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Blog Archive

• • 2023 •
• On PhD advisory committees
  motivation, PhD
• • 2022 •
• Fisher information (with a cat)
  Immanuel, bias–variance trade-off, Fisher information, dialogue
• Does science need statistical tests?
  p-hacking, dialogue, statistics
• Journal clubs, ranked from worst to best
  science, journal club, opinion
• • 2021 •
• A gentle introduction to the Cramér-Rao lower bound (with a cat)
  Immanuel, dialogue, Fisher information
• A tutorial on t-SNE (3)
  series: focus on, statistics, data visualization, bioinformatics
• How to teach yourself math
  mathematics, motivation, learning
• • 2020 •
• The most important quality of a scientist
  science, management, opinion
• Scientific models
  science, model, dialogue
• • 2019 •
• A tutorial on t-SNE (2)
  perplexity, t-SNE, entropy
• Focus on: the Kullback-Leibler divergence
  Kullback-Leibler divergence, series: focus on
• • 2018 •
• On open peer review
  science, peer review, opinion
• A tutorial on t-SNE (1)
  series: focus on, statistics, data visualization, bioinformatics
• Pro recruitment tip: ask your mum!
  recruitment, leadership
• The curse of large numbers (Big Data considered harmful)
  statistics, hypothesis testing, big data, p-values
• Interview with Miguel Beato
  interview
• • 2017 •
• A tutorial on Burrows-Wheeler indexing methods (3)
  series: focus on, suffix array, Burrows-Wheeler transform, full text indexing, bioinformatics
• A tutorial on Burrows-Wheeler indexing methods (2)
  series: focus on, suffix array, Burrows-Wheeler transform, full text indexing, bioinformatics
• When scientific models fail
  models, science, evolution
• Against recruitment panel interviews
  recruitment, management
• Three lessons from peer coaching
  motivation, management, coaching, leadership
• • 2016 •
• One or two tails?
  statistics, p-hacking
• A tutorial on Burrows-Wheeler indexing methods (1)
  Burrows-Wheeler transform, suffix array, series: focus on, full text indexing, bioinformatics
• Did Mendel fake his results?
  statistics, p-hacking, genetics, fraud
• How to teach research?
  motivation, management, leadership
• • 2015 •
• ENCODE data, Principal Components and racism
  ENCODE, racism, series: genetics and racism, Principal Component Analysis
• Stick breaking and DNA alignment
  heuristic, sequence alignment, bioinformatics, spacings, stick breaking
• Bayesian networks and causation
  statistics, Bayesian networks, causes, correlation
• What is bioinformatics about?
  PubMed, journals, bioinformatics, information retrieval
• Why do bioinformatics?
  software pollution, benchmark, bioinformatics
• If cars were made by bioinformaticians...
  cars, bioinformatics, software
• • 2014 •
• Longest runs and DNA alignments
  sequence alignment, BLAST, bioinformatics
• Why Linux is awesome
  open source, self-learning, Linux
• Nature on code sharing
  bioinformatics revolution, open source, reproducible research, obfuscated open source
• Bioinformatics without Excel
  Excel, self-learning, bioinformatics
• A flurry of copycats on PubMed
  PubMed, journals, information retrieval
• (Mis)using the KS test for p-hacking
  statistics, p-hacking
• Shadow libraries
  journals, shadow libraries
• Detecting trends in culture
  Changepoint detection, PubMed, information retrieval
• Once upon a BLAST
  series: focus on, BLAST, sequence alignment, bioinformatics
• June babies and bioinformatics
  extreme value fallacy, Gumbel, extreme value theory, bioinformatics
• How to write a cover letter
  post-doc, PhD
• Four illusions
  motivation, management, illusions, leadership
• So you want to be a group leader
  motivation, management, leadership
• Infinite expectations
  black swans, diffusion, brownian motion, probability
• • 2013 •
• Who understands the histone code?
  histone code, position effect variegation, epigenetics
• The rise of epigenetics
  chromatin, histone code, PubMed, epigenetics
• Meet planktonrules
  interview, series: IMDB reviews, planktonrules
• How to stop sucking and be awesome instead
  motivation, PhD
• 100% non functional
  ENCODE, junk DNA, intelligent design
• One shade of authorship attribution
  planktonrules, Python, machine learning, R, IMDB, series: IMDB reviews, automatic authorship attribution
• Genetics and racism (3)
  breed, series: genetics and racism, species, race
• ... and academic reprints for all
  pdftk, pdf, reprint, DRM
• Genetics and racism (2)
  craniometry, genetics, racism, series: genetics and racism
• • 2012 •
• Genetics and racism (1)
  variability, crimestop, genetics, series: genetics and racism
• Unpredictable?
  information, randomness, probability, random generator
• Does the Earth have a mind?
  Turing test, ecology, consciousness, Gaia theory
• Is there a gene for alcoholism? (2)
  information, genetics, neurogenetics, genetic determinism, series: is there a gene for alcoholism?, missing heritability
• Lessons from Intelligent Design
  evolution, crimestop, intelligent design, consciousness, creationism
• Let’s Disqus
  Disqus, meta, Cross Validated
• Focus on: multiple testing
  multiple testing, familywise error rate, p-values, R, false discovery rate, series: focus on, hypothesis testing
• The most dangerous number
  multiple testing, confirmation bias, hypothesis testing, p-values
• Is there a gene for alcoholism? (1)
  causality, genetics, series: is there a gene for alcoholism?, independence, information
• The chaos and the doubt
  law of large numbers, Bayesian statistics, coherence, probability
• The autistic computer
  neurosciences, algorithmics, natural language processing, synesthesia
• The geometry of style
  planktonrules, co-inertia analysis, information retrieval, IMDB, principal component analysis, series: IMDB reviews
• Are you human?
  Python, Information retrieval, movies, IMDB, series: IMDB reviews, crawler
• The elements of style
  movies, series: IMDB reviews, information retrieval, IMDB, natural language processing
• Did Sweden cheat at Eurovision?
  Twitter, Eurovision, information retrieval
• Lost in punctuation
  information, series: IMDB reviews, information retrieval, IMDB, movies
• Poetry and optimality
  information, independence, probability
• The fallacy of (in)dependence
  information, causality, probability, independence
• The reverend’s gambit
  Bayesian statistics, probability, p-values
• Why p-values are crap
  R, random walks, probability, p-values
• The Brownian labyrinth
  stochastic processes, R, random walks
• Drunk man walking
  stochastic processes, R, probability, random walks
• What’s in a title?
  PubMed, journals, information retrieval
• I’m the boss!!
  motivation, journals, dialogue