Hilmar Lapp
Dir, IT
Current Research Interests
My research program revolves around using knowledge representation techniques and machine reasoning to make data recorded as natural language descriptions fully computable. My focus has been on evolutionary phenotypes recorded as morphological character and character state descriptions, and specifically on building computational infrastructure that allows the evolutionary science community to compute with the knowledge-based semantics of such descriptions. I am one of the PIs for the NSF-funded collaborative project "Enabling machine-actionable semantics for comparative analysis of trait evolution" (SCATE
), a project under the Phenoscape
umbrella, for which I served as co-PI.
More recently I also work on computable semantics of phylogenetic clade definitions, whether published in the literature or authored ad-hoc. In this regard, I am PI of the (also NSF-funded) project on creating a standard and computational infrastructure for phyloreferencing .
More recently I also work on computable semantics of phylogenetic clade definitions, whether published in the literature or authored ad-hoc. In this regard, I am PI of the (also NSF-funded) project on creating a standard and computational infrastructure for phyloreferencing .
Current Appointments & Affiliations
Contact Information
- 304 Research Drive, North Building 119, Durham, NC 27708
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Hilmar.Lapp@duke.edu
+1 919 613 4661
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GCB Computational Solutions Core
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Homepage
- Research
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Selected Grants
- Collaborative Research: ABI Innovation: Enabling machine-actionable semantics for comparative analyses of trait evolution awarded by National Science Foundation 2017 - 2020
- Collaborative Research: ABI Innovation: An Ontology-Based system for Querying Life in a Post-Taxonomic Age awarded by National Science Foundation 2015 - 2020
- Phenoscape Knowledgebase Interop Codefest 2017 - 2018
- Phenoscape Development awarded by University of North Carolina - Chapel Hill 2011 - 2017
- HARDAC+:Reproducible HPC for next-generation genomics 2016 - 2017
- Collaborative Research-ABI Innovation: A novel database and ontology for evolutionary analyses of mammalian feeding awarded by National Science Foundation 2011 - 2016
- ABI Development: Dryad: Scalable and Sustainable Infrastructure for the Publication of Data awarded by National Science Foundation 2012 - 2015
- National Evolutionary Synthesis Center awarded by National Science Foundation 2009 - 2014
- A Digital Repository for Evolutionary Biology awarded by National Science Foundation 2008 - 2013
- Publications & Artistic Works
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Selected Publications
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Academic Articles
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Mabee, P., Balhoff, J., Dahdul, W., Lapp, H., Mungall, C., & Vision, T. (2019). A logical model of homology for comparative biology. https://doi.org/10.1101/588822Full Text
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Shen, N., Zhao, J., Schipper, J. L., Zhang, Y., Bepler, T., Leehr, D., … Gordan, R. (2018). Divergence in DNA Specificity among Paralogous Transcription Factors Contributes to Their Differential In Vivo Binding.. Cell Syst, 6(4), 470-483.e8. https://doi.org/10.1016/j.cels.2018.02.009Full Text Link to Item
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Dahdul, W., Manda, P., Cui, H., Balhoff, J. P., Dececchi, T. A., Ibrahim, N., … Mabee, P. M. (2018). Annotation of phenotypes using ontologies: a gold standard for the training and evaluation of natural language processing systems.. Database : The Journal of Biological Databases and Curation, 2018. https://doi.org/10.1093/database/bay110Full Text
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Harris, N. L., Wiencko, H., Chapman, B., Cock, P. J. A., Hokamp, K., Lapp, H., … Greshake Tzovaras, B. (2018). The 2018 Bioinformatics Open Source Conference (GCCBOSC 2018).. F1000research, 7. https://doi.org/10.12688/f1000research.15936.1Full Text Open Access Copy
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Stoltzfus, A., Rosenberg, M., Lapp, H., Budd, A., Cranston, K., Pontelli, E., … Vos, R. (2017). Community and Code: Nine Lessons from Nine NESCent Hackathons. https://doi.org/10.12688/f1000research.11429.1Full Text
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Harris, N. L., Cock, P. J. A., Chapman, B., Fields, C. J., Hokamp, K., Lapp, H., … Wiencko, H. (2017). The 2017 Bioinformatics Open Source Conference (BOSC).. F1000research, 6. https://doi.org/10.12688/f1000research.12929.1Full Text
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Jombart, T., Archer, F., Schliep, K., Kamvar, Z., Harris, R., Paradis, E., … Lapp, H. (2017). apex: phylogenetics with multiple genes.. Molecular Ecology Resources, 17(1), 19–26. https://doi.org/10.1111/1755-0998.12567Full Text Open Access Copy
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Kamvar, Z. N., López-Uribe, M. M., Coughlan, S., Grünwald, N. J., Lapp, H., & Manel, S. (2017). Developing educational resources for population genetics in R: an open and collaborative approach.. Molecular Ecology Resources, 17(1), 120–128. https://doi.org/10.1111/1755-0998.12558Full Text
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Paradis, E., Gosselin, T., Grünwald, N. J., Jombart, T., Manel, S., & Lapp, H. (2017). Towards an integrated ecosystem of R packages for the analysis of population genetic data.. Molecular Ecology Resources, 17(1), 1–4. https://doi.org/10.1111/1755-0998.12636Full Text
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Boettiger, C., Chamberlain, S., Vos, R., & Lapp, H. (2016). RNeXML: A package for reading and writing richly annotated phylogenetic, character and trait data in R. Methods in Ecology and Evolution, 7(3), 352–357. https://doi.org/10.1111/2041-210X.12469Full Text Open Access Copy
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Harris, N. L., Cock, P. J. A., Lapp, H., Chapman, B., Davey, R., Fields, C., … Munoz-Torres, M. (2016). The 2015 Bioinformatics Open Source Conference (BOSC 2015).. Plos Computational Biology, 12(2). https://doi.org/10.1371/journal.pcbi.1004691Full Text Open Access Copy
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Druzinsky, R. E., Balhoff, J. P., Crompton, A. W., Done, J., German, R. Z., Haendel, M. A., … Wall, C. E. (2016). Muscle Logic: New Knowledge Resource for Anatomy Enables Comprehensive Searches of the Literature on the Feeding Muscles of Mammals.. Plos One, 11(2). https://doi.org/10.1371/journal.pone.0149102Full Text Open Access Copy
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Edmunds, R. C., Su, B., Balhoff, J. P., Eames, B. F., Dahdul, W. M., Lapp, H., … Westerfield, M. (2016). Phenoscape: Identifying Candidate Genes for Evolutionary Phenotypes.. Molecular Biology and Evolution, 33(1), 13–24. https://doi.org/10.1093/molbev/msv223Full Text
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Harris, N. L., Cock, P. J. A., Chapman, B., Fields, C. J., Hokamp, K., Lapp, H., … Wiencko, H. (2016). The 2016 Bioinformatics Open Source Conference (BOSC).. F1000research, 5. https://doi.org/10.12688/f1000research.9663.1Full Text Open Access Copy
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Dececchi, T. A., Balhoff, J. P., Lapp, H., & Mabee, P. M. (2015). Toward Synthesizing Our Knowledge of Morphology: Using Ontologies and Machine Reasoning to Extract Presence/Absence Evolutionary Phenotypes across Studies.. Systematic Biology, 64(6), 936–952. https://doi.org/10.1093/sysbio/syv031Full Text
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Manda, P., Balhoff, J. P., Lapp, H., Mabee, P., & Vision, T. J. (2015). Using the phenoscape knowledgebase to relate genetic perturbations to phenotypic evolution.. Genesis (New York, N.Y. : 2000), 53(8), 561–571. https://doi.org/10.1002/dvg.22878Full Text
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Deans, A. R., Lewis, S. E., Huala, E., Anzaldo, S. S., Ashburner, M., Balhoff, J. P., … Mabee, P. (2015). Finding our way through phenotypes.. Plos Biology, 13(1). https://doi.org/10.1371/journal.pbio.1002033Full Text Open Access Copy
