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Computational Methods in Systems Biology: 13th International Conference, CMSB 2015, Nantes, France, September 16-18, 2015, Proceedings

1, 2015

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Predicting weighted unobserved nodes in a regulatory network using answer set programming

BMC bioinformatics, 2023-08, Vol.24 (Suppl 1), p.1-321, Article 321

2023

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Induction of Human Trophoblast Stem Cells from Somatic Cells and Pluripotent Stem Cells

Cell reports (Cambridge), 2020-11, Vol.33 (8), p.108419-108419, Article 108419

2020

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Meneco, a Topology-Based Gap-Filling Tool Applicable to Degraded Genome-Wide Metabolic Networks

PLoS computational biology, 2017-01, Vol.13 (1), p.e1005276-e1005276

2017

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Computational discovery of dynamic cell line specific Boolean networks from multiplex time-course data

PLoS computational biology, 2018-10, Vol.14 (10), p.e1006538-e1006538

2018

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StochPy: a comprehensive, user-friendly tool for simulating stochastic biological processes

PloS one, 2013-11, Vol.8 (11), p.e79345-e79345

2013

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Fuzzy Stochastic Petri Nets for Modeling Biological Systems with Uncertain Kinetic Parameters

PloS one, 2016-02, Vol.11 (2), p.e0149674-e0149674

2016

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Source reconstruction accuracy of MEG and EEG Bayesian inversion approaches

PloS one, 2012-12, Vol.7 (12), p.e51985-e51985

2012

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Quantifying loopy network architectures

PloS one, 2012-06, Vol.7 (6), p.e37994-e37994

2012

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Computational Methods in Systems Biology

BioSystems, 2016-11, Vol.149, p.1-2

2016

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Application of differential evolution algorithm on self-potential data

PloS one, 2012-12, Vol.7 (12), p.e51199-e51199

2012

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A Logic for Checking the Probabilistic Steady-State Properties of Reaction Networks

Journal of computational biology, 2017-08, Vol.24 (8), p.734

2017

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Efficient methods and readily customizable libraries for managing complexity of large networks

PloS one, 2018-05, Vol.13 (5), p.e0197238-e0197238

2018

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Ambiguity in logic-based models of gene regulatory networks: An integrative multi-perturbation analysis

PloS one, 2018-11, Vol.13 (11), p.e0206976-e0206976

2018

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Stochastic Frontier approach and Data Envelopment Analysis to Total Factor Productivity and efficiency measurement of Bangladeshi rice

PloS one, 2012-10, Vol.7 (10), p.e46081-e46081

2012

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Hierarchical ordering of reticular networks

PloS one, 2012-06, Vol.7 (6), p.e36715-e36715

2012

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Bayesian Integrative Modeling of Genome-Scale Metabolic and Regulatory Networks

Informatics (Basel), 2020-03, Vol.7 (1), p.1

2020

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Probabilistic Modeling of Microbial Metabolic Networks for Integrating Partial Quantitative Knowledge Within the Nitrogen Cycle

Frontiers in microbiology, 2019-01, Vol.9 (JAN), p.3298-3298

2019

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Flux Balance Analysis with Objective Function Defined by Proteomics Data-Metabolism of Mycobacterium tuberculosis Exposed to Mefloquine

PloS one, 2015-07, Vol.10 (7), p.e0134014-e0134014

2015

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OPINION PAPER Evolutionary Constraint-Based Formulation Requires New Bi-level Solving Techniques

Computational Methods in Systems Biology, 2015, p.279-281

2015

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Using hidden markov models to improve quantifying physical activity in accelerometer data - a simulation study

PloS one, 2014-12, Vol.9 (12), p.e114089-e114089

2014

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Combinations of Cytochrome P450 Gene Polymorphisms Enhancing the Risk for Sporadic Colorectal Cancer Related to Red Meat Consumption

Cancer epidemiology, biomarkers & prevention, 2007-07, Vol.16 (7), p.1460-1467

2007

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MI-Sim: A MATLAB package for the numerical analysis of microbial ecological interactions

PloS one, 2017-03, Vol.12 (3), p.e0173249-e0173249

2017

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Avoiding the Enumeration of Infeasible Elementary Flux Modes by Including Transcriptional Regulatory Rules in the Enumeration Process Saves Computational Costs

PloS one, 2015-06, Vol.10 (6), p.e0129840-e0129840

2015

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Computational Methods in Systems Biology: 13th International Conference, CMSB 2015, Nantes, France, September 16-18, 2015, Proceedings

Predicting weighted unobserved nodes in a regulatory network using answer set programming

Induction of Human Trophoblast Stem Cells from Somatic Cells and Pluripotent Stem Cells

Integrated pseudotime analysis of human pre-implantation embryo single-cell transcriptomes reveals the dynamics of lineage specification

Meneco, a Topology-Based Gap-Filling Tool Applicable to Degraded Genome-Wide Metabolic Networks

Computational discovery of dynamic cell line specific Boolean networks from multiplex time-course data

StochPy: a comprehensive, user-friendly tool for simulating stochastic biological processes

Fuzzy Stochastic Petri Nets for Modeling Biological Systems with Uncertain Kinetic Parameters

Source reconstruction accuracy of MEG and EEG Bayesian inversion approaches

Quantifying loopy network architectures

Computational Methods in Systems Biology

Application of differential evolution algorithm on self-potential data

A Logic for Checking the Probabilistic Steady-State Properties of Reaction Networks

Efficient methods and readily customizable libraries for managing complexity of large networks

Ambiguity in logic-based models of gene regulatory networks: An integrative multi-perturbation analysis

Stochastic Frontier approach and Data Envelopment Analysis to Total Factor Productivity and efficiency measurement of Bangladeshi rice

Hierarchical ordering of reticular networks

Bayesian Integrative Modeling of Genome-Scale Metabolic and Regulatory Networks

Probabilistic Modeling of Microbial Metabolic Networks for Integrating Partial Quantitative Knowledge Within the Nitrogen Cycle

Flux Balance Analysis with Objective Function Defined by Proteomics Data-Metabolism of Mycobacterium tuberculosis Exposed to Mefloquine

OPINION PAPER Evolutionary Constraint-Based Formulation Requires New Bi-level Solving Techniques

Using hidden markov models to improve quantifying physical activity in accelerometer data - a simulation study

Combinations of Cytochrome P450 Gene Polymorphisms Enhancing the Risk for Sporadic Colorectal Cancer Related to Red Meat Consumption

MI-Sim: A MATLAB package for the numerical analysis of microbial ecological interactions

Avoiding the Enumeration of Infeasible Elementary Flux Modes by Including Transcriptional Regulatory Rules in the Enumeration Process Saves Computational Costs

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