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Background: Nowadays, the reconstruction of genome scale metabolic models is a non-automatized and interactive process based on decision taking. This lengthy process usually requires a full year of one person's work in order to satisfactory…
The recent advances in sequencing technologies enables the assembly of individual genomes to the reference quality. How to integrate multiple genomes from the same species and to make the integrated representation accessible to biologists…
Single-particle cryo-electron microscopy (cryo-EM) has recently joined X-ray crystallography and NMR spectroscopy as a high-resolution structural method to resolve biological macromolecules. In a cryo-EM experiment, the microscope produces…
Rapid development of modern sequencing platforms enabled an unprecedented growth of protein families databases. The abundance of sets composed of hundreds of thousands sequences is a great challenge for multiple sequence alignment…
Digital information can be encoded in the building-block sequence of macro-molecules, such as RNA and single-stranded DNA. Methods of "writing" and "reading" macromolecular strands are currently available, but they are slow and expensive.…
Motivation: Next-generation sequencing tools have enabled producing of huge amount of genomic information at low cost. Unfortunately, presence of sequencing errors in such data affects quality of downstream analyzes. Accuracy of them can be…
Molecular electronics and other technologies whose components comprise individual molecules have been pursued for half a century because the molecular scale represents the limit of miniaturisation of objects whose structure is tuneable for…
DNA-coated particles are promising as building blocks for functional and finite-sized assemblies because they can be programmed with orthogonal interactions owing to the sequence-specific hybridization of DNA strands. To fully exploit this…
The cell cycle is one of the most fundamental biological processes important for understanding normal physiology and various pathologies such as cancer. Single cell RNA sequencing technologies give an opportunity to analyse the cell cycle…
We present a parallel algorithm and scalable implementation for genome analysis, specifically the problem of finding overlaps and alignments for data from "third generation" long read sequencers. While long sequences of DNA offer enormous…
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…
A critical problem in the emerging high-throughput genotyping protocols is to minimize the number of polymerase chain reaction (PCR) primers required to amplify the single nucleotide polymorphism loci of interest. In this paper we study PCR…
Single-cell technologies have revolutionized biomedical research by enabling scalable measurement of the genome, transcriptome, and proteome of multiple systems at single-cell resolution. Now widely applied to cancer models, these assays…
Analyses of targeted genomic sequencing data from next-generation-sequencing (NGS) technologies typically involves mapping reads to a reference sequence or clustering reads. For a number of species a reference genome is not available so the…
By using the Jensen-Shannon divergence, genomic DNA can be divided into compositionally distinct domains through a standard recursive segmentation procedure. Each domain, while significantly different from its neighbours, may however share…
This paper presents an accurate short-read mapper for next-generation sequencing data which is widely used in the 1000 Genomes Project, and human clinical and other species genome studies.
Single-cell technologies are revolutionizing the entire field of biology. The large volumes of data generated by single-cell technologies are high-dimensional, sparse, heterogeneous, and have complicated dependency structures, making…
High throughput sequencing (HTS)-based technology enables identifying and quantifying non-culturable microbial organisms in all environments. Microbial sequences have enhanced our understanding of the human microbiome, the soil and plant…
We study a minimal model for genome evolution whose elementary processes are single site mutation, duplication and deletion of sequence regions and insertion of random segments. These processes are found to generate long-range correlations…
Detection of extremely rare variant alleles, such as tumour DNA, within a complex mixture of DNA molecules is experimentally challenging due to sequencing errors. Barcoding of target DNA molecules in library construction for next-generation…