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In genomics, pattern matching against a sequence of nucleotides plays a pivotal role for DNA sequence alignment and comparing genomes. This helps tackling some diseases, such as cancer in humans. The complexity of searching biological…
Genome sequencing is the basis for many modern biological and medicinal studies. With recent technological advances, metagenomics has become a problem of interest. This problem entails the analysis and reconstruction of multiple DNA…
DNA labeling is a tool in molecular biology and biotechnology to visualize, detect, and study DNA at the molecular level. In this process, a DNA molecule is labeled by a set of specific patterns, referred to as labels, and is then imaged.…
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…
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…
DNA sequence alignment is important today as it is usually the first step in finding gene mutation, evolutionary similarities, protein structure, drug development and cancer treatment. Covid-19 is one recent example. There are many…
Time series subsequence anomaly detection is an important task in a large variety of real-world applications ranging from health monitoring to AIOps, and is challenging due to the following reasons: 1) how to effectively learn complex…
The classification of DNA sequences is a key research area in bioinformatics as it enables researchers to conduct genomic analysis and detect possible diseases. In this paper, three state-of-the-art algorithms, namely Convolutional Neural…
Described are two algorithms to find long approximate palindromes in a string, for example a DNA sequence. A simple algorithm requires O(n)-space and almost always runs in $O(k.n)$-time where n is the length of the string and k is the…
In this paper, we present an optical computing method for string data alignment applicable to genome information analysis. By applying moire technique to spatial encoding patterns of deoxyribonucleic acid (DNA) sequences, association…
One of the most computationally intensive tasks in computational biology is de novo genome assembly, the decoding of the sequence of an unknown genome from redundant and erroneous short sequences. A common assembly paradigm identifies…
Reconstructing components of a genomic mixture from data obtained by means of DNA sequencing is a challenging problem encountered in a variety of applications including single individual haplotyping and studies of viral communities.…
De novo assembly is the process of reconstructing the genome sequence of an organism from sequencing reads. Genome sequences are essential to biology, and assembly has been a central problem in bioinformatics for four decades. Until…
Branched junction molecule assembly of DNA nanostructures, pioneered by Seeman's laboratory in the 1980s, has become increasingly sophisticated, as have the assembly targets. A critical design step is finding minimal sets of branched…
In this paper, we consider recommender systems with side information in the form of graphs. Existing collaborative filtering algorithms mainly utilize only immediate neighborhood information and have a hard time taking advantage of deeper…
The prevalent technique for DNA sequencing consists of two main steps: shotgun sequencing, where many randomly located fragments, called reads, are extracted from the overall sequence, followed by an assembly algorithm that aims to…
We present a framework for the design of optimal assembly algorithms for shotgun sequencing under the criterion of complete reconstruction. We derive a lower bound on the read length and the coverage depth required for reconstruction in…
With recent high-throughput technology we can synthesize large heterogeneous collections of DNA structures, and also read them all out precisely in a single procedure. Can we use these tools, not only to do things faster, but also to devise…
DNA sequencing is the physical/biochemical process of identifying the location of the four bases (Adenine, Guanine, Cytosine, Thymine) in a DNA strand. As semiconductor technology revolutionized computing, modern DNA sequencing technology…
We present a new approach for solving (minimum disagreement) correlation clustering that results in sublinear algorithms with highly efficient time and space complexity for this problem. In particular, we obtain the following algorithms for…