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Statistical Analysis of Molecular Signal Recording
(Public Library of Science, 2013)
A molecular device that records time-varying signals would enable new approaches in neuroscience. We have recently proposed such a device, termed a “molecular ticker tape”, in which an engineered DNA polymerase (DNAP) ...
CRISPR/Cas9-Mediated Phage Resistance Is Not Impeded by the DNA Modifications of Phage T4
(Public Library of Science, 2014)
Bacteria rely on two known DNA-level defenses against their bacteriophage predators: restriction-modification and Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)-CRISPR-associated (Cas) systems. Certain ...
Improving Lambda Red Genome Engineering in Escherichia coli via Rational Removal of Endogenous Nucleases
(Public Library of Science, 2012)
Lambda Red recombineering is a powerful technique for making targeted genetic changes in bacteria. However, many applications are limited by the frequency of recombination. Previous studies have suggested that endogenous ...
RNA - ligand interactions:(I) magnesium binding sites in yeast tRNA Phe
(Oxford University Press (OUP), 1977)
X-ray crystallagraphic studies studies indicate that there are at least four site-specifically bound hydrated Mg2+ ions, [Mg(H2O)n]2+, in yeast tRNAPhe. The size and the octahedral coordination geometry, rather than the ...
Simulating Serial-Target Antibacterial Drug Synergies Using Flux Balance Analysis
(Public Library of Science, 2016)
Flux balance analysis (FBA) is an increasingly useful approach for modeling the behavior of metabolic systems. However, standard FBA modeling of genetic knockouts cannot predict drug combination synergies observed between ...
Improved Cell-Free RNA and Protein Synthesis System
(Public Library of Science, 2014)
Cell-free RNA and protein synthesis (CFPS) is becoming increasingly used for protein production as yields increase and costs decrease. Advances in reconstituted CFPS systems such as the Protein synthesis Using Recombinant ...
Multiplex Sequencing of 1.5 Mb of the <i>Mycobacterium leprae</i> Genome
(Cold Spring Harbor Laboratory, 1997-08-01)
The nucleotide sequence of 1.5 Mb of genomic DNA from Mycobacterium leprae was determined using computer-assisted multiplex sequencing technology. This brings the 2.8-Mb M. leprae genome sequence to ∼66% completion. The ...
Conservation of DNA Regulatory Motifs and Discovery of New Motifs in Microbial Genomes
(Cold Spring Harbor Laboratory, 2000-06-01)
Regulatory motifs can be found by local multiple alignment of upstream regions from coregulated sets of genes, or regulons. We searched for regulatory motifs using the program AlignACE together with a set of filters that ...
Computation-Based Discovery of Related Transcriptional Regulatory Modules and Motifs Using an Experimentally Validated Combinatorial Model
(Cold Spring Harbor Laboratory, 2002-07)
Gene expression is regulated by transcription factors that interact with cis-regulatory elements. Predicting these elements from sequence data has proven difficult. We describe here a successful computational search for ...
Global RNA Half-Life Analysis in Escherichia coli Reveals Positional Patterns of Transcript Degradation
(Cold Spring Harbor Laboratory, 2003-01-14)
Subgenic-resolution oligonucleotide microarrays were used to study global RNA degradation in wild-type Escherichia coli MG1655. RNA chemical half-lives were measured for 1036 open reading frames (ORFs) and for 329 known ...