Alignment-free protein interaction network comparison

NetCoffee: a fast and accurate global alignment approach to identify functionally conserved proteins in multiple networks

(2013) Jialu Hu et al.   BIOINFORMATICS

BEAMS: backbone extraction and merge strategy for the global many-to-many alignment of multiple PPI networks

(2013) Ferhat Alkan et al.   BIOINFORMATICS

A combinatorial approach to graphlet counting

(2013) Tomaž Hočevar et al.   BIOINFORMATICS

Alignment-Free Sequence Comparison Based on Next-Generation Sequencing Reads

(2013) Kai Song et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

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

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

Global network alignment using multiscale spectral signatures

(2012) R. Patro et al.   BIOINFORMATICS

Surprising results on phylogenetic tree building methods based on molecular sequences

(2012) Gaston H Gonnet   BMC BIOINFORMATICS

The Importance of Age and High Degree, in Protein-Protein Interaction Networks

(2012) Tiago Rito et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

Differential network biology

(2012) Trey Ideker et al.   Molecular Systems Biology

Taxonomies of networks from community structure

(2012) Jukka-Pekka Onnela et al.   PHYSICAL REVIEW E

What Evidence Is There for the Homology of Protein-Protein Interactions?

(2012) Anna C. F. Lewis et al.   PLoS Computational Biology

Integrative network alignment reveals large regions of global network similarity in yeast and human

(2011) Oleksii Kuchaiev et al.   BIOINFORMATICS

Evidence for the additions of clustered interacting nodes during the evolution of protein interaction networks from network motifs

(2011) Zhongyang Liu et al.   BMC EVOLUTIONARY BIOLOGY

New powerful statistics for alignment-free sequence comparison under a pattern transfer model

(2011) Xuemei Liu et al.   JOURNAL OF THEORETICAL BIOLOGY

Measuring the Evolutionary Rewiring of Biological Networks

(2011) Chong Shou et al.   PLoS Computational Biology

How threshold behaviour affects the use of subgraphs for network comparison

(2010) Tiago Rito et al.   BIOINFORMATICS

phangorn: phylogenetic analysis in R

(2010) Klaus Peter Schliep   BIOINFORMATICS

Evolutionary analysis reveals low coverage as the major challenge for protein interaction network alignment

(2010) Waqar Ali et al.   Molecular BioSystems

IsoRankN: spectral methods for global alignment of multiple protein networks

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

From evidence to inference: Probing the evolution of protein interaction networks

(2009) Oliver Ratmann et al.   HFSP Journal

Automatic Parameter Learning for Multiple Local Network Alignment

(2009) Jason Flannick et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

Alignment-Free Sequence Comparison (I): Statistics and Power

(2009) Gesine Reinert et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

Human Protein Reference Database--2009 update

(2008) T. S. Keshava Prasad et al.   NUCLEIC ACIDS RESEARCH

Database resources of the National Center for Biotechnology Information

(2008) E. W. Sayers et al.   NUCLEIC ACIDS RESEARCH

Global alignment of multiple protein interaction networks with application to functional orthology detection

(2008) R. Singh et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA