Analyzing DAP-seq data from GEO!

Finding DNA-binding sites using DAP-seq data

I am learning to take advantage of the mass amount of data made publicly available for plant scientists! I don't have a coding background or much formal training at all, so I am trying to teach myself some basics. As I learn ...More

PB2020 Online Workshop: Mathematical Modeling Across Scales in Plant Biology 

The Online workshop is now on July 31st from 2-4 pm EDT. If you can’t make this, everything will be recorded. Even the workshop exercises will be available afterward, so you only miss out if you don’t sign up. Keep reading if you want to know how ...More

Interview: Clearing out the undergrowth with the sequencing of two fern genomes. 

Interview with Dr. Fay-Wei Li from the Boyce Thompson Institute

Where do you start when you want to sequence the first representative species of an entire class of land plants? Ferns are notorious for having gigantic genomes, with some as large as 145 Gb (more than a thousand times larger than Arabidopsis th ...More

Material for our #PlantBio18 "Reproducibility for Everyone" workshop

Here we present the extended support material for our 'Reproducibility for Everyone' workshop at ASPB #PlantBio18. All material is available under a CC BY 4.0 license. Please feel free to remix, copy, distribute, use, improve, and snowball The exte ...More

Bioinformatics core competencies for undergraduate life sciences education

Abstract Although bioinformatics is becoming increasingly central to research in the life sciences, bioinformatics skills and knowledge are not well integrated into undergraduate biology education. This curricular gap prevents biology students from ...More

Interview: Technology as a tool in teaching quantitative biology at the secondary and undergraduate levels

Interview with Shelby Scott and Miranda Chen of the University of Tennessee Knoxville

Shelby Scott and Miranda Chen recently published the article Technology as a tool in teaching quantitative biology at the secondary and undergraduate levels. You can find the paper here. In this interview, the authors describe what the ...More

Interview: Increasing transcriptomic complexity through alternative splicing in response to abiotic stress.

Interview with Dr. Pankaj Jaiswal of Oregon State University

Dr. Pankaj Jaiswal's group at Oregon State University recently published an article in Frontiers in Plant Science (find it here) that combines two types of RNA-sequencing techniques to shed light on how the poplar transcriptome is resp ...More

Interview: Accessible chromatin profiles in plants

Interview with Kelsey Maher, Marko Bajic, and Roger Deal of Emory University

Kelsey and Marko (co-first authors) and Roger (corresponding author) at Emory University recently published an article in Plant Cell (find it here) that used high throughput techniques (INTACT and ATAC-seq) to identify conserved t ...More

Interview: Bayesian statistics for meta-analysis of genomic data

Interview with Dr. Huo of University of Florida

Dr. Huo of the University of Florida recently published a preprint on new methodology for meta-analysis of genomic data: Bayesian latent hierarchical model for transcriptomic meta-analysis to detect biomarkers with clustered meta-pat ...More