.......................................................................................................................................... v Introduction ..................................................................................................................................... 1 Objectives ...................................................................................................

We consider a fully model-based approach for the analysis of distance sampling data. Distance sampling has been widely used to estimate abundance (or density) of animals or plants in a spatially explicit study area. There is, however, no readily available method of making statistical inference on the relationships between abundance and environmental covariates. Spatial Poisson process likelihoo...

Fast and accurate quantification and differential analysis of transcriptomes by Harold Joseph Pimentel Doctor of Philosophy in Computer science University of California, Berkeley Professor Lior Pachter, Chair As access to DNA sequencing has become ubiquitous to scientists, the use of sequencers has expanded from determining the genomes of individuals to performing molecular probing assays. Thes...

Motivation Current metagenomics approaches allow analyzing the composition of microbial communities at high resolution. Important changes to the composition are known to even occur on strain level and to go hand in hand with changes in disease or ecological state. However, specific challenges arise for strain level analysis due to highly similar genome sequences present. Only a limited number o...

To know the abundance of fishes and their size distribution in semi-intensive rearing systems traditional ponds is an aspect key to plan manage efficiently sales lots. Usually this information obtained by means sampling which mandatory supposes a direct catch stressful time consuming management fishes. Therefore, work we propose use non-invasive procedures based on multibeam sonars or imaging c...

We analyzed 1950s survey data with generalized estimating equations (GEEs) to quantify factors that influence the rate that bait is lost from pelagic longlines. Hook depth, bait species, local tuna abundance, and the timing of longline operations strongly influenced loss rates. Loss rates increased with tuna abundance and soak time. They declined with hook depth and were low for firm-bodied bai...