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BioNetGen 2.2: advances in rule-based modeling

Bioinformatics (Oxford, England), 2016-11, Vol.32 (21), p.3366-3368

2016

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Characterization and modeling of the Haemophilus influenzae core and supragenomes based on the complete genomic sequences of Rd and 12 clinical nontypeable strains

Genome biology, 2007-06, Vol.8 (6), p.R103-R103, Article R103

2007

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Comparative Genomic Analyses of Seventeen Streptococcus pneumoniae Strains: Insights into the Pneumococcal Supragenome

Journal of Bacteriology, 2007-11, Vol.189 (22), p.8186-8195

2007

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Exact hybrid particle/population simulation of rule-based models of biochemical systems

PLoS computational biology, 2014-04, Vol.10 (4), p.e1003544-e1003544

2014

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Comparative supragenomic analyses among the pathogens Staphylococcus aureus, Streptococcus pneumoniae, and Haemophilus influenzae using a modification of the finite supragenome model

BMC genomics, 2011-04, Vol.12 (1), p.187-187, Article 187

2011

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Modeling and Hemofiltration Treatment of Acute Inflammation

Processes, 2016-12, Vol.4 (4), p.38-38

2016

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Real-time optimization of cytokine-selective hemoadsorption devices for treatment of acute inflammation

Journal of critical care, 2011-04, Vol.26 (2), p.e14-e14

2011

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A compartmental model reveals a mechanism for misregulation of neutrophil trafficking in sepsis

Journal of critical care, 2009-09, Vol.24 (3), p.e29-e30

2009

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Evaluation of Parallel Tempering to Accelerate Bayesian Parameter Estimation in Systems Biology

2018 26th Euromicro International Conference on Parallel, Distributed and Network-based Processing (PDP), 2018, p.690-697

2018

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Exact Hybrid Particle/Population Simulation of Rule-Based Models of Biochemical Systems: e1003544

PLoS computational biology, 2014-04, Vol.10 (4)

2014

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Compartmental rule-based modeling of biochemical systems

Proceedings of the 2009 Winter Simulation Conference (WSC), 2009, p.908-919

2009

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Advances in rule-based modeling: Compartments, energy, and hybrid simulation, with application to sepsis and cell signaling

Hogg, Justin S

2013

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Energy-based modeling in BioNetGen

2016 IEEE International Conference on Bioinformatics and Biomedicine (BIBM), 2016, p.1460-1467

2016

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Comparative genomic analyses of seventeen Streptococcus pneumoniae strains : Insights into the pneumococcal supragenome : Biofilms 2007: broadened horizon and new emphases

Journal of bacteriology, 2007, Vol.189 (22), p.8186-8195

2007

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Acute Inflammation Treatment via Particle Filter State Estimation and MPC

IFAC Proceedings Volumes, 2010, Vol.43 (5), p.272-277

2010

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Compartmental rule-based modeling of biochemical systems

Winter Simulation Conference, 2009, p.908-919

2009

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Kronos and Krios: Evidence for Accretion of a Massive, Rocky Planetary System in a Comoving Pair of Solar-type Stars

The Astrophysical journal, 2018-02, Vol.854 (2), p.138

2018

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Alternative Lengthening of Telomeres and Loss of DAXX/ATRX Expression Predicts Metastatic Disease and Poor Survival in Patients with Pancreatic Neuroendocrine Tumors

Clinical cancer research, 2017-01, Vol.23 (2), p.600-609

2017

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‘Excited Delirium’ Reflects System of Control, Not Care for MH Crises

Psychiatric news, 2024-01, Vol.59 (1)

2024

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NUDT21 limits CD19 levels through alternative mRNA polyadenylation in B cell acute lymphoblastic leukemia

Nature immunology, 2022-10, Vol.23 (10), p.1424-1432

2022

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Demographic Factors and Instantaneous Lower Extremity Injury Occurrence in a National Collegiate Athletic Association Division I Population

Journal of athletic training, 2023-05, Vol.58 (5), p.393-400

2023

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Examining differential success in recruitment using respondent driven sampling (RDS) in a multi-site study of gay, bisexual and other men who have sex with men

BMC medical research methodology, 2023-06, Vol.23 (1), p.136-12, Article 136

2023

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E7820, an anti-cancer sulfonamide, degrades RBM39 in patients with splicing factor mutant myeloid malignancies: a phase II clinical trial

Leukemia, 2023-12, Vol.37 (12), p.2512-2516

2023

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Minor intron retention drives clonal hematopoietic disorders and diverse cancer predisposition

Nature genetics, 2021-05, Vol.53 (5), p.707-718

2021

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Impaired Proteolysis of Noncanonical RAS Proteins Drives Clonal Hematopoietic Transformation

Cancer discovery, 2022-10, Vol.12 (10), p.2434-2453

2022

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BioNetGen 2.2: advances in rule-based modeling

Characterization and modeling of the Haemophilus influenzae core and supragenomes based on the complete genomic sequences of Rd and 12 clinical nontypeable strains

Comparative Genomic Analyses of Seventeen Streptococcus pneumoniae Strains: Insights into the Pneumococcal Supragenome

Exact hybrid particle/population simulation of rule-based models of biochemical systems

Comparative supragenomic analyses among the pathogens Staphylococcus aureus, Streptococcus pneumoniae, and Haemophilus influenzae using a modification of the finite supragenome model

Modeling and Hemofiltration Treatment of Acute Inflammation

Real-time optimization of cytokine-selective hemoadsorption devices for treatment of acute inflammation

A compartmental model reveals a mechanism for misregulation of neutrophil trafficking in sepsis

Evaluation of Parallel Tempering to Accelerate Bayesian Parameter Estimation in Systems Biology

Exact Hybrid Particle/Population Simulation of Rule-Based Models of Biochemical Systems: e1003544

Compartmental rule-based modeling of biochemical systems

Advances in rule-based modeling: Compartments, energy, and hybrid simulation, with application to sepsis and cell signaling

Energy-based modeling in BioNetGen

Comparative genomic analyses of seventeen Streptococcus pneumoniae strains : Insights into the pneumococcal supragenome : Biofilms 2007: broadened horizon and new emphases

Acute Inflammation Treatment via Particle Filter State Estimation and MPC

Compartmental rule-based modeling of biochemical systems

Kronos and Krios: Evidence for Accretion of a Massive, Rocky Planetary System in a Comoving Pair of Solar-type Stars

Alternative Lengthening of Telomeres and Loss of DAXX/ATRX Expression Predicts Metastatic Disease and Poor Survival in Patients with Pancreatic Neuroendocrine Tumors

‘Excited Delirium’ Reflects System of Control, Not Care for MH Crises

NUDT21 limits CD19 levels through alternative mRNA polyadenylation in B cell acute lymphoblastic leukemia

Demographic Factors and Instantaneous Lower Extremity Injury Occurrence in a National Collegiate Athletic Association Division I Population

Examining differential success in recruitment using respondent driven sampling (RDS) in a multi-site study of gay, bisexual and other men who have sex with men

E7820, an anti-cancer sulfonamide, degrades RBM39 in patients with splicing factor mutant myeloid malignancies: a phase II clinical trial

Minor intron retention drives clonal hematopoietic disorders and diverse cancer predisposition

Impaired Proteolysis of Noncanonical RAS Proteins Drives Clonal Hematopoietic Transformation

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