Inform Development of Regenerative Therapies Identify regulatory units for regeneration Identify...
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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)
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Expression Data Summary for a Gene in a Single Organism
Appendage Regeneration
Heart Regeneration
Comparative Models of Regeneration Database (RegenDB)
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Expression Data for a Transcript in a Single Experiment
Comparative Models of Regeneration Database (RegenDB)
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Predicted microRNA Binding Sites for the 3p UTR of a Single Transcript
Comparative Models of Regeneration Database (RegenDB)
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Comparative Models of Regeneration Database (RegenDB)Expression Data Summary for Homologs in Similar Tissues
Axolotl
Zebrafish
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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
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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
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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.
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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)
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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.
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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.
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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).
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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