At the heart of genomics lies the precise determination of an organism's DNA sequence.
Palacios-Flores et al. present a simple, sensitive, precise, and essentially non-statistical …

When addressing a genomic question, having a reliable and adequate reference genome is
of utmost importance. This drives the necessity to refine and customize reference genomes …

This thesis concerns itself with the development of methods for comparing genomes.
Chapter 2 is a comparative genomics investigation of coding regions across multiple …

High-throughput sequencing is enabling remarkably deep surveys of genomic variation. It is
now possible to completely sequence multiple individuals from a single species, yet the …

Over the past twenty-five years, we have gone from completing the first eukaryotic genome
assembly to the new goal of sequencing and completing genome assemblies representing …

INTRODUCTION Modern genomics depends on inexpensive short-read sequencing.
Sequenced reads up to a few hundred base pairs in length are computationally mapped to …

Completely sequencing genomes is expensive, and to save costs we often analyze new
genomic data in the context of a reference genome. This approach distorts our image of the …

Recent advances in sequencing technology make it possible to comprehensively catalog
genetic variation in population samples, creating a foundation for understanding human …

Comparative genomics, using the model organism approach, has provided powerful insights
into the structure and evolution of whole genomes. Unfortunately, only a small fraction of …

As the number of available genome sequences from both closely related species and
individuals within species increased, theoretical and methodological convergences between …