Cargando…

A strategy for evaluating pathway analysis methods

BACKGROUND: Researchers have previously developed a multitude of methods designed to identify biological pathways associated with specific clinical or experimental conditions of interest, with the aim of facilitating biological interpretation of high-throughput data. Before practically applying such...

Descripción completa

Detalles Bibliográficos
Autores principales:	Yu, Chenggang, Woo, Hyung Jun, Yu, Xueping, Oyama, Tatsuya, Wallqvist, Anders, Reifman, Jaques
Formato:	Online Artículo Texto
Lenguaje:	English
Publicado:	BioMed Central 2017
Materias:	Methodology Article
Acceso en línea:	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5640951/ https://www.ncbi.nlm.nih.gov/pubmed/29029625 http://dx.doi.org/10.1186/s12859-017-1866-7

Ejemplares similares

Inferring high-confidence human protein-protein interactions
por: Yu, Xueping, et al.
Publicado: (2012)

Genotype distribution-based inference of collective effects in genome-wide association studies: insights to age-related macular degeneration disease mechanism
por: Woo, Hyung Jun, et al.
Publicado: (2016)

A Novel Scoring Approach for Protein Co-Purification Data Reveals High Interaction Specificity
por: Yu, Xueping, et al.
Publicado: (2009)

Influence of Protein Abundance on High-Throughput Protein-Protein Interaction Detection
por: Ivanic, Joseph, et al.
Publicado: (2009)

Exploiting large-scale drug-protein interaction information for computational drug repurposing
por: Liu, Ruifeng, et al.
Publicado: (2014)

PathNet: a tool for pathway analysis using topological information
por: Dutta, Bhaskar, et al.
Publicado: (2012)

A systems biology strategy to identify molecular mechanisms of action and protein indicators of traumatic brain injury
por: Yu, Chenggang, et al.
Publicado: (2015)

Collective Genetic Interaction Effects and the Role of Antigen-Presenting Cells in Autoimmune Diseases
por: Woo, Hyung Jun, et al.
Publicado: (2017)

Development and analysis of an in vivo-compatible metabolic network of Mycobacterium tuberculosis
por: Fang, Xin, et al.
Publicado: (2010)

The development of PIPA: an integrated and automated pipeline for genome-wide protein function annotation
por: Yu, Chenggang, et al.
Publicado: (2008)

A systems biology framework for modeling metabolic enzyme inhibition of Mycobacterium tuberculosis
por: Fang, Xin, et al.
Publicado: (2009)

Evidence of probabilistic behaviour in protein interaction networks
por: Ivanic, Joseph, et al.
Publicado: (2008)

Probing the Extent of Randomness in Protein Interaction Networks
por: Ivanic, Joseph, et al.
Publicado: (2008)

Modeling Phenotypic Metabolic Adaptations of Mycobacterium tuberculosis H37Rv under Hypoxia
por: Fang, Xin, et al.
Publicado: (2012)

Reconstituting protein interaction networks using parameter-dependent domain-domain interactions
por: Memišević, Vesna, et al.
Publicado: (2013)

Data-driven prediction of adverse drug reactions induced by drug-drug interactions
por: Liu, Ruifeng, et al.
Publicado: (2017)

Novel Burkholderia mallei Virulence Factors Linked to Specific Host-Pathogen Protein Interactions
por: Memišević, Vesna, et al.
Publicado: (2013)

Prediction of Metabolic Flux Distribution from Gene Expression Data Based on the Flux Minimization Principle
por: Song, Hyun-Seob, et al.
Publicado: (2014)

Erratum to: Genotype distribution-based inference of collective effects in genome-wide association studies: insights to age-related macular degeneration disease mechanism
por: Woo, Hyung Jun, et al.
Publicado: (2016)

Bridging the gap between gene expression and metabolic phenotype via kinetic models
por: Vital-Lopez, Francisco G, et al.
Publicado: (2013)

Biofilm Formation Mechanisms of Pseudomonas aeruginosa Predicted via Genome-Scale Kinetic Models of Bacterial Metabolism
por: Vital-Lopez, Francisco G., et al.
Publicado: (2015)

Genetic interaction effects reveal lipid-metabolic and inflammatory pathways underlying common metabolic disease risks
por: Woo, Hyung Jun, et al.
Publicado: (2018)

Using a genome-scale metabolic network model to elucidate the mechanism of chloroquine action in Plasmodium falciparum
por: Tewari, Shivendra G., et al.
Publicado: (2017)

Using host-pathogen protein interactions to identify and characterize Francisella tularensis virulence factors
por: Wallqvist, Anders, et al.
Publicado: (2015)

DOVIS: an implementation for high-throughput virtual screening using AutoDock
por: Zhang, Shuxing, et al.
Publicado: (2008)

DOVIS 2.0: an efficient and easy to use parallel virtual screening tool based on AutoDock 4.0
por: Jiang, Xiaohui, et al.
Publicado: (2008)

Metabolic host responses to malarial infection during the intraerythrocytic developmental cycle
por: Wallqvist, Anders, et al.
Publicado: (2016)

A high-throughput pipeline for designing microarray-based pathogen diagnostic assays
por: Vijaya Satya, Ravi, et al.
Publicado: (2008)

Metabolic alterations in the erythrocyte during blood-stage development of the malaria parasite
por: Tewari, Shivendra G., et al.
Publicado: (2020)

Collective interaction effects associated with mammalian behavioral traits reveal genetic factors connecting fear and hemostasis
por: Woo, Hyung Jun, et al.
Publicado: (2018)

QuartetS: a fast and accurate algorithm for large-scale orthology detection
por: Yu, Chenggang, et al.
Publicado: (2011)

QuartetS-DB: a large-scale orthology database for prokaryotes and eukaryotes inferred by evolutionary evidence
por: Yu, Chenggang, et al.
Publicado: (2012)

DBSecSys 2.0: a database of Burkholderia mallei and Burkholderia pseudomallei secretion systems
por: Memišević, Vesna, et al.
Publicado: (2016)

PSPP: A Protein Structure Prediction Pipeline for Computing Clusters
por: Lee, Michael S., et al.
Publicado: (2009)

DBSecSys: a database of Burkholderia mallei secretion systems
por: Memišević, Vesna, et al.
Publicado: (2014)

Short-term metabolic adjustments in Plasmodium falciparum counter hypoxanthine deprivation at the expense of long-term viability
por: Tewari, Shivendra G., et al.
Publicado: (2019)

Volumetric characteristics of idiopathic pulmonary fibrosis lungs: computational analyses of high-resolution computed tomography images of lung lobes
por: Sul, Bora, et al.
Publicado: (2019)

Inter-study and time-dependent variability of metabolite abundance in cultured red blood cells
por: Tewari, Shivendra G., et al.
Publicado: (2021)

In silico microarray probe design for diagnosis of multiple pathogens
por: Vijaya Satya, Ravi, et al.
Publicado: (2008)

Mechanisms of action of Coxiella burnetii effectors inferred from host-pathogen protein interactions
por: Wallqvist, Anders, et al.
Publicado: (2017)

Cannot write session to /tmp/vufind_sessions/sess_v9n1tv4ssogcqqpg82d9q7ehtk