Representing a set of reconciliations in a compact way

International audienceComparative genomic studies are often conducted by reconciliation analyses comparing gene and species trees. One of the issues with reconciliation approaches is that an exponential number of optimal scenarios is possible. The resulting complexity is masked by the fact that a majority of reconciliation software pick up a random optimal solution that is returned to the end-user. However, the alternative solutions should not be ignored since they tell different stories that parsimony considers as viable as the output solution. In this paper, we describe a polynomial space and time algorithm to build a minimum reconciliation graph -- a graph that summarizes the set of all most parsimonious reconciliations. Amongst numerous applications, it is shown how this graph allows counting the number of non-equivalent most parsimonious reconciliations

The development of new methodology for determination of vincristine (VCR) in human serum using LC-MS/MS-based method for medical diagnostics

In this article, we have presented the development and validation of a rapid and sensitive reversed-phase liquid chromatography with tandem mass spectrometry (LC-MS/MS) method for the determination of vincristine (VCR) in patient serum samples. Chromatographic separation was achieved on a Kinetex(®) (Singapore) column using a mobile phase consisting of 25 mM acetic acid and 0.3% formic acid (A) and methanol (B) in a gradient elution mode at a flow rate of 0.3 mL/min. The VCR and internal standard (vinblastine) were monitored using the multiple reaction monitoring mode under positive electrospray ionization. The lower limit of quantification (LLOQ) was 0.67 ng/mL, and the upper limit of quantification (ULOQ) was 250 ng/mL for VCR. The calculated values of LOD and LOQ for VCR were 0.075 and 0.228 ng/mL, respectively. The calibration curve was linear over the VCR concentration range of 1.0–250 ng/mL in serum. The intra- and inter-day precision and precision were within the generally accepted criteria for the bioanalytical method (<15%). The method was successfully applied to the analysis of serum samples in clinical practice

Representing a set of reconciliations in a compact way.

Comparative genomic studies are often conducted by reconciliation analyses comparing gene and species trees. One of the issues with reconciliation approaches is that an exponential number of optimal scenarios is possible. The resulting complexity is masked by the fact that a majority of reconciliation software pick up a random optimal solution that is returned to the end-user. However, the alternative solutions should not be ignored since they tell different stories that parsimony considers as viable as the output solution. In this paper, we describe a polynomial space and time algorithm to build a minimum reconciliation graph - a graph that summarizes the set of all most parsimonious reconciliations. Amongst numerous applications, it is shown how this graph allows counting the number of non-equivalent most parsimonious reconciliations