ZFIN ID: ZDB-PERS-030612-2
Howe, Doug
Email: dhowe@zfin.org
URL:
Affiliation: ZFIN Database Team
Address: Zebrafish Information Network 5291 University of Oregon Eugene, OR 97403-5291 USA
Country: United States
Phone: (541) 346-2355
Fax: (541) 346-4548
Orcid ID: 0000-0001-5831-7439


BIOGRAPHY AND RESEARCH INTERESTS
2011-Present
Data Curation Manager
Zebrafish Model Organism Database

2003-2011 Scientific Curator
Zebrafish Model Organism Database
Eugene, OR

1998-2003 Postdoctoral Fellow
Department of Pharmacology
University of Washington
Seattle, WA
Molecular and Behavioral Analysis of the role of PKA in Neuronal and Glial Signal Transduction In Vivo

2001-2002 Computer Programming Courses
North Seattle Community College
Seattle, WA

1992-1998 Ph.D., Neurobiology
University of North Carolina
Chapel Hill, NC
Signal Transduction in Neurons and Glia

1988-1992 B.S. Biology
University of New Hampshire
Durham, New Hampshire

CERTIFICATIONS
4/26/2017: Microsoft Professional Program in Data Science


PUBLICATIONS
Howe, D.G., Bradford, Y.M., Eagle, A., Fashena, D., Frazer, K., Kalita, P., Mani, P., Martin, R., Moxon, S.T., Paddock, H., Pich, C., Ramachandran, S., Ruzicka, L., Schaper, K., Shao, X., Singer, A., Toro, S., Van Slyke, C., Westerfield, M. (2016) The Zebrafish Model Organism Database: new support for human disease models, mutation details, gene expression phenotypes and searching. Nucleic acids research. 45(D1):D758-D768
Howe, D.G., Bradford, Y.M., Eagle, A., Fashena, D., Frazer, K., Kalita, P., Mani, P., Martin, R., Moxon, S.T., Paddock, H., Pich, C., Ramachandran, S., Ruzicka, L., Schaper, K., Shao, X., Singer, A., Toro, S., Van Slyke, C., Westerfield, M. (2016) A scientist's guide for submitting data to ZFIN. Methods in cell biology. 135:451-81
Ruzicka, L., Bradford, Y.M., Frazer, K., Howe, D.G., Paddock, H., Ramachandran, S., Singer, A., Toro, S., Van Slyke, C.E., Eagle, A.E., Fashena, D., Kalita, P., Knight, J., Mani, P., Martin, R., Moxon, S.A., Pich, C., Schaper, K., Shao, X., Westerfield, M. (2015) ZFIN, the Zebrafish Model Organism Database: Updates and new directions. Genesis (New York, N.Y. : 2000). 53(8):498-509
Alam-Faruque, Y., Hill, D.P., Dimmer, E.C., Harris, M.A., Foulger, R.E., Tweedie, S., Attrill, H., Howe, D.G., Thomas, S.R., Davidson, D., Woolf, A.S., Blake, J.A., Mungall, C.J., O'Donovan, C., Apweiler, R., Huntley, R.P. (2014) Representing Kidney Development Using the Gene Ontology. PLoS One. 9:e99864
Khodiyar, V.K., Howe, D., Talmud, P.J., Breckenridge, R., Lovering, R.C. (2013) From zebrafish heart jogging genes to mouse and human orthologs: using Gene Ontology to investigate mammalian heart development.. F1000 Research. 2:1-17
Howe, D.G., Bradford, Y.M., Conlin, T., Eagle, A.E., Fashena, D., Frazer, K., Knight, J., Mani, P., Martin, R., Moxon, S.A., Paddock, H., Pich, C., Ramachandran, S., Ruef, B.J., Ruzicka, L., Schaper, K., Shao, X., Singer, A., Sprunger, B., Van Slyke, C.E., and Westerfield, M. (2013) ZFIN, the Zebrafish Model Organism Database: increased support for mutants and transgenics. Nucleic acids research. 41(D1):D854-860
Bradford, Y., Conlin, T., Dunn, N., Fashena, D., Frazer, K., Howe, D.G., Knight, J., Mani, P., Martin, R., Moxon, S.A., Paddock, H., Pich, C., Ramachandran, S., Ruef, B.J., Ruzicka, L., Bauer Schaper, H., Schaper, K., Shao, X., Singer, A., Sprague, J., Sprunger, B., Van Slyke, C., and Westerfield, M. (2011) ZFIN: enhancements and updates to the zebrafish model organism database. Nucleic acids research. 39(suppl 1):D822-D829
Howe, D.G., Frazer, K., Fashena, D., Ruzicka, L., Bradford, Y., Ramachandran, S., Ruef, B.J., Van Slyke, C., Singer, A., and Westerfield, M. (2011) Data extraction, transformation, and dissemination through ZFIN. Meth. Cell. Biol.. 104:311-325
Sprague, J., Bayraktaroglu, L., Bradford, Y., Conlin, T., Dunn, N., Fashena, D., Frazer, K., Haendel, M., Howe, D.G., Knight, J., Mani, P., Moxon, S.A., Pich, C., Ramachandran, S., Schaper, K., Segerdell, E., Shao, X., Singer, A., Song, P., Sprunger, B., Van Slyke, C.E., and Westerfield, M. (2008) The Zebrafish Information Network: the zebrafish model organism database provides expanded support for genotypes and phenotypes. Nucleic acids research. 36:D768-772
Sprague, J., Bayraktaroglu, L., Clements, D., Conlin, T., Fashena, D., Frazer, K., Haendel, M., Howe, D.G., Mani, P., Ramachandran, S., Schaper, K., Segerdell, E., Song, P., Sprunger, B., Taylor, S., Van Slyke, C.E., and Westerfield, M. (2006) The Zebrafish Information Network: the zebrafish model organism database. Nucleic acids research. 34:D581-585

