%% BioMed_Central_Bib_Style_v1.01

\begin{thebibliography}{10}
\providecommand{\url}[1]{[#1]}
\providecommand{\urlprefix}{}

\bibitem{Miller:2003:BioTech}
Miller CJ, Kassem HS, Pepper SD, Hey Y, Ward TH, Margison GP:
  \textbf{Mycoplasma infection significantly alters microarray gene expression
  profiles}. \emph{BioTechniques} 2003, \textbf{35}(4):812--814,
  \urlprefix\url{[http://www.biotechniques.com/BiotechniquesJournal/2003/Octob%
er/]}.

\bibitem{Drexler:2002:Cytotechnology}
Drexler HG, Uphoff CC: \textbf{Mycoplasma contamination of cell cultures:
  Incidence, sources, effects, detection, elimination, prevention}.
  \emph{Cytotechnology} 2002, \textbf{39}(2):75--90,
  \urlprefix\url{[http://dx.doi.org/doi:10.1023/A:1022913015916]}.

\bibitem{barrett:2007:geo}
Barrett T, Troup DB, Wilhite SE, Ledoux P, Rudnev D, Evangelista C, Kim IF,
  Soboleva A, Tomashevsky M, Edgar R: \textbf{{NCBI GEO:} mining tens of
  millions of expression profiles--database and tools update}. \emph{Nucleic
  Acids Research} 2007, \textbf{35}(Database issue):D760--D765,
  \urlprefix\url{[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve\&%
db=pubmed\&dopt=Abstract\&list_uids=17099226]}.

\bibitem{Astarloa:2009:BT}
Aldecoa-Otalora E, Langdon WB, Cunningham P, Arno MJ: \textbf{Unexpected
  presence of mycoplasma probes on human microarrays}. \emph{BioTechniques}
  2009, \textbf{47}(6):1013--1016,
  \urlprefix\url{[http://dx.doi.org/doi:10.2144/000113271]}.

\bibitem{Langdon:2013:geccocomp}
Langdon WB: \textbf{Correlation of Microarray Probes give Evidence for
  Mycoplasma Contamination in Human Studies}. In \emph{GECCO-2013 Workshop:
  MedGEC Medical Applications of Genetic and Evolutionary Computation}. Edited
  by Smith SL, Cagnoni S, Patton RM, Amsterdam: ACM 2013:1447--1454,
  \urlprefix\url{[http://doi.acm.org/10.1145/2464576.2482725]}.

\bibitem{langdon:evobio12}
Langdon WB, Arno M: \textbf{{\em In Silico} Infection of the Human Genome}. In
  \emph{10th European Conference on Evolutionary Computation, Machine Learning
  and Data Mining in Bioinformatics, {EvoBIO 2012}}, \emph{Volume 7246 of
  \emph{LNCS}}. Edited by Giacobini M, Vanneschi L, Bush WS, Malaga, Spain:
  Springer Verlag 2012:245--249,
  \urlprefix\url{[http://dx.doi.org/doi:10.1007/978-3-642-29066-4_22]}.

\bibitem{nature09534}
{Durbin, {\em et al}} RM: \textbf{A map of human genome variation from
  population-scale sequencing}. \emph{Nature} 2010,
  \textbf{467}(7319):1061--1073,
  \urlprefix\url{[http://dx.doi.org/10.1038/nature09534]}.

\bibitem{Langmead:2009:GB}
Langmead B, Trapnell C, Pop M, Salzberg S: \textbf{Ultrafast and
  memory-efficient alignment of short {DNA} sequences to the human genome}.
  \emph{Genome Biology} 2009, \textbf{10}(3):R25,
  \urlprefix\url{[http://genomebiology.com/2009/10/3/R25]}.

\bibitem{10.1371/journal.pone.0017288}
Schmieder R, Edwards R: \textbf{Fast Identification and Removal of Sequence
  Contamination from Genomic and Metagenomic Datasets}. \emph{PLoS ONE} 2011,
  \textbf{6}(3),
  \urlprefix\url{[http://dx.doi.org/10.1371%2Fjournal.pone.0017288]}.

\bibitem{ncbi_blast}
Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ:
  \textbf{Gapped {BLAST} and {PSI-BLAST} a new generation of protein database
  search programs}. \emph{Nucleic Acids Research} 1997,
  \textbf{25}(17):3389--3402,
  \urlprefix\url{[http://nar.oxfordjournals.org/content/25/17/3389.abstract]}.

\bibitem{Am.J.Hum.Genet.vol.91-pp.839}
Jun G, Flickinger M, Hetrick KN, Romm JM, Doheny KF, Abecasis GR, Boehnke M,
  Kang HM: \textbf{Detecting and estimating contamination of human {DNA}
  samples in sequencing and array-based genotype data}. \emph{American Journal
  of Human Genetics} 2012, \textbf{91}(5):839--848,
  \urlprefix\url{[http://dx.doi.org/10.1016/j.ajhg.2012.09.004]}.

\bibitem{Cibulskis:2011:BI}
Cibulskis K, McKenna A, Fennell T, Banks E, DePristo M, Getz G:
  \textbf{ContEst: estimating cross-contamination of human samples in
  next-generation sequencing data}. \emph{Bioinformatics} 2011,
  \textbf{27}(18):2601--2602,
  \urlprefix\url{[http://bioinformatics.oxfordjournals.org/content/27/18/2601.%
abstract]}.

