Publications

PQN-75 is expressed in the pharyngeal gland cells of C. elegans and is dispensable for germline development

Simple and fast quantification of DNA damage by real-time PCR, and its application to nuclear and mitochondrial DNA from multiple tissues of aging zebrafish

Zhu S, Coffman JA. BMC Res Notes 2017 Jul 11;10(1):269. doi: 10.1186/s13104-017-2593-x. PMID: 28693618; PMCID: PMC5504608.

IKKα regulates human keratinocyte migration through surveillance of the redox environment

Lisse TS, Rieger S. J Cell Sci. 2017 Mar 1;130(5):975-988. doi: 10.1242/jcs.197343. PubMed PMID: 28122935.

The protein tyrosine phosphatase 1B inhibitor MSI-1436 stimulates regeneration of heart and multiple other tissues

Smith A, Nguyen K, Rando TA, Zasloff M, Strange K, Yin VP. Nature pj Regenerative Medicine 2017, March 3;2:doi:10.1038/s41536-017-0008-1.

The landscape of extreme genomic variation in the highly adaptable Atlantic killifish. Genome Biol Evol.

Reid NM, Jackson CE, Gilbert D, Minx P, Montague MJ, Hampton TH, Helfrich LW, King BL, Nacci DE, Aluru N, et al. 2017 Feb 13. doi: 10.1093/gbe/evx023. [Epub ahead of print] PubMed PMID: 28201664. PMCID:PMC5381573.

ELLI-1, a novel germline protein, modulates RNAi activity and P-granule accumulation in Caenorhabditis elegans

Andralojc KM, Campbell AC, Kelly AL, Terrey M, Tanner PC, Gans IM, Senter-Zapata MJ, Khokhar ES, Updike DL. PLoS Genet. 2017 Feb 9;13(2):e1006611. doi: 10.1371/journal.pgen.1006611. PubMed PMID: 28182654; PubMed Central PMCID: PMC5325599.

Assessing Health Span in Caenorhabditis elegans: Lessons From Short-Lived Mutants

Rollins JA, Howard AC, Dobbins SK, Washburn EH, Rogers AN. J Gerontol A Biol Sci Med Sci. 2017 Feb 2. doi: 10.1093/gerona/glw248. [Epub ahead of print] PubMed PMID: 28158466.

Prioritizing studies on regeneration in nontraditional model organisms

King BL, Yin VP. Regen Med. 2017 Jan;12(1):1-3. doi: 10.2217/rme-2016-0159. PubMed PMID: 27925505.

The Comparative Toxicogenomics Database: update 2017

Davis AP, Grondin CJ, Johnson RJ, Sciaky D, King BL, McMorran R, Wiegers J, Wiegers TC, Mattingly CJ. Nucleic Acids Res. 2017 Jan 4;45(D1):D972-D978. doi: 10.1093/nar/gkw838. PubMed PMID: 27651457; PubMed Central PMCID: PMC5210612.

Leucine-rich repeat containing protein LRRC8A is essential for swelling-activated Cl- currents and embryonic development in zebrafish

Yamada T, Wondergem R, Morrison R, Yin VP, Strange K. Physiol Rep. 2016 Oct;4(19). pii: e12940. doi: 10.14814/phy2.12940. PubMed PMID:27688432.

Global gene profiling of aging lungs in Atp8b1 mutant mice

Soundararajan R, Stearns TM, Czachor A, Fukumoto J, Turn C, Westermann-Clark E, Breitzig M, Tan L, Lockey RF, King BL, Kolliputi N. Aging (Albany NY). 2016 Sep 29;8(9):2232-2252. doi: 10.18632/aging.101056. PubMed PMID: 27689529.

Cortisol-treated zebrafish embryos develop into pro-inflammatory adults with aberrant immune gene regulation

Hartig EI, Zhu S, King BL, Coffman JA. Biol Open. 2016 Aug 15;5(8):1134-41. doi: 10.1242/bio.020065. PubMed PMID: 27444789; PubMed Central PMCID:PMC5004618.

A Conserved MicroRNA Regulatory Circuit Is Differentially Controlled during Limb/Appendage Regeneration

King BL, Yin VP. PLoS One. 2016 Jun 29;11(6):e0157106. doi: 10.1371/journal.pone.0157106. eCollection 2016. PubMed PMID: 27355827; PubMed Central PMCID:PMC4927183.

