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20002019
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Research Output 2000 2019

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Article
2019

Definition Of The Minimal Contents For The Molecular Simulation Of The Yeast Cytoplasm

Kompella, V. P. S., Stansfield, I., Romano, M. C. & Mancera, R. L., Oct 2019, In : Frontiers in Molecular Biosciences. 6, 9 p., 97.

Research output: Contribution to journalArticle

Open Access
File
Yeast
Proteins
Chemical analysis
Cell growth
Biomolecules
2018
6 Citations (Scopus)
4 Downloads (Pure)

Deciphering mRNA Sequence Determinants of Protein Production Rate

Szavits-Nossan, J., Ciandrini, L. & Romano, M. C., 23 Mar 2018, In : Physical Review Letters. 120, 12, 128101.

Research output: Contribution to journalArticle

Open Access
File
determinants
proteins
ribosomes
genome
nucleotides
2 Citations (Scopus)
4 Downloads (Pure)

Power series solution of the inhomogeneous exclusion process

Szavits-Nossan, J., Romano, M. C. & Ciandrini, L., 29 May 2018, In : Physical Review. E, Statistical, Nonlinear and Soft Matter Physics. 97, 5, 13 p., 052139.

Research output: Contribution to journalArticle

Open Access
File
Power Series Solution
Asymmetric Simple Exclusion Process
Exclusion Process
power series
exclusion
2017
7 Citations (Scopus)
5 Downloads (Pure)

Novel mRNA-specific effects of ribosome drop-off on translation rate and polysome profile

Bonnin, P., Kern, N., Young, N. T., Stansfield, I. & Romano, M. C., May 2017, In : PLoS Computational Biology . 13, 5, e1005555.

Research output: Contribution to journalArticle

Open Access
File
polyribosomes
Polyribosomes
ribosomes
Ribosomes
Messenger RNA
2016
7 Citations (Scopus)
8 Downloads (Pure)

Identification of the mRNA targets of tRNA-specific regulation using genome-wide simulation of translation

Gorgoni, B., Ciandrini, L., McFarland, M. R., Romano, M. C. & Stansfield, I., 2 Nov 2016, In : Nucleic Acids Research. 44, 19, p. 9231-9244 14 p.

Research output: Contribution to journalArticle

Open Access
File
Transfer RNA
Genome
Messenger RNA
Ribosomes
Codon
7 Citations (Scopus)
7 Downloads (Pure)

Synthetic biology routes to bio-artificial intelligence

Nesbeth, D. N., Zaikin, A., Saka, Y., Romano, M. C., Giuraniuc, C. V., Kanakov, O. & Laptyeva, T., 30 Nov 2016, In : Essays in Biochemistry. 60, 4, p. 381-391 11 p.

Research output: Contribution to journalArticle

Open Access
File
Synthetic Biology
Synthetic Genes
Gene Regulatory Networks
Artificial Intelligence
Artificial intelligence
2015
22 Citations (Scopus)
7 Downloads (Pure)

Integrative Model of Oxidative Stress Adaptation in the Fungal Pathogen Candida albicans

Chandrasekaran, K., Kaloriti, D., Tillmann, A. T., Yin, Z., Herrero De Dios, C., Jacobsen, M. D., Belmonte, R. C., Cameron, G., Haynes, K., Grebogi, C., de Moura, A. P. S., Gow, N. A. R., Thiel, M., Quinn, J., Brown, A. J. P. & Romano, M. C., 14 Sep 2015, In : PloS ONE. 10, 9, 0137750.

Research output: Contribution to journalArticle

Open Access
File
Oxidative stress
Candida
Pathogens
Candida albicans
Oxidative Stress
2014
12 Citations (Scopus)

Controlling translation elongation efficiency: tRNA regulation of ribosome flux on the mRNA

Gorgoni, B., Marshall, E., McFarland, M. R., Romano, M. C. & Stansfield, I., Feb 2014, In : Biochemical Society Transactions. 42, 1, p. 160-165 6 p.

