Benjamin King


Ph.D. University of Maine 2016

Research Interests

Many aspects of human health can be traced to the ability of cells to sense and respond to infection, injury or other environmental changes.  Cells orchestrate these essential biological processes through complex networks of genes, proteins and metabolites.  The focus of my laboratory is to utilize genomic and computational approaches to understand the mechanisms of stress responses.  Increased understanding of how these networks normally function will inform the development of therapies that restore their function when needed.

Within these networks, genes function together with multiple layers of genetic regulation that include both protein coding and non-coding genes.  Network models provide a powerful framework to predict the regulatory roles of genes.  Current projects involve using genome-level data to build and analyze these networks.  A specific focus is on non-coding RNAs, including microRNAs and long non-coding RNAs, that have important regulatory roles in heath and disease.


Selected Publications

  • King BL, Yin VP. A conserved gene regulatory circuit is dynamically controlled during limb/appendage regeneration in the vertebrates. PLoS ONE. 2016.1(6):e0157106. Featured in Science Shot on June 29, 2016 DOI: 10.1126/science.aag0632.
  • Grondin CJ, Davis AP, Wiegers TC, King BL, Wiegers JA, Reif DM, Hoppin JA, Mattingly CJ. Advancing exposure science through chemical data curation and integration in the Comparative Toxicogenomics Database. Environ Health Perspect. 2016; 124(10):1592-1599.
  • Fromm B, Billipp T, Peck LE, Johansen M, Tarver JE, King BL, Newcomb JM, Sempere LF, Flatmark K, Hovig E, Peterson KJ. (2015) A Uniform System for the Annotation of Vertebrate microRNA Genes and the Evolution of the Human microRNAome. Annu Rev Genet. 49:213-42.
  • 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. Natural selection canalizes expression variation of environmentally induced plasticity-enabling genes. Mol Biol Evol. 2014; 31(11):3002-15.
  • Tarver JE, Sperling EA, Nailor A, Heimberg AM, Robinson JM, King BL, Pisani D, Donoghue PC, Peterson KJ. miRNAs: small genes with big potential in metazoan phylogenetics. Mol Biol Evol. 2013 Nov;30(11):2369-82.
  • King BL, Davis AP, Rosenstein MC, Wiegers TC, Mattingly CJ. Ranking transitive chemical-disease inferences using local network topology in the comparative toxicogenomics database. PLoS One. 2012;7(11):e46524.
  • King BL, Gillis JA, Carlisle HR, Dahn RD. (2011) A natural deletion of the HoxC cluster in elasmobranch fishes. Science, 334(6062):1517. Reviewed in Research Highlights Nature 480(22/29): 419, 2011.
  • International Stem Cell Initiative. Characterization of human embroyonic stem cell lines by the International Stem Cell Initiative. Nature Biotechnology, 2007; 25(7), 803-816.
  • Petkov PM, Graber JH, Churchill GA, DiPetrillo K, King BL, Paigen K. Evidence of a large-scale functional organization of mammalian chromosomes. PLoS Genetics. 2005; 1(3), e33.
  • Zhu Y, King BL, Parvizi B, Brunk BP, Stoeckert, Jr, CJ, Quackenbush J, Richardson J, Bult CJ. Integrating Computationally Assembled Mouse Transcript Sequences with the Mouse Genome (MGI) Database. Genome Biology. 2003; 4(2), R16.
  • The FANTOM Consortium and RIKEN Genome Exploration Research Group Phase I & II Team. (2002). Analysis of the mouse transcriptome based on functional annotation of 60,770 full-length cDNAs. Nature, 420, 563-73.
  • The RIKEN Genome Exploration Research Group Phase II Team and the FANTOM Consortium. (2001). Functional annotation of a full-length mouse cDNA collection. Nature, 409, 685-690.
  • Alm RA, Ling LS, Moir DT, King BL, Brown ED, Doig PC, Smith DR, Noonan B, Guild BC, deJonge BL, Carmel G, Tummino PJ, Caruso A, Uria-Nickelsen M, Mills DM, Ives C, Gibson R, Merberg D, Mills SD, Jiang Q, Taylor DE, Vovis GF, Trust TJ. (1999). Genome-sequence comparison of two unrelated isolates of the human gastric pathogen Helicobacter pylori. Nature, 397(6715),176-80.

Dissertation Students

Michael Babcock

Kodey Silknitter