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Dahdul, W., Dececchi, T. A., Ibrahim, N., Lapp, H., & Mabee, P. (2015). Moving the mountain: analysis of the effort required to transform comparative anatomy into computable anatomy.. Database : The Journal of Biological Databases and Curation, 2015. https://doi.org/10.1093/database/bav040Full Text
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Harris, N. L., Cock, P. J. A., Chapman, B. A., Goecks, J., Hotz, H.-R., & Lapp, H. (2015). The Bioinformatics Open Source Conference (BOSC) 2013.. Bioinformatics (Oxford, England), 31(2), 299–300. https://doi.org/10.1093/bioinformatics/btu413Full Text
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Summary of the First Workshop on Sustainable Software for Science: Practice and Experiences (WSSSPE1). (2014). Journal of Open Research Software, 2(1), e6–e6. https://doi.org/10.5334/jors.anFull Text Open Access Copy
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Katayama, T., Wilkinson, M. D., Aoki-Kinoshita, K. F., Kawashima, S., Yamamoto, Y., Yamaguchi, A., … Takagi, T. (2014). BioHackathon series in 2011 and 2012: penetration of ontology and linked data in life science domains.. Journal of Biomedical Semantics, 5(1). https://doi.org/10.1186/2041-1480-5-5Full Text Open Access Copy
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Lapp, H., Guralnick, R., & Westneat, M. (2014). Liberating Our Beautiful Trees: A Call to Arms. https://doi.org/10.7287/peerj.preprints.206v1Full Text
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Balhoff, J. P., Dahdul, W. M., Dececchi, T. A., Lapp, H., Mabee, P. M., & Vision, T. J. (2014). Annotation of phenotypic diversity: decoupling data curation and ontology curation using Phenex.. Journal of Biomedical Semantics, 5(1). https://doi.org/10.1186/2041-1480-5-45Full Text
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Druzinsky, R., Mungall, C., Haendel, M., Lapp, H., & Mabee, P. (2013). What is an anatomy ontology?. Anatomical Record (Hoboken, N.J. : 2007), 296(12), 1797–1799. https://doi.org/10.1002/ar.22805Full Text
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Midford, P. E., Dececchi, T. A., Balhoff, J. P., Dahdul, W. M., Ibrahim, N., Lapp, H., … Blackburn, D. C. (2013). The vertebrate taxonomy ontology: a framework for reasoning across model organism and species phenotypes.. Journal of Biomedical Semantics, 4(1). https://doi.org/10.1186/2041-1480-4-34Full Text Open Access Copy
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Harris, N., Cock, P., Chapman, B., Goecks, J., Hotz, H.-R., & Lapp, H. (2013). The Bioinformatics Open Source Conference (BOSC) 2013. https://doi.org/10.7287/peerj.preprints.83Full Text
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Rodrigo, A., Alberts, S., Cranston, K., Kingsolver, J., Lapp, H., McClain, C., … Wiegmann, B. (2013). Science incubators: synthesis centers and their role in the research ecosystem.. Plos Biology, 11(1). https://doi.org/10.1371/journal.pbio.1001468Full Text Open Access Copy
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Stoltzfus, A., Lapp, H., Matasci, N., Deus, H., Sidlauskas, B., Zmasek, C. M., … Jordan, G. (2013). Phylotastic! Making tree-of-life knowledge accessible, reusable and convenient.. Bmc Bioinformatics, 14. https://doi.org/10.1186/1471-2105-14-158Full Text Open Access Copy
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Prlić, A., & Lapp, H. (2012). The PLOS Computational Biology Software Section.. Plos Computational Biology, 8(11). https://doi.org/10.1371/journal.pcbi.1002799Full Text
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Robbins, R. J., Amaral-Zettler, L., Bik, H., Blum, S., Edwards, J., Field, D., … Wooley, J. (2012). RCN4GSC Workshop Report: Managing Data at the Interface of Biodiversity and (Meta)Genomics, March 2011.. Standards in Genomic Sciences, 7(1), 159–165. https://doi.org/10.4056/sigs.3156511Full Text Open Access Copy
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Vos, R. A., Balhoff, J. P., Caravas, J. A., Holder, M. T., Lapp, H., Maddison, W. P., … Stoltzfus, A. (2012). NeXML: rich, extensible, and verifiable representation of comparative data and metadata.. Systematic Biology, 61(4), 675–689. https://doi.org/10.1093/sysbio/sys025Full Text
