Genomics
Predicting the response of a specific cancer to a therapy is a major goal in modern oncology that should ultimately lead to a personalised treatment. High-throughput screenings of potentially active compounds against a panel of genomically…
Enterococcus faecalis is the third cause of nosocomial infections. To obtain the first comprehensive view of transcriptional organizations in this bacterium, we used a modified RNA-seq approach enabling to discriminate primary from…
The high throughput and cost-effectiveness afforded by short-read sequencing technologies, in principle, enable researchers to perform 16S rRNA profiling of complex microbial communities at unprecedented depth and resolution. Existing…
High-throughput pooled resequencing offers significant potential for whole genome population sequencing. However, its main drawback is the loss of haplotype information. In order to regain some of this information, we present LDx, 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…
For many traits, including susceptibility to common diseases in humans, causal loci uncovered by genetic mapping studies explain only a minority of the heritable contribution to trait variation. Multiple explanations for this "missing…
Long noncoding RNAs (lncRNAs) are a recently discovered class of non-protein coding RNAs which have now increasingly been shown to be involved in a wide variety of biological processes as regulatory molecules. Little is known regarding the…
Deep sequencing has enabled the investigation of a wide range of environmental microbial ecosystems, but the high memory requirements for {\em de novo} assembly of short-read shotgun sequencing data from these complex populations are an…
Global transposable characteristics in the complete DNA sequence of the Saccharomyces cevevisiae yeast is determined by using the metric representation and recurrence plot methods. In the form of the correlation distance of nucleotide…
It is shown how to take advantage of the frequent occurrence of double-strand breaks in the genome of prokaryotic cells, in order to reduce their high efficient reproductive capability. The analysis examines the physical status of the free…
Large-scale dynamical properties of complete chromosome DNA sequences of eukaryotes are considered. By the proposed deterministic models with intermittency and symbolic dynamics we describe a wide spectrum of large-scale patterns inherent…
A major challenge in next-generation genome sequencing (NGS) is to assemble massive overlapping short reads that are randomly sampled from DNA fragments. To complete assembling, one needs to finish a fundamental task in many leading…
The Set Covering Machine (SCM) is a greedy learning algorithm that produces sparse classifiers. We extend the SCM for datasets that contain a huge number of features. The whole genetic material of living organisms is an example of such a…
Module network inference is an established statistical method to reconstruct co-expression modules and their upstream regulatory programs from integrated multi-omics datasets measuring the activity levels of various cellular components…
Gene regulatory network inference uses genome-wide transcriptome measurements in response to genetic, environmental or dynamic perturbations to predict causal regulatory influences between genes. We hypothesized that evolution also acts as…
We develop a cross-platform open-source Java application (BACOM2) with graphic user interface (GUI), and users also can use a XML file to set the parameters of algorithm model, file paths and the dataset of paired samples. BACOM2 implements…
Existing sequence alignment algorithms use heuristic scoring schemes which cannot be used as objective distance metrics. Therefore one relies on measures like the p- or log-det distances, or makes explicit, and often simplistic, assumptions…
The prevalence of common chronic non-communicable diseases (CNCDs) far overshadows the prevalence of both monogenic and infectious diseases combined. All CNCDs, also called complex genetic diseases, have a heritable genetic component that…
An active microbiota, reaching up to 10 E+7 cells/g, was found to inhabit a naturally occurring asphalt lake characterized by low water activity and elevated temperature. Geochemical and molecular taxonomic approaches revealed novel and…
We use nucleosome maps obtained by high-throughput sequencing to study sequence specificity of intrinsic histone-DNA interactions. In contrast with previous approaches, we employ an analogy between a classical one-dimensional fluid of…