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Vahid Shahrezaei, PhD - Publications

Affiliations: 
Mathematics Imperial College, London, London, England, United Kingdom 
Area:
Stochastic processes, Genetic networks
Website:
http://www3.imperial.ac.uk/people/v.shahrezaei
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9/56 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2018 Bertaux F, Marguerat S, Shahrezaei V. Division rate, cell size and proteome allocation: impact on gene expression noise and implications for the dynamics of genetic circuits. Royal Society Open Science. 5: 172234. PMID 29657814 DOI: 10.1098/Rsos.172234  0.312
2015 Shahrezaei V, Marguerat S. Connecting growth with gene expression: of noise and numbers. Current Opinion in Microbiology. 25: 127-35. PMID 26093364 DOI: 10.1016/J.Mib.2015.05.012  0.305
2013 Delaney KR, Shahrezaei V. Uncaging calcium in neurons. Cold Spring Harbor Protocols. 2013: 1115-24. PMID 24298037 DOI: 10.1101/Pdb.Top079491  0.576
2010 Ollivier JF, Shahrezaei V, Swain PS. Scalable rule-based modelling of allosteric proteins and biochemical networks. Plos Computational Biology. 6: e1000975. PMID 21079669 DOI: 10.1371/Journal.Pcbi.1000975  0.301
2008 Shahrezaei V, Swain PS. The stochastic nature of biochemical networks. Current Opinion in Biotechnology. 19: 369-74. PMID 18662776 DOI: 10.1016/J.Copbio.2008.06.011  0.311
2006 Shahrezaei V, Cao A, Delaney KR. Ca2+ from one or two channels controls fusion of a single vesicle at the frog neuromuscular junction. The Journal of Neuroscience : the Official Journal of the Society For Neuroscience. 26: 13240-9. PMID 17182774 DOI: 10.1523/Jneurosci.1418-06.2006  0.582
2005 Shahrezaei V, Delaney KR. Brevity of the Ca2+ microdomain and active zone geometry prevent Ca2+-sensor saturation for neurotransmitter release. Journal of Neurophysiology. 94: 1912-9. PMID 15888526 DOI: 10.1152/Jn.00256.2005  0.588
2004 Shahrezaei V, Delaney KR. Consequences of molecular-level Ca2+ channel and synaptic vesicle colocalization for the Ca2+ microdomain and neurotransmitter exocytosis: a monte carlo study. Biophysical Journal. 87: 2352-64. PMID 15454435 DOI: 10.1529/Biophysj.104.043380  0.592
2004 Otsu Y, Shahrezaei V, Li B, Raymond LA, Delaney KR, Murphy TH. Competition between phasic and asynchronous release for recovered synaptic vesicles at developing hippocampal autaptic synapses. The Journal of Neuroscience : the Official Journal of the Society For Neuroscience. 24: 420-33. PMID 14724240 DOI: 10.1523/Jneurosci.4452-03.2004  0.533
Low-probability matches (unlikely to be authored by this person)
2020 Sun XM, Bowman A, Priestman M, Bertaux F, Martinez-Segura A, Tang W, Whilding C, Dormann D, Shahrezaei V, Marguerat S. Size-Dependent Increase in RNA Polymerase II Initiation Rates Mediates Gene Expression Scaling with Cell Size. Current Biology : Cb. PMID 32059768 DOI: 10.1016/J.Cub.2020.01.053  0.291
2008 Shahrezaei V, Swain PS. Analytical distributions for stochastic gene expression. Proceedings of the National Academy of Sciences of the United States of America. 105: 17256-61. PMID 18988743 DOI: 10.1073/Pnas.0803850105  0.29
2008 Shahrezaei V, Ollivier JF, Swain PS. Colored extrinsic fluctuations and stochastic gene expression. Molecular Systems Biology. 4: 196. PMID 18463620 DOI: 10.1038/Msb.2008.31  0.285
2014 Robb ML, Shahrezaei V. Stochastic cellular fate decision making by multiple infecting lambda phage. Plos One. 9: e103636. PMID 25105971 DOI: 10.1371/Journal.Pone.0103636  0.284