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Mabee, B. P., Balhoff, J. P., Dahdul, W. M., Lapp, H., Midford, P. E., Vision, T. J., & Westerfield, M. (2012). 500,000 fish phenotypes: The new informatics landscape for evolutionary and developmental biology of the vertebrate skeleton.. Zeitschrift Fur Angewandte Ichthyologie = Journal of Applied Ichthyology, 28(3), 300–305. https://doi.org/10.1111/j.1439-0426.2012.01985.xFull Text Open Access Copy
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Dahdul, W. M., Balhoff, J. P., Blackburn, D. C., Diehl, A. D., Haendel, M. A., Hall, B. K., … Mabee, P. M. (2012). A unified anatomy ontology of the vertebrate skeletal system.. Plos One, 7(12). https://doi.org/10.1371/journal.pone.0051070Full Text Open Access Copy
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Wall, C. E., Vinyard, C. J., Williams, S. H., Gapeyev, V., Liu, X., Lapp, H., & German, R. Z. (2011). Overview of FEED, the feeding experiments end-user database.. Integrative and Comparative Biology, 51(2), 215–223. https://doi.org/10.1093/icb/icr047Full Text Open Access Copy
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Lapp, H., Morris, R. A., Catapano, T., Hobern, D., & Morrison, N. (2011). Organizing our knowledge of biodiversity. Bulletin of the American Society for Information Science and Technology, 37(4), 38–42. https://doi.org/10.1002/bult.2011.1720370411Full Text
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Jung, S., Menda, N., Redmond, S., Buels, R. M., Friesen, M., Bendana, Y., … Main, D. (2011). The Chado Natural Diversity module: a new generic database schema for large-scale phenotyping and genotyping data.. Database : The Journal of Biological Databases and Curation, 2011. https://doi.org/10.1093/database/bar051Full Text
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Katayama, T., Arakawa, K., Nakao, M., Ono, K., Aoki-Kinoshita, K. F., Yamamoto, Y., … Takagi, T. (2010). The DBCLS BioHackathon: standardization and interoperability for bioinformatics web services and workflows. The DBCLS BioHackathon Consortium*.. Journal of Biomedical Semantics, 1(1). https://doi.org/10.1186/2041-1480-1-8Full Text
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Dahdul, W. M., Lundberg, J. G., Midford, P. E., Balhoff, J. P., Lapp, H., Vision, T. J., … Mabee, P. M. (2010). The teleost anatomy ontology: anatomical representation for the genomics age.. Systematic Biology, 59(4), 369–383. https://doi.org/10.1093/sysbio/syq013Full Text
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Strier, K. B., Altmann, J., Brockman, D. K., Bronikowski, A. M., Cords, M., Fedigan, L. M., … Alberts, S. C. (2010). The Primate Life History Database: A unique shared ecological data resource.. Methods in Ecology and Evolution, 1(2), 199–211. https://doi.org/10.1111/j.2041-210X.2010.00023.xFull Text
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Dahdul, W. M., Balhoff, J. P., Engeman, J., Grande, T., Hilton, E. J., Kothari, C., … Mabee, P. M. (2010). Evolutionary characters, phenotypes and ontologies: curating data from the systematic biology literature.. Plos One, 5(5). https://doi.org/10.1371/journal.pone.0010708Full Text Open Access Copy
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Balhoff, J. P., Dahdul, W. M., Kothari, C. R., Lapp, H., Lundberg, J. G., Mabee, P., … Vision, T. J. (2010). Phenex: ontological annotation of phenotypic diversity.. Plos One, 5(5). https://doi.org/10.1371/journal.pone.0010500Full Text Open Access Copy
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Sidlauskas, B., Ganapathy, G., Hazkani-Covo, E., Jenkins, K. P., Lapp, H., McCall, L. W., … Kidd, D. M. (2010). Linking big: the continuing promise of evolutionary synthesis.. Evolution; International Journal of Organic Evolution, 64(4), 871–880. https://doi.org/10.1111/j.1558-5646.2009.00892.xFull Text
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Field, D., Sansone, S., Delong, E. F., Sterk, P., Friedberg, I., Gaudet, P., … Thessen, A. (2010). Meeting Report: BioSharing at ISMB 2010.. Standards in Genomic Sciences, 3(3), 254–258. https://doi.org/10.4056/sigs/1403501Full Text
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Lapp, H., Bala, S., Balhoff, J. P., Bouck, A., Goto, N., Holder, M., … Vision, T. J. (2007). The 2006 NESCent Phyloinformatics Hackathon: A Field Report.. Evolutionary Bioinformatics Online, 3, 287–296.
