List of works by Jason A. Papin

3165 Diseased and Healthy Gastrointestinal Tissue Data Mining requires an Engaged Transdisciplinary team

A community-driven global reconstruction of human metabolism. ⬇️

scientific article

A metabolic network approach for the identification and prioritization of antimicrobial drug targets

scientific article

A scalable systems analysis approach for regulated metabolic networks

scientific article

A simplified metabolic network reconstruction to promote understanding and development of flux balance analysis tools

scientific article published in February 2019

A thirteen-gene expression signature predicts survival of patients with pancreatic cancer and identifies new genes of interest

scientific article

Accelerating the Drug Development Pipeline with Genome-Scale Metabolic Network Reconstructions

article

Advancing code sharing in the computational biology community

scientific article published on 02 June 2022

An engineering design approach to systems biology

scientific article

Analysis of metabolic capabilities using singular value decomposition of extreme pathway matrices

scientific article

Bioinformatics and cellular signaling

scientific journal article

Biomedical applications of genome-scale metabolic network reconstructions of human pathogens

scientific article published on 7 December 2017

Characterizing emergent properties of immunological systems with multi-cellular rule-based computational modeling

scientific article

Clinical, molecular and genetic validation of a murine orthotopic xenograft model of pancreatic adenocarcinoma using fresh human specimens

scientific article

Clostridioides difficile: Sometimes It Pays To Be Difficult

scientific article published on 01 September 2020

Community standards to facilitate development and address challenges in metabolic modeling

scientific article published on 01 August 2020

Comparative analyses of parasites with a comprehensive database of genome-scale metabolic models

scientific article published on 23 February 2022

Comparative metabolic systems analysis of pathogenic Burkholderia

scientific article

Comparison of network-based pathway analysis methods

scientific article

Comprehensive analysis of receptor tyrosine kinase activation in human melanomas reveals autocrine signaling through IGF-1R

scientific article

Computational Models of Algae Metabolism for Industrial Applications

Computing Biology

scientific article published on 12 July 2016

Computing the Dynamic Supramolecular Structural Proteome

scientific article published on 19 January 2017

Core Competencies for Undergraduates in Bioengineering and Biomedical Engineering: Findings, Consequences, and Recommendations

scientific article published on 05 February 2020

Correction: Dynamic Analysis of Integrated Signaling, Metabolic, and Regulatory Networks.

scientific article

Cross-modulation of pathogen-specific pathways enhances malnutrition during enteric co-infection with Giardia lamblia and enteroaggregative Escherichia coli

scientific article

Dephosphorylation of beta-arrestin 1 in glioblastomas

scientific article

Determination of redundancy and systems properties of the metabolic network of Helicobacter pylori using genome-scale extreme pathway analysis.

scientific article published on May 2002

Development of network-based pathway definitions: the need to analyze real metabolic networks

article

Do genome-scale models need exact solvers or clearer standards?

scientific article published on 14 October 2015

Dynamic analysis of integrated signaling, metabolic, and regulatory networks

scientific article

Evaluating the efficacy of an algae-based treatment to mitigate elicitation of antibiotic resistance

scientific article published on 20 July 2019

Extreme pathway lengths and reaction participation in genome-scale metabolic networks

scientific article

Flux balance analysis in the era of metabolomics

scientific article (publication date: 7 March 2006)

Flux balance analysis: interrogating genome-scale metabolic networks

scientific article

From "What Is?" to "What Isn't?" Computational Biology

scientific article

Functional integration of a metabolic network model and expression data without arbitrary thresholding.

scientific article

Functional states of the genome-scale Escherichia coli transcriptional regulatory system

scientific article

Gene Essentiality and Metabolism in Bordetella pertussis

article

Genome-Scale Characterization of Toxicity-Induced Metabolic Alterations in Primary Hepatocytes

scientific article published on 01 December 2019

Genome-Scale Model-Based Identification of Metabolite Indicators for Early Detection of Kidney Toxicity

scientific article published on 01 February 2020

Genome-scale metabolic modeling reveals increased reliance on valine catabolism in clinical isolates of Klebsiella pneumoniae

scientific article published in 2022

Genome-scale metabolic network analysis of the opportunistic pathogen Pseudomonas aeruginosa PAO1

scientific article

Genome-scale microbial in silico models: the constraints-based approach.

scientific article

Genome-scale reconstruction and analysis of the Pseudomonas putida KT2440 metabolic network facilitates applications in biotechnology

scientific article

Genome-wide functional annotation and structural verification of metabolic ORFeome of Chlamydomonas reinhardtii

scientific article

Genotypic and phenotypic analyses of a Pseudomonas aeruginosa chronic bronchiectasis isolate reveal differences from cystic fibrosis and laboratory strains

scientific article

Gram-negative Microbiota Blooms in Premature Twins Discordant for Parenteral Nutrition-associated Cholestasis

scientific article published on 14 January 2020

Growth-Altering Microbial Interactions Are Highly Sensitive to Environmental Context

