Quantitative and logic modelling of molecular and gene networks

NAIL, a software toolset for inferring, analyzing and visualizing regulatory networks

(2014) Daniel G. Hurley et al.   BIOINFORMATICS

A model integration approach linking signalling and gene-regulatory logic with kinetic metabolic models

(2014) A. Ryll et al.   BIOSYSTEMS

Integrated metabolic spatial-temporal model for the prediction of ammonia detoxification during liver damage and regeneration

(2014) Freimut Schliess et al.   HEPATOLOGY

Constraint-based models predict metabolic and associated cellular functions

(2014) Aarash Bordbar et al.   NATURE REVIEWS GENETICS

Multiscale digitalArabidopsispredicts individual organ and whole-organism growth

(2014) Yin Hoon Chew et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Defining an essential transcription factor program for naive pluripotency

(2014) S.- J. Dunn et al.   SCIENCE

Construction and Validation of a Regulatory Network for Pluripotency and Self-Renewal of Mouse Embryonic Stem Cells

(2014) Huilei Xu et al.   PLoS Computational Biology

Hard-wired heterogeneity in blood stem cells revealed using a dynamic regulatory network model

(2013) Nicola Bonzanni et al.   BIOINFORMATICS

The systems biology simulation core algorithm

(2013) Roland Keller et al.   BMC Systems Biology

Path2Models: large-scale generation of computational models from biochemical pathway maps

(2013) Finja Büchel et al.   BMC Systems Biology

High-throughput sequencing reveals the disruption of methylation of imprinted gene in induced pluripotent stem cells

(2013) Gang Chang et al.   CELL RESEARCH

Moving from Basic Toward Systems Pharmacodynamic Models

(2013) William J. Jusko   JOURNAL OF PHARMACEUTICAL SCIENCES

Reverse engineering and identification in systems biology: strategies, perspectives and challenges

(2013) A. F. Villaverde et al.   Journal of the Royal Society Interface

A competitive protein interaction network buffers Oct4-mediated differentiation to promote pluripotency in embryonic stem cells

(2013) S. Munoz Descalzo et al.   Molecular Systems Biology

Programming biological models in Python using PySB

(2013) C. F. Lopez et al.   Molecular Systems Biology

Network deconvolution as a general method to distinguish direct dependencies in networks

(2013) Soheil Feizi et al.   NATURE BIOTECHNOLOGY

A community-driven global reconstruction of human metabolism

(2013) Ines Thiele et al.   NATURE BIOTECHNOLOGY

The MIntAct project—IntAct as a common curation platform for 11 molecular interaction databases

(2013) Sandra Orchard et al.   NUCLEIC ACIDS RESEARCH

The 2014Nucleic Acids ResearchDatabase Issue and an updated NAR online Molecular Biology Database Collection

(2013) Xosé M. Fernández-Suárez et al.   NUCLEIC ACIDS RESEARCH

The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of Pathway/Genome Databases

(2013) Ron Caspi et al.   NUCLEIC ACIDS RESEARCH

The Reactome pathway knowledgebase

(2013) David Croft et al.   NUCLEIC ACIDS RESEARCH

Integration of Biochemical and Electrical Signaling-Multiscale Model of the Medium Spiny Neuron of the Striatum

(2013) Michele Mattioni et al.   PLoS One

Integrative Modelling of the Influence of MAPK Network on Cancer Cell Fate Decision

(2013) Luca Grieco et al.   PLoS Computational Biology

Guidelines for the use and interpretation of assays for monitoring autophagy

(2012) Daniel J. Klionsky et al.   Autophagy

Stochastic Boolean networks: An efficient approach to modeling gene regulatory networks

(2012) Jinghang Liang et al.   BMC Systems Biology

TIGRESS: Trustful Inference of Gene REgulation using Stability Selection

(2012) Anne-Claire Haury et al.   BMC Systems Biology

CellNOptR: a flexible toolkit to train protein signaling networks to data using multiple logic formalisms

(2012) Camille Terfve et al.   BMC Systems Biology

A Whole-Cell Computational Model Predicts Phenotype from Genotype

(2012) Jonathan R. Karr et al.   CELL

Circuitry and Dynamics of Human Transcription Factor Regulatory Networks

(2012) Shane Neph et al.   CELL

Architecture of the human regulatory network derived from ENCODE data

(2012) Mark B. Gerstein et al.   NATURE

Wisdom of crowds for robust gene network inference

(2012) Daniel Marbach et al.   NATURE METHODS

Serotonergic transcriptional networks and potential importance to mental health

(2012) Evan S Deneris et al.   NATURE NEUROSCIENCE

STRING v9.1: protein-protein interaction networks, with increased coverage and integration

(2012) Andrea Franceschini et al.   NUCLEIC ACIDS RESEARCH

The ConsensusPathDB interaction database: 2013 update

(2012) Atanas Kamburov et al.   NUCLEIC ACIDS RESEARCH

State–time spectrum of signal transduction logic models

(2012) Aidan MacNamara et al.   PHYSICAL BIOLOGY

Modeling of Tumor Progression in NSCLC and Intrinsic Resistance to TKI in Loss of PTEN Expression

