基因组学
We study the fraction $f$ of nucleotides involved in the formation of a cactus--like secondary structure of random heteropolymer RNA--like molecules. In the low--temperature limit we study this fraction as a function of the number $c$ of…
Summary: BWA-MEM is a new alignment algorithm for aligning sequence reads or long query sequences against a large reference genome such as human. It automatically chooses between local and end-to-end alignments, supports paired-end reads…
Background: Predictive, stable and interpretable gene signatures are generally seen as an important step towards a better personalized medicine. During the last decade various methods have been proposed for that purpose. However, one…
Approaches for testing sets of variants, such as a set of rare or common variants within a gene or pathway, for association with complex traits are important. In particular, set tests allow for aggregation of weak signal within a set, can…
For DNA sequences of various species we construct the Google matrix G of Markov transitions between nearby words composed of several letters. The statistical distribution of matrix elements of this matrix is shown to be described by a power…
Counting the frequencies of k-mers in read libraries is often a first step in the analysis of high-throughput sequencing experiments. Infrequent k-mers are assumed to be a result of sequencing errors. The frequent k-mers constitute a…
In a letter published in Molecular Biology Evolution [10], Chen and Zhang argue that the variation of the mutation rate along the Escherichia coli genome that we recently reported [3] cannot be evolutionarily optimised. To support this…
Identifying targets for personalized targeted therapy is the pathologist's domain and a treasure. For decades, pathologists have had to learn, understand, adopt and implement many new laboratory techniques as they arrived on the scene.…
Motivation: Rapid technological progress in DNA sequencing has stimulated interest in compressing the vast datasets that are now routinely produced. Relatively little attention has been paid to compressing the quality scores that are…
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…
Popular sequence alignment tools such as BWA convert a reference genome to an indexing data structure based on the Burrows-Wheeler Transform (BWT), from which matches to individual query sequences can be rapidly determined. However the…
The genetic code underlying protein synthesis is a canonical example of a degenerate biological system. Degeneracies in physical and biological systems can be lifted by external perturbations thus allowing degenerate systems to exhibit a…
Summary: We present an extension of CUSHAW2 for fast and accurate alignments of SOLiD color-space short-reads. Our extension introduces a double-seeding approach to improve mapping sensitivity, by combining maximal exact match seeds and…
Background: Computational analysis of next-generation sequencing data is outpaced by data generation in many cases. In one such case, paired-end reads can be produced from the Illumina sequencing method faster than they can be overlapped by…
We present a nonparametric Bayesian method for disease subtype discovery in multi-dimensional cancer data. Our method can simultaneously analyse a wide range of data types, allowing for both agreement and disagreement between their…
We show that a normalized alignment free similarity measure, called D2z, can be used to detect potential regulatory relations for gene sets when little is known about the regulatory elements involved. One scenario where such gene sets arise…
Background: The delineation of genomic copy number abnormalities (CNAs) from cancer samples has been instrumental for identification of tumor suppressor genes and oncogenes and proven useful for clinical marker detection. An increasing…
In this paper we introduce a novel parallel pipeline for fast and accurate mapping of RNA sequences on servers equipped with multicore processors. Our software, named HPG-Aligner, leverages the speed of the Burrows-Wheeler Transform to map…
It is widely held that a substantial genetic component underlies Bipolar Disorder (BD) and other neuropsychiatric disease traits. Recent efforts have been aimed at understanding the genetic basis of disease susceptibility, with genome-wide…
Breakage-Fusion-Bridge (BFB) is a mechanism of genomic instability characterized by the joining and subsequent tearing apart of sister chromatids. When this process is repeated during multiple rounds of cell division, it leads to patterns…