About

Angelo Valleriani

What drives me

I am a theoretical physicist turned into a multidisciplinary scientist. Curiosity and the love for mathematical methods has brought me to work on very different topics, from which I take inspiration for my classes.

Current topics of research are related to malaria, cancer, bones, and gene expression. In the past I have been working on theoretical particle physics, ecology and evolutionary modeling, physical chemistry, theoretical biophysics, network theory.

From early on, I have been also teaching. I always taught out of my personal inspiration and only topics I was interested in. Indeed, my job as a researcher does not include any compulsory teaching. The reason why I am teaching is that I like it, it is a very interesting form of learning and focusing on topics of my own interest. I taught mostly about stochastic modeling, which is a very flexible and fascinating mathematical methodology strongly related to statistical physics.

Now my current focus in teaching is applied statistics. The reason I like this topic is that it merges both the theoretical part of understanding the role of randomness, the mathematical treatment of the randomness, and the experimental detail that starts ideally with the design of an experiment.

For the way my brain is wired up, I tend to focus on the mathematics behind the methods. But I understand that when teaching, it is good to leave many details away and focus on intuition. People interested in the mathematical details will have to go through the books one step at a time.
I teach statistics classes at professional level within the scope of my job. There, the people attending the courses have already some previous knowledge and they have also some application in mind.

The courses offered here, instead, are not a replacement and not a copy of those provided at the professional level. Here, I try to help researchers in strong need for a quick start or a quick overview of the many classical methods in statistics. The courses are particularly suited to experimental young researchers in biology and other natural sciences.

Resume

Since Nov. 2000

Group leader at the Max Planck Institute of Colloids and Interfaces

Nov. 1998

Visiting Scientist in the Theory Division of the Max Planck Institute of Colloids and Interfaces, Golm, Germany

Nov. 1996

Visiting Scientist for two years at the Max Planck Institute for Physics of Complex Systems in Dresden, Germany

Oct. 1996

Ph.D. Degree in High Energy Physics at SISSA (Trieste, Italy); Thesis Supervisor: Dr. G. Mussardo
Thesis Title: Form Factors and Correlation Functions

Feb. 1993

Start one year compulsory military service as Civil Service

Nov. 1992

Admitted, as best qualified after exam, to the Ph.D. course in High Energy Physics at SISSA (Trieste, Italy)

July 1992

Laurea Degree in Theoretical Physics at the University of Bologna with full marks and honours.
Thesis Supervisors: Prof. R. Soldati and Dr. F. Ravanini
Thesis Title: Conformal Invariance, Renormalization Group and Integrable Models in Two-Dimensional Quantum Field Theories

July 1985

Scientific Lycée Degree with full marks

Resume

Since Nov. 2000

Group leader at the Max Planck Institute of Colloids and Interfaces

Nov. 1998

Visiting Scientist in the Theory Division of the Max Planck Institute of Colloids and Interfaces, Golm, Germany

Nov. 1996

Visiting Scientist for two years at the Max Planck Institute for Physics of Complex Systems in Dresden, Germany

Oct. 1996

Ph.D. Degree in High Energy Physics at SISSA (Trieste, Italy); Thesis Supervisor: Dr. G. Mussardo
Thesis Title: Form Factors and Correlation Functions

Feb. 1993

Start one year compulsory military service as Civil Service

Nov. 1992

Admitted, as best qualified after exam, to the Ph.D. course in High Energy Physics at SISSA (Trieste, Italy)

