List of works - Gary An

A Computational, Tissue-Realistic Model of Pressure Ulcer Formation in Individuals with Spinal Cord Injury

scientific article published on 25 June 2015

A case report of thoracic compartment syndrome in the setting of penetrating chest trauma and review of the literature

scientific article published on 30 July 2010

A comparative approach for the investigation of biological information processing: an examination of the structure and function of computer hard drives and DNA

scientific article

A proposal for augmenting biological model construction with a semi-intelligent computational modeling assistant

scientific article published on December 2012

Addressing the translational dilemma: dynamic knowledge representation of inflammation using agent-based modeling

scientific article published on January 2012

Agent-based dynamic knowledge representation of Pseudomonas aeruginosa virulence activation in the stressed gut: Towards characterizing host-pathogen interactions in gut-derived sepsis

scientific article

Agent-based model of epithelial host-pathogen interactions in anastomotic leak

scientific article published on January 2013

Agent-based model of fecal microbial transplant effect on bile acid metabolism on suppressing Clostridium difficile infection: an example of agent-based modeling of intestinal bacterial infection

scientific article

Agent-based models in translational systems biology.

scientific article

Agent-based models of inflammation in translational systems biology: A decade later

scientific article published on 01 July 2019

An agent-based modeling framework linking inflammation and cancer using evolutionary principles: description of a generative hierarchy for the hallmarks of cancer and developing a bridge between mechanism and epidemiological data

scientific article

Augmenting Surgery via Multi-scale Modeling and Translational Systems Biology in the Era of Precision Medicine: A Multidisciplinary Perspective

scientific article

Bayesian inference of the lung alveolar spatial model for the identification of alveolar mechanics associated with acute respiratory distress syndrome

scientific article

Blister fluid composition in a pediatric patient with toxic epidermal necrolysis

scientific article published in July 2008

Chemical scalp burns after hair highlights.

scientific article published on March 2007

Closing the scientific loop: bridging correlation and causality in the petaflop age.

scientific article published in July 2010

Collagen degradation and MMP9 activation by Enterococcus faecalis contribute to intestinal anastomotic leak

scientific article published on May 2015

Computational disease modeling - fact or fiction?

scientific article

Concepts for developing a collaborative in silico model of the acute inflammatory response using agent-based modeling

scientific article published in March 2006

Control of presacral hemorrhage after penetrating trauma: a new technique

scientific article

Detection of intra-abdominal injury using diagnostic peritoneal lavage after shotgun wound to the abdomen.

scientific article published on February 2003

Dynamic knowledge representation using agent-based modeling: ontology instantiation and verification of conceptual models

scientific article published on January 2009

Even ephemeral endotoxin exposure establishes endotoxin tolerance.

scientific article published in April 2008

Evisceration after abdominal stab wounds: is laparotomy required?

scientific article published on October 1999

Examining the Relationship between Pre-Malignant Breast Lesions, Carcinogenesis and Tumor Evolution in the Mammary Epithelium Using an Agent-Based Model

scientific article

Examining the controllability of sepsis using genetic algorithms on an agent-based model of systemic inflammation

scientific article published on 15 February 2018

Examining the pathogenesis of breast cancer using a novel agent-based model of mammary ductal epithelium dynamics

scientific article

Extreme-scale Dynamic Exploration of a Distributed Agent-based Model with the EMEWS Framework

scientific article published on 30 August 2018

From data patterns to mechanistic models in acute critical illness.

scientific article

How implementation of systems biology into clinical trials accelerates understanding of diseases.

scientific article

Hypercalcemia in patients in the burn intensive care unit

scientific article published on 01 September 2007

Immature oxidative stress management as a unifying principle in the pathogenesis of necrotizing enterocolitis: insights from an agent-based model.

scientific article published on 4 January 2012

In Silico Augmentation of the Drug Development Pipeline: Examples from the study of Acute Inflammation.

