bioconductor: minet | Projects | Ecosyste.ms: Papers

10.1186/s13029-015-0043-5

CyNetworkBMA: a Cytoscape app for inferring gene regulatory networks
Cited by: 5
Author(s): Maciej Fronczuk, Adrian E. Raftery, Ka Yee Yeung
Software Mentions: 8
Published: over 8 years ago

Stability Indicators in Network Reconstruction
Cited by: 19
Author(s): Michele Filosi, Roberto Visintainer, Samantha Riccadonna, Giuseppe Jurman, Cesare Furlanello
Software Mentions: 7
Published: over 10 years ago

10.1186/1471-2105-12-492

Structural Measures for Network Biology Using QuACN
Cited by: 18
Author(s): Laurin A. J. Mueller, Karl G. Kugler, Armin Graber, Frank Emmert‐Streib, Matthias Dehmer
Software Mentions: 7
Published: over 12 years ago

10.1371/journal.pone.0035077

Hub-Centered Gene Network Reconstruction Using Automatic Relevance Determination
Cited by: 20
Author(s): M. Bock, Soichi Ogishima, Hiroshi Tanaka, Stefan Krämer, Lars Kaderali
Software Mentions: 6
Published: about 12 years ago

10.1186/s12859-015-0856-x

3off2: A network reconstruction algorithm based on 2-point and 3-point information statistics
Cited by: 13
Author(s): Séverine Affeldt, Louis Verny, Hervé Isambert
Software Mentions: 6
Published: over 8 years ago

10.1186/1752-0509-8-47

Fast Bayesian inference for gene regulatory networks using ScanBMA
Cited by: 78
Author(s): William Chad Young, Adrian E. Raftery, Ka Yee Yeung
Software Mentions: 6
Published: over 10 years ago

10.1093/bioinformatics/bts363

Integrating literature-constrained and data-driven inference of signalling networks
Cited by: 36
Author(s): Federica Eduati, Javier De Las Rivas, Barbara Di Camillo, Gianna Toffolo, Julio Sáez-Rodríguez
Software Mentions: 6
Published: about 12 years ago

10.1371/journal.pone.0060045

The Structure of a Gene Co-Expression Network Reveals Biological Functions Underlying eQTLs
Cited by: 37
Author(s): Nathalie Villa-Vialaneix, Laurence Liaubet, Thibault Laurent, Pierre Chérel, Adrien Gamot, Magali SanCristobal
Software Mentions: 6
Published: over 11 years ago

10.1371/journal.pone.0026146

Graph Constrained Discriminant Analysis: A New Method for the Integration of a Graph into a Classification Process
Cited by: 5
Author(s): Vincent Guillemot, Arthur Tenenhaus, Laurent Le Brusquet, Vincent Frouin
Software Mentions: 6
Published: almost 13 years ago

10.1371/journal.pone.0077776

Extension of Life Span by Impaired Glucose Metabolism in Caenorhabditis elegans Is Accompanied by Structural Rearrangements of the Transcriptomic Network
Cited by: 20
Author(s): Stefan Priebe, Uwe Menzel, Kim Zarse, Marco Groth, Matthias Platzer, Michael Ristow, Reinhard Guthke
Software Mentions: 6
Published: over 10 years ago

10.1371/journal.pone.0251666

PEPN-GRN: A Petri net-based approach for the inference of gene regulatory networks from noisy gene expression data
Cited by: 4
Author(s): Deepika Vatsa, Sumeet Agarwal
Software Mentions: 5
Published: about 3 years ago

10.1186/s12864-016-3075-6

Non-linear interactions between candidate genes of myocardial infarction revealed in mRNA expression profiles
Cited by: 17
Author(s): Katherine E. Hartmann, Michał Seweryn, Samuel K. Handelman, Grzegorz A. Rempała, Wolfgang Sadée
Software Mentions: 5
Published: almost 8 years ago

