A comprehensive account of both basic and advanced material in phylogeny estimation,
focusing on computational and statistical issues. No background in biology or computer …

Data storage optimizations (DS, eg low latency for data access) in data center networks
(DCN) are difficult online-making problems. Previously, they are done with heuristics under …

This book develops a new approach called parameter advising for finding a parameter
setting for a sequence aligner that yields a quality alignment of a given set of input …

A common way to integrate and analyze large amounts of biological “omic” data is through
pathway reconstruction: using condition-specific omic data to create a subnetwork of a …

Computational tools used for genomic analyses are becoming more accurate but also
increasingly sophisticated and complex. This introduces a new problem in that these pieces …

Background While the multiple sequence alignment output by an aligner strongly depends
on the parameter values used for its alignment scoring function (ie choice of gap penalties …

The multiple sequence alignments computed by an aligner for different settings of its
parameters, as well as the alignments computed by different aligners using their default …

Transcript assemblers are tools to reconstruct expressed transcripts from RNA-seq data.
These tools have a large number of tunable parameters, and accurate transcript assembly …

Multiple sequence alignment is a fundamental problem in bioinformatics, which is why a
large number of tools are used to align sequences under a prescribed (biologically inspired) …

Bioinformatics is a growing field that attracts many researchers and continues to prove its
value and significance. Since the early days of discovering genomic martial and using it to …