Publications

Journal Article

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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Journal Article

Thai, E.; Costa, G.; Weyrich, A.; Murugan, R.; Oyen, D.; Prieto, K.; Bosch, A.; Valleriani, A.; Wu, N. C.; Pholcharee, T. et al.; Scally, S. W.; Wilson, I. A.; Wardemann, H.; Julien, J.-P.; Levashina, E. A.: 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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Journal Article

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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Journal Article

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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Full

Journal Article

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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Journal Article

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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Journal Article

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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Journal Article

McShane, E.; Sin, C.; Zauber, H.; Wells, J.; Donnelly, N.; Wang, X.; Hou, J.; Chen, W.; Storchova, Z.; Marsh, J. et al.; Valleriani, A.; Selbach, M.: Kinetic analysis of protein stability reveals age-dependent degradation. Cell 167 (3), pp. 803 - 815.e21 (2016)

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10.

Journal Article

Olarte, C.; Chiarugi, D.; Falaschi, M.; Hermith, D.: A proof theoretic view of spatial and temporal dependencies in biochemical systems. Theoretical Computer Science 641, pp. 25 - 42 (2016)

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11.

Journal Article

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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12.

Journal Article

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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13.

Journal Article

Sin, C.; Chiarugi, D.; Valleriani, A.: Degradation parameters from pulse-chase experiments. PLoS One 11 (5), e0155028 (2016)

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14.

Journal Article

Valleriani, A.: A conditional likelihood is required to estimate the selection coefficient in ancient DNA. Scientific Reports 6, 31561 (2016)

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15.

Journal Article

Bodei, C.; Bortolussi, L.; Chiarugi, D.; Guerriero, M. L.; Policriti, A.; Romanel, A.: On the impact of discreteness and abstractions on modelling noise in gene regulatory networks. Computational Biology and Chemistry 56, pp. 98 - 108 (2015)

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16.

Journal Article

Chiarugi, D.; Falaschi, M.; Hermith, D.; Olarte, C.: Verification of spatial and temporal modalities in biochemical systems. Electronic Notes in Theoretical Computer Science 316, pp. 29 - 44 (2015)

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17.

Journal Article

Chiarugi, D.; Falaschi, M.; Hermith, D.; Olarte, C.; Torella, L.: Modelling non-Markovian dynamics in biochemical reactions. BMC Systems Biology 9 (Suppl 3), S8 (2015)

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18.

Journal Article

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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19.

Journal Article

Keller, P.; Rœlly, S.; Valleriani, A.: On time duality for Markov chains. Stochastic Models 31 (1), pp. 98 - 118 (2015)

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20.

Journal Article

Paradisi, P.; Allegrini, P.; Chiarugi, D.: A renewal model for the emergence of anomalous solute crowding in liposomes. BMC Systems Biology 9 (Suppl 3), S7 (2015)

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21.

Journal Article

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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22.

Journal Article

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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23.

Journal Article

Valleriani, A.: Circular analysis in complex stochastic systems. Scientific Reports 5, 17986 (2015)

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24.

Journal Article

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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25.

Journal Article

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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26.

Journal Article

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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27.

Journal Article

Deneke, C.; Lipowsky, R.; Valleriani, A.: Effect of ribosome shielding on mRNA stability. Physical Biology 10 (4), 046008 (2013)

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28.

Journal Article

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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29.

Journal Article

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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30.

Journal Article

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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31.

Journal Article

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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32.

Journal Article

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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33.

Journal Article

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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34.

Journal Article

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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35.

Journal Article

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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36.

Journal Article

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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37.

Journal Article

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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38.

Journal Article

Menche, J.; Valleriani, A.; Lipowsky, R.: Dynamical processes on dissortative scale-free networks. EPL 89 (1), 18002 (2010)

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39.

Journal Article

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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40.

Journal Article

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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41.

Journal Article

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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42.

Journal Article

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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43.

Journal Article

Valleriani, A.; Liepelt, S.; Lipowsky, R.: Dwell time distributions for kinesin's mechanical steps. EPL 82 (2), 28011 (2008)

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44.

Journal Article

Valleriani, A.; Meene, T.: Multilevel selection in a gradient. Ecological Modelling 208 (2-4), pp. 159 - 164 (2007)

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45.

Journal Article

Valleriani, A.: Evolutionarily stable germination strategies with time-correlated yield. Theoretical Population Biology 70 (3), pp. 255 - 261 (2006)

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46.

Journal Article

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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47.

Journal Article

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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48.

Journal Article

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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49.

Journal Article

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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50.

Journal Article

Valleriani, A.: Algebraic determination of the evolutionary stable germination fraction. Theoretical Population Biology 68 (3), pp. 197 - 203 (2005)

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51.

Journal Article

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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52.

Journal Article

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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53.

Journal Article

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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54.

Journal Article

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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Book (1)

55.

Book

Lässig, M.; Valleriani, A. (Eds.): Biological evolution and statistical physics. Springer, Berlin (2002), 337 pp.

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Book Chapter (2)

56.

Book Chapter

Chiarugi, D.; Falaschi, M.; Olarte, C.; Palamidessi, C.: A Declarative View of Signaling Pathways. In: Lecture Notes in Computer Science, Vol. 9465. Springer, Cham (2015)

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57.

Book Chapter

Bastolla, U.; Lässig, M.; Manrubia, S. C.; Valleriani, A.: Dynamics and topology of species networks. In: Biological evolution and statistical physics, pp. 299 - 311 (Ed. Valleriani, A.). Springer, Berlin (2002)

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Meeting Abstract (1)

58.

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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Thesis - PhD (1)

59.

Thesis - PhD

Sin, C.: Post-transcriptional control of gene expression. Dissertation, 238 pp., Universität Potsdam, Potsdam (2016)

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Working Paper (2)

60.

Working Paper

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

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External

61.

Working Paper

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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Full

Editorial (1)

62.

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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