Publications and Presentations

Project Publications:

  1. 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 Aug 12;3:191. doi: 10.12688/f1000research.4996.1. eCollection 2014. PubMed PMID: 25309735; PubMed Central PMCID: PMC4184313.
  2. 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. Community annotation and bioinformatics workforce development in concert--Little Skate Genome Annotation Workshops and Jamborees. Database (Oxford). 2012 Mar 20;2012:bar064. doi: 10.1093/database/bar064. Print 2012. PubMed PMID: 22434832; PubMed Central PMCID:PMC3308154. *authors contributed equally

Supported Publications: (Did Skatebase Support your Publication? Let us know!)

  1. Onimaru K, Kuraku S, Takagi W, Hyodo S, Sharpe J, Tanaka M. A shift in anterior-posterior positional information underlies the fin-to-limb evolution. Elife. 2015 Aug 18;4. doi: 10.7554/eLife.07048. PubMed PMID: 26283004; PubMed Central PMCID: PMC4538735.
  2. Presnell JS, Schnitzler CE, Browne WE. KLF/SP Transcription Factor Family Evolution: Expansion, Diversification, and Innovation in Eukaryotes. Genome Biol Evol. 2015 Jul 30;7(8):2289-309. doi: 10.1093/gbe/evv141. PubMed PMID: 26232396; PubMed Central PMCID: PMC4558859.
  3. Zou J, Redmond AK, Qi Z, Dooley H, Secombes CJ. The CXC chemokine receptors of fish: Insights into CXCR evolution in the vertebrates. Gen Comp Endocrinol. 2015 May 1;215:117-31. doi: 10.1016/j.ygcen.2015.01.004. Epub 2015 Jan 23. Review. PubMed PMID: 25623148.
  4. Suzuki S, Kasai K, Yamauchi K. Characterization of little skate (Leucoraja erinacea) recombinant transthyretin: Zinc-dependent 3,3',5-triiodo-l-thyronine binding. Gen Comp Endocrinol. 2015 Jun-Jul;217-218:43-53. doi: 10.1016/j.ygcen.2015.04.006. Epub 2015 Apr 9. PubMed PMID: 25863347.
  5. Lopes-Marques M, Ruivo R, Delgado I, Wilson JM, Aluru N, Castro LF. Basal Gnathostomes provide unique insights into the evolution of vitamin B12 binders. Genome Biol Evol. 2014 Dec 31;7(2):457-64. doi: 10.1093/gbe/evu289. PubMed PMID: 25552533; PubMed Central PMCID: PMC4350170.
  6. Noro M, Sugahara F, Kuraku S. Reevaluating Emx gene phylogeny: homopolymeric amino acid tracts as a potential factor obscuring orthology signals in cyclostome genes. BMC Evol Biol. 2015 May 4;15:78. doi: 10.1186/s12862-015-0351-z. PubMed PMID: 25935411; PubMed Central PMCID: PMC4464114.
  7. Venkatesh B, Lee AP, Ravi V, Maurya AK, Lian MM, Swann JB, Ohta Y, Flajnik MF, Sutoh Y, Kasahara M, Hoon S, Gangu V, Roy SW, Irimia M, Korzh V, Kondrychyn I, Lim ZW, Tay BH, Tohari S, Kong KW, Ho S, Lorente-Galdos B, Quilez J, Marques-Bonet T, Raney BJ, Ingham PW, Tay A, Hillier LW, Minx P, Boehm T, Wilson RK, Brenner S, Warren WC. Elephant shark genome provides unique insights into gnathostome evolution. Nature. 2014 Jan 9;505(7482):174-9. doi: 10.1038/nature12826. Erratum in: Nature. 2014 Sep 25;513(7519):574. PubMed PMID: 24402279; PubMed Central PMCID: PMC3964593.
