@article{RusconiVallerianiDunlopetal.2012,
  author    = {Rusconi, Marco and Valleriani, Angelo and Dunlop, John William Chapman and Kurths, J{\"u}rgen and Weinkamer, Richard},
  title     = {Quantitative approach to the stochastics of bone remodeling},
  series = {epl : a letters journal exploring the frontiers of physics},
  volume    = {97},
  journal   = {epl : a letters journal exploring the frontiers of physics},
  number    = {2},
  publisher = {EDP Sciences},
  address   = {Mulhouse},
  issn      = {0295-5075},
  doi       = {10.1209/0295-5075/97/28009},
  pages     = {6},
  year      = {2012},
  abstract  = {During life bones constantly adapt their structure to their mechanical environment via a mechanically controlled process called bone remodeling. For trabecular bone, this process modifies the thickness of each trabecula leading occasionally to full resorption. We describe the irreversible dynamics of the trabecular thickness distribution (TTD) by means of a Markov chain discrete in space and time. By using thickness data from adult patients, we derive the transition probabilities in the chain. This allows a quantification, in terms of geometrical quantities, of the control of bone remodeling and thus to determine the evolution of the TTD with age.},
  language  = {en}
}
@article{ZhangFedyuninKirchneretal.2012,
  author    = {Zhang, Gong and Fedyunin, Ivan and Kirchner, Sebastian and Xiao, Chuanle and Valleriani, Angelo and Ignatova, Zoya},
  title     = {FANSe: an accurate algorithm for quantitative mapping of large scale sequencing reads},
  series = {Nucleic acids research},
  volume    = {40},
  journal   = {Nucleic acids research},
  number    = {11},
  publisher = {Oxford Univ. Press},
  address   = {Oxford},
  issn      = {0305-1048},
  doi       = {10.1093/nar/gks196},
  pages     = {11},
  year      = {2012},
  abstract  = {The most crucial step in data processing from high-throughput sequencing applications is the accurate and sensitive alignment of the sequencing reads to reference genomes or transcriptomes. The accurate detection of insertions and deletions (indels) and errors introduced by the sequencing platform or by misreading of modified nucleotides is essential for the quantitative processing of the RNA-based sequencing (RNA-Seq) datasets and for the identification of genetic variations and modification patterns. We developed a new, fast and accurate algorithm for nucleic acid sequence analysis, FANSe, with adjustable mismatch allowance settings and ability to handle indels to accurately and quantitatively map millions of reads to small or large reference genomes. It is a seed-based algorithm which uses the whole read information for mapping and high sensitivity and low ambiguity are achieved by using short and non-overlapping reads. Furthermore, FANSe uses hotspot score to prioritize the processing of highly possible matches and implements modified Smith-Watermann refinement with reduced scoring matrix to accelerate the calculation without compromising its sensitivity. The FANSe algorithm stably processes datasets from various sequencing platforms, masked or unmasked and small or large genomes. It shows a remarkable coverage of low-abundance mRNAs which is important for quantitative processing of RNA-Seq datasets.},
  language  = {en}
}
@article{KellerValleriani2012,
  author    = {Keller, Peter and Valleriani, Angelo},
  title     = {Single-molecule stochastic times in a reversible bimolecular reaction},
  series = {The journal of chemical physics : bridges a gap between journals of physics and journals of chemistr},
  volume    = {137},
  journal   = {The journal of chemical physics : bridges a gap between journals of physics and journals of chemistr},
  number    = {8},
  publisher = {American Institute of Physics},
  address   = {Melville},
  issn      = {0021-9606},
  doi       = {10.1063/1.4747337},
  pages     = {7},
  year      = {2012},
  abstract  = {In this work, we consider the reversible reaction between reactants of species A and B to form the product C. We consider this reaction as a prototype of many pseudobiomolecular reactions in biology, such as for instance molecular motors. We derive the exact probability density for the stochastic waiting time that a molecule of species A needs until the reaction with a molecule of species B takes place. We perform this computation taking fully into account the stochastic fluctuations in the number of molecules of species B. We show that at low numbers of participating molecules, the exact probability density differs from the exponential density derived by assuming the law of mass action. Finally, we discuss the condition of detailed balance in the exact stochastic and in the approximate treatment.},
  language  = {en}
}
@unpublished{KellerRoellyValleriani2012,
  author    = {Keller, Peter and Roelly, Sylvie and Valleriani, Angelo},
  title     = {On time duality for quasi-birth-and-death processes},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-56973},
  year      = {2012},
  abstract  = {We say that (weak/strong) time duality holds for continuous time quasi-birth-and-death-processes if, starting from a fixed level, the first hitting time of the next upper level and the first hitting time of the next lower level have the same distribution. We present here a criterion for time duality in the case where transitions from one level to another have to pass through a given single state, the so-called bottleneck property. We also prove that a weaker form of reversibility called balanced under permutation is sufficient for the time duality to hold. We then discuss the general case.},
  language  = {en}
}