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At any time humans need accurate information to solve different problems. For example, how to perform a task, what happens in the news, what the hundreds of tweets say, etc. On the other hand, electronic information has ...

This thesis, entitled €High Performance Computing for solving large sparse systems. Optical Diffraction Tomography as a case of study€ investigates the computational issues related to the resolution of linear systems o...

Digital technologies have revolutionized studying, analyzing, and interpreting human culture, history, and society. Digital humanities (DH) combine traditional disciplines such as literature, history, and philosophy with...

MOTIVATION: Modern data acquisition based on high-throughput technology is often facing the problem of missing data. Algorithms commonly used in the analysis of such large-scale data often depend on a complete set. Missi...

SUMMARY: It is expected that emerging digital gene expression (DGE) technologies will overtake microarray technologies in the near future for many functional genomics applications. One of the fundamental data analysis ta...

MOTIVATION: Most existing methods for DNA sequence analysis rely on accurate sequences or genotypes. However, in applications of the next-generation sequencing (NGS), accurate genotypes may not be easily obtained (e.g. m...

MOTIVATION: In 2001 and 2002, we published two papers (Bioinformatics, 17, 282-283, Bioinformatics, 18, 77-82) describing an ultrafast protein sequence clustering program called cd-hit. This program can efficiently clust...

MOTIVATION: DnaSP is a software package for a comprehensive analysis of DNA polymorphism data. Version 5 implements a number of new features and analytical methods allowing extensive DNA polymorphism analyses on large da...

MOTIVATION: Next-generation sequencing technologies generate millions of short sequence reads, which are usually aligned to a reference genome. In many applications, the key information required for downstream analysis i...