July 1992

July 1985

Scientific Lycée Degree with full marks

Publications

Articles

Tsirigoni, A.-M.; Göktas, M.; Atris, Z.; Valleriani, A.; Vila Verde, A.; Blank, K. G.: Chain sliding versus β-sheet formation upon shearing single α-helical coiled coils. Macromolecular Bioscience 23 (5), 202200563 (2023)
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Giacomini, G.; Graziani, C.; Lachi, V.; Bongini, P.; Pancino, N.; Bianchini, M.; Chiarugi, D.; Valleriani, A.; Andreini, P.: A neural networks approach for the analysis of reproducible ribo–seq profiles. Algorithms 15 (8), 274 (2022)
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Mohr, E.; Hinnenthal, T.; Gryzik, S.; Hoang, Y.; Lischke, T.; Retzlaff, J.; Mekonnen, A.; Paul, F.; Valleriani, A.; Radbruch, A. et al.: Bin-based visualization of cytokine-co-expression patterns of IL-10-producing CD4 T cell subsets. European Journal of Immunology 52 (10), S. 1684 – 1687 (2022)
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Siciliano, G.; Costa, G.; Suárez-Cortés, P.; Valleriani, A.; Alano, P.; Levashina, E. A.: Critical steps of Plasmodium falciparum ookinete maturation. Frontiers in Microbiology 11, 269 (2020)
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Thai, E.; Costa, G.; Weyrich, A.; Murugan, R.; Oyen, D.; Prieto, K.; Bosch, A.; Valleriani, A.; Wu, N. C.; Pholcharee, T. et al.: A high-affinity antibody against the CSP N-terminal domain lacks Plasmodium falciparum inhibitory activity. Journal of Experimental Medicine 217 (11), e20200061 (2020)
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Broeker, N. K.; Roske, Y.; Valleriani, A.; Stephan, M. S.; Andres, D.; Koetz, J.; Heinemann, U.; Barbirz, S.: Time-resolved DNA release from an O-antigen–specific Salmonella bacteriophage with a contractile tail. Journal of Biological Chemistry 294 (31), pp. 11751 – 11761 (2019)
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Bergues Pupo, A. E.; Göktas, M.; Tunn, I.; López García, P.; Vila Verde, A.; Blank, K.; Valleriani, A.: Goodness of fit testing in dynamic single-molecule force spectroscopy. The Journal of Chemical Physics 149, 244120 (2018)
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Bühning , M.; Valleriani, A.; Leimkühler, S.: The role of SufS is restricted to Fe−S cluster biosynthesis in Escherichia coli. Biochemistry 56 (14), pp. 1987 – 2000 (2017)
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Stange, M.; Hintsche, M.; Sachse, K.; Gerhardt, M.; Valleriani, A.; Beta, C.: Analyzing the spatial positioning of nuclei in polynuclear giant cells. Journal of Physics D: Applied Physics 50 (46), 464001 (2017)
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Wiechecki, K.; Manohar, S.; Silva, G.; Tchourine, K.; Jacob, S.; Valleriani, A.; Vogel, C.: Integrative meta-analysis reveals that most yeast proteins are very stable. bioRxiv (2017)
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Bartholomäus, A.; Fedyunin, I.; Feist, P.; Sin, C.; Zhang, G.; Valleriani, A.; Ignatova, Z.: Bacteria differently regulate mRNA abundance to specifically respond to various stresses. Philosophical Transactions of the Royal Society of London – Series A: Mathematical Physical and Engineering Sciences 374 (2063), 20150069 (2016)
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McShane, E.; Sin, C.; Zauber, H.; Wells, J.; Donnelly, N.; Wang, X.; Hou, J.; Chen, W.; Storchova, Z.; Marsh, J. et al.: Kinetic analysis of protein stability reveals age-dependent degradation. Cell 167 (3), pp. 803 – 815.e21 (2016)
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Rusconi, M.; Valleriani, A.: Predict or classify: the deceptive role of time-locking in brain signal classification. Scientific Reports 6, 28236 (2016)
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Sin, C.; Chiarugi, D.; Valleriani, A.: Quantitative assessment of ribosome drop-off in E. coli. Nucleic Acids Research 44 (6), pp. 2528 – 2537 (2016)
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Sin, C.; Chiarugi, D.; Valleriani, A.: Degradation parameters from pulse-chase experiments. PLoS One 11 (5), e0155028 (2016)
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Valleriani, A.: A conditional likelihood is required to estimate the selection coefficient in ancient DNA. Scientific Reports 6, 31561 (2016)
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Keller, P.; Rœlly, S.; Valleriani, A.: A quasi random walk to model a biological transport process. Methodology and Computing in Applied Probability 17 (1), pp. 125 – 137 (2015)
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Keller, P.; Rœlly, S.; Valleriani, A.: On time duality for Markov chains. Stochastic Models 31 (1), pp. 98 – 118 (2015)
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Rading, M. M.; Sandmann, M.; Steup, M.; Chiarugi, D.; Valleriani, A.: Weak correlation of starch and volume in synchronized photosynthetic cells. Physical Review E 91 (1), 012711 (2015)
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Sin, C.; Chiarugi, D.; Valleriani, A.: Single-molecule modeling of mRNA degradation by miRNA: lessons from data. BMC Systems Biology 9 (Suppl 3), S2 (2015)
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Valleriani, A.: Circular analysis in complex stochastic systems. Scientific Reports 5, 17986 (2015)
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Li, X.; Kolomeisky, A. B.; Valleriani, A.: Pathway structure determination in complex stochastic networks with non-exponential dwell times. The Journal of Chemical Physics 140 (18), 84102 (2014)
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Li, X.; Kolomeisky, A. B.; Valleriani, A.: Stochastic kinetics on networks: when slow is fast. Journal of Physical Chemistry B 118 (35), pp. 10419 – 10425 (2014)
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Valleriani, A.; Li, X.; Kolomeisky, A. B.: Unveiling the hidden structure of complex stochastic biochemical networks. The Journal of Chemical Physics 140 (6), 064101 (2014)
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Deneke, C.; Lipowsky, R.; Valleriani, A.: Effect of ribosome shielding on mRNA stability. Physical Biology 10 (4), 046008 (2013)
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Deneke, C.; Lipowsky, R.; Valleriani, A.: Complex degradation processes lead to non-exponential decay patterns and age-dependent decay rates of messenger RNA. PLoS One 8 (2), e55442 (2013)
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Deneke, C.; Rudorf, S.; Valleriani, A.: Transient Phenomena in Gene Expression after Induction of Transcription. PLoS One 7 (4), e35044 (2012)
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Keller, P.; Valleriani, A.: Single-molecule stochastic times in a reversible bimolecular reaction. The Journal of Chemical Physics 137 (8), 084106 (2012)
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Rusconi, M.; Valleriani, A.; Dunlop, J. W. C.; Kurths, J.; Weinkamer, R.: Quantitative approach to the stochastics of bone remodeling. EPL 97 (2), 28009 (2012)
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Zhang, G.; Fedyunin, I.; Kirchner, S.; Xiao, C. L.; Valleriani, A.; Ignatova, Z.: FANSe: an accurate algorithm for quantitative mapping of large scale sequencing reads. Nucleic Acids Research (London) 40 (11), e83 (2012)
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Menche, J.; Valleriani, A.; Lipowsky, R.: Sequences of phase transitions in Ising models on correlated networks. Physical Review E 83 (6), 061129 (2011)
