GORC: A large contextual citation graph of academic papers

Lo K*, Wang LL*, Neumann M, Kinney R, Weld DS

arXiv: 1911.02782


Extracting evidence of supplement-drug interactions from literature

Wang LL, Tafjord O, Jain S, Cohan A, Skjonsberg S, Schoenick C, Botner N, Ammar W.

Machine Learning for Health (ML4H) Workshop at NeurIPS 2019

arXiv: 1909.08135


Gender trends in computer science authorship

Wang LL, Gabriel Stanovsky, Luca Weihs, Oren Etzioni

arXiv: 1906.07883


Predicting instances of Pathway Ontology classes for pathway integration

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

Journal of Biomedical Semantics

DOI: 10.1186/s13326-019-0202-8

PMID: 31196182


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

DOI: 10.18653/v1/W18-2306

ACL ID: W18-2306

arXiv: 1806.07976


PhenotypeXpression: sub-classification of disease states using public gene expression data and literature

Wang LL, Lin H, Bao X, Sengupta S, Busby B, and Butler RR III.

bioRXiv: 10.1101/461301v2


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.

DOI: 10.18653/v1/N18-3011

ACL ID: N18-3011

arXiv: 1805.02262


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

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


Similarity metrics for determining overlap among biological pathways

Wang LL, Gennari, JH.

Proceedings of the International Conference on Biomedical Ontology, 2017.

CEUR Workshop Proceedings


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

Wang LL, Gennari JH, Abernethy NF.

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

CEUR Workshop Proceedings


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

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


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

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

AMIA Annual Symposium Proceedings, 2015.

PMID: 26958311


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

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

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




Biological Pathway Analysis: Trends and Applications

BIME 591, Winter 2017

Department of Biomedical Informatics and Medical Education

University of Washington


Talks & tutorials


Ontology-based integration of biological pathway data

22 May 2019
AKBC Scientific Literature Knowledge Bases Workshop
Amherst, MA

Ontologies and algorithms for integrating biological pathway data

11 October 2018
BIME 590: seminar series
Seattle, WA

A Brief Introduction to Ontology

24 July 2018
KPMP Ontology Workshop
Seattle, WA

A SPARQL Tutorial

24 January 2018
BIME 550: Knowledge Representation, Winter 2018
Department of Biomedical Informatics and Medical Education
University of Washington


PhD Dissertation


Ontology-driven pathway data integration

March 2019

Department of Biomedical Informatics and Medical Education

University of Washington