Growth-altering microbial interactions are responsive to chemical context

scientific article

Guiding the Refinement of Biochemical Knowledgebases with Ensembles of Metabolic Networks and Machine Learning

scientific article published on 08 January 2020

Harnessing systems biology approaches to engineer functional microvascular networks

scientific article

Hierarchical thinking in network biology: the unbiased modularization of biochemical networks.

scientific article

High temporal resolution of glucosyltransferase dependent and independent effects of Clostridium difficile toxins across multiple cell types

scientific article

History of Antibiotic Adaptation Influences Microbial Evolutionary Dynamics During Subsequent Treatment

article

History of antibiotic adaptation influences microbial evolutionary dynamics during subsequent treatment

scientific article

How can computation advance microbiome research? ⬇️

scientific article published on 21 September 2017

Identifying metabolic adaptations characteristic of cardiotoxicity using paired transcriptomics and metabolomics data integrated with a computational model of heart metabolism

scientific article published on 29 February 2024

Improving reproducibility in computational biology research

scientific article published on 19 May 2020

In vivo physiological and transcriptional profiling reveals host responses to Clostridium difficile toxin A and toxin B

scientific article

Increased urinary trimethylamine N-oxide (TMAO) following Cryptosporidium infection and protein malnutrition independent of microbiome effects

scientific article

Inference of Network Dynamics and Metabolic Interactions in the Gut Microbiome

scientific article

Inferring Metabolic Mechanisms of Interaction within a Defined Gut Microbiota

scientific article published on 05 September 2018

Influential Parameters for the Analysis of Intracellular Parasite Metabolomics.

scientific article published on 18 April 2018

Influential parameters for the analysis of intracellular parasite metabolomics

Integrated Experimental and Computational Analyses Reveal Differential Metabolic Functionality in Antibiotic-Resistant Pseudomonas aeruginosa

scientific article published on 02 January 2019

Integration of expression data in genome-scale metabolic network reconstructions

scientific article

Leveraging the effects of chloroquine on resistant malaria parasites for combination therapies

scientific article published on 15 April 2019

Linking genome-scale metabolic modeling and genome annotation

scientific article

MEMOTE for standardized genome-scale metabolic model testing

scientific article published on 01 March 2020

Managing Uncertainty in Metabolic Network Structure and Improving Predictions Using EnsembleFBA

Managing uncertainty in metabolic network structure and improving predictions using EnsembleFBA

scientific article

Matrix formalism to describe functional states of transcriptional regulatory systems

scientific article

Matrix rigidity regulates cancer cell growth by modulating cellular metabolism and protein synthesis

scientific article

Mechanistic exploration of phthalimide neovascular factor 1 using network analysis tools

scientific article

Mechanistic identification of biofluid metabolite changes as markers of acetaminophen-induced liver toxicity in rats

scientific article published on 08 April 2019

Mechanistic systems modeling to guide drug discovery and development

scientific article

Medusa: Software to build and analyze ensembles of genome-scale metabolic network reconstructions

scientific article published on 29 April 2020

Memote: A community-driven effort towards a standardized genome-scale metabolic model test suite

MetDraw: automated visualization of genome-scale metabolic network reconstructions and high-throughput data

scientific article

Metabolic Network Reconstructions to Predict Drug Targets and Off-Target Effects

scientific article published on 01 January 2020

Metabolic mechanisms of interaction within a defined gut microbiota

Metabolic network analysis integrated with transcript verification for sequenced genomes.

scientific article

Metabolic network analysis of Pseudomonas aeruginosa during chronic cystic fibrosis lung infection

scientific article

Metabolic network analysis predicts efficacy of FDA-approved drugs targeting the causative agent of a neglected tropical disease

scientific article

Metabolic network modeling of microbial communities

scientific article

Metabolic network reconstruction of Chlamydomonas offers insight into light-driven algal metabolism.

scientific article

Metabolic network-guided binning of metagenomic sequence fragments.

scientific article

Metabolic pathways in the post-genome era.

scientific article

Metabolic reconstruction, constraint-based analysis and game theory to probe genome-scale metabolic networks

scientific article published on 06 August 2010

Metabolic systems analysis to advance algal biotechnology

scientific article

MicroRNAs induced in melanoma treated with combination targeted therapy of Temsirolimus and Bevacizumab

scientific article

Miniaturized plate readers for low-cost, high-throughput phenotypic screening

scientific article

Minimum Bactericidal Concentration of Ciprofloxacin to Pseudomonas aeruginosa Determined Rapidly Based on Pyocyanin Secretion

scientific article published on 04 March 2020

Multiscale Computational Modeling in Vascular Biology: From Molecular Mechanisms to Tissue-Level Structure and Function