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Nagar, A.; Valleriani, A.; Lipowsky, R.: Translation by ribosomes with mRNA degradation: exclusion processes on aging tracks. Journal of Statistical Physics 145 (5), pp. 1385 – 1404 (2011)
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Rading, M. M.; Engel, T. A.; Lipowsky, R.; Valleriani, A.: Stationary size distributions of growing cells with binary and multiple cell division. Journal of Statistical Physics 145 (1), pp. 1 – 22 (2011)
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Valleriani, A.; Zhang, G.; Nagar, A.; Ignatova, Z.; Lipowsky, R.: Length-dependent translation of messenger RNA by ribosomes. Physical Review E 83 (4), 042903 (2011)
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Menche, J.; Valleriani, A.; Lipowsky, R.: Asymptotic properties of degree-correlated scale-free networks. Physical Review E 81 (4), 046103 (2010)
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Menche, J.; Valleriani, A.; Lipowsky, R.: Dynamical processes on dissortative scale-free networks. EPL 89 (1), 18002 (2010)
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Valleriani, A.; Ignatova, Z.; Nagar, A.; Lipowsky, R.: Turnover of messenger RNA: polysome statistics beyond the steady state. EPL 89 (5), 58003 (2010)
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Zhang, G.; Fedyunin, I.; Miekley, O.; Valleriani, A.; Moura, A.; Ignatova, Z.: Global and local depletion of ternary complex limits translational elongation. Nucleic Acids Research 38 (14), pp. 4778 – 4787 (2010)
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Lipowsky, R.; Beeg, J.; Dimova, R.; Klumpp, S.; Liepelt, S.; Müller, M. J. I.; Valleriani, A.: Active bio-systems: from single motor molecules to cooperative cargo transport. Biophysical Reviews and Letters 4 (1 & 2), pp. 77 – 137 (2009)
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Lipowsky, R.; Liepelt, S.; Valleriani, A.: Energy Conversion by Molecular Motors Coupled to Nucleotide Hydrolysis. Journal of Statistical Physics 135 (5-6 Sp. Iss.), pp. 951 – 975 (2009)
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Valleriani, A.; Liepelt, S.; Lipowsky, R.: Dwell time distributions for kinesin’s mechanical steps. EPL 82 (2), 28011 (2008)
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Valleriani, A.; Meene, T.: Multilevel selection in a gradient. Ecological Modelling 208 (2-4), pp. 159 – 164 (2007)
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Valleriani, A.: Evolutionarily stable germination strategies with time-correlated yield. Theoretical Population Biology 70 (3), pp. 255 – 261 (2006)
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Valleriani, A.; Tielborger, K.: Effect of age on germination of dormant seeds. Theoretical Population Biology 70 (1), pp. 1 – 9 (2006)
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Bastolla, U.; Lässig, M.; Manrubia, S. C.; Valleriani, A.: Biodiversity in model ecosystems, I: coexistence conditions for competing species. Journal of Theoretical Biology 235 (4), pp. 521 – 530 (2005)
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Bastolla, U.; Lässig, M.; Manrubia, S. C.; Valleriani, A.: Biodiversity in model ecosystems, II: species assembly and food web structure. Journal of Theoretical Biology 235 (4), pp. 531 – 539 (2005)
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Tielborger, K.; Valleriani, A.: Can seeds predict their future? Germination strategies of density-regulated desert annuals. Oikos 111 (2), pp. 235 – 244 (2005)
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Valleriani, A.: Algebraic determination of the evolutionary stable germination fraction. Theoretical Population Biology 68 (3), pp. 197 – 203 (2005)
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Bastolla, U.; Lässig, M.; Manrubia, S. C.; Valleriani, A.: Diversity patterns from ecological models at dynamical equilibrium. Journal of Theoretical Biology 212, pp. 11 – 34 (2001)
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Cuniberti, G.; Valleriani, A.; Vega, J. L.: Effects of regulation on a self-organized market. Quantitative Finance 3 (1), pp. 332 – 335 (2001)
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Lässig, M.; Bastolla, U.; Manrubia, S. C.; Valleriani, A.: Shape of ecological networks. Physical Review Letters 86 (19), pp. 4418 – 4421 (2001)
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Cafiero, R.; de los Rios, P.; Valleriani, A.; Vega, J. L.: Levy-nearest-neighbors Bak-Sneppen model. Physical Review E 60 (2), pp. R 1111 – R 1114 (1999)
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Cafiero, R.; Valleriani, A.; Vega, J.L.: Damage-spreading in the parallel Bak-Sneppen model. The European Physical Journal B: Condensend Matter Physics 7, pp. 505 – 508 (1999)
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Valleriani, A.; Vega, J. L.: Damage spreading in the Bak-Sneppen model. Journal of Physics A: Mathematical and General 32 (1), pp. 105 – 114 (1999)
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Cafiero, R.; De Los Rios, P.; Dittes, F.-M.; Valleriani, A.; Vega, J. L.: Power-law behavior in a nonextremal Bak-Sneppen model. Physical Review E 58 (3), pp. 3993 – 3996 (1998)
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De Los Rios, P.; Valleriani, A.; Luis Vega, J.: Self-organized criticality in deterministic systems with disorder. Physical Review E 57, pp. 6451 – 6459 (1998)
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Cafiero, R.; Valleriani, A.; Vega, J.L.: Damage-spreading in the Bak-Sneppen model without noise. The European Physical Journal B: Condensend Matter Physics 4 (4), pp. 405 – 408 (1998)
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Marsili, M.; Valleriani, A.: Self organization of interacting polya urns. The European Physical Journal B: Condensend Matter Physics 3 (4), pp. 417 – 420 (1998)
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De Los Rios, P.; Valleriani, A.; Vega, J. L.: Self-organized criticality driven by deterministic rules. Physical Review E 56, pp. 4876 – 4879 (1997)
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Acerbi, C.; Mussardo, G.; Valleriani, A.: On the form factors of relevant operators and their cluster property. Journal of Physics A: Mathematical and General 30 (9), pp. 2895 – 2913 (1997)
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Acerbi, C.; Valleriani, A.; Mussardo, G.: Form factors and correlation functions of the stress-energy tensor in massive deformation of the minimal models (E(n))(1)circle times(E(n))(1)/(E(n))(2). International Journal of Modern Physics A 11 (30), pp. 5327 – 5364 (1996)
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Valleriani, A.: Random walk with a boundary line as a free massive boson with a defect line. Journal of Physics A: Mathematical and General 29 (16), pp. 4885 – 4893 (1996)
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Ravanini, F.; Valleriani, A.; Tateo, R.: Dynkin TBA’s. International Journal of Modern Physics A 08 (10), pp. 1707 – 1727 (1993)
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Ravanini, F.; Tateo, R.; Valleriani, A.: A new family of diagonal ADE-related scattering theories. Physics Letters B 293, pp. 361 – 366 (1992)
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Complete List