  8. Hyodo S, Kakumura K, Takagi W, Hasegawa K, Yamaguchi Y. Morphological and functional characteristics of the kidney of cartilaginous fishes: with special reference to urea reabsorption. Am J Physiol Regul Integr Comp Physiol. 2014 Dec 15;307(12):R1381-95. doi: 10.1152/ajpregu.00033.2014. Epub 2014 Oct 22. Review. PubMed PMID: 25339681.
  9. Roch GJ, Busby ER, Sherwood NM. GnRH receptors and peptides: skating backward. Gen Comp Endocrinol. 2014 Dec 1;209:118-34. doi: 10.1016/j.ygcen.2014.07.025. Epub 2014 Aug 5. Review. PubMed PMID: 25107740.
  10. Rossier BC, Baker ME, Studer RA. Epithelial sodium transport and its control by aldosterone: the story of our internal environment revisited. Physiol Rev. 2015 Jan;95(1):297-340. doi: 10.1152/physrev.00011.2014. Review. PubMed PMID: 25540145
  11. Osugi T, Ubuka T, Tsutsui K. Review: evolution of GnIH and related peptides structure and function in the chordates. Front Neurosci. 2014 Aug 15;8:255. doi: 10.3389/fnins.2014.00255. eCollection 2014. Review. PubMed PMID: 25177268; PubMed Central PMCID: PMC4133751.
  12. Macqueen DJ, Wilcox AH. Characterization of the definitive classical calpain family of vertebrates using phylogenetic, evolutionary and expression analyses. Open Biol. 2014 Apr 9;4:130219. doi: 10.1098/rsob.130219. PubMed PMID: 24718597; PubMed Central PMCID: PMC4043111.
  13. Yegorov S, Bogerd J, Good SV. The relaxin family peptide receptors and their ligands: new developments and paradigms in the evolution from jawless fish to mammals. Gen Comp Endocrinol. 2014 Dec 1;209:93-105. doi: 10.1016/j.ygcen.2014.07.014. Epub 2014 Jul 29. Review. PubMed PMID: 25079565.
  14. Hyodo S, Kakumura K, Takagi W, et al. Morphological and functional characteristics of the kidney of cartilaginous fishes: with special reference to urea reabsorption. Comp Biochem Physiol C Toxicol Pharmacol. 2014;307(12):R1381–R1395. doi:10.1152/ajpregu.00033.2014.
  15. Falcón J, Coon SL, Besseau L, Cazaméa-Catalan D, Fuentès M, Magnanou E, Paulin CH, Boeuf G, Sauzet S, Jørgensen EH, Mazan S, Wolf YI, Koonin EV, Steinbach PJ, Hyodo S, Klein DC. Drastic neofunctionalization associated with evolution of the timezyme AANAT 500 Mya. Proc Natl Acad Sci U S A. 2014 Jan 7;111(1):314-9. doi: 10.1073/pnas.1312634110. Epub 2013 Dec 18. PubMed PMID: 24351931; PubMed Central PMCID: PMC3890824.
  16. Braasch I, Guiguen Y, Loker R, Letaw JH, Ferrara A, Bobe J, Postlethwait JH. Connectivity of vertebrate genomes: Paired-related homeobox (Prrx) genes in spotted gar, basal teleosts, and tetrapods. Comp Biochem Physiol C Toxicol Pharmacol. 2014 Jan 30. pii: S1532-0456(14)00007-6. doi: 10.1016/j.cbpc.2014.01.005. [Epub ahead of print] PubMed PMID: 24486528.
  17. Moore DB, Gillentine MA, Botezatu NM, Wilson KA, Benson AE, Langeland JA. Asynchronous Evolutionary Origins of Aβ and BACE1. Mol Biol Evol. 2014;31(3):1436.doi: 10.1093/molbev/mst262. PubMed PMID: 24361992.
  18. Modrell MS, Hockman D, Uy B, Buckley D, Sauka-Spengler T, Bronner ME, Baker CV. A fate-map for cranial sensory ganglia in the sea lamprey. Dev Biol. 2014 Jan 15;385(2):405-16.doi:10.1016/j.ydbio.2013.10.021. PubMed PMID: 24513489.
