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We present Meraculous2, an update to the Meraculous short-read assembler that includes (1) handling of allelic variation using "bubble" structures within the de Bruijn graph, (2) improved gap closing, and (3) an improved scaffolding…
In digital baseband processing, the forward error correction (FEC) unit belongs to the most demanding components in terms of computational complexity and power consumption. Hence, efficient implementation of FEC decoders is crucial for next…
The de novo assembly of large, complex genomes is a significant challenge with currently available DNA sequencing technology. While many de novo assembly software packages are available, comparatively little attention has been paid to…
We present a novel approach to solving combinatorial assignment problems in particle physics without the need to introduce prior knowledge or assumptions about the particles' decay. The correct assignment of decay products to parent…
Random linear network coding (RLNC) in theory achieves the max-flow capacity of multicast networks, at the cost of high decoding complexity. To improve the performance-complexity tradeoff, we consider the design of sparse network codes. A…
DNA Data storage has recently attracted much attention due to its durable preservation and extremely high information density (bits per gram) properties. In this work, we propose a hybrid coding strategy comprising of generalized…
DNA samples are often pooled, either by experimental design, or because the sample itself is a mixture. For example, when population allele frequencies are of primary interest, individual samples may be pooled together to lower the cost of…
The polarization-adjusted convolutional (PAC) codes concatenate the polar transform and the convolutional transform to improve the decoding performance of the finite-length polar codes, where the rate-profile is used to construct the PAC…
Recent studies have shown that a Deep Convolutional Neural Network (DCNN) pretrained on a large image dataset can be used as a universal image descriptor, and that doing so leads to impressive performance for a variety of image…
Biological sequence analysis relies on the ability to denoise the imprecise output of sequencing platforms. We consider a common setting where a short sequence is read out repeatedly using a high-throughput long-read platform to generate…
Decoding of convolutional codes poses a significant challenge for coding theory. Classical methods, based on e.g. Viterbi decoding, suffer from being computationally expensive and are restricted therefore to codes of small complexity. Based…
Currently, third-generation sequencing techniques, which allow to obtain much longer DNA reads compared to the next-generation sequencing technologies, are becoming more and more popular. There are many possibilities to combine data from…
Large pools of synthetic DNA molecules have been recently used to reliably store significant volumes of digital data. While DNA as a storage medium has enormous potential because of its high storage density, its practical use is currently…
At the core of high throughput DNA sequencing platforms lies a bio-physical surface process that results in a random geometry of clusters of homogenous short DNA fragments typically hundreds of base pairs long - bridge amplification. The…
We study the amount of reliable information that can be stored in a DNA-based storage system composed of short DNA molecules. In this regime, Shomorony and Heckel (2022) put forward a conjecture on the scaling of the number of information…
We propose an assembly algorithm {\sc Barnacle} for sequences generated by the clone-based approach. We illustrate our approach by assembling the human genome. Our novel method abandons the original physical-mapping-first framework. As we…
Recent advances in machine translation (MT) have shown that Minimum Bayes Risk (MBR) decoding can be a powerful alternative to beam search decoding, especially when combined with neural-based utility functions. However, the performance of…
We report an accurate method to determine DNA barcodes from the dwell time measurement of protein tags (barcodes) along the DNA backbone using Brownian dynamics simulation of a model DNA and use a recursive theoretical scheme which improves…
In this paper a novel biclustering algorithm based on artificial intelligence (AI) is introduced. The method called EBIC aims to detect biologically meaningful, order-preserving patterns in complex data. The proposed algorithm is probably…
Nanopore sequencing technology remains highly error-prone, making efficient error correction essential in DNA-based data storage. Prior work addressed high error rates using convolutional codes with their decoder coupled with the…