Books, Chapters & more

Books

Lässig, M.; Valleriani, A. (Hg.): Biological evolution and statistical physics. Springer, Berlin (2002), 337 S.
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Book Chapters

Valleriani, A.: Stochastic modeling of complex macromolecular decay. In: Lectures in Pure and Applied Mathematics, Bd. 4, S. 1 – 28. Potsdam University Press, Potsdam (2017)
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Bastolla, U.; Lässig, M.; Manrubia, S. C.; Valleriani, A.: Dynamics and topology of species networks. In: Biological evolution and statistical physics, S. 299 – 311 (Hg. Valleriani, A.). Springer, Berlin (2002)
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Meeting Abstract

Rudorf, S.; Valleriani, A.; Lipowsky, R.: Dependence of Protein Synthesis on TRNA Concentrations. In Biophysical Journal, 104 (2 Suppl. 1), p. 257A – 257A. Cell Press, Cambridge, Mass. (2013)
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Working Paper

Valleriani, A.; Chiarugi, D.: A workbench for the translational control of gene expression. bioRxiv (2020)
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Editorial

Lipowsky, R.; Valleriani, A.: Active biomimetic systems: force generation and cargo transport by molecular machines. Biophysical Reviews and Letters 4 (1 & 2), pp. 1 – 4 (2009)
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