Publications

2021

Hernansaiz-Ballesteros, R. D., Földi, C., Cardelli, L., Nagy, L. G., & Csikász-Nagy, A. (2021). Evolution of opposing regulatory interactions underlies the emergence of eukaryotic cell cycle checkpoints. Scientific Reports, 11(1), 1-10. Link

Szep, G., Dalchau, N., & Csikasz-Nagy, A. (2021). Parameter Inference with Bifurcation Diagrams. arXiv preprint arXiv:2106.04243. Accepted in Advances in Neural Information Processing Systems, 34 Link to preprint

Reguly, I. Z., Csercsik, D., Juhasz, J., Tornai, K., Bujtar, Z., Horvath, G., Keömley-Horváth, B., Kós, T., Cserey, G., Iván, K., Pongor, S., Szederkényi, G., Röst, G., Csikász-Nagy, A. (2021). Microsimulation based quantitative analysis of COVID-19 management strategies. medRxiv. 10.1101/2021.06.20.21259214 Link

2020

Howell, R. S., Klemm, C., Thorpe, P. H., & Csikasz-Nagy, A. (2020). Unifying the mechanism of mitotic exit control in a spatio-temporal logical model. PLoS Biology, 18(11): e3000917. Link

Grant, P. K., Szep, G., Patange, O., Halatek, J., Coppard, V., Csikász-Nagy, A., Haseloff, J., Locke, JCW., Dalchau, N. & Phillips, A. (2020). Interpretation of morphogen gradients by a synthetic bistable circuit. Nature Communications, 11(1), 1-8. Link

Melnik, A., Cappelletti, V., Vaggi, F., Piazza, I., Tognetti, M., Schwarz, C., Cereghetti, G., Ahmed, M.A., Soste, M., Matlack, K., de Souza, N., Csikász-Nagy, A., Picotti, P. (2020). Comparative analysis of the intracellular responses to disease-related aggregation-prone proteins. Journal of Proteomics, 103862. Link

Yang, G., Csikász-Nagy, A., Waites, W., Xiao, G., & Cavaliere, M. (2020). information cascades and the collapse of cooperation. Scientific Reports, 10(1), 1-13. Link

Jenkins, K., Mateeva, T., Szabó, I., Melnik, A., Picotti, P., Csikász-Nagy, A., & Rosta, E. (2020). Combining data integration and molecular dynamics for target identification in∝-synuclein-aggregating neurodegenerative diseases: Structural insights on Synaptojanin-1. Computational and Structural Biotechnology Journal, 18, 1032-1042 Link

Cardelli, L., Laurenti, L., & Csikasz-Nagy, A. (2020). Coupled membrane transporters reduce noise. Physical Review E, 101(1), 012414. Link

2019

Moreno, D.F., Jenkins, K., Morlot, S., Charvin, G., Csikász-Nagy, A., and Aldea, M. (2019). Proteostasis collapse, a hallmark of aging, hinders the chaperone-Start network and arrests cells in G1 eLife, 8:e48240. Link

Moreno, D. F., Parisi, E., Yahya, G., Vaggi, F., Csikász-Nagy, A., & Aldea, M. (2019). Competition in the chaperone-client network subordinates cell-cycle entry to growth and stress. Life Science Alliance, 2(2), e201800277. Link

Howell, R. S., Csikász-Nagy, A., & Thorpe, P. H. (2019). Comparative analysis of Synthetic Physical Interactions with the yeast centrosome. bioRxiv, 514166. Link

2018

Rizzetto, S., & Csikász-Nagy, A. (2018). Toward Large-Scale Computational Prediction of Protein Complexes. In Computational Cell Biology (pp. 271-295). Humana Press, New York, NY. LINK

Hernansaiz-Ballesteros, R., Jenkins, K., & Csikász-Nagy, A. (2018). Computational Models of Cell Cycle Transitions. In Computational Cell Biology (pp. 297-316). Humana Press, New York, NY. LINK

Rizzetto, S., Moyseos, P., Baldacci, B., Priami, C., & Csikász-Nagy, A. (2018). Context-dependent prediction of protein complexes by SiComPre. NPJ systems biology and applications, 4(1), 37. LINK

Hernansaiz-Ballesteros, RD., Cardelli, L., Csikász-Nagy, A. (2018) Single molecules can operate as primitive biological sensors, switches and oscillators BMC Systems Biology 12:70 LINK

Laurenti, L., Csikász-Nagy, A., Kwiatkowska, M., Cardelli, L. (2018) Molecular Filters for Noise Reduction Biophysical Journal 114: 12, 3000 – 3011 LINK

