Data-driven spatio-temporal modelling of glioblastoma

Authors: Jørgensen, Andreas Christ Sølvsten, Hill, Ciaran Scott, Sturrock, Marc, Tang, Wenhao, Karamched, Saketh R., Gorup, Dunja, Lythgoe, Mark F., Parrinello, Simona, Marguerat, Samuel, Shahrezaei, Vahid

Subject Terms: Quantitative Biology - Quantitative Methods

Access URL: http://arxiv.org/abs/2210.01537

Inference of a three-gene network underpinning epidermal stem cell development in Caenorhabditis elegans

Authors: Brożek, Alicja ^{1, 5}, Ceccarelli, Arianna ^{2, 3, 5}, Sølvsten Jørgensen, Andreas Christ ^{2, 4}, Hintze, Mark ¹, Shahrezaei, Vahid ^{2, ∗∗}, Barkoulas, Michalis ^{1, 6, ∗}

Source: In iScience 21 February 2025 28(2)

S-multi-SNE: Semi-Supervised Classification and Visualisation of Multi-View Data

Authors: Rodosthenous, Theodoulos, Shahrezaei, Vahid, Evangelou, Marina

Subject Terms: Computer Science - Machine Learning, Computer Science - Human-Computer Interaction, Statistics - Machine Learning

Access URL: http://arxiv.org/abs/2111.03519

Global transcription regulation revealed from dynamical correlations in time-resolved single-cell RNA sequencing

Authors: Volteras, Dimitris, Shahrezaei, Vahid, Thomas, Philipp

Source: In Cell Systems 21 August 2024 15(8):694-708

Multi-view Data Visualisation via Manifold Learning

Authors: Rodosthenous, Theodoulos, Shahrezaei, Vahid, Evangelou, Marina

Subject Terms: Statistics - Machine Learning, Computer Science - Machine Learning, Statistics - Computation

Access URL: http://arxiv.org/abs/2101.06763

Selective advantage of epigenetically disrupted cancer cells via phenotypic inertia

Authors: Loukas, Ioannis, Simeoni, Fabrizio, Milan, Marta, Inglese, Paolo, Patel, Harshil, Goldstone, Robert, East, Philip, Strohbuecker, Stephanie, Mitter, Richard, Talsania, Bhavik, Tang, Wenhao, Ratcliffe, Colin D.H., Sahai, Erik, Shahrezaei, Vahid, Scaffidi, Paola

Source: In Cancer Cell 9 January 2023 41(1):70-87

The impact of random microenvironmental fluctuations on tumor control probability

Authors: Forouzannia, Farinaz, Shahrezaei, Vahid, Kohandel, Mohammad

Source: In Journal of Theoretical Biology 21 January 2021 509

Size-Dependent Increase in RNA Polymerase II Initiation Rates Mediates Gene Expression Scaling with Cell Size

Authors: Sun, Xi-Ming, Bowman, Anthony, Priestman, Miles, Bertaux, Francois, Martinez-Segura, Amalia, Tang, Wenhao, Whilding, Chad, Dormann, Dirk, Shahrezaei, Vahid, Marguerat, Samuel

Source: In Current Biology 6 April 2020 30(7):1217-1230

Heterogeneity of Striatal Dopamine Function in Schizophrenia: Meta-analysis of Variance

Authors: Brugger, Stefan P., Angelescu, Ilinca, Abi-Dargham, Anissa, Mizrahi, Romina, Shahrezaei, Vahid, Howes, Oliver D.

Source: In Biological Psychiatry 1 February 2020 87(3):215-224

BayNorm: Bayesian gene expression recovery, imputation and normalization for single-cell RNA-sequencing data

Authors: Tang, Wenhao, Bertaux, François, Thomas, Philipp, Stefanelli, Claire, Saint, Malika, Marguerat, Samuel, Shahrezaei, Vahid

Source: Bioinformatics. 36(4):1174-1181

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCvdc_100099355462.0x000001&indx=1&recIds=ETOCvdc_100099355462.0x000001

Multi-signal regulation of the GSK-3β homolog Rim11 controls meiosis entry in budding yeast.

