--- /dev/null
+
+\paragraph{prokaryote}
+In~\cite{SMMR+13}, the authors compare some smooth tubercle baciles isolates
+with M. tuberculosis regarding
+branching, core genome,
+genome sizes, and
+number of scars.
+To achieve this, the authors
+\begin{enumerate}
+\item compare the hamming distance and the bootstrap probability between 12 gene segments;
+\item compute pairwise comparisons of some selected SNPs data;
+\item use NeighborNet analysis, based on pairwise alignments of some selected
+ SNPs data.
+\end{enumerate}
+
+In~\cite{10.1371/journal.pone.0052841} the authors analyse 435 Mycobacterium Tuberculosis complex isolates of the same clade. By focusing on the H37Rv genome,
+they produce 13382 SNPs. Later, they compare 44 genomes to this one
+regarding these SNP. The way they extract this phylogenetical tree is
+not detailed. They focus then on Percy256 and Percy556 since both these
+genomes have a very long branch split from the M. Canetti. They deduce then
+a new lineage.
+
+
+
+\paragraph{eukaryote}
+In~\cite{CGOT10}, the authors show how to reconstruct an ancestral genome of seven eukaryotes species (Saccharomyces cerevisiae, Candida glabrata, Zygosaccharomyces rouxii, Kluyveromyces lactis, Ashbya gossypii, Kluyveromyces thermotolerans, Saccharomyces kluyveri).
+Their method is as follows:
+\begin{enumerate}
+\item the starting point is a set of markers covering a large
+ part of the extant genomes and which are believed to
+ be present in a unique exemplar in the ancestral genome.
+\item first method: rearrangement methods and particularely median method. Authors even provide informations about medians in case of duplicated genomes or not.
+\item second method: physical mapping techniques by trying to guess
+ which genes should be close to each other,
+ and propose a mapping that maximize an objective function.
+\end{enumerate}
--- /dev/null
+@article{SMMR+13,
+title={Genomic analysis of smooth tubercle bacilli provides insights into ancestry and pathoadaptation of Mycobacterium tuberculosis},
+url={http://www.nature.com/ng/journal/v45/n2/full/ng.2517.html},
+DOI={10.1038/ng.2517},
+volume={45},
+number={2},
+journal={Nature Genetics},
+author={Philip Supply and Michael Marceau and Sophie Mangenot and David Roche and Carine Rouanet and Varun Khanna and Laleh Majlessi and Alexis Criscuolo and Julien Tap and Alexandre Pawlik},
+year={2013},
+ pages={172–179}}
+
+@article{CGOT10,
+title={Yeast Ancestral Genome Reconstructions: The Possibilities of Computational Methods II},
+author={Cedric Chauve and Haris Gavranovic and Aida Ouangraoua and Eric Tannier},
+journal={Journal of Computational Biology},
+month=sep,
+year={2010},
+volume=17,
+number=9,
+pages={1097--1112},
+DOI={10.1089/cmb.2010.0092}
+}
+
+@incollection{,
+year={2009},
+isbn={978-3-642-04743-5},
+booktitle={Comparative Genomics},
+volume={5817},
+series={Lecture Notes in Computer Science},
+editor={Ciccarelli, FrancescaD. and Miklós, István},
+doi={10.1007/978-3-642-04744-2_1},
+title={Yeast Ancestral Genome Reconstructions: The Possibilities of Computational Methods},
+url={http://dx.doi.org/10.1007/978-3-642-04744-2_1},
+publisher={Springer Berlin Heidelberg},
+author={Tannier, Eric},
+pages={1-12}
+}
+
+
+@article{10.1371/journal.pone.0052841,
+ author = {Blouin, Yann AND Hauck, Yolande AND Soler, Charles AND Fabre, Michel AND Vong, Rithy AND Dehan, Céline AND Cazajous, Géraldine AND Massoure, Pierre-Laurent AND Kraemer, Philippe AND Jenkins, Akinbowale AND Garnotel, Eric AND Pourcel, Christine AND Vergnaud, Gilles},
+ journal = {PLoS ONE},
+ publisher = {Public Library of Science},
+ title = {Significance of the Identification in the Horn of Africa of an Exceptionally Deep Branching <italic>Mycobacterium tuberculosis</italic> Clade},
+ year = {2012},
+ month = {12},
+ volume = {7},
+ url = {http://dx.doi.org/10.1371%2Fjournal.pone.0052841},
+ pages = {e52841},
+ abstract = {<p>Molecular and phylogeographic studies have led to the definition within the <italic>Mycobacterium tuberculosis</italic> complex (MTBC) of a number of geotypes and ecotypes showing a preferential geographic location or host preference. The MTBC is thought to have emerged in Africa, most likely the Horn of Africa, and to have spread worldwide with human migrations. Under this assumption, there is a possibility that unknown deep branching lineages are present in this region. We genotyped by spoligotyping and multiple locus variable number of tandem repeats (VNTR) analysis (MLVA) 435 MTBC isolates recovered from patients. Four hundred and eleven isolates were collected in the Republic of Djibouti over a 12 year period, with the other 24 isolates originating from neighbouring