2018 Uhía I, Priestman M, Joyce G, Krishnan N, Shahrezaei V, Robertson BD. Analysis of ParAB dynamics in mycobacteria shows active movement of ParB and differential inheritance of ParA. Plos One. 13: e0199316. PMID 29920558 DOI: 10.1371/Journal.Pone.0199316  0.282
2020 Beltran T, Shahrezaei V, Katju V, Sarkies P. Epimutations driven by small RNAs arise frequently but most have limited duration in Caenorhabditis elegans. Nature Ecology & Evolution. PMID 32868918 DOI: 10.1038/S41559-020-01293-Z  0.282
2017 Priestman M, Thomas P, Robertson BD, Shahrezaei V. Mycobacteria Modify Their Cell Size Control under Sub-Optimal Carbon Sources. Frontiers in Cell and Developmental Biology. 5: 64. PMID 28748182 DOI: 10.3389/Fcell.2017.00064  0.28
2012 Joyce G, Williams KJ, Robb M, Noens E, Tizzano B, Shahrezaei V, Robertson BD. Cell division site placement and asymmetric growth in mycobacteria. Plos One. 7: e44582. PMID 22970255 DOI: 10.1371/Journal.Pone.0044582  0.273
2017 Sturrock M, Li S, Shahrezaei V. The influence of nuclear compartmentalisation on stochastic dynamics of self-repressing gene expression. Journal of Theoretical Biology. 424: 55-72. PMID 28483564 DOI: 10.1016/J.Jtbi.2017.05.003  0.27
2014 Dushek O, Lellouch AC, Vaux DJ, Shahrezaei V. Biosensor architectures for high-fidelity reporting of cellular signaling. Biophysical Journal. 107: 773-82. PMID 25099816 DOI: 10.1016/J.Bpj.2014.06.021  0.269
2019 Tang W, Bertaux F, Thomas P, Stefanelli C, Saint M, Marguerat S, Shahrezaei V. bayNorm: Bayesian gene expression recovery, imputation and normalisation for single cell RNA-sequencing data. Bioinformatics (Oxford, England). PMID 31584606 DOI: 10.1093/Bioinformatics/Btz726  0.265
1998 Ejtehadi MR, Hamedani N, Seyed-Allaei H, Shahrezaei V, Yahyanejad M. Highly designable protein structures and inter-monomer interactions Journal of Physics a: Mathematical and General. 31: 6141-6155. DOI: 10.1088/0305-4470/31/29/006  0.264
2010 Malleshaiah MK, Shahrezaei V, Swain PS, Michnick SW. The scaffold protein Ste5 directly controls a switch-like mating decision in yeast. Nature. 465: 101-5. PMID 20400943 DOI: 10.1038/Nature08946  0.262
2011 Dushek O, van der Merwe PA, Shahrezaei V. Ultrasensitivity in multisite phosphorylation of membrane-anchored proteins. Biophysical Journal. 100: 1189-97. PMID 21354391 DOI: 10.1016/J.Bpj.2011.01.060  0.259
1998 Ejtehadi MR, Hamedani N, Seyed-Allaei H, Shahrezaei V, Yahyanejad M. Stability of preferable structures for a hydrophobic-polar model of protein folding Physical Review E - Statistical Physics, Plasmas, Fluids, and Related Interdisciplinary Topics. 57: 3298-3301. DOI: 10.1103/Physreve.57.3298  0.255
2016 Archer N, Walsh MD, Shahrezaei V, Hebenstreit D. Modeling Enzyme Processivity Reveals that RNA-Seq Libraries Are Biased in Characteristic and Correctable Ways. Cell Systems. PMID 27840077 DOI: 10.1016/J.Cels.2016.10.012  0.252
1999 Ejtehadi MR, Hamedani N, Shahrezaei V. Geometrically reduced number of protein ground state candidates Physical Review Letters. 82: 4723-4726. DOI: 10.1103/Physrevlett.82.4723  0.249
1999 Shahrezaei V, Hamedani N, Ejtehadi MR. Protein ground state candidates in a simple model: an enumeration study. Physical Review. E, Statistical Physics, Plasmas, Fluids, and Related Interdisciplinary Topics. 60: 4629-36. PMID 11970324 DOI: 10.1103/Physreve.60.4629  0.248
2019 Dyer NP, Shahrezaei V, Hebenstreit D. LiBiNorm: an htseq-count analogue with improved normalisation of Smart-seq2 data and library preparation diagnostics. Peerj. 7: e6222. PMID 30740268 DOI: 10.7717/Peerj.6222  0.248