10.3389/fpls.2019.01535

A Bioinformatics Approach to Explore MicroRNAs as Tools to Bridge Pathways Between Plants and Animals. Is DNA Damage Response (DDR) a Potential Target Process?
Cited by: 9
Author(s): Massimo Bellato, Davide De Marchi, Carla Gualtieri, Elisabetta Sauta, Paolo Magni, Anca Macovei, Lorenzo Pasotti
Software Mentions: 5
Published: over 4 years ago

10.1371/journal.pone.0200094

A robust gene regulatory network inference method base on Kalman filter and linear regression
Cited by: 35
Author(s): Jamshid Pirgazi, Alireza Khanteymoori
Software Mentions: 5
Published: about 6 years ago

10.1186/1471-2105-9-461

minet: A R/Bioconductor Package for Inferring Large Transcriptional Networks Using Mutual Information
Cited by: 469
Author(s): Patrick Meyer, Frédéric Lafitte, Gianluca Bontempi
Software Mentions: 4
Published: over 15 years ago

10.3390/biom10040557

Deciphering Master Gene Regulators and Associated Networks of Human Mesenchymal Stromal Cells
Cited by: 6
Author(s): Elena Sánchez-Luis, Andrea Joaquín-García, Francisco J. Campos‐Laborie, Fermín Sánchez‐Guijo, Javier De Las Rivas
Software Mentions: 4
Published: over 4 years ago

10.1242/jeb.238915

Metabolic response of dolphins to short-term fasting reveals physiological changes that differ from the traditional fasting model
Cited by: 10
Author(s): Dorian S. Houser, Davina Derous, Alex Douglas, David Lusseau
Software Mentions: 4
Published: about 3 years ago

10.1038/s41598-017-18205-0

Tissue Tropism in Host Transcriptional Response to Members of the Bovine Respiratory Disease Complex
Cited by: 26
Author(s): Susanta K. Behura, P. C. Tizioto, JaeWoo Kim, Natália Vinhal Grupioni, Christopher M. Seabury, Robert D. Schnabel, Laurel J. Gershwin, Alison L. Van Eenennaam, Rachel L. Toaff-Rosenstein, Holly L. Neibergs, Luciana Correia de Almeida Regitano, Jeremy F. Taylor
Software Mentions: 4
Published: over 6 years ago

10.1186/1471-2105-12-292

Unraveling gene regulatory networks from time-resolved gene expression data -- a measures comparison study
Cited by: 43
Author(s): Sabrina Hempel, Aneta Koseska, Zoran Nikoloski, Jürgen Kurths
Software Mentions: 4
Published: about 13 years ago

10.1371/journal.pone.0171240

Expectation propagation for large scale Bayesian inference of non-linear molecular networks from perturbation data
Cited by: 5
Author(s): Zahra Narimani, Hamid Beigy, Ashar Ahmad, Ali Masoudi‐Nejad, Holger Fröhlich
Software Mentions: 4
Published: over 7 years ago

10.3390/ijms22189693

Fetal Brain Elicits Sexually Conflicting Transcriptional Response to the Ablation of Uterine Forkhead Box A2 (Foxa2) in Mice
Cited by: 5
Author(s): Pramod Dhakal, Monica Strawn, Ananya Samal, Susanta K. Behura
Software Mentions: 3
Published: almost 3 years ago

10.1186/s12859-015-0710-1

Prior knowledge driven Granger causality analysis on gene regulatory network discovery
Cited by: 16
Author(s): Shun Yao, Shinjae Yoo, D. Yu
Software Mentions: 3
Published: almost 9 years ago

10.1186/s12859-016-0885-0

Deciphering transcriptional regulations coordinating the response to environmental changes
Cited by: 1
Author(s): Vicente Acuña, Andrés Aravena, Carito Guziołowski, Damien Eveillard, Anne Siegel, Alejandro Maass
Software Mentions: 3
Published: over 8 years ago

