ArticleBioinformatics (Oxford, England)2018
ssbio: a Python framework for structural systems biology.
Article in Bioinformatics (Oxford, England), 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 23 papers, 1 of them a synthesis that pooled it.
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
23 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Pooled it
- Plant-associated fungi co-opt ancient antimicrobials for host manipulation.Science advances · 2026Article
- Article
- Laboratory Evolution Reveals Transcriptional Mechanisms Underlying Thermal Adaptation of Escherichia coli.Genome biology and evolution · 2025Article
- Decoding glycosylation potential from protein structure across human glycoproteins with a multi-view recurrent neural network.bioRxiv : the preprint server for biology · 2024Article
- Constraint-Based Reconstruction and Analyses of Metabolic Models: Open-Source Python Tools and Applications to Cancer.Frontiers in oncology · 2022Review
- Automated prediction of site and sequence of protein modification with ATRP initiators.PloS one · 2022Article
- Path to improving the life cycle and quality of genome-scale models of metabolism.Cell systems · 2021Review
- Genome-scale metabolic modeling reveals key features of a minimal gene set.Molecular systems biology · 2021Article
- The role of artificial intelligence in the battle against antimicrobial-resistant bacteria.Current genetics · 2021Review
- Article
- The Expanding Computational Toolbox for Engineering Microbial Phenotypes at the Genome Scale.Microorganisms · 2020Review
- Reconstructing organisms in silico: genome-scale models and their emerging applications.Nature reviews. Microbiology · 2020Review
- Systems biology analysis of the Clostridioides difficile core-genome contextualizes microenvironmental evolutionary pressures leading to genotypic and phenotypic divergence.NPJ systems biology and applications · 2020Article
- The Bitome: digitized genomic features reveal fundamental genome organization.Nucleic acids research · 2020Article
- Towards gaining sight of multiscale events: utilizing network models and normal modes in hybrid methods.Current opinion in structural biology · 2020Review
- Adaptations of Escherichia coli strains to oxidative stress are reflected in properties of their structural proteomes.BMC bioinformatics · 2020Article
- An atlas of human metabolism.Science signaling · 2020Article
- Combining Strengths for Multi-genome Visual Analytics Comparison.Bioinformatics and biology insights · 2019Article
- A computational knowledge-base elucidates the response of Staphylococcus aureus to different media types.PLoS computational biology · 2019Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
9 authors.
Funding
Abstract
Summary: Working with protein structures at the genome-scale has been challenging in a variety of ways. Here, we present ssbio, a Python package that provides a framework to easily work with structural information in the context of genome-scale network reconstructions, which can contain thousands of individual proteins. The ssbio package provides an automated pipeline to construct high quality genome-scale models with protein structures (GEM-PROs), wrappers to popular third-party programs to compute associated protein properties, and methods to visualize and annotate structures directly in Jupyter notebooks, thus lowering the barrier of linking 3D structural data with established systems workflows. Availability and implementation: ssbio is implemented in Python and available to download under the MIT license at http://github.com/SBRG/ssbio. Documentation and Jupyter notebook tutorials are available at http://ssbio.readthedocs.io/en/latest/. Interactive notebooks can be launched using Binder at https://mybinder.org/v2/gh/SBRG/ssbio/master?filepath=Binder.ipynb. Supplementary information: Supplementary data are available at Bioinformatics online.
Indexed as
Identifiers
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.