2020 Rodosthenous T, Shahrezaei V, Evangelou M. Integrating multi-OMICS data through sparse Canonical Correlation Analysis for the prediction of complex traits: A comparison study. Bioinformatics (Oxford, England). PMID 32437529 DOI: 10.1093/Bioinformatics/Btaa530  0.232
2019 Tang W, Ranganathan N, Shahrezaei V, Larrouy-Maumus G. MALDI-TOF mass spectrometry on intact bacteria combined with a refined analysis framework allows accurate classification of MSSA and MRSA. Plos One. 14: e0218951. PMID 31247021 DOI: 10.1371/Journal.Pone.0218951  0.231
2012 Schley D, Tanaka RJ, Leungchavaphongse K, Shahrezaei V, Ward J, Grant C, Charleston B, Rhodes CJ. Modelling the influence of foot-and-mouth disease vaccine antigen stability and dose on the bovine immune response. Plos One. 7: e30435. PMID 22363437 DOI: 10.1371/Journal.Pone.0030435  0.228
2000 Shahrezaei V, Ejtehadi MR. Geometry selects highly designable structures Journal of Chemical Physics. 113: 6437-6442. DOI: 10.1063/1.1308514  0.226
2015 Smith S, Shahrezaei V. General transient solution of the one-step master equation in one dimension. Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics. 91: 062119. PMID 26172673 DOI: 10.1103/Physreve.91.062119  0.221
2012 Szomolay B, Shahrezaei V. Bell-shaped and ultrasensitive dose-response in phosphorylation-dephosphorylation cycles: the role of kinase-phosphatase complex formation. Bmc Systems Biology. 6: 26. PMID 22531112 DOI: 10.1186/1752-0509-6-26  0.214
2020 England P, Tang W, Kostrzewa M, Shahrezaei V, Larrouy-Maumus G. Discrimination of bovine milk from non-dairy milk by lipids fingerprinting using routine matrix-assisted laser desorption ionization mass spectrometry. Scientific Reports. 10: 5160. PMID 32198427 DOI: 10.1038/S41598-020-62113-9  0.205
2019 Brugger SP, Angelescu I, Abi-Dargham A, Mizrahi R, Shahrezaei V, Howes OD. Heterogeneity of Striatal Dopamine Function in Schizophrenia: Meta-analysis of Variance. Biological Psychiatry. PMID 31561858 DOI: 10.1016/J.Biopsych.2019.07.008  0.191
2019 Saint M, Bertaux F, Tang W, Sun XM, Game L, Köferle A, Bähler J, Shahrezaei V, Marguerat S. Single-cell imaging and RNA sequencing reveal patterns of gene expression heterogeneity during fission yeast growth and adaptation. Nature Microbiology. PMID 30718845 DOI: 10.1038/s41564-018-0330-4  0.172
2023 Tang W, Jørgensen ACS, Marguerat S, Thomas P, Shahrezaei V. Modelling capture efficiency of single-cell RNA-sequencing data improves inference of transcriptome-wide burst kinetics. Bioinformatics (Oxford, England). PMID 37354494 DOI: 10.1093/bioinformatics/btad395  0.158
2022 Kleijn IT, Martínez-Segura A, Bertaux F, Saint M, Kramer H, Shahrezaei V, Marguerat S. Growth-rate-dependent and nutrient-specific gene expression resource allocation in fission yeast. Life Science Alliance. 5. PMID 35228260 DOI: 10.26508/lsa.202101223  0.153
2021 Thomas P, Shahrezaei V. Coordination of gene expression noise with cell size: analytical results for agent-based models of growing cell populations. Journal of the Royal Society, Interface. 18: 20210274. PMID 34034535 DOI: 10.1098/rsif.2021.0274  0.151
2022 Lasri A, Shahrezaei V, Sturrock M. Benchmarking imputation methods for network inference using a novel method of synthetic scRNA-seq data generation. Bmc Bioinformatics. 23: 236. PMID 35715748 DOI: 10.1186/s12859-022-04778-9  0.144
2021 Hintze M, Katsanos D, Shahrezaei V, Barkoulas M. Phenotypic Robustness of Epidermal Stem Cell Number in Is Modulated by the Activity of the Conserved N-acetyltransferase /NAT10. Frontiers in Cell and Developmental Biology. 9: 640856. PMID 34084768 DOI: 10.3389/fcell.2021.640856  0.143
