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genomics + data mining
ICDM2012 Keynote
Needles in Stacks of Needles: genomics + data mining
visual abstract
abstract
In 2001, the first human genome sequence was published. Now, just over 10 years later, we capable of sequencing a genome in just a few days. Massive parallel sequencing projects now make it possible to study the cancers of thousands of individuals. New data mining approaches are required to robustly interrogate the data for causal relationships among the inherently noisy biology. How does one identify genetic changes that are specific and causal to a disease within the rich variation that is either natural or merely correlated? The problem is one of finding a needle in a stack of needles. I will provide a non-specialist introduction to data mining methods and challenges in genomics, with a focus on the role visualization plays in the exploration of the underlying data.
references
The title of the talk was drawn from the paper
Gregory M. Cooper & Jay Shendure Needles in stacks of needles: finding disease-causal variants in a wealth of genomic data Nature Reviews Genetics 12, 628-640 (September 2011)
I will be posting a full list of references for the talk shortly.
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news + thoughts
Music for the Moon: Flunk's 'Down Here / Moon Above'
The Sanctuary Project is a Lunar vault of science and art. It includes two fully sequenced human genomes, sequenced and assembled by us at Canada's Michael Smith Genome Sciences Centre.
The first disc includes a song composed by Flunk for the (eventual) trip to the Moon.
But how do you send sound to space? I describe the inspiration, process and art behind the work.
Happy 2021 `\pi` Day—
A forest of digits
Celebrate `\pi` Day (March 14th) and finally see the digits through the forest.
This year is full of botanical whimsy. A Lindenmayer system forest – deterministic but always changing. Feel free to stop and pick the flowers from the ground.
And things can get crazy in the forest.
Check out art from previous years: 2013 `\pi` Day and 2014 `\pi` Day, 2015 `\pi` Day, 2016 `\pi` Day, 2017 `\pi` Day, 2018 `\pi` Day and 2019 `\pi` Day.
Testing for rare conditions
All that glitters is not gold. —W. Shakespeare
The sensitivity and specificity of a test do not necessarily correspond to its error rate. This becomes critically important when testing for a rare condition — a test with 99% sensitivity and specificity has an even chance of being wrong when the condition prevalence is 1%.
We discuss the positive predictive value (PPV) and how practices such as screen can increase it.
Altman, N. & Krzywinski, M. (2021) Points of significance: Testing for rare conditions. Nature Methods 18:224–225.
Standardization fallacy
We demand rigidly defined areas of doubt and uncertainty! —D. Adams
A popular notion about experiments is that it's good to keep variability in subjects low to limit the influence of confounding factors. This is called standardization.
Unfortunately, although standardization increases power, it can induce unrealistically low variability and lead to results that do not generalize to the population of interest. And, in fact, may be irreproducible.
Not paying attention to these details and thinking (or hoping) that standardization is always good is the "standardization fallacy". In this column, we look at how standardization can be balanced with heterogenization to avoid this thorny issue.
Voelkl, B., Würbel, H., Krzywinski, M. & Altman, N. (2021) Points of significance: Standardization fallacy. Nature Methods 18:5–6.
Graphical Abstract Design Guidelines
Clear, concise, legible and compelling.
Making a scientific graphical abstract? Refer to my practical design guidelines and redesign examples to improve organization, design and clarity of your graphical abstracts.