NON-ZEBRAFISH PUBLICATIONS
Huntley RP, Sitnikov D, Orlic-Milacic M, Balakrishnan R, D'Eustachio P, Gillespie ME, Howe D, Kalea AZ, Maegdefessel L, Osumi-Sutherland D, Petri V, Smith JR, Van Auken K, Wood V, Zampetaki A, Mayr M, Lovering RC (2016). Guidelines for the functional annotation of microRNAs using the Gene Ontology. RNA. 2016 Feb 25.

Gene Ontology Consortium (2015). Gene Ontology Consortium: going forward. Nucl.Ac.Res. 43:D1049-56.

Gene Ontology Consortium (2013). Gene Ontology annotations and resources. Nucl.Ac.Res. 41:D530-5.

Good BM, Howe DG, Lin SM, Kibbe WA, Su AI (2011). Mining the Gene Wiki for functional genomic knowledge. BMC Genomics 12:603.

Gene Ontology Consortium (2011). The Gene Ontology: enhancements for 2011.Nucl.Ac.Res. 40:D559-64.

Gaudet P, Bairoch A, Field D, Sansone SA, Taylor C, Attwood TK, Bateman A, Blake JA, Bult CJ, Cherry JM, Chisholm RL, Cochrane G, Cook CE, Eppig JT, Galperin MY, Gentleman R, Goble CA, Gojobori T, Hancock JM, Howe DG, Imanishi T, Kelso J, Landsman D, Lewis SE, Karsch Mizrachi I, Orchard S, Ouellette BF, Ranganathan S, Richardson L, Rocca-Serra P, Schofield PN, Smedley D, Southan C, Tan TW, Tatusova T, Whetzel PL, White O, Yamasaki C (2011) BioDBCore Working Group. Towards BioDBcore: a community-defined information specification for biological databases. Database (Oxford). Jan 4;baq027.

Gaudet P, Bairoch A, Field D, Sansone SA, Taylor C, Attwood TK, Bateman A, Blake JA, Bult CJ, Cherry JM, Chisholm RL, Cochrane G, Cook CE, Eppig JT, Galperin MY, Gentleman R, Goble CA, Gojobori T, Hancock JM, Howe DG, Imanishi T, Kelso J, Landsman D, Lewis SE, Mizrachi IK, Orchard S, Ouellette BF, Ranganathan S, Richardson L, Rocca-Serra P, Schofield PN, Smedley D, Southan C, Tan TW, Tatusova T, Whetzel PL, White O, Yamasaki C; BioDBCore Working Group (2011) Towards BioDBcore: a community-defined information specification for biological databases. Nucleic Acids Res. Jan;39(Database issue):D7-10.

