Study reference library¶
Other people's courses, written up as one book per course from everything the course provides. The companion to the study knowledge base, which holds the notes themselves — the split is by authorship, not by subject.
12 course books, 473 chapters. 12 further sources are converted but not yet written as books — 18 pages. Books and paywalled papers are deliberately absent.
Course books¶
Rewritten, not reformatted. Each book merges a course's slides, recordings, notes and problem sets into chapters, names every course offering it was written from, and carries the licence those offerings permit. The books are generated and are never edited by hand.
Computational biology¶
- MIT 6047 — 16 chapters, CC BY-NC-SA 4.0
- MIT 7.091J — 23 chapters, CC BY-NC-SA 4.0
- MIT 8.591J 2004 — 20 chapters, CC BY-NC-SA 4.0
- MIT 8.591J 2014 — 24 chapters, CC BY-NC-SA 4.0
- MIT 8.592J — 15 chapters, CC BY-NC-SA 4.0
Omics statistics¶
- GTPB Psls20 — 42 chapters, CC BY 4.0
- StatOmics Sga21 — 41 chapters, CC BY-NC-SA 4.0
Probability¶
- MIT 6.041SC — 26 chapters, CC BY-NC-SA 4.0
Statistical computing¶
- Berkeley Stat 243 — 46 chapters, CC BY 4.0
Statistics¶
- Berkeley Stat 153 — 128 chapters, CC BY 4.0
- Berkeley Stat 156 — 9 chapters, CC BY-NC 4.0
- Berkeley Stat 210A — 83 chapters, CC BY 4.0
Papers¶
41 papers and theses, each summarised in our own words. The full text is here too for the 12 whose licence allows it; the rest are summaries only and link to the original.
Computational biology¶
- Carilli 2026 — Genetic Interrogation of Expression Regulation — summary
- Fang 2025 — A biophysical approach to normalization and trajectory inference in single-cell RNA sequencing data analysis — summary
- Felce 2026 — Biophysical Modeling for Gene Expression and Evolution — summary
- Gálvez Merchán 2023 — Studies of mRNA expression and degradation — summary
- Gardiner & Chaturvedi 1977 — The Poisson Representation. I. A New Technique for Chemical Master Equations — summary
- Gillespie 1976 — A General Method for Numerically Simulating the Stochastic Time Evolution of Coupled Chemical Reactions — summary
- Gillespie 2000 — The chemical Langevin equation — summary
- Gillespie 2001 — Approximate accelerated stochastic simulation of chemically reacting systems — summary
- Gorin et al. 2022 — Interpretable and tractable models of transcriptional noise for the rational design of single-molecule quantification experiments — summary and full text
- Gorin, Yoshida & Pachter 2022 — Transient and delay chemical master equations — summary and full text
- Gorin 2023 — Stochastic foundations for single-cell RNA sequencing — summary
- Gorin & Pachter 2020 — Intrinsic and extrinsic noise are distinguishable in a synthesis – export – degradation model of mRNA production — summary and full text
- Gorin & Pachter 2021 — Analytical solutions of the chemical master equation with bursty production and isomerization reactions — summary and full text
- Grima, Schmidt & Newman 2012 — Steady-state fluctuations of a genetic feedback loop: an exact solution — summary
- Jahnke & Huisinga 2007 — Solving the chemical master equation for monomolecular reaction systems analytically — summary
- Luebbert 2024 — Complexity of Transcriptomic Data Analysis and Implications for Biological Discovery — summary
- Munsky & Khammash 2006 — The finite state projection algorithm for the solution of the chemical master equation — summary
- Paulsson 2004 — Summing up the noise in gene networks — summary
- Peccoud & Ycart 1995 — Markovian Modelling of Gene Product Synthesis — summary
- Shahrezaei & Swain 2008 — Analytical distributions for stochastic gene expression — summary
- Singh & Bokes, 2012 — Consequences of mRNA Transport on Stochastic Variability in Protein Levels — summary
- Tang et al. 2020 — bayNorm: Bayesian gene expression recovery, imputation and normalization for single-cell RNA-sequencing data — summary and full text
- Tang et al. 2023 — Modelling capture efficiency of single-cell RNA-sequencing data improves inference of transcriptome-wide burst kinetics — summary and full text
- Thomas, Popović & Grima, 2014 — Phenotypic switching in gene regulatory networks — summary
- Vastola & Holmes 2020 — The chemical Langevin equation: a path integral view of Gillespie's derivation — summary
Omics statistics¶
- Ahlmann-Eltze & Huber 2021 — Transformation and Preprocessing of Single-Cell RNA-Seq Data — summary
- Cargnelli et al. 2026 — Benchmarking computational decontamination of ambient RNA — summary and full text
- Caskey & Rich et al. 2026 — Single-Cell Genomics Decontamination with CellSweep — summary and full text
- Fleming et al. 2023 — Unsupervised removal of systematic background noise from droplet-based single-cell experiments using CellBender — summary
- Janssen et al. 2023 — The effect of background noise and its removal on the analysis of single-cell expression data — summary and full text
- Kouiroukidis & Evangelidis 2011 — The Effects of Dimensionality Curse in High Dimensional kNN Search — summary
- Marioni et al. 2008 — RNA-seq: An assessment of technical reproducibility and comparison with gene expression arrays — summary
- Wang et al. 2024 — scCDC: a computational method for gene-specific contamination detection and correction in single-cell and single-nucleus RNA-seq data — summary and full text
- Yang et al. 2020 — Decontamination of ambient RNA in single-cell RNA-seq with DecontX — summary and full text
- Young & Behjati 2020 — SoupX removes ambient RNA contamination from droplet-based single-cell RNA sequencing data — summary and full text
Statistical computing¶
Statistics¶
- Cao, Zeng & Fine 2015 — Regression analysis of sparse asynchronous longitudinal data — summary
- Efron 2008 — Microarrays, Empirical Bayes and the Two-Groups Model — summary
- Fisher & Kennedy 2019 — Visually Communicating and Teaching Intuition for Influence Functions — summary
- Hines et al. 2021 — Demystifying statistical learning based on efficient influence functions — summary
- Lo, Mendell & Rubin 2001 — Testing the number of components in a normal mixture — summary
Converted sources¶
Converted, not adapted. The text is its author's, reformatted and split so that every part has a URL. A page built from a PDF carries a warning, because prose survives a PDF and mathematics does not.
Probability¶
- Berkeley Stat 201A Fall 2024 — 1 page, CC BY 4.0
- Berkeley Stat 205A Fall 2024 — 1 page, CC BY 4.0
- Berkeley Stat 205B Spring 2026 — 2 pages, CC BY 4.0
- Berkeley Stat 206A Fall 2024 — 1 page, CC BY 4.0
- Berkeley Stat 206B Spring 2025 — 2 pages, CC BY 4.0
- Berkeley Stat 206B Spring 2026 — 2 pages, CC BY 4.0
Statistics¶
- Berkeley Stat 158 Spring 2025 — 1 page, CC BY 4.0
- Berkeley Stat 201B Fall 2024 — 1 page, CC BY 4.0
- Berkeley Stat 210B Spring 2025 — 2 pages, CC BY 4.0
- Berkeley Stat 230A Spring 2025 — 3 pages, CC BY 4.0
- Berkeley Stat 230A Spring 2026 — 1 page, CC BY 4.0
Stochastic processes¶
- Berkeley Stat 150 Spring 2026 — 1 page, CC BY 4.0