2016 ACS Synthetic Biology Issues
Summary
- Total Articles Analyzed: 169
- Total Figures in All Articles: 886
- Figures Compatible with SBOL Visual: 217 (24.49%)
- Figures Compatible with SBOL Visual & Fully Compliant: 136 (62.67%)
- Figures Compatible with SBOL Visual & Following Best Practices: 90 (41.47%)
Individual issues
January
| Article | No. of SBOL Visual compliant images | No. of SBOL Visual images following Best practices | |
|---|---|---|---|
| Metabolic Engineering toward Sustainable Production of Nylon-6 | 1 | 1 | ⭐ |
| Orthogonal Modular Gene Repression in Escherichia coli Using Engineered CRISPR/Cas9 | 4 | 0 | |
| CIDAR MoClo: Improved MoClo Assembly Standard and New E. coli Part Library Enable Rapid Combinatorial Design for Synthetic and Traditional Biology | 2 | 2 | ⭐ |
February
| Article | No. of SBOL Visual compliant images | No. of SBOL Visual images following Best practices | |
|---|---|---|---|
| Slowing Translation between Protein Domains by Increasing Affinity between mRNAs and the Ribosomal Anti-Shine–Dalgarno Sequence Improves Solubility | 1 | 0 |
March
| Article | No. of SBOL Visual compliant images | No. of SBOL Visual images following Best practices | |
|---|---|---|---|
| Multiple Gene Repression in Cyanobacteria Using CRISPRi | 1 | 1 | ⭐ |
| Assays To Detect the Formation of Triphosphates of Unnatural Nucleotides: Application to Escherichia coli Nucleoside Diphosphate Kinase | 1 | 1 | ⭐ |
| Circumvention of Learning Increases Intoxication Efficacy of Nematicidal Engineered Bacteria | 1 | 1 | ⭐ |
| Measurements of Gene Expression at Steady State Improve the Predictability of Part Assembly | 3 | 3 | ⭐ |
April
| Article | No. of SBOL Visual compliant images | No. of SBOL Visual images following Best practices | |
|---|---|---|---|
| Automatic Control of Gene Expression in Mammalian Cells | 1 | 0 |
June
| Article | No. of SBOL Visual compliant images | No. of SBOL Visual images following Best practices | |
|---|---|---|---|
| Improving Synthetic Biology Communication: Recommended Practices for Visual Depiction and Digital Submission of Genetic Designs | 1 | 1 | ⭐ |
| Genotype Specification Language | 1 | 1 | ⭐ |
| A Converter from the Systems Biology Markup Language to the Synthetic Biology Open Language | 4 | 4 | ⭐ |
| The SBOL Stack: A Platform for Storing, Publishing, and Sharing Synthetic Biology Designs | 1 | 1 | ⭐ |
| Sharing Structure and Function in Biological Design with SBOL 2.0 | 3 | 3 | ⭐ |
| Double Dutch: A Tool for Designing Combinatorial Libraries of Biological Systems | 3 | 3 | ⭐ |
July
| Article | No. of SBOL Visual compliant images | No. of SBOL Visual images following Best practices | |
|---|---|---|---|
| Two Distinct Cyclodipeptide Synthases from a Marine Actinomycete Catalyze Biosynthesis of the Same Diketopiperazine Natural Product | 1 | 1 | ⭐ |
| Optical Control of Peroxisomal Trafficking | 1 | 0 | |
| Multiplexed Targeted Genome Engineering Using a Universal Nuclease-Assisted Vector Integration System | 3 | 3 | ⭐ |
| Refactoring the Six-Gene Photosystem II Core in the Chloroplast of the Green Algae Chlamydomonas reinhardtii | 1 | 0 | |
| Synthetic Quorum Sensing and Cell–Cell Communication in Gram-Positive Bacillus megaterium | 1 | 0 | |
| Molecular Buffers Permit Sensitivity Tuning and Inversion of Riboswitch Signals | 3 | 0 | |
| Entrainment and Control of Bacterial Populations: An in Silico Study over a Spatially Extended Agent Based Model | 1 | 0 | |
| A Minimal Model of Ribosome Allocation Dynamics Captures Trade-offs in Expression between Endogenous and Synthetic Genes | 2 | 2 | ⭐ |
| Bacterial Genome Editing with CRISPR-Cas9: Deletion, Integration, Single Nucleotide Modification, and Desirable “Clean” Mutant Selection in Clostridium beijerinckii as an Example | 4 | 4 | ⭐ |
| Repurposing Synechocystis PCC6803 UirS–UirR as a UV-Violet/Green Photoreversible Transcriptional Regulatory Tool in E. coli | 1 | 1 | ⭐ |
| CRISPR/Cas9 Based Genome Editing of Penicillium chrysogenum | 4 | 4 | ⭐ |
August
| Article | No. of SBOL Visual compliant images | No. of SBOL Visual images following Best practices | |
