BELIEF): evaluation in the BioCreative V BEL and IAT track.

Evaluation of the Tobacco Heating System 2.2. Part 4: 90-day OECD 413 rat inhalation study with systems toxicology endpoints demonstrates reduced exposure effects compared with cigarette smoke.

Evaluation of the Tobacco Heating System 2.2. Part 7: Systems toxicological assessment of a mentholated version revealed reduced cellular and molecular exposure effects compared with mentholated and non-mentholated cigarette smoke.

Evaluation of the Tobacco Heating System 2.2. Part 6: 90-day OECD 413 rat inhalation study with systems toxicology endpoints demonstrates reduced exposure effects of a mentholated version compared with mentholated and non-mentholated cigarette smoke.

Semi-Automated Curation Allows Causal Network Model Building for the Quantification of Age-Dependent Plaque Progression in ApoE Mouse.

Evaluation of the tobacco heating system 2.2. Part 9: Application of systems pharmacology to identify exposure response markers in peripheral blood of smokers switching to THS2.2.

A systems toxicology approach for comparative assessment: Biological impact of an aerosol from a candidate modified-risk tobacco product and cigarette smoke on human organotypic bronchial epithelial cultures.

Evaluation of the Tobacco Heating System 2.2 (THS2.2). Part 5: microRNA expression from a 90-day rat inhalation study indicates that exposure to THS2.2 aerosol causes reduced effects on lung tissue compared with cigarette smoke.

Comparative systems toxicology analysis of cigarette smoke and aerosol from a candidate modified risk tobacco product in organotypic human gingival epithelial cultures: A 3-day repeated exposure study.

Crowd-Sourced Verification of Computational Methods and Data in Systems Toxicology: A Case Study with a Heat-Not-Burn Candidate Modified Risk Tobacco Product.

Aerosol from Tobacco Heating System 2.2 has reduced impact on mouse heart gene expression compared with cigarette smoke.

Characterization of the Vitrocell® 24/48 aerosol exposure system for its use in exposures to liquid aerosols.

Multicomponent aerosol particle deposition in a realistic cast of the human upper respiratory tract.

Novel approaches to develop community-built biological network models for potential drug discovery.

Toxicity of the main electronic cigarette components, propylene glycol, glycerin, and nicotine, in Sprague-Dawley rats in a 90-day OECD inhalation study complemented by molecular endpoints.

Supporting evidence-based analysis for modified risk tobacco products through a toxicology data-sharing infrastructure.

Effects of cigarette smoking on color stability of dental resin composites.

Assessment of mitochondrial function following short- and long-term exposure of human bronchial epithelial cells to total particulate matter from a candidate modified-risk tobacco product and reference cigarettes.

Comparative biological impacts of an aerosol from carbon-heated tobacco and smoke from cigarettes on human respiratory epithelial cultures: A systems toxicology assessment.

Assessment of the impact of aerosol from a potential modified risk tobacco product compared with cigarette smoke on human organotypic oral epithelial cultures under different exposure regimens.

The biological effects of long-term exposure of human bronchial epithelial cells to total particulate matter from a candidate modified-risk tobacco product.

A 90-day OECD TG 413 rat inhalation study with systems toxicology endpoints demonstrates reduced exposure effects of the aerosol from the carbon heated tobacco product version 1.2 (CHTP1.2) compared with cigarette smoke. II. Systems toxicology assessment.

A 90-day OECD TG 413 rat inhalation study with systems toxicology endpoints demonstrates reduced exposure effects of the aerosol from the carbon heated tobacco product version 1.2 (CHTP1.2) compared with cigarette smoke. I. Inhalation exposure, clinical pathology and histopathology.

Interrogating the microbiome: experimental and computational considerations in support of study reproducibility.

Delivery efficiencies of constituents of combustion-derived aerosols across the air-liquid interface during in vitro exposures.

In vitro systems toxicology-based assessment of the potential modified risk tobacco product CHTP 1.2 for vascular inflammation- and cytotoxicity-associated mechanisms promoting adhesion of monocytic cells to human coronary arterial endothelial cells.

Systems toxicology meta-analysis of assessment studies: biological impact of a candidate modified-risk tobacco product aerosol compared with cigarette smoke on human organotypic cultures of the aerodigestive tract.

Comparative effects of a candidate modified-risk tobacco product Aerosol and cigarette smoke on human organotypic small airway cultures: a systems toxicology approach.

The sbv IMPROVER Systems Toxicology Computational Challenge: Identification of Human and Species-Independent Blood Response Markers as Predictors of Smoking Exposure and Cessation Status.

Proteomics and Lipidomics in Inflammatory Bowel Disease Research: From Mechanistic Insights to Biomarker Identification.

Embracing Transparency Through Data Sharing.