\bibitem{Pippard:1957:Thermodynamics}
Pippard AB: \emph{Elements of Classical Thermodynamics}. Cambridge University
  Press 1957,
  \urlprefix\url{[http://adsabs.harvard.edu/abs/1957ectf.book.....P]}.

\bibitem{Shannon.Weaver:64}
Shannon CE, Weaver W: \emph{The Mathematical Theory of Communication}. Urbana,
  Il, USA: The University of Illinois Press 1964,
  \urlprefix\url{[http://www.press.uillinois.edu/books/catalog/67qhn3ym9780252%
725463.html]}.

\end{thebibliography}

\newcommand{\BMCxmlcomment}[1]{}

\BMCxmlcomment{

<refgrp>

<bibl id="B1">
  <title><p>Mycoplasma infection significantly alters microarray gene
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  <aug>
    <au><snm>Miller</snm><fnm>CJ</fnm></au>
    <au><snm>Kassem</snm><fnm>HS</fnm></au>
    <au><snm>Pepper</snm><fnm>SD</fnm></au>
    <au><snm>Hey</snm><fnm>Y</fnm></au>
    <au><snm>Ward</snm><fnm>TH</fnm></au>
    <au><snm>Margison</snm><fnm>GP</fnm></au>
  </aug>
  <source>BioTechniques</source>
  <pubdate>2003</pubdate>
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  <issue>4</issue>
  <fpage>812</fpage>
  <lpage>-814</lpage>
  <url>http://www.biotechniques.com/BiotechniquesJournal/2003/October/</url>
</bibl>

<bibl id="B2">
  <title><p>Mycoplasma contamination of cell cultures: Incidence, sources,
  effects, detection, elimination, prevention</p></title>
  <aug>
    <au><snm>Drexler</snm><fnm>HG</fnm></au>
    <au><snm>Uphoff</snm><fnm>CC</fnm></au>
  </aug>
  <source>Cytotechnology</source>
  <publisher>Springer Netherlands</publisher>
  <pubdate>2002</pubdate>
  <volume>39</volume>
  <issue>2</issue>
  <fpage>75</fpage>
  <lpage>-90</lpage>
  <url>http://dx.doi.org/doi:10.1023/A:1022913015916</url>
</bibl>

<bibl id="B3">
  <title><p>{NCBI GEO:} mining tens of millions of expression
  profiles--database and tools update</p></title>
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    <au><snm>Troup</snm><fnm>DB</fnm></au>
    <au><snm>Wilhite</snm><fnm>SE</fnm></au>
    <au><snm>Ledoux</snm><fnm>P</fnm></au>
    <au><snm>Rudnev</snm><fnm>D</fnm></au>
    <au><snm>Evangelista</snm><fnm>C</fnm></au>
    <au><snm>Kim</snm><fnm>IF</fnm></au>
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    <au><snm>Tomashevsky</snm><fnm>M</fnm></au>
    <au><snm>Edgar</snm><fnm>R</fnm></au>
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  <source>Nucleic Acids Research</source>
  <publisher>National Center for Biotechnology Information, National Library of
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  USA.</publisher>
  <pubdate>2007</pubdate>
  <volume>35</volume>
  <issue>Database issue</issue>
  <fpage>D760</fpage>
  <lpage>-D765</lpage>
  <url>http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve\&db=pubmed\&%
dopt=Abstract\&list_uids=17099226</url>
</bibl>

<bibl id="B4">
  <title><p>Unexpected presence of mycoplasma probes on human
  microarrays</p></title>
  <aug>
    <au><snm>Aldecoa Otalora</snm><fnm>E</fnm></au>
    <au><snm>Langdon</snm><fnm>WB</fnm></au>
    <au><snm>Cunningham</snm><fnm>P</fnm></au>
    <au><snm>Arno</snm><fnm>MJ</fnm></au>
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  <source>BioTechniques</source>
  <pubdate>2009</pubdate>
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</bibl>

<bibl id="B5">
  <title><p>Correlation of Microarray Probes give Evidence for Mycoplasma
  Contamination in Human Studies</p></title>
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    <au><snm>Langdon</snm><fnm>W. B.</fnm></au>
  </aug>
  <source>GECCO-2013 Workshop: MedGEC Medical Applications of Genetic and
  Evolutionary Computation</source>
  <publisher>Amsterdam: ACM</publisher>
  <editor>Stephen L. Smith and Stefano Cagnoni and Robert M. Patton</editor>
  <pubdate>2013</pubdate>
  <fpage>1447</fpage>
  <lpage>-1454</lpage>
  <url>http://doi.acm.org/10.1145/2464576.2482725</url>
</bibl>

<bibl id="B6">
  <title><p>{\em In Silico} Infection of the Human Genome</p></title>
  <aug>
    <au><snm>Langdon</snm><fnm>W. B.</fnm></au>
    <au><snm>Arno</snm><fnm>M.J.</fnm></au>
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  <source>10th European Conference on Evolutionary Computation, Machine
  Learning and Data Mining in Bioinformatics, {EvoBIO 2012}</source>
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  <editor>Mario Giacobini and Leonardo Vanneschi and William S. Bush</editor>
  <series><title><p>LNCS</p></title></series>
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</bibl>

<bibl id="B7">
  <title><p>A map of human genome variation from population-scale
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<bibl id="B8">
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<bibl id="B9">
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<bibl id="B11">
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<bibl id="B12">
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<bibl id="B13">
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<bibl id="B14">
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</refgrp>
} % end of \BMCxmlcomment
