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The study of DNA charge dynamics is a highly interdisciplinary field that bridges physics, chemistry, biology, and medicine, and plays a critical role in processes such as DNA damage detection, protein-DNA interactions, and DNA-based…
Spannotation is an open source user-friendly tool developed for image annotation for semantic segmentation specifically in autonomous navigation tasks. This study provides an evaluation of Spannotation, demonstrating its effectiveness in…
Evolution is an extraordinary engine for enzymatic diversity, yet the chemistry it has explored remains a narrow slice of what DNA can encode. Deep generative models can design new proteins that bind ligands, but none have created enzymes…
An RNA sequence is a word over an alphabet on four elements $\{A,C,G,U\}$ called bases. RNA sequences fold into secondary structures where some bases match one another while others remain unpaired. Pseudoknot-free secondary structures can…
We introduce YATO, an open-source, easy-to-use toolkit for text analysis with deep learning. Different from existing heavily engineered toolkits and platforms, YATO is lightweight and user-friendly for researchers from cross-disciplinary…
In the past few years, Differentiable Neural Architecture Search (DNAS) rapidly imposed itself as the trending approach to automate the discovery of deep neural network architectures. This rise is mainly due to the popularity of DARTS, one…
In this work, we investigate a challenging problem, which has been considered to be an important criterion in designing codewords for DNA computing purposes, namely secondary structure avoidance in single-stranded DNA molecules. In short,…
Decoding how linear DNA encodes regulatory information remains a central challenge. Existing decoding approaches lack interpretability and struggle to reveal the underlying coding principles. Here, we present the interpretability-first,…
Designing RNA molecules has garnered recent interest in medicine, synthetic biology, biotechnology and bioinformatics since many functional RNA molecules were shown to be involved in regulatory processes for transcription, epigenetics and…
We present a modular DNA origami design approach to address the challenges of assembling geometrically complex nanoscale structures, including those with nonuniform Gaussian curvature. This approach features a core structure that completely…
Protein design has become a critical method in advancing significant potential for various applications such as drug development and enzyme engineering. However, protein design methods utilizing large language models with solely pretraining…
This paper addresses the complex issue of one-shot face stylization, focusing on the simultaneous consideration of appearance and structure, where previous methods have fallen short. We explore deformation-aware face stylization that…
Computational RNA design tasks are often posed as inverse problems, where sequences are designed based on adopting a single desired secondary structure without considering 3D conformational diversity. We introduce gRNAde, a geometric RNA…
DNA monolayers with inherent chirality play a pivotal role across various domains, including biosensors, DNA chips, and bioelectronics. Nonetheless, conventional DNA chiral monolayers, typically constructed from single-stranded DNA (ssDNA)…
Summary: Biospectrogam is an open-source software for the spectral analysis of DNA and protein sequences. The software can fetch (from NCBI server), import and manage biological data. One can analyze the data using Digital Signal Processing…
This paper introduces PyGAD, an open-source easy-to-use Python library for building the genetic algorithm. PyGAD supports a wide range of parameters to give the user control over everything in its life cycle. This includes, but is not…
SNOMED Clinical Terms (SNOMED CT) is one of the most widespread ontologies in the life sciences, with more than 300,000 concepts and relationships, but is distributed with no associated software tools. In this paper we present MySNOM, a…
With the advancement of Deep Neural Networks (DNN) and large amounts of sensor data from Internet of Things (IoT) systems, the research community has worked to reduce the computational and resource demands of DNN to compute on low-resourced…
Theano is a Python library that allows to define, optimize, and evaluate mathematical expressions involving multi-dimensional arrays efficiently. Since its introduction, it has been one of the most used CPU and GPU mathematical compilers -…
Marcello, in 1997, formally proved that chemical kinetics can make a universal computer i.e they can replicate any digital circuit. Recently, Soloveichik et al. showed that chemical kinetics can perform fast and reliable Turing Universal…