Multiscale computational analysis of Xenopus laevis morphogenesis reveals key insights of systems-level behavior

scientific article

Multiscale computational models of complex biological systems

scientific article

Nano-motion dynamics are determined by surface-tethered selectin mechanokinetics and bond formation

scientific article

Network analysis reveals differential metabolic functionality in antibiotic-resistant Pseudomonas aeruginosa

scholarly article published 18 April 2018

Network-based analysis of metabolic regulation in the human red blood cell

scientific article (publication date: 21 November 2003)

Novel Co-Culture Plate Enables Growth Dynamic-Based Assessment Of Contact-Independent Microbial Interactions

article

Novel Drivers of Virulence in Clostridioides difficile Identified via Context-Specific Metabolic Network Analysis

scientific article published on 05 October 2021

Novel Plasmodium falciparum metabolic network reconstruction identifies shifts associated with clinical antimalarial resistance

scientific article published on 19 July 2017

Novel Plasmodium falciparum metabolic network reconstruction identifies shifts associated with clinical antimalarial resistance

Novel co-culture plate enables growth dynamic-based assessment of contact-independent microbial interactions

scientific article published on 2 August 2017

Novel multiscale modeling tool applied to Pseudomonas aeruginosa biofilm formation

scientific article

Novel pathway compendium analysis elucidates mechanism of pro-angiogenic synthetic small molecule

scientific article

One thousand simple rules

Phthalimide neovascular factor 1 (PNF1) modulates MT1-MMP activity in human microvascular endothelial cells

scientific article

Predicting biological system objectives de novo from internal state measurements

scientific article

Predicting changes in renal metabolism after compound exposure with a genome-scale metabolic model

scientific article published on 30 December 2020

Protein- and zinc-deficient diets modulate the murine microbiome and metabolic phenotype

scientific article

Proteomic and network analysis characterize stage-specific metabolism in Trypanosoma cruzi

scientific article

Publisher Correction: MEMOTE for standardized genome-scale metabolic model testing

scientific article published on 01 April 2020

Quantifying cumulative phenotypic and genomic evidence for procedural generation of metabolic network reconstructions

scientific article published on 07 February 2022

Reconciled rat and human metabolic networks for comparative toxicogenomics and biomarker predictions

scientific article

Reconciliation of genome-scale metabolic reconstructions for comparative systems analysis

scientific article

Reconciling high-throughput gene essentiality data with metabolic network reconstructions

article

Reconciling high-throughput gene essentiality data with metabolic network reconstructions

scientific article published on 11 April 2019

Reconstruction of cellular signalling networks and analysis of their properties

scientific article

Reconstruction of the metabolic network of Pseudomonas aeruginosa to interrogate virulence factor synthesis

scientific article

SIMPLE: a sequential immunoperoxidase labeling and erasing method

scientific article

Systems analyses characterize integrated functions of biochemical networks

scientific article

Systems analysis of metabolism in the pathogenic trypanosomatid Leishmania major

scientific article

Systems analysis of small signaling modules relevant to eight human diseases

scientific article

Systems analysis of the transcriptional response of human ileocecal epithelial cells to Clostridium difficile toxins and effects on cell cycle control

scientific article

Systems level analysis of the Chlamydomonas reinhardtii metabolic network reveals variability in evolutionary co-conservation

scientific article

Systems-level metabolism of the altered Schaedler flora, a complete gut microbiota

scientific article

TIGER: Toolbox for integrating genome-scale metabolic models, expression data, and transcriptional regulatory networks

scientific article

Ten simple rules for biologists learning to program

scientific article published on 4 January 2018

Ten simple rules for launching an academic research career

scientific article published in 2022

The JAK-STAT signaling network in the human B-cell: an extreme signaling pathway analysis

scientific article published on July 2004

The application of flux balance analysis in systems biology

scientific article

The blossoming of methods and software in computational biology

scientific article published on 17 August 2023

The genome-scale metabolic extreme pathway structure in Haemophilus influenzae shows significant network redundancy.

scientific article published in March 2002

Topological analysis of mass-balanced signaling networks: a framework to obtain network properties including crosstalk

scientific article published in March 2004

Transcriptome-guided parsimonious flux analysis improves predictions with metabolic networks in complex environments

scientific article published on 16 April 2020

Whole-genome metabolic network reconstruction and constraint-based modeling

scientific article

Wisdom of crowds in computational biology.

scientific article published on 23 May 2019

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