Linear-time computation of minimal absent words using suffix array.

Background: An absent word of a word y of length n is a word that does not occur in y. It is a minimal absent word if all its proper factors occur in y. Minimal absent words have been computed in genomes of organisms from all domains of life; their computation also provides a fast alternative for measuring approximation in sequence comparison.

Querying highly similar sequences.

In this paper, we present a solution to the extreme similarity sequencing problem. The extreme similarity sequencing problem consists of finding occurrences of a pattern p in a set S(0), S(1), …, S(k), of sequences of equal length, where S(i), for all 1≤i≤k, differs from S(0) by a constant number of errors - around 10 in practice. We present an asymptotically fast O(n + occ logocc) time algorithm, as well as a practical O(nk/w) time algorithm for solving this problem, where n is the length of a sequence, occ is the number of candidate occurrences reported by our technique, w is the size of the machine word, and the total number of errors is bounded by k - the number of sequences.

Segmentation of biological target volumes on multi-tracer PET images based on information fusion for achieving dose painting in radiotherapy.

Medical imaging plays an important role in radiotherapy. Dose painting consists in the application of a nonuniform dose prescription on a tumoral region, and is based on an efficient segmentation of biological target volumes (BTV). It is derived from PET images, that highlight tumoral regions of enhanced glucose metabolism (FDG), cell proliferation (FLT) and hypoxia (FMiso).

A fast and efficient algorithm for mapping short sequences to a reference genome.

Novel high-throughput (Deep) sequencing technology methods have redefined the way genome sequencing is performed. They are able to produce tens of millions of short sequences (reads) in a single experiment and with a much lower cost than previous sequencing methods. In this paper, we present a new algorithm for addressing the problem of efficiently mapping millions of short reads to a reference genome.

Algorithms for mapping short degenerate and weighted sequences to a reference genome.

Novel high-throughput (Deep) sequencing technologies have redefined the way genome sequencing is performed. They are able to produce millions of short sequences in a single experiment and with a much lower cost than previous methods. In this paper, we address the problem of efficiently mapping and classifying millions of short sequences to a reference genome, based on whether they occur exactly once in the genome or not, and by taking into consideration probability scores.

Analysis of virtual two-dimensional gels based upon affinity capillary electrophoresis hyphenated to ion trap-mass spectrometry.

Affinity capillary electrophoresis (ACE) is a robust tool for the study of noncovalent biomolecular interactions and to determine the binding constants. It is advantageous due to the speed of analysis, the high and reproducible separation efficiencies, the low consumption of analytes, the ability to study several interactions at the same time, and to cover a wide range of affinity. The use of an ion trap-mass spectrometer as a sensitive and specific detector, coupled on-line with a classical UV detector, permits extracting simultaneously the electropherograms corresponding to each ionic species.

Whole-genome shotgun assembly and comparison of human genome assemblies.

We report a whole-genome shotgun assembly (called WGSA) of the human genome generated at Celera in 2001. The Celera-generated shotgun data set consisted of 27 million sequencing reads organized in pairs by virtue of end-sequencing 2-kbp, 10-kbp, and 50-kbp inserts from shotgun clone libraries. The quality-trimmed reads covered the genome 5.