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The plant hormone auxin is thought to provide positional information for patterning during development. It is still unclear, however, precisely how auxin is distributed across tissues and how the hormone is sensed in space and time. The control of gene expression in response to auxin involves a complex network of over 50 potentially interacting(More)
The hidden Markov tree models were introduced by Crouse et al. in 1998 for modeling nonindependent, non-Gaussian wavelet transform coefficients. In their paper, they developed the equivalent of the forward-backward algorithm for hidden Markov tree models and called it the "upward-downward algorithm". This algorithm is subject to the same numerical(More)
How biological systems generate reproducible patterns with high precision is a central question in science. The shoot apical meristem (SAM), a specialized tissue producing plant aerial organs, is a developmental system of choice to address this question. Organs are periodically initiated at the SAM at specific spatial positions and this spatiotemporal(More)
Models that combine Markovian states with implicit geometric state occupancy distributions and semi-Markovian states with explicit state occupancy distributions, are investigated. This type of model retains the flexibility of hidden semi-Markov chains for the modeling of short or medium size homogeneous zones along sequences but also enables the modeling of(More)
The knowledge of the state sequences that explain a given observed sequence for a known hidden Markovian model is the basis of various methods that may be divided into three categories: (i) enumeration of state sequences; (ii) summary of the possible state sequences in state profiles; (iii) computation of a global measure of the state sequence uncertainty.(More)
Root architecture is a crucial part of plant adaptation to soil heterogeneity and is mainly controlled by root branching. The process of root system development can be divided into two successive steps: lateral root initiation and lateral root development/emergence which are controlled by different fluxes of the plant hormone auxin. While shoot architecture(More)
Plant architecture is the result of repetitions that occur through growth and branching processes. During plant ontogeny, changes in the morphological characteristics of plant entities are interpreted as the indirect translation of different physiological states of the meristems. Thus connected entities can exhibit either similar or very contrasted(More)
The Lifetime Reproductive Success (LRS) of an individual i.e. the number of young raised during its lifespan is an indicator of its contribution to future generations and thus a measure of fitness. Nevertheless, the LRS is hard to estimate because of the difficulty to keep track of the outcome of each breeding attempt (successful or failed and, if(More)
Biological context Vascular plants produce new organs at the tip of the stem in a very organized fashion. This patterning process occurs in small groups of stem cells, the so-called shoot apical meristems (SAM), and generates regular patterns called phyllotaxis. The phyllotaxis of the model plant Arabidopsis thaliana follows a Fibonacci spiral, the most(More)
This study aims to explore and model the changes in growth unit (GU) branching patterns during tree ontogeny. The question was addressed in apple trees cv. "Fuji", by analysing the relative impact of GU length and within-tree position. The development of two 6-year-old trees was recorded over 6 years. The fate of axillary buds along each GU was represented(More)