ArticleCurrent genomics2014
Genome scale modeling in systems biology: algorithms and resources.
Article in Current genomics, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
13 citing papers in PubMed.
- PathIN: an integrated tool for the visualization of pathway interaction networks.Computational and structural biotechnology journal · 2023Article
- PathExNET: A tool for extracting pathway expression networks from gene expression statistics.Computational and structural biotechnology journal · 2021Article
- Integrating Single-Step GWAS and Bipartite Networks Reconstruction Provides Novel Insights into Yearling Weight and Carcass Traits in Hanwoo Beef Cattle.Animals : an open access journal from MDPI · 2020Article
- Identification of biomarkers in common chronic lung diseases by co-expression networks and drug-target interactions analysis.Molecular medicine (Cambridge, Mass.) · 2020Article
- Advances in Astrocyte Computational Models: From Metabolic Reconstructions to Multi-omic Approaches.Frontiers in neuroinformatics · 2020Article
- ProtExA: A tool for post-processing proteomics data providing differential expression metrics, co-expression networks and functional analytics.Computational and structural biotechnology journal · 2020Article
- Systems Bioinformatics: increasing precision of computational diagnostics and therapeutics through network-based approaches.Briefings in bioinformatics · 2019Review
- Multiple Pathways Involved in Palmitic Acid-Induced Toxicity: A System Biology Approach.Frontiers in neuroscience · 2019Article
- Metabolic network-based stratification of hepatocellular carcinoma reveals three distinct tumor subtypes.Proceedings of the National Academy of Sciences of the United States of America · 2018Article
- Metabolic Network-Based Identification and Prioritization of Anticancer Targets Based on Expression Data in Hepatocellular Carcinoma.Frontiers in physiology · 2018Article
- Dynamic modeling of folliculogenesis signaling pathways in the presence of miRNAs expression.Journal of ovarian research · 2017Article
- Genome-Scale Reconstruction of the Human Astrocyte Metabolic Network.Frontiers in aging neuroscience · 2017Article
- Neuroblastoma, a Paradigm for Big Data Science in Pediatric Oncology.International journal of molecular sciences · 2016Review
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
5 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
In recent years, in silico studies and trial simulations have complemented experimental procedures. A model is a description of a system, and a system is any collection of interrelated objects; an object, moreover, is some elemental unit upon which observations can be made but whose internal structure either does not exist or is ignored. Therefore, any network analysis approach is critical for successful quantitative modeling of biological systems. This review highlights some of most popular and important modeling algorithms, tools, and emerging standards for representing, simulating and analyzing cellular networks in five sections. Also, we try to show these concepts by means of simple example and proper images and graphs. Overall, systems biology aims for a holistic description and understanding of biological processes by an integration of analytical experimental approaches along with synthetic computational models. In fact, biological networks have been developed as a platform for integrating information from high to low-throughput experiments for the analysis of biological systems. We provide an overview of all processes used in modeling and simulating biological networks in such a way that they can become easily understandable for researchers with both biological and mathematical backgrounds. Consequently, given the complexity of generated experimental data and cellular networks, it is no surprise that researchers have turned to computer simulation and the development of more theory-based approaches to augment and assist in the development of a fully quantitative understanding of cellular dynamics.
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What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.