@article{KellerRoellyValleriani2015,
  author    = {Keller, Peter and Roelly, Sylvie and Valleriani, Angelo},
  title     = {A Quasi Random Walk to Model a Biological Transport Process},
  series = {Methodology and computing in applied probability},
  volume    = {17},
  journal   = {Methodology and computing in applied probability},
  number    = {1},
  publisher = {Springer},
  address   = {Dordrecht},
  issn      = {1387-5841},
  doi       = {10.1007/s11009-013-9372-5},
  pages     = {125 -- 137},
  year      = {2015},
  abstract  = {Transport molecules play a crucial role for cell viability. Amongst others, linear motors transport cargos along rope-like structures from one location of the cell to another in a stochastic fashion. Thereby each step of the motor, either forwards or backwards, bridges a fixed distance and requires several biochemical transformations, which are modeled as internal states of the motor. While moving along the rope, the motor can also detach and the walk is interrupted. We give here a mathematical formalization of such dynamics as a random process which is an extension of Random Walks, to which we add an absorbing state to model the detachment of the motor from the rope. We derive particular properties of such processes that have not been available before. Our results include description of the maximal distance reached from the starting point and the position from which detachment takes place. Finally, we apply our theoretical results to a concrete established model of the transport molecule Kinesin V.},
  language  = {en}
}
@unpublished{KellerRoellyValleriani2013,
  author    = {Keller, Peter and Roelly, Sylvie and Valleriani, Angelo},
  title     = {A quasi-random-walk to model a biological transport process},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-63582},
  year      = {2013},
  abstract  = {Transport Molecules play a crucial role for cell viability. Amongst others, linear motors transport cargos along rope-like structures from one location of the cell to another in a stochastic fashion. Thereby each step of the motor, either forwards or backwards, bridges a fixed distance. While moving along the rope the motor can also detach and is lost. We give here a mathematical formalization of such dynamics as a random process which is an extension of Random Walks, to which we add an absorbing state to model the detachment of the motor from the rope. We derive particular properties of such processes that have not been available before. Our results include description of the maximal distance reached from the starting point and the position from which detachment takes place. Finally, we apply our theoretical results to a concrete established model of the transport molecule Kinesin V.},
  language  = {en}
}
@article{StangeHintscheSachseetal.2017,
  author    = {Stange, Maike and Hintsche, Marius and Sachse, Kirsten and Gerhardt, Matthias and Valleriani, Angelo and Beta, Carsten},
  title     = {Analyzing the spatial positioning of nuclei in polynuclear giant cells},
  series = {Journal of Physics D: Applied Physics},
  volume    = {50},
  journal   = {Journal of Physics D: Applied Physics},
  number    = {46},
  publisher = {IOP Publ. Ltd.},
  address   = {Bristol},
  issn      = {0022-3727},
  doi       = {10.1088/1361-6463/aa8da0},
  pages     = {8},
  year      = {2017},
  abstract  = {How cells establish and maintain a well-defined size is a fundamental question of cell biology. Here we investigated to what extent the microtubule cytoskeleton can set a predefined cell size, independent of an enclosing cell membrane. We used electropulse-induced cell fusion to form giant multinuclear cells of the social amoeba Dictyostelium discoideum. Based on dual-color confocal imaging of cells that expressed fluorescent markers for the cell nucleus and the microtubules, we determined the subcellular distributions of nuclei and centrosomes in the giant cells. Our two- and three-dimensional imaging results showed that the positions of nuclei in giant cells do not fall onto a regular lattice. However, a comparison with model predictions for random positioning showed that the subcellular arrangement of nuclei maintains a low but still detectable degree of ordering. This can be explained by the steric requirements of the microtubule cytoskeleton, as confirmed by the effect of a microtubule degrading drug.},
  language  = {en}
}
@article{BartholomaeusFedyuninFeistetal.2016,
  author    = {Bartholom{\"a}us, Alexander and Fedyunin, Ivan and Feist, Peter and Sin, Celine and Zhang, Gong and Valleriani, Angelo and Ignatova, Zoya},
  title     = {Bacteria differently regulate mRNA abundance to specifically respond to various stresses},
  series = {Geology},
  volume    = {374},
  journal   = {Geology},
  publisher = {Royal Society},
  address   = {London},
  issn      = {1364-503X},
  doi       = {10.1098/rsta.2015.0069},
  pages     = {16},
