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2018    2017    2016    2015    2014    2013


Klein A, Sarker A, Cai H, Weissenbacher D, Gonzalez G. Social Media Mining for Birth Defects Research: A Rule-Based, Bootstrapping Approach to Collecting Data for Rare Health-Related Events on Twitter. Journal of Biomedical Informatics. 2018 Nov; Vol. 87:68-78. doi: 10.1016/j.jbi.2018.10.001.

Golder S, Chiuve S, Weissenbacher D, Klein A, O’Connor K, Bland M, Malin M, Bhattacharya M, Scarazzini L, Gonzalez G. Pharmacoepidemiologic Evaluation of Birth Defects from Health‑Related Postings in Social Media During Pregnancy. Drug Safety. 2018 Oct. doi: 10.1007/s40264-018-0731-6. (For abstract)

Sarker A, Belousov M, Friedrichs J, Hakala K, Kiritchenko S, Mehryary F, Han S, Tran T, Rios A, Kavuluru R, De Bruijn B, Ginter F, Mahata D, Mohammad S, Nenadic G, Gonzalez G. Data and Systems for Medication-related Text Classification and Concept Normalization from Twitter: Insights from the Social Media Mining for Health (SMM4H)-2017 Shared Task. Journal of the American Medical Informatics Association, ocy114. doi: 10.1093/jamia/ocy114.

Smith K, Golder S, Sarker A, Loke Y, O’Connor K, Gonzalez-Hernandez G. Methods to Compare Adverse Events in Twitter to FAERS, Drug Information Databases, and Systematic Reviews: Proof of Concept with Adalimumab. Drug Safety. 2018 Aug. doi: 10.1007/s40264-018-0707-6. PMID: 30167992.


Sarker A, Chandrashekar P, Magge A, Cai H, Klein A, Gonzalez G. Discovering Cohorts of Pregnant Women From Social Media for Safety Surveillance and Analysis. Journal of Medical Internet Research. 2017 Oct; 19(10): e361.

Gonzalez G, Sarker A, O’Connor K, Savova G. Capturing the patient’s perspective: a review of advances in natural language processing of health-related text. Yearbook of medical informatics. 2017; 26 (01), 214-227.

Klein A, Sarker A, Rouhizadeh M, O’Connor K, Gonzalez G. Detecting Personal Medication Intake in Twitter: An Annotated Corpus and Baseline Classification System. BioNLP 2017. 136-142.

Sarker A, Gonzalez G. A corpus for mining drug-related knowledge from Twitter chatter: language models and their utilities. Data in Brief. 2016 Nov 23;10:122-131. eCollection 2017 Feb. PMID: 27981203.

Sarker A, Malone D, Gonzalez G. Authors’ Reply to Jouanjus and Colleagues’ Comment on “Social Media Mining for Toxicovigilance: Automatic Monitoring of Prescription Medication Abuse from Twitter”. Drug Safety. 2017 Feb;40(2):187-188. doi: 10.1007/s40264-016-0498-6. PMID: 28070742

Sarker A, Magge A, Sharma A. Dermatologic concerns communicated through Twitter. International Journal of Dermatology. 2017 Feb 12. doi: 10.1111/ijd.13506. PMID: 28191639.


Korkontzelos I, Nikfarjam A, Shardlow M, Sarker A, Ananidou S, Gonzalez G. Improving extraction of adverse drug reactions from tweets and forum posts using sentiment analysis features. Journal of Biomedical Informatics. 2016; Vol. 62. 148—158.

Tahsin T, Weissenbacher D, Rivera 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. 2016 Sep;23(5):934-41. doi: 10.1093/jamia/ocv172. Epub 2016 Jan 17.


Sarker A, O’Connor K, Ginn R, Scotch M, Smith K, Malone D, Gonzalez G. Social Media Mining for Toxicovigilance: Automatic Monitoring of Prescription Medication Abuse from Twitter. Drug Safety. 2015; 39(3):231—240.

Sarker A, Mollá D, Paris C. Automatic evidence quality prediction to support evidence-based decision making. Artificial Intelligence in Medicine. 2015; 64(2). 89—103.

Sarker A, Ginn R, Nikfarjam A, O’Connor K, Smith K, Jayaraman S, Upadhaya T, Gonzalez G. Utilizing social media data for pharmacovigilance: a review. Journal of Biomedical Informatics. 2015; Vol. 54. 202—212.

Nikