Benjamin King, Ph.D.

Education

B.S. (1994) Boston University

M.S. (1996) Boston University

Ph.D. (2016) University of Maine

 

 

 

Research Interests

Systems Biology of Stress Responses

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.

 

Featured Publication

  • King BL, Rosenstein MC, Smith A, Dykeman CA, Smith GA, Yin VP. RegenDbase: a comparative database of noncoding RNA regulation of tissue regeneration circuits across multiple taxa. NPJ Regen. Med. 2018. 3:10. doi: 10.1038/s41536-018-0049-0.
  • King BL, Yin VP. A conserved gene regulatory circuit is dynamically controlled during limb/appendage regeneration in three vertebrates. PLoS ONE. 2016.1(6):e0157106. Featured in Science Shot on June 29, 2016 DOI: 10.1126/science.aag0632.
  • 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.

 

All Publications

  • King BL, Rosenstein MC, Smith A, Dykeman CA, Smith GA, Yin VP. RegenDbase: a comparative database of noncoding RNA regulation of tissue regeneration circuits across multiple taxa. NPJ Regen. Med. 2018. 3:10. doi: 10.1038/s41536-018-0049-0.
  • Hersh TA, Dimond AL, Ruth BA, Lupica NV, Bruce JC, Kelley JM, King BL, Lutton BV. A role for the CXCR4-CXCL12 axis in the little skate, Leucoraja erinacea. Am J Physiol Regul Integr Comp Physiol. 2018. doi:10.1152/ajpregu.00322.2017.
  • Reid NM, Jackson CE, Gilbert D, Minx P, Montague MJ, Hampton TH, Helfrich LW, King BL, Nacci DE, Aluru N, Karchner SI, Colbourne JK, Hahn ME, Shaw JR, Oleksiak MF, Crawford DL, Warren WC, Whitehead A. The landscape of extreme genomic variation in the highly adaptable Atlantic killifish. Genome Biol Evol. 2017. doi: 10.1093/gbe/evx023.
  • King BL, Yin VP. Prioritizing studies on regeneration in nontraditional model organisms. Regen Med. 2017; 12(1):1-3.
  • Soundararajan R, Stearns TM, Czachor A, Fukumoto J, Turn C, Westermann-Clark E, Breitzig M, Tan L, Lockey RF, King BL, Kolliputi N. Global gene profiling of aging lungs in Atp8b1 mutant mice. Aging (Albany NY). 2016;8(9):2232-2252.
  • Davis AP, Grondin CJ, Johnson RJ, Sciaky D, King BL, McMorran R, Wiegers J, Wiegers TC, Mattingly CJ. The Comparative Toxicogenomics Database: update 2017. Nucleic Acids Res. 2016 Sep 19. pii: gkw838. [Epub ahead of print] PubMed PMID: 27651457.
  • Hartig EI, Zhu S, King BL, Coffman JA. Cortisol-treated zebrafish embryos develop into pro-inflammatory adults with aberrant immune gene regulation. Biol Open. 2016; 5(8):1134-41. PubMed PMID: 27444789.
  • King BL, Yin VP. A conserved gene regulatory circuit is dynamically controlled during limb/appendage regeneration in three vertebrates. PLoS ONE. 2016; 1(6):e0157106. Featured in Science Shot on June 29, 2016 DOI: 10.1126/science.aag0632.
  • Davis, AP, Wiegers TC, King BL, Wiegers J, Grondin CJ, Sciaky D, Johnson RJ, Mattingly CJ. Generating Gene Ontology-Disease inferences to explore mechanisms of human disease at the Comparative Toxicogenomics Database. PLoS ONE. 2016; 11(5):e0155530.
  • 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.
  • Lee EC, Kim H, Ditano J, Manion D, King BL, Strange K. Abnormal Osmotic Avoidance Behavior in C. elegans Is Associated with Increased Hypertonic Stress Resistance and Improved Proteostasis. PLoS One. 2016; 11(4):e0154156.
  • Lisse TS, King BL, Rieger S. Comparative transcriptomic profiling of hydrogen peroxide signaling networks in zebrafish and human keratinocytes: Implications toward conservation, migration and wound healing. Sci Rep. 2016; 6:20328.
