Publications
(Equal contribution is shown by †, joint corresponding authorship * )
coming soon ...
XM Sun, A Bowman, M Priestman, F Bertaux, A Martinez-Segura, W Tang, D Dormann, V Shahrezaei*, S Marguerat*
bioRxiv, 754788
Ohm's Law for emergent gene expression under fitness pressure
M Ciechonska, M Sturrock, A Grob, G Larrouy-Maumus, V Shahrezaei*, M Isalan*
bioRxiv, 693234
A bacterial size law revealed by a coarse-grained model of cell physiology
F Bertaux, J Von Kügelgen, S Marguerat, V Shahrezaei
bioRxiv, 078998
Already published …
W Tang, N Ranganathan, V Shahrezaei*, G Larrouy-Maumus*
PloS one 14 (6), e0218951 (2019)
NP Dyer, V Shahrezaei, D Hebenstreit
PeerJ 7, e6222 (2019)
bayNorm: Bayesian gene expression revovery, imputaiton and normalisation for single cell RNA-sequencing data
Tang, W., Bertaux, F., Stefanelli, C., Saint, M., Marguerat, S.*, Shahrezaei, V.*
bioRxiv 384586 (2018) (accepted in Bioinformatics; 2019)
Single Cell Phenotyping and RNA sequencing reveal novel patterns of gene expression heterogeneity and regulation during growth and stress adaptation in a unicellular eukaryote
Saint, M., Bertaux, F., Tang, W., Sun, X., Game, L., Koferle, A., Bahler, J., Shahrezaei, V.*, Marguerat, S.*
Nature microbiology 4 (3), 480-491 (2019)
Analysis of ParAB dynamics in mycobacteria shows active movement of ParB and differential inheritance of ParA
Uhia I., Priestman, M., Joyce G., Krishnan N., Shahrezaei, V., Robertson, B.D.
Divsion rate, cell size and proteome allocation: impact on gene expression noise and implications for the dynamics of genetic circuits
Bertaux, F., Marguerat S.* , Shahrezaei, V.*
Royal Society Open Science 5, 172234 (2018)
Mycobacteria Modify Their Cell Size Control under Sub-Optimal Carbon Sources
Priestman, M., Thomas, P., Robertson, B.D.*, Shahrezaei, V.*
Front. Cell Dev. Biol. 5:64 (2017)
The influence of nuclear compartmentalisation on stochastic dynamics of self-repressing gene expression
Sturrock, M.*, Li, S., Shahrezaei, V.*
Journal of Theoretical Biology 424, 55-72 (2017).
Modelling enzyme processivity reveals that RNA-seq libraries are biased in characteristic and correctable ways.
Archer, N., Walsh, M., Shahrezaei, V.*, Hebenstreit, D.*
Cell Systems 3, 467-479.e12 (2016).
Connecting growth with gene expression: of noise and numbers.
Shahrezaei, V.*, Marguerat S.*
Curr. Opin. Microbiol. 25, 127-135 (2015).
General transient solution of the one-step master equation in one dimension.
Smith, S., Shahrezaei, V.
Phys. Rev. E 91, 062119 (2015)
Mycobacterial Growth.
Uhia-Castro I., Williams K.J., Shahrezaei, V., Robertson B.D.
Cold Spring Harbor Perspec Med doi: 10.1101/cshperspect.a021097 (2015).
Stochastic cellular fate decision making by multiple infecting Lambda phage.
Robb M., Shahrezaei, V.
A novel biosensor architecture is predicted to reduce nonlinear reporting of signaling protein activity.
Dushek O.*, Lellouch A., Vaux D., Shahrezaei, V*.
Biophycial J. 107, 773-82 (2014).
Uncaging Calcium in Neurons
Delaney K.R., Shahrezaei, V.
Cold Spring Harb Protoc. (2013).
Cell division-site placement and asymmetric growth in mycobacteria.
Joyce, G., Williams, K.J., Robb M., Noens, E., Tizzano, B., Shahrezaei, V., Robertson, B.D.
Bell-shaped and ultrasensitive dose-response in phosphorylation-dephosphorylation cycles: the role of kinase-phosphatase complex formation.
Szomolay B., Shahrezaei, V.
BMC Systems Biology 6, 26 (2012).
Mathematical modelling of bovine immunodynamcis in response to multiple foot-and mouth disease virus vaccinations: the effect of antigen stability and doses.
Schley, D., Leungchavaphogse, K., Tanaka, R., Shahrezaei, V., Ward, J., Charleston, B. and Rhodes, C.J.
PLOS One 7, e30435 (2012).
Ultrasensitivity in multisite membrane protein phosphorylations.
Dushek, O.*, van der Merwe, P.A., Shahrezaei, V.*
Biophys. J. 100, 1189-1197 (2011).
Scalable rule-based modelling of allosteric proteins and biochemical networks.
Ollivier J.F., Shahrezaei, V., Swain, P.S.
PLOS Computational Biology 6, e1000975 (2010).
The Ste5 scaffold protein directly controls a switch-like mating decision in yeast.
Malleshaiah, M.†, Shahrezaei, V.†, Swain, P.S., Michnick, S.W.
Nature 465, 101-105 (2010).
Evaluated on Faculty of 100 Biology: http://f1000.com/7337956; Media coverage by Eureka (the Times’ monthly science magazine), The Metro, The Canberra Times, Irish Sun and several other newspapers and science websites.
The stochastic nature of biochemical networks.
Shahrezaei, V., Swain, P.S.
Curr. Opin. Biotechnol. 19, 369-374 (2008).
Analytical distributions for stochastic gene expression.
Shahrezaei, V., Swain, P.S.
Proc Natl Acad Sci USA 105, 17256 (2008).
Selected for the virtual journal of biological physics.
Colored extrinsic fluctuations and stochastic gene expression
Shahrezaei, V., Ollivier, J., Swain, P.S.
Mol. Syst. Biol. 4, 196 (2008).
Calcium from one or two channels controls fusion of a single vesicle at the frog neuromuscular junction.
Shahrezaei, V.†, Cao, A.†, Delaney, K.R.
J. Neurosci. 26, 13240-13249 (2006).
Recommended by Noble laureate Erwin Neher on Faculty of 1000 Biology: http://f1000.com/1059717
Brevity of the Ca2+ microdomain and active zone geometry prevent Ca2+-sensor saturation for neurotransmitter release.
Shahrezaei, V., Delaney, K.R.
J. Neurophysiol. 94, 1912-1919 (2005).
Consequences of molecular-level Ca2+ channel and synaptic vesicle colocalization for the Ca2+ microdomain and neurotransmitter exocytosis: a Monte Carlo study.
Shahrezaei, V., Delaney, K.R.
Biophys. J. 87, 2352-2364 (2004).
Competition between phasic and asynchronous release for recovered synaptic vesicles at developing hippocampal autaptic synapses.
Otsu, Y., Shahrezaei, V., Li, B., Raymond, L.A., Delaney, K.R., Murphy, T.H.
J. Neurosci. 24, 420-433 (2004).
Geometry selects highly designable structures.
Shahrezaei, V., Ejtehadi, M.R.
J. Chem. Phys. 113, 6437-6442 (2000).
Protein ground state candidates in a simple model: an exact enumeration study.
Shahrezaei, V., Hamedani, N., Ejtehadi, M.R.
Phys. Rev. E 60, 4629-4636 (1999).
Geometrically Reduced Number of Protein Ground State Candidates.
Ejtehadi, M.R., Hamedani, N., Shahrezaei, V.
Phys. Rev. Lett. 82, 4723-4726 (1999).
Highly designable protein structures and inter monomer interactions.
Ejtehadi, M.R., Hamedani, N., Seyed-Allaei, H., Shahrezaei, V., Yahyanejad, M.
J. Phys. A: Math. Gen. 31, 6141-6155 (1998).
Stability of preferable structures for an HP model of protein folding.
Ejtehadi, M.R., Hamedani, N., Seyed-Allaei, H., Shahrezaei, V., Yahyanejad, M.
Phys. Rev. E 57, 3298-3301 (1998).
Book Chapters, etc
Delaney, K.R., Shahrezaei, V. Calcium and Transmitter Release. In: The Encyclopedia of Life Sciences, 2nd Edition, John Wiley & Sons (2005).
Delaney K.R., Shahrezaei, V. Uncaging Calcium in Neurons. In: R. Yuste, A. Konnerth, eds. Imaging in Neuroscience and Development: A Laboratory Manual. Cold Spring Harbor Laboratory Press, NY (2005).
Ejtehadi, M.R., Shahrezaei, V., Hamedani, N. Turk. J. Phys. 24, 227-293 (2000) (TUBITAK, Regional Conference on Mathematical Physics IX, Feza Gursey Institute, Istanbul, August 1999).
Ejtehadi, M.R., Hamedani, N., Seyed-Allaei, H., Shahrezaei, V., Yahyanejad, M. Preferred structures and monomer-monomer interaction. In: P. Grassberger, G. Bakema, W. Nadler, eds. Monte Carlo approach to Biopolymers and protein folding. World scientific, Singapore, (1998).