(Q30352074)

18 August 2017

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

1 reference

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

18 August 2017

1 reference

corrigendum / erratum

0 references

4

Manolis Kellis

1 reference

18 August 2017

Soheil Feizi

1

1 reference

PMCID

3773370

18 August 2017

Daniel Marbach

series ordinal

2

1 reference

PMCID

3773370

18 August 2017

Muriel Médard

series ordinal

3

1 reference

18 August 2017

14 July 2013

1 reference

18 August 2017

1 reference

18 August 2017

31

1 reference

18 August 2017

8

1 reference

18 August 2017

726-733

1 reference

Improved contact prediction in proteins: using pseudolikelihoods to infer Potts models

18 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3773370

TIGRESS: Trustful Inference of Gene REgulation using Stability Selection.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3773370

Protein structure prediction from sequence variation

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3773370

Wisdom of crowds for robust gene network inference

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3773370

Accurate de novo structure prediction of large transmembrane protein domains using fragment-assembly and correlated mutation analysis

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3773370

Three-dimensional structures of membrane proteins from genomic sequencing

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3773370

Protein 3D structure computed from evolutionary sequence variation

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3773370

Direct-coupling analysis of residue coevolution captures native contacts across many protein families

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3773370

PSICOV: precise structural contact prediction using sparse inverse covariance estimation on large multiple sequence alignments

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3773370

RegulonDB version 7.0: transcriptional regulation of Escherichia coli K-12 integrated within genetic sensory response units (Gensor Units)

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3773370

DREAM4: Combining genetic and dynamic information to identify biological networks and dynamical models

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3773370

From knockouts to networks: establishing direct cause-effect relationships through graph analysis.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3773370

Inferring regulatory networks from expression data using tree-based methods

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3773370

Advantages and limitations of current network inference methods

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3773370

Estimating the directed information to infer causal relationships in ensemble neural spike train recordings

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3773370

Revealing strengths and weaknesses of methods for gene network inference

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3773370

Disentangling direct from indirect co-evolution of residues in protein alignments

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3773370

Identification of direct residue contacts in protein-protein interaction by message passing

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3773370

Genome-wide partial correlation analysis of Escherichia coli microarray data.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3773370

Network-based prediction of protein function

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3773370

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

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3773370

Integrated biclustering of heterogeneous genome-wide datasets for the inference of global regulatory networks

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3773370

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

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3773370

The Inferelator: an algorithm for learning parsimonious regulatory networks from systems-biology data sets de novo

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3773370

An improved map of conserved regulatory sites for Saccharomyces cerevisiae

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3773370

Chemogenomic profiling on a genome-wide scale using reverse-engineered gene networks

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3773370

Discovery of meaningful associations in genomic data using partial correlation coefficients

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3773370

Inferring cellular networks using probabilistic graphical models

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3773370

Evaluating causal relations in neural systems: granger causality, directed transfer function and statistical assessment of significance

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3773370

Scientific collaboration networks. II. Shortest paths, weighted networks, and centrality

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3773370

Using graphical models and genomic expression data to statistically validate models of genetic regulatory networks

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3773370

Using Bayesian networks to analyze expression data

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3773370

Mutual information relevance networks: functional genomic clustering using pairwise entropy measurements

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3773370

How frequent are correlated changes in families of protein sequences?

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3773370

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3773370

Correlation of co-ordinated amino acid substitutions with function in viruses related to tobacco mosaic virus

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3773370

The Structure and Function of Complex Networks

3 June 2018

1 reference

Mutual information without the influence of phylogeny or entropy dramatically improves residue contact prediction.

21 January 2018

1 reference

Superadditive correlation.

21 January 2018

1 reference

21 January 2018

1 reference

Computational discovery of gene modules and regulatory networks

21 January 2018

1 reference

Inferring gene regulatory networks by ANOVA.

21 January 2018

1 reference

Finding community structure in networks using the eigenvectors of matrices.

21 January 2018

1 reference

The Strength of Weak Ties: A Network Theory Revisited

21 January 2018

1 reference

High-dimensional graphs and variable selection with the Lasso

21 January 2018

1 reference

inferred from DOI database lookup

7 January 2021

based on heuristic

Identifiers

DOI

10.1038/NBT.2635

1 reference

18 August 2017

1 reference

18 August 2017

1 reference

PMCID

3773370