Related papers: Genome assembly, from practice to theory: safe, co…
Embeddings of graphs into distributions of trees that preserve distances in expectation are a cornerstone of many optimization algorithms. Unfortunately, online or dynamic algorithms which use these embeddings seem inherently randomized and…
Maximal clique enumeration (MCE) is a fundamental problem in graph theory and is used in many applications, such as social network analysis, bioinformatics, intelligent agent systems, cyber security, etc. Most existing MCE algorithms focus…
Background: In the metagenome assembly of a microbiome community, we may think abundant species would be easier to assemble due to their deeper coverage. However, this conjucture is rarely tested. We often do not know how many abundant…
How to compare whole genome sequences at large scale has not been achieved via conventional methods based on pair-wisely base-to-base comparison; nevertheless, no attention was paid to handle in-one-sitting a number of genomes crossing…
De novo assembly enables investigations of unknown genomes, paving the way for personalized medicine and disease management. However, it faces immense computational challenges arising from the excessive data volumes and algorithmic…
One of the most important algorithmic applications of quantum walks is to solve spatial search problems. A widely used quantum algorithm for this problem, introduced by Childs and Goldstone [Phys. Rev. A 70, 022314 (2004)], finds a marked…
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…
Systems Biology is a fundamental field and paradigm that introduces a new era in Biology. The crux of its functionality and usefulness relies on metabolic networks that model the reactions occurring inside an organism and provide the means…
Some recent results have introduced external-memory algorithms to compute self-indexes of a set of strings, mainly via computing the Burrows-Wheeler Transform (BWT) of the input strings. The motivations for those results stem from…
We address the induced matching enumeration problem. An edge set $M$ is an induced matching of a graph $G =(V,E)$. The enumeration of matchings are widely studied in literature, but the induced matching has not been paid much attention. A…
Advances in data collecting technologies in genomics have significantly increased the need for tools designed to study the genetic basis of many diseases. Effective statistical methods should excel in both prediction accuracy and biomarker…
Finding large cliques or cliques missing a few edges is a fundamental algorithmic task in the study of real-world graphs, with applications in community detection, pattern recognition, and clustering. A number of effective…
In Gaussian graphical model selection, noise-corrupted samples present significant challenges. It is known that even minimal amounts of noise can obscure the underlying structure, leading to fundamental identifiability issues. A recent line…
A pangenome captures the genetic diversity across multiple individuals simultaneously, providing a more comprehensive reference for genome analysis than a single linear genome, which may introduce allele bias. A widely adopted pangenome…
One of the major successes in computational biology has been the unification, using the graphical model formalism, of a multitude of algorithms for annotating and comparing biological sequences. Graphical models that have been applied…
We consider the problem of enumerating all instances of a given pattern graph in a large data graph. Our focus is on determining the input/output (I/O) complexity of this problem. Let $E$ be the number of edges in the data graph, $k=O(1)$…
Quasi-cliques are dense incomplete subgraphs of a graph that generalize the notion of cliques. Enumerating quasi-cliques from a graph is a robust way to detect densely connected structures with applications to bio-informatics and social…
We consider string matching with variable length gaps. Given a string $T$ and a pattern $P$ consisting of strings separated by variable length gaps (arbitrary strings of length in a specified range), the problem is to find all ending…
A new method involving particle diagrams is introduced and developed into a rigorous framework for carrying out embedded random matrix calculations. Using particle diagrams and the attendant methodology including loop counting it becomes…
High-confidence prediction of complex traits such as disease risk or drug response is an ultimate goal of personalized medicine. Although genome-wide association studies have discovered thousands of well-replicated polymorphisms associated…