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Journal Articles
- 2021
[j20]Randi Vita
, Jie Zheng, Rebecca C. Jackson, Damion M. Dooley, James A. Overton, Mark A. Miller, Daniel C. Berrios, Richard H. Scheuermann, Yongqun He, Hande Küçük-McGinty, Mathias Brochhausen, Aisyah Yu Lin, Sagar B. Jain, Marcus C. Chibucos, John Judkins, Michelle G. Giglio, Irene Y. Feng, Gully Burns, Matthew H. Brush, Bjoern Peters, Christian J. Stoeckert Jr.:
Standardization of assay representation in the Ontology for Biomedical Investigations. Database J. Biol. Databases Curation 2021 (2021)- [j19]José Luis Ambite, Lily Fierro, Jonathan Gordon, Gully A. P. C. Burns, Florian Geigl, Kristina Lerman, John D. Van Horn:
BD2K Training Coordinating Center's ERuDIte: The Educational Resource Discovery Index for Data Science. IEEE Trans. Emerg. Top. Comput. 9(1): 316-328 (2021) - 2019
- [j18]Gully A. Burns, Xiangci Li, Nanyun Peng:
Building deep learning models for evidence classification from the open access biomedical literature. Database J. Biol. Databases Curation 2019: baz034 (2019) - 2016
- [j17]Gully A. P. C. Burns, Pradeep Dasigi, Anita de Waard, Eduard H. Hovy:
Automated detection of discourse segment and experimental types from the text of cancer pathway results sections. Database J. Biol. Databases Curation 2016 (2016) - 2014
- [j16]Gully Burns, Yolanda Gil, Yan Liu, Natalia Villanueva-Rosales, Sebastian Risi, Joel Lehman, Jeff Clune, Christian Lebiere, Paul S. Rosenbloom, Frank van Harmelen, James A. Hendler, Pascal Hitzler, Krzysztof Janowicz, Samarth Swarup:
Reports on the 2013 AAAI Fall Symposium Series. AI Mag. 35(2): 69-74 (2014) - 2013
- [j15]Kyle H. Ambert, Aaron M. Cohen, Gully A. P. C. Burns, Eilis Boudreau, M. Kemal Sönmez:
Virk: an active learning-based system for bootstrapping knowledge base development in the neurosciences. Frontiers Neuroinformatics 7: 38 (2013) - [j14]David B. Keator, Karl G. Helmer, Jason Steffener, Jessica A. Turner, Theo G. M. van Erp, Syam Gadde, Naveen Ashish, Gully A. P. C. Burns, B. Nolan Nichols:
Towards structured sharing of raw and derived neuroimaging data across existing resources. NeuroImage 82: 647-661 (2013) - [j13]Gully A. P. C. Burns, Jessica A. Turner:
Modeling functional Magnetic Resonance Imaging (fMRI) experimental variables in the Ontology of Experimental Variables and Values (OoEVV). NeuroImage 82: 662-670 (2013) - 2012
- [j12]Lynette Hirschman, Gully A. P. C. Burns, Martin Krallinger, Cecilia N. Arighi, K. Bretonnel Cohen, Alfonso Valencia, Cathy H. Wu, Andrew Chatr-aryamontri, Karen G. Dowell, Eva Huala, Anália Lourenço, Robert S. Nash, Anne-Lise Veuthey, Thomas C. Wiegers, Andrew G. Winter:
Text mining for the biocuration workflow. Database J. Biol. Databases Curation 2012 (2012) - [j11]Yongqun He, Luca Toldo, Gully Burns, Cui Tao, Darrell R. Abernethy:
A 2012 Workshop: Vaccine and Drug Ontology in the Study of Mechanism and Effect (VDOSME 2012). J. Biomed. Semant. 3: 12 (2012) - [j10]Cartic Ramakrishnan, Abhishek Patnia, Eduard H. Hovy, Gully A. P. C. Burns:
Layout-aware text extraction from full-text PDF of scientific articles. Source Code Biol. Medicine 7: 7 (2012) - 2011
