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Assembling genomic sequences from a set of overlapping reads is one of the most fundamental problems in computational biology. Algorithms addressing the assembly problem fall into two broad categories -- based on the data structures which…
We introduce the graph parameter readability and study it as a function of the number of vertices in a graph. Given a digraph D, an injective overlap labeling assigns a unique string to each vertex such that there is an arc from x to y if…
We present an algorithm for maintaining maximal matching in a graph under addition and deletion of edges. Our data structure is randomized that takes O(log n) expected amortized time for each edge update where n is the number of vertices in…
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.…
This paper introduces a new family of reconstruction codes which is motivated by applications in DNA data storage and sequencing. In such applications, DNA strands are sequenced by reading some subset of their substrings. While previous…
The problem of matching a query string to a directed graph, whose vertices are labeled by strings, has application in different fields, from data mining to computational biology. Several variants of the problem have been considered,…
Given a set of strings, the shortest common superstring problem is to find the shortest possible string that contains all the input strings. The problem is NP-hard, but a lot of work has gone into designing approximation algorithms for…
(An updated version of this manuscript has been accepted to Scientific Reports in 2016, please refer to http://www.nature.com/articles/srep31900) The highly anticipated transition from next generation sequencing (NGS) to third generation…
Aligning a sequence to a walk in a labeled graph is a problem of fundamental importance to Computational Biology. For finding a walk in an arbitrary graph with $|E|$ edges that exactly matches a pattern of length $m$, a lower bound based on…
We consider the problem of maintaining a $(1-\epsilon)$-approximation to the densest subgraph (DSG) in an undirected multigraph as it undergoes edge insertions and deletions (the fully dynamic setting). Sawlani and Wang [SW20] developed a…
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…
Covering alignment problems arise from recent developments in genomics; so called pan-genome graphs are replacing reference genomes, and advances in haplotyping enable full content of diploid genomes to be used as basis of sequence…
We revisit the complexity of approximate pattern matching in an elastic-degenerate string. Such a string is a sequence of $n$ finite sets of strings of total length $N$, and compactly describes a collection of strings obtained by first…
This paper addresses the persistent challenge of accurately digitizing paper-based electrocardiogram (ECG) recordings, with a particular focus on robustly handling single leads compromised by signal overlaps-a common yet under-addressed…
Motivation: Second generation sequencing technology makes it feasible for many researches to obtain enough sequence reads to attempt the de novo assembly of higher eukaryotes (including mammals). De novo assembly not only provides a tool…
A connected graph $G$ with at least $2m + 2n + 2$ vertices which contains a perfect matching is $E(m, n)$-{\it extendable}, if for any two sets of disjoint independent edges $M$ and $N$ with $|M| = m$ and $|N|= n$, there is a perfect…
We present a data structure that can maintain a simple planar graph under edge contractions in linear total time. The data structure supports adjacency queries and provides access to neighbor lists in $O(1)$ time. Moreover, it can report…
Subgraph matching is to find all subgraphs in a data graph that are isomorphic to an existing query graph. Subgraph matching is an NP-hard problem, yet has found its applications in many areas. Many learning-based methods have been proposed…
The phylogenetic tree construction is to infer the evolutionary relationship between species from the experimental data. However, the experimental data are often imperfect and conflicting each others. Therefore, it is important to extract…
Motivated by systems where the information is represented by a graph, such as neural networks, associative memories, and distributed systems, we present in this work a new class of codes, called codes over graphs. Under this paradigm, the…