Synthetic Microbiology (Becskei)

Delaney, Colin E. et al. (2024) ‘H3K9 methylation-independent activity for HPL-2/HP1 in heterochromatin foci, gene repression, and organogenesis’, bioRxiv [Preprint]. bioRxiv: Cold Spring Harbor Laboratory. Available at: https://doi.org/10.1101/2024.09.29.615660.

Rahaman, Sayanur et al. (2023) ‘Polysome propensity and tunable thresholds in coding sequence length enable differential mRNA stability’, Science Advances, 9(39), p. eadh9545. Available at: https://doi.org/10.1126/sciadv.adh9545.

Becskei, Attila and Rahaman, Sayanur (2022) ‘The life and death of RNA across temperatures’, Computational and structural biotechnology journal, 20, pp. 4325–4336. Available at: https://doi.org/10.1016/j.csbj.2022.08.008.

Jaquet, Vincent et al. (2022) ‘Determinants of the temperature adaptation of mRNA degradation’, Nucleic Acids Research, 50(2), pp. 1092–1110. Available at: https://doi.org/10.1093/nar/gkab1261.

Iakovlev, Mikhail, Faravelli, Simone and Becskei, Attila (2021) ‘Gene Families With Stochastic Exclusive Gene Choice Underlie Cell Adhesion in Mammalian Cells’, Frontiers in Cell and Developmental Biology, 9, p. 642212. Available at: https://doi.org/10.3389/fcell.2021.642212.

Becskei, Attila (2020) ‘Tuning up Transcription Factors for Therapy’, Molecules, 25(8), p. 1902. Available at: https://doi.org/10.3390/molecules25081902.

Baudrimont, Antoine et al. (2019) ‘Contribution of RNA Degradation to Intrinsic and Extrinsic Noise in Gene Expression’, Cell reports, 26(13), pp. 3752–3761.e5. Available at: https://doi.org/10.1016/j.celrep.2019.03.001.

Wada, Takeo, Wallerich, Sandrine and Becskei, Attila (2019) ‘Synthetic transcription factors switch from local to long-range control during cell differentiation’, ACS Synthetic Biology, 8(2), pp. 223–231. Available at: https://doi.org/10.1021/acssynbio.8b00369.

Wada, Takeo, Wallerich, Sandrine and Becskei, Attila (2018) ‘Stochastic Gene Choice during Cellular Differentiation’, Cell reports, 24(13), pp. 3503–3512. Available at: https://doi.org/10.1016/j.celrep.2018.08.074.

Baudrimont, Antoine et al. (2017) ‘Multiplexed gene control reveals rapid mRNA turnover’, Science Advances, 3(7), p. e1700006. Available at: https://doi.org/10.1126/sciadv.1700006.

Gencoglu, Mumun, Schmidt, Alexander and Becskei, Attila (2017) ‘Measurement of in vivo protein binding affinities in a signaling network with mass spectrometry’, ACS Synthetic Biology, 6(7), pp. 1305–1314. Available at: https://doi.org/10.1021/acssynbio.6b00282.

Jaquet, Vincent, Hsu, Chieh and Becskei, Attila (2017) ‘Measurement of bistability in a multidimensional parameter space’, Integrative Biology, 9(2), pp. 167–177. Available at: https://doi.org/10.1039/c6ib00242k.

Maleki, Farzaneh and Becskei, Attila (2017) ‘An open-loop approach to calculate noise-induced transitions’, Journal of Theoretical Biology, 415, pp. 145–157. Available at: https://doi.org/10.1016/j.jtbi.2016.12.012.

Wada, Takeo and Becskei, Attila (2017) ‘Impact of Methods on the Measurement of mRNA Turnover’, International Journal of Molecular Sciences, 18(12), p. 12. Available at: https://doi.org/10.3390/ijms18122723.

Hsu, Chieh et al. (2016) ‘Protein Dimerization Generates Bistability in Positive Feedback Loops’, Cell Reports, 16(5), pp. 1204–10. Available at: https://doi.org/10.1016/j.celrep.2016.06.072.

Hsu, Chieh et al. (2016) ‘Contribution of bistability and noise to cell fate transitions determined by feedback opening’, Journal of Molecular Biology, 428(20), pp. 4115–4128. Available at: https://doi.org/10.1016/j.jmb.2016.07.024.

Baudrimont, Antoine and Becskei, Attila (2015) ‘Gene regulation: Expression feels two pulses’, Nature, pp. 46–7. Available at: https://doi.org/10.1038/nature15634.

Májer, Imre, Hajihosseini, Amirhossein and Becskei, Attila (2015) ‘Identification of optimal parameter combinations for the emergence of bistability’, Physical biology, 12(6), p. 066011. Available at: https://doi.org/10.1088/1478-3975/12/6/066011.

Bonde, Marie Mi et al. (2014) ‘Quantification of pre-mRNA escape rate and synergy in splicing’, Nucleic acids research, 42(20), pp. 12847–60. Available at: https://doi.org/10.1093/nar/gku1014.

Stölting, Meline Nogueira Lucena et al. (2013) ‘Myoblasts inhibit prostate cancer growth by paracrine secretion of tumor necrosis factor-α’, Journal of Urology, 189(5), pp. 1952–9. Available at: https://doi.org/10.1016/j.juro.2012.10.071.

