Related papers: Champuru 2: Improved scoring of alignments and a u…
End-to-end encryption (E2EE) provides strong technical protections to individuals from interferences. Governments and law enforcement agencies around the world have however raised concerns that E2EE also allows illegal content to be shared…
Recently, due to the genomic sequence analysis in several types of cancer, the genomic data based on {\em copy number profiles} ({\em CNP} for short) are getting more and more popular. A CNP is a vector where each component is a…
Sequence alignment is common nowadays as it is used in many fields to determine how closely two sequences are related and at times to see how little they differ. In computational biology / Bioinformatics, there are many algorithms developed…
We present CHAMPION: a software developed to automatically detect time-dependent bonds between atoms based on their dynamics, classify the local graph topology around them, and analyze the physicochemical properties of these topologies by…
The configuration model is a standard tool for uniformly generating random graphs with a specified degree sequence, and is often used as a null model to evaluate how much of an observed network's structure can be explained by its degree…
Recent years have seen more and more demand for a unified framework to address multiple realistic image retrieval tasks concerning both category and attributes. Considering the scale of modern datasets, hashing is favorable for its low…
A lot of search approaches have been explored for the selection of features in pattern classification domain in order to discover significant subset of the features which produces better accuracy. In this paper, we introduced a Harmony…
We present an unique way to detect basepair mismatches in DNA leading to different epigenetic disorder by the method of nanopore sequencing. Based on a tight-binding formulation of graphene nanopore based device, using Greens function…
HEP-Frame is a new C++ package designed to efficiently perform analyses of data sets from a very large number of events, like those available at the Large Hadron Collider (LHC) at CERN, Geneva. It mainly targets high performance servers and…
We have developed a novel method to rapidly obtain homologous genomic data for phylogenetics directly from next-generation sequencing reads without the use of a reference genome. This software, called SISRS, avoids the time consuming steps…
A genome read data set can be quickly and efficiently remapped from one reference to another similar reference (e.g., between two reference versions or two similar species) using a variety of tools, e.g., the commonly-used CrossMap tool.…
Summary: Raw nanopore signals can be analyzed while they are being generated, a process known as real-time analysis. Real-time analysis of raw signals is essential to utilize the unique features that nanopore sequencing provides, enabling…
The computational problem of inferring the full haplotype of a cell starting from read sequencing data is known as haplotype assembly, and consists in assigning all heterozygous Single Nucleotide Polymorphisms (SNPs) to exactly one of the…
High throughput sequencing is a technology that allows for the generation of millions of reads of genomic data regarding a study of interest, and data from high throughput sequencing platforms are usually count compositions. Subsequent…
Existing studies for gait recognition primarily utilized sequences of either binary silhouette or human parsing to encode the shapes and dynamics of persons during walking. Silhouettes exhibit accurate segmentation quality and robustness to…
Motivation: Sequence mapping is the cornerstone of modern genomics. However, most existing sequence mapping algorithms are insufficiently general. Results: We introduce context schemes: a method that allows the unambiguous recognition of a…
Frequency estimation of elements is an important task for summarizing data streams and machine learning applications. The problem is often addressed by using streaming algorithms with sublinear space data structures. These algorithms allow…
Hypergraphs are generalisation of graphs in which a hyperedge can connect any number of vertices. It can describe n-ary relationships and high-order information among entities compared to conventional graphs. In this paper, we study the…
In the last decade a number of algorithms and associated software have been developed to align next generation sequencing (NGS) reads with relevant reference genomes. The accuracy of these programs may vary significantly, especially when…
About 90% of the computing resources available to the LHCb experiment has been spent to produce simulated data samples for Run 2 of the Large Hadron Collider at CERN. The upgraded LHCb detector will be able to collect larger data samples,…