Research output: Contribution to journalArticle

Transfer RNA
Ribosomes
Elongation
Fluxes
Gene expression
11 Citations (Scopus)

Minimal model of transcriptional elongation processes with pauses

Wang, J., Pfeuty, B., Thommen, Q., Romano Blasco, M. C. & Lefranc, M., 11 Nov 2014, In : Physical Review. E, Statistical, Nonlinear and Soft Matter Physics. 90, 5, p. 1-4 4 p., 050701.

Research output: Contribution to journalArticle

Minimal Model
Elongation
elongation
Transcription
exclusion
13 Citations (Scopus)
4 Downloads (Pure)

Ribosome recycling induces optimal translation rate at low ribosomal availability

Marshall, E., Stansfield, I. & Romano, M. C., 6 Sep 2014, In : Journal of the Royal Society Interface. 11, 98, 9 p., 20140589 .

Research output: Contribution to journalArticle

Open Access
File
Ribosomes
Recycling
Availability
Messenger RNA
Proteins
10 Citations (Scopus)

Stepping and Crowding of Molecular Motors: Statistical Kinetics from an Exclusion Process Perspective

Ciandrini, L., Romano, M. C. & Parmeggiani, A., 2 Sep 2014, In : Biophysical Journal. 107, 5, p. 1176-1184 9 p.

Research output: Contribution to journalArticle

Crowding
Enzymes
Biological Phenomena
Dyneins
Kinesin
2013
24 Citations (Scopus)

A yeast tRNA mutant that causes pseudohyphal growth exhibits reduced rates of CAG codon translation

Kemp, A., Betney, R., Ciandrini, L., Schwenger, A. C., Romano, M. C. & Stansfield, I., Jan 2013, In : Molecular Microbiology. 87, 2, p. 284–300 27 p.

Research output: Contribution to journalArticle

Transfer RNA
Codon
Open Reading Frames
Anticodon
Yeasts
9 Citations (Scopus)
5 Downloads (Pure)

From START to FINISH: the influence of osmotic stress on the cell cycle

Radmaneshfar, E., Kaloriti, D., Gustin, M. C., Gow, N. A. R., Brown, A. J. P., Grebogi, C., Romano, M. C. & Thiel, M., 10 Jul 2013, In : PloS ONE. 8, 7, 14 p., e68067.

Research output: Contribution to journalArticle

Open Access
File
59 Citations (Scopus)
5 Downloads (Pure)
Open Access
File
Gene Ontology
polyribosomes
Polyribosomes
ribosomes
Ribosomes

The wiper model: avalanche dynamics in an exclusion process

Politi, A. & Romano, M. C., Oct 2013, In : Journal of statistical mechanics-Theory and experiment. 2013, 18 p., 10015.

Research output: Contribution to journalArticle

15 Citations (Scopus)

Transport on a lattice with dynamical defects

Turci, F., Parmeggiani, A., Pitard, E., Romano, M. C. & Ciandrini, L., 2013, In : Physical Review. E, Statistical, Nonlinear and Soft Matter Physics. 87, 1, 8 p., 012705.

Research output: Contribution to journalArticle

ribosomes
Defects
Substrate
defects
Lattice Dynamics
2012
25 Citations (Scopus)

A max-plus model of ribosome dynamics during mRNA translation

Brackley, C. A., Broomhead, D. S., Romano, M. C. & Thiel, M., 21 Jun 2012, In : Journal of Theoretical Biology. 303, -, p. 128-140 13 p.

Research output: Contribution to journalArticle

Protein Biosynthesis
ribosomes
Ribosomes
Messenger RNA
translation (genetics)
16 Citations (Scopus)
8 Downloads (Pure)

A systems biology analysis of long and short-term memories of osmotic stress adaptation in fungi

You, T., Ingram, P., Jacobsen, M. D., Cook, E., McDonagh, A., Thorne, T., Lenardon, M. D., de Moura, A. P. S., Romano, M. C., Thiel, M., Stumpf, M., Gow, N. A. R., Haynes, K., Grebogi, C., Stark, J. & Brown, A. J. P., 25 May 2012, In : BMC Research Notes. 5, 16 p., 258.

