For citations, I would recommend natbib for its flexibility, particularly when named citation styles are used, but it also has useful features for plain and those of that ilk.
\documentclass[phd]{gbuthesis}
%% For citations, I would recommend natbib for its
%% flexibility, particularly when named citation styles are used, but
%% it also has useful features for plain and those of that ilk.
%% The natbib package gives you the following definitons
%% that extend the simple \cite:
% \citet{key} ==>> Jones et al. (1990)
% \citet*{key} ==>> Jones, Baker, and Smith (1990)
% \citep{key} ==>> (Jones et al., 1990)
% \citep*{key} ==>> (Jones, Baker, and Smith, 1990)
% \citep[chap. 2]{key} ==>> (Jones et al., 1990, chap. 2)
% \citep[e.g.][]{key} ==>> (e.g. Jones et al., 1990)
% \citep[e.g.][p. 32]{key} ==>> (e.g. Jones et al., p. 32)
% \citeauthor{key} ==>> Jones et al.
% \citeauthor*{key} ==>> Jones, Baker, and Smith
% \citeyear{key} ==>> 1990
\usepackage{natbib}
%\setlength{\bibsep}{0pt}
%\bibliographystyle{apalike}
\usepackage{graphicx}
\usepackage{graphics}
\usepackage[english]{babel}
\usepackage{float,epsfig, floatflt,here}
\usepackage{amsmath,amssymb,amsthm,mathtools}
%\usepackage{fancyhdr}
\usepackage{makeidx}
\usepackage{hyperref}
\usepackage{moreverb}
\usepackage{tabularx}
\usepackage{tabulary}
\makeindex
\title{My Project Report}
\author{Amit K Awasthi}
\rollno{00/GBU/001}
\department{Departemtn of Applied Mathematics}
\school{School of Vocational Studies and Applied Sciences}
\supervisor{Amit K Awasthi}
\supervisoraffil{Assiatnat Professor, GBU}
%\def\cosupervisors{No one More}
%\def\cosupervisorsaffil{Assiatnat Professor, GBU}
\date{DEC, 2017}
\begin{document}
\pagenumbering{roman}
%%%% Create the title page and standard declaration.
\maketitle
\declaration
\certificateofsupervisor
\input{Chapters/abstract}
\input{Chapters/acknowledgement}
\tableofcontents
\listoftables
\listoffigures
\pagenumbering{arabic}
\include{Chapters/Chapter1}
First ref \cite{re:bunch:rankone} and \cite{re:toolan:as03}. I called only two.
\begin{appendix}
\include{Appendices/AppendixA}
\end{appendix}
\bibliographystyle{plain}
\bibliography{Bibliography/refrences}
\end{document}