Stability indicators in network reconstruction (Q35108162)

6 August 2017

title

Stability indicators in network reconstruction (English)

1 reference

6 August 2017

Michele Filosi

1

0 references

Roberto Visintainer

Roberto Visintainer

2

0 references

Samantha Riccadonna

Samantha Riccadonna

3

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Cesare Furlanello

Cesare Furlanello

5

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Giuseppe Jurman

Giuseppe Jurman

4

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language of work or name

English

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publication date

27 February 2014

1 reference

6 August 2017

1 reference

6 August 2017

volume

9

1 reference

6 August 2017

issue

2

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6 August 2017

page(s)

e89815

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Creative Commons Attribution 4.0 International

6 August 2017

copyright license

start time

27 February 2014

1 reference

April 2022 Public Data File from Crossref

copyright status

copyrighted

0 references

describes a project that uses

WGCNA

WGCNA

WGCNA R package

1 reference

CZ Software Mentions: A large dataset of software mentions in the biomedical literature

WGCNA

0 references

cites work

microRNA: a promising diagnostic biomarker and therapeutic target for hepatocellular carcinoma

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3937450

Network deconvolution as a general method to distinguish direct dependencies in networks

9 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3937450

Inference of gene regulatory networks with sparse structural equation models exploiting genetic perturbations

9 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3937450

An overview of the statistical methods used for inferring gene regulatory networks and protein-protein interaction networks

9 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3937450

Interactions of miR-323/miR-326/miR-329 and miR-130a/miR-155/miR-210 as prognostic indicators for clinical outcome of glioblastoma patients

9 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3937450

Network Inference and Biological Dynamics

9 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3937450

Minerva and minepy: a C engine for the MINE suite and its R, Python and MATLAB wrappers

9 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3937450

Comparison of co-expression measures: mutual information, correlation, and model based indices

9 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3937450

Wisdom of crowds for robust gene network inference

9 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3937450

Identifying biological network structure, predicting network behavior, and classifying network state with High Dimensional Model Representation (HDMR)

9 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3937450

IntScore: a web tool for confidence scoring of biological interactions

9 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3937450

Gene regulatory network inference: evaluation and application to ovarian cancer allows the prioritization of drug targets

9 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3937450

Gene regulation is governed by a core network in hepatocellular carcinoma.

9 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3937450

Transcriptional network inference from functional similarity and expression data: a global supervised approach

9 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3937450

Comparing statistical methods for constructing large scale gene networks

9 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3937450

Detecting novel associations in large data sets

9 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3937450

Inference of complex biological networks: distinguishability issues and optimization-based solutions

9 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3937450

DART: Denoising Algorithm based on Relevance network Topology improves molecular pathway activity inference

9 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3937450

Verification of systems biology research in the age of collaborative competition

9 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3937450

GeneNetWeaver:in silicobenchmark generation and performance profiling of network inference methods

9 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3937450

The role of indirect connections in gene networks in predicting function

9 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3937450

Emerging roles of microRNA in the intracellular signaling networks of hepatocellular carcinoma

9 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3937450

Gene Expression Network Reconstruction by Convex Feature Selection when Incorporating Genetic Perturbations

9 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3937450

miRBase: integrating microRNA annotation and deep-sequencing data

9 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3937450

Downregulation of p53-inducible microRNAs 192, 194, and 215 impairs the p53/MDM2 autoregulatory loop in multiple myeloma development

9 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3937450

Advantages and limitations of current network inference methods

9 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3937450

Gender-Specific Reduction of Estrogen-Sensitive Small RNA, miR-30b, in Subjects With Schizophrenia

9 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3937450

Reprogramming of miRNA networks in cancer and leukemia

9 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3937450

Revealing strengths and weaknesses of methods for gene network inference

9 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3937450

Development of the human cancer microRNA network

9 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3937450

Towards a rigorous assessment of systems biology models: the DREAM3 challenges

9 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3937450

PhenomiR: a knowledgebase for microRNA expression in diseases and biological processes

9 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3937450

The neuronal microRNA miR-326 acts in a feedback loop with notch and has therapeutic potential against brain tumors

9 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3937450

MicroRNA expression, survival, and response to interferon in liver cancer

9 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3937450

Reverse engineering and verification of gene networks: principles, assumptions, and limitations of present methods and future perspectives.

