Related papers: Optimal Assembly for High Throughput Shotgun Seque…
We introduce a Bayesian genetic algorithm for reconstructing atomic models of nanoparticles from a single projection using Z-contrast imaging. The number of atoms in a projected atomic column obtained from annular dark field scanning…
With the advent of high-throughput profiling methods, interest in reverse engineering the structure and dynamics of biochemical networks is high. Recently an algorithm for reverse engineering of biochemical networks was developed by…
The sequence in which a complex product is assembled directly impacts the ease and efficiency of the assembly process, whether executed by a human or a robot. A sequence that gives the assembler the greatest freedom of movement is therefore…
Among the distance based algorithms in phylogenetic tree reconstruction, the neighbor-joining algorithm has been a widely used and effective method. We propose a new algorithm which counts the number of consistent quartets for cherry…
In this paper, we present new efficiently solvable cases of the Minimum Uncovering Branching problem, an optimization problem with applications in cancer genomics introduced by Hujdurovi\'c, Husi\'c, Milani\v{c}, Rizzi, and Tomescu in 2018.…
We describe properties and constructions of constraint-based codes for DNA-based data storage which account for the maximum repetition length and AT/GC balance. We present algorithms for computing the number of sequences with maximum…
Encoding data as a set of unordered strings is receiving great attention as it captures one of the basic features of DNA storage systems. However, the challenge of constructing optimal redundancy codes for this channel remained elusive. In…
The experimenter must perform a legitimate search in the entire set of feasible censoring schemes to identify the optimal type II progressive censoring scheme, when applied to a life-testing experiment. Current recommendations are limited…
We consider the problem of how many samples from a Gaussian multi-index model are required to weakly reconstruct the relevant index subspace. Despite its increasing popularity as a testbed for investigating the computational complexity of…
This paper studies sequencing and mapping methods that rely solely on pooling and shotgun sequencing of clones. First, we scrutinize and improve the recently proposed Clone-Array Pooled Shotgun Sequencing (CAPSS) method, which delivers a…
Motivated by mass-spectrometry protein sequencing, we consider a simply-stated problem of reconstructing a string from the multiset of its substring compositions. We show that all strings of length 7, one less than a prime, or one less than…
Limited spectrum coverage is a problem in shotgun proteomics. Replicates are generated to improve the spectrum coverage. When integrating peptide identification results obtained from replicates, the state-of-the-art algorithm PeptideProphet…
The optimal robot assembly planning problem is challenging due to the necessity of finding the optimal solution amongst an exponentially vast number of possible plans, all while satisfying a selection of constraints. Traditionally, robotic…
Gene finding is the task of identifying the locations of coding sequences within the vast amount of genetic code contained in the genome. With an ever increasing quantity of raw genome sequences, gene finding is an important avenue towards…
Motivation: Eugene Myers in his string graph paper (Myers, 2005) suggested that in a string graph or equivalently a unitig graph, any path spells a valid assembly. As a string/unitig graph also encodes every valid assembly of reads, such a…
Identifying palindromes in sequences has been an interesting line of research in combinatorics on words and also in computational biology, after the discovery of the relation of palindromes in the DNA sequence with the HIV virus. Efficient…
Next-generation sequencing technologies generate millions of short sequence reads, which are usually aligned to a reference genome. In many applications, the key information required for downstream analysis is the number of reads mapping to…
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…
The problem of reconstructing strings from substring information has found many applications due to its importance in genomic data sequencing and DNA- and polymer-based data storage. One practically important and challenging paradigm…
The problem of reconstructing strings from their substring spectra has a long history and in its most simple incarnation asks for determining under which conditions the spectrum uniquely determines the string. We study the problem of coded…