We describe a strategy for de novo peptide sequencing based on matched pairs of tandem mass spectra (MS/MS) obtained by collision induced dissociation (CID) and 351 nm ultraviolet photodissociation (UVPD). Each precursor ion is isolated twice with the mass spectrometer switching between CID and UVPD activation modes to obtain a complementary MS/MS pair. To interpret these paired spectra, we mod...

A major limitation of high-throughput DNA sequencing is the high rate of erroneous base calls produced. For instance, Illumina sequencing machines produce errors at a rate of ~0.1-1 × 10(-2) per base sequenced. These technologies typically produce billions of base calls per experiment, translating to millions of errors. We have developed a unique library preparation strategy, "circle sequencing...

We address the classical uniformly related machine scheduling problem with minsum objective. The problem is solvable in polynomial time by the algorithm of Horowitz and Sahni. In that solution, each machine sequences its jobs shortest first. However when jobs may choose the machine on which they are processed, while keeping the same sequencing rule per machine, the resulting Nash equilibria are...

As Internet access spreads to all nations of the globe, it is becoming increasingly important to be able to access information in a language other than that in which it was written. A survey of the free machine translation (MT) systems available on the Internet yields unsatisfying results; MT systems simply have not been able to improve fast enough to satisfy the demand for reliable, accurate t...

Computational learning especially, deep and machine have a huge impact. This current research topic gathered two fundamental concepts, approaches applied to array-based biomedical data such as next generation sequencing (NGS) medical imaging data.

selecting an appropriate manufacturing machine is a very important and complex problem for firms, which usually have to deal with both qualitative and quantitative criteria. taking into account the differences among machines in terms of cost, speed, quality and after sale services, type and number of machines are important parameters to consider. therefore, the goal of this paper is to propose ...

A major limitation of high-throughput DNA sequencing is the high rate of erroneous base calls produced. For instance, Illumina sequencing machines produce errors at a rate of ∼0.1–1 × 10 per base sequenced. These technologies typically produce billions of base calls per experiment, translating to millions of errors. We have developed a unique library preparation strategy, “circle sequencing,” w...

Testing complex manufacturing systems, such as an ASML [ASML, 2006] lithographic machine, takes up to 45% of the total development time of a system. The problem of which tests must be executed in what sequence to ensure in the shortest possible test time that the system works, the test sequencing problem, was already solved by Pattipati [Pattipati et al., 1991; Pattipati and Alexandridis, 1990]...

The diversity of microbial species in a metagenomic study is commonly assessed using 16S rRNA gene sequencing. With the rapid developments in genome sequencing technologies, the focus has shifted towards the sequencing of hypervariable regions of 16S rRNA gene instead of full length gene sequencing. Therefore, 16S Classifier is developed using a machine learning method, Random Forest, for faste...

Large scale DNA sequencing projects require gel readers with high throughput and good base-calling accuracy with as little manual intervention as possible. The automatic sequencing machines now available meet these requirements quite well, indeed, a single ABI 373A machine can read at least around 500 samples/200 000 nt per week. Thus, a full-time sequencing laboratory will need to produce thou...