Related papers: Calculating complexity of large randomized librari…
Recently, several groups have used error-prone polymerase chain reactions to construct mutant libraries containing up to 27 nucleotide mutations per gene on average, and reported a striking observation: although retention of protein…
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…
Biologists use random transposon mutagenesis to construct knockout libraries for bacteria. Random mutagenesis offers cost and efficiency benefits over the standard site directed mutagenesis, but one can no longer ensure that all the…
An analogy between combinatorial chemistry and Monte Carlo computer simulation is pursued. Examples of how to design libraries for both materials discovery and protein molecular evolution are given. For materials discovery, the concept of…
Sequencing by synthesis is used in many next-generation DNA sequencing technologies. Some of the technologies, especially those exploring the principle of single-molecule sequencing, allow incomplete nucleotide incorporation in each cycle.…
Genetic information is encoded in a linear sequence of nucleotides, represented by letters ranging from thousands to billions. Mutations refer to changes in the DNA or RNA nucleotide sequence. Thus, mutation detection is vital in all areas…
Radionuclide identification is a radioanalytical method employed in various scientific disciplines that utilize alpha-particle or gamma-ray spectrometric assays, ranging from astrophysics to nuclear medicine. Radionuclide libraries in…
Variation and selection are the core principles of Darwinian evolution, yet quantitatively relating the diversity of a population to its capacity to respond to selection is challenging. Here, we examine this problem at a molecular level in…
Modern biomedicine is challenged to predict the effects of genetic variation. Systematic functional assays of point mutants of proteins have provided valuable empirical information, but vast regions of sequence space remain unexplored.…
Accelerating the discovery of structural materials is essential for applications in hard and refractory alloys, hypersonic platforms, nuclear systems, and other extreme environment technologies. Progress is often constrained by slow…
Fast numerical libraries have been a cornerstone of scientific computing for decades, but this comes at a price. Programs may be tied to vendor specific software ecosystems resulting in polluted, non-portable code. As we enter an era of…
The unbounded permutations of biological molecules, including proteins and their constituent peptides, presents a dilemma in identifying the components of complex biosamples. Sequence search algorithms used to identify peptide spectra can…
1) We introduce random discrete Morse theory as a computational scheme to measure the complicatedness of a triangulation. The idea is to try to quantify the frequence of discrete Morse matchings with a certain number of critical cells. Our…
Understanding how machine learning models respond to distributional shifts is a key research challenge. Mazes serve as an excellent testbed due to varied generation algorithms offering a nuanced platform to simulate both subtle and…
The potential number of drug like small molecules is estimated to be between 10^23 and 10^60 while current databases of known compounds are orders of magnitude smaller with approximately 10^8 compounds. This discrepancy has led to an…
Software code complexity is a well-studied property to determine software component health. However, the existing code complexity metrics do not directly take into account the fault-proneness aspect of the code. We propose a metric called…
When confronted with a substance of unknown identity, researchers often perform mass spectrometry on the sample and compare the observed spectrum to a library of previously-collected spectra to identify the molecule. While popular, this…
The number of substitutions (of nucleotides, amino acids, ...) that take place during the evolution of a sequence is a stochastic variable of fundamental importance in the field of molecular evolution. Although the mean number of…
Motivated by genome-wide association studies, we consider a standard linear model with one additional random effect in situations where many predictors have been collected on the same subjects and each predictor is analyzed separately.…
Software quality is considered as one of the most important challenges in software engineering. It has many dimensions which differ from users' point of view that depend on their requirements. Therefore, those dimensions lead to difficulty…