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good papers

@paperperday

2 months

The Effects of Codon Usage on Protein Structure and Folding

2

97

591

good papers

@paperperday

1 month

Coding, or non-coding, that is the question "blurry boundary between what is coding and what is non-coding"

1

106

476

good papers

@paperperday

28 days

Cracking the Code: Reprogramming the Genetic Script in Prokaryotes and Eukaryotes to Harness the Power of Noncanonical Amino Acids

2

81

313

good papers

@paperperday

9 months

column-free protein purification with an aggregation tag Discovery and Identification of a Novel Tag of HlyA60 for Protein Active Aggregate Formation in Escherichia coli

3

71

302

good papers

@paperperday

7 months

Engineering Cas9: next generation of genomic editors

0

70

273

good papers

@paperperday

10 months

From microbiome composition to functional engineering, one step at a time

1

77

245

good papers

@paperperday

1 year

Dynamic plasmid copy number control for synthetic biology

0

59

220

good papers

@paperperday

8 months

The ribosome as a small-molecule sensor

1

37

212

good papers

@paperperday

1 year

Advancing Synthetic Biology Through Cell-Free Protein Synthesis

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50

192

good papers

@paperperday

1 year

The design of synthetic gene circuits in plants: new components, old challenges

0

52

192

good papers

@paperperday

11 months

Recent advances in systems metabolic engineering

0

52

189

good papers

@paperperday

2 years

A primer to directed evolution: current methodologies and future directions

0

47

174

good papers

@paperperday

9 months

Manipulating gene expression levels in mammalian cell factories: an outline of synthetic molecular toolboxes to achieve multiplexed control

0

37

170

good papers

@paperperday

1 year

Machine learning for metabolic pathway optimization: A review

1

47

164

good papers

@paperperday

9 days

Horizontal gene transfer and beyond: the delivery of biological matter by bacterial membrane vesicles to host and bacterial cells

1

39

170

good papers

@paperperday

8 months

Cultivating the uncultured: Harnessing the “sandwich agar plate” approach to isolate heme-dependent bacteria from marine sediment "our method allows for the interaction between isolates and helper organisms throughout the incubation/ isolation process"

1

43

164

good papers

@paperperday

4 months

Synthetic intrinsically disordered protein fusion tags that enhance protein solubility

Synthetic intrinsically disordered protein fusion tags that enhance protein solubility

Nature Communications - Insoluble protein expression continues to be a bottleneck for biotechnology. Here, Chilkoti and colleagues report a method for generating and identifying hypersoluble...

www.nature.com

0

32

165

good papers

@paperperday

6 months

Next generation probiotics: Engineering live biotherapeutics

0

41

162

good papers

@paperperday

4 months

Genetically encoded Boolean logic operators to sense and integrate phenylpropanoid metabolite levels in plants

0

29

158

good papers

@paperperday

6 months

The minimum energy required to build a cell "The energy for synthesising the genome, transcriptome, proteome, and lipid bilayer of four cell types: Escherichia coli, Saccharomyces cerevisiae, an average mammalian cell and JCVI-syn3A were estimated."

The minimum energy required to build a cell

Scientific Reports - The minimum energy required to build a cell

www.nature.com

1

41

155

good papers

@paperperday

1 year

Bacterial secretion system functions: evidence of interactions and downstream implications

1

34

154

good papers

@paperperday

2 months

Directed evolution of material-producing microorganisms "direct evolution of cellulose-producing microorganisms for enhanced bio-fabrication"

2

33

154

good papers

@paperperday

6 months

Mobile genetic element-based gene editing and genome engineering: Recent advances and applications "Characteristics of the 4 types of mobile genetic elements (DNA transposons, retrotransposons, retrons, and CRISPR-associated transposons)"

2

35

145

good papers

@paperperday

2 years

Minireview: Engineering evolution to reconfigure phenotypic traits in microbes for biotechnological applications "...review covers the representative studies among the 700 ALE studies, outlining key ideas, principles, and mechanisms..."

