A review of stochastic block models and extensions for graph clustering von Lee, Clement, Wilkinson, Darren J.

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MGnify: the microbiome sequence data analysis resource in 2023 von Richardson, Lorna, Allen, Ben, Baldi, Germana, Beracochea, Martin, Bileschi, Maxwell L, Burdett, Tony, Burgin, Josephine, Caballero-Pérez, Juan, Cochrane, Guy, Colwell, Lucy J, Curtis, Tom, Escobar-Zepeda, Alejandra, Gurbich, Tatiana A, Kale, Varsha, Korobeynikov, Anton, Raj, Shriya, Rogers, Alexander B, Sakharova, Ekaterina, Sanchez, Santiago, Wilkinson, Darren J, Finn, Robert D

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EBI Metagenomics in 2017: enriching the analysis of microbial communities, from sequence reads to assemblies von Mitchell, Alex L, Scheremetjew, Maxim, Denise, Hubert, Potter, Simon, Tarkowska, Aleksandra, Qureshi, Matloob, Salazar, Gustavo A, Pesseat, Sebastien, Boland, Miguel A, Hunter, Fiona M I, ten Hoopen, Petra, Alako, Blaise, Amid, Clara, Wilkinson, Darren J, Curtis, Thomas P, Cochrane, Guy, Finn, Robert D

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Stochastic modelling for quantitative description of heterogeneous biological systems von Wilkinson, Darren J.

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Controlled vocabularies and semantics in systems biology von Courtot, Mélanie, Juty, Nick, Knüpfer, Christian, Waltemath, Dagmar, Zhukova, Anna, Dräger, Andreas, Dumontier, Michel, Finney, Andrew, Golebiewski, Martin, Hastings, Janna, Hoops, Stefan, Keating, Sarah, Kell, Douglas B, Kerrien, Samuel, Lawson, James, Lister, Allyson, Lu, James, Machne, Rainer, Mendes, Pedro, Pocock, Matthew, Rodriguez, Nicolas, Villeger, Alice, Wilkinson, Darren J, Wimalaratne, Sarala, Laibe, Camille, Hucka, Michael, Le Novère, Nicolas

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The Systems Biology Markup Language (SBML): Language Specification for Level 3 Version 2 Core Release 2 von Hucka, Michael, Bergmann, Frank T, Chaouiya, Claudine, Dräger, Andreas, Hoops, Stefan, Keating, Sarah M, König, Matthias, Novère, Nicolas Le, Myers, Chris J, Olivier, Brett G, Sahle, Sven, Schaff, James C, Sheriff, Rahuman, Smith, Lucian P, Waltemath, Dagmar, Wilkinson, Darren J, Zhang, Fengkai

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A Bayesian approach to modelling the impact of hydrodynamic shear stress on biofilm deformation von Oyebamiji, Oluwole K, Wilkinson, Darren J, Jayathilake, Pahala Gedara, Rushton, Steve P, Bridgens, Ben, Li, Bowen, Zuliani, Paolo

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Colonyzer: automated quantification of micro-organism growth characteristics on solid agar von Lawless, Conor, Wilkinson, Darren J, Young, Alexander, Addinall, Stephen G, Lydall, David A

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The Systems Biology Markup Language (SBML): Language Specification for Level 3 Version 2 Core von Hucka, Michael, Bergmann, Frank T., Dräger, Andreas, Hoops, Stefan, Keating, Sarah M., Le Novère, Nicolas, Myers, Chris J., Olivier, Brett G., Sahle, Sven, Schaff, James C., Smith, Lucian P., Waltemath, Dagmar, Wilkinson, Darren J.

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A whole-body mathematical model of cholesterol metabolism and its age-associated dysregulation von Mc Auley, Mark T, Wilkinson, Darren J, Jones, Janette J L, Kirkwood, Thomas B L

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Bayesian parameter inference for stochastic biochemical network models using particle Markov chain Monte Carlo von Golightly, Andrew, Wilkinson, Darren J.

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Emulating computer experiments of transport infrastructure slope stability using Gaussian processes and Bayesian inference von Svalova, Aleksandra, Helm, Peter, Prangle, Dennis, Rouainia, Mohamed, Glendinning, Stephanie, Wilkinson, Darren J.

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Emulating computer experiments of transport infrastructure slope stability using Gaussian processes and Bayesian inference—ADDENDUM von Svalova, Aleksandra, Helm, Peter, Prangle, Dennis, Rouainia, Mohamed, Glendinning, Stephanie, Wilkinson, Darren J.

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A Hierarchical Model of Nonhomogeneous Poisson Processes for Twitter Retweets von Lee, Clement, Wilkinson, Darren J.

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Pentose phosphate pathway function affects tolerance to the G-quadruplex binder TMPyP4 von Andrew, Elizabeth J, Merchan, Stephanie, Lawless, Conor, Banks, A Peter, Wilkinson, Darren J, Lydall, David

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Systems Biology Markup Language (SBML) Level 3 Package: Distributions, Version 1, Release 1 von Smith, Lucian P., Moodie, Stuart L., Bergmann, Frank T., Gillespie, Colin, Keating, Sarah M., König, Matthias, Myers, Chris J., Swat, Maciek J., Wilkinson, Darren J., Hucka, Michael

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A mathematical model of aging-related and cortisol induced hippocampal dysfunction von McAuley, Mark T, Kenny, Rose Anne, Kirkwood, Thomas B L, Wilkinson, Darren J, Jones, Janette J L, Miller, Veronica M

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Bayesian methods in bioinformatics and computational systems biology von Wilkinson, Darren J.

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Do simple models lead to generality in ecology? von Evans, Matthew R., Grimm, Volker, Johst, Karin, Knuuttila, Tarja, de Langhe, Rogier, Lessells, Catherine M., Merz, Martina, O’Malley, Maureen A., Orzack, Steve H., Weisberg, Michael, Wilkinson, Darren J., Wolkenhauer, Olaf, Benton, Tim G.

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Composable models for online Bayesian analysis of streaming data von Law, Jonathan, Wilkinson, Darren J.

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