I decided to use Latex to write my thesis. Luckily, Rickard E. Faith had gone through the trouble to design a LaTeX style compatible with the requirements of the UNC Graduate School. Unfortunately, the guidlines had changed, so i modified the style to fit the newer guidlines and my own preferences better. Download the newer style here.
Commenting of the style file is sparse, so i included a code example (abbreviated version of the root document of my thesis) below. And if you want to see the end-product, you can download the beginning 30 pages of my thesis here. Information and tools for the use of EndNote libraries in LateX documents can be found on Noah Hoffman's page. Alternatively, i have written some simple python scripts that can be used to fetch records from ncbi pubmed in xml format and then convert these to bibtex format. BibDesk, a Mac OS X application written by Mike McCracken et al., can then be used to administer the bibtex database and insert citations into latex documents through copy/paste or through the services menu.
\documentclass[12pt, double, citemod, twoside]{report}
%OPTIONSHERE: double (double spaced),
% single (single spaced),
% citemod (use parantheses instead of brackes in text for citations),
% draft,
% nofront (leave out front matter),
% nolists
\newif\ifpdf
\ifx\pdfoutput\undefined
\pdffalse % we are not running PDFLaTeX
\else
\pdfoutput=1 % we are running PDFLaTeX
\pdfcompresslevel=0 %this determines the level of compression of the final pdf file
\pdftrue
\fi
\ifpdf
\usepackage[pdftex]{graphicx}
\else
\usepackage{graphicx}
\fi
\usepackage{uncthesis, amssymb, xspace}
\usepackage{amssymb, times, mathptm, longtable}
%%%--------------------------------------COMMANDS/ENV
\newcommand{\ug}{\ensuremath{\mu}g\xspace}
\newcommand{\ul}{\ensuremath{\mu}l\xspace}
\newcommand{\cg}{\ensuremath{^\circ}C\xspace}
\newcommand{\uM}{\ensuremath{\mu}M\xspace}
%%%modify float behaviour to allow large floats to be placed more easily
\renewcommand{\floatpagefraction}{0.3}
\renewcommand{\topfraction}{1}
\renewcommand{\textfraction}{0}
%%%modify widow/orphan behaviour (avoid orphans !!)
\widowpenalty=10000
\clubpenalty=10000
\raggedbottom
%%%--------------------------------------COMMANDS/ENV
\thesistype{dissertation}
\thesisuniversity{University of North Carolina at Chapel Hill}
\thesisdegree{Doctor of Philosophy}
\thesisdepartment{Department of Biochemistry and Biophysics}
\thesistitle{Evolution of human immunodeficiency virus type 1 genotype
and phenotype in response to strong selective pressure from protease
inhibitors}
\thesisauthor{Wolfgang Resch}
\thesisadvisor{Dr. One}
\thesisreadera{Dr. Two}
\thesisreaderb{Dr. Three}
\thesisreaderc{Dr. Four}
\thesisreaderd{Dr. Five}
%ABBEREVIATIONS---------------------------------------------BEG
\abbrev{\env}{\textit{env}\xspace}{HIV-1 envelope gene}
\abbrev{\Env}{Env\xspace}{HIV-1 envelope protein}
%ABBEREVIATIONS---------------------------------------------END
\begin{document}
%FRONT MATTER---------------------------------------------------
\thesismaketitle
%for a copyright page uncomment the following line
%\thesismakecopyright
\begin{abstract}
\input{frontmatter/020128_abstract}
\end{abstract}
\begin{dedication}
\input{frontmatter/dedication}
\end{dedication}
\begin{acknowledgments}
\input{frontmatter/acknowledgments}
\end{acknowledgments}
\unctoc %table of contents
\unclof %list of figures
\unclot %list of tables
\uncloa %list of abbreviations
%BODY OF THESIS------------------------------------------------
\chapter{Introduction}
Human immunodeficiency virus type 1 (\hiv) is a member of the
lentivirus genus of the \emph{retroviridae} family of viruses.
\emph{Retroviridae} are positive-stranded RNA viruses with a linear,
non-segmented genome 7-12kb in length. Replication occurs through a
characteristic double-stranded DNA intermediate integrated into the
host genome. Lentiviruses, such as \hiv, simian immunodeficiency virus,
and equine infectious anemia virus, have been shown to replicate to
high levels and display a great degree of sequence diversity
\cite{20007473112-3121,19871612321-331,1993259359-362,1995692955-967,
199325951021749-1754}.
%%and much more
\begin{spacing}{1}
\bibliographystyle{unsrt}
\bibliography{020113_allRef}
\end{spacing}
\end{document}