Multiplex methods provide effective integration of multi-omic data in genome-scale models

Quantitative proteomic analysis reveals a simple strategy of global resource allocation in bacteria

(2015) S. Hui et al.   Molecular Systems Biology

Model-driven discovery of underground metabolic functions inEscherichia coli

(2015) Gabriela I. Guzmán et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Analysis and design of molecular machines

(2015) C. Angione et al.   THEORETICAL COMPUTER SCIENCE

Predictive analytics of environmental adaptability in multi-omic network models

(2015) Claudio Angione et al.   Scientific Reports

A Hybrid of Metabolic Flux Analysis and Bayesian Factor Modeling for Multiomic Temporal Pathway Activation

(2015) Claudio Angione et al.   ACS Synthetic Biology

Network-based analysis of comorbidities risk during an infection: SARS and HIV case studies

(2014) Mohammad Moni et al.   BMC BIOINFORMATICS

Recent advances in the reconstruction of metabolic models and integration of omics data

(2014) Rajib Saha et al.   CURRENT OPINION IN BIOTECHNOLOGY

Similarity network fusion for aggregating data types on a genomic scale

(2014) Bo Wang et al.   NATURE METHODS

Constraint-based models predict metabolic and associated cellular functions

(2014) Aarash Bordbar et al.   NATURE REVIEWS GENETICS

Transcript level and sequence determinants of protein abundance and noise in Escherichia coli

(2014) Joao C. Guimaraes et al.   NUCLEIC ACIDS RESEARCH

Communicability reveals a transition to coordinated behavior in multiplex networks

(2014) Ernesto Estrada et al.   PHYSICAL REVIEW E

The structure and dynamics of multilayer networks

(2014) S. Boccaletti et al.   PHYSICS REPORTS-REVIEW SECTION OF PHYSICS LETTERS

Network-level architecture and the evolutionary potential of underground metabolism

(2014) R. A. Notebaart et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

An exact arithmetic toolbox for a consistent and reproducible structural analysis of metabolic network models

(2014) Leonid Chindelevitch et al.   Nature Communications

toyLIFE: a computational framework to study the multi-level organisation of the genotype-phenotype map

(2014) Clemente F. Arias et al.   Scientific Reports

Systematic Evaluation of Methods for Integration of Transcriptomic Data into Constraint-Based Models of Metabolism

(2014) Daniel Machado et al.   PLoS Computational Biology

Systems biology and brain activity in neuronal pathways by smart device and advanced signal processing

(2014) Gastone Castellani et al.   Frontiers in Genetics

Pareto Optimality in Organelle Energy Metabolism Analysis

(2013) Claudio Angione et al.   IEEE-ACM Transactions on Computational Biology and Bioinformatics

Incorporation of flexible objectives and time-linked simulation with flux balance analysis

(2013) Elsa W. Birch et al.   JOURNAL OF THEORETICAL BIOLOGY

A design automation framework for computational bioenergetics in biological networks

(2013) Claudio Angione et al.   Molecular BioSystems

An in vivo control map for the eukaryotic mRNA translation machinery

(2013) H. Firczuk et al.   Molecular Systems Biology

COLOMBOS v2.0: an ever expanding collection of bacterial expression compendia: Table 1.

(2013) Pieter Meysman et al.   NUCLEIC ACIDS RESEARCH

Growing Multiplex Networks

(2013) V. Nicosia et al.   PHYSICAL REVIEW LETTERS

Inferring Carbon Sources from Gene Expression Profiles Using Metabolic Flux Models

(2012) Aaron Brandes et al.   PLoS One

MultiMetEval: Comparative and Multi-Objective Analysis of Genome-Scale Metabolic Models

(2012) Piotr Zakrzewski et al.   PLoS One

Multidimensional Optimality of Microbial Metabolism

(2012) R. Schuetz et al.   SCIENCE

A comprehensive genome-scale reconstruction of Escherichia coli metabolism--2011

(2011) J. D. Orth et al.   Molecular Systems Biology

Variance of Gene Expression Identifies Altered Network Constraints in Neurological Disease

(2011) Jessica C. Mar et al.   PLoS Genetics

Integrative clustering of multiple genomic data types using a joint latent variable model with application to breast and lung cancer subtype analysis

(2009) Ronglai Shen et al.   BIOINFORMATICS

Feedback regulation of opposing enzymes generates robust, all-or-none bistable responses

(2008) James E. Ferrell   CURRENT BIOLOGY