Related papers: The Tandem Duplication Distance is NP-hard
Quasiperiodicity in strings was introduced almost 30 years ago as an extension of string periodicity. The basic notions of quasiperiodicity are cover and seed. A cover of a text $T$ is a string whose occurrences in $T$ cover all positions…
The problem of approximate string matching is important in many different areas such as computational biology, text processing and pattern recognition. A great effort has been made to design efficient algorithms addressing several variants…
A (tandem) duplication of length $ k $ is an insertion of an exact copy of a substring of length $ k $ next to its original position. This and related types of impairments are of relevance in modeling communication in the presence of…
During cancer progression, malignant cells accumulate somatic mutations that can lead to genetic aberrations. In particular, evolutionary events akin to segmental duplications or deletions can alter the copy-number profile (CNP) of a set of…
When estimating a phylogeny from a multiple sequence alignment, researchers often assume the absence of recombination. However, if recombination is present, then tree estimation and all downstream analyses will be impacted, because…
Hairpin completion, derived from the hairpin formation observed in DNA biochemistry, is an operation applied to strings, particularly useful in DNA computing. Conceptually, a right hairpin completion operation transforms a string $S$ into…
The matching distance is a computationally tractable topological measure to compare multi-filtered simplicial complexes. We design efficient algorithms for approximating the matching distance of two bi-filtered complexes to any desired…
Let T be a triangulation of a simple polygon. A flip in T is the operation of removing one diagonal of T and adding a different one such that the resulting graph is again a triangulation. The flip distance between two triangulations is the…
The double digest problem is a common NP-hard approach to constructing physical maps of DNA sequences. This paper presents a new approach called the enhanced double digest problem. Although this new problem is also NP-hard, it can be solved…
The computation of genomic distances has been a very active field of computational comparative genomics over the last 25 years. Substantial results include the polynomial-time computability of the inversion distance by Hannenhalli and…
Data compression plays an important role to deal with high volumes of DNA sequences in the field of Bioinformatics. Again data compression techniques directly affect the alignment of DNA sequences. So the time needed to decompress a…
A binary tanglegram is a pair <S,T> of binary trees whose leaf sets are in one-to-one correspondence; matching leaves are connected by inter-tree edges. For applications, for example in phylogenetics or software engineering, it is required…
Many consensus string problems are based on Hamming distance. We replace Hamming distance by the more flexible (e.g., easily coping with different input string lengths) dynamic time warping distance, best known from applications in time…
We present the first dynamic algorithms for Dyck and tree edit distances with subpolynomial update times. Dyck edit distance measures how far a parenthesis string is from a well-parenthesized expression, while tree edit distance quantifies…
Trace reconstruction is the problem of learning an unknown string $x$ from independent traces of $x$, where traces are generated by independently deleting each bit of $x$ with some deletion probability $q$. In this paper, we initiate the…
Shannon's entropy is a definitive lower bound for statistical compression. Unfortunately, no such clear measure exists for the compressibility of repetitive strings. Thus, ad hoc measures are employed to estimate the repetitiveness of…
Motivated by the study of genome rearrangements, the NP-hard Minimum Common String Partition problems asks, given two strings, to split both strings into an identical set of blocks. We consider an extension of this problem to unbalanced…
We study codes that can correct backtracking errors during nanopore sequencing. In this channel, a sequence of length $n$ over an alphabet of size $q$ is being read by a sliding window of length $\ell$, where from each window we obtain only…
DNA as a data storage medium has several advantages, including far greater data density compared to electronic media. We propose that schemes for data storage in the DNA of living organisms may benefit from studying the reconstruction…
Gibbons and Korach studied a fundamental problem in 1997: given an observed sequence of reads and writes of a multi-threaded program, does there exist an interleaving which is sequentially consistent? Apart from applications in testing…