(2012) Gholamreza Bidkhori et al.   PLoS One

Theoretical insights into bacterial chemotaxis

(2012) Marcus J. Tindall et al.   Wiley Interdisciplinary Reviews-Systems Biology and Medicine

An overview of existing modeling tools making use of model checking in the analysis of biochemical networks

(2012) Miguel Carrillo et al.   Frontiers in Plant Science

Reproducible computational biology experiments with SED-ML - The Simulation Experiment Description Markup Language

(2011) Dagmar Waltemath et al.   BMC Systems Biology

Origin of bistability underlying mammalian cell cycle entry

(2011) G. Yao et al.   Molecular Systems Biology

Gene network inference and visualization tools for biologists: application to new human transcriptome datasets

(2011) Daniel Hurley et al.   NUCLEIC ACIDS RESEARCH

SABIO-RK--database for biochemical reaction kinetics

(2011) U. Wittig et al.   NUCLEIC ACIDS RESEARCH

KEGG for integration and interpretation of large-scale molecular data sets

(2011) M. Kanehisa et al.   NUCLEIC ACIDS RESEARCH

A Hybrid Model of Mammalian Cell Cycle Regulation

(2011) Rajat Singhania et al.   PLoS Computational Biology

Minimum Information About a Simulation Experiment (MIASE)

(2011) Dagmar Waltemath et al.   PLoS Computational Biology

Logic-Based Models for the Analysis of Cell Signaling Networks

(2010) Melody K. Morris et al.   BIOCHEMISTRY

BoolNet—an R package for generation, reconstruction and analysis of Boolean networks

(2010) Christoph Müssel et al.   BIOINFORMATICS

Discovering pathways by orienting edges in protein interaction networks

(2010) Anthony Gitter et al.   NUCLEIC ACIDS RESEARCH

BRENDA, the enzyme information system in 2011

(2010) M. Scheer et al.   NUCLEIC ACIDS RESEARCH

The Genetic Landscape of a Cell

(2010) M. Costanzo et al.   SCIENCE

Mathematical Modelling of Cell-Fate Decision in Response to Death Receptor Engagement

(2010) Laurence Calzone et al.   PLoS Computational Biology

iBioSim: a tool for the analysis and design of genetic circuits

(2009) C. J. Myers et al.   BIOINFORMATICS

Logical modelling of regulatory networks with GINsim 2.3

(2009) A. Naldi et al.   BIOSYSTEMS

Transforming Boolean models to continuous models: methodology and application to T-cell receptor signaling

(2009) Dominik M Wittmann et al.   BMC Systems Biology

A Yeast Synthetic Network for In Vivo Assessment of Reverse-Engineering and Modeling Approaches

(2009) Irene Cantone et al.   CELL

Reverse engineering and verification of gene networks: Principles, assumptions, and limitations of present methods and future perspectives

(2009) Feng He et al.   JOURNAL OF BIOTECHNOLOGY

Sampling-rate-dependent probabilistic Boolean networks

(2009) Golnaz Vahedi et al.   JOURNAL OF THEORETICAL BIOLOGY

Comparing different ODE modelling approaches for gene regulatory networks

(2009) A. Polynikis et al.   JOURNAL OF THEORETICAL BIOLOGY

The Systems Biology Graphical Notation

(2009) Nicolas Le Novère et al.   NATURE BIOTECHNOLOGY

Pulsatile Stimulation Determines Timing and Specificity of NF- B-Dependent Transcription

(2009) L. Ashall et al.   SCIENCE

Human Induced Pluripotent Stem Cells Free of Vector and Transgene Sequences

(2009) J. Yu et al.   SCIENCE

Fuzzy Logic Analysis of Kinase Pathway Crosstalk in TNF/EGF/Insulin-Induced Signaling

(2009) Bree B. Aldridge et al.   PLoS Computational Biology

Synchronous versus asynchronous modeling of gene regulatory networks

(2008) A. Garg et al.   BIOINFORMATICS

Characterization of the proneural gene regulatory network during mouse telencephalon development

(2008) Julia M Gohlke et al.   BMC BIOLOGY

An Extended Transcriptional Network for Pluripotency of Embryonic Stem Cells

(2008) Jonghwan Kim et al.   CELL

Simulation of the regulation of EGFR endocytosis and EGFR-ERK signaling by endophilin-mediated RhoA-EGFR crosstalk

(2008) Choong Yong Ung et al.   FEBS LETTERS

Modeling the segmentation clock as a network of coupled oscillations in the Notch, Wnt and FGF signaling pathways

(2008) Albert Goldbeter et al.   JOURNAL OF THEORETICAL BIOLOGY

Models from experiments: combinatorial drug perturbations of cancer cells

(2008) Sven Nelander et al.   Molecular Systems Biology

Design principles of biochemical oscillators

(2008) Béla Novák et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Cataloging and organizing p73 interactions in cell cycle arrest and apoptosis

(2008) Melda Tozluoğlu et al.   NUCLEIC ACIDS RESEARCH

Notch Signalling Synchronizes the Zebrafish Segmentation Clock but Is Not Needed To Create Somite Boundaries

(2008) Ertuğrul M. Özbudak et al.   PLoS Genetics

An allosteric model of calmodulin explains differential activation of PP2B and CaMKII

(2008) M. I. Stefan et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA