Below is a list of my lab notebooks. The important ones (i.e. the ones leading to publications) are available below as PDFs (these are huge files . . . patience is key). All others are available as originals in either the Murray lab or the Botstein lab.

My initial goal when I started this practice was to establish a permanent digital record of published experiments, to promote transparency, and to motivate myself to keep good records. As it turns out, I am not the only person doing this; this trend has become known as Open Notebook Science.


Evolution 7: Expression of heterologous transcription factors in hybrid yeast
Microarray timecourse experiments following induction of transcription factors in hybrid yeasts.
Available in the Botstein lab.

Evolution 6: Frequency-dependent selection
A study of action of frequency-dependent selection in yeast.
Available in the Botstein lab.

Evolution 5: Heterologous interference in the yeast mating pathway
Experiments addressing the effect of heterologous proteins on the function of protein complexes.
Available in the Botstein lab.

Evolution 4: Rise of alpha-factor resistant strains
A long-term evolution experiment tracking the emergence and fate of spontaneous sterile mutations.
Companion notebook to the Lang, Botstein, and Desai (2011) Genetics paper
[PDF] - 44.6 Mb, 152 pages

Evolution 3: Clustering of the GAL genes in yeast
Experiments designed to determine why the GAL1-GAL10-GAL7 genomic organization is highly conserved.
Companion notebook to the Lang and Botstein (2011) PLoS ONE paper
[PDF] - 33.9 Mb, 101 pages

Evolution 2: Carbon assimilation in Saccharomyces kudriavzevii
Experiments investigating the basis for the gain of inulin assimilation and the loss of the GAL pathway in this yeast.
Available in the Botstein lab.

Evolution 1: Fitness of alpha-factor resistant strains
Experiments showing that basal signaling through the mating pathway entails a fitness cost.
Companion notebook to the Lang, Murray, and Botstein (2009) PNAS paper
[PDF] - 82.7 Mb, 202 pages

Mutation rate 5: Target size to phenotypic mutations
Accurately determining the phenotypic mutation rate and the target size for phenotypic mutations.
Companion notebook to the Lang and Murray (2008) Genetics paper
[PDF] - 45.5 Mb, 110 pages

Mutation rate 4: Mutation rate and strain background
Experiments looking at the basis for observed mutation rate variation in different strain backgrounds.
Available in the Murray lab.

Mutation rate 3: Mutation rate across Chromosome VI.
Experiments showing that mutation rate varies across yeast Chromosome VI and that this variation is correlated with replication timing.
Companion notebook to the Lang and Murray paper (2011) Genome Biology and Evolution paper
[PDF] - 80.9 Mb, 200 pages

Mutation rate 2: Mutation rate and osmotic stress
Experiments investigating the 4-fold elevation of mutation rate under osmotic stress.
Available in the Murray lab.

Mutation rate 1
First mutation rate notebook containing many of the original observations upon which later notebooks are based.
Available in the Murray lab.