Related papers: Combining oligo pools and Golden Gate cloning to c…
Recombinant protein production is pivotal in molecular biology, enabling profound insights into cellular processes through biophysical, biochemical, and structural analyses of the purified samples. The demand for substantial biomolecule…
Golden Gate cloning has become a powerful and widely used DNA assembly method. Its modular nature and the reusability of standardized parts allow rapid construction of transcription units and multi-gene constructs. Importantly, its modular…
Golden Gate cloning has become one of the most popular DNA assembly techniques. Its modular and hierarchical structure allows the construction of complex DNA fragments. Over time, Golden Gate cloning allows for the creation of a repository…
The design of large libraries of oligonucleotides having constant GC-content and satisfying Hamming distance constraints between oligonucleotides and their Watson-Crick complements is important in reducing hybridization errors in DNA…
Protein variant libraries produced by site-directed mutagenesis are a useful tool utilized by protein engineers to explore variants with potentially improved properties, such as activity and stability. These libraries are commonly built by…
Cell-free transcription and translation (TXTL) systems have emerged as a powerful tool for testing genetic regulatory elements and circuits. Cell-free prototyping can dramatically accelerate the design-build-test cycle of new functions in…
Golden Gate cloning has revolutionized synthetic biology. Its concept of modular, highly characterized libraries of parts that can be combined into higher order assemblies allows engineering principles to be applied to biological systems.…
We describe efficient methods for screening clone libraries, based on pooling schemes which we call ``random $k$-sets designs''. In these designs, the pools in which any clone occurs are equally likely to be any possible selection of $k$…
The exponential increase in storage demand and low lifespan of data storage devices has resulted in long-term archival and preservation emerging as a critical bottlenecks in data storage. In order to meet this demand, researchers are now…
DNA-encoded libraries (DELs) are a powerful approach for rapidly screening large numbers of diverse compounds. One of the key challenges in using DELs is library design, which involves choosing the building blocks that will be…
We study the problem of selecting control clones in DNA array hybridization experiments. The problem arises in the OFRG method for analyzing microbial communities. The OFRG method performs classification of rRNA gene clones using binary…
Composite DNA is a recent novel method to increase the information capacity of DNA-based data storage above the theoretical limit of 2 bits/symbol. In this method, every composite symbol does not store a single DNA nucleotide but a mixture…
Inspired by the effectiveness of genetic algorithms and the importance of synthesizability in molecular design, we present SynGA, a simple genetic algorithm that operates directly over synthesis routes. Our method features custom crossover…
This paper presents a Python library to model pooling problems, a class of network flow problems with many engineering applications. The library automatically generates a mixed-integer quadratically-constrained quadratic optimization…
Single-stranded libraries generated from ancient DNA extracts have specific sequencing requirements. The short library molecules typically associated with ancient DNA templates are expected to behave differently during the annealing to the…
An algorithm implemented in an open-source python library was developed for building periodic coincidence site lattice (CSL) grain boundary models in a universal fashion. The software framework aims to generate tilt and twist grain…
The main obstacles for the practical deployment of DNA-based data storage platforms are the prohibitively high cost of synthetic DNA and the large number of errors introduced during synthesis. In particular, synthetic DNA products contain…
The short lifespan of traditional data storage media, coupled with an exponential increase in storage demand, has made long-term archival a fundamental problem in the data storage industry and beyond. Consequently, researchers are looking…
Deep learning hyper-parameter optimization is a tough task. Finding an appropriate network configuration is a key to success, however most of the times this labor is roughly done. In this work we introduce a novel library to tackle this…
Oligonucleotide arrays are used in a wide range of genomic analyses, such as gene expression profiling, comparative genomic hybridization, chromatin immunoprecipitation, SNP detection, etc. During fabrication, the sites of an…