Research output: Contribution to journalArticle

Open Access
File
Systems Biology
Long-Term Memory
Osmotic Pressure
Fungi
Short-Term Memory
53 Citations (Scopus)

Combinatorial stresses kill pathogenic Candida species

Kaloriti, D., Tillmann, A., Cook, E., Jacobsen, M., You, T., Lenardon, M., Ames, L., Barahona, M., Chandrasekaran, K., Coghill, G., Goodman, D., Gow, N. A. R., Grebogi, C., Ho, H-L., Ingram, P., McDonagh, A., de Moura, A. P. S., Pang, W., Puttnam, M., Radmaneshfar, E. & 10 others, Romano, M. C., Silk, D., Stark, J., Stumpf, M., Thiel, M., Thorne, T., Usher, J., Yin, Z., Haynes, K. & Brown, A. J. P., Oct 2012, In : Medical Mycology. 50, 7, p. 699-709 11 p.

Research output: Contribution to journalArticle

Candida glabrata
Candida albicans
Candida
Oxidative Stress
Growth
35 Citations (Scopus)

Mixed population of competing totally asymmetric simple exclusion processes with a shared reservoir of particles

Greulich, P., Ciandrini, L., Allen, R. & Romano, M. C., 27 Jan 2012, In : Physical Review. E, Statistical, Nonlinear and Soft Matter Physics. 85, 1, 11 p., 011142.

Research output: Contribution to journalArticle

Asymmetric Simple Exclusion Process
exclusion
lattice parameters
Mean Field
Entire
7 Citations (Scopus)

Multiple phase transitions in a system of exclusion processes with limited reservoirs of particles and fuel carriers

Brackley, C., Ciandrini, L. & Romano, M. C., 6 Mar 2012, In : Journal of statistical mechanics-Theory and experiment. 2012, 3, 23 p., P03002 .

Research output: Contribution to journalArticle

Exclusion Process
exclusion
resources
Phase Transition
Resources
2011
8 Citations (Scopus)
5 Downloads (Pure)
Open Access
File
Chemical Kinetics
Reaction kinetics
Yeast
Open Reading Frames
Modeling and Simulation
23 Citations (Scopus)

Inferring direct coupling by means of recurrences

Zou, Y., Romano, M. C., Thiel, M., Marwan, N. & Kurths, J., Apr 2011, In : International Journal of Bifurcation and Chaos. 21, 4, p. 1099-1111 13 p.

Research output: Contribution to journalArticle

Recurrence
Time series
Time series analysis
Hinges
Multivariate Time Series
28 Citations (Scopus)
5 Downloads (Pure)

The dynamics of supply and demand in mRNA translation

Brackley, C. A., Romano, M. C. & Thiel, M., 13 Oct 2011, In : PLoS Computational Biology . 7, 10, 16 p., e1002203.

Research output: Contribution to journalArticle

Open Access
File
supply balance
Protein Biosynthesis
Transfer RNA
Elongation
Messenger RNA
2010
3 Citations (Scopus)

An automated algorithm for the generation of dynamically reconstructed trajectories

Komalapriya, C., Romano, M. C., Thiel, M., Marwan, N., Kurths, J., Kiss, I. Z. & Hudson, J. L., Mar 2010, In : Chaos. 20, 1, 9 p., 013107.

Research output: Contribution to journalArticle

Trajectories
trajectories
Trajectory
Optimal Parameter
Term
52 Citations (Scopus)
9 Downloads (Pure)

Distinguishing Direct from Indirect Interactions in Oscillatory Networks with Multiple Time Scales

Nawrath, J., Romano, M. C., Thiel, M., Kiss, I. Z., Wickramasinghe, M., Timmer, J., Kurths, J. & Schelter, B., 22 Jan 2010, In : Physical Review Letters. 104, 3, 4 p., 038701.

Research output: Contribution to journalArticle

Open Access
File
oscillators
synchronism
interactions
8 Citations (Scopus)
6 Downloads (Pure)

Introduction to Focus Issue: Dynamics in Systems Biology

Brackley, C. A., Ebenhoeh, O., Grebogi, C., Kurths, J., de Moura, A., Romano, M. C. & Thiel, M., Dec 2010, In : Chaos. 20, 4, 3 p., 045101.

