Awards
Best Poster Award to postdoctoral associate Lorena Endara for her poster: Endara, L. J.G. Burleigh, H. Cui. 2015 Semi-automated extraction of phenomic characters from taxonomic descriptions: Natural Language Processing Approaches for the Tree of Life. Presented at SEPEEG Meeting 2015. Eatonton, Georgia, USA.

Best Student Poster award to AVAToL Phenomics project member Anna Yu (advisor Dr. Edward Theriot), University of Texas at Austin awarded at the 23rd International Diatom Symposium, Nanjing China, 2014, for her poster “Using Crowd Sourcing Tools to Build the Next Generation Phenomic Tree of Life – Using Cyclotella as an Example.”

NSF Graduate Fellowship to Michael Lam, Oregon State University, 2014, advised by Tom Dietterich and Sinisa Todorovic

 

Peer-Reviewed Publications

Blank CE, Cui H, Moore LR, Walls RL. 2016. MicrO: An Ontology of Phenotypic and Metabolic Characters, Assays, and Culture Media Found in Prokaryotic Taxonomic Descriptions, Journal of Biomedical Semantics 7:18. DOI:10.1186/s13326-016-0060-6.

Burleigh, G. et al. 2013. Next Generation Phenomics for the Tree of Life. PLoS Currents.

Cranston, K., L. J. Harmon, M. A. O’Leary, and C. Lisle. 2014. Best practices for data sharing in phylogenetic research. PLoS Currents Tree of Life. 1-8. In Review.

Daly, M., L. Endara, J.G. Burleigh. 2015. Peeking behind the page: using Natural Language Processing to identify and explore the characters used to classify sea anemones. Zoologischer Anzeiger 256 (54-60).​

Endara, L., H.A. Cole, J.G. Burleigh, N. Nagalingum, J.A.Macklin, J.Liu, H. Cui Building A Community Plant Glossary Using Taxonomic Descriptions (submitted to TAXON)

Liu, J., L. Endara, and J.G. Burleigh. 2015. MatrixConverter: Facilitating construction of phenomic character matrices. Applications in Plant Science. 3:(2):apps.1400088.

Miller, M., T. Schwartz, B. E. Pickett, S. He, E. B. Klem, R. H. Scheuermann, M. Passarotti, S. Kaufman, M. A. O’Leary. 2015. A RESTful API for access to phylogenetic tools via the CIPRES Science Gateway. Evolutionary Bioinformatics. 11: 1-6.

Thacker RW, Díaz MC, Kerner A, Vignes-Lebbe R, Segerdell E, Haendel MA, Mungall CJ. 2014. The Porifera Ontology (PORO): enhancing sponge systematics with an anatomy ontology. Journal of Biomedical Semantics 5:39. doi: 10.1186/2041-1480-5-39.

 

Scientific Talks
Mao, J., L.R. Moore, C. Blank, H. Cui. An Information Extraction Tool for Microbial Characters. Poster accepted and to be presented at iConference 2016.

Endara, L. J.G. Burleigh, H. Cui. 2015 Semi-automated extraction of phenomic characters from taxonomic descriptions: Natural Language Processing Approaches for the Tree of Life. Presented at SEPEEG Meeting 2015. Eatonton, Georgia, USA. (won best poster)

Nagalingum, N., L. Endara, and J. Gordon Burleigh. Semi-automated generation of morphological matrices: examples using the cycads. Australasian Systematic Botany Society Meeting, Canberra, Australia, November, 2015.

Burleigh, J.G., L. Endara, and H. Cui. Extracting and Using Phenomic Data from Taxonomic Descriptions. Seminar Botany Department, NMNH, Washington, DC, October, 2015.

Nagalingum, N., L. Endara, H. Cui, and J. Gordon Burleigh. Phylogenetic relationships and classification of Cycas. 10th International Conference on Cycad Biology, Medellín, Columbia, Aug. 2015.

Burleigh, J.G., L. Endara, N. Nagalingum, and H. Cui. Semi-automated approaches for extracting phylogenetically informative datasets from taxonomic descriptions. Botany 2015 Conference, Edmonton, Alberta, Canada, July, 2015.

