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Motivation: Despite significant advances in Third-Generation Sequencing (TGS) technologies, Next-Generation Sequencing (NGS) technologies remain dominant in the current sequencing market. This is due to the lower error rates and richer…
Sequencing a genome to determine an individual's DNA produces an enormous number of short nucleotide subsequences known as reads, which must be reassembled to reconstruct the full genome. We present a method for analyzing this type of data…
DNA has immense potential as an emerging data storage medium. The principle of DNA storage is the conversion and flow of digital information between binary code stream, quaternary base, and actual DNA fragments. This process will inevitably…
Nanopore sequencing is an emerging new technology for sequencing DNA, which can read long fragments of DNA (~50,000 bases) in contrast to most current short-read sequencing technologies which can only read hundreds of bases. While nanopore…
Self-adaptation solutions need to periodically monitor, reason about, and adapt a running system. The adaptation step involves generating an adaptation strategy and applying it to the running system whenever an anomaly arises. In this…
Data-efficient image classification is a challenging task that aims to solve image classification using small training data. Neural network-based deep learning methods are effective for image classification, but they typically require…
The study of functional genomics--particularly in non-model organisms has been dramatically improved over the last few years by use of transcriptomes and RNAseq. While these studies are potentially extremely powerful, a computationally…
A quest to determine the complete sequence of a human DNA from telomere to telomere started three decades ago and was finally completed in 2021. This accomplishment was a result of a tremendous effort of numerous experts who engineered…
Technologies for sequencing (reading) and synthesizing (writing) DNA have progressed on a Moore's law-like trajectory over the last three decades. This has motivated the idea of using DNA for data storage. Theoretically, DNA-based storage…
A major hindrance to studies of microbial diversity has been that the vast majority of microbes cannot be cultured in the laboratory and thus are not amenable to traditional methods of characterization. Environmental shotgun sequencing…
Machine learning, and representation learning in particular, has the potential to facilitate drug discovery by screening billions of compounds. For example, a successful approach is representing the molecules as a graph and utilizing graph…
The computational problem of inferring the full haplotype of a cell starting from read sequencing data is known as haplotype assembly, and consists in assigning all heterozygous Single Nucleotide Polymorphisms (SNPs) to exactly one of the…
Message-passing based approaches form the default backbone of most learning architectures on graph-structured data. However, the rapid progress of modern deep learning architectures in other domains, particularly sequence modeling, raises…
We provide an overview of current approaches to DNA-based storage system design and accompanying synthesis, sequencing and editing methods. We also introduce and analyze a suite of new constrained coding schemes for both archival and random…
Sequencing by tunneling is a next-generation approach to read single-base information using electronic tunneling transverse to the single-stranded DNA (ssDNA) backbone while the latter is translocated through a narrow channel. The original…
De novo genome assembly is the process of stitching short DNA sequences to generate longer DNA sequences, without using any reference sequence for alignment. It enables high-throughput genome sequencing and thus accelerates the discovery of…
Pairwise alignment of DNA sequencing data is a ubiquitous task in bioinformatics and typically represents a heavy computational burden. State-of-the-art approaches to speed up this task use hashing to identify short segments (k-mers) that…
DNA pattern matching is essential for many widely used bioinformatics applications. Disease diagnosis is one of these applications, since analyzing changes in DNA sequences can increase our understanding of possible genetic diseases. The…
A major challenge in next-generation genome sequencing (NGS) is to assemble massive overlapping short reads that are randomly sampled from DNA fragments. To complete assembling, one needs to finish a fundamental task in many leading…
Gene finding is the task of identifying the locations of coding sequences within the vast amount of genetic code contained in the genome. With an ever increasing quantity of raw genome sequences, gene finding is an important avenue towards…