2023 Kleijn IT, Marguerat S, Shahrezaei V. A coarse-grained resource allocation model of carbon and nitrogen metabolism in unicellular microbes. Journal of the Royal Society, Interface. 20: 20230206. PMID 37751876 DOI: 10.1098/rsif.2023.0206  0.135
2023 Bertaux F, Kleijn IT, Marguerat S, Shahrezaei V. Fission yeast obeys a linear size law under nutrient titration. Micropublication Biology. 2023. PMID 37193545 DOI: 10.17912/micropub.biology.000833  0.135
2022 Ciechonska M, Sturrock M, Grob A, Larrouy-Maumus G, Shahrezaei V, Isalan M. Emergent expression of fitness-conferring genes by phenotypic selection. Pnas Nexus. 1: pgac069. PMID 36741458 DOI: 10.1093/pnasnexus/pgac069  0.121
2022 Jørgensen ACS, Ghosh A, Sturrock M, Shahrezaei V. Efficient Bayesian inference for stochastic agent-based models. Plos Computational Biology. 18: e1009508. PMID 36197919 DOI: 10.1371/journal.pcbi.1009508  0.114
2020 Bertaux F, von Kügelgen J, Marguerat S, Shahrezaei V. A bacterial size law revealed by a coarse-grained model of cell physiology. Plos Computational Biology. 16: e1008245. PMID 32986690 DOI: 10.1371/journal.pcbi.1008245  0.105
2015 Uhía I, Williams KJ, Shahrezaei V, Robertson BD. Mycobacterial Growth. Cold Spring Harbor Perspectives in Medicine. PMID 25957314 DOI: 10.1101/cshperspect.a021097  0.102
2022 Loukas I, Simeoni F, Milan M, Inglese P, Patel H, Goldstone R, East P, Strohbuecker S, Mitter R, Talsania B, Tang W, Ratcliffe CDH, Sahai E, Shahrezaei V, Scaffidi P. Selective advantage of epigenetically disrupted cancer cells via phenotypic inertia. Cancer Cell. PMID 36332625 DOI: 10.1016/j.ccell.2022.10.002  0.101
2023 Jørgensen ACS, Hill CS, Sturrock M, Tang W, Karamched SR, Gorup D, Lythgoe MF, Parrinello S, Marguerat S, Shahrezaei V. Data-driven spatio-temporal modelling of glioblastoma. Royal Society Open Science. 10: 221444. PMID 36968241 DOI: 10.1098/rsos.221444  0.097
2020 Forouzannia F, Shahrezaei V, Kohandel M. The impact of random microenvironmental fluctuations on Tumor control probability. Journal of Theoretical Biology. 110494. PMID 32979339 DOI: 10.1016/j.jtbi.2020.110494  0.092
2015 Shahrezaei V, Marguerat S. Connecting growth with gene expression: Of noise and numbers Current Opinion in Microbiology. 25: 127-135. DOI: 10.1016/j.mib.2015.05.012  0.09
2009 Shahrezaei V, Swain PS. Analytical distributions for stochastic gene expression (Proceedings of the National Academy of Sciences of the United States of America (2008) 105, 45, (17256-17261) DOI:10.1073/pnas.0803850105) Proceedings of the National Academy of Sciences of the United States of America. 106: 346. DOI: 10.1073/pnas.0811545106  0.075
2022 Pizzato J, Tang W, Bernabeu S, Bonnin RA, Bille E, Farfour E, Guillard T, Barraud O, Cattoir V, Plouzeau C, Corvec S, Shahrezaei V, Dortet L, Larrouy-Maumus G. Discrimination of Escherichia coli, Shigella flexneri, and Shigella sonnei using lipid profiling by MALDI-TOF mass spectrometry paired with machine learning. Microbiologyopen. 11: e1313. PMID 36004556 DOI: 10.1002/mbo3.1313  0.07
2000 Ejtehadi MR, Shahrezaei V, Hamedani N. Global Results in Space of Inter-Monomer Interactions for HP Lattice Model Turkish Journal of Physics. 24: 277-293.  0.061
2015 Smith S, Shahrezaei V. General transient solution of the one-step master equation in one dimension Physical Review E - Statistical, Nonlinear, and Soft Matter Physics. 91. DOI: 10.1103/PhysRevE.91.062119  0.046
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