Seminal papers that have shaped my scientific experience. Resources I have accessed over the years that have been extremely useful.
Genetics
Constructing genetic map
Critical and example papers include:
Quantitiative trait locus analysis
Critical papers include:
Churchill and Doerge (1996) Permutations tests for multiple loci affecting a quantitative character. Genetics 142:285-294.
Transgressive segregation
Critical papers include:
deVicente and Tanksley (1993) QTL analysis of transgressive segregation in an interspecific tomato cross. Genetics 134:585-596.
Genomics
Toolsets for analyzing genomes
EMBOSS provides a diverse set of programs to analyze genome, transcriptome, and proteome data GenomeQC sets out a framework for benchmarking different assembly strategies ORFcor for correcting gene models post-annotation
Visualization of genes and genomes
gggenes
dgenies provides dotplots for large genomes
smudgeplot provides visualization of ploidy and heterozygosity structure
Assembling complex regions of the genome
Molecular Evolution
PAML
MrBayes uses Bayesian inference and model choice over several phylogenetic and evolutionary models.
Plant-Microbe Interaction
R genes versus QTLs
There has been a long-standing debate about the potential relationship between R gene-mediated resistance and minor effect QTLs identified based on field-based phenotyping.
Critical papers include:
Li et al. (1999) A “defeated” rice resistance gene acts as a QTL against a virulent strain of Xanthomonas oryzae pv. oryzae. Molecular Genomics and Genetics 261:58-63.
Data, visualization, and figures
Compendium of data visualization tools.
Vecteezy is a free vector art searchable repository.
Color and color blindness resources.
Easyfig
gggenes
Diversity of tools in ggplot
High-throughput sequencing
Tools for mapping high-throughput sequencing data
RNAseqlopedia
RNAseq tutorial from the Griffith Lab
Counts, TPM, RPKM, and FPKM
Estimating genome size using k-mer frequency
Bioinformatics
Data Carpentry
Bioinformatics Core Training
Data Science Skills in Research
Teaching Resources in Bioinformatics for Life Sciences
Plant biology
Statistics
DABEST: Data Analysis using Bootstrap-Coupled ESTimation
A good tutorial in mixed linear models
Graphic design
Canvas design reports, flyers, posters, and other diverse media with a range of templates
Language
Mailchimp manages large e-mail mailing lists
Random
I should have loved biology by James Somers
Last updated: 2020 November 30