James Schnable

James Schnable

E-mail: schnable@unl.edu

Curriculum Vitae (pdf)

Assistant Professor




As a side effect of some of my own research I generated a dataset of other group's published maize expression data, all analyzed with the same computational pipeline to generate comparable expression values for the same genes. This was a resource that let people ask "I'm really interested in gene X, can you tell me where it is expressed?" or even "I have a QTL for trait Y, can you tell me which genes within my QTL have expression patterns that would make them good candidates for the trait I am studying?"

Eventually I figured I might as well build a web interface so I wouldn't need to look up the expression values for genes in specific regions manually each time and qTeller was born. qTeller lets any researcher look at the expression of their favorite gene across multiple tissues and genetic backgrounds or pull out expression data (as well as multiple sets of functional and comparative genomic data) for a genomic interval of interest -- the two most common examples being a QTL or a region to which a mutant has been mapped.

Syntenic Ortholog Grass Gene Sets

By using syntenic (the conserved order of genes along a chromosome) combined with aggrediate statistics on gene divergence, it becomes possible to identify high confidence orthologs in different grass species, enabling all sorts of powerful comparative genomics. Unlike a BLAST search, an analysis using synteny will also report gene losses and predicted locations for lost genes, instead of simply reporting the most closely related paralog.

Identifying syntenic orthologs is still a rather involved process and takes much longer than a simple BLAST search. To aid in research I provide pre-generated lists of syntenic genes amoung the grasses.

Classic Maize Genes

The classical maize gene list is a human proofed mapping of 464 well studied, cloned, genetic loci in maize to maizesequence.org gene model IDs (the IDs starting with GRMZM, AC or AF). Proofing the list allowed an assessment of the sorts of errors the automated gene annotation of the maize genome was making, and the final list is a valuable "sanity check" for all sorts of whole genome studies. A great example of this is Davidsen RM et al 2011 where the authors used RNA-seq to measure gene expression in a wide range of maize reproductive tissues and used the classical maize gene list to make sure their data was showing the same patterns of expression already observed in studies of individual well studied genes.

Sequenced Plant Genomes

From until 2008, plant biologists could count the number of species with sequenced genomes on one hand. But the year I entered grad school saw the publication of three additional genomes and the speed of publication has only increased since then to the point where it's hard to keep track of what genomes are avaliable at any given time, or quickly figure out what the best outgroup would be to use in a comparative genomics study.

The sequenced plant genomes page I maintain at CoGePedia keeps track of which genomes have been published and which are still under Fort Lauderdale restrictions, how each genome was sequenced and assembled, who did the work, where to find the datasets, and how sequenced plant species are related to each other.

The sequenced plant genomes page is the single highest traffic webpage on CoGePedia, drawing more than 500 visits per month, with the bulk coming from the US, India, and China. The page also has more citations in google scholar than half of my actual peer reviewed publications.