scientific article

Inflammation and Disease: Modelling and Modulation of the Inflammatory Response to Alleviate Critical Illness

scientific article published on 23 August 2018

Insights into the pathogenesis of ulcerative colitis from a murine model of stasis-induced dysbiosis, colonic metaplasia, and genetic susceptibility

scientific article

Integrating physiology across scales and formalizing hypothesis exploration with agent-based modeling.

scientific article published on 26 March 2015

Integration of TGF-β- and EGFR-based signaling pathways using an agent-based model of epithelial restitution.

scientific article published on 30 October 2012

Intestinal tissues induce an SNP mutation in Pseudomonas aeruginosa that enhances its virulence: possible role in anastomotic leak

scientific article published in 2012

Introduction of a Framework for Dynamic Knowledge Representation of the Control Structure of Transplant Immunology: Employing the Power of Abstraction with a Solid Organ Transplant Agent-Based Model

scientific article published on 6 November 2015

Introduction of an agent-based multi-scale modular architecture for dynamic knowledge representation of acute inflammation

scientific article published on 27 May 2008

Investigation of inflammation and tissue patterning in the gut using a Spatially Explicit General-purpose Model of Enteric Tissue (SEGMEnT).

scientific article

Investigation of the essential role of platelet-tumor cell interactions in metastasis progression using an agent-based model

scientific article published on 12 April 2014

Kinetics and isotype assessment of antibodies targeting the spike protein receptor-binding domain of severe acute respiratory syndrome-coronavirus-2 in COVID-19 patients as a function of age, biological sex and disease severity

scientific article published on 07 October 2020

Learning-accelerated discovery of immune-tumour interactions

scientific article published on 07 June 2019

Linking Inflammation, Cardiorespiratory Variability, and Neural Control in Acute Inflammation via Computational Modeling

scientific article

Mathematical modeling in medicine: a means, not an end.

scientific article published in January 2005

Mathematical models of the acute inflammatory response.

scientific article published in October 2004

Mechanistic simulations of inflammation: current state and future prospects.

scientific article published on 26 August 2008

Multi-scale Modeling in Clinical Oncology: Opportunities and Barriers to Success.

scientific article

Multiscale Modeling in the Clinic: Drug Design and Development

scientific article published on 17 February 2016

Optimization and Control of Agent-Based Models in Biology: A Perspective.

scientific article published on 8 November 2016

Phenomenological issues related to the measurement, mechanisms and manipulation of complex biological systems

scientific article published on 01 January 2006

Proceedings of the first international summit on intestinal anastomotic leak, Chicago, Illinois, October 4-5, 2012.

scientific article published on 12 September 2014

Purpura fulminans in an adult patient with Haemophilus influenzae sepsis: case report and review of the literature.

scientific article

Rapid community-driven development of a SARS-CoV-2 tissue simulator ⬇️

scientific article published on 06 April 2020

Removal of inflammatory ascites is associated with dynamic modification of local and systemic inflammation along with prevention of acute lung injury: in vivo and in silico studies

scientific article published on April 2014

Sepsis: from pattern to mechanism and back.

scientific article published on January 2012

Small to large, lots to some, many to few: in silico navigation of the Translational Dilemma

scientific article published in April 2012

Systems biology and inflammation

scientific article published on 01 January 2010

The Basic Immune Simulator: an agent-based model to study the interactions between innate and adaptive immunity

scientific article

The Crisis of Reproducibility, the Denominator Problem and the Scientific Role of Multi-scale Modeling

scientific article published on 07 September 2018

The Hospital Microbiome Project: Meeting Report for the 1st Hospital Microbiome Project Workshop on sampling design and building science measurements, Chicago, USA, June 7th-8th 2012.

scientific article published on 15 April 2013

The Hospital Microbiome Project: Meeting report for the 2nd Hospital Microbiome Project, Chicago, USA, January 15(th), 2013.

scientific article

The molecular Koch's postulates and surgical infection: a view forward

scientific article published on June 2010

Toll-like receptor 2 ligands on the staphylococcal cell wall downregulate superantigen-induced T cell activation and prevent toxic shock syndrome.