Wound-Induced Polyploidy Is Required for Tissue Repair

Losick VP. Adv Wound Care (New Rochelle). 2016 Jun 1;5(6):271-278. Review. PubMed PMID: 27274437; PubMed Central PMCID:PMC4876532.

Generating Gene Ontology-Disease Inferences to Explore Mechanisms of Human Disease at the Comparative Toxicogenomics Database

Davis, AP, Wiegers TC, King BL, Wiegers J, Grondin CJ, Sciaky D, Johnson RJ, Mattingly CJ. PLoS One. 2016 May 12;11(5):e0155530. doi: 10.1371/journal.pone.0155530. eCollection 2016. PubMed PMID:27171405; PubMed Central PMCID:PMC4865041.

Advancing Exposure Science through Chemical Data Curation and Integration in the Comparative Toxicogenomics Database

Grondin CJ, Davis AP, Wiegers TC, King BL, Wiegers JA, Reif DM, Hoppin JA, Mattingly CJ. Environ Health Perspect. 2016. http://dx.doi.org/10.1289/EHP174. PubMed PMID:27170236.

Abnormal Osmotic Avoidance Behavior in C. elegans Is Associated with Increased Hypertonic Stress Resistance and Improved Proteostasis

Lee EC, Kim H, Ditano J, Manion D, King BL, Strange K. PLoS One. 2016 Apr 25;11(4):e0154156. doi: 10.1371/journal.pone.0154156. eCollection 2016. PubMed PMID:27111894; PubMed Central PMCID:PMC4844114.

Paclitaxel-induced epithelial damage and ectopic MMP-13 expression promotes neurotoxicity in zebrafish

Lisse TS, Middleton LJ, Pellegrini AD, Martin PB, Spaulding EL, Lopes O, Brochu EA, Carter EV, Waldron A, Rieger S. PNAS 2016 113 (15) E2189-E2198; published ahead of print March 28, 2016, doi:10.1073/pnas.1525096113. PubMed PMID:27035978; PubMed Central PMCID:PMC4839466.

Wound-Induced Polyploidization: Regulation by Hippo and JNK Signaling and Conservation in Mammals

Losick VP, Jun AS, Spradling AC.  PLoS One. 2016 Mar 9;11(3):e0151251. doi: 10.1371/journal.pone.0151251. eCollection 2016. PubMed PMID: 26958853; PubMed Central PMCID: PMC4784922.

Comparative transcriptomic profiling of hydrogen peroxide signaling networks in zebrafish and human keratinocytes: Implications toward conservation, migration and wound healing

Lisse TS, King BL, Rieger S.  Sci Rep. 2016 Feb 5;6:20328. doi: 10.1038/srep20328. PubMed PMID: 26846883; PubMed Central PMCID:PMC4742856.

The Interrelationships of Placental Mammals and the Limits of Phylogenetic Inference

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. Genome Biol Evol. 2016 Jan 5;8(2):330-44. doi: 10.1093/gbe/evv261. PubMed PMID:26733575; PubMed Central PMCID:PMC4779606.

Developmental control of transcriptional and proliferative potency during the evoltionary emergence of animals

Arenas-Mena C, Coffman JA.  Dev Dyn. 2015 Oct;244(10):1193-201. doi: 10.1002/dvdy.24305. Epub 2015 Aug 4. PubMed PMID: 26173445; PubMed Central PMCID:PMC4705838.

Calcium activated K⁺ channels in the electroreceptor of the skate confirmed by cloning. Details of subunits and splicing.

King BL, Shi LF, Kao P, Clusin WT. Gene. 2016 Mar 1;578(1):63-73. doi: 10.1016/j.gene.2015.12.010. Epub 2015 Dec 11. PubMed PMID: 26687710; PubMed Central PMCID:PMC4724458.

Dynamic microRNA-101a and Fosab expression controls zebrafish heart regeneration

Beauchemin M, Smith A, Yin VP. Development 2015 142: 4026-4037; doi: 10.1242/dev.126649. PubMed PMID:26628091; PubMed Central PMCID:PMC4712838.

