A gene (or genetic) regulatory network (GRN) is a collection of molecular regulators that interact with each other and with other substances in the cell to govern the gene expression levels of mRNA and proteins which, in turn, determine the function of the cell. Wikipedia (CC BY-SA 3.0)
2023 Articles
21 703 articles
Predicting the behavior of cerebral aneurysms, a different approach is necessary
- Saleha Azeem, Mohsin Rashid, Zaid Aljuboori, Saleha Azeem, Mohsin Rashid, Zaid Aljuboori
- None, 10.25259/sni_1035_2022
An oracle predicts regulators of cell identity
- Jeffrey A Farrell, Jeffrey A Farrell, Jeffrey A Farrell, Jeffrey A Farrell, Jeffrey A Farrell
- Nature, 10.1038/d41586-023-00251-6
wpLogicNet: logic gate and structure inference in gene regulatory networks
- Seyed Amir Malekpour, Maryam Shahdoust, Rosa Aghdam, …, Maryam Shahdoust, Rosa Aghdam, Mehdi Sadeghi
- Bioinformatics, 10.1093/bioinformatics/btad072
EnsInfer: a simple ensemble approach to network inference outperforms any single method
- Bingran Shen, Gloria Coruzzi, Dennis Shasha, …, Bingran Shen, Gloria Coruzzi, Dennis Shasha
- BMC Bioinformatics, 10.1186/s12859-023-05231-1
Sensitivity Analysis of Genome-Scale Metabolic Flux Prediction
- Puhua Niu, Maria J Soto, Shuai Huang, …, Francis J Alexander, Ian Blaby, Xiaoning Qian
- J Comput Biol, 10.1089/cmb.2022.0368
kboolnet: a toolkit for the verification, validation, and visualization of reaction-contingency (rxncon) models
- Willow Carretero Chavez, Marcus Krantz, Edda Klipp, …, Marcus Krantz, Edda Klipp, Irina Kufareva
- BMC Bioinformatics, 10.1186/s12859-023-05329-6
Multiscale computational modeling offers key to understanding molecular logic underpinning development and disease
- Himanshu Kaul, Himanshu Kaul, Himanshu Kaul, Himanshu Kaul
- Biotechniques, 10.2144/btn-2023-0039
MCPNet: a parallel maximum capacity-based genome-scale gene network construction framework
- Tony Pan, Sriram P Chockalingam, Maneesha Aluru, …, Sriram P Chockalingam, Maneesha Aluru, Srinivas Aluru
- Bioinformatics, 10.1093/bioinformatics/btad373
Inferring gene regulatory networks using transcriptional profiles as dynamical attractors
- Ruihao Li, Jordan C Rozum, Morgan M Quail, …, Clarissa J Nobile, Réka Albert, Aaron D Hernday
- PLoS Comput Biol, 10.1371/journal.pcbi.1010991
2022 Articles
2 223 articles
Accurate determination of causalities in gene regulatory networks by dissecting downstream target genes
- Zhigang Jia, Xiujun Zhang, Zhigang Jia, Xiujun Zhang
- None, 10.3389/fgene.2022.923339
REFINING CELLULAR PATHWAY MODELS USING AN ENSEMBLE OF HETEROGENEOUS DATA SOURCES
- Alexander M Franks, Florian Markowetz, Edoardo M Airoldi, …, Alexander M Franks, Florian Markowetz, Edoardo M Airoldi
- None, 10.1214/16-aoas915
NetSHy: network summarization via a hybrid approach leveraging topological properties
- Thao Vu, Elizabeth M Litkowski, Weixuan Liu, …, Russell P Bowler, Farnoush Banaei-Kashani, Katerina J Kechris
- Bioinformatics, 10.1093/bioinformatics/btac818
Functional Resilience of Mutually Repressing Motifs Embedded in Larger Networks
- Pradyumna Harlapur, Atchuta Srinivas Duddu, Kishore Hari, …, Kishore Hari, Prakash Kulkarni, Mohit Kumar Jolly
- Biomolecules, 10.3390/biom12121842
Inference of regulatory networks through temporally sparse data
- Mohammad Alali, Mahdi Imani, Mohammad Alali, …, Mahdi Imani, Mohammad Alali, Mahdi Imani
- None, 10.3389/fcteg.2022.1017256
Inferring gene regulatory networks from single-cell gene expression data via deep multi-view contrastive learning
- Zerun Lin, Le Ou-Yang, Zerun Lin, …, Le Ou-Yang, Zerun Lin, Le Ou-Yang
- Brief Bioinform, 10.1093/bib/bbac586
A generic parallel framework for inferring large-scale gene regulatory networks from expression profiles: application to Alzheimer’s disease network
- Softya Sebastian, Swarup Roy, Jugal Kalita, …, Softya Sebastian, Swarup Roy, Jugal Kalita
- Brief Bioinform, 10.1093/bib/bbac482
Leveraging class hierarchy for detecting missing annotations on hierarchical multi-label classification
- Miguel Romero, Felipe Kenji Nakano, Jorge Finke, …, Jorge Finke, Camilo Rocha, Celine Vens
- Comput Biol Med, 10.1016/j.compbiomed.2022.106423
Systematic comparison of modeling fidelity levels and parameter inference settings applied to negative feedback gene regulation
- Adrien Coulier, Prashant Singh, Marc Sturrock, …, Prashant Singh, Marc Sturrock, Andreas Hellander
- PLoS Comput Biol, 10.1371/journal.pcbi.1010683
A Comparison of Weighted Stochastic Simulation Methods for the Analysis of Genetic Circuits
- Mohammad Ahmadi, Payton J Thomas, Lukas Buecherl, …, Chris Winstead, Chris J Myers, Hao Zheng
- ACS Synth Biol, 10.1021/acssynbio.2c00553