scientific article published in June 2009

Toward computational identification of multiscale "tipping points" in acute inflammation and multiple organ failure

scientific article published on 21 April 2012

Towards anatomic scale agent-based modeling with a massively parallel spatially explicit general-purpose model of enteric tissue (SEGMEnT_HPC).

scientific article

Toxic Epidermal Necrolysis with Gastrointestinal Involvement: A Case Report and Review of the Literature

scientific article published on 30 March 2016

Trans-mediastinal gunshot wounds: are "stable" patients really stable?

scientific article published on 6 September 2002

Translational Systems Biology of Inflammation: Potential Applications to Personalized Medicine ⬇️

scientific article published on September 1, 2010

Translational systems biology of inflammation

scientific article

Translational systems biology using an agent-based approach for dynamic knowledge representation: An evolutionary paradigm for biomedical research

scientific article published on 01 January 2010

List of works by Gary An

A Computational, Tissue-Realistic Model of Pressure Ulcer Formation in Individuals with Spinal Cord Injury

A case report of thoracic compartment syndrome in the setting of penetrating chest trauma and review of the literature

A comparative approach for the investigation of biological information processing: an examination of the structure and function of computer hard drives and DNA

A proposal for augmenting biological model construction with a semi-intelligent computational modeling assistant

Addressing the translational dilemma: dynamic knowledge representation of inflammation using agent-based modeling

Agent-based dynamic knowledge representation of Pseudomonas aeruginosa virulence activation in the stressed gut: Towards characterizing host-pathogen interactions in gut-derived sepsis

Agent-based model of epithelial host-pathogen interactions in anastomotic leak

Agent-based model of fecal microbial transplant effect on bile acid metabolism on suppressing Clostridium difficile infection: an example of agent-based modeling of intestinal bacterial infection

Agent-based models in translational systems biology.

Agent-based models of inflammation in translational systems biology: A decade later

An agent-based modeling framework linking inflammation and cancer using evolutionary principles: description of a generative hierarchy for the hallmarks of cancer and developing a bridge between mechanism and epidemiological data

Augmenting Surgery via Multi-scale Modeling and Translational Systems Biology in the Era of Precision Medicine: A Multidisciplinary Perspective

Bayesian inference of the lung alveolar spatial model for the identification of alveolar mechanics associated with acute respiratory distress syndrome

Blister fluid composition in a pediatric patient with toxic epidermal necrolysis

Chemical scalp burns after hair highlights.

Closing the scientific loop: bridging correlation and causality in the petaflop age.

Collagen degradation and MMP9 activation by Enterococcus faecalis contribute to intestinal anastomotic leak

Computational disease modeling - fact or fiction?

Concepts for developing a collaborative in silico model of the acute inflammatory response using agent-based modeling

Control of presacral hemorrhage after penetrating trauma: a new technique

Detection of intra-abdominal injury using diagnostic peritoneal lavage after shotgun wound to the abdomen.

Dynamic knowledge representation using agent-based modeling: ontology instantiation and verification of conceptual models

Even ephemeral endotoxin exposure establishes endotoxin tolerance.

Evisceration after abdominal stab wounds: is laparotomy required?

Examining the Relationship between Pre-Malignant Breast Lesions, Carcinogenesis and Tumor Evolution in the Mammary Epithelium Using an Agent-Based Model

Examining the controllability of sepsis using genetic algorithms on an agent-based model of systemic inflammation

Examining the pathogenesis of breast cancer using a novel agent-based model of mammary ductal epithelium dynamics

Extreme-scale Dynamic Exploration of a Distributed Agent-based Model with the EMEWS Framework

From data patterns to mechanistic models in acute critical illness.

How implementation of systems biology into clinical trials accelerates understanding of diseases.

Hypercalcemia in patients in the burn intensive care unit

Immature oxidative stress management as a unifying principle in the pathogenesis of necrotizing enterocolitis: insights from an agent-based model.

