deletions | additions       diff --git a/Cell cycle.tex b/Cell cycle.tex  deleted file mode 100644  index 7e35b95..0000000  --- a/Cell cycle.tex  +++ /dev/null 
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\subsection{Cell cycle}  TODO: cell cycle and nuclear are  The hidden Markov model for the cell cycle phase follows the same model than the one for the circadian phase, minus the baseline hidden state that wasn't necessary. Formally, it links the observed cell area $a_t$ to the cell cycle phase $\phi_t$ through a waveform $w(\phi)$ and an amplitude $a_t$: $a_t = \exp(\alpha_t) w(\phi_t) +\xi$. The complete model and its parameters are given in Section \ref{sec:HMM_methods}.  diff --git a/layout.md b/layout.md  index 051bd42..f8a1887 100644  --- a/layout.md  +++ b/layout.md 
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Introduction.tex  Estimating phases from signal.tex  figures/InferedPhaseCircadian/traceAndPhase.png  Cell cycle.tex  Nuclear area predicts cell cycle phases.tex  figures/FucciFigure/paperFigure.png  Estimating coupling functions from phases.tex