Stochastic Processes in Complex and Biological Systems


Angelo Valleriani

This page contains some essential information about my research interests.

A scientific blog can be found at the following link:

Circular analysis in complex stochastic systems
It is not possible to derive the details of microscopic mechanisms from macroscopic observations alone. It is shown here that in a simple system like a random walk on a line, an attempt to derive the jumping probabilities from sampled trajectories leads to a wrong model. This work connects to issues of circular analysis, where data and models achieve an artificial agreement by means of selection of good results. See more in: 

Angelo Valleriani
Circular analysis in complex stochastic systems
Scientific Reports 5, 17986 (2015)
http://www.nature.com/articles/srep17986

 

Single-molecule modeling of mRNA degradation by miRNA: Lessons from data
By using advanced methods in stochastic modeling of single-molecule dynamics we show that the standard biochemical network underlying the degradation of mRNA by miRNA is not supported by data. We propose instead a modification of the network according to which the order of biochemical reactions is sometimes inverted. In principle, this should lead to a new set of experimental verification. See more in: 

Celine Sin, Davide Chiarugi, Angelo Valleriani
Single-molecule modeling of mRNA degradation by miRNA: Lessons from data
BMC Systems Biology 9, S2 (2015)
http://www.biomedcentral.com/1752-0509/9/S3/S2

 

Effect of ribosome shielding on mRNA stability
Ribosomes protect the messenger RNA from being degraded. We used hazard rate methods to define a model of coverage according to which the mRNA is covered by ribosomes during its life and becomes stable. This model fits the stability data for E. coli. See more in: 

Carlus Deneke, Reinhard Lipowsky, Angelo Valleriani
Effect of ribosome shielding on mRNA stability
Physical Biology 10, 046008 (2013)
http://iopscience.iop.org/article/10.1088/1478-3975/10/4/046008/pdf

 

Complex degradation processes lead to non-exponential decay patterns and age-dependent decay rates of messenger RNA
The degradation of messenger RNA is regulated by a complex biochemical reaction network. Each single mRNA molecule undergoes a series of biochemical modifications until complete degradation is achieved. Accordingly, the decay pattern measured in stability assays cannot be exponential. This paper explains the underlying theory for the first time in the literature on mRNA stability. See more in: 

Carlus Deneke, Reinhard Lipowsky, Angelo Valleriani
Complex degradation processes lead to non-exponential decay patterns and age-dependent decay rates of messenger RNA
PLoS ONE 8, e55442 (2013) 
http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0055442

 

Transient phenomena in gene expression after induction of transcription
The transient phase between the starting point of transcription and the steady state is characterized by the degradation of the messenger RNA. When the degradation is age dependent, the transient phase is non trivial and depends on several characteristics of the life-time distribution of the mRNA. This paper exploits methods of hazard rte theory to show that the time to steadystate is not trivial, It shows also for the first time in the field of mRNA stability that the distribution of the number of mRNA is always Poisson independently of the life-time distribution. See more in: 

Carlus Deneke, Sophia Rudorf, Angelo Valleriani
Transient Phenomena in Gene Expression after Induction of Transcription
PLoS ONE 7, e35044 (2013) 
http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0035044

 

 

(more will come in the next weeks)