-Object oriented software systems are subject to frequent modifications either during development (iterative, agile software development) or software evolution. For such systems which have large number of classes, detection of design defects is a complex task. Bad smells are used to identify design defects in object oriented software design. Identification of bad smells allows us to apply appro...

Simulated data sets have been found to be useful in developing software systems because (1) they allow one to study the effect of a particular phenomenon in isolation, and (2) one has complete information about the true solution against which to measure the results of the software. In developing a software suite for assembling a whole human genome shotgun data set, we have developed a simulator...

Tracking output is a very attractive source of labeled data sets that, in turn, could be used to train other systems for tracking, detection, recognition and categorization. In this context, long tracking sequences are of particular importance because they provide richer information, multiple views, wider range of appearances. This paper addresses two obstacles to the use of tracking data for t...

This paper studies sequencing and mapping methods that rely solely on pooling and shotgun sequencing of clones. First, we scrutinize and improve the recently proposed Clone-Array Pooled Shotgun Sequencing (CAPSS) method, which delivers a BAC-linked assembly of a whole genome sequence. Secondly, we introduce a novel physical mapping method, called Clone-Array Pooled Shotgun Mapping (CAPS-MAP), w...

Although the transcriptome, proteome, and interactome of several eukaryotic model organisms have been described in detail, lipidomes remain relatively uncharacterized. Using Saccharomyces cerevisiae as an example, we demonstrate that automated shotgun lipidomics analysis enabled lipidome-wide absolute quantification of individual molecular lipid species by streamlined processing of a single sam...

In order to quantitatively comprehend the essence of whole genome shotgun sequencing, a Monte-Carlo simulation was carried out. It was estimated that even a vast genome such as human genome can be sequenced at a moderate redundancy ( 7) with a satisfactory accuracy (10 error rate), resulting in a high sequencing speed and much lower cost. Switching from a random process (i.e., shotgun) to a dir...

Shotgun metagenomic sequencing does not depend on gene-targeted primers or PCR amplification; thus, it is not affected by primer bias or chimeras. However, searching rRNA genes from large shotgun Illumina data sets is computationally expensive, and no approach exists for unsupervised community analysis of small-subunit (SSU) rRNA gene fragments retrieved from shotgun data. We present a pipeline...

Post-translational modifications of proteins play an important role in the regulation cellular processes. The mass spectrometry analysis proteome offers huge potential for study how protein inhibitors affect phosphosignaling mechanisms inside cells. We have recently proposed PHONEMeS, a method that uses high-content shotgun phosphoproteomic data to build logical network models signal perturbati...