llwang.net

Journal & Conference Publications

 

Ontology alignment in the biomedical domain using entity definitions and context

Wang LL, Bhagavatula C, Neumann M, Lo K, Wilhelm C, Ammar W.

Proceedings of the 56th Annual Meeting of the Association for Computational Linguistics, BioNLP, 2018.

arXiv: 1806.07976

ACL anthology

 

Ontology-based integration of pathway databases using Pathway Ontology annotations [pdf]

Wang LL, Shimoyama ME, Hayman GT, Smith JR, Tutaj M, Gennari, JH.

Proceedings of the 26th Conference on Intelligent Systems for Molecular Biology, Bio-Ontologies COSI, 2018.

 

Construction of the literature graph in Semantic Scholar

Ammar W, Groeneveld D, Bhagavatula C, Beltagy I, Crawford M, Downey D, Dunkelberger J, Elgohary A, Feldman S, Ha V, Kinney R, Kohlmeier S, Lo K, Murray T, Ooi H, Peters M, Power J, Skjonsberg S, Wang LL, Wilhelm C, Yuan Z, van Zuylen M, Etzioni O.

Proceedings of the 2018 Conference of the North American Chapter of the Association for Computational Linguistics, Industry.

arXiv: 1805.02262

 

Similarity metrics for determining overlap among biological pathways [pdf]

Wang LL, Gennari, JH.

Proceedings of the International Conference on Biomedical Ontology, 2017.

 

Fluctuation analysis of peak expiratory flow and its associations with treatment failure in asthma [pdf]

Kaminsky DA, Wang LL, Bates JH, Thamrin C, Shade DM, Dixon AE, Wise RA, Peters S, Irvin CG.

American Journal of Respiratory and Critical Care Medicine, 2017.

DOI: 10.1164/rccm.201601-0076OC

PMID: 27814453

 

Development of a novel Markov chain model for the prediction of head and neck squamous cell carcinoma dissemination

Jung H, Law A, Grunblatt E, Wang LL, Kusano A, Mejino JLV, Whipple ME.

AMIA Annual Symposium Proceedings, 2016.

PMID: 28269942

 

An analysis of differences in biological pathway resources [pdf]

Wang LL, Gennari JH, Abernethy NF.

Proceedings of the Joint International Conference on Biological Ontology and BioCreative, 2016.

CEUR Workshop Proceedings

 

Biological model development as an opportunity to provide content auditing for the foundational model of anatomy ontology [pdf]

Wang LL, Grunblatt E, Jung H, Kalet IJ, Whipple ME.

AMIA Annual Symposium Proceedings, 2015.

PMID: 26958311

 

Electrical impedance myography in duchenne muscular dystrophy and health controls: a multi-center study of reliability and validity [pdf]

Zaidman CM, Wang LL, Connolly AM, Florence J, Wong BL, Parsons JA, Apkon S, Goyal N, Williams E, Escolar D, Rutkove SB, Bohorquez JL; DART-EIM Clinical Evaluators Consortium.

Muscle & Nerve, 2015.

DOI: 10.1002/mus.24611

PMID: 25702806

 

Electrical impedance myography for monitoring motor neuron loss in the SOD1 G93A amyotrophic lateral sclerosis rat [pdf]

Wang LL, Spieker AJ, Li J, Rutkove SB.

Clinical Neurophysiology, 2011.

DOI: 10.1016/j.clinph.2011.04.021

PMID: 21612980

 

Assessment of alterations in the electrical impedance of muscle after experimental nerve injury via finite-element analysis [pdf]

Wang LL, Ahad M, McEwan A, Li J, Jafarpoor M, Rutkove SB.

IEEE Transactions on Biomedical Engineering, 2011.

DOI: 10.1109/TBME.2011.2104957

PMID: 21224171

 

Conference Activity

2018.

Quantifying the effects of gene entity disambiguation for GSEA
To be presented at the AMIA Annual Symposium
November 5, 2018, San Francisco, CA, USA

Ontology alignment in the biomedical domain using entity definitions and context
Presented at the Bio-NLP workshop at ACL
July 19, 2018, Melbourne, Victoria, Australia

Ontology-based integration of pathway databases using Pathway Ontology annotations
Presented at the Bio-Ontologies COSI at ISMB
July 9, 2018, Chicago, IL, USA

2017.

Similarity metrics for determining overlap among biological pathways
Presented at ICBO
September 15, 2017, Newcastle upon Tyne, UK.

Detection and Functional Classification of Fusion Genes Using Pathway Expression Profiles
Presented at the AMIA Joint Summits on Translational Science
March 28, 2017, San Francisco, CA

2016.

Discovering representational differences between pathway knowledge bases for pathway resource merging
Presented at the AMIA Annual Symposium
November 15, 2016, Chicago, IL

Auditing tree-like organ systems in the FMA using network motifs
Presented at the AMIA Annual Symposium
November 15, 2016, Chicago, IL

An analysis of differences in biological pathway resources
Presented at ICBO and BioCreative
August 3, 2016, Corvallis, OR

Identifying and resolving inconsistencies in biological pathway resources
Presented at the NLM informatics training conference
June 27, 2016, Columbus, OH

2015.

Biological model development as an opportunity to provide content auditing for the foundational model of anatomy ontology
Presented at the AMIA Annual Symposium
November 16, 2015, San Francisco, CA

Development of a discharge ontology to support postanesthesia discharge decision making
Presented at ICBO
July 27, 2015, Lisbon, Portugal

Ontological content auditing during model creation using the foundational model of anatomy
Presented at the NLM informatics training conference
June 23, 2015, Bethesda, MD

2014 & before.

Detrended fluctuation analysis of peak expiratory flow and its association with destabilization of asthma control
Presented at the international conference of the American Thoracic Society
May 16, 2014, San Diego, CA

Electrical impedance myography in DMD: a multi-center study of reliability and relationships to strength and function
Presented at the 18th international congress of the World Muscle Society
October, 2013, Asilomar, CA

 

Courses Taught

 

Biological Pathway Analysis: Trends and Applications

BIME 591, Winter 2017

Department of Biomedical Informatics and Medical Education

University of Washington

Guest lectures.

"A SPARQL Tutorial"
BIME 550: Knowledge Representation, Winter 2018
Department of Biomedical Informatics and Medical Education
University of Washington