- [j9]Thomas A. Russ, Cartic Ramakrishnan, Eduard H. Hovy, Mihail Bota, Gully A. P. C. Burns:
Knowledge Engineering Tools for Reasoning with Scientific Observations and Interpretations: a Neural Connectivity Use Case. BMC Bioinform. 12: 351 (2011) - [j8]Marcelo Tallis, Richard H. Thompson, Thomas A. Russ, Gully A. P. C. Burns:
Knowledge Synthesis with Maps of Neural Connectivity. Frontiers Neuroinformatics 5: 24 (2011) - [j7]Karl G. Helmer, José Luis Ambite, Joseph Ames, Rachana Ananthakrishnan, Gully Burns, Ann L. Chervenak, Ian T. Foster, Lee Liming, David B. Keator, Fabio Macciardi, Ravi K. Madduri, John-Paul Navarro, Steven G. Potkin, Bruce R. Rosen, Seth Ruffins, Robert Schuler, Jessica A. Turner, Arthur W. Toga, Christina Williams, Carl Kesselman:
Enabling collaborative research using the Biomedical Informatics Research Network (BIRN). J. Am. Medical Informatics Assoc. 18(4): 416-422 (2011) - 2006
- [j6]Gully A. P. C. Burns, Wei-Cheng Cheng, Richard H. Thompson, Larry W. Swanson:
The NeuARt II system: a viewing tool for neuroanatomical data based on published neuroanatomical atlases. BMC Bioinform. 7: 531 (2006) - [j5]Arshad M. Khan, Joel D. Hahn, Wei-Cheng Cheng, Alan G. Watts, Gully A. P. C. Burns:
NeuroScholar's electronic laboratory notebook and its application to neuroendocrinology. Neuroinformatics 4(2): 139-161 (2006) - 2003
- [j4]Gully A. P. C. Burns, Arshad M. Khan, Shahram Ghandeharizadeh, Mark A. O'Neill, Yi-Shin Chen:
Tools and approaches for the construction of knowledge models from the neuroscientific literature. Neuroinformatics 1(1): 81-109 (2003) - 2002
- [j3]Gully A. P. C. Burns, Fang Bian, Wei-Cheng Cheng, Shyam Kapadia, Cyrus Shahabi, Shahram Ghandeharizadeh:
Software engineering tools and approaches for neuroinformatics: the design and implementation of the View-Primitive Data Model framework (VPDMf). Neurocomputing 44-46: 1049-1056 (2002) - 2001
- [j2]Gully Burns, Klaas E. Stephan, Bertram Ludäscher, Amarnath Gupta, Rolf Kötter:
Towards a federated neuroscientific knowledge management system using brain atlases. Neurocomputing 38-40: 1633-1641 (2001) - 1999
- [j1]Gully Burns:
Neuroscholar 1.00, a neuroinformatics databasing website. Neurocomputing 26-27: 963-970 (1999)
Conference and Workshop Papers
- 2021
- [c30]Xiangci Li, Gully A. Burns, Nanyun Peng:
A Paragraph-level Multi-task Learning Model for Scientific Fact-Verification. SDU@AAAI 2021 - [c29]Te-Lin Wu, Shikhar Singh, Sayan Paul, Gully A. Burns, Nanyun Peng:
MELINDA: A Multimodal Dataset for Biomedical Experiment Method Classification. AAAI 2021: 14076-14084 - [c28]Xiangci Li, Gully A. Burns, Nanyun Peng:
Scientific Discourse Tagging for Evidence Extraction. EACL 2021: 2550-2562 - 2019
- [c27]José Luis Ambite, Jonathan Gordon, Lily Fierro, Gully Burns, Joel Mathew:
Linking Educational Resources on Data Science. AAAI 2019: 9404-9409 - [c26]Xiangyang Shi, Yue Wu, Huaigu Cao, Gully Burns, Prem Natarajan:
Layout-aware Subfigure Decomposition for Complex Figures in the Biomedical Literature. ICASSP 2019: 1343-1347 - 2018
- [c25]John Darrell Van Horn, Lily Fierro, Jeana Kamdar, Jonathan Gordon, Crystal Stewart, Avnish Bhattrai, Sumiko Abe, Xiaoxiao Lei, Caroline O'Driscoll, Aakanchha Sinha, Priyambada Jain, Gully Burns, Kristina Lerman, José Luis Ambite:
Democratizing data science through data science training. PSB 2018: 292-303 - [c24]Gully Burns, Xiangyang Shi, Yue Wu, Huaigu Cao, Premkumar Natarajan:
Towards Evidence Extraction : Analysis of Scientific Figures from Studies of Molecular Interactions. SemSci@ISWC 2018: 34-42 - [c23]Gully Burns, Xiangyang Shi, Yue Wu, Huaigu Cao, Prem Natarajan:
Towards Evidence Extraction: Analysis of Scientific Figures from Studies of Molecular Interactions. ISWC (Best Workshop Papers) 2018: 95-102 - 2017
- [c22]José Luis Ambite, Lily T. Fierro, Florian Geigl, Jonathan Gordon, Gully A. P. C. Burns, Kristina Lerman, Jeana Kamdar, Crystal Stewart, Avnish Bhattrai, Xiaoyu Lei, Sumiko Abe, John D. Van Horn:
The BD2K Training Coordinating Center's Data Science Education Platform. AMIA 2017 - [c21]Emily Sheng, Prem Natarajan, Jonathan Gordon, Gully Burns:
An Investigation into the Pedagogical Features of Documents. BEA@EMNLP 2017: 109-120 - [c20]Jonathan Gordon, Stephen Aguilar, Emily Sheng, Gully Burns:
Structured Generation of Technical Reading Lists. BEA@EMNLP 2017: 261-270 - [c19]Gully A. Burns, Randi Vita, James A. Overton, Ward Fleri, Bjoern Peters:
Semantic Modeling for Accelerated Immune Epitope Database (IEDB) Biocuration. K-CAP Workshops 2017: 7-12 - [c18]Gully Burns, Pradeep Dasigi, Eduard H. Hovy:
Extracting Evidence Fragments for Distant Supervision of Molecular Interactions. SemSci@ISWC 2017: 7-14 - [c17]José Luis Ambite, Lily Fierro, Florian Geigl, Jonathan Gordon, Gully A. P. C. Burns, Kristina Lerman, John D. Van Horn:
BD2K ERuDIte: the Educational Resource Discovery Index for Data Science. WWW (Companion Volume) 2017: 1203-1211 - 2016
- [c16]Jonathan Gordon, Linhong Zhu, Aram Galstyan, Prem Natarajan, Gully Burns:
Modeling Concept Dependencies in a Scientific Corpus. ACL (1) 2016 - [c15]Gully A. P. C. Burns, Anita de Waard, Pradeep Dasigi, Eduard H. Hovy:
Cycles of Scientific Investigation in Discourse - Machine Reading Methods for the Primary Research Contributions of a Paper. ICBO/BioCreative 2016 - [c14]Gully A. P. C. Burns, Ulf Hermjakob, José Luis Ambite:
Abstract Meaning Representations as Linked Data. ISWC (2) 2016: 12-20 - 2013
- [c13]Kyle H. Ambert, Aaron M. Cohen, Gully A. P. C. Burns, Eilis Boudreau, M. Kemal Sönmez:
Finna: A Paragraph Prioritization System for Biocuration in the Neurosciences. AAAI Fall Symposia 2013 - [c12]Gully A. P. C. Burns, Yolanda Gil, Yan Liu, Natalia Villanueva-Rosales:
Organizing Committee. AAAI Fall Symposia 2013 - [c11]Gully A. P. C. Burns, Yolanda Gil, Yan Liu, Natalia Villanueva-Rosales:
Preface. AAAI Fall Symposia 2013 - [c10]Vít Novácek, Gully Burns:
SKIMMR: machine-aided skim-reading. IUI Companion 2013: 59-60 - 2012
- [c9]Marcelo Tallis, Drashti Dave, Gully A. P. C. Burns:
Preliminary Meta-Analyses of Experimental Design with Examples from HIV Vaccine Protection Studies. AAAI Fall Symposium: Discovery Informatics 2012 - 2011
- [c8]Sandeep Pokkunuri, Cartic Ramakrishnan, Ellen Riloff, Eduard H. Hovy, Gully Burns:
The Role of Information Extraction in the Design of a Document Triage Application for Biocuration. BioNLP@ACL 2011: 46-55 - 2009