  • King BL, Shi LF, Kao P, Clusin WT. Calcium activated K(+) channels in the electroreceptor of the skate confirmed by cloning. Details of subunits and splicing. Gene. 2016; 578(1):63-73.
  • Tarver JE, Dos Reis M, Mirarab S, Moran RJ, Parker S, O’Reilly JE, King BL, O’Connell MJ, Asher RJ, Warnow T, Peterson KJ, Donoghue PC, Pisani D. The Interrelationships of Placental Mammals and the Limits of Phylogenetic Inference. Genome Biol Evol. 2016; 8(2):330-44.
  • Fromm B, Billipp T, Peck LE, Johansen M, Tarver JE, King BL, Newcomb JM, Sempere LF, Flatmark K, Hovig E, Peterson KJ. A Uniform System for the Annotation of Vertebrate microRNA Genes and the Evolution of the Human microRNAome. Annu Rev Genet. 2015; 49:213-42.
  • Soundararajan R, Stearns TM, Griswold AL, Mehta A, Czachor A, Fukumoto J, Lockey RF, King BL, Kolliputi N. Detection of canonical A-to-G editing events at 3′ UTRs and microRNA target sites in human lungs using next-generation sequencing. Oncotarget. 2015; 6(34):35726-36.
  • Hanke N, King BL, Vaske B, Haller H, Schiffer M. A Fluorescence-Based Assay for Proteinuria Screening in Larval Zebrafish (Danio rerio). Zebrafish. 2015; 12(5):372-6.
  • Carrier TJ, King BL, Coffman JA. Gene Expression Changes Associated With the Developmental Plasticity of Sea Urchin Larvae in Response to Food Availability. Biol Bull. 2015 Jun;228(3):171-80.
  • Davis AP, Grondin CJ, Lennon-Hopkins K, Saraceni-Richards C, Sciaky D, King BL, Wiegers TC, Mattingly CJ. The Comparative Toxicogenomics Database’s 10th year anniversary: update 2015. Nucleic Acids Res. 2015; 43(Database issue):D914-20.
  • 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.
  • 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. F1000Res. 2014; 3:191.
  • Field DJ, Gauthier JA, King BL, Pisani D, Lyson TR, Peterson KJ. Toward consilience in reptile phylogeny: miRNAs support an archosaur, not lepidosaur, affinity for turtles. Evol Dev. 2014; 16(4):189-96.
  • 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. A CTD-Pfizer collaboration: manual curation of 88,000 scientific articles text mined for drug-disease and drug-phenotype interactions. Database (Oxford). 2013; 2013(0):bat080.
  • 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; 30(11):2369-82.
  • Peterson KJ, Su YH, Arnone MI, Swalla B, King BL. MicroRNAs support the monophyly of enteropneust hemichordates. J Exp Zool B Mol Dev Evol. 2013; 320(6):368-74.
  • Davis AP, Murphy CG, Johnson R, Lay JM, Lennon-Hopkins K, Saraceni-Richards C, Sciaky D, King BL, Rosenstein MC, Wiegers TC, Mattingly CJ. The Comparative Toxicogenomics Database: update 2013. Nucleic Acids Res. 2013; 41(D1):D1104-14.
  • Christie AE, Roncalli V, Lona PB, McCoole MD, King BL, Bucklin A, Hartline DK, Lenz PH. In silico characterization of the insect diapause-associated protein couch potato (CPO) in Calanus finmarchicus (Crustacea: Copepoda). Comp Biochem Physiol Part D Genomics Proteomics. 2012; 8(1):45-57
  • 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
  • Duncan JF, Silva KA, Johnson CJ, King BL, Szatkiewicz JP, Kamdar SP, Ong DE, Napoli JL, Wang J, King LE Jr, Whiting DA, McElwee KJ, Sundberg JP, Everts HB. Endogenous Retinoids in the Pathogenesis of Alopecia Areata. J Invest Dermatol. 2012 133(2):334-43.
  • Collin GB, Marshall JD, King BL, Milan G, Maffei P, Jagger DJ, Naggert JK. The Alstrom Syndrome Protein, ALMS1, Interacts with α- Actinin and Components of the Endosome Recycling Pathway. PLoS ONE. 2012;7(5):e37925.
