Automating parameter selection to avoid implausible biological pathway models

ResponseNet v.3: revealing signaling and regulatory pathways connecting your proteins and genes across human tissues

(2019) Omer Basha et al.   NUCLEIC ACIDS RESEARCH

Assessment of network module identification across complex diseases

(2019) Sarvenaz Choobdar et al.   NATURE METHODS

Genome-wide CRISPR/Cas9 Screen Identifies Host Factors Essential for Influenza Virus Replication

(2018) Julianna Han et al.   Cell Reports

Network inference reveals novel connections in pathways regulating growth and defense in the yeast salt response

(2018) Matthew E. MacGilvray et al.   PLoS Computational Biology

Influenza A Virus Cell Entry, Replication, Virion Assembly and Movement

(2018) Dan Dou et al.   Frontiers in Immunology

Synthesizing Signaling Pathways from Temporal Phosphoproteomic Data

(2018) Ali Sinan Köksal et al.   Cell Reports

STRING v11: protein–protein association networks with increased coverage, supporting functional discovery in genome-wide experimental datasets

(2018) Damian Szklarczyk et al.   NUCLEIC ACIDS RESEARCH

The Gene Ontology Resource: 20 years and still GOing strong

(2018)   NUCLEIC ACIDS RESEARCH

Learning Parameter-Advising Sets for Multiple Sequence Alignment

(2017) Dan DeBlasio et al.   IEEE-ACM Transactions on Computational Biology and Bioinformatics

Network propagation: a universal amplifier of genetic associations

(2017) Lenore Cowen et al.   NATURE REVIEWS GENETICS

The Reactome Pathway Knowledgebase

(2017) Antonio Fabregat et al.   NUCLEIC ACIDS RESEARCH

Optimal classifier for imbalanced data using Matthews Correlation Coefficient metric

(2017) Sabri Boughorbel et al.   PLoS One

Parameter advising for multiple sequence alignment

(2015) Dan DeBlasio et al.   BMC BIOINFORMATICS

Meta- and Orthogonal Integration of Influenza “OMICs” Data Defines a Role for UBR4 in Virus Budding

(2015) Shashank Tripathi et al.   Cell Host & Microbe

Reconstruction of the temporal signaling network in Salmonella-infected human cells

(2015) Gungor Budak et al.   Frontiers in Microbiology

Influenza Virus-Host Interactome Screen as a Platform for Antiviral Drug Development

(2014) Tokiko Watanabe et al.   Cell Host & Microbe

PhosphoSitePlus, 2014: mutations, PTMs and recalibrations

(2014) Peter V. Hornbeck et al.   NUCLEIC ACIDS RESEARCH

Revealing the Hidden Language of Complex Networks

(2014) Ömer Nebil Yaveroğlu et al.   Scientific Reports

Accuracy Estimation and Parameter Advising for Protein Multiple Sequence Alignment

(2013) John Kececioglu et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

Simultaneous Reconstruction of Multiple Signaling Pathways via the Prize-Collecting Steiner Forest Problem

(2013) Nurcan Tuncbag et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

ResponseNet2.0: revealing signaling and regulatory pathways connecting your proteins and genes—now with human data

(2013) Omer Basha et al.   NUCLEIC ACIDS RESEARCH

How advancement in biological network analysis methods empowers proteomics

(2012) Wilson W. B. Goh et al.   PROTEOMICS

Human diseases through the lens of network biology

(2012) Laura I. Furlong   TRENDS IN GENETICS

Computationally efficient measure of topological redundancy of biological and social networks

(2011) Réka Albert et al.   PHYSICAL REVIEW E

ANAT: A Tool for Constructing and Analyzing Functional Protein Networks

(2011) N. Yosef et al.   Science Signaling

Automated Network Analysis Identifies Core Pathways in Glioblastoma

(2010) Ethan Cerami et al.   PLoS One

Finding undetected protein associations in cell signaling by belief propagation

(2010) M. Bailly-Bechet et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Use of Data-Biased Random Walks on Graphs for the Retrieval of Context-Specific Networks from Genomic Data

(2010) Kakajan Komurov et al.   PLoS Computational Biology

NetPath: a public resource of curated signal transduction pathways

(2010) Kumaran Kandasamy et al.   GENOME BIOLOGY

Bridging high-throughput genetic and transcriptional data reveals cellular responses to alpha-synuclein toxicity

(2009) Esti Yeger-Lotem et al.   NATURE GENETICS

Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources

(2009) Da Wei Huang et al.   Nature Protocols

iRefIndex: A consolidated protein interaction database with provenance

(2008) Sabry Razick et al.   BMC BIOINFORMATICS