Related papers: RNA as a Nanoscale Data Transmission Medium: Error…
The control over DNA elongation in nanofluidic devices holds great potential for large-scale genomic analysis. So far, the manipulation of DNA in nanochannels has been mostly carried out with electrophoresis and seldom with hydrodynamics,…
Data selection has proven its merit for improving Neural Machine Translation (NMT), when applied to authentic data. But the benefit of using synthetic data in NMT training, produced by the popular back-translation technique, raises the…
We have micromachined a silicon-chip device that transports DNA with a Brownian ratchet that rectifies the Brownian motion of microscopic particles. Transport properties for a DNA 50mer agree with theoretical predictions, and the DNA…
Knowledge Distillation is an effective method of transferring knowledge from a large model to a smaller model. Distillation can be viewed as a type of model compression, and has played an important role for on-device ASR applications. In…
RNA is a fundamental class of biomolecules that mediate a large variety of molecular processes within the cell. Computational algorithms can be of great help in the understanding of RNA structure-function relationship. One of the main…
{\it Transcription} is the process whereby RNA molecules are polymerized by molecular machines, called RNA polymerase (RNAP), using the corresponding DNA as the template. Recent {\it in-vivo} experiments with single cells have established…
A simple DNA-based data storage scheme is demonstrated in which information is written using "addressing" oligonucleotides. In contrast to other methods that allow arbitrary code to be stored, the resulting DNA is suitable for downstream…
One of the primary sequencing methods gaining prominence in DNA storage is nanopore sequencing, attributed to various factors. In this work, we consider a simplified model of the sequencer, characterized as a channel. This channel takes a…
The practical NAND flash memory suffers from various non-stationary noises that are difficult to be predicted. Furthermore, the data retention noise induced channel offset is unknown during the readback process. This severely affects the…
The Human Genome Project has led to an exponential increase in data related to the sequence, structure, and function of biomolecules. Bioinformatics is an interdisciplinary research field that primarily uses computational methods to analyze…
To increase the information capacity of DNA storage, composite DNA letters were introduced. We propose a novel channel model for composite DNA in which composite sequences are decomposed into ordered standard non-composite sequences. The…
Replication is a key technique in the design of efficient and reliable distributed systems. As information grows, it becomes difficult or even impossible to store all information at every replica. A common approach to deal with this problem…
The editing of transcribed RNA by other molecules such that the form of the final product differs from that specified in the corresponding DNA sequence is ubiquitous. This paper uses an abstract, tunable Boolean genetic regulatory network…
Single-cell RNA-seq data are challenging because of the sparseness of the read counts, the tiny expression of many relevant genes, and the variability in the efficiency of RNA extraction for different cells. We consider a simple…
Using a combination of theory and computer simulations, we study the translocation of an RNA molecule, pulled through a solid-state nanopore by an optical tweezer, as a method to determine its secondary structure. The resolution with which…
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,…
RNA sequencing (RNA-seq) enables characterization and quantification of individual transcriptomes as well as detection of patterns of allelic expression and alternative splicing. Current RNA-seq protocols depend on high-throughput…
Recurrent Neural Networks are powerful machine learning frameworks that allow for data to be saved and referenced in a temporal sequence. This opens many new possibilities in fields such as handwriting analysis and speech recognition. This…
Inspired by RNA-editing as occurs in transcriptional processes in the living cell, we introduce an abstract notion of string adjustment, called guided rewriting. This formalism allows simultaneously inserting and deleting elements. We prove…
Synthetic DNA approaches 227.5 exabytes per gram of storage density with stability over millennial timescales. Realising this capacity requires error-correction codes that recover data from substantial synthesis and sequencing errors.…