Searching for repetitions in biological networks: methods, resources and tools

Optimizing a global alignment of protein interaction networks

(2013) Leonid Chindelevitch et al.   BIOINFORMATICS

SPINAL: scalable protein interaction network alignment

(2013) Ahmet E. Aladağ et al.   BIOINFORMATICS

mentha: a resource for browsing integrated protein-interaction networks

(2013) Alberto Calderone et al.   NATURE METHODS

EvoDesign: de novo protein design based on structural and evolutionary profiles

(2013) Pralay Mitra et al.   NUCLEIC ACIDS RESEARCH

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

(2013) Sayed Mohammad Ebrahim Sahraeian et al.   PLoS One

RNA-Seq Atlas—a reference database for gene expression profiling in normal tissue by next-generation sequencing

(2012) Markus Krupp et al.   BIOINFORMATICS

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

GraphAlignment: Bayesian pairwise alignment of biological networks

(2012) Michal Kolář et al.   BMC Systems Biology

HuPho: the human phosphatase portal

(2012) Susanna Liberti et al.   FEBS Journal

Yeast one-hybrid assays: A historical and technical perspective

(2012) John S. Reece-Hoyes et al.   METHODS

ChIP–seq and beyond: new and improved methodologies to detect and characterize protein–DNA interactions

(2012) Terrence S. Furey   NATURE REVIEWS GENETICS

The BioGRID interaction database: 2013 update

(2012) Andrew Chatr-aryamontri et al.   NUCLEIC ACIDS RESEARCH

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

(2012) Giovanni Ciriello et al.   PLoS One

Extracting string motif bases for quorum higher than two

(2012) Simona E. Rombo   THEORETICAL COMPUTER SCIENCE

AURA: Atlas of UTR Regulatory Activity

(2011) E. Dassi et al.   BIOINFORMATICS

Multifunctional proteins revealed by overlapping clustering in protein interaction network

(2011) Emmanuelle Becker et al.   BIOINFORMATICS

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

(2011) Oleksii Kuchaiev et al.   BIOINFORMATICS

GraphCrunch 2: Software tool for network modeling, alignment and clustering

(2011) Oleksii Kuchaiev et al.   BMC BIOINFORMATICS

Biological network motif detection: principles and practice

(2011) E. Wong et al.   BRIEFINGS IN BIOINFORMATICS

Interactome Networks and Human Disease

(2011) Marc Vidal et al.   CELL

Asymmetric Comparison and Querying of Biological Networks

(2011) N Ferraro et al.   IEEE-ACM Transactions on Computational Biology and Bioinformatics

A Coclustering Approach for Mining Large Protein-Protein Interaction Networks

(2011) C. Pizzuti et al.   IEEE-ACM Transactions on Computational Biology and Bioinformatics

SubMAP: Aligning Metabolic Pathways with Subnetwork Mappings

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

Biological Network Querying Techniques: Analysis and Comparison

(2011) Valeria Fionda et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

MADMX: A Strategy for Maximal Dense Motif Extraction

(2011) Roberto Grossi et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

Next-generation transcriptome assembly

(2011) Jeffrey A. Martin et al.   NATURE REVIEWS GENETICS

UniPathway: a resource for the exploration and annotation of metabolic pathways

(2011) Anne Morgat et al.   NUCLEIC ACIDS RESEARCH

The IntAct molecular interaction database in 2012

(2011) S. Kerrien et al.   NUCLEIC ACIDS RESEARCH

Gene Expression Atlas update--a value-added database of microarray and sequencing-based functional genomics experiments

(2011) M. Kapushesky 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 User's Guide to the Encyclopedia of DNA Elements (ENCODE)

(2011)   PLOS BIOLOGY

High-resolution genome-wide in vivo footprinting of diverse transcription factors in human cells

(2010) A. P. Boyle et al.   GENOME RESEARCH

Network medicine: a network-based approach to human disease

(2010) Albert-László Barabási et al.   NATURE REVIEWS GENETICS

UniPROBE, update 2011: expanded content and search tools in the online database of protein-binding microarray data on protein-DNA interactions

(2010) K. Robasky et al.   NUCLEIC ACIDS RESEARCH

Pathway Commons, a web resource for biological pathway data

(2010) E. G. Cerami et al.   NUCLEIC ACIDS RESEARCH

NCBI GEO: archive for functional genomics data sets--10 years on

(2010) T. Barrett 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

Reactome: a database of reactions, pathways and biological processes

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

IsoRankN: spectral methods for global alignment of multiple protein networks

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

A new graph-based method for pairwise global network alignment

(2009) Gunnar W Klau   BMC BIOINFORMATICS

Optimal extraction of motif patterns in 2D

(2009) Simona E. Rombo   INFORMATION PROCESSING LETTERS

A technique to search for functional similarities in protein-protein interaction networks

(2009) Valeria Fionda et al.   International Journal of Data Mining and Bioinformatics

MINT, the molecular interaction database: 2009 update

(2009) Arnaud Ceol et al.   NUCLEIC ACIDS RESEARCH

Structure prediction for CASP8 with all-atom refinement using Rosetta

(2009) Srivatsan Raman et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Bayesian Modeling of the Yeast SH3 Domain Interactome Predicts Spatiotemporal Dynamics of Endocytosis Proteins

(2009) Raffi Tonikian et al.   PLOS BIOLOGY

ITFP: an integrated platform of mammalian transcription factors

(2008) G. Zheng et al.   BIOINFORMATICS

Align human interactome with phenome to identify causative genes and networks underlying disease families

(2008) Xuebing Wu et al.   BIOINFORMATICS

Biomolecular network querying: a promising approach in systems biology

(2008) Shihua Zhang et al.   BMC Systems Biology

Mining Bridge and Brick Motifs From Complex Biological Networks for Functionally and Statistically Significant Discovery

(2008) Chia-Ying Cheng et al.   IEEE TRANSACTIONS ON SYSTEMS MAN AND CYBERNETICS PART B-CYBERNETICS

Human Protein Reference Database--2009 update

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

The implications of human metabolic network topology for disease comorbidity

(2008) D.- S. Lee et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

Motif patterns in 2D

(2007) Alberto Apostolico et al.   THEORETICAL COMPUTER SCIENCE