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Stajich, J. E., & Lapp, H. (2006). Open source tools and toolkits for bioinformatics: significance, and where are we?. Briefings in Bioinformatics, 7(3), 287–296. https://doi.org/10.1093/bib/bbl026Full Text
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Ching, K. A., Cooke, M. P., Tarantino, L. M., & Lapp, H. (2006). Data and animal management software for large-scale phenotype screening.. Mammalian Genome : Official Journal of the International Mammalian Genome Society, 17(4), 288–297. https://doi.org/10.1007/s00335-005-0145-5Full Text
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Gurkan, C., Lapp, H., Alory, C., Su, A. I., Hogenesch, J. B., & Balch, W. E. (2005). Large-scale profiling of Rab GTPase trafficking networks: the membrome.. Molecular Biology of the Cell, 16(8), 3847–3864. https://doi.org/10.1091/mbc.E05-01-0062Full Text
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Gurkan, C., Lapp, H., Hogenesch, J. B., & Balch, W. E. (2005). Exploring trafficking GTPase function by mRNA expression profiling: use of the SymAtlas web-application and the Membrome datasets.. Methods in Enzymology, 403, 1–10. https://doi.org/10.1016/s0076-6879(05)03001-6Full Text
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Walker, J. R., Su, A. I., Self, D. W., Hogenesch, J. B., Lapp, H., Sturchler, C., … Bilbe, G. (2004). Erratum: Applications of a rat multiple tissue gene expression data set (Genome Research (2004) vol. 14 (742-749)). Genome Research, 14(7).
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Su, A. I., Wiltshire, T., Batalov, S., Lapp, H., Ching, K. A., Block, D., … Hogenesch, J. B. (2004). A gene atlas of the mouse and human protein-encoding transcriptomes.. Proceedings of the National Academy of Sciences of the United States of America, 101(16), 6062–6067. https://doi.org/10.1073/pnas.0400782101Full Text
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Walker, J. R., Su, A. I., Self, D. W., Hogenesch, J. B., Lapp, H., Maier, R., … Bilbe, G. (2004). Applications of a rat multiple tissue gene expression data set.. Genome Research, 14(4), 742–749. https://doi.org/10.1101/gr.2161804Full Text
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Brändle, N., Bischof, H., & Lapp, H. (2003). Robust DNA microarray image analysis. Machine Vision and Applications, 15(1), 11–28. https://doi.org/10.1007/s00138-002-0114-xFull Text
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Stajich, J. E., Block, D., Boulez, K., Brenner, S. E., Chervitz, S. A., Dagdigian, C., … Birney, E. (2002). The Bioperl toolkit: Perl modules for the life sciences.. Genome Research, 12(10), 1611–1618. https://doi.org/10.1101/gr.361602Full Text
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Su, A. I., Welsh, J. B., Sapinoso, L. M., Kern, S. G., Dimitrov, P., Lapp, H., … Hampton, G. M. (2001). Molecular classification of human carcinomas by use of gene expression signatures.. Cancer Research, 61(20), 7388–7393.
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Brändle, N., Bischof, H., & Lapp, H. (2001). A generic and robust approach for the analysis of spot array images. Proceedings of Spie the International Society for Optical Engineering, 4266, 1–12. https://doi.org/10.1117/12.427983Full Text
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Brändle, N., Chen, H. Y., Bischof, H., & Lapp, H. (2000). Robust parametric and semi-parametric spot fitting for spot array images.. Proceedings. International Conference on Intelligent Systems for Molecular Biology, 8, 46–56.
