Related papers: On-line Assembling Mitochondrial DNA from de novo …

In this thesis, we address the problem of identifying and quantifying variants (alternative splicing and genomic polymorphism) in RNA-seq data when no reference genome is available, without assembling the full transcripts. Based on the…

The classification of DNA sequences is a key research area in bioinformatics as it enables researchers to conduct genomic analysis and detect possible diseases. In this paper, three state-of-the-art algorithms, namely Convolutional Neural…

We present a new simulation scheme which allows an efficient sampling of reconfigurable supramolecular structures made of polymeric constructs functionalized by reactive binding sites. The algorithm is based on the configurational bias…

This work presents the application of the artificial neural networks, trained and structurally optimized by genetic algorithms, for modeling of crude distillation process at PKN ORLEN S.A. refinery. Models for the main fractionator…

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…

Genome assembly from the high-throughput sequencing (HTS) reads is a fundamental yet challenging computational problem. An intrinsic challenge is the uncertainty caused by the widespread repetitive elements. Here we get around the…

In this paper we propose a novel network adaption method called Differentiable Network Adaption (DNA), which can adapt an existing network to a specific computation budget by adjusting the width and depth in a differentiable manner. The…

A method based on mapping a symbolic sequence into a set of patterns (strings resulting from the sequence parsing) is proposed as a tool for the reconstruction of ancestral sequences. The set union of patterns comprises all the patterns…

A number of bioinformatic or biostatistical methods are available for analyzing DNA copy number profiles measured from microarray or sequencing technologies. In the absence of rich enough gold standard data sets, the performance of these…

In this letter, we introduce a new syndrome-based decoder where a deep neural network (DNN) estimates the error pattern from the reliability and syndrome of the received vector. The proposed algorithm works by iteratively selecting the most…

In this paper, we propose an online multi-spectral neuron tracing method with uniquely designed modules, where no offline training are required. Our method is trained online to update our enhanced discriminative correlation filter to…

Mining subgraphs with interesting structural properties from networks (or graphs) is a computationally challenging task. In this paper, we propose two algorithms for enumerating all connected induced subgraphs of a given cardinality from…

This paper proposes a novel algorithm to reassemble an arbitrarily shredded image to its original status. Existing reassembly pipelines commonly consist of a local matching stage and a global compositions stage. In the local stage, a key…

A cut-down de Bruijn sequence is a cyclic string of length $L$, where $1 \leq L \leq k^n$, such that every substring of length $n$ appears at most once. Etzion [Theor. Comp. Sci 44 (1986)] gives an algorithm to construct binary cut-down de…

Motivation: RNA-seq has made feasible the analysis of a whole set of expressed mRNAs. Mapping-based assembly of RNA-seq reads sometimes is infeasible due to lack of high-quality references. However, de novo assembly is very challenging due…

We propose a new compression scheme for genomic data given as sequence fragments called reads. The scheme uses a reference genome at the decoder side only, freeing the encoder from the burdens of storing references and performing…

Genome assembly is a prominent problem studied in bioinformatics, which computes the source string using a set of its overlapping substrings. Classically, genome assembly uses assembly graphs built using this set of substrings to compute…

Filtered diode array spectrometers are routinely employed to infer the temporal evolution of spectral power from x-ray sources, but uniquely extracting spectral content from a finite set of broad, spectrally overlapping channel spectral…

Transcriptome assembly from RNA-Seq reads is an active area of bioinformatics research. The ever-declining cost and the increasing depth of RNA-Seq have provided unprecedented opportunities to better identify expressed transcripts. However,…

The de Bruijn graph plays an important role in bioinformatics, especially in the context of de novo assembly. However, the representation of the de Bruijn graph in memory is a computational bottleneck for many assemblers. Recent papers…