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We review the recent progress in computational approaches to protein design which builds on advances in statistical-mechanical protein folding theory. In particular, we evaluate the degeneracy of the protein code (i.e. how many sequences…
As the chief informational molecule of life, DNA is subject to extensive physical manipulations. The energy required to deform double-helical DNA depends on sequence, and this mechanical code of DNA influences gene regulation, such as…
Learning effective protein representations is critical in a variety of tasks in biology such as predicting protein function or structure. Existing approaches usually pretrain protein language models on a large number of unlabeled amino acid…
We live in a period where bio-informatics is rapidly expanding, a significant quantity of genomic data has been produced as a result of the advancement of high-throughput genome sequencing technology, raising concerns about the costs…
Natural protein sequences that self-assemble to form globular structures are compact with high packing densities in the folded states. It is known that proteins unfold upon addition of denaturants, adopting random coil structures. The…
Proteins are linear molecular chains that often fold to function. The topology of folding is widely believed to define its properties and function, and knot theory has been applied to study protein structure and its implications. More that…
A theoretical construction of the genetic material establishes the unique and ideal character of DNA. A similar conclusion is reached for amino acids and proteins.
Most DNA sequencing technologies are based on the shotgun paradigm: many short reads are obtained from random unknown locations in the DNA sequence. A fundamental question, studied in arXiv:1203.6233, is what read length and coverage depth…
Recent advances in operating and manipulating DNA have provided unique experimental possibilities in many fields of DNA research, especially in gene therapy. Researchers have deployed many techniques, experimental and theoretical, to study…
These lectures will address two questions. Is there a simple variational principle underlying the existence of secondary motifs in the native state of proteins? Is there a general approach which can qualitatively capture the salient…
Labeling of DNA molecules is a fundamental technique for DNA visualization and analysis. This process was mathematically modeled in [1], where the received sequence indicates the positions of the used labels. In this work, we develop error…
The formation of DNA loops by proteins and protein complexes is ubiquitous to many fundamental cellular processes, including transcription, recombination, and replication. Here we review recent advances in understanding the properties of…
DNA storage has emerged as an important area of research. The reliability of DNA storage system depends on designing the DNA strings (called DNA codes) that are sufficiently dissimilar. In this work, we introduce DNA codes that satisfy a…
Predicting how genetic variation affects phenotypic outcomes at the organismal, cellular, and molecular levels requires deciphering the cis-regulatory code, the sequence rules by which non-coding regions regulate genes. In this perspective,…
The representation, or encoding, utilized in evolutionary algorithms has a substantial effect on their performance. Examination of the suitability of widely used representations for quality diversity optimization (QD) in robotic domains has…
Cryptography is the science that secures data and communication over the network by applying mathematics and logic to design strong encryption methods. In the modern era of e-business and e-commerce the protection of confidentiality,…
DNA sequencing allows for the determination of the genetic code of an organism, and therefore is an indispensable tool that has applications in Medicine, Life Sciences, Evolutionary Biology, Food Sciences and Technology, and Agriculture. In…
The tendencies described in this work were revealed in the course of examination of adenine and uracil distribution in the mRNA encoding sequence. The study also discusses the usage of codons occupied by the amino acid arginine in the table…
Much evolutionary information is stored in the fluctuations of protein length distributions. The genome size and non-coding DNA content can be calculated based only on the protein length distributions. So there is intrinsic relationship…
A new version of DNA walks, where nucleotides are regarded unequal in their contribution to a walk is introduced, which allows us to study thoroughly the "fine structure" of nucleotide sequences. The approach is based on the assumption that…