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Teal, T. K., Cranston, K. A., Lapp, H., White, E., Wilson, G., Ram, K., & Pawlik, A. (n.d.). Data Carpentry: Workshops to Increase Data Literacy for Researchers. International Journal of Digital Curation, 10(1), 135–143. https://doi.org/10.2218/ijdc.v10i1.351Full Text
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Other Articles
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Rees, J., Cranston, K., Lapp, H., & Vision, T. (2013). Response to GBIF request for consultation on data licenses. https://doi.org/10.6084/m9.figshare.799766Full Text
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Cranston, K., Vision, T., O Meara, B., & Lapp, H. (2013). A grassroots approach to software sustainability. https://doi.org/10.6084/m9.figshare.790739Full Text
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Huang, D., & Lapp, H. (n.d.). Software Engineering as Instrumentation for the Long Tail of Scientific Software. https://doi.org/10.6084/m9.figshare.791560Full Text
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Conference Papers
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Mabee, P. M., Balhoff, J. P., Dahdul, W. M., Lapp, H., Mungall, C. J., & Vision, T. J. (2018). Reasoning over anatomical homology in the Phenoscape KB. In Ceur Workshop Proceedings (Vol. 2285).
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Manda, P., Mungall, C. J., Balhoff, J. P., Lapp, H., & Vision, T. J. (2016). Investigating the importance of anatomical homology for cross-species phenotype comparisons using semantic similarity. - Accepted at pacific symposium on biocomputing, 2016. In Pacific Symposium on Biocomputing (pp. 132–143).
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Balhoff, J. P., Dececchi, T. A., Mabee, P., & Lapp, H. (2014). Presence-absence reasoning for evolutionary phenotypes. In Phenotype Day at International Conference on Intelligent Systems for Molecular Biology (Isbm 2014).Open Access Copy
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Sereno, P. C., Ibrahim, N., Mabee, P. M., Vision, T. J., & Lapp, H. (2012). PHENOSCAPE: A NEW ANATOMICAL ONTOLOGY OF VERTEBRATES. In Journal of Vertebrate Paleontology (Vol. 32, pp. 170–171). N Carolina Museum Nat Sci, Raleigh, NC: TAYLOR & FRANCIS INC.Link to Item
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Balhoff, J. P., Midford, P. E., & Lapp, H. (2011). Integrating anatomy and phenotype ontologies with taxonomic hierarchies. In Ceur Workshop Proceedings (Vol. 833, pp. 426–427).
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Dahdul, W., Balhoff, J., Lapp, H., Midford, P., Vision, T., Westerfield, M., & Mabee, P. (2011). Phenoscape: Use cases and anatomy ontology requirements for linking evolutionary and model organism phenotypes. In Ceur Workshop Proceedings (Vol. 833, pp. 428–429).
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Balhoff, J. P., Midford, P. E., & Lapp, H. (2011). Integrating anatomy and phenotype ontologies with taxonomic hierarchies. In Icbo: International Conference on Biomedical Ontology (2011) Proceedings (Vol. 5, pp. 8–9).
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Vision, T., Blake, J., Lapp, H., Mabee, P., & Westerfield, M. (2011). Similarity between semantic description sets: Addressing needs beyond data integration. In Ceur Workshop Proceedings (Vol. 783).
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Chen, H. Y., Brändle, N., Bischof, H., & Lapp, H. (2000). Robust spot fitting for genetic spot array images. In Ieee International Conference on Image Processing (Vol. 3).
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Brändle, N., Lapp, H., & Bischof, H. (1999). Automatic grid fitting for genetic spot array images containing guide spots. In Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics) (Vol. 1689, pp. 357–366).
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Carral, D., Hitzler, P., Lapp, H., & Rudolph, S. (n.d.). On the Ontological Modeling of Trees. In E. Blomqvist, O. Corcho, M. Horridge, D. Carral, & R. Hoekstra (Eds.), Proceedings of the 8th Workshop on Ontology Design and Patterns (Wop 2017). Vienna, Austria: CEUR.Open Access Copy Link to Item
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Datasets
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Cellinese, N., & Lapp, H. (2015). An Ontology-Based System for Querying Life in a Post-Taxonomic Age. https://doi.org/10.6084/m9.figshare.1401984.v1Data Access
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