- [c7]Bruce William Herr II, Edmund M. Talley, Gully A. P. C. Burns, David Newman, Gavin LaRowe:
The NIH Visual Browser: An Interactive Visualization of Biomedical Research. IV 2009: 505-509 - [c6]Gully A. P. C. Burns, Thomas A. Russ:
Biomedical knowledge engineering tools based on experimental design: a case study based on neuroanatomical tract-tracing experiments. K-CAP 2009: 173-174 - 2008
- [c5]Donghui Feng, Gully Burns, Eduard H. Hovy:
Adaptive Information Extraction for Complex Biomedical Tasks. BioNLP 2008: 120-121 - [c4]Donghui Feng, Gully Burns, Jingbo Zhu, Eduard H. Hovy:
Towards Automated Semantic Analysis on Biomedical Research Articles. IJCNLP 2008: 871-876 - 2007
- [c3]Gully Burns, Donghui Feng, Tommy Ingulfsen, Eduard H. Hovy:
Infrastructure for Annotation-Driven Information Extraction from the Primary Scientific Literature: Principles and Practice. IEEE SCW 2007: 122-129 - [c2]Donghui Feng, Gully Burns, Eduard H. Hovy:
Extracting Data Records from Unstructured Biomedical Full Text. EMNLP-CoNLL 2007: 837-846 - 1999
- [c1]Cyrus Shahabi, Ali E. Dashti, Gully A. P. C. Burns, Shahram Ghandeharizadeh, Ning Jiang, Larry W. Swanson:
Visualization of Spatial Neuroanatomical Data. VISUAL 1999: 801-808
Parts in Books or Collections
- 2008
- [p1]Gully Burns, Donghui Feng, Eduard H. Hovy:
Intelligent Approaches to Mining the Primary Research Literature: Techniques, Systems, and Examples. Computational Intelligence in Medical Informatics 2008: 17-50
Informal and Other Publications
- 2020
- [i7]Te-Lin Wu, Shikhar Singh, Sayan Paul, Gully A. Burns, Nanyun Peng:
MELINDA: A Multimodal Dataset for Biomedical Experiment Method Classification. CoRR abs/2012.09216 (2020) - [i6]Xiangci Li, Gully A. Burns, Nanyun Peng:
A Paragraph-level Multi-task Learning Model for Scientific Fact-Verification. CoRR abs/2012.14500 (2020) - 2019
- [i5]Xiangci Li, Gully A. Burns, Nanyun Peng:
Discourse Tagging for Scientific Evidence Extraction. CoRR abs/1909.04758 (2019) - [i4]John D. Van Horn, Sumiko Abe, José Luis Ambite, Teresa K. Attwood, Niall Beard, Louisa Bellis, Avnish Bhattrai, Alex A. T. Bui, Gully Burns, Lily Fierro, Jonathan Gordon, Jeffrey S. Grethe, Jeana Kamdar, Xiaoyu Lei, Kristina Lerman, Annette McGrath, Nicola J. Mulder, Caroline O'Driscoll, Crystal Stewart, Sonika Tyagi:
Advancing the international data science workforce through shared training and education. F1000Research 8: 251 (2019) - 2017
- [i3]Pradeep Dasigi, Gully A. P. C. Burns, Eduard H. Hovy, Anita de Waard:
Experiment Segmentation in Scientific Discourse as Clause-level Structured Prediction using Recurrent Neural Networks. CoRR abs/1702.05398 (2017) - [i2]Emily Sheng, Prem Natarajan, Jonathan Gordon, Gully Burns:
An Investigation into the Pedagogical Features of Documents. CoRR abs/1708.00179 (2017) - 2012
- [i1]David B. Keator, Karl G. Helmer, Jason Steffener, Jessica A. Turner, Theo G. M. van Erp, Syam Gadde, Naveen Ashish, Gully A. P. C. Burns, B. Nolan Nichols, Satrajit S. Ghosh:
Towards structured sharing of raw and derived neuroimaging data across existing resources. CoRR abs/1209.5922 (2012)
Coauthor Index
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