====== UE4:  Mathematics for systems biology======

==== Project ====
Choose one among the following papers for your study:

== Part 1: Christophe Ambroise == 
  - [[http://www-stat.stanford.edu/~tibs/SAM/pnassam.pdf| paper ]] of Tusher, Tibshirani and Chu (2001) about Signifiance Analysis of Microarrays,
    - {{:members:cambroise:teaching:pnas-2008-leek-18718-23.pdf| paper }} of  Leek and Storey (2008) about a general framework for multiple testing dependence,
  - {{:members:cambroise:teaching:bioinformatics-2003-bolstad-185-93.pdf| paper }} of Benjamin M. Bolstad, Rafael A. Irizarry, Magnus Åstrand, Terence P. Speed (2003) about normalization.



== Part 2: Catherine Matias ==
  - {{:members:cambroise:teaching:sor08.pdf| Statistical aspects of motifs exceptionality}} . Ref: S. Schbath and S. Robin. ”How can pattern statistics be useful for DNA motif discovery?”. In Glaz, Pozdnyakov, and Wallenstein, editors, Scan Statistics, Statistics for Industry and Technology, pages 319–350. Birkhauser Boston, 2009. 
  - {{:members:cambroise:teaching:nucl._acids_res.-2002-nicolas-1418-26.pdf|Sequence segmentation through HMMs}}. Ref P. Nicolas et al., ”Mining bacillus subtilis chromosome heterogeneities using hidden Markov models”, Nucleic Acids Res., 30(6):1418–1426, 2002. 
  - {{:members:cambroise:teaching:krogh.pdf| HMM profils. Ref: Krogh et al., ”Hidden Markov Models in Computational Biology: Applications to Protein Modeling”}}, J. Mol. Biol. 235/1501-1531, 1994. 
  
== Part 3: Florence D'Alché-Buc ==

 https://www.ibisc.univ-evry.fr/~dalche/Site/mlbni.html