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statistics + data
Since 2013, our Nature Methods Points of Significance column has been offering crisp explanations and practical suggestions about best practices in statistical analysis and reporting. To all our coauthors — thank you and see you in the next column!
Nature Methods: Points of Significance
Martin Krzywinski is a staff scientist at Canada’s Michael Smith Genome Sciences Centre.
Naomi Altman is a Professor of Statistics at The Pennsylvania State University.
contributing authors
Jasleen Grewal is a graduate student in the Jones lab at Canada's Michael Smith Genome Sciences Centre.
Kiranmoy Das is a faculty member at the Indian Statistical Institute in Kolkata, India.
Luca Greco is an Assistant Professor of Statistics at the University of Sannio in Benevento, Italy.
Geroge Luta Associate Professor of Biostatistics at the Georgetown University in Washington, DC, USA.
Byran Smucker is an Associate Professor of Statistics at Miami University in Oxford, OH, USA.
Danilo Bzdok is an Assistant Professor at the Department of Psychiatry, RWTH Aachen University, Germany, and a Visiting Professor at INRIA/Neurospin Saclay in France.
Jake Lever is a Postdoctoral Research Fellow in Bioengineering at Stanford University in Stanford, California, USA.
Paul Blainey is an Assistant Professor of Biological Engineering at MIT and Core Member of the Broad Institute.
Anthony Kulesa is a graduate student in the Department of Biological Engineering at MIT.
Jorge López Puga is a Professor of Research Methodology at UCAM Universidad Católica de Murcia.
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news + thoughts
Points of Significance celebrates 50th column
We are celebrating the publication of our 50th column!
To all our coauthors — thank you and see you in the next column!
Uncertainty and the management of epidemics
When modelling epidemics, some uncertainties matter more than others.
Public health policy is always hampered by uncertainty. During a novel outbreak, nearly everything will be uncertain: the mode of transmission, the duration and population variability of latency, infection and protective immunity and, critically, whether the outbreak will fade out or turn into a major epidemic.
The uncertainty may be structural (which model?), parametric (what is `R_0`?), and/or operational (how well do masks work?).
This month, we continue our exploration of epidemiological models and look at how uncertainty affects forecasts of disease dynamics and optimization of intervention strategies.
We show how the impact of the uncertainty on any choice in strategy can be expressed using the Expected Value of Perfect Information (EVPI), which is the potential improvement in outcomes that could be obtained if the uncertainty is resolved before making a decision on the intervention strategy. In other words, by how much could we potentially increase effectiveness of our choice (e.g. lowering total disease burden) if we knew which model best reflects reality?
This column has an interactive supplemental component (download code) that allows you to explore the impact of uncertainty in `R_0` and immunity duration on timing and size of epidemic waves and the total burden of the outbreak and calculate EVPI for various outbreak models and scenarios.
Bjørnstad, O.N., Shea, K., Krzywinski, M. & Altman, N. (2020) Points of significance: Uncertainty and the management of epidemics. Nature Methods 17.
Background reading
Bjørnstad, O.N., Shea, K., Krzywinski, M. & Altman, N. (2020) Points of significance: Modeling infectious epidemics. Nature Methods 17:455–456.
Bjørnstad, O.N., Shea, K., Krzywinski, M. & Altman, N. (2020) Points of significance: The SEIRS model for infectious disease dynamics. Nature Methods 17:557–558.
Cover of Nature Genetics August 2020
Our design on the cover of Nature Genetics's August 2020 issue is “Dichotomy of Chromatin in Color” . Thanks to Dr. Andy Mungall for suggesting this terrific title.
The cover design accompanies our report in the issue Gagliardi, A., Porter, V.L., Zong, Z. et al. (2020) Analysis of Ugandan cervical carcinomas identifies human papillomavirus clade–specific epigenome and transcriptome landscapes. Nature Genetics 52:800–810.
Poster Design Guidelines
Clear, concise, legible and compelling.
The PDF template is a poster about making posters. It provides design, typography and data visualiation tips with minimum fuss. Follow its advice until you have developed enough design sobriety and experience to know when to go your own way.
The SEIRS model for infectious disease dynamics
Realistic models of epidemics account for latency, loss of immunity, births and deaths.
We continue with our discussion about epidemic models and show how births, deaths and loss of immunity can create epidemic waves—a periodic fluctuation in the fraction of population that is infected.
This column has an interactive supplemental component (download code) that allows you to explore epidemic waves and introduces the idea of the phase plane, a compact way to understand the evolution of an epidemic over its entire course.
Bjørnstad, O.N., Shea, K., Krzywinski, M. & Altman, N. (2020) Points of significance: The SEIRS model for infectious disease dynamics. Nature Methods 17:557–558.
Background reading
Bjørnstad, O.N., Shea, K., Krzywinski, M. & Altman, N. (2020) Points of significance: Modeling infectious epidemics. Nature Methods 17:455–456.
Gene Machines
Shifting soundscapes, textures and rhythmic loops produced by laboratory machines.
In commemoration of the 20th anniversary of Canada's Michael Smith Genome Sciences Centre, Segue was commissioned to create an original composition based on audio recordings from the GSC's laboratory equipment, robots and computers—to make “music” from the noise they produce.
Virus Mutations Reveal How COVID-19 Really Spread
Genetic sequences of the coronavirus tell story of when the virus arrived in each country and where it came from.
Our graphic in Scientific American's Graphic Science section in the June 2020 issue shows a phylogenetic tree based on a snapshot of the data model from Nextstrain as of 31 March 2020.
Cover of Nature Cancer April 2020
Our design on the cover of Nature Cancer's April 2020 issue shows mutation spectra of patients from the POG570 cohort of 570 individuals with advanced metastatic cancer.
The cover design accompanies our report in the issue Pleasance, E., Titmuss, E., Williamson, L. et al. (2020) Pan-cancer analysis of advanced patient tumors reveals interactions between therapy and genomic landscapes. Nat Cancer 1:452–468.