SMETANA: Accurate and Scalable Algorithm for Probabilistic Alignment of Large-Scale Biological Networks

Structure and dynamics of molecular networks: A novel paradigm of drug discovery

(2013) Peter Csermely et al.   PHARMACOLOGY & THERAPEUTICS

RESQUE: Network reduction using semi-Markov random walk scores for efficient querying of biological networks

(2012) Sayed Mohammad Ebrahim Sahraeian et al.   BIOINFORMATICS

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

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

C-GRAAL: Common-neighbors-based global GRAph ALignment of biological networks

(2012) Vesna Memišević et al.   Integrative Biology

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

(2012) Giovanni Ciriello et al.   PLoS One

A Network Synthesis Model for Generating Protein Interaction Network Families

(2012) Sayed Mohammad Ebrahim Sahraeian et al.   PLoS One

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

(2011) Oleksii Kuchaiev et al.   BIOINFORMATICS

Comparative Analysis of Biological Networks: Hidden Markov model and Markov chain-based approach

(2011) Byung-Jun Yoon et al.   IEEE SIGNAL PROCESSING MAGAZINE

SubMAP: Aligning Metabolic Pathways with Subnetwork Mappings

(2011) Ferhat Ay et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

Aligning graphs and finding substructures by a cavity approach

(2010) S. Bradde et al.   EPL

A Novel Low-Complexity HMM Similarity Measure

(2010) Sayed Mohammad Ebrahim Sahraeian et al.   IEEE SIGNAL PROCESSING LETTERS

PicXAA: greedy probabilistic construction of maximum expected accuracy alignment of multiple sequences

(2010) Sayed Mohammad Ebrahim Sahraeian et al.   NUCLEIC ACIDS RESEARCH

IsoBase: a database of functionally related proteins across PPI networks

(2010) D. Park et al.   NUCLEIC ACIDS RESEARCH

The BioGRID Interaction Database: 2011 update

(2010) C. Stark et al.   NUCLEIC ACIDS RESEARCH

The STRING database in 2011: functional interaction networks of proteins, globally integrated and scored

(2010) D. Szklarczyk et al.   NUCLEIC ACIDS RESEARCH

Domain-oriented edge-based alignment of protein interaction networks

(2009) X. Guo et al.   BIOINFORMATICS

Functionally guided alignment of protein interaction networks for module detection

(2009) Waqar Ali et al.   BIOINFORMATICS

IsoRankN: spectral methods for global alignment of multiple protein networks

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

Global alignment of protein-protein interaction networks by graph matching methods

(2009) M. Zaslavskiy et al.   BIOINFORMATICS

A new graph-based method for pairwise global network alignment

(2009) Gunnar W Klau   BMC BIOINFORMATICS

Automatic Parameter Learning for Multiple Local Network Alignment

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

Effective Identification of Conserved Pathways in Biological Networks Using Hidden Markov Models

(2009) Xiaoning Qian et al.   PLoS One

NetworkBLAST: comparative analysis of protein networks

(2008) M. Kalaev et al.   BIOINFORMATICS

Human Protein Reference Database--2009 update

(2008) T. S. Keshava Prasad 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

Age-Dependent Evolution of the Yeast Protein Interaction Network Suggests a Limited Role of Gene Duplication and Divergence

(2008) Wan Kyu Kim et al.   PLoS Computational Biology

Mining physical protein-protein interactions from the literature

(2008) Minlie Huang et al.   GENOME BIOLOGY