1

38

146

good papers

@paperperday

1 year

Improving the soluble expression of difficult-to-express proteins in prokaryotic expression system via protein engineering and synthetic biology strategies

0

29

138

good papers

@paperperday

5 months

Inteins: A Swiss army knife for synthetic biology

2

33

136

good papers

@paperperday

3 months

"we provide a roadmap for increasing electroporation efficiency in non-model bacteria

bioRxiv Synthetic Biology

@bioRxiv_synbio

3 months

Using Cupriavidus necator H16 to provide a roadmap for increasing electroporation efficiency in non-model bacteria #biorxiv_synbio

0

3

15

0

28

137

good papers

@paperperday

4 months

CRISPR Tools for Engineering Prokaryotic Systems: Recent Advances and New Applications

0

24

134

good papers

@paperperday

3 months

Recent advances in engineering microorganisms for the production of natural food colorants

1

36

133

good papers

@paperperday

25 days

Strategies to overcome the challenges of low or no expression of heterologous proteins in Escherichia coli

0

37

132

good papers

@paperperday

23 days

Principles of bacterial innate immunity against viruses how to sense phage infection

2

28

127

good papers

@paperperday

5 months

The Damietta Server: a comprehensive protein design toolkit

0

35

125

good papers

@paperperday

2 years

Approaches for bacteriophage genome engineering

In recent years, bacteriophage research has been boosted by a rising interest in using phage therapy to treat antibiotic-resistant bacterial infections. In addition, there is a desire to use phages...

www.cell.com

0

26

120

good papers

@paperperday

3 months

RNA modifying enzymes shape tRNA biogenesis and function "we described how tRNA modifying enzymes affect tRNAs at all stages of the tRNA lifecycle by modifying and folding tRNAs."

1

34

121

good papers

@paperperday

5 months

High temperature delays and low temperature accelerates evolution of a new protein phenotype "YFP from GFP evolved most slowly at high temperature and most rapidly at low temperature"

High temperature delays and low temperature accelerates evolution of a new protein phenotype

Nature Communications - The effect of temperature fluctuations on the evolution of new phenotypes is largely unknown. Using experimental evolution of fluorescent protein in E. coli, this study...

www.nature.com

1

27

117

good papers

@paperperday

1 year

Genome engineering on size reduction and complexity simplification: A review

1

30

114

good papers

@paperperday

2 months

genetically encoded fluorescent temperature sensor Extremely Sensitive Genetically Encoded Temperature Indicator Enabling Measurement at the Organelle Level

Extremely Sensitive Genetically Encoded Temperature Indicator Enabling Measurement at the Organelle...

Intracellular temperature is a fundamental parameter in biochemical reactions. Genetically encoded fluorescent temperature indicators (GETIs) have been developed to visualize intracellular thermoge...

pubs.acs.org

0

23

114

good papers

@paperperday

2 months

Tuning tRNAs for improved translation

0

19

111

good papers

@paperperday

5 months

Split Proteins and Reassembly Modules for Biological Applications

0

21

113

good papers

@paperperday

2 months

Synthetic Microbial Ecology: Engineering Habitats for Modular Consortia

1

30

109

good papers

@paperperday

2 months

Evolution and stability of complex microbial communities driven by trade-offs "two distant strains in phenotypic space can coexist in the same environment, but only if one strain creates an ecological niche for the other that it cannot itself occupy."

0

29

112

good papers

@paperperday

1 month

"programmable DNA conjugation between specific cells through synthetic cell-cell adhesion" A whole-cell platform for discovering synthetic cell adhesion molecules in bacteria

2

23

111

good papers

@paperperday

3 months

Concepts of a synthetic minimal cell: Information molecules, metabolic pathways, and vesicle reproduction

0

19

107

good papers

@paperperday

1 year

Biosensors in microalgae: A roadmap for new opportunities in synthetic biology and biotechnology

1

30

102

good papers

@paperperday

5 months

Harnessing RNA-based DNA repair pathways for targeted gene editing

David Edgell

@megatev

5 months

📢New gene editing technology . This is result of amazing collaboration with @SpecificBio and supported by @NSERC_CRSNG @MitacsCanada @LumiraVentures @adMare_Bio @westernuBiochem @SchulichMedDent 🧵👇

1

14

53

0

21

106

good papers

@paperperday

12 days

Engineering Microbial Consortia as Living Materials: Advances and Prospectives

Yong Lai

@YongLaiLab

16 days

We are excited to share our review paper on materials design by synthetic biology. We discuss both top-down and bottom-up approaches to engineering living materials composed of microbial consortia. More exciting research is coming soon. @ACSSynBio

1

9

37

0

27

108

good papers

@paperperday

8 months

Ultrahigh-throughput screening-assisted in vivo directed evolution for enzyme engineering "an in vivo continuous evolution system was developed based on DNA Pol I and a temperature-sensitive variant of the mismatch repair protein MutS in E. coli"

0

21

106

good papers

@paperperday

10 months

Catcher/Tag Toolbox: Biomolecular Click-Reactions For Protein Engineering Beyond Genetics

0

17

101

good papers

@paperperday

1 year

A Self-Regenerating Artificial Cell, that is One Step Closer to Living Cells: Challenges and Perspectives

1

23

102

good papers

@paperperday

1 month

START = toehold switch + riboswitch sensor START: A Versatile Platform for Bacterial Ligand Sensing with Programmable Performances

1

24

104

good papers

@paperperday

10 months

Synthetic Cells Revisited: Artificial Cells Construction Using Polymeric Building Blocks

0

20

98

good papers

@paperperday

1 year

Toward Microbiome Engineering "genetic intractability after DNA transfer (SOS response, depletion of tRNAs, dysregulation of host pathways, codon usage/nucleotide bias, incompatible plasmid replicons, host replication stalling, outer membrane structures)"

0

28

101

good papers

@paperperday

9 months

Customizing cellular signal processing by synthetic multi-level regulatory circuits

0

20

98

good papers

@paperperday

3 months

Tunable translation-level CRISPR interference by dCas13 and engineered gRNA in bacteria "The difference between transcription-level control and translation-level control toward polycistronic gene repression"

0

13

101

good papers

@paperperday

5 months

“Metabolic burden” explained: stress symptoms and its related responses induced by (over)expression of (heterologous) proteins in Escherichia coli

1

27

100

good papers

@paperperday

1 month

"bacteria-derived membrane vesicles deliver DNA and iron to microalgae, promoting the growth of the iron-depleted algal cultures" Algicidal bacteria-derived membrane vesicles as shuttles mediating cross-kingdom interactions between bacteria and algae

1

28

99

good papers

@paperperday

1 year

Advancements in synthetic biology-based bacterial cancer therapy: A modular design approach

0

16

99

good papers

@paperperday

13 days

"Expression of mammalian caveolin-1 in E. coli induces the formation of nanovesicles (caveosphere), which accumulate in the cytoplasm and can be purified. The caveospheres can be functionally decorated via caveolin fusion proteins for targeted delivery and tumor killing."

biorxiv_bioengineering

@biorxiv_bioeng

16 days

A modular encapsulation system for precision delivery of proteins, nucleic acids and therapeutics #biorxiv_bioeng

0

3

13

1

22

100

good papers

@paperperday

6 months

Engineered bacteria in tumor immunotherapy

0

22

96

good papers

@paperperday

1 year

Microbial Primer: An introduction to biofilms – what they are, why they form and their impact on built and natural environments

0

18

91

good papers

@paperperday

1 year

Riboswitches, from cognition to transformation

0

11

92

good papers

@paperperday

5 months

Optogenetic Control of Bacterial Cell-Cell Adhesion Dynamics: Unraveling the Influence on Biofilm Architecture and Functionality "photoswitchable adhesins between bacteria"

0

24

94

good papers

@paperperday

4 months

"we create an artificial biosynthetic pathway that controls the abundance of the toxic RuBisCO substrate RuBP and converts RuBisCO-derived 3PG to glycerate, which we quantitatively monitor using an evolved transcriptional biosensor."

Ahmed H. Badran

@AhmedHBadran

4 months

RuBisCO is one of the most exciting bioengineering targets, but studying and improving its catalytic abilities can be very challenging. To address this, we came up with an intracellular strategy to monitor and evolve RuBisCO at scale! Check out our new preprint below🪴

2

9

100

0

21

92

good papers

@paperperday

1 year

"inserts and linear vectors was mixed at a molar ratio of approximately 3:1 and treated with 0.5 U of T5 exonuclease at 0°C for 5 min. Then, the mixture was transformed into E. coli to generate recombinant plasmids."

Frontiers - Bioengineering and Biotechnology

@FrontBioeng

1 year

New Research: TLTC, a T5 exonuclease–mediated low-temperature DNA cloning method #bioengineering #biotech

0

4

43

0

14

90

good papers

@paperperday

10 days

Compartmentalization of pathway sequential enzymes into synthetic protein compartments for metabolic flux optimization in Escherichia coli "The recruitment of pathway enzymes into synthetic organelles"

1

29

93

good papers

@paperperday

1 year

Engineering bacteriophages for enhanced host range and efficacy: insights from bacteriophage-bacteria interactions

0

16

92

good papers

@paperperday

1 year

Recent advances in non-model bacterial chassis construction

0

27

90

good papers

@paperperday

26 days

Induction of bacterial expression at the mRNA level by light "combining transcriptional and translational optogenetic tools increases light-induced gene expression >1000-fold."

1

16

92

good papers

@paperperday

1 month

"a method for recovering complete viral genomes from complex environmental samples" Targeted whole-genome recovery of single viral species in a complex environmental sample

0

15

89

good papers

@paperperday

4 months

5′UTR G-quadruplex structure enhances translation in size dependent manner "We found that the presence of the G-quadruplex in the 5′UTR led to enhanced translation both in vitro and in E. coli."

1

18

87

good papers

@paperperday

9 months

"autoregulation can also be leveraged to promote the design of evolutionarily robust synthetic gene circuits" Competition and evolutionary selection among core regulatory motifs in gene expression control

Competition and evolutionary selection among core regulatory motifs in gene expression control

Nature Communications - Regulators represent a bioenergetic cost in gene expression control. Here, the author shows how functionally equivalent regulatory motifs have fundamentally different...

www.nature.com

0

15

84

good papers

@paperperday

10 months

"characterizations of two mutational paths in unprecedented details (23 intermediates), we unveiled a molecular picture of an evolutionary bifurcation, a phenomenon in which such a mutational event can trigger the segregation of two trajectories"

bioRxiv Evobio

@biorxiv_evobio

10 months

Origin Of Evolutionary Bifurcation In An Enzyme #biorxiv_evobio

0

15

23

0

17

87

good papers

@paperperday

4 months

Microbial Synthetic Epigenetic Tools Design and Applications

0

13

86

good papers

@paperperday

2 months

Sustainable power generation from sewage with engineered microorganisms as electrocatalysts

0

18

87

good papers

@paperperday

2 years

Designing artificial synthetic promoters for accurate, smart and versatile gene expression in plants

1

26

88

good papers

@paperperday

3 months

Systems and Methods for Continuous Evolution of Enzymes "we summarize the working mechanisms of recently developed continuous evolution strategies, discuss examples of their applications focusing on enzyme evolution"

1

18

84

good papers

@paperperday

10 months

A novel protein purification scheme based on salt inducible self-assembling peptides

0

14

85

good papers

@paperperday

6 months

Genetic circuits for metabolic flux optimization

0

15

84

good papers

@paperperday

1 year

A polycistronic system for multiplexed and precalibrated expression of multigene pathways in fungi "We identify a 9-bp nucleotide sequence that enables the efficient translation of synthetic bicistronic cassettes in yeast and filamentous fungi."

1

23

83

good papers

@paperperday

7 months

Two horizontally acquired bacterial genes steer the exceptionally efficient and flexible nitrogenous waste cycling in whiteflies "Hijacking bacterial uricolytic enzyme genes reveals why fertilizer applications often leads to whitefly outbreaks"

2

24

83

good papers

@paperperday

7 months

Context-dependent redesign of robust synthetic gene circuits

0

25

84

good papers

@paperperday

1 year

High-Complexity One-Pot Golden Gate Assembly from @NEBiolabs

0

22

83

good papers

@paperperday

5 months

Click, Compute, Create: A Review of Web-based Tools for Enzyme Engineering

0

18

78

good papers

@paperperday

9 months

Plasmid-encoded toxin defence mediates mutualistic microbial interactions

0

19

80

good papers

@paperperday

6 months

A novel nucleic acid linker for multi-gene expression enhances plant and animal synthetic biology "we discovered a 9bp linker for polycistronic gene expression in yeast. Here, we validate polycistronic expression in the maize protoplast & human T cells."

2

15

80

good papers

@paperperday

1 year

Applications of synthetic biology in medical and pharmaceutical fields

0

21

77

good papers

@paperperday

2 years

Understanding a protein fold: the physics, chemistry, and biology of α-helical coiled coils "what are the sequence-to-structure relationships that govern coiled-coil folding and assembly, and how to design de novo coiled coils with confidence?"

0

20

79

good papers

@paperperday

3 years

Bacterial cooperation through horizontal gene transfer

1

15

79

good papers

@paperperday

16 days

Design of microbial catalysts for two-stage processes "A two-stage bioprocess that separates the cell growth phase from the product synthesis phase can resolve the tradeoff between growth & product synthesis"

0

15

79

good papers

@paperperday

2 years

Bacterial survivors: evaluating the mechanisms of antibiotic persistence

3

23

77

good papers

@paperperday

2 years

SynBioStrainFinder: A microbial strain database of manually curated CRISPR/Cas genetic manipulation system information for biomanufacturing recommend CRISPR tools for microbial strains

SynBioStrainFinder: A microbial strain database of manually curated CRISPR/Cas genetic manipulation...

Background Microbial strain information databases provide valuable data for microbial basic research and applications. However, they rarely contain information on the genetic operating system of...

microbialcellfactories.biomedcentral.com

0

14

77

good papers

@paperperday

10 months

Mutation bias and adaptation in bacteria

0

22

77

good papers

@paperperday

4 months

CRISPR-powered RNA sensing in vivo 4 categories of RNA sensors: programmable reassembly of split sgRNA, RNA-triggered RNA processing and protein cleavage, miRNA-triggered RNA interference, strand displacement reactions

0

14

75

good papers

@paperperday

4 months

"InducTn-seq, which leverages inducible mutagenesis for temporal control of Tn5 transposition. InducTn-seq generates millions of transposon mutants from a single colony."

bioRxiv Microbiology

@biorxiv_micrbio

4 months

Inducible transposon mutagenesis for genome-scale forward genetics #biorxiv_micrbio

0

24

61

1

13

73

good papers

@paperperday

1 year

Engineering a complex, multiple enzyme-mediated synthesis of natural plant pigments in the silkworm, Bombyx mori red silkworm cocoon

0

26

72

good papers

@paperperday

1 year

The diverse structural modes of tRNA binding and recognition "it's not surprising that tRNAs are also used in other cellular pathways and exploited by viruses and pathogens, we summarize the examples of tRNA-like molecules and tRNA-derived fragments."

1

20

74

good papers

@paperperday

10 months

Unravelling the enigma of the human microbiome: Evolution and selection of sequencing technologies

9

20

71

good papers

@paperperday

7 months

Convenient synthesis and delivery of a megabase-scale designer accessory chromosome empower biosynthetic capacity "efficient assembly and delivery of a de novo designed 1.024 Mb synthetic accessory chromosome"

0

22

71

good papers

@paperperday

2 years

Engineering artificial photosynthetic life-forms through endosymbiosis from @angadmehta & co

Engineering artificial photosynthetic life-forms through endosymbiosis

Nature Communications - The endosymbiotic theory posits that chloroplasts in eukaryotes arise from bacterial endosymbionts. Here, the authors engineer the yeast/cyanobacteria chimeras and show that...

www.nature.com

0

18

70

good papers

@paperperday

1 year

Boolean logic in synthetic biology and biomaterials: Towards living materials in mammalian cell therapeutics

0

13

70