Graciela Gonzalez-Hernandez, M.S., Ph.D.

faculty photo
Associate Professor of Informatics in Biostatistics and Epidemiology
Department: Biostatistics and Epidemiology

Contact information
The Perelman School of Medicine
University of Pennsylvania
404 Blockley Hall
423 Guardian Drive
Philadelphia, PA 19104-6021
Office: 215-746-1101
Education:
BS (Computer Science)
University of Texas, 1992.
MS (Computer Systems Engineering)
University of Texas, 1994.
PhD (Computer Systems Engineering)
University of Texas, 2000.
Permanent link
 
> Perelman School of Medicine   > Faculty   > Details

Description of Research Expertise

Dr. Gonzalez is a recognized expert and leader in natural language processing (NLP) applied to bioinformatics, medical/clinical informatics, and public health informatics. Her system (BANNER) for named entity recognition has been downloaded over 6000 times from 82 countries, and remains the best performing openly available gene tagging system to date. Her recent work is focused on NLP applications for public health monitoring and surveillance, and is funded by R01s from the National Library of Medicine (NLM) and the National Institute of Allergy and Infectious Diseases (NIAID).

Her work on social media mining for pharmacovigilance has resulted in 10 publications in prestigious conferences and journals, such as work on ADR extraction in JAMIA (PMID 25755127) and prescription drug abuse in Drug Safety (PMID 26748505). A JBI publication (PMID 25720841) was selected last September among the 10 articles with greatest potential social impact (https://www.elsevier.com/atlas/nominations-2015) from papers in over 2500 journals by Elsevier/Atlas. Her work in this area also caught the attention of the FDA, from which she received a grant to develop these methods for monitoring nutritional supplements.

Her work on enriching geospatial information for phylogeography, in collaboration with Dr. Matthew Scotch, uses NLP for the automatic extraction of relevant geospatial data from the literature and its linkage to GenBank records. Preliminary work in this area resulted in publications in JAMIA (PMID 26911818) and Oxford Bioinformatics (PMID 26072502) and a presentation at ISMB in Dublin in 2015.

Dr Gonzalez was director of the Data Core on a P30 award from the NIA from 2008 to 2016, and served as a member of the NIH BLIRC panel from 2008 to 2013. She is a regular reviewer for a number of prestigious journals and conferences, including Nature’s Scientific Reports, PLoS One, PLoS Computational Biology, and the Journal of the American Medical Informatics Association (JAMIA), among others.

Selected Publications

Sarker Abeed, O'Connor Karen, Ginn Rachel, Scotch Matthew, Smith Karen, Malone Dan, Gonzalez Graciela: Social Media Mining for Toxicovigilance: Automatic Monitoring of Prescription Medication Abuse from Twitter. Drug safety 39(3): 231-240, March 2016.

Paul MJ, Sarker A, Brownstein JS, Nikfarjam A, Scotch M, Smith KL, Gonzalez G: Social Media Mining for Public Health Monitoring and Surveillance. Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing 21: 581-592, Jan 2016 Notes: proceeding represents original peer-reviewed research.

Korkontzelos I, Nikfarjam A, Shardlow M, Sarker A, Ananiadou S, Gonzalez G: Improving extraction of adverse drug reactions from tweets and forum posts using sentiment analysis features. Journal of Biomedical Informatics 62: 148-58, Aug 2016.

Leaman R., Wojtulewicz L, Sullivan R, Skariah A, Yang J, Gonzalez G: Towards internet-age pharmacovigilance: extracting adverse drug reactions from user posts to health-related social network. Proceedings of the 2010 Workshop on Biomedical Natural Language Processing (BioNLP), Association for Computational Linguistics (ACL) Page: 117-125, Jul 2010 Notes: proceeding represents original peer-reviewed research.

Nikfarjam Azadeh, Gonzalez Graciela H: Pattern mining for extraction of mentions of Adverse Drug Reactions from user comments. AMIA ... Annual Symposium proceedings / AMIA Symposium. AMIA Symposium 2011: 1019-26, 2011 Notes: proceeding represents original peer-reviewed research.

O'Connor Karen, Pimpalkhute Pranoti, Nikfarjam Azadeh, Ginn Rachel, Smith Karen L, Gonzalez Graciela: Pharmacovigilance on twitter? Mining tweets for adverse drug reactions. AMIA ... Annual Symposium proceedings / AMIA Symposium. AMIA Symposium 2014: 924-33, 2014 Notes: proceeding represents original peer-reviewed research.

Sullivan Ryan, Sarker Abeed, O'Connor Karen, Goodin Amanda, Karlsrud Mark, Gonzalez Graciela: Finding potentially unsafe nutritional supplements from user reviews with topic modeling. Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing 21: 528-39, Jan 2016 Notes: proceeding represents original peer-reviewed research.

Sarker Abeed, Gonzalez Graciela: Portable automatic text classification for adverse drug reaction detection via multi-corpus training. Journal of biomedical informatics 53: 196-207, Feb 2015.