  • Walker MB, King BL, Paigen K. Clusters of Ancestrally Related Genes that Show Paralogy in Whole or in Part are a Major Feature of the Genomes of Humans and Other Species. PLoS ONE. 2012; 7(4): e35274.
  • Wang Q, Arighi CN, King BL, Polson SW, Vincent J, Chen C, Huang H, Kingham BF, Page ST, Farnum Rendino M, Thomas WK, Udwary DW, Wu CH; the North East Bioinformatics Collaborative Curation Team. Community annotation and bioinformatics workforce development in concert–Little Skate Genome Annotation Workshops and Jamborees. Database (Oxford). 2012; 2012(0):bar064.
  • Tossidou I, Niedenthal R, Klaus M, Teng B, Worthmann K, King BL, Peterson KJ, Haller H, Schiffer M. CD2AP regulates SUMOylation of CIN85 in podocytes. Mol Cell Biol. 2012; 32(6):1068-79.
  • Lyson TR, Sperling EA, Heimberg AM, Gauthier JA, King BL, Peterson KJ. MicroRNAs support a turtle + lizard clade. Biol Lett. 2012; 8(1):104-7.
  • King BL, Gillis JA, Carlisle HR, Dahn RD. A natural deletion of the HoxC cluster in elasmobranch fishes. Science. 2011 Dec 16;334(6062):1517. Reviewed in Research Highlights Nature 480(22/29): 419, 2011.
  • Howell GR, Macalinao DG, Sousa GL, Walden M, Soto I, Kneeland SC, Barbay JM, King BL, Marchant JK, Hibbs M, Stevens B, Barres BA, Clark AF, Libby RT, John SW.  Molecular clustering identifies complement and endothelin induction as early events in a mouse model of glaucoma. J Clin Invest. 2011; 121(4):1429-44.
  • Lee Y, Smith RS, Jordan W, King BL, Won J, Valpuesta JM, Naggert JK, Nishina PM. Prefoldin 5 is required for normal sensory and neuronal development in a murine model. J Biol Chem. 2011; 286(1):726-36.
  • Davis AP, King BL, Mockus S, Murphy CG, Saraceni-Richards C, Rosenstein M, Wiegers T, Mattingly CJ. The Comparative Toxicogenomics Database: update 2011. Nucleic Acids Res. 2011; 39(Database issue):D1067-72.
  • Hasham M, Donghia N, Coffey E, Maynard J, Snow K, Ames J, Wiplan R, He Y, King BL, Mills KD. Widespread genomic breaks from activation induced cytidine deaminase are prevented by homologous recombination.  Nature Immunology. 2010; 11(9):820-6.
  • Bleich A, Büchler G, Beckwith J, Petell LM, Affourtit JP, King BL, Shaffer DJ, Roopenian DC, Hedrich HJ, Sundberg JP, Leiter EH.  Cdcs1 a major colitis susceptibility locus in mice; Subcongenic analysis reveals genetic complexity.  Inflammatory Bowel Disease. 2010;16(5):765-75.
  • Reinholdt LG, Czechanski A, Kamdar S, King BL, Sun F, Handel MA.  Meiotic behavior of aneuploid chromatin in mouse models of Down syndrome.  Chromosoma. 2009; 118(6), 723-36.
  • Leiter EH, Reifsnyder PC, Wallace R, Li R, King B, Churchill GC.  NOD x 129.H2(g7) backcross delineates 129S1/SvImJ-derived genomic regions modulating type 1 diabetes development in mice.  Diabetes. 2009; 58(7),1700-3.
  • Eppig JJ, O’Brien MJ, Wigglesworth K, Nicholson A, Zhang W, King B.  Effect of in vitro maturation of mouse oocytes on the health and lifespan of adult offspring,  Human Reproduction. 2009. 24(4), 922-8.
  • Korstanje R, Desai J, Lazar G, King B, Rollins J, Spurr M, Joseph J, Kadambi S, Li Y, Cherry A, Matteson PG, Paigen B, Millonig JH.  Quantitative trait loci affecting phenotypic variation in the vacuolated lens mouse mutant, a multigenic mouse model of neural tube defects.  Physiological Genomics. 2008; 35(3), 296-304.
