Inform Development of Regenerative Therapies Identify regulatory units for regeneration Identify genes inactivated in animal systems that cannot regenerate

User-Friendly Interface That Features: Multiple integrated datasets Multiple organisms

Needed to Integrate Increasingly Large Datasets Needed to compare different models and tissues Primary publications often limited to individual datasets

Comparative Models of Regeneration Database (RegenDB)

Expression Data Summary for a Gene in a Single Organism

Appendage Regeneration

Heart Regeneration

Comparative Models of Regeneration Database (RegenDB)

Expression Data for a Transcript in a Single Experiment

Comparative Models of Regeneration Database (RegenDB)

Predicted microRNA Binding Sites for the 3p UTR of a Single Transcript

Comparative Models of Regeneration Database (RegenDB)

Comparative Models of Regeneration Database (RegenDB)Expression Data Summary for Homologs in Similar Tissues

Axolotl

Zebrafish

Applied Bioinformatics Course at MDI Biological Laboratory

FASTQ Files

Tertiary Analysis1. Analysis of Read Counts

e.g., Differentially expressed genes2. Analysis of Gene Lists

1. Enrichment2. Pathway and networks

3. Analysis of Expression Patterns

Secondary Analysis1. Read Preprocessing & Diagnostics2. Align Reads to Reference

3. Analysis of Aligned Readse.g., Read counts per gene from RNA-Seq

Jointly Funded by Maine and New Hampshire IDeA Programs

Conceptual Model of Functional Relationships Between Environmental Challenge, Plasticity, and Canalization

Shaw JR, Hampton TH, King BL, Whitehead A, Galvez F, Gross RH, Keith N, Notch E, Jung D, Glaholt SP, Chen CY, Colbourne JK, Stanton BA. (2014) Mol Biol Evol 31:3002-3015

microRNA Acquisition Consistent With Fossil Record

Tarver JE, Sperling EA, Nailor A, Heimberg AM, Robinson JM, King BL, Pisani D, Donoghue PC, Peterson KJ. (2013). Mol Biol Evol. 30(11):2369-82.

Evolutionary History of microRNA Genes Across Animal Kingdom

Fromm B, Billipp T, Peck LE, Johansen M, Tarver JE, King BL, Newcomb JM, Sempere LF, Flatmark K, Hovig E, Peterson KJ. Ann Rev Genetics (in press)

Holocephalan and Elasmobranch Resources in Public Nucleotide and Protein Databases

Wyffels J, King BL, Vincent J, Chen C, Wu CH, Polson SW. SkateBase, an elasmobranch genome project and collection of molecular resources for chondrichthyan fishes. (2014) F1000Res. 3:191.

Phenotypes Inferred to Diseases Through Shared Chemicals

Davis AP, Wiegers TC, Roberts PM, King BL, Lay JM, Lennon-Hopkins K, Sciaky D, Johnson R, Keating H, Greene N, Hernandez R, McConnell KJ, Enayetallah AE, Mattingly CJ. (2013) Database (Oxford). 2013:bat080.

Identification of RNA Editing Sites in Normal Lung Samples

Analysis Pipeline

Soundararajan R, Stearns TM, Griswold AL, Mehta A, Czachor A, Fukumoto J, Lockey RF, King BL, Kolliputi, N. Oncotarget (in press).

Skate Mitochondrial Genome

Wang Q, Arighi CN, King BL, Polson SW, Vincent J, Chen C, Huang H, Kingham BF, Page ST, Rendino MF, Thomas WK, Udwary DW, Wu CH; North East Bioinformatics Collaborative Curation Team. (2012) Database (Oxford). 2012:bar064.

Leucoraja erinacea