Khodiyar VK, Hill DP, Howe D, Berardini TZ, Tweedie S, Talmud PJ, Breckenridge R, Bhattarcharya S, Riley P, Scambler P, Lovering RC (2011) The representation of heart development in the gene ontology. Dev Biol. 2011 Mar 23.

The Gene Ontology Consortium (2010) The Gene Ontology in 2010: extensions and refinements. Nucl.Ac.Res. 38:D331-335.

Hirschman J, Berardini TZ, Drabkin H, Howe D (2010) A MOD(ern) perspecive on literature curation. Mol. Genet. Genomics 283(5):415-425.

Su, AI, Howe, DG (2010) Mining the Gene Wiki to prioritize literature curation efforts. The Future of the Web for Collaborative Science 2010

Hill DP, Berardini TZ, Howe DG, Van Auken KM (2010) Representing ontogeny through ontology: A developmental biologist's guide to the gene ontology. Mol. Reprod. Dev. 77(4):314-329.

LePendu P., Dou D., Howe, D. (2009) Detecting Inconsistencies in the Gene Ontology Using Ontology Databases with Not-gadgets. Lecture Notes in Computer Science 5871:948-965.

The Reference Genome Group of the Gene Ontology Consortium (2009) The Gene Ontology���s Reference Genome Project: A Unified Framework for Functional Annotation across Species. PLoS Comput. Biol. 5(7): e1000431. doi:10.1371/journal.pcbi.1000431

The Gene Ontology Consortium The Gene Ontology Project in 2008. (2008) Nuc.Ac.Res. 36:D440-D444.

Howe DG, Costanzo M, Fey P, Gojobori T, Hannick L, Hide, W, Hill DP, Kania R, Schaeffer M, St Pierre S, Twigger S, White O, Rhee SY (2008) Big Data: The future of biocuration. Nature 455:47-50.

Gene Ontology Consortium (2006) The Gene Ontology (GO) project in 2006. Nucleic Acids Research 34 (Database issue):D322-D326.

Howe DG, Clark CM, Yan H, Willis BS, Schneider DA, McKnight GS, Kapur RP (2005) Inhibition of Protein Kinase A in Murine Enteric Neurons Causes Lethal Intestinal Pseudo-obstruction. J. Neurobiology 66:256-272.

Kapur RP, Clarke CM, Doggett B, Taylor BE, Baldessari A, Parisi MA, Howe, DG (2005) Hox11L1 expression by precursors of enteric smooth muscle: an alternative explanation for megacecum in Hox11L1 -/- mice. Pediatr. Dev. Pathol. 8:148-161.

Amieux PS, Howe DG, Knickerbocker H, Lee DC, Su T, Laszlo GS, Idzerda RL, McKnight GS (2002). Increased basal PKA activity inhibits the formation of mesoderm-derived structures in the developing mouse embryo. J.Biol.Chem. 277(30): 27294-304.

Howe DG,Wiley JC, and McKnight GS (2002). Molecular and behavioral effects of a null mutation in all PKA Cbeta isoforms. Mol.Cell.Neurosci. 20(3): 515-524.

Howe DG and McCarthy KD (2000). Retroviral inhibition of Schwann cell cyclic AMP-dependent protein kinase inhibits myelination but not mitosis stimulated by interaction with neurons. J. Neurosci. 20(10):3513-3521.

Howe DG and McCarthy KD (1998). A dicistronic retroviral vector and culture model for analysis of neuron-Schwann cell interactions. J. Neurosci. Methods 83(2): 133-142.

He M, Howe DG and McCarthy KD (1996). Oligodendroglial signal transduction systems are regulated by neuronal contact. J. Neurochem. 67(4): 1491-1499.

Fagerberg WR and Howe DG (1996). A quantitative study of tissue dynamics in venuses flytrap Dionaea muscipula (Droseraceae). II. Trap reopening. American J. Botany. 83(7): 836-842.