  year      = {2016},
  abstract  = {Environmental stress is detrimental to cell viability and requires an adequate reprogramming of cellular activities to maximize cell survival. We present a global analysis of the response of Escherichia coli to acute heat and osmotic stress. We combine deep sequencing of total mRNA and ribosome-protected fragments to provide a genome-wide map of the stress response at transcriptional and translational levels. For each type of stress, we observe a unique subset of genes that shape the stress-specific response. Upon temperature upshift, mRNAs with reduced folding stability up-and downstream of the start codon, and thus with more accessible initiation regions, are translationally favoured. Conversely, osmotic upshift causes a global reduction of highly translated transcripts with high copy numbers, allowing reallocation of translation resources to not degraded and newly synthesized mRNAs.},
  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{ZhangFedyuninMiekleyetal.2010,
  author    = {Zhang, Gong and Fedyunin, Ivan and Miekley, Oskar and Valleriani, Angelo and Moura, Alessandro and Ignatova, Zoya},
  title     = {Global and local depletion of ternary complex limits translational elongation},
  issn      = {0305-1048},
  doi       = {10.1093/Nar/Gkq196},
  year      = {2010},
  abstract  = {The translation of genetic information according to the sequence of the mRNA template occurs with high accuracy and fidelity. Critical events in each single step of translation are selection of transfer RNA (tRNA), codon reading and tRNA-regeneration for a new cycle. We developed a model that accurately describes the dynamics of single elongation steps, thus providing a systematic insight into the sensitivity of the mRNA translation rate to dynamic environmental conditions. Alterations in the concentration of the aminoacylated tRNA can transiently stall the ribosomes during translation which results, as suggested by the model, in two outcomes: either stress-induced change in the tRNA availability triggers the premature termination of the translation and ribosomal dissociation, or extensive demand for one tRNA species results in a competition between frameshift to an aberrant open-reading frame and ribosomal drop-off. Using the bacterial Escherichia coli system, we experimentally draw parallels between these two possible mechanisms.},
  language  = {en}
}
@article{RusconiVallerianiDunlopetal.2009,
  author    = {Rusconi, Marco and Valleriani, Angelo and Dunlop, John William Chapman and Kurths, J{\"u}rgen and Weinkamer, Richard},
  title     = {Insights into the control of trabecular bone remodelling obtained by a Markov model},
  issn      = {8756-3282},
  doi       = {10.1016/j.bone.2009.03.467},
  year      = {2009},
  language  = {en}
}
@article{VallerianiZhangNagaretal.2011,
  author    = {Valleriani, Angelo and Zhang, Gong and Nagar, Apoorva and Ignatova, Zoya and Lipowsky, Reinhard},
  title     = {Length-dependent translation of messenger RNA by ribosomes},
  series = {Physical review : E, Statistical, nonlinear and soft matter physics},
  volume    = {83},
  journal   = {Physical review : E, Statistical, nonlinear and soft matter physics},
  number    = {4},
  publisher = {American Physical Society},
  address   = {College Park},
  issn      = {1539-3755},
  doi       = {10.1103/PhysRevE.83.042903},
  pages     = {4},
  year      = {2011},
  abstract  = {A simple measure for the efficiency of protein synthesis by ribosomes is provided by the steady state amount of protein per messenger RNA (mRNA), the so-called translational ratio, which is proportional to the translation rate. Taking the degradation of mRNA into account, we show theoretically that both the translation rate and the translational ratio decrease with increasing mRNA length, in agreement with available experimental data for the prokaryote Escherichia coli. We also show that, compared to prokaryotes, mRNA degradation in eukaryotes leads to a less rapid decrease of the translational ratio. This finding is consistent with the fact that, compared to prokaryotes, eukaryotes tend to have longer proteins.},
  language  = {en}
}
@article{KellerRoellyValleriani2015,
  author    = {Keller, Peter and Roelly, Sylvie and Valleriani, Angelo},
  title     = {On time duality for Markov Chains},
  series = {Stochastic models},
  volume    = {31},
  journal   = {Stochastic models},
  number    = {1},
  publisher = {Taylor \& Francis Group},
  address   = {Philadelphia},
  issn      = {1532-6349},
  doi       = {10.1080/15326349.2014.969736},
  pages     = {98 -- 118},
  year      = {2015},
