http://mcb111.org/w06/w06-lecture.html
Has some nice textbook downloads – e.g.
http://mcb111.org/w06/KollerFriedman.pdf
QT:{{”
There are many good books to learn about probabilistic models. “Probabilistic graphical models: principles and techniques” (by Koller & Friedman) is a comprehensive source about more general probabilistic models than the one we are going to study here.
“}}
Subset of chap 7 focuses on GMRF
good tutorial/textbook chaper/review paper on Poisson regression :
Below are a few readings that discuss how to fit a generalized linear mixed model.
1. Breslow & Clayton (1993), JASA, Approximate Inference in
Generalized Linear Mixed Models.
https://doi.org/10.2307/2290687
A classic statistical paper introducing the Laplace approximation and penalized quasi-likelihood for GLMMs
2. Bates (2011), Mixed models in R using the lme4 package Part 5: Generalized linear mixed models
https://lme4.r-forge.r-project.org/slides/2011-03-16-Amsterdam/5GLMMH.pdf 3. Bates, D., Mächler, M., Bolker, B., & Walker, S. (2015). Fitting linear mixed-effects models using lme4. Journal of statistical software, 67, 1-48.
https://doi.org/10.18637/jss.v067.i01
4. Bates (2025), Computational methods for mixed models
https://cran.r-project.org/web/packages/lme4/vignettes/Theory.pdf
These are written by the authors of the lme4 package, discussing the details of how a mixed-effects model (more specifically, a generalized linear mixed-effects model) is trained using the PIRLS approach.
1. Paulsson (2005) – “Models of stochastic gene expression”
https://www.sciencedirect.com/science/article/abs/pii/S1571064505000138 Nice pedagogical review of the master equation framework – covers the conceptual foundations and different analytical approaches.
2. Shahrezaei & Swain (2008) – “Analytical distributions for stochastic gene expression”
https://pubmed.ncbi.nlm.nih.gov/18988743/
This one derives the exact analytical solutions to the master equation for protein/mRNA distributions.
The Paulsson paper is probably better as a tutorial.
However, it’s a bit difficult to connect to protein & mRNA.
What Is a Blepharoplasty? What to Know About the Popular Eyelid
Surgery – WSJ https://www.wsj.com/style/beauty/blepharoplasty-eyelid-lift-cosmetic-surgery-cc865580
A New Concern About Weight Loss Drugs: What if They Work Too Well? – The New York Times
https://www.nytimes.com/2026/02/18/well/weight-loss-drugs-retatrutide.html
https://en.wikipedia.org/wiki/Cytotoxic_T-lymphocyte_associated_protein_4 QT:{{” Cytotoxic T-lymphocyte associated protein 4, (CTLA-4) also known as CD152 (cluster of differentiation 152), is a protein receptor that functions as an immune checkpoint and downregulates immune responses. “}}
Hipparchus star catalog – Wikipedia https://share.google/Q6kPwSnZDc5AUGKv8
linkstream2 microblog 