Dalchau, N., Szép, G., Hernansaiz-Ballesteros, R., Barnes, C.P., Cardelli, L., Phillips, A., Csikász-Nagy A. (2018) Computing with biological switches and clocks Nat Comput. 17: 761–779 . LINK

Geymonat, M., Chessel, A., Dodgson, J., Punter, H., Horns, F., Csikasz-Nagy, A., & Carazo-Salas, R. E. (2018). Activation of polarized cell growth by inhibition of cell polarity. bioRxiv, 402990. LINK

2017

Dodgson, J., Chessel, A., Vaggi, F., Giordan, M., Yamamoto, M., Arai, K., Madrid M., Geymonat M., Abenza J.F., Cansado J., Sato M., Csikasz-Nagy A., Carazo-Salas R.E. (2017). Reconstructing regulatory pathways by systematically mapping protein localization interdependency networks. bioRxiv, 116749. LINK

Weil, T., Santamaría, R., Lee, W., Rung, J., Tocci, N., Abbey, D., Bezerra A.R., Carreto L., Moura G.R., Bayés M., Gut I.G., Csikasz-Nagy A, Cavalieri D., Berman J., Santos M.A.S: (2017). Adaptive Mistranslation Accelerates the Evolution of Fluconazole Resistance and Induces Major Genomic and Gene Expression Alterations in Candida albicans. mSphere, 2(4), e00167-17. LINK

Aldea M, Jenkins K, Csikász-Nagy A. (2017) Growth Rate as a Direct Regulator of the Start Network to Set Cell Size. Front Cell Dev Biol.5:57.

Cardelli L, Hernansaiz-Ballesteros RD, Dalchau N, Csikász-Nagy A. (2017) Efficient Switches in Biology and Computer Science. PLoS Comput Biol 13(1):e1005100

Palmisano A, Zámborszky J, Oguz C, Csikász-Nagy A. (2017) Molecular Network Dynamics of Cell Cycle Control: Periodicity of Start and Finish. Methods Mol Biol. 1524:331-349. Link

2016

Giordan M, Csikasz-Nagy A, Collings AM, Vaggi F. (2016) The effects of an editor serving as one of the reviewers during the peer-review process. F1000Res. 5:683

Cardelli L, Csikász-Nagy A, Dalchau N, Tribastone M, Tschaikowski M. (2016) Noise Reduction in Complex Biological Switches. Scientific Reports. 6:20214. doi: 10.1038/srep20214

Csikász-Nagy, A., & Mura, I. (2016). Role of Computational Modeling in Understanding Cell Cycle Oscillators. Cell Cycle Oscillators: Methods and Protocols, 59-70. DOI 10.1007/978-1-4939-2957-3

2015

Rizzetto S, Priami C, Csikász-Nagy A. (2015) Qualitative and Quantitative Protein Complex Prediction Through Proteome-Wide Simulations. PLoS Comput Biol. 11(10):e1004424. doi: 10.1371/journal.pcbi.1004424

Rivero D, Berná L, Stefanini I, Baruffini E, Bergerat A, Csikász-Nagy A, De Filippo C, Cavalieri D. (2015) Hsp12p and PAU genes are involved in ecological interactions between natural yeast strains. Environ Microbiol. doi: 10.1111/1462-2920.12950.

Kakui Y, Sunaga T, Arai K, Dodgson J, Ji L, Csikász-Nagy A, Carazo-Salas R, Sato M. (2015) Module-based construction of plasmids for chromosomal integration of the fission yeast Schizosaccharomyces pombe. Open Biol 5(6). pii: 150054

Honeth G, Schiavinotto T, Vaggi F, Marlow R, Kanno T, Shinomiya I, Lombardi S, Buchupalli B, Graham R, Gazinska P, Ramalingam V, Burchell J, Purushotham AD, Pinder SE, Csikasz-Nagy A, Dontu G. (2015) Models of Breast Morphogenesis Based on Localization of Stem Cells in the Developing Mammary Lobule. Stem Cell Reports 4,: 699-711.