  abstract  = {For an irreducible continuous time Markov chain, we derive the distribution of the first passage time from a given state i to another given state j and the reversed passage time from j to i, each under the condition of no return to the starting point. When these two distributions are identical, we say that i and j are in time duality. We introduce a new condition called permuted balance that generalizes the concept of reversibility and provides sufficient criteria, based on the structure of the transition graph of the Markov chain. Illustrative examples are provided.},
  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}
}
@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{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}
}
@inproceedings{VallerianiRoellyKulik2017,
  author    = {Valleriani, Angelo and Roelly, Sylvie and Kulik, Alexei Michajlovič},
  title     = {Stochastic processes with applications in the natural sciences},
  series = {Lectures in pure and applied mathematics},
  booktitle = {Lectures in pure and applied mathematics},
  number    = {4},
  editor    = {Roelly, Sylvie and H{\"o}gele, Michael and Rafler, Mathias},
  publisher = {Universit{\"a}tsverlag Potsdam},
  address   = {Potsdam},
  isbn      = {978-3-86956-414-2},
  issn      = {2199-4951},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-401802},
  pages     = {ix, 124},
  year      = {2017},
  abstract  = {The interdisciplinary workshop STOCHASTIC PROCESSES WITH APPLICATIONS IN THE NATURAL SCIENCES was held in Bogot{\´a}, at Universidad de los Andes from December 5 to December 9, 2016. It brought together researchers from Colombia, Germany, France, Italy, Ukraine, who communicated recent progress in the mathematical research related to stochastic processes with application in biophysics. The present volume collects three of the four courses held at this meeting by Angelo Valleriani, Sylvie Rœlly and Alexei Kulik. A particular aim of this collection is to inspire young scientists in setting up research goals within the wide scope of fields represented in this volume. Angelo Valleriani, PhD in high energy physics, is group leader of the team "Stochastic processes in complex and biological systems" from the Max-Planck-Institute of Colloids and Interfaces, Potsdam. Sylvie Rœlly, Docteur en Math{\´e}matiques, is the head of the chair of Probability at the University of Potsdam. Alexei Kulik, Doctor of Sciences, is a Leading researcher at the Institute of Mathematics of Ukrainian National Academy of Sciences.},
  language  = {en}
}
@article{BuehningVallerianiLeimkuehler2017,
  author    = {B{\"u}hning, Martin and Valleriani, Angelo and Leimk{\"u}hler, Silke},
  title     = {The role of SufS is restricted to Fe-S cluster biosynthesis in escherichia coli},
  series = {Biochemistry},
  volume    = {56},
  journal   = {Biochemistry},
  publisher = {American Chemical Society},
  address   = {Washington},
  issn      = {0006-2960},
  doi       = {10.1021/acs.biochem.7b00040},
  pages     = {1987 -- 2000},
  year      = {2017},
  abstract  = {In Escherichia coli, two different systems that are important for the coordinate formation of Fe-S clusters have been identified, namely, the ISC and SUF systems. The ISC system is the housekeeping Fe-S machinery, which provides Fe-S clusters for numerous cellular proteins. The IscS protein of this system was additionally revealed to be the primary sulfur donor for several sulfur-containing molecules with important biological functions, among which are the molybdenum cofactor (Moco) and thiolated nucleosides in tRNA. Here, we show that deletion of central components of the ISC system in addition to IscS leads to an overall decrease in Fe-S cluster enzyme and molybdoenzyme activity in addition to a decrease in the number of Fe-S-dependent thiomodifications of tRNA, based on the fact that some proteins involved in Moco biosynthesis and tRNA thiolation are Fe-S-dependent. Complementation of the ISC deficient strains with the suf operon restored the activity of Fe-S-containing proteins, including the MoaA protein, which is involved in the conversion of 5′GTP to cyclic pyranopterin monophosphate in the fist step of Moco biosynthesis. While both systems share a high degree of similarity, we show that the function of their respective l-cysteine desulfurase IscS or SufS is specific for each cellular pathway. It is revealed that SufS cannot play the role of IscS in sulfur transfer for the formation of 2-thiouridine, 4-thiouridine, or the dithiolene group of molybdopterin, being unable to interact with TusA or ThiI. The results demonstrate that the role of the SUF system is exclusively restricted to Fe-S cluster assembly in the cell.},
  language  = {en}
}
@article{BroekerRoskeVallerianietal.2019,
  author    = {Broeker, Nina K. and Roske, Yvette and Valleriani, Angelo and Stephan, Mareike Sophia and Andres, Dorothee and Koetz, Joachim and Heinemann, Udo and Barbirz, Stefanie},
  title     = {Time-resolved DNA release from an O-antigen-specific Salmonella bacteriophage with a contractile tail},
  series = {The journal of biological chemistry},
  volume    = {294},
  journal   = {The journal of biological chemistry},