Research output: Contribution to journalArticle

Open Access
File
Graph theory
Circuit theory
Systems Biology
Mathematical Analysis
biology
14 Citations (Scopus)

Limited resources in a driven diffusion process

Brackley, C. A., Romano, M. C., Grebogi, C. & Thiel, M., 13 Aug 2010, In : Physical Review Letters. 105, 7, 4 p., 078102.

Research output: Contribution to journalArticle

resources
availability
amino acids
depletion
molecules
50 Citations (Scopus)
3 Downloads (Pure)
Open Access
File
Asymmetric Exclusion Process
exclusion
Asymmetric Simple Exclusion Process
Messenger RNA
ribosomes
8 Citations (Scopus)

Slow sites in an exclusion process with limited resources

Brackley, C. A., Romano, M. C. & Thiel, M., Nov 2010, In : Physical Review. E, Statistical, Nonlinear and Soft Matter Physics. 82, 5 Pt 1, 051920.

Research output: Contribution to journalArticle

ribonucleic acids
Exclusion Process
Queuing
exclusion
Messenger RNA
2009
5 Citations (Scopus)

Analysis of high-resolution microelectrode EEG recordings in an animal model of spontaneous limbic seizures

Komalapriya, C., Romano, M. C., Thiel, M., Schwarz, U., Kurths, J., Simonotto, J., Furman, M., Ditto, W. L. & Carney, P. R., Feb 2009, In : International Journal of Bifurcation and Chaos. 19, 2, p. 605–617 13 p.

Research output: Contribution to journalArticle

Animal Model
Microelectrodes
Electroencephalography
Precursor
Spectrum analysis
21 Citations (Scopus)

Hypothesis test for synchronization: Twin surrogates revisited

Romano, M. C., Thiel, M., Kurths, J., Mergenthaler, K. & Engbert, R., 31 Mar 2009, In : Chaos. 19, 1, 14 p., 015108.

Research output: Contribution to journalArticle

eye movements
Eye movements
Hypothesis Test
synchronism
Synchronization
71 Citations (Scopus)

Influence of paced maternal breathing on fetal–maternal heart rate coordination

Van Leeuwen, P., Geue, D., Thiel, M., Cysarz, D., Lange, S., Romano, M. C., Wessel, N., Kurths, J. & Groenemeyer, D. H., 18 Aug 2009, In : PNAS. 106, 33, p. 13661-13666 6 p.

Research output: Contribution to journalArticle

Respiration
Heart Rate
Mothers
Respiratory Rate
Cardiac Arrhythmias
36 Citations (Scopus)

Queueing phase transition: Theory of Translation

Romano, M. C., Thiel, M., Stansfield, I. & Grebogi, C., 15 May 2009, In : Physical Review Letters. 102, 19, 4 p., 198104.

Research output: Contribution to journalArticle

proteins
configurations
2008
1 Citation (Scopus)

Continuous wavelet transform in the analysis of burst synchronization in a coupled laser system

Bergner, A., Meucci, R., Al Naimee, K., Romano, M. C., Thiel, M., Kurths, J. & Arecchi, F. T., 25 Jul 2008, In : Physical Review. E, Statistical, Nonlinear and Soft Matter Physics. 78, 1, 7 p., 016211.

Research output: Contribution to journalArticle

23 Citations (Scopus)

Generating surrogates from recurrences

Thiel, M., Romano, M. C., Kurths, J., Rolfs, M. & Kliegl, R., 28 Feb 2008, In : Philosophical Transactions of the Royal Society A: Mathematical, Physical & Engineering Sciences. 366, 1865, p. 545-557 13 p.

Research output: Contribution to journalArticle

15 Citations (Scopus)

Reconstruction of a system's dynamics from short trajectories

Komalapriya, C., Thiel, M., Romano, M. C., Marwan, N., Schwarz, U. & Kurths, J., 24 Dec 2008, In : Physical Review. E, Statistical, Nonlinear and Soft Matter Physics. 78, 6, 11 p., 066217.