Hsu, Chieh et al. (2012) ‘Stochastic signalling rewires the interaction map of a multiple feedback network during yeast evolution’, Nature communications, 3, p. 682. Available at: https://doi.org/10.1038/ncomms1687.

Becskei, Attila et al. (2011) ‘Modeling of chromosomal epigenetic silencing processes’, Transcription, 2(4), pp. 173–178. Available at: https://doi.org/10.4161/trns.2.4.16344.

Ratna, Prasuna and Becskei, Attila (2011) ‘Construction of cis-regulatory input functions of yeast promoters’, in Becskei, Attila (ed.) Yeast Genetic Networks. Basel: Springer Nature (Methods in Molecular Biology), pp. 45–61. Available at: https://doi.org/10.1007/978-1-61779-086-7_3.

Kelemen, János Z. et al. (2010) ‘Spatial epigenetic control of mono- and bistable gene expression’, PLoS Biology, 8(3), p. e1000332. Available at: https://doi.org/10.1371/journal.pbio.1000332.

Sun, Li and Becskei, Attila (2010) ‘Systems biology: The cost of feedback control’, Nature, pp. 163–4. Available at: https://doi.org/10.1038/467163a.

Becskei, Attila (2009) ‘Linearization through distortion: a new facet of negative feedback in signalling’, Molecular Systems Biology, 5, p. 255. Available at: https://doi.org/10.1038/msb.2009.14.

Buetti-Dinh, Antoine et al. (2009) ‘Control and signal processing by transcriptional interference’, Molecular Systems Biology, 5, p. 300. Available at: https://doi.org/10.1038/msb.2009.61.

Byun, Reine and Becskei, Attila (2009) ‘Biology inspires engineering’, Genome Biology, p. 317. Available at: https://doi.org/10.1186/gb-2009-10-11-317.

Ratna, Prasuna et al. (2009) ‘Synergy of repression and silencing gradients along the chromosome’, Journal of Molecular Biology, 387(4), pp. 826–39. Available at: https://doi.org/10.1016/j.jmb.2009.02.025.

Becskei, Attila and Grusby, Michael J. (2007) ‘Contribution of IL-12R mediated feedback loop to Th1 cell differentiation’, FEBS Letters, 581(27), pp. 5199–206. Available at: https://doi.org/10.1016/j.febslet.2007.10.007.

Acar, Murat, Becskei, Attila and van Oudenaarden, Alexander (2005) ‘Enhancement of cellular memory by reducing stochastic transitions’, Nature, 435(7039), pp. 228–32. Available at: https://doi.org/10.1038/nature03524.

Becskei, Attila, Kaufmann, Benjamin B. and van Oudenaarden, Alexander (2005) ‘Contributions of low molecule number and chromosomal positioning to stochastic gene expression’, Nature Genetics, 37(9), pp. 937–44. Available at: https://doi.org/10.1038/ng1616.

Becskei, Attila and Mattaj, Iain W. (2005) ‘Quantitative models of nuclear transport’, Current Opinion in Cell Biology, 17(1), pp. 27–34. Available at: https://doi.org/10.1016/j.ceb.2004.12.010.

Ozbudak, Ertugrul M., Becskei, Attila and van Oudenaarden, Alexander (2005) ‘A system of counteracting feedback loops regulates Cdc42p activity during spontaneous cell polarization’, Developmental Cell, 9(4), pp. 565–71. Available at: https://doi.org/10.1016/j.devcel.2005.08.014.

Becskei, Attila, Boselli, Monica G. and van Oudenaarden, Alexander (2004) ‘Amplitude control of cell-cycle waves by nuclear import’, Nature Cell Biology, 6(5), pp. 451–7. Available at: https://doi.org/10.1038/ncb1124.

Becskei, Attila and Mattaj, Iain W. (2003) ‘The strategy for coupling the RanGTP gradient to nuclear protein export’, Proceedings of the National Academy of Sciences of the United States of America, 100(4), pp. 1717–22. Available at: https://doi.org/10.1073/pnas.252766999.

Louis, Matthieu and Becskei, Attila (2002) ‘Binary and graded responses in gene networks’, Science Signaling, 2002(143), p. pe33. Available at: https://doi.org/10.1126/stke.2002.143.pe33.

Becskei, A., Séraphin, B. and Serrano, L. (2001) ‘Positive feedback in eukaryotic gene networks: cell differentiation by graded to binary response conversion’, The EMBO Journal, 20(10), pp. 2528–35. Available at: https://doi.org/10.1093/emboj/20.10.2528.

Becskei, A. and Serrano, L. (2000) ‘Engineering stability in gene networks by autoregulation’, Nature, 405(6786), pp. 590–3. Available at: https://doi.org/10.1038/35014651.

Jancsó, G. et al. (1998) ‘Beta-amyloid (1-42) peptide impairs blood-brain barrier function after intracarotid infusion in rats’, Neuroscience Letters, 253(2), pp. 139–41. Available at: https://doi.org/10.1016/s0304-3940(98)00622-3.