Results 41 to 50 of about 946,920 (339)

SERGIO: a single-cell expression simulator guided by gene regulatory networks

Cell Systems, 2020
Summary A common approach to benchmarking of single-cell transcriptomics tools is to generate synthetic data sets that statistically resemble experimental data.
Payam Dibaeinia, S. Sinha
semanticscholar   +1 more source

RENGE infers gene regulatory networks using time-series single-cell RNA-seq data with CRISPR perturbations

Communications Biology, 2023
Single-cell RNA-seq analysis coupled with CRISPR-based perturbation has enabled the inference of gene regulatory networks with causal relationships.
Masato Ishikawa, Seiichi Sugino, Yoshie Masuda, Yusuke Tarumoto, Yusuke Seto, Nobuko Taniyama, Fumi Wagai, Yuhei Yamauchi, Yasuhiro Kojima, Hisanori Kiryu, Kosuke Yusa, Mototsugu Eiraku, Atsushi Mochizuki   +12 more
doaj   +1 more source

Stochastic neural network models for gene regulatory networks [PDF]

, 2003
Recent advances in gene-expression profiling technologies provide large amounts of gene expression data. This raises the possibility for a functional understanding of genome dynamics by means of mathematical modelling.
Burrage K., Tian, T., Tian T., Burrage, K.   +3 more
core   +1 more source

Gene Regulatory Networks in Coronary Artery Disease [PDF]

, 2023
Purpose of ReviewCoronary artery disease is a complex disorder and the leading cause of mortality worldwide. As technologies for the generation of high-throughput multiomics data have advanced, gene regulatory network modeling has become an increasingly ...
Cheng, Jenny, Yang, Xia, Lusis, Aldons J, Cheng, Michael   +3 more
core   +1 more source

Nonparametric Bayesian inference for perturbed and orthologous gene regulatory networks [PDF]

, 2012
Motivation: The generation of time series transcriptomic datasets collected under multiple experimental conditions has proven to be a powerful approach for disentangling complex biological processes, allowing for the reverse engineering of gene ...
Penfold, Christopher A., Buchanan-Wollaston, Vicky, Wild, David L., Denby, Katherine J.   +3 more
core   +1 more source

Comprehensive information-based differential gene regulatory networks analysis (CIdrgn): Application to gastric cancer and chemotherapy-responsive gene network identification.

PLoS ONE, 2023
Biological condition-responsive gene network analysis has attracted considerable research attention because of its ability to identify pathways or gene modules involved in the underlying mechanisms of diseases.
Heewon Park, Seiya Imoto, Satoru Miyano
doaj   +2 more sources

GeRNet: a gene regulatory network tool [PDF]

Biosystems, 2017
Gene regulatory networks (GRNs) are crucial in every process of life since they govern the majority of the molecular processes. Therefore, the task of assembling these networks is highly important. In particular, the so called model-free approaches have an advantage modeling the complexities of dynamic molecular networks, since most of the gene ...
Julieta Sol Dussaut, Cristian Andrés Gallo, Fiorella Cravero, María Jimena Martínez, Jessica Andrea Carballido, Ignacio Ponzoni   +5 more
openaire   +3 more sources

Supervised inference of gene-regulatory networks

BMC Bioinformatics, 2008
Background Inference of protein interaction networks from various sources of data has become an important topic of both systems and computational biology.
Vohradsky Jiri, To Cuong C
doaj   +1 more source

Behavior-related gene regulatory networks: A new level of organization in the brain

Proceedings of the National Academy of Sciences of the United States of America, 2020
Neuronal networks are the standard heuristic model today for describing brain activity associated with animal behavior. Recent studies have revealed an extensive role for a completely distinct layer of networked activities in the brain—the gene ...
S. Sinha, Beryl M. Jones, Ian M. Traniello, S. A. Bukhari, M. Halfon, H. Hofmann, Sui Huang, P. Katz, Jason Keagy, Vincent J. Lynch, M. Sokolowski, L. Stubbs, Shayan Tabe-Bordbar, M. Wolfner, G. Robinson   +14 more
semanticscholar   +1 more source

Prioritizing transcriptional factors in gene regulatory networks with PageRank [PDF]

, 2021
Biological states are controlled by orchestrated transcriptional factors (TFs) within gene regulatory networks. Here we show TFs responsible for the dynamic changes of biological states can be prioritized with temporal PageRank.
Ding, Hongxu, Seninge, Lucas, Yang, Ying, Gong, Henry, Xue, Yuanqing, Safavi, Rojin, Stuart, Joshua M, Califano, Andrea   +7 more
core   +1 more source