  • Serreze DV, Choisy-Rossi CM, Grier AE, Holl TM, Chapman HD, Gahagan JR, Osborne MA, Zhang W, King BL, Brown A, Roopenian D, Marron MP.  Through Regulation of TCR Expression Levels, an Idd7 Region Gene(s) Interactively Contributes to the Impaired Thymic Deletion of Autoreactive Diabetogenic CD8+ T Cells in Nonobese Diabetic Mice.  Journal of Immunology. 2008; 180(5), 3250-3259.
  • International Stem Cell Initiative.  Characterization of human embroyonic stem cell lines by the International Stem Cell Initiative.  Nature Biotechnology, 2007; 25(7), 803-816.
  • Yuan R, Flurkey K, Van Aelst-Bouma R, Zhang W, King B, Austad S, Miller RA, Harrison DE. Altered growth characteristics of skin fibroblasts from wild-derived mice and genetic loci regulating fibroblast clone size.  Aging Cell. 2006; 5, 203-212.
  • Pan H-J, Agate DS, King BL, Wu MK, Roderick SL, Leiter EH, Cohen DE. A polymorphism in New Zealand inbred mouse strains that inactivates phosphatidylcholine transfer protein.  FEBS Letters.  2006; 580, 5953-5958.
  • 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.
  • Bult CJ, Blake JA, Richardson JE, Kadin JA, Eppig JT, Baldarelli RM, Barsanti K, Baya M, Beal JS, Boddy WJ, Bradt DW, Burkart DL, Butler NE, Campbell J, Corey R, Corbani LE, Cousins S, Dene H, Drabkin HJ, Frazer K, Garippa DM, Glass LH, Goldsmith CW, Grant PL, King BL, Lennon-Pierce M, Lewis J, Lu I, Lutz CM, Maltais LJ, McKenzie LM, Miers D, Modrusan D, Ni L, Ormsby JE, Qi D, Ramachandran S, Reddy TB, Reed DJ, Sinclair R, Shaw DR, Smith CL, Szauter P, Taylor B, Vanden Borre P, Walker M, Washburn L, Witham I, Winslow J, Zhu Y; Mouse Genome Database Group.  The Mouse Genome Database (MGD): integrating biology with the genome.  Nucleic Acids Research. 2004; 32(Database issue), D476-81.
  • Baldarelli RM., Hill DP, Blake JA, Adachi J, Furuno M, Bradt D, Corbani LE, Cousins S, Frazer KS, Qi D, Yang L, Ramachandran S, Reed D, Zhu Y, Kasukawa T, Ringwald M, King BL, Maltais LJ, McKenzie LM, Schriml LM, Maglott D, Church DM, Pruitt K, Eppig JT, Richardson JE, Kadin JA, Bult CJ.  Connecting sequence and biology in the laboratory mouse.  Genome Research. 2003; 13(6B), 1505-19.
  • 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.
  • Peterson KA, King BL, Hagge-Greenberg A, Roix JJ, Bult CJ, O’Brien TP.  Functional and comparative genomic analysis of the piebald deletion region of mouse chromosome 14.  Genomics. 2002; 80,  172-84.
  • The FANTOM Consortium and RIKEN Genome Exploration Research Group Phase I & II Team.  Analysis of the mouse transcriptome based on functional annotation of 60,770 full-length cDNAs. Nature. 2002; 420, 563-73.
  • The RIKEN Genome Exploration Research Group Phase II Team and the FANTOM Consortium. Functional annotation of a full-length mouse cDNA collection.  Nature.  2001; 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.  Genome-sequence comparison of two unrelated isolates of the human gastric pathogen Helicobacter pylori.  Nature. 1999. 397(6715),176-80.
  • DeLisi C, Cornette J, King BL, Silverman MD. Molecular modeling method and system.  U.S. Patent number 5,583,973 issued December 10, 1996.
  • King BL, Vajda S, DeLisi C. Empirical free energy as a target function in docking and design: application to HIV-1 protease inhibitors. FEBS Letters. 1996; 384, 87-91.
  • Cornette JL, King BL, Silverman MD, DeLisi C. Graphical representations of the class I MHC binding cleft. Molecular Graphics. 1993; 11, 174-179, 187.