Related papers: On the Coverage Required for Diploid Genome Assemb…
Genome assembly asks to reconstruct an unknown string from many shorter substrings of it. Even though it is one of the key problems in Bioinformatics, it is generally lacking major theoretical advances. Its hardness stems both from…
We consider a random geometric graph with vertices sampled from a probability measure supported on $\mathbb R^d$, and study its connectivity. We show the graph is typically disconnected, unless the sampling density has superexponential…
We investigate the structure and reconstruction complexity of Manacher arrays. First, we establish a combinatorial lower bound, proving that the number of rooted tandem repeat trees with $n+1$ genes exceeds the number of distinct Manacher…
DNA rearrangement processes recombine gene segments that are organized on the chromosome in a variety of ways. The segments can overlap, interleave or one may be a subsegment of another. We use directed graphs to represent segment…
Each human genome is a 3 billion base pair set of encoding instructions. Decoding the genome using deep learning fundamentally differs from most tasks, as we do not know the full structure of the data and therefore cannot design…
Cellular coverage quality estimation has been a critical task for self-organized networks. In real-world scenarios, deep-learning-powered coverage quality estimation methods cannot scale up to large areas due to little ground truth can be…
Background - The process of generating raw genome sequence data continues to become cheaper, faster, and more accurate. However, assembly of such data into high-quality, finished genome sequences remains challenging. Many genome assembly…
Molecular self-assembly plays a very important role in various aspects of technology as well as in biological systems. Governed by the covalent, hydrogen or van der Waals interactions - self-assembly of alike molecules results in a large…
Ptychography is a well-studied phase imaging method that makes non-invasive imaging possible at a nanometer scale. It has developed into a mainstream technique with various applications across a range of areas such as material science or…
In this paper, a new information theoretic framework for graph matching is introduced. Using this framework, the graph isomorphism and seeded graph matching problems are studied. The maximum degree algorithm for graph isomorphism is…
Polyploidization is an evolutionary process by which a species acquires multiple copies of its complete set of chromosomes. The reticulate nature of the signal left behind by it means that phylogenetic networks offer themselves as a…
In genome-scale constraint-based metabolic models, gene deletion strategies are essential for achieving growth-coupled production, where cell growth and target metabolite synthesis occur simultaneously. Despite the inherently networked…
Understanding genetic variation, e.g., through mutations, in organisms is crucial to unravel their effects on the environment and human health. A fundamental characterization can be obtained by solving the haplotype assembly problem, which…
Motivations Short-read accuracy is important for downstream analyses such as genome assembly and hybrid long-read correction. Despite much work on short-read correction, present-day correctors either do not scale well on large data sets or…
Coverage of image features play an important role in many vision algorithms since their distribution affect the estimated homography. This paper presents a Genetic Algorithm (GA) in order to select the optimal set of features yielding…
Maximum weight matching is one of the most fundamental combinatorial optimization problems with a wide range of applications in data mining and bioinformatics. Developing distributed weighted matching algorithms is challenging due to the…
The huge amount of data acquired by high-throughput sequencing requires data reduction for effective analysis. Here we give a clustering algorithm for genome-wide open chromatin data using a new data reduction method. This method regards…
We introduce a new concept of a subgraph class called a superbubble for analyzing assembly graphs, and propose an efficient algorithm for detecting it. Most assembly algorithms utilize assembly graphs like the de Bruijn graph or the overlap…
We study the classic set cover problem from the perspective of sub-linear algorithms. Given access to a collection of $m$ sets over $n$ elements in the query model, we show that sub-linear algorithms derived from existing techniques have…
A common starting point for drug design is to find small chemical groups or "fragments" that form interactions with distinct subregions in a protein binding pocket. The subsequent challenge is to assemble these fragments into a molecule…