Detection of canonical A-to-G editing events at 3′ UTRs and microRNA target sites in human lungs using next-generation sequencing

Soundararajan R, Stearns TM, Griswold AL, Mehta A, Czachor A, Fukumoto J, Lockey RF, King BL, Kolliputi N. Oncotarget. 2015 Nov 3;6(34):35726-36. doi: 10.18632/oncotarget.6132. PubMed PMID: 26486088; PubMed Central PMCID: PMC4742137.

A Fluorescence-Based Assay for Proteinuria Screening in Larval Zebrafish (Danio rerio)

Hanke N, King BL, Vaske B, Haller H, Schiffer M. Zebrafish. 2015 Oct;12(5):372-6. doi: 10.1089/zeb.2015.1093. Epub 2015 Jun 30. PubMed PMID:26125680; PubMed Central PMCID: PMC4593894.

A Uniform System for the Annotation of Vertebrate microRNA Genes and the Evolution of the Human microRNAome

Fromm B, Billipp T, Peck LE, Johansen M, Tarver JE, King BL, Newcomb JM, Sempere LF, Flatmark K, Hovig E, Peterson KJ. Annu Rev Genet. 2015;49:213-42. doi: 10.1146/annurev-genet-120213-092023. Epub 2015 Oct 14. Review. PubMed PMID: 26473382; PubMed Central PMCID: PMC4743252.

Specifying and protecting germ cell fate

Strome S, Updike D. Nat Rev Mol Cell Biol. 2015 Jul;16(7):406-16. doi: 10.1038/nrm4009. Review. PubMed PMID: 26122616; PubMed Central PMCID:PMC4698964.

Gene Expression Changes Associated With the Developmental Plasticity of Sea Urchin Larvae in Response to Food Availability

Carrier TJ, King BL, Coffman JA. Biol Bull. 2015 Jun;228(3):171-80. PubMed PMID: 26124444; PubMed Central PMCID:PMC4706744.

CSR-1 and P granules suppress sperm-specific transcription in the C. elegans germline

Campbell AC, Updike DL. Development 2015 142: 1745-1755; doi: 10.1242/dev.121434. PubMed PMID:25968310; PubMed Central PMCID:PMC4440928.

A Forward Genetic Screen for Suppressors of Somatic P Granules in Caenorhabditis elegans

Kelly AL, Senter-Zapata MJ, Campbell AC, Lust HE, Theriault ME, Andralojc KM, Updike DL. G3 (Bethesda). 2015 Jun 22;5(10):2209-15. doi: 10.1534/g3.115.019257. PubMed PMID: 26100681; PubMed Central PMCID:PMC4593002.

Exosome Delivered Anticancer Drugs Across the Blood-Brain Barrier for Brain Cancer Therapy in Danio Rerio

Yang T, Martin P, Fogarty B, Brown A, Schurman K, Phipps R, Yin VP, Lockman P, Bai S. Pharm Res. 2015 Jun;32(6):2003-14. doi: 10.1007/s11095-014-1593-y. Epub 2015 Jan 22. PubMed PMID:25609010; PubMed Central PMCID:PMC4520542.

The role of nuclear hormone receptors in cutaneous wound repair

Rieger S, Zhao H, Martin P, Abe K, Lisse TS. Cell Biochem Funct. 2015 Jan;33(1):1-13. doi: 10.1002/cbf.3086. Epub 2014 Dec 22. PubMed PMID:25529612; PubMed Central PMCID:PMC4357276.

The Comparative Toxicogenomics Database’s 10th year anniversary: update 2015

Davis AP, Grondin CJ, Lennon-Hopkins K, Saraceni-Richards C, Sciaky D, King BL, Wiegers TC, Mattingly CJ. Nucleic Acids Res. 2015 Jan;43(Database issue):D914-20. doi: 10.1093/nar/gku935. Epub 2014 Oct 17. PubMed PMID:25326323; PubMed Central PMCID:PMC4384013.

On the meaning of chance in biology

Coffman JA. Biosemiotics. 2014 Dec 1;7(3):377-388. PubMed PMID: 25870720; PubMed Central PMCID:PMC4392722.

Cloning of a functional 25-hydroxyvitamin D-1α-hydroxylase in zebrafish (Danio rerio)

Chun RF, Blatter E, Elliott S, Fitz-Gibbon S, Rieger S, Sagasti A, Adams JS, Hewison M. Cell Biochem Funct. 2014 Dec;32(8):675-82. doi: 10.1002/cbf.3071. Epub 2014 Oct 7. PubMed PMID:25290078; PubMed Central PMCID:PMC4363119.

Natural selection canalizes expression variation of environmentally induced plasticity-enabling genes

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. Mol Biol Evol. 2014 Nov;31(11):3002-15. doi: 10.1093/molbev/msu241. Epub 2014 Aug 25. PubMed PMID:25158801; PubMed Central PMCID:PMC4209136.

SkateBase, an elasmobranch genome project and collection of molecular resources for chondrichthyan fishes

Wyffels J, King BL, Vincent J, Chen C, Wu CH, Polson SW. F1000Res. 2014 Aug 12;3:191. doi: 10.12688/f1000research.4996.1. eCollection 2014. PubMed PMID:25309735; PubMed Central PMCID:PMC4184313.

Toward consilience in reptile phylogeny: miRNAs support an archosaur, not lepidosaur, affinity for turtles

Field DJ, Gauthier JA, King BL, et al. Evol Dev. 2014 Jul;16(4):189-96. doi: 10.1111/ede.12081. Epub 2014 May 5. PubMed PMID:24798503; PubMed Central PMCID:PMC4215941.

Germ-Granule Components Prevent Somatic Development in the C. elegans Germline

Updike DL, Knutson AK, Egelhofer TA, Campbell AC, Strome S. Curr Biol. 2014 May 5;24(9):970-5. doi: 10.1016/j.cub.2014.03.015. Epub 2014 Apr 17. PubMed PMID:24746798; Pub Med Central PMCID:PMC4036631.

The voltage-gated anion channels encoded by clh-3 regulate egg laying in C. elegans by modulating motor neuron excitability

Branicky R, Miyazaki H, Strange K, Schafer WR.  J Neurosci. 2014 Jan 15;34(3):764-75. doi: 10.1523/JNEUROSCI.3112-13.2014. PubMed PMID: 24431435; PubMed Central PMCID:PMC3891957.

Oral-aboral axis specification in the sea urchin embryo, IV: hypoxia radializes embryos by preventing the initial spatialization of nodal activity

Coffman JA, Wessels A, DeSchiffart C, Rydlizky K. Dev Biol. 2014 Feb 15;386(2):302-7. doi: 10.1016/j.ydbio.2013.12.035. Epub 2013 Dec 31. PubMed PMID:24384388; PubMed Central PMCID:PMC3929957.

A unique covalent bond in basement membrane is a primordial innovation for tissue evolution

Fidler AL, Vanacore RM, Chetyrkin SV, Pedchenko VK, Bhave G, Yin VP, et al. Proc Natl Acad Sci USA. 2014 Jan 7;111(1):331-6. doi: 10.1073/pnas.1318499111. Epub 2013 Dec 16. PubMed PMID:24344311; PubMed Central PMCID:PMC3890831.

miRNAs: small genes with big potential in metazoan phylogenetics

Tarver JE, Sperling EA, Nailor A, Heimberg AM, Robinson JM, King BL, et al. Mol Biol Evol. 2013 Nov;30(11):2369-82. doi: 10.1093/molbev/mst133. Epub 2013 Aug 2. Review. PubMed PMID:23913097.

A CTD-Pfizer collaboration: manual curation of 88,000 scientific articles text mined for drug-disease and drug-phenotype interactions

Davis AP, Wiegers TC, Roberts PM, King BL, et al. Database (Oxford). 2013 Nov 28;2013:bat080. doi: 10.1093/database/bat080. Print 2013. PubMed PMID:24288140; PubMed Central PMCID:PMC3842776.

Developmental cis-regulatory analysis of the cyclin D gene in the sea urchin Strongylocentrotus purpuratus

McCarty CM, Coffman JA. Biochem Biophys Res Commun. 2013 Oct 25;440(3):413-8. doi: 10.1016/j.bbrc.2013.09.094. Epub 2013 Oct 1. PubMed Central PMCID:PMC3871186.