Cardiac gene regulatory networks in Drosophila [PDF]
Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms, 2009 The Drosophila system has proven a powerful tool to help unlock the regulatory processes that occur during specification and differentiation of the embryonic heart. In this review, we focus upon a temporal analysis of the molecular events that result in heart formation in Drosophila, with a particular emphasis upon how genomic and other cutting-edge ...
Anton L, Bryantsev, Richard M, Cripps
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Modelling stem cell differentiation related processes—A practical overview for biologists
FEBS Letters, EarlyView.Stem cell differentiation is complex and difficult to control experimentally. This review introduces suitable computational modelling approaches that can support stem cell research, from mechanistic ODE and abstract models to multiscale and deep learning methods.
Ricco Zeegelaar +4 more
wiley +1 more source
Linking Cytoscape and the corynebacterial reference database CoryneRegNet [PDF]
, 2008 Baumbach J, Apeltsin L. Linking Cytoscape and the corynebacterial reference database CoryneRegNet. BMC Genomics. 2008;9(1): 184.Background: Recently, the research community has seen an influx of data relating to transcriptional regulatory interactions of
Baumbach Jan +5 more
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Inferring context-sensitive probablistic boolean networks from gene expression data under multi-biological conditions [PDF]
, 2007 In recent years biological microarrays have emerged as a high-throughput data acquisition technology in bioinformatics. In conjunction with this, there is an increasing need to develop frameworks for the formal analysis of biological pathways. A modeling
Stephen Marshall +3 more
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ViBEx: A Visualization Tool for Gene Expression Analysis
BioMedInformaticsBackground: Variations in the states of Gene Regulatory Networks significantly influence disease outcomes and drug development. Boolean Networks serve as a tool to conceptualize and understand the complex relationships between genes.
Michael H. Terrefortes-Rosado +3 more
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Constructing tissue-specific transcriptional regulatory networks via a Markov random field
BMC Genomics, 2018 Background Recent advances in sequencing technologies have enabled parallel assays of chromatin accessibility and gene expression for major human cell lines.
Shining Ma, Tao Jiang, Rui Jiang
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Modeling regulatory network topology improves genome-wide analyses of complex human traits
Nature Communications, 2021 Gene regulatory networks are a useful means of inferring functional interactions from large-scale genomic data. Here, the authors develop a Bayesian framework integrating GWAS summary statistics with gene regulatory networks to identify genetic ...
Xiang Zhu, Zhana Duren, Wing Hung Wong
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Design and analysis strategies for robust microbiome ageing research
FEBS Letters, EarlyView.The gut microbiome changes with age and associates with age‐related morbidity and mortality, establishing it as a potential biomarker and intervention target for ageing. Realising this potential requires methodological rigour, yet distinguishing biological signals from methodological artefacts remains challenging across cohorts. This review provides an
Mark Olenik +5 more
wiley +1 more source
On robust stability of stochastic genetic regulatory networks with time delays: A delay fractioning approach [PDF]
, 2009 Copyright [2009] IEEE. This material is posted here with permission of the IEEE. Such permission of the IEEE does not in any way imply IEEE endorsement of any of Brunel University's products or services.
Wang, Z, Liang, J, Wang, Y
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Neuronal and glial 3D chromatin architecture informs the cellular etiology of brain disorders
Nature Communications, 2021 The cellular heterogeneity in brain obscures the identification of robust cellular regulatory networks. Here the authors integrate genome-wide chromosome conformation data from sorted neurons and glia, with transcriptomic and enhancer profiles, to ...
Benxia Hu +14 more
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