ComPlEx: conservation and divergence of co-expression networks in A. thaliana, Populus and O. sativa

PLANEX: the plant co-expression database

(2013) Won Yim et al.   BMC PLANT BIOLOGY

The evolutionary origins of modularity

(2013) J. Clune et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

PINALOG: a novel approach to align protein interaction networks—implications for complex detection and function prediction

(2012) Hang T. T. Phan et al.   BIOINFORMATICS

Beyond differential expression: the quest for causal mutations and effector molecules

(2012) Nicholas J Hudson et al.   BMC GENOMICS

GraphAlignment: Bayesian pairwise alignment of biological networks

(2012) Michal Kolář et al.   BMC Systems Biology

Comparative studies of gene expression and the evolution of gene regulation

(2012) Irene Gallego Romero et al.   NATURE REVIEWS GENETICS

Comparative co-expression analysis in plant biology

(2012) SARA MOVAHEDI et al.   PLANT CELL AND ENVIRONMENT

BAR expressolog identification: expression profile similarity ranking of homologous genes in plant species

(2012) Rohan V. Patel et al.   PLANT JOURNAL

Comparing Statistical Methods for Constructing Large Scale Gene Networks

(2012) Jeffrey D. Allen et al.   PLoS One

AlignNemo: A Local Network Alignment Method to Integrate Homology and Topology

(2012) Giovanni Ciriello et al.   PLoS One

Evaluation of Gene Association Methods for Coexpression Network Construction and Biological Knowledge Discovery

(2012) Sapna Kumari et al.   PLoS One

A systems biology model of the regulatory network in Populus leaves reveals interacting regulators and conserved regulation

(2011) Nathaniel Street et al.   BMC PLANT BIOLOGY

Human-specific loss of regulatory DNA and the evolution of human-specific traits

(2011) Cory Y. McLean et al.   NATURE

PlaNet: Combined Sequence and Expression Comparisons across Plant Networks Derived from Seven Species

(2011) M. Mutwil et al.   PLANT CELL

Comparative Network Analysis Reveals That Tissue Specificity and Gene Function Are Important Factors Influencing the Mode of Expression Evolution in Arabidopsis and Rice

(2011) S. Movahedi et al.   PLANT PHYSIOLOGY

Gene Coexpression Network Alignment and Conservation of Gene Modules between Two Grass Species: Maize and Rice

(2011) S. P. Ficklin et al.   PLANT PHYSIOLOGY

Measuring the Evolutionary Rewiring of Biological Networks

(2011) Chong Shou et al.   PLoS Computational Biology

Are There Laws of Genome Evolution?

(2011) Eugene V. Koonin   PLoS Computational Biology

Evolution of biological interaction networks: from models to real data

(2011) Mark GF Sun et al.   GENOME BIOLOGY

Topological network alignment uncovers biological function and phylogeny

(2010) O. Kuchaiev et al.   Journal of the Royal Society Interface

Ten years of genetics and genomics: what have we achieved and where are we heading?

(2010) Edith Heard et al.   NATURE REVIEWS GENETICS

COMODO: an adaptive coclustering strategy to identify conserved coexpression modules between organisms

(2010) Peyman Zarrineh et al.   NUCLEIC ACIDS RESEARCH

DREAM3: Network Inference Using Dynamic Context Likelihood of Relatedness and the Inferelator

(2010) Aviv Madar et al.   PLoS One

Cross species analysis of microarray expression data

(2009) Y. Lu et al.   BIOINFORMATICS

IsoRankN: spectral methods for global alignment of multiple protein networks

(2009) C.-S. Liao et al.   BIOINFORMATICS

Reverse-engineering the Arabidopsis thaliana transcriptional network under changing environmental conditions

(2009) Javier Carrera et al.   GENOME BIOLOGY

A cross-species transcriptomics approach to identify genes involved in leaf development

(2008) Nathaniel Street et al.   BMC GENOMICS

Comparative analysis of the transcriptomes ofPopulus trichocarpaandArabidopsis thalianasuggests extensive evolution of gene expression regulation in angiosperms

(2008) Tania Quesada et al.   NEW PHYTOLOGIST

Comparative Analysis of Divergent and Convergent Gene Pairs and Their Expression Patterns in Rice, Arabidopsis, and Populus

(2008) N. Krom et al.   PLANT PHYSIOLOGY