|---|---|---|---|
| Using RNA as Molecular Code for Programming Cellular Function | 2 | 2 | ⭐ |
| VisBOL: Web-Based Tools for Synthetic Biology Design Visualization | 2 | 2 | ⭐ |
September
| Article | No. of SBOL Visual compliant images | No. of SBOL Visual images following Best practices | |
|---|---|---|---|
| Programming Surface Chemistry with Engineered Cells | 1 | 1 | ⭐ |
| Quorum Sensing Communication Modules for Microbial Consortia | 3 | 2 | |
| DATEL: A Scarless and Sequence-Independent DNA Assembly Method Using Thermostable Exonucleases and Ligase | 2 | 2 | ⭐ |
October
| Article | No. of SBOL Visual compliant images | No. of SBOL Visual images following Best practices | |
|---|---|---|---|
| Mammalian Synthetic Biology: Time for Big MACs | 2 | 2 | ⭐ |
| EcoFlex: A Multifunctional MoClo Kit for E. coli Synthetic Biology | 2 | 0 | |
| Expanding Biosensing Abilities through Computer-Aided Design of Metabolic Pathways | 1 | 0 | |
| Library-Aided Probing of Linker Determinants in Hybrid Photoreceptors | 1 | 0 | |
| An Implementation-Focused Bio/Algorithmic Workflow for Synthetic Biology | 3 | 2 | |
| SEVA Linkers: A Versatile and Automatable DNA Backbone Exchange Standard for Synthetic Biology | 2 | 0 |
November
| Article | No. of SBOL Visual compliant images | No. of SBOL Visual images following Best practices | |
|---|---|---|---|
| Construction and Characterization of a Synthetic MicroRNA Cluster for Multiplex RNA Interference in Mammalian Cells | 4 | 0 | |
| A Cell–Cell Communication-Based Screening System for Novel Microbes with Target Enzyme Activities | 1 | 1 | ⭐ |
| EcoExpress—Highly Efficient Construction and Expression of Multicomponent Protein Complexes in Escherichia coli | 1 | 1 | ⭐ |
| Optimum Rebalancing of the 3-Hydroxypropionic Acid Production Pathway from Glycerol in Escherichia coli | 1 | 0 | |
| Metabolic Engineering of Escherichia coli for the Production of 3-Hydroxypropionic Acid and Malonic Acid through β-Alanine Route | 1 | 0 | |
| Microbial Synthesis of 5-Aminolevulinic Acid and Its Coproduction with Polyhydroxybutyrate | 3 | 3 | ⭐ |
| Biosensing Vibrio cholerae with Genetically Engineered Escherichia coli | 3 | 3 | ⭐ |
| Development of Colorimetric-Based Whole-Cell Biosensor for Organophosphorus Compounds by Engineering Transcription Regulator DmpR | 1 | 1 | ⭐ |
| Semirational Approach for Ultrahigh Poly(3-hydroxybutyrate) Accumulation in Escherichia coli by Combining One-Step Library Construction and High-Throughput Screening | 1 | 1 | ⭐ |
December
| Article | No. of SBOL Visual compliant images | No. of SBOL Visual images following Best practices | |
|---|---|---|---|
| The Geobacillus Plasmid Set: A Modular Toolkit for Thermophile Engineering | 1 | 1 | ⭐ |
| Combinatorial Pairwise Assembly Efficiently Generates High Affinity Binders and Enables a “Mix-and-Read” Detection Scheme | 1 | 0 | |
| Design and Assembly of DNA Sequence Libraries for Chromosomal Insertion in Bacteria Based on a Set of Modified MoClo Vectors | 3 | 0 | |
| Tapping the Unused Potential of Photosynthesis with a Heterologous Electron Sink | 1 | 1 | ⭐ |
| C-Brick: A New Standard for Assembly of Biological Parts Using Cpf1 | 3 | 0 | |
| Programming Saposin-Mediated Compensatory Metabolic Sinks for Enhanced Ubiquinone Production | 1 | 0 | |
| A Parts Database with Consensus Parameter Estimation for Synthetic Circuit Design | 2 | 2 | ⭐ |
| Development of Design Rules for Reliable Antisense RNA Behavior in E. coli | 5 | 2 | |
| Converting a Natural Protein Compartment into a Nanofactory for the Size-Constrained Synthesis of Antimicrobial Silver Nanoparticles | 1 | 1 | ⭐ |
| OptSSeq: High-Throughput Sequencing Readout of Growth Enrichment Defines Optimal Gene Expression Elements for Homoethanologenesis | 5 | 5 | ⭐ |
| Multigene Pathway Engineering with Regulatory Linkers (M-PERL) | 4 | 4 | ⭐ |
| Biosynthesis of the High-Value Plant Secondary Product Benzyl Isothiocyanate via Functional Expression of Multiple Heterologous Enzymes in Escherichia coli | 2 | 0 |
