Laboratory Notebooks

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). The 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 notes.
As it turns out, I am not the only person doing this; this trend has become known as Open Notebook Science. In a 2011 PLoS ONE paper, I included the full notebook as supplemental material. You can read about this on Mike Eisen's blog: Notebook S1: Scientific publishing awesomeness

Evolution 9: Bulk-fitness assays. Our first major project at Lehigh. Quantifying the fitness effect of hundreds of mutations from evolved populations One of two companion notebooks to the Buskirk et al. (2017) PNAS paper.
pdf [52.1 Mb, 200 pages]

Evolution 8: Sequencing evolved populations. A collaboration with The Genome Institute at Washington University to perform whole-genome whole-population timecourse sequencing on evolved populations. Companion notebook to the Lang et al. (2013) Nature paper.
pdf [27.1 Mb, 158 pages]

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

Evolution 6: Frequency-dependent selection. A study of frequency-dependent selection in yeast.
Available in the Lang 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 Lang 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 [30.3 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 [18.3 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 Lang 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 [42.6 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 [18.9 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 [43.4 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.