  19. Boehm T, Swann, JB. Origen and evolution of adaptive immunity. Annu Rev Anim Biosci. 2014.2:259-283.doi: 10.1146/annurev-animal-022513-114201. PubMed PMID:
  20. Richards VP, Suzuki H, Stanhope MJ, Shivji MS. Characterization of the heart transcriptome of the white shark (Carcharodon carcharias). BMC Genomics. 2013 Oct 11;14:697. doi: 10.1186/1471-2164-14-697. PubMed PMID: 24112713; PubMed Central PMCID: PMC3832898.
  21. Lopes-Marques M, Cunha I, Reis-Henriques MA, Santos MM, Castro LF. Diversity and history of the long-chain acyl-CoA synthetase (Acsl) gene family in vertebrates. BMC Evol Biol. 2013 Dec 12;13:271. doi: 10.1186/1471-2148-13-271. PubMed PMID: 24330521; PubMed Central PMCID: PMC3890633.
  22. Gillis J.A., M.S. Modrell,C.V. Baker. Developmental evidence for serial homology of the vertebrate jaw and gill arch skeleton.Nat Commun. 2013;4:1436.doi:10.1038/ncomms2429. PubMed PMID: 23385581; PubMed Central PMCID:PMC3600657.
  23. Amemiya CT, J. Alföldi, A.P. Lee, S. Fan, H. Philippe, I. Maccallum, I. Braasch, T. Manousaki, I. Schneider, N. Rohner, C. Organ, D. Chalopin, J.J. Smith, M. Robinson, R.A. Dorrington, M. Gerdol, B. Aken, M.A. Biscotti, M. Barucca, D. Baurain, A.M. Berlin, G.L. Blatch, F. Buonocore, T. Burmester, M.S. Campbell, A. Canapa, J.P. Cannon, A. Christoffels, G. De Moro, A.L. Edkins, L. Fan, A.M. Fausto, N. Feiner, M. Forconi, J. Gamieldien, S. Gnerre, A. Gnirke, J.V. Goldstone, W. Haerty, M.E. Hahn, U. Hesse, S. Hoffmann, J. Johnson, S.I. Karchner, S Kuraku, M. Lara, J.Z. Levin, G.W. Litman, E. Mauceli, T. Miyake, M.G. Mueller, D.R. Nelson, A. Nitsche, E. Olmo, T. Ota, A. Pallavicini, S. Panji, B. Picone, C.P. Ponting, S.J. Prohaska, D. Przybylski, N.R. Saha, V. Ravi, F.J. Ribeiro, T. Sauka-Spengler, G. Scapigliati, S.M. Searle, T. Sharpe, O. Simakov, P.F. Stadler, J.J. Stegeman, K. Sumiyama, D. Tabbaa, H. Tafer, J. Turner-Maier, P. van Heusden, S. White, L. Williams, M. Yandell, H. Brinkmann, J.N. Volff, C.J. Tabin, N. Shubin, M. Schartl, D.B. Jaffe, J.H. Postlethwait, B. Venkatesh, F. Di Palma, E.S. Lander, A. Meyer, K. Lindblad-Toh. The African coelacanth genome provides insights into tetrapod evolution.Nature.2013 Apr 18;496(7445):311-6.doi: 10.1038/nature12027. PubMed PMID: 23598338; PubMed Central PMCID:PMC3633110.
  24. Frankenberg S., M.B. Renfree. On the origin of POU5F1. BMC Biol. 2013 May 9;11:56. doi: 10.1186/1741-7007-11-56. PubMed PMID: 23659605; PubMed Central PMCID: PMC3665618.