9 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3937450

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

9 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3937450

WGCNA: an R package for weighted correlation network analysis

9 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3937450

p53-Responsive micrornas 192 and 215 are capable of inducing cell cycle arrest

9 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3937450

Elevated expression of the miR-17-92 polycistron and miR-21 in hepadnavirus-associated hepatocellular carcinoma contributes to the malignant phenotype

9 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3937450

MicroRNA gene expression profile of hepatitis C virus-associated hepatocellular carcinoma

9 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3937450

Association of MicroRNA expression in hepatocellular carcinomas with hepatitis infection, cirrhosis, and patient survival.

9 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3937450

MicroRNA-21 (miR-21) post-transcriptionally downregulates tumor suppressor Pdcd4 and stimulates invasion, intravasation and metastasis in colorectal cancer

9 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3937450

Indeterminacy of reverse engineering of Gene Regulatory Networks: the curse of gene elasticity

9 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3937450

Large-scale mapping and validation of Escherichia coli transcriptional regulation from a compendium of expression profiles

9 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3937450

microRNAs exhibit high frequency genomic alterations in human cancer

9 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3937450

ARACNE: An Algorithm for the Reconstruction of Gene Regulatory Networks in a Mammalian Cellular Context

9 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3937450

A general framework for weighted gene co-expression network analysis

9 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3937450

Metabolic pathways variability and sequence/networks comparisons

9 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3937450

Comprehensive analysis of microRNA expression patterns in hepatocellular carcinoma and non-tumorous tissues

9 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3937450

MicroRNA profiling reveals distinct signatures in B cell chronic lymphocytic leukemias

9 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3937450

Missing value estimation methods for DNA microarrays

9 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3937450

Discovering functional relationships between RNA expression and chemotherapeutic susceptibility using relevance networks

9 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3937450

Basic local alignment search tool

9 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3937450

A novel Bayesian network inference algorithm for integrative analysis of heterogeneous deep sequencing data

9 July 2018

1 reference

https://api.crossref.org/works/10.1371/JOURNAL.PONE.0089815

Identifiability and inference of pathway motifs by epistasis analysis

21 January 2018

1 reference

https://api.crossref.org/works/10.1371/JOURNAL.PONE.0089815

Inferring gene networks: dream or nightmare?

21 January 2018

1 reference

https://api.crossref.org/works/10.1371/JOURNAL.PONE.0089815

Empirically determining the sample size for large-scale gene network inference algorithms

21 January 2018

1 reference

https://api.crossref.org/works/10.1371/JOURNAL.PONE.0089815

Revealing differences in gene network inference algorithms on the network level by ensemble methods.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371/JOURNAL.PONE.0089815

Identification of metastasis-related microRNAs in hepatocellular carcinoma

21 January 2018

1 reference

https://api.crossref.org/works/10.1371/JOURNAL.PONE.0089815

Validation of gene regulatory networks: scientific and inferential

21 January 2018

1 reference

https://api.crossref.org/works/10.1371/JOURNAL.PONE.0089815

Evolutionary reconstruction of networks

21 January 2018

1 reference

https://api.crossref.org/works/10.1371/JOURNAL.PONE.0089815

Perturbation analysis of complete synchronization in networks of phase oscillators

21 January 2018

1 reference

https://api.crossref.org/works/10.1371/JOURNAL.PONE.0089815

Mathematics. A correlation for the 21st century

21 January 2018

1 reference

https://api.crossref.org/works/10.1371/JOURNAL.PONE.0089815

Hive plots--rational approach to visualizing networks.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371/JOURNAL.PONE.0089815

Coordinated regulation of cell cycle transcripts by p53-Inducible microRNAs, miR-192 and miR-215.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371/JOURNAL.PONE.0089815

Clinical significance and prognostic value of microRNA expression signatures in hepatocellular carcinoma

21 January 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/24587057

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Finding correlations in big data

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/24587057

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1371/JOURNAL.PONE.0089815

1 reference

6 August 2017

0 references

1 reference

1 reference

6 August 2017

1 reference