Lundberg, J. G., K. Luckenbill, M. Arce-H., D. Hendrickson, P. Mabee, M. A. O’Leary, and J. P. Sullivan. 2015. Ictaluridae 2015: Systematic Challenges, Opportunities and New Approaches. Joint meeting of Ichthyologists and Herpetologists (JMIH) hosted by University of Nevada, Reno. July 15-19.

Burleigh, J. G. 2015. “2015 Synthesizing Genomic and Phenomic Data for the Tree of Life” National Science Foundation, Washington, DC, February, 2015.

M. Lam, J. Doppa, S. Todorovic, and T. Dietterich, “HC-Search: A new tool for structured prediction in computer vision,” in Proc. IEEE Computer Vision Pattern Recognition (CVPR), Boston, MA, 2015

Burleigh, J. G. 2014. “Extracting Phenomic Data from Taxonomic Descriptions”. Big Data Symposium, Biodiversity Synthesis Center (BioSynC), Field Museum of Natural History, Chicago, IL, November, 2014.

Blank CE, Hsin-Hui Wu E, Cui H, Moore LR, Burleigh JG, Liu J, Gasparich GE. 2014. AVAToL microbial phenomics: an ontology and natural language processing tools to facilitate trait evolution stdueis for the archaeal domain of life. Evolution 2014 meeting, Raleigh, NC, June 20-24. Contributed talk.

Blank CE, Moore LR, Cui H, Hsin-Hui Wu E, Burleigh G, Liu J, Slonczewski JL, Barich D, Gasparich GE. 2014. AVAToL microbial phenomics: developing a microbial ontology and natural language processing tools to automate the study of the evolution of microbial traits. Joint Aquatic Sciences Meeting, Portland, OR, May 18-23. Contributed poster.

Daly, M., A. Reft, E. Law, and M. O’Leary. 2014. “The wisdom of the crowd: a crowd-sourcing task for character discovery from nematocyst ultrastructure” Society for Integrative and Comparative Biology, Austin, Texas.

Endara, L., Liu, J., Burleigh, J.G., Nagalingum, N., Cui, H. 2014. Transformation of Taxonomic Literature to a Taxon-Character Matrix for Phylogenetics. Evolution meeting, contributed talk.

Uyeda J, Blank CE, Moore LR, Harmon L. 2014. Billion year old rate shifts in microbial evolution. Evolution 2014 meeting, Raleigh, NC, June 20-24. Contributed presentation.

Yu, M., E. C. Theriot, M. A. O’Leary, A. J. Alverson, M. Julius, A. L. Cirranello, J. Irvine, and M. Passarotti. 2014. Use Crowd Sourcing Tools to build The Next Generation Phenomic Tree of Life – Using Cyclotella as an example. 23rd International Diatom Symposium. Nanjing, China.

Cui, H. et al. 2013. Towards phenotype extraction from microbial descriptions. iEvoBio

Moore, L. R., C. Blank, J.G. Burleigh, H. Cui, G. Gasparich, J. Liu, S. Ranade. 2013. Next Generation Microbial
Phenomics, Australian Association for Microbiology Annual Scientific Meeting (poster).

Todorovic, S. 2013 “Fine-Grained Recognition for Building the Tree of Life”. Second Workshop on Fine-Grained
Categorization

Yu, M. et al. 2013. Next generation phenomics for the diatom tree of life – usig Thalassiosirales as an example.
North American Diatom Symposium.

Daly, M., Burleigh, J. G., O’Leary, M. A. 2014. Next generation phenomics for the Tree of Life. ICIM3 meeting, contributed talk.

Lam, M., S. Todorovic, T. Dietterich, and J. R. Doppa (in press). “HC-Search: A new tool for structured prediction in computer vision”. IEEE Conference on Computer Vision and Pattern Recognition. Sydney, Australia.

 

Participants in the “Next Generation Phenomics for the Tree of Life” meeting, Biosphere 2, Arizona, January 2015

Participants in the “Next Generation Phenomics for the Tree of Life” meeting, Ohio State University, November 2013

 

Participants in the “Next Generation Phenomics for the Tree of Life” meeting, Stony Brook University, September, 2012