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I am using a bioinformatics template with a user defined bioinfo.cls file.

This is the section where the "Reference" environment is defined.

% ***********
% References *
% ***********

\providecommand{\newblock}{}
\newenvironment{thebibliography}{%
  \section{\bibname}%
  \begingroup
  \small
  \begin{list}{}{%
      \setlength{\topsep}{\z@}%
      \setlength{\labelsep}{\z@}%
      \settowidth{\labelwidth}{\z@}%
      \setlength{\leftmargin}{4mm}%
      \setlength{\itemindent}{-4mm}}\small}
{\end{list}\endgroup}

\RequirePackage{natbib}
\RequirePackage{cite}

And this is how they were initially adding the references.

\begin{thebibliography}{}
        \bibitem[Bofelli {\it et~al}., 2000]{Boffelli03} Bofelli,F., Name2, Name3 (2003) Article title, {\it Journal Name}, {\bf 199}, 133-154.
        \bibitem[Bag {\it et~al}., 2001]{Bag01} Bag,M., Name2, Name3 (2001) Article title, {\it Journal Name}, {\bf 99}, 33-54.
        \bibitem[Yoo \textit{et~al}., 2003]{Yoo03}
        Yoo,M.S. \textit{et~al}. (2003) Oxidative stress regulated genes
        in nigral dopaminergic neurnol cell: correlation with the known
        pathology in Parkinson's disease. \textit{Brain Res. Mol. Brain
            Res.}, \textbf{110}(Suppl. 1), 76--84.
        \bibitem[Lehmann, 1986]{Leh86}
        Lehmann,E.L. (1986) Chapter title. \textit{Book Title}. Vol.~1, 2nd edn. Springer-Verlag, New York.
        \bibitem[Crenshaw and Jones, 2003]{Cre03}
        Crenshaw, B.,III, and Jones, W.B.,Jr (2003) The future of clinical
        cancer management: one tumor, one chip. \textit{Bioinformatics},
        doi:10.1093/bioinformatics/btn000.
        \bibitem[Auhtor \textit{et~al}. (2000)]{Aut00}
        Auhtor,A.B. \textit{et~al}. (2000) Chapter title. In Smith, A.C.
        (ed.), \textit{Book Title}, 2nd edn. Publisher, Location, Vol. 1, pp.
        ???--???.
        \bibitem[Bardet, 1920]{Bar20}
        Bardet, G. (1920) Sur un syndrome d'obesite infantile avec
        polydactylie et retinite pigmentaire (contribution a l'etude des
        formes cliniques de l'obesite hypophysaire). PhD Thesis, name of
        institution, Paris, France.
    \end{thebibliography}

I want to use BibTex instead by using the .bib files. I tried adding it in the file but the references don't show up.

closed as unclear what you're asking by Mensch, user13907, egreg, Zarko, Paul Gessler Sep 28 '16 at 0:58

Please clarify your specific problem or add additional details to highlight exactly what you need. As it's currently written, it’s hard to tell exactly what you're asking. See the How to Ask page for help clarifying this question. If this question can be reworded to fit the rules in the help center, please edit the question.

  • The initially added refferences, are they in the tex file? – HATEthePLOT Feb 23 '16 at 9:19
  • No i commented them. – Alchemist Feb 23 '16 at 9:23
  • Can you provide the template and a MWE, so we can experiment with it? – HATEthePLOT Feb 23 '16 at 9:25
  • You have been asked yesterday already for the class file. You should not change it. – Johannes_B Feb 23 '16 at 9:42
  • I want to use BibTex instead by using the .bib files. This sentence contradicts itself. If you want to use BibTeX, you gotta use a database. Have you checked with the journal editors if you are allowed to use BibTeX? – Johannes_B Feb 23 '16 at 9:43