ReviewNature reviews. Genetics2011
Software for systems biology: from tools to integrated platforms.
Review in Nature reviews. Genetics, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 122 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
122 citing papers in PubMed.
- Creating an engine of scientific discovery, an Indo-Japan perspective: learnings from IJNTC 2025 workshop.NPJ systems biology and applications · 2026Review
- Reviewability and supportability: New complementary principles to empower research software practices.Computational and structural biotechnology journal · 2024Review
- Towards a comprehensive assessment of QSP models: what would it take?Journal of pharmacokinetics and pharmacodynamics · 2024Review
- Ten simple rules for training scientists to make better software.PLoS computational biology · 2024Article
- Enabling Personalization for Digital Cognitive Stimulation to Support Communication With People With Dementia: Pilot Intervention Study as a Prelude to AI Development.JMIR formative research · 2024Article
- In Silico Clinical Trials: Is It Possible?Methods in molecular biology (Clifton, N.J.) · 2024Article
- Ten simple rules for managing laboratory information.PLoS computational biology · 2023Article
- Biologically informed NeuralODEs for genome-wide regulatory dynamics.Research square · 2023Article
- Application of Multiple Omics to Understand Postoperative Delirium Pathophysiology in Humans.Gerontology · 2023Review
- Reconstructing data-driven governing equations for cell phenotypic transitions: integration of data science and systems biology.Physical biology · 2022Review
- Isotope Calculation Gadgets: A Series of Software for Isotope-Tracing Experiments in Garuda Platform.Metabolites · 2022Article
- Analyzing the Systems Biology Effects of COVID-19 mRNA Vaccines to Assess Their Safety and Putative Side Effects.Pathogens (Basel, Switzerland) · 2022Article
- AI-driven laboratory workflows enable operation in the age of social distancing.SLAS technology · 2022Article
- Systems approaches to investigate the role of NF-κB signaling in aging.The Biochemical journal · 2022Review
- Teaching computational systems biology with an eye on quantitative systems pharmacology at the undergraduate level: Why do it, who would take it, and what should we teach?Frontiers in systems biology · 2022Article
- Relationship Between Dimensionality and Convergence of Optimization Algorithms: A Comparison Between Data-Driven Normalization and Scaling Factor-Based Methods Using PEPSSBI.Methods in molecular biology (Clifton, N.J.) · 2022Article
- Large scale text mining for deriving useful insights: A case study focused on microbiome.Frontiers in physiology · 2022Article
- A Network-Guided Approach to Discover Phytochemical-Based Anticancer Therapy: Targeting MARK4 for Hepatocellular Carcinoma.Frontiers in oncology · 2022Article
- Bacterial Metabolomics: Sample Preparation Methods.Biochemistry research international · 2022Review
- WinBEST-KIT: Biochemical Reaction Simulator for Analyzing Multi-Layered Metabolic Pathways.Bioengineering (Basel, Switzerland) · 2021Article
62 more citing papers are in PubMed but not listed here.
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
Understanding complex biological systems requires extensive support from software tools. Such tools are needed at each step of a systems biology computational workflow, which typically consists of data handling, network inference, deep curation, dynamical simulation and model analysis. In addition, there are now efforts to develop integrated software platforms, so that tools that are used at different stages of the workflow and by different researchers can easily be used together. This Review describes the types of software tools that are required at different stages of systems biology research and the current options that are available for systems biology researchers. We also discuss the challenges and prospects for modelling the effects of genetic changes on physiology and the concept of an integrated platform.
Indexed as
Identifiers
22048662What 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.