2014

Zámborszky J, Csikász-Nagy A, Hong CI. (2014) Neurospora crassa as a model organism to explore the interconnected network of the cell cycle and the circadian clock. Fungal Genet Biol 71:52-7

Fernandes de Abreu, D.A., Caballero, A., Fardel, P., Stroustrup, N., Chen, Z., Lee, K., Keyes, W.D., Nash, Z.M., López-Moyado, I.F., Vaggi, F., Cornils, A., Regenass, M., Neagu, A., Ostojic, I., Liu, C., Cho, Y., Sifoglu, D., Shen, Y., Fontana, W., Lu, H., Csikasz-Nagy, A., Murphy, C.T., Antebi, A., Blanc, E., Apfeld, J., Zhang, Y., Alcedo, J., and Ch'ng, Q. (2014). An Insulin-to-Insulin Regulatory Network Orchestrates Phenotypic Specificity in Development and Physiology. PLoS Genet 10: e1004225.

Vaggi F, Schiavinotto T, Lawson JLD, Chessel A, Dodgson J, Geymonat M, Sato M, Carazo-Salas RE, Csikász-Nagy A (2014) A network approach to mixing delegates at meetings. eLife 3:e02273

Hong CI, Zámborszky J, Baek M, Labiscsak L, Ju K, Lee H, Larrondo LF, Goity A, Chong HS, Belden WJ, Csikász-Nagy A. (2014) Circadian Rhythms Synchronize Mitosis in Neurospora crassa. Proc Natl Acad Sci USA 111(4):1397-402

2013

Csikász-Nagy A, Sato M, Carazo Salas RE. (2013) Projecting cell polarity into the next decade. Philos Trans R Soc Lond B Biol Sci. 368(1629):20130001.

Bajpai A, Feoktistova A, Chen JS, McCollum D, Sato M, Carazo-Salas RE, Gould KL, Csikász-Nagy A. (2013) Dynamics of SIN Asymmetry Establishment. PLOS Computational Biology 9(7):e1003147

Csikász-Nagy A, Escudero LM, Guillaud M, Sedwards S, Baum B, Cavaliere M. (2013) Cooperation and competition in the dynamics of tissue architecture during homeostasis and tumorigenesis. Seminars in Cancer Biology 23:293-298

Dodgson J, Chessel A, Yamamoto M, Vaggi F, Cox S, Rosten E, Albrecht D, Geymonat M, Csikász-Nagy A, Sato M, Carazo-Salas RE. (2013) Spatial segregation of polarity factors into distinct cortical clusters is required for cell polarity control. Nature Communications 4:1834

Amara F, Colombo R, Cazzaniga P, Pescini D, Csikasz-Nagy A, Muzi Falconi M, Besozzi D, Plevani P, (2013) In vivo and in silico analysis of PCNA ubiquitylation in the activation of the Post Replication Repair pathway in S. cerevisiae. BMC Systems Biology 7:24

2012

Vaggi F, Dodgson J, Bajpai A, Chessel A, Jordan F, Sato M, Carazo-Salas RE, Csikász-Nagy A. (2012) Linkers of cell polarity and cell cycle regulation in the fission yeast protein interaction network. PLoS Computational Biology 8(10): e1002732

Cardelli L, Csikász-Nagy A. (2012) The Cell Cycle Switch Computes Approximate Majority. Scientific Reports 2:656

Ferrezuelo F., Colomina N., Palmisano A., Garí E., Gallego C., Csikász-Nagy A. & Aldea M. (2012) The critical size is set at a single-cell level by growth rate to attain homeostasis and adaptation. Nature Communications 3:1012

Romanel A, Cardelli L, Jensen LJ, Csikász-Nagy A (2012) Transcriptional regulation is a major controller of cell cycle transition dynamics. PLoS One 7: e29716

Cavaliere M, Sedwards, S, Tarnita CE, Nowak MA, Csikász-Nagy A (2012) Prosperity is associated with instability in dynamical networks. J Theor Biol 299:126-138

Moriya H, Chino A, Kapuy O, Csikász-Nagy A, Novak B. (2011) Overexpression limits of fission yeast cell-cycle regulators in vivo and in silico. Mol Sys Biol 7:556

2011

Csikász-Nagy A, Cardelli L, Soyer OS (2011) Response dynamics of phosphorelays suggest their potential utility in cell signaling J R Soc Interface 8(57):480-8

2010

Conradie R, Bruggeman FJ, Ciliberto A, Csikász-Nagy A, Novák B, Westerhoff HV, Snoep JL.(2010) Restriction point control of the mammalian cell cycle via the cyclin E/Cdk2:p27 complex. FEBS J. 277(2):357-67

Csikász-Nagy A, Mura I. (2010) Role of mRNA gestation and senescence in noise reduction during the cell cycle. In Silico Biol. 10:0006.

