Seminal papers that have shaped my scientific experience. Resources I have accessed over the years that have been extremely useful.


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.


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

dgenies provides dotplots for large genomes
smudgeplot provides visualization of ploidy and heterozygosity structure

Assembling complex regions of the genome

HiCanu HapCUT2

Molecular Evolution

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.
Diversity of tools in ggplot

High-throughput sequencing

Tools for mapping high-throughput sequencing data
RNAseq tutorial from the Griffith Lab
Counts, TPM, RPKM, and FPKM
Estimating genome size using k-mer frequency


Data Carpentry
Bioinformatics Core Training
Data Science Skills in Research
Teaching Resources in Bioinformatics for Life Sciences

Plant biology

What plants are important


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


Top 10,000 English words


Mailchimp manages large e-mail mailing lists


I should have loved biology by James Somers

Last updated: 2020 November 30