2017 ACS Synthetic Biology Issues
Summary
- Total Articles Analyzed: 242
- Total Figures in All Articles: 1266
- Figures Compatible with SBOL Visual: 285 (22.51%)
- Figures Compatible with SBOL Visual & Fully Compliant: 187 (65.61%)
- Figures Compatible with SBOL Visual & Following Best Practices: 115 (40.35%)
Individual issues
January
| Article | No. of SBOL Visual compliant images | No. of SBOL Visual images following Best practices | |
|---|---|---|---|
| Rapid and Inexpensive Evaluation of Nonstandard Amino Acid Incorporation in Escherichia coli | 1 | 1 | ⭐ |
| Designing Synthetic Flexible Gene Regulation Networks Using RNA Devices in Cyanobacteria | 1 | 1 | ⭐ |
| Short Synthetic Terminators for Assembly of Transcription Units in Vitro and Stable Chromosomal Integration in Yeast S. cerevisiae | 5 | 2 | |
| Improving Metabolic Pathway Efficiency by Statistical Model-Based Multivariate Regulatory Metabolic Engineering | 3 | 3 | ⭐ |
February
| Article | No. of SBOL Visual compliant images | No. of SBOL Visual images following Best practices | |
|---|---|---|---|
| Discovery of a Phosphonoacetic Acid Derived Natural Product by Pathway Refactoring | 1 | 0 | |
| Direct Combinatorial Pathway Optimization | 1 | 0 | |
| Artificial Symmetry-Breaking for Morphogenetic Engineering Bacterial Colonies | 5 | 4 | |
| Synthetic Biogenesis of Bacterial Amyloid Nanomaterials with Tunable Inorganic–Organic Interfaces and Electrical Conductivity | 1 | 0 | |
| Resource Sharing Controls Gene Expression Bursting | 1 | 0 | |
| Characterization of Endogenous and Reduced Promoters for Oxygen-Limited Processes Using Escherichia coli | 1 | 1 | ⭐ |
| Reproducibility of High-Throughput Plate-Reader Experiments in Synthetic Biology | 1 | 0 |
March
| Article | No. of SBOL Visual compliant images | No. of SBOL Visual images following Best practices | |
|---|---|---|---|
| Standardized Markerless Gene Integration for Pathway Engineering in Yarrowia lipolytica | 1 | 0 | |
| Introduction of Premature Stop Codons as an Evolutionary Strategy To Rescue Signaling Network Function | 2 | 0 | |
| Synthetic Core Promoters as Universal Parts for Fine-Tuning Expression in Different Yeast Species | 1 | 0 | |
| Reprogramming the Transcriptional Response to Hypoxia with a Chromosomally Encoded Cyclic Peptide HIF-1 Inhibitor | 2 | 0 | |
| A Novel Approach for Gene Expression Optimization through Native Promoter and 5′ UTR Combinations Based on RNA-seq, Ribo-seq, and TSS-seq of Streptomyces coelicolor | 1 | 0 |
April
| Article | No. of SBOL Visual compliant images | No. of SBOL Visual images following Best practices | |
|---|---|---|---|
| Engineering a Thermostable Keto Acid Decarboxylase Using Directed Evolution and Computationally Directed Protein Design | 1 | 0 | |
| Quantitative Tracking of Combinatorially Engineered Populations with Multiplexed Binary Assemblies | 1 | 0 | |
| Controlling Multicycle Replication of Live-Attenuated HIV-1 Using an Unnatural Genetic Switch | 2 | 2 | ⭐ |
May
| Article | No. of SBOL Visual compliant images | No. of SBOL Visual images following Best practices | |
|---|---|---|---|
| AGOS: A Plug-and-Play Method for the Assembly of Artificial Gene Operons into Functional Biosynthetic Gene Clusters | 3 | 3 | ⭐ |
| Efficient Genome Editing of a Facultative Thermophile Using Mesophilic spCas9 | 2 | 1 | |
| Mechanistic Modeling of Genetic Circuits for ArsR Arsenic Regulation | 2 | 2 | ⭐ |
| An Engineered Survival-Selection Assay for Extracellular Protein Expression Uncovers Hypersecretory Phenotypes in Escherichia coli | 1 | 0 |
June
| Article | No. of SBOL Visual compliant images | No. of SBOL Visual images following Best practices | |
|---|---|---|---|
| Engineering Iron Responses in Mammalian Cells by Signal-Induced Protein Proximity | 3 | 0 | |
| Recursive DNA Assembly Using Protected Oligonucleotide Duplex Assisted Cloning (PODAC) | 2 | 2 | ⭐ |
| Extracellular Self-Assembly of Functional and Tunable Protein Conjugates from Bacillus subtilis | 1 | 1 | ⭐ |
| Tailoring Escherichia coli for the l-Rhamnose PBAD Promoter-Based Production of Membrane and Secretory Proteins | 3 | 0 | |
| Heterologous Biosynthesis of Spinosad: An Omics-Guided Large Polyketide Synthase Gene Cluster Reconstitution in Streptomyces | 4 | 4 | ⭐ |
| A Modular Toolkit for Generating Pichia pastoris Secretion Libraries | 5 | 5 | ⭐ |
| Development of a Biosensor Concept to Detect the Production of Cluster-Specific Secondary Metabolites | 2 | 1 | |
| A Scalable Epitope Tagging Approach for High Throughput ChIP-Seq Analysis | 1 | 1 | ⭐ |
| Formation of Nitrogenase NifDK Tetramers in the Mitochondria of Saccharomyces cerevisiae | 1 | 1 | ⭐ |
| Obtaining a Panel of Cascade Promoter-5′-UTR Complexes in Escherichia coli | 1 | 0 | |
| The Impact of DNA Topology and Guide Length on Target Selection by a Cytosine-Specific Cas9 | 2 | 2 | ⭐ |
July
| Article | No. of SBOL Visual compliant images | No. of SBOL Visual images following Best practices | |
|---|---|---|---|
| DNAplotlib: Programmable Visualization of Genetic Designs and Associated Data | 5 | 5 | ⭐ |
| SBOLDesigner 2: An Intuitive Tool for Structural Genetic Design | 3 | 3 | ⭐ |
| A Validator and Converter for the Synthetic Biology Open Language | 2 | 2 | ⭐ |
| Simulation Approach for Timing Analysis of Genetic Logic Circuits | 2 | 2 | ⭐ |
| Automated Design Framework for Synthetic Biology Exploiting Pareto Optimality | 1 | 1 | ⭐ |
| sbml-diff: A Tool for Visually Comparing SBML Models in Synthetic Biology | 1 | 1 | ⭐ |
| Improvement of Squalene Production from CO2 in Synechococcus elongatus PCC 7942 by Metabolic Engineering and Scalable Production in a Photobioreactor | 2 | 0 | |
| Measurement of In Vivo Protein Binding Affinities in a Signaling Network with Mass Spectrometry | 2 | 1 | |
| Genome Engineering of Virulent Lactococcal Phages Using CRISPR-Cas9 | 3 | 0 | |
| Deconvolution of Gene Expression Noise into Spatial Dynamics of Transcription Factor–Promoter Interplay | 4 | 4 | ⭐ |
| EMMA: An Extensible Mammalian Modular Assembly Toolkit for the Rapid Design and Production of Diverse Expression Vectors | 6 | 6 | ⭐ |
| Construction and Rescue of a Functional Synthetic Baculovirus | 2 | 2 | ⭐ |
| Repurposing a Two-Component System-Based Biosensor for the Killing of Vibrio cholerae | 2 | 2 | ⭐ |
August
| Article | No. of SBOL Visual compliant images | No. of SBOL Visual images following Best practices | |
|---|---|---|---|
| Amplifying Riboswitch Signal Output Using Cellular Wiring | 2 | 2 | ⭐ |
| Rational Design of an Ultrasensitive Quorum-Sensing Switch | 1 | 1 | ⭐ |
| Genome-Wide Abolishment of Mobile Genetic Elements Using Genome Shuffling and CRISPR/Cas-Assisted MAGE Allows the Efficient Stabilization of a Bacterial Chassis | 1 | 1 | ⭐ |
| A New Improved and Extended Version of the Multicell Bacterial Simulator gro | 1 | 1 | ⭐ |
| Synthetic Protein Scaffolds for Biosynthetic Pathway Colocalization on Lipid Droplet Membranes | 2 | 2 | ⭐ |
| Programming Post-Translational Control over the Metabolic Labeling of Cellular Proteins with a Noncanonical Amino Acid | 1 | 1 | ⭐ |
| Sort-Seq Approach to Engineering a Formaldehyde-Inducible Promoter for Dynamically Regulated Escherichia coli Growth on Methanol | 1 | 1 | ⭐ |
September
| Article | No. of SBOL Visual compliant images | No. of SBOL Visual images following Best practices | |
|---|---|---|---|
| Engineering a Native Inducible Expression System in Shewanella oneidensis to Control Extracellular Electron Transfer | 2 | 2 | ⭐ |
| Multiplex Genome Editing by Natural Transformation (MuGENT) for Synthetic Biology in Vibrio natriegens | 2 | 2 | ⭐ |
| Rapid Generation of Universal Synthetic Promoters for Controlled Gene Expression in Both Gas-Fermenting and Saccharolytic Clostridium Species | 2 | 1 | |
| Mini Photobioreactors for in Vivo Real-Time Characterization and Evolutionary Tuning of Bacterial Optogenetic Circuit | 1 | 0 |
October
| Article | No. of SBOL Visual compliant images | No. of SBOL Visual images following Best practices | |
|---|---|---|---|
| Developing a Genetically Encoded, Cross-Species Biosensor for Detecting Ammonium and Regulating Biosynthesis of Cyanophycin | 2 | 2 | ⭐ |
| Rapid and Programmable Protein Mutagenesis Using Plasmid Recombineering | 2 | 2 | ⭐ |
| A Synthetic Circuit for Mercury Bioremediation Using Self-Assembling Functional Amyloids | 1 | 0 | |
| Fundamental Design Principles for Transcription-Factor-Based Metabolite Biosensors | 3 | 0 | |
| Evidence for Improved Encapsulated Pathway Behavior in a Bacterial Microcompartment through Shell Protein Engineering | 1 | 1 | ⭐ |
| A Versatile Toolbox for the Control of Protein Levels Using Nε-Acetyl-l-lysine Dependent Amber Suppression | 4 | 0 | |
| Engineered Control of Genetic Variability Reveals Interplay among Quorum Sensing, Feedback Regulation, and Biochemical Noise | 1 | 1 | ⭐ |
| Multiple T-DNA Delivery to Plants Using Novel Mini Binary Vectors with Compatible Replication Origins | 4 | 4 | ⭐ |
| Development of Chemical and Metabolite Sensors for Rhodococcus opacus PD630 | 1 | 1 | ⭐ |
November
| Article | No. of SBOL Visual compliant images | No. of SBOL Visual images following Best practices | |
|---|---|---|---|
| The Timing of Transcriptional Regulation in Synthetic Gene Circuits | 3 | 0 | |
| A Tug-of-War Mechanism for Pattern Formation in a Genetic Network | 2 | 0 | |
| A Small-Molecule Inducible Synthetic Circuit for Control of the SOS Gene Network without DNA Damage | 1 | 1 | ⭐ |
| Orthogonal Ribosome Biofirewall | 5 | 0 | |
| Genetic Design via Combinatorial Constraint Specification | 2 | 2 | ⭐ |
| Systematic Approaches to Efficiently Produce 2,3-Butanediol in a Marine Cyanobacterium | 1 | 1 | ⭐ |
| Construction of Recombinant Pdu Metabolosome Shells for Small Molecule Production in Corynebacterium glutamicum | 2 | 2 | ⭐ |
| Dynamic Blue Light-Inducible T7 RNA Polymerases (Opto-T7RNAPs) for Precise Spatiotemporal Gene Expression Control | 2 | 0 |
December
| Article | No. of SBOL Visual compliant images | No. of SBOL Visual images following Best practices | |
|---|---|---|---|
| Production of Functional Anti-Ebola Antibodies in Pichia pastoris | 1 | 0 | |
| Managing the SOS Response for Enhanced CRISPR-Cas-Based Recombineering in E. coli through Transient Inhibition of Host RecA Activity | 1 | 0 | |
| Leaf LIMS: A Flexible Laboratory Information Management System with a Synthetic Biology Focus | 1 | 1 | ⭐ |
| Engineering Isoprene Synthase Expression and Activity in Cyanobacteria | 1 | 1 | ⭐ |
| Genetic Constructor: An Online DNA Design Platform | 2 | 0 |
