Related papers: On-line Assembling Mitochondrial DNA from de novo …
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…
As the global need for large-scale data storage is rising exponentially, existing storage technologies are approaching their theoretical and functional limits in terms of density and energy consumption, making DNA based storage a potential…
(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…
Gene assembly in ciliates is one of the most involved DNA processings going on in any organism. This process transforms one nucleus (the micronucleus) into another functionally different nucleus (the macronucleus). We continue the…
Optical molecular tomographic imaging is to reconstruct the concentration distribution of photon-molecular probes in a small animal from measured photon fluence rates. The localization and quantification of molecular probes is related to…
Genome analysis fundamentally starts with a process known as read mapping, where sequenced fragments of an organism's genome are compared against a reference genome. Read mapping is currently a major bottleneck in the entire genome analysis…
The identification of low-energy conformers for a given molecule is a fundamental problem in computational chemistry and cheminformatics. We assess here a conformer search that employs a genetic algorithm for sampling the low-energy segment…
For single-cell or metagenomic sequencing projects, it is necessary to sequence with a very high mean coverage in order to make sure that all parts of the sample DNA get covered by the reads produced. This leads to huge datasets with lots…
Decoding sequences that stem from multiple transmissions of a codeword over an insertion, deletion, and substitution channel is a critical component of efficient deoxyribonucleic acid (DNA) data storage systems. In this paper, we consider a…
In just the last decade, a multitude of bio-technologies and software pipelines have emerged to revolutionize genomics. To further their central goal, they aim to accelerate and improve the quality of de novo whole-genome assembly starting…
This paper focuses on pattern matching in the DNA sequence. It was inspired by a previously reported method that proposes encoding both pattern and sequence using prime numbers. Although fast, the method is limited to rather small pattern…
In this paper, we propose a shape optimization pipeline for propeller blades, applied to naval applications. The geometrical features of a blade are exploited to parametrize it, allowing to obtain deformed blades by perturbating their…
Proteomics is the large-scale analysis of the proteins. The common method for identifying proteins and characterising their amino acid sequences is to digest the proteins into peptides, analyse the peptides using mass spectrometry and…
The possibility of prescribing local interactions between nano- and microscopic components that direct them to assemble in a predictable fashion is a central goal of nanotechnology research. In this article we advance a new paradigm in…
Recently, deep neural network (DNN) has been widely adopted in the design of intelligent communication systems thanks to its strong learning ability and low testing complexity. However, most current offline DNN-based methods still suffer…
The paper describes an algorithm to compute a consensus sequence from a set of DNA sequences of approximatively identical length generated by 3rd sequencing generation technologies. Its purpose targets DNA storage and is guided by specific…
Motivation: Intimately tied to assembly quality is the complexity of the de Bruijn graph built by the assembler. Thus, there have been many paradigms developed to decrease the complexity of the de Bruijn graph. One obvious combinatorial…
Retrosynthetic planning, which aims to find a reaction pathway to synthesize a target molecule, plays an important role in chemistry and drug discovery. This task is usually modeled as a search problem. Recently, data-driven methods have…
Artificial synthesis of DNA molecules is an essential part of the study of biological mechanisms. The design of a synthetic DNA molecule usually involves many objectives. One of the important objectives is to eliminate short sequence…
In the small phylogeny problem we, are given a phylogenetic tree and gene orders of the extant species and our goal is to reconstruct all of the ancestral genomes so that the number of evolutionary operations is minimized. Algorithms for…