Related papers: Baa.pl: A tool to evaluate de novo genome assembli…
Modern high-throughput gene perturbation screens are key technologies at the forefront of genetic research. Combined with rich phenotypic descriptors they enable researchers to observe detailed cellular reactions to experimental…
The discovery of nucleic acids and the structure of DNA have brought considerable advances in the understanding of life. The development of next-generation sequencing technologies has led to a large-scale generation of data, for which…
The AGP format is a tab-separated table format describing how components of a genome assembly fit together. A standard submission format for genome assemblies is a fasta file giving the sequence of contigs along with an AGP file showing how…
Genome assembly using high throughput data with short reads, arguably, remains an unresolvable task in repetitive genomes, since when the length of a repeat exceeds the read length, it becomes difficult to unambiguously connect the flanking…
Summary: Accurate phenotype prediction from genomic sequences is a highly coveted task in biological and medical research. While machine-learning holds the key to accurate prediction in a variety of fields, the complexity of biological data…
The combination of multiple classifiers using ensemble methods is increasingly important for making progress in a variety of difficult prediction problems. We present a comparative analysis of several ensemble methods through two case…
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…
The detection of genomic structural variation (SV) has advanced tremendously in recent years due to progress in high-throughput sequencing technologies. Novel sequence insertions, insertions without similarity to a human reference genome,…
RNAnet provides a bridge between two widely used Human gene databases. Ensembl describes DNA sequences and transcripts but not experimental gene expression. Whilst NCBI's GEO contains actual expression levels from Human samples. RNAnet…
Analysis of DNA samples is an important step in forensics, and the speed of analysis can impact investigations. Comparison of DNA sequences is based on the analysis of short tandem repeats (STRs), which are short DNA sequences of 2-5 base…
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…
By means of the concept of Factorial Moments we examine DNA sequences from Yeast to distinguish coding and non-coding regions. It is found that the FM may be a powerful tool for analysis of DNA sequences. PACS numbers:…
Genome sequencing is the basis for many modern biological and medicinal studies. With recent technological advances, metagenomics has become a problem of interest. This problem entails the analysis and reconstruction of multiple DNA…
We now need more than ever to make genome analysis more intelligent. We need to read, analyze, and interpret our genomes not only quickly, but also accurately and efficiently enough to scale the analysis to population level. There currently…
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…
Detecting changepoints in a time series of length $N$ entails evaluating up to $2^{N-1}$ possible changepoint models, making exhaustive enumeration computationally infeasible. Genetic algorithms (GAs) provide a stochastic way to identify…
Rapid analysis of DNA sequences is important in preventing the evolution of different viruses and bacteria during an early phase, early diagnosis of genetic predispositions to certain diseases (cancer, cardiovascular diseases), and in DNA…
Being able to store and transmit human genome sequences is an important part in genomic research and industrial applications. The complete human genome has 3.1 billion base pairs (haploid), and storing the entire genome naively takes about…
Genome assembly tools based on the de Bruijn graph framework rely on a parameter k, which represents a trade-off between several competing effects that are difficult to quantify. There is currently a lack of tools that would automatically…
For a genomically unstable cancer, a single tumour biopsy will often contain a mixture of competing tumour clones. These tumour clones frequently differ with respect to their genomic content (copy number of each gene) and structure (order…