  number    = {31},
  publisher = {American Society for Biochemistry and Molecular Biology},
  address   = {Bethesda},
  issn      = {1083-351X},
  doi       = {10.1074/jbc.RA119.008133},
  pages     = {11751 -- 11761},
  year      = {2019},
  abstract  = {Myoviruses, bacteriophages with T4-like architecture, must contract their tails prior to DNA release. However, quantitative kinetic data on myovirus particle opening are lacking, although they are promising tools in bacteriophage-based antimicrobial strategies directed against Gram-negative hosts. For the first time, we show time-resolved DNA ejection from a bacteriophage with a contractile tail, the multi-O-antigen-specific Salmonella myovirus Det7. DNA release from Det7 was triggered by lipopolysaccharide (LPS) O-antigen receptors and notably slower than in noncontractile-tailed siphoviruses. Det7 showed two individual kinetic steps for tail contraction and particle opening. Our in vitro studies showed that highly specialized tailspike proteins (TSPs) are necessary to attach the particle to LPS. A P22-like TSP confers specificity for the Salmonella Typhimurium O-antigen. Moreover, crystal structure analysis at 1.63 angstrom resolution confirmed that Det7 recognized the Salmonella Anatum O-antigen via an E15-like TSP, DettilonTSP. DNA ejection triggered by LPS from either host showed similar velocities, so particle opening is thus a process independent of O-antigen composition and the recognizing TSP. In Det7, at permissive temperatures TSPs mediate O-antigen cleavage and couple cell surface binding with DNA ejection, but no irreversible adsorption occurred at low temperatures. This finding was in contrast to short-tailed Salmonella podoviruses, illustrating that tailed phages use common particle-opening mechanisms but have specialized into different infection niches.},
  language  = {en}
}
@article{VallerianiIgnatovaNagaretal.2010,
  author    = {Valleriani, Angelo and Ignatova, Zoya and Nagar, Apoorva and Lipowsky, Reinhard},
  title     = {Turnover of messenger RNA : polysome statistics beyond the steady state},
  issn      = {0295-5075},
  doi       = {10.1209/0295-5075/89/58003},
  year      = {2010},
  abstract  = {The interplay between turnover or degradation and ribosome loading of messenger RNA (mRNA) is studied theoretically using a stochastic model that is motivated by recent experimental results. Random mRNA degradation affects the statistics of polysomes, i.e., the statistics of the number of ribosomes per mRNA as extracted from cells. Since ribosome loading of newly created mRNA chains requires some time to reach steady state, a fraction of the extracted mRNA/ ribosome complexes does not represent steady state conditions. As a consequence, the mean ribosome density obtained from the extracted complexes is found to be inversely proportional to the mRNA length. On the other hand, the ribosome density profile shows an exponential decrease along the mRNA for prokaryotes and becomes uniform in eukaryotic cells. Copyright (C) EPLA, 2010},
  language  = {en}
}
@article{RadingSandmannSteupetal.2015,
  author    = {Rading, M. Michael and Sandmann, Michael and Steup, Martin and Chiarugi, Davide and Valleriani, Angelo},
  title     = {Weak correlation of starch and volume in synchronized photosynthetic cells},
  series = {Physical review : E, Statistical, nonlinear and soft matter physics},
  volume    = {91},
  journal   = {Physical review : E, Statistical, nonlinear and soft matter physics},
  number    = {1},
  publisher = {American Physical Society},
  address   = {College Park},
  issn      = {1539-3755},
  doi       = {10.1103/PhysRevE.91.012711},
  pages     = {11},
  year      = {2015},
  abstract  = {In cultures of unicellular algae, features of single cells, such as cellular volume and starch content, are thought to be the result of carefully balanced growth and division processes. Single-cell analyses of synchronized photoautotrophic cultures of the unicellular alga Chlamydomonas reinhardtii reveal, however, that the cellular volume and starch content are only weakly correlated. Likewise, other cell parameters, e.g., the chlorophyll content per cell, are only weakly correlated with cell size. We derive the cell size distributions at the beginning of each synchronization cycle considering growth, timing of cell division and daughter cell release, and the uneven division of cell volume. Furthermore, we investigate the link between cell volume growth and starch accumulation. This work presents evidence that, under the experimental conditions of light-dark synchronized cultures, the weak correlation between both cell features is a result of a cumulative process rather than due to asymmetric partition of biomolecules during cell division. This cumulative process necessarily limits cellular similarities within a synchronized cell population.},
  language  = {en}
}