  25. Västermark Å., A. Krishnan, M.E. Houle, R. Fredriksson, J.M. Cerdá-Reverter, H.B. Schiöth. Identification of distant Agouti-like sequences and re-evaluation of the evolutionary history of the Agouti-related peptide (AgRP). PLoS One. 2012;7(7):e40982. doi: 10.1371/journal.pone.0040982. Epub 2012 Jul 16. PubMed PMID: 22815886; PubMed Central PMCID: PMC3397983.
  26. Gaudet P, C. Arighi, F. Bastian, A.Bateman, J.A. Blake, M.J. Cherry, P. D'Eustachio, R. Finn, M. Giglio, L. Hirschman, R. Kania, W. Klimke, M.J. Martin, I. Karsch-Mizrachi, M. Munoz-Torres, D. Natale, C. O'Donovan, F. Ouellette, K.D. Pruitt, M. Robinson-Rechavi, S.A. Sansone, P. Schofield, G. Sutton, K. Van Auken, S. Vasudevan, C. Wu, J. Young, R. Mazumder. Recent advances in biocuration: meeting report from the Fifth International Biocuration Conference. Database (Oxford). 2012 Oct 29;2012:bas036. doi: 10.1093/database/bas036. Print 2012. PubMed PMID: 23110974; PubMed Central PMCID: PMC3483532.
  27. Tossidou I., R. Niedenthal, M. Klaus, B. Teng, K. Worthmann, B.L. King, K.J. Peterson, H. Haller, M. Schiffer. CD2AP regulates SUMOylation of CIN85 in podocytes. Mol Cell Biol. 2012 Mar;32(6):1068-79. doi: 10.1128/MCB.06106-11. Epub 2011 Dec 27. PubMed PMID: 22203040; PubMed Central PMCID: PMC3295011.
  28. King B.L., J.A. Gillis, H.R. Carlisle, R.D. Dahn. A natural deletion of the HoxC cluster in elasmobranch fishes. Science. 2011 Dec 16;334(6062):1517. PubMed PMID:22174244.
  29. Schneider, I., I. Aneas, A.R. Gehrke, R.D. Dahn, M.A. Nobrega, N.H. Shubin. Appendage expression driven by the Hoxd Global Control Region is an ancient gnathostome feature. Proc Natl Acad Sci U S A. 2011 Aug 2;108(31):12782-6. Epub 2011 Jul 15. PubMed PMID:21765002; PubMed Central PMCID: PMC3150877.

Project Presentations:

  1. Wyffels, J., Cain, W., King, B., Vincent, J., Wu, C., Polson, S., and The North East Bioinformatics Collaborative (NEBC). "Integrated wet and dry lab education using The Skate Genome Project", 6th Biennial Northeast Regional IDeA Conference, Bar Harbor, ME, September 24–26, 2015.
  2. Wyffels, J., King, B.L., Vincent, J., Chen, C., Polson, S.W., Wu, C. "Transcriptome Sequencing, De novo Assembly, and Annotation of Three Chondrichthyan Fishes, Leucoraja erinacea, Scyliorhinus canicula, and Callorhinchus milii.", 30th American Elasmobranch Society & 94rd American Society of Ichthyologists and Herpetologists Joint Meeting, Chattanooga, Tennessee, 30 July – 3 August 2014.
  3. Wyffels, J.T. and The North East Bioinformatics Collaborative. “The Skate Genome Project: An Educational Model for Gene and Protein Annotation”, The Plant and Animal Genome XXII Conference, San Diego, CA, Jan 10-14, 2014.
  4. Wyffels, J.T. and The North East Bioinformatics Collaborative. “The Skate Genome Project: SkateBase Updates and Scientific Outreach”, 5th Biennial Northeast Regional IDeA Conference, Newark, DE, August 14-16, 2013.
  5. King, B.L., “The Skate Genome Project”, 5th Biennial Northeast Regional IDeA Conference, Newark, DE, August 14-16, 2013.