Sarker Abeed, Ginn Rachel, Nikfarjam Azadeh, O'Connor Karen, Smith Karen, Jayaraman Swetha, Upadhaya Tejaswi, Gonzalez Graciela: Utilizing social media data for pharmacovigilance: A review. Journal of biomedical informatics 54: 202-12, Apr 2015.

Nikfarjam Azadeh, Sarker Abeed, O'Connor Karen, Ginn Rachel, Gonzalez Graciela: Pharmacovigilance from social media: mining adverse drug reaction mentions using sequence labeling with word embedding cluster features. Journal of the American Medical Informatics Association : JAMIA 22(3): 671-81, May 2015.

Weissenbacher Davy, Tahsin Tasnia, Beard Rachel, Figaro Mari, Rivera Robert, Scotch Matthew, Gonzalez Graciela: Knowledge-driven geospatial location resolution for phylogeographic models of virus migration. Bioinformatics (Oxford, England) 31(12): i348-56, Jun 2015 Notes: proceeding represents original peer-reviewed research.

4Tahsin T, Weissenbacher D, Rivera R, Beard R, Firago M, Wallstrom G, Scotch M, Gonzalez G; : A high-precision rule-based extraction system for expanding geospatial metadata in GenBank records. Journal of the American Medical Informatics Association 23(5): 934-41, Sep 2016.

Furniss Stephanie K, Yao Robert, Gonzalez Graciela: Automatic gene prioritization in support of the inflammatory contribution to Alzheimer's disease. AMIA Joint Summits on Translational Science proceedings AMIA Summit on Translational Science 2014: 42-7, 2014 Notes: proceeding represents original peer-reviewed research.

Gonzalez Graciela, Uribe Juan C, Tari Luis, Brophy Colleen, Baral Chitta: Mining gene-disease relationships from biomedical literature: weighting protein-protein interactions and connectivity measures. Pacific Symposium on Biocomputing Page: 28-39, 2007 Notes: proceeding represents original peer-reviewed research.

Nikfarjam Azadeh, Emadzadeh Ehsan, Gonzalez Graciela: Towards generating a patient's timeline: extracting temporal relationships from clinical notes. Journal of biomedical informatics 46 Suppl: S40-7, Dec 2013.

Jonnalagadda S, Gonzalez G: Can distributional statistics aid clinical concept extraction? Proceedings of the 2010 i2b2/VA Workshop on Challenges in Natural Language Processing for Clinical Data 2010 Notes: proceeding represents original peer-reviewed research.

Sullivan Ryan, Yao Robert, Jarrar Randa, Buchhalter Jeffrey, Gonzalez Graciela: Text Classification towards Detecting Misdiagnosis of an Epilepsy Syndrome in a Pediatric Population. AMIA ... Annual Symposium proceedings / AMIA Symposium. AMIA Symposium 2014: 1082-7, 2014 Notes: proceeding represents original peer-reviewed research.

Gonzalez Graciela H, Tahsin Tasnia, Goodale Britton C, Greene Anna C, Greene Casey S: Recent Advances and Emerging Applications in Text and Data Mining for Biomedical Discovery. Briefings in bioinformatics 17(1): 33-42, Jan 2016.

Hakenberg Jörg, Gerner Martin, Haeussler Maximilian, Solt Illés, Plake Conrad, Schroeder Michael, Gonzalez Graciela, Nenadic Goran, Bergman Casey M: The GNAT library for local and remote gene mention normalization. Bioinformatics (Oxford, England) 27(19): 2769-71, Oct 2011.

Lee Jang H, Gonzalez Graciela H: Towards integrative gene prioritization in Alzheimer's disease. Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing Page: 4-13, 2011 Notes: proceeding represents original peer-reviewed research.

Jonnalagadda Siddhartha, Gonzalez Graciela: BioSimplify: an open source sentence simplification engine to improve recall in automatic biomedical information extraction. AMIA ... Annual Symposium proceedings / AMIA Symposium. AMIA Symposium 2010: 351-5, 2010 Notes: proceeding represents original peer-reviewed research.

Hakenberg Jörg, Plake Conrad, Leaman Robert, Schroeder Michael, Gonzalez Graciela: Inter-species normalization of gene mentions with GNAT. Bioinformatics (Oxford, England) 24(16): i126-132, Aug 2008.

Leaman Robert, Gonzalez Graciela: BANNER: an executable survey of advances in biomedical named entity recognition. Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing Page: 652-63, 2008 Notes: proceeding represents original peer-reviewed research.

Sullivan R, Leaman R, and Gonzalez G: The DIEGO Lab Graph Based Gene Normalization System. International Conference on Machine Learning and Applications and Workshops (ICMLA) Page: 78-83, Dec 2011 Notes: proceeding represents original peer-reviewed research.

Jonnalagadda SR, Leaman R, Coehn T*, Gonzalez G: A Distributional Semantics Approach to Simultaneous Recognition of Multiple Classes of Named Entities. Proceedings of the 11th International Conference on Intelligent Text Processing and Computational Linguistics, CICLing 2010 Page: 224-235, 2010 Notes: proceeding represents original peer-reviewed research.

back to top
Last updated: 05/12/2017
The Trustees of the University of Pennsylvania