2009

Csikász-Nagy A. (2009) Computational Systems Biology of the Cell Cycle. Brief Bioinform. 10(4):424-34

Soyer OS, Kuwahara H, Csikász-Nagy A. (2009) Regulating the total level of a signaling protein can vary its dynamics in a range from switch like ultrasensitivity to adaptive responses. FEBS J. 276(12), 3290-3298

Hong CI., Zámborszky J. & Csikász-Nagy A. (2009) Minimum Criteria for DNA Damage-Induced Phase Advances in Circadian Rhythms. PLoS Comput Biol. 5(5):e1000384

Csikász-Nagy A., Kapuy O., Toth A., Pal C., Jensen, L.J. Uhlmann, F. Tyson, J.J. & Novák B. (2009) Cell cycle regulation by feed-forward loops coupling transcription and phosphorylation. Mol Sys Biol 5:236

2008

Mura I, Csikász-Nagy A. (2008) Stochastic Petri Net extension of a yeast cell cycle model. J Theor Biol. 254(4), 850-60

Csikász-Nagy A, Soyer OS. (2008) Adaptive dynamics with a single two-state protein. J R Soc Interface. Suppl 1:S41-7.

Lovrics A, Zsély IG, Csikász-Nagy A, Zádor J, Turányi T, et al. (2008) Analysis of a budding yeast cell cycle model using the shapes of local sensitivity functions. Int J Chem Kinet 40: 710-720.

Csikász-Nagy, A., Győrffy, B., Alt, W., Tyson, J.J. & Novák, B., (2008) Spatial controls for growth zone formation during the fission yeast cell cycle. Yeast, 25: 59–69.

2007

Zámborszky J., Hong CI. & Csikász-Nagy A. (2007) Computational Analysis of Mammalian Cell Division Gated by a Circadian Clock: Quantized Cell Cycles and Cell Size Control. J Biol Rhythms, 22: 542-53.

Novák B., Tyson JJ., Győrffy B. & Csikász-Nagy A. (2007) Irreversible cell cycle transitions due to systems-level feedback. Nat Cell Biol, 9, 724 - 728

Csikász-Nagy A., Kapuy O., Győrffy B., Tyson, J.J. & Novák, B., (2007) Modeling the Septation Initiation Network (SIN) in Fission Yeast Cells. Curr Genet, 51, 245-255

2006

Lovrics A., Csikász-Nagy A., Zsély I.G., Zádor J., Turányi T. & Novák B. (2006) Time scale and dimension analysis of a budding yeast cell cycle model. BMC Bioinformatics, 7, 494

Csikasz-Nagy A, Battogtokh D, Chen KC, Novák B & Tyson JJ. (2006) Analysis of a generic model of eukaryotic cell cycle regulation. Biophys J 90, 4361-4379

2004

Chen KC, Calzone L, Csikasz-Nagy A, Cross FR, Novak B, Tyson JJ. (2004) Integrative Analysis of Cell Cycle Control in Budding Yeast. Mol Biol Cell 15, 3841-3862.

2002

Tyson, J.J., Csikász-Nagy, A. & Novák, B. (2002): The Dynamics of Cell Cycle Regulation. Bioessays 24, 1095-1109

Sveiczer, Á., Csikász-Nagy, A. & Novák, B. (2002): Morphogenetic checkpoint in fission yeast? Yes! Microbiology 148, 2270-2271

2000

Sveiczer, Á., Csikász-Nagy, A., Gyorffy, B., Tyson, J. J., Novák, B. (2000) Modeling the fission yeast cell cycle: quantized cycle times in wee1^- cdc25D mutant cells. Proc Natl Acad Sci USA, 97, 7865-7870

Chen, KC., Csikasz-Nagy, A., Gyorffy, B., Val, J., Novak, B., & Tyson, J.J. (2000) Kinetic Analysis of a Molecular Model of the Budding Yeast Cell Cycle. Mol Biol Cell 11, 369–391

1999

Novák, B., Tóth, A., Csikász-Nagy, A., Gyorffy, B., Tyson, J.J. & Nasmyth, K. (1999) Finishing the Cell Cycle. J Theor Biol 199, 223-233

1998

Novák, B., Csikász-Nagy, A., Gyorffy, B., Chen, K. & Tyson, J.J. (1998) Mathematical model of the fission yeast cell cycle with checkpoint controls at the G1/S, G2/M and metaphase/anaphase transitions. Biophs Chem 72, 185-200

Novák, B., Csikász-Nagy, A., Gyorffy, B., Nasmyth, K. & Tyson, J.J. (1998) Model Scenarios for the Evolution of the Eukaryotic Cell Cycle. Phil Trans R Soc Lond B, 353, 2063-2076