Research output: Contribution to journalArticle

2007
6 Citations (Scopus)

Analytical description of recurrence plots of dynamical systems with nontrivial recurrences

Zou, Y., Thiel, M., Romano, M. C. & Kurths, J., Dec 2007, In : International Journal of Bifurcation and Chaos. 17, 12, p. 4273-4283 11 p.

Research output: Contribution to journalArticle

Recurrence Plot
Quasi-periodic Motion
Recurrence
Dynamical systems
Dynamical system
16 Citations (Scopus)

Characterization of stickiness by means of recurrence

Zou, Y., Thiel, M., Romano, M. C. & Kurths, J., 12 Oct 2007, In : Chaos. 17, 4, 8 p., 043101.

Research output: Contribution to journalArticle

86 Citations (Scopus)
Conditional probability
Recurrence
Asymmetry
asymmetry
Coupled System
26 Citations (Scopus)

Recurrence analysis of strange nonchaotic dynamics

Ngamga, E. J., Nandi, A., Ramaswamy, R., Romano, M. C., Thiel, M. & Kurths, J., 29 Mar 2007, In : Physical Review. E, Statistical, Nonlinear and Soft Matter Physics. 75, 3, 8 p., 036222.

Research output: Contribution to journalArticle

strange attractors
Strange attractor
Recurrence
Chaotic Motion
Additive Noise
1583 Citations (Scopus)

Recurrence Plots for the Analysis of Complex Systems

Marwan, N., Romano, M. C., Thiel, M. & Kurths, J., 12 Jan 2007, In : Physics Reports. 438, 5-6, p. 237-329 93 p.

Research output: Contribution to journalArticle

2006
4 Citations (Scopus)

Recurrence plot analyses suggests a novel reference system in newborn spontaneous movements

Aszmann, B., Thiel, M., Romano, M. C. & Niemitz, C., Aug 2006, In : Behavior Research Methods. 38, 3, p. 400-406 7 p.

Research output: Contribution to journalArticle

17 Citations (Scopus)

Shrimp Structure and Associated Dynamics in Parametrically Excited Oscillators

Zou, Y., Thiel, M., Romano, M. C., Bi, Q. & Kurths, J., 2006, In : International Journal of Bifurcation and Chaos. 16, 12, p. 3567-3579 13 p.

Research output: Contribution to journalArticle

Convergence of numerical methods
Parameter Space
Large scale systems
Numerical analysis
Entropy
23 Citations (Scopus)

Spurious Structures in Recurrence Plots Induced by Embedding

Thiel, M., Romano, M. C. & Kurths, J., 2006, In : Nonlinear Dynamics. 44, 1-4, p. 299-305 7 p.

Research output: Contribution to journalArticle

85 Citations (Scopus)

Twin surrogates to test for complex synchronisation

Thiel, M., Romano, M. C., Kurths, J., Rolfs, M. & Kliegl, R., Aug 2006, In : Europhysics Letters. 75, 4, p. 535-541 6 p.

Research output: Contribution to journalArticle

2005
124 Citations (Scopus)

Detection of Synchronization for Non-Phase Coherent and Non-stationary Data

Romano, M. C., Thiel, M., Kurths, J., Kiss, I. Z. & Hudson, J. L., 2005, In : Europhysics Letters. 71, 3, p. 466-472 7 p.

Research output: Contribution to journalArticle

2004
128 Citations (Scopus)

Estimation of dynamical invariants without embedding by recurrence plots

Thiel, M., Romano, M. C., Kurths, J. & Read, P., Jun 2004, In : Chaos. 14, 2, p. 234-243 10 p.

Research output: Contribution to journalArticle

100 Citations (Scopus)

How much information is contained in a Recurrence Plot?

Thiel, M., Romano, M. C. & Kurths, J., Sep 2004, In : Physics Letters A. 330, 5, p. 343-349 6 p.

Research output: Contribution to journalArticle

84 Citations (Scopus)

Multivariate Recurrence Plots

Romano, M. C., Thiel, M., Kurths, J. & von Bloh, W., Sep 2004, In : Physics Letters A. 330, 3-4, p. 214-223 10 p.

Research output: Contribution to journalArticle