countries. All major <italic>M. tuberculosis</italic> lineages were identified, with only two <italic>M. africanum</italic> and one <italic>M. bovis</italic> isolates. Upon comparison with typing data of worldwide origin we observed that several isolates showed clustering characteristics compatible with new deep branching. Whole genome sequencing (WGS) of seven isolates and comparison with available WGS data from 38 genomes distributed in the different lineages confirms the identification of ancestral nodes for several clades and most importantly of one new lineage, here referred to as lineage 7. Investigation of specific deletions confirms the novelty of this lineage, and analysis of its precise phylogenetic position indicates that the other three superlineages constituting the MTBC emerged independently but within a relatively short timeframe from the Horn of Africa. The availability of such strains compared to the predominant lineages and sharing very ancient ancestry will open new avenues for identifying some of the genetic factors responsible for the success of the modern lineages. Additional deep branching lineages may be readily and efficiently identified by large-scale MLVA screening of isolates from sub-Saharan African countries followed by WGS analysis of a few selected isolates.</p>},
+ number = {12},
+ doi = {10.1371/journal.pone.0052841}
+}
-\documentclass{acm_proc_article-sp}
+\documentclass{article}
\usepackage{subfig}
\usepackage{color}
\usepackage{graphicx}
\title{Ancetre}
-\author{Jean-Fran\c cois Couchot, Raphael Couturier, and Christophe Guyeux*\\
+\author{Jean-Fran\c cois Couchot, and Christophe Guyeux*\\
FEMTO-ST Institute, UMR 6174 CNRS\\
Computer Science Laboratory DISC,
University of Franche-Comt\'{e},
Besan\c con, France.\\
- \{jean-francois.couchot, raphael.couturier, christophe.guyeux\}@femto-st.fr\\
+ \{jean-francois.couchot, christophe.guyeux\}@femto-st.fr\\
$*:$ Authors in alphabetic order.\\
}
\newcommand{\JFC}[1]{\begin{color}{green}\textit{}\end{color}}
%IEEEtran, journal, \LaTeX, paper, template.
-\keywords{Steganography, least-significant-bit (LSB)-based steganography, edge detection, Canny filter, security, syndrome treillis code}
\maketitle
\begin{abstract}
-A novel steganographic method called STABYLO is introduced in this research work.
-Its main avantage for being is to be much lighter than the so-called
-Highly Undetectable steGO (HUGO) method, a well known state of the art
-steganographic process. Additionally to this effectiveness,
-quite comparable results through noise measures like PSNR-HVS-M,
-BIQI, and weighted PSNR (wPSNR) are obtained.
-To achieve the proposed goal, famous experimented components of signal processing,
-coding theory, and cryptography are combined together, leading to
-a scheme that can reasonably face up-to-date steganalysers.
\end{abstract}
\section{Introduction}\label{sec:intro}
-\input{intro.tex}
-
+%\input{intro.tex}
+\input{art}
\section{Presentation of the Proposed Approach}\label{sec:ourapproach}
-\input{ourapproach.tex}
+
\section{Experiments}\label{sec:experiments}
-\input{experiments}
+
\section{First Stage: Genomes as Lists of Homologous Classes}
\section{Conclusion}\label{sec:concl}
-The STABYLO algorithm, whose acronym means STeganography
-with cAnny, Bbs, binarY embedding at LOw cost, has been introduced
-in this document as an efficient method having comparable, though
-somewhat smaller, security than the well known
-Highly Undetectable steGO (HUGO) steganographic scheme.
-This edge-based steganographic approach embeds a Canny
-detection filter, the Blum-Blum-Shub cryptographically secure
-pseudorandom number generator, together with Syndrome-Treillis Codes
-for minimizing distortion.
-After having introduced with details the proposed method,
-we have evaluated it through noise measures (namely, the PSNR, PSNR-HVS-M,
-BIQI, and weighted PSNR) and using well established steganalysers.
-
-For future work, the authors' intention is to investigate systematically
-all the existing edge detection methods, to see if the STABYLO evaluation scores can
-be improved by replacing Canny with another edge filter. We will try
-to take into account the least significant bits too during all the
-stages of the algorithm, hoping by doing so to be closer to the HUGO scores against
-steganalyzers. Other steganalyzers than the ones used in this document will be
-examined for the sake of completeness. Finally, the
-systematic replacement of all the LSBs of edges by binary digits provided
-by the BBS generator will be investigated, and the consequences of such a
-replacement, in terms of security, will be discussed.
-
\bibliographystyle{plain}
\bibliography{biblio}