Authors: Kociemba, Johanna, Jørgensen, Andreas Christ Sølvsten, Tadić, Nika, Harris, Anthony, Sideri, Theodora, Chan, Wei Yee, Ibrahim, Fairouz, Ünal, Elçin, Skehel, Mark, Shahrezaei, Vahid, Argüello-Miranda, Orlando, van Werven, Folkert Jacobus

Source: EMBO Journal; Aug2024, Vol. 43 Issue 15, p3256-3286, 31p

Analytical distributions for stochastic gene expression

Authors: Shahrezaei, Vahid, Swain, Peter S.

Source: Proc Natl Acad Sci U S A. 2008 Nov 11;105(45):17256-61

Subject Terms: Quantitative Biology - Molecular Networks, Quantitative Biology - Quantitative Methods

Access URL: http://arxiv.org/abs/0812.3344

Colored extrinsic fluctuations and stochastic gene expression

Authors: Shahrezaei, Vahid, Ollivier, Julien F, Swain, Peter S

Source: Molecular Systems Biology 4:196 (2008)

Subject Terms: Quantitative Biology - Molecular Networks, Quantitative Biology - Quantitative Methods

Access URL: http://arxiv.org/abs/0809.2973

Single-cell imaging and RNA sequencing reveal patterns of gene expression heterogeneity during fission yeast growth and adaptation

Authors: Saint, Malika, Bertaux, François, Tang, Wenhao, Sun, Xi-Ming, Game, Laurence, Köferle, Anna, Bähler, Jürg, Shahrezaei, Vahid, Marguerat, Samuel

Source: Nature microbiology. 4(3):480-491

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCvdc_100130017296.0x000001&indx=1&recIds=ETOCvdc_100130017296.0x000001

Discrimination of Escherichia coli, Shigella flexneri, and Shigella sonnei using lipid profiling by MALDI‐TOF mass spectrometry paired with machine learning

Authors: Pizzato, Jade, Tang, Wenhao, Bernabeu, Sandrine, Bonnin, Rémy A., Bille, Emmanuelle, Farfour, Eric, Guillard, Thomas, Barraud, Olivier, Cattoir, Vincent, Plouzeau, Chloe, Corvec, Stéphane, Shahrezaei, Vahid, Dortet, Laurent, Larrouy‐Maumus, Gerald

Source: MicrobiologyOpen. 11(4)

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCvdc_100170290625.0x000001&indx=1&recIds=ETOCvdc_100170290625.0x000001

The influence of nuclear compartmentalisation on stochastic dynamics of self-repressing gene expression

Authors: Sturrock, Marc, Li, Shiyu, Shahrezaei, Vahid

Source: In Journal of Theoretical Biology 7 July 2017 424:55-72

Benchmarking imputation methods for network inference using a novel method of synthetic scRNA-seq data generation.

Authors: Lasri, Ayoub¹ (AUTHOR), Shahrezaei, Vahid² (AUTHOR), Sturrock, Marc¹ (AUTHOR) marcsturrock@rcsi.ie

Source: BMC Bioinformatics. 6/17/2022, Vol. 23 Issue 1, p1-26. 26p.

Subject Terms: *GENE regulatory networks, *MULTISCALE modeling

Multi-view data visualisation via manifold learning.

Authors: Rodosthenous, Theodoulos¹, theodoulosr@gmail.com, Shahrezaei, Vahid¹, Evangelou, Marina¹

Source: PeerJ Computer Science; May2024, p1-36, 36p

Modeling Enzyme Processivity Reveals that RNA-Seq Libraries Are Biased in Characteristic and Correctable Ways

Authors: Archer, Nathan, Walsh, Mark D., Shahrezaei, Vahid, Hebenstreit, Daniel

Source: In Cell Systems 23 November 2016 3(5):467-479

Connecting growth with gene expression: of noise and numbers

Authors: Shahrezaei, Vahid, Marguerat, Samuel

Source: In Current Opinion in Microbiology June 2015 25:127-135