10.1186/s12859-017-1576-1

Enhanced construction of gene regulatory networks using hub gene information
Cited by: 62
Author(s): Daren Yu, Jong-Tae Lim, Xinlei Wang, Faming Liang, Guanghua Xiao
Software Mentions: 3
Published: over 7 years ago

10.1186/s12864-017-3775-6

The midgut transcriptome of Aedes aegypti fed with saline or protein meals containing chikungunya virus reveals genes potentially involved in viral midgut escape
Cited by: 42
Author(s): Shao-Jing Dong, Susanta K. Behura, Alexander W. E. Franz
Software Mentions: 3
Published: about 7 years ago

10.1371/journal.pone.0031194

A Relative Variation-Based Method to Unraveling Gene Regulatory Networks
Cited by: 12
Author(s): Yali Wang, Tong Zhou
Software Mentions: 3
Published: over 12 years ago

10.1371/journal.pone.0188016

Estimation of the proteomic cancer co-expression sub networks by using association estimators
Cited by: 2
Author(s): Cihat Erdoğan, Zeyneb Kurt, Banu Di̇ri̇
Software Mentions: 3
Published: over 6 years ago

10.1016/j.cels.2017.08.014

Gene Regulatory Network Inference from Single-Cell Data Using Multivariate Information Measures
Cited by: 386
Author(s): Thalia E. Chan, Michael Stumpf, Ann C. Babtie
Software Mentions: 3
Published: almost 7 years ago

10.3390/cells2020306

Reverse Engineering Cellular Networks with Information Theoretic Methods
Cited by: 53
Author(s): Alejandro F. Villaverde, John Ross, Julio R. Banga
Software Mentions: 3
Published: about 11 years ago

10.12688/f1000research.9050.2

CoNet app: inference of biological association networks using Cytoscape
Cited by: 238
Author(s): Karoline Faust, Jeroen Raes
Software Mentions: 3
Published: almost 8 years ago

10.1155/2019/6212681

Identifying and Validating Genes with DNA Methylation Data in the Context of Biological Network for Chinese Patients with Graves’ Orbitopathy
Cited by: 6
Author(s): Tingting Shi, Lin Hua, Xin Zhong, Li Yu, Wei Liu, Yilin Yang
Software Mentions: 3
Published: over 5 years ago

10.1155/2015/140819

MIrExpress: A Database for Gene Coexpression Correlation in Immune Cells Based on Mutual Information and Pearson Correlation
Cited by: 13
Author(s): Luman Wang, Qiaochu Mo, Jianxin Wang
Software Mentions: 3
Published: over 9 years ago

10.1186/s12859-016-1324-y

CMIP: a software package capable of reconstructing genome-wide regulatory networks using gene expression data
Cited by: 19
Author(s): Guangyong Zheng, Yaochen Xu, Xiujun Zhang, Zhi-Ping Liu, Zhuo Wang, Luonan Chen, Xin‐Guang Zhu
Software Mentions: 2
Published: over 7 years ago

10.18632/aging.100944

The effects of graded levels of calorie restriction: VII. Topological rearrangement of hypothalamic aging networks
Cited by: 18
Author(s): Davina Derous, Sharon E. Mitchell, Cara L Green, Yingchun Wang, Jing Han, Luonan Chen, Daniel E. L. Promislow, David Lusseau, John R. Speakman, Alex Douglas
Software Mentions: 2
Published: over 8 years ago

10.1098/rsos.140270

Prognostic models in coronary artery disease: Cox and network approaches
Cited by: 2
Author(s): Antonio M. Mora, Rosa Sicari, Lauro Cortigiani, Clara Carpeggiani, Eugenio Picaño, Enrico Capobianco
Software Mentions: 2
Published: over 9 years ago

10.1186/s12918-016-0331-y

Information theoretic approaches for inference of biological networks from continuous-valued data
Cited by: 12
Author(s): David Budden, Edmund J. Crampin
Software Mentions: 2
Published: almost 8 years ago

Ecosyste.ms: Papers

Projects: bioconductor: minet

Papers Mentioning minet 36