The Curious Engineer

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Bits of DNA

liorpachter.wordpress.com

Reviews and commentary on computational biology by Lior Pachter

ScienceMathAI / ML

’15’20’25
Posts
131 from 19 Aug 2013 to 12 Sep 2026
Posting
now and then (5 in the last year)
Kind
personal blog
Feed
https://liorpachter.wordpress.com/feed/

2026 4

  1. Align AI and Mathematics—to Something Else
  2. Hausdorff
  3. Nowakia
  4. The Quickening

2025 4

  1. Review of Cold Spring Harbor Laboratory’s Obituary for Dr. James Watson
  2. Zbąszyń
  3. Reply to: Reply to: False positives in the study of memory-related gene expression
  4. Epistemic failure of epistemic failure

2024 4

  1. The Journal of Scientific Integrity
  2. A note on “How the Gaza Ministry of Health Fakes Casualty Numbers”
  3. All of Us failed
  4. Women in mathematics – a case study

2023 2

  1. Gregg L. Semenza’s retractions
  2. Ting Guo, sexual assault allegations, and the UC Davis Young Scholars Program

2022 1

  1. A decade of molecular cell atlases

2021 1

  1. The amoral nonsense of Orchid’s embryo selection

2020 7

  1. Williams math professor investigating voter fraud in Pennsylvania finds no evidence
  2. Mathematical analysis of “mathematical analysis” of a vitamin D COVID-19 trial
  3. The lethal nonsense of Michael Levitt
  4. Sexual harassment case number 1,052
  5. $ How to profit from COVID-19 testing $
  6. Black lives matter
  7. Diversity matters

2019 15

  1. How many doubly manlocked scientists are there?
  2. An outrage at UC Davis
  3. Zero-data RNA-seq
  4. Is Python really faster than C++ ?
  5. High velocity RNA velocity
  6. Rotating the knee (plot) and related yoga
  7. How to solve an NP-complete problem in linear time
  8. Single-cell RNA-seq for dummies
  9. Near-optimal pre-processing of single-cell RNA-seq
  10. Introduction to single-cell RNA-seq technologies
  11. Nonsense methods tend to produce nonsense results
  12. Sub-Poisson loading for single-cell RNA-seq
  13. Technologies of narcissism
  14. Open sourcing bioinstruments
  15. Fast and accurate gene differential expression by testing transcript compatibility counts

2018 13

  1. How to write a paper in four minutes
  2. Yuval Peres
  3. I was wrong (part 3)
  4. The combinatorics of authorship in the biological sciences
  5. Rate changes decrease substitutions
  6. Mathematics matters
  7. Low IQ scores predict excellence in data science
  8. The benefits of multiplexing
  9. James Watson in his own words
  10. Waterman’s egg
  11. GDE² = DGE² + DTU² = DTE₁² + DTE₂²
  12. Bioinformatics on a Rock64
  13. Terry Speed: a “male feminist”

2017 8

  1. How to cite the GTEx project
  2. A rebuttal
  3. I was wrong (part 2)
  4. How not to perform a differential expression analysis (or science)
  5. 0 = 1
  6. The joy of (blogging) Bach
  7. My aperiodic rhombic bathroom
  8. A citation is not a citation is not a citation

2016 9

  1. The Happy Ending in 2016
  2. Confusion matrix terminology is taxicab trigonometry
  3. Something the NIH can learn from NASA
  4. It cannot possibly be true
  5. Caltech
  6. The ice-cream-cone-proof
  7. The relative impact factor of glamour journals is 2.166
  8. The Heroes of CRISPR
  9. A statistical companion to “Stochastic Gene Expression in a Single Cell”

2015 14

  1. What is a read mapping?
  2. Straining metagenomics
  3. Unsolved problems with the common core
  4. A sleuth for RNA-Seq
  5. In biology n does not go to infinity
  6. How to average genome-wide data
  7. The myths of bioinformatics software
  8. Pondering p-values before breakfast
  9. I was wrong
  10. Pachter’s P-value Prize
  11. The most embarrassing citation ever?
  12. Near-optimal RNA-Seq quantification with kallisto
  13. Subset sums
  14. Colori

2014 24

  1. The two cultures of mathematics and biology
  2. The perfect human is Puerto Rican
  3. To some a citation is worth $3 per year
  4. The two-body opportunity
  5. The Middle East is not one-dimensional
  6. Do you know your great-great-great-great-great-great-great-great-great-great-great-great-great-great-great-great-great-great-great-great-great-great-great-great-great-great-great-great-great-grandfathers?
  7. Removing unwanted variation (from the literature)
  8. Digital normalization revealed
  9. Year-end review
  10. Nicholas Wade’s troublesome inheritance
  11. What is principal component analysis?
  12. Bessel’s correction and the dangers of MOOCs
  13. Time to end ordered authorship
  14. Estimating number of transcripts from RNA-Seq measurements (and why I believe in paywall)
  15. Does researching casual marijuana use cause brain abnormalities?
  16. Designing roofs and drawing phylogenetic trees
  17. Reproducibility vs. usability
  18. Using statistical methods to estimate and take into account experimental measurement errors: a case study using high throughput proteomics data
  19. Number deconvolution
  20. Why I read the network nonsense papers
  21. The network nonsense of Manolis Kellis
  22. The network nonsense of Albert-László Barabási
  23. Why do you look at the speck in your sister’s quilt plot and pay no attention to the plank in your own heat map?
  24. This paper is full of sh*t

2013 25

  1. Nature is irrational
  2. Time to end letter grades
  3. Molecular “restoration studies” of extinct forms of life
  4. Multiple testing an issue for 23andme
  5. Iterative [proportional fitting of a log-linear model for] correction of Hi-C data reveals hallmarks of chromosome organization
  6. Linearity of expectation
  7. Zero-cell RNA-Seq
  8. Claude Shannon, population geneticist
  9. Stories from the Supplement
  10. Response to: “GTEx is throwing away 90% of their data”
  11. Random numbers, reproducibility and SAMtools
  12. GTEx is throwing away 90% of their data
  13. Non-uniform coverage of transcripts in RNA-Seq experiments
  14. Ukkonen’s condition for assembly
  15. Finite decimal expansion, infinite time constants and structural controllability of networks
  16. The tabular hall of shame
  17. The Needleman-Wunsch algorithm
  18. UniFrac revealed
  19. Don’t believe the Affymetrix anti-hype
  20. Fibonacci numbers and splicing complexity
  21. Magnitude of effect vs. statistical significance
  22. The phylogeny of oranges is a point in a phylogenetic orange
  23. Catching a bus
  24. Sailfish
  25. Genesis of *Seq