In Silico Augmentation of the Drug Development Pipeline: Examples from the study of Acute Inflammation.

Inflammation and Disease: Modelling and Modulation of the Inflammatory Response to Alleviate Critical Illness

Insights into the pathogenesis of ulcerative colitis from a murine model of stasis-induced dysbiosis, colonic metaplasia, and genetic susceptibility

Integrating physiology across scales and formalizing hypothesis exploration with agent-based modeling.

Integration of TGF-β- and EGFR-based signaling pathways using an agent-based model of epithelial restitution.

Intestinal tissues induce an SNP mutation in Pseudomonas aeruginosa that enhances its virulence: possible role in anastomotic leak

Introduction of a Framework for Dynamic Knowledge Representation of the Control Structure of Transplant Immunology: Employing the Power of Abstraction with a Solid Organ Transplant Agent-Based Model

Introduction of an agent-based multi-scale modular architecture for dynamic knowledge representation of acute inflammation

Investigation of inflammation and tissue patterning in the gut using a Spatially Explicit General-purpose Model of Enteric Tissue (SEGMEnT).

Investigation of the essential role of platelet-tumor cell interactions in metastasis progression using an agent-based model

Kinetics and isotype assessment of antibodies targeting the spike protein receptor-binding domain of severe acute respiratory syndrome-coronavirus-2 in COVID-19 patients as a function of age, biological sex and disease severity

Learning-accelerated discovery of immune-tumour interactions

Linking Inflammation, Cardiorespiratory Variability, and Neural Control in Acute Inflammation via Computational Modeling

Mathematical modeling in medicine: a means, not an end.

Mathematical models of the acute inflammatory response.

Mechanistic simulations of inflammation: current state and future prospects.

Multi-scale Modeling in Clinical Oncology: Opportunities and Barriers to Success.

Multiscale Modeling in the Clinic: Drug Design and Development

Optimization and Control of Agent-Based Models in Biology: A Perspective.

Phenomenological issues related to the measurement, mechanisms and manipulation of complex biological systems

Proceedings of the first international summit on intestinal anastomotic leak, Chicago, Illinois, October 4-5, 2012.

Purpura fulminans in an adult patient with Haemophilus influenzae sepsis: case report and review of the literature.

Rapid community-driven development of a SARS-CoV-2 tissue simulator ⬇️

Removal of inflammatory ascites is associated with dynamic modification of local and systemic inflammation along with prevention of acute lung injury: in vivo and in silico studies

Sepsis: from pattern to mechanism and back.

Small to large, lots to some, many to few: in silico navigation of the Translational Dilemma

Systems biology and inflammation

The Basic Immune Simulator: an agent-based model to study the interactions between innate and adaptive immunity

The Crisis of Reproducibility, the Denominator Problem and the Scientific Role of Multi-scale Modeling

The Hospital Microbiome Project: Meeting Report for the 1st Hospital Microbiome Project Workshop on sampling design and building science measurements, Chicago, USA, June 7th-8th 2012.

The Hospital Microbiome Project: Meeting report for the 2nd Hospital Microbiome Project, Chicago, USA, January 15(th), 2013.

The molecular Koch's postulates and surgical infection: a view forward

Toll-like receptor 2 ligands on the staphylococcal cell wall downregulate superantigen-induced T cell activation and prevent toxic shock syndrome.

Toward computational identification of multiscale "tipping points" in acute inflammation and multiple organ failure

Towards anatomic scale agent-based modeling with a massively parallel spatially explicit general-purpose model of enteric tissue (SEGMEnT_HPC).

Toxic Epidermal Necrolysis with Gastrointestinal Involvement: A Case Report and Review of the Literature

Trans-mediastinal gunshot wounds: are "stable" patients really stable?

Translational Systems Biology of Inflammation: Potential Applications to Personalized Medicine ⬇️

Translational systems biology of inflammation

Translational systems biology using an agent-based approach for dynamic knowledge representation: An evolutionary paradigm for biomedical research