Tobacco Heating System 2.2 has a limited impact on DNA methylation of candidate enhancers in mouse lung compared with cigarette smoke.

A lung/liver-on-a-chip platform for acute and chronic toxicity studies.

Assessment of a 72-hour repeated exposure to Swedish snus extract and total particulate matter from 3R4F cigarette smoke on gingival organotypic cultures.

Effects of Natural Monoamine Oxidase Inhibitors on Anxiety-Like Behavior in Zebrafish.

Corrigendum to "The biological effects of long-term exposure of human bronchial epithelial cells to total particulate matter from a candidate modified-risk tobacco product" published in Toxicology in Vitro, Volume 50, August 2018, Pages 95-108.

How complex should an in vitro model be? Evaluation of complex 3D alveolar model with transcriptomic data and computational biological network models.

A six-month systems toxicology inhalation/cessation study in ApoE mice to investigate cardiovascular and respiratory exposure effects of modified risk tobacco products, CHTP 1.2 and THS 2.2, compared with conventional cigarettes.

Assessing the lung cancer risk reduction potential of candidate modified risk tobacco products.

Construction of a Suite of Computable Biological Network Models Focused on Mucociliary Clearance in the Respiratory Tract.

A lower impact of an acute exposure to electronic cigarette aerosols than to cigarette smoke in human organotypic buccal and small airway cultures was demonstrated using systems toxicology assessment.

Biological changes in C57BL/6 mice following 3 weeks of inhalation exposure to cigarette smoke or e-vapor aerosols.

GladiaTOX: GLobal Assessment of Dose-IndicAtor in TOXicology.

Toxicological assessment of Tobacco Heating System 2.2: Findings from an independent peer review.

A Meta-Analysis of the Performance of a Blood-Based Exposure Response Gene Signature Across Clinical Studies on the Tobacco Heating System 2.2 (THS 2.2).

Impact of sample preparation upon intracellular metabolite measurements in 3D cell culture systems.

Mitochondria as a possible target for nicotine action.

Antiparasitic properties of leaf extracts derived from selected Nicotiana species and Nicotiana tabacum varieties.

Effects of different discoloration challenges and whitening treatments on dental hard tissues and composite resin restorations.

3D human microvessel-on-a-chip model for studying monocyte-to-endothelium adhesion under flow - application in systems toxicology.

NPA: an R package for computing network perturbation amplitudes using gene expression data and two-layer networks.

Application of a multi-layer systems toxicology framework for in vitro assessment of the biological effects of Classic Tobacco e-liquid and its corresponding aerosol using an e-cigarette device with MESH™ technology.

Respirable aerosol exposures of nicotine dry powder formulations to , , and pre-clinical models demonstrate consistency of pharmacokinetic profiles.

The extraction of complex relationships and their conversion to biological expression language (BEL) overview of the BioCreative VI (2017) BEL track.

Structural, functional, and molecular impact on the cardiovascular system in ApoE mice exposed to aerosol from candidate modified risk tobacco products, Carbon Heated Tobacco Product 1.2 and Tobacco Heating System 2.2, compared with cigarette smoke.

Neurobehavioral effects of selected tobacco constituents in rodents following subchronic administration.

Comparison of monoamine oxidase inhibition by cigarettes and modified risk tobacco products.

An electrophysiological characterization of naturally occurring tobacco alkaloids and their action on human α4β2 and α7 nicotinic acetylcholine receptors.

Systems toxicology assessment of a representative e-liquid formulation using human primary bronchial epithelial cells.

Assessment of Single-Photon Ionization Mass Spectrometry for Online Monitoring of Aerosol Exposure Experiments.

In Vitro High-Content Imaging-Based Phenotypic Analysis of Bronchial 3D Organotypic Air-Liquid Interface Cultures.

Anthropometry-based generation of personalized and population-specific human airway models.

Alternatives to Animal Use in Risk Assessment of Mixtures.

The reduction of DSS-induced colitis severity in mice exposed to cigarette smoke is linked to immune modulation and microbial shifts.

Mitochondrial Network and Biogenesis in Response to Short and Long-Term Exposure of Human BEAS-2B Cells to Aerosol Extracts from the Tobacco Heating System 2.2.

Comparison of experimentally measured and computational fluid dynamic predicted deposition and deposition uniformity of monodisperse solid particles in the Vitrocell® AMES 48 air-liquid-interface in-vitro exposure system.

Lipid-based biomarkers for CVD, COPD, and aging - A translational perspective.

Evaluation of toxicity of aerosols from flavored e-liquids in Sprague-Dawley rats in a 90-day OECD inhalation study, complemented by transcriptomics analysis.

Human multi-organ chip co-culture of bronchial lung culture and liver spheroids for substance exposure studies.

Multi-omics systems toxicology study of mouse lung assessing the effects of aerosols from two heat-not-burn tobacco products and cigarette smoke.

An Intestine-on-a-Chip Model of Plug-and-Play Modularity to Study Inflammatory Processes.

Analysis of chemical deposits on tooth enamel exposed to total particulate matter from cigarette smoke and tobacco heating system 2.2 aerosol by novel GC-MS deconvolution procedures.

Systems Toxicology Approach for Testing Chemical Cardiotoxicity in Larval Zebrafish.

Inflammatory Bowel Disease-Associated Changes in the Gut: Focus on Kazan Patients.

Reduced Chronic Toxicity and Carcinogenicity in A/J Mice in Response to Life-Time Exposure to Aerosol From a Heated Tobacco Product Compared With Cigarette Smoke.

Respiratory Effects of Exposure to Aerosol From the Candidate Modified-Risk Tobacco Product THS 2.2 in an 18-Month Systems Toxicology Study With A/J Mice.

Anatabine ameliorates intestinal inflammation and reduces the production of pro-inflammatory factors in a dextran sulfate sodium mouse model of colitis.

Comparing the preclinical risk profile of inhalable candidate and potential candidate modified risk tobacco products: A bridging use case.

A meta-analysis of microRNAs expressed in human aerodigestive epithelial cultures and their role as potential biomarkers of exposure response to nicotine-containing products.

Ceramide ratios are affected by cigarette smoke but not heat-not-burn or e-vapor aerosols across four independent mouse studies.

Impact of switching to a heat-not-burn tobacco product on CYP1A2 activity.

Comparison of the biological impact of aerosol of e-vapor device with MESH® technology and cigarette smoke on human bronchial and alveolar cultures.

Profiling of a Natural Alkaloid, Anatabine, in Rodents: Pharmacokinetics and Anti-Inflammatory Efficacy.

Impact of whole-body versus nose-only inhalation exposure systems on systemic, respiratory, and cardiovascular endpoints in a 2-month cigarette smoke exposure study in the ApoE mouse model.

Development of an Advanced Multicellular Intestinal Model for Assessing Immunomodulatory Properties of Anti-Inflammatory Compounds.

Effects of whitening toothpaste and bleaching treatment on resin composite discoloration caused by cigarette smoke and electronic vapor aerosol.

A 6-month inhalation toxicology study in Apoe mice demonstrates substantially lower effects of e-vapor aerosol compared with cigarette smoke in the respiratory tract.

Differential effects of alkaloids on memory in rodents.

Systems biology approach highlights mechanistic differences between Crohn's disease and ulcerative colitis.

Effects of plant alkaloids on mitochondrial bioenergetic parameters.

Subchronic effects of plant alkaloids on anxiety-like behavior in zebrafish.

Systems Toxicology Approach for Assessing Developmental Neurotoxicity in Larval Zebrafish.

Effects of nicotinic acetylcholine receptor-activating alkaloids on anxiety-like behavior in zebrafish.

Impact of 6-Month Exposure to Aerosols From Potential Modified Risk Tobacco Products Relative to Cigarette Smoke on the Rodent Gastrointestinal Tract.

Systems toxicology study reveals reduced impact of heated tobacco product aerosol extract relative to cigarette smoke on premature aging and exacerbation effects in aged aortic cells in vitro.

Comparison of the basic morphology and function of 3D lung epithelial cultures derived from several donors.

A simple method for decellularizing a cell-derived matrix for bone cell cultivation and differentiation.

Assessment of in vitro kinetics and biological impact of nebulized trehalose on human bronchial epithelium.

Impact of aerosols on liver xenobiotic metabolism: A comparison of two methods of exposure.

Iota-carrageenan extracted from red algae is a potent inhibitor of SARS-CoV-2 infection in reconstituted human airway epithelia.

Translational Modeling of Chloroquine and Hydroxychloroquine Dosimetry in Human Airways for Treating Viral Respiratory Infections.

A Literature Review and Framework Proposal for Halitosis Assessment in Cigarette Smokers and Alternative Nicotine-Delivery Products Users.

AI-driven laboratory workflows enable operation in the age of social distancing.

Pulmonary Delivery of Aerosolized Chloroquine and Hydroxychloroquine to Treat COVID-19: In Vitro Experimentation to Human Dosing Predictions.

Influence of tobacco smoking on the development of halitosis.

Discriminating Spontaneous From Cigarette Smoke and THS 2.2 Aerosol Exposure-Related Proliferative Lung Lesions in A/J Mice by Using Gene Expression and Mutation Spectrum Data.

Effects of cigarette smoke exposure on a mouse model of multiple sclerosis.

Differentiating the Neuropharmacological Properties of Nicotinic Acetylcholine Receptor-Activating Alkaloids.