  6. Wu, C. H., “Community Annotation & Bioinformatics Workforce Development In Concert: Little Skate Genome Annotation Workshops & Jamborees “,5th Biennial Northeast Regional IDeA Conference, Newark, DE, August 14-16, 2013.
  7. Wyffels, J. T. and The North East Bioinformatics Collaborative., “The Skate Genome Project”, 29th American Elasmobranch Society & 93rd American Society of Ichthyologists and Herpetologists Joint Meeting, Albuquerque, NM, July 10-15, 2013.
  8. Vincent, J., “Skate Genome Project: Cyber-Enabled Bioinformatics Collaboration”, The Association of Biomolecular Resource Facilities, Palm Springs, CA, March 2-5, 2011.
  9. King, B.L., "The Skate Genome Project", 4th Northeast INBRE Regional Meeting, Newport, RI, Aug. 12, 2011.
  10. Polson, S.W. "NECC Little Skate Genome Annotation Workshops and Jamborees", 2011 Annual North East Cyberinfrastructure Consortium Meeting, Orono, ME, March 15, 2011.
  11. King, B.L., "The Genome Sequence Project for The Little Skate, Leucoraja erinacea", 2011 Annual North East Cyberinfrastructure Consortium Meeting, Orono, ME, March 15, 2011.
  12. King, B.L., “The Skate Genome Project”, Annual INBRE Principal Investigator Meeting, NCRR, NIH, Bethesda, MD, Oct. 4, 2010.

Project Posters:

  1. King, B.L., Thomas, W.K., Vincent, J., Shaikh, Z., Polson, S.W., Wu, C., and The North East Bioinformatics Collaborative (NEBC). " Bioinformatics Training and Research Collaborations among Northeast IDeA Programs", 6th Biennial Northeast Regional IDeA Conference, Bar Harbor, ME, September 24–26, 2015.
  2. Wyffels, J. and The North East Bioinformatics Collaborative (NEBC). "The Skate Genome Project: A Model for Scientific Collaboration and Education", 5th Biennial NIH, NCRR National IDeA Symposium of Biomedical Research Excellence (NISBRE), Washington DC, June 16-18, 2014.
  3. King, B.L. and The North East Bioinformatics Collaborative (NEBC)."Comparative Analysis of Three Cartilaginous Fish Transcriptomes To Advance Studies of Human Gene Function", 5th Biennial NIH, NCRR National IDeA Symposium of Biomedical Research Excellence (NISBRE), Washington DC, June 16-18, 2014.
  4. King, B.L. and The North East Bioinformatics Collaborative. "The Skate Genome Project", 38th Maine Biological and Medical Sciences Symposium, Mount Desert Island Biological Laboratory, Salisbury Cove, ME, April 15, 2011.
  5. Farnum Rendino, M., J. Vincent ,K. Miaskiewicz, M. Kaplarevic , H. Huang, S. Polson, J. Koskies, S. Cousins, B. Segee, C. Wu, V. Nemeth, and J. Van Houten. "NECC Shared Data Center: Enabling Collaborative Research Through Shared Infrastructure", 2011 Annual North East Cyberinfrastructure Consortium Meeting, Orono, ME, March 15, 2011.
  6. Arighi, C. and the North East Cyberinfrastructure Consortium. "Skate Genome Project: a Cyber-Enabled Research and Workforce Development”, Plant and Animal Genome XIX _meeting, San Diego, CA. January 15 - 19, 2011.
  7. Wang, Q., B. King, C. Arighi, H. Huang, M. Kaplarevic, B. Kingham, J. Vincent, M. Farnum Rendino, R.D. Dahn, C. Mattingly, C. Chichester, J. Fueyo, W.K. Thomas, C.H. Wu. “Skate Genome Project: Cyber-Enabled Research and Workforce Development”, National IDeA Symposium of Biomedical Research Excellence Symposium, Bethesda, MD, June 16-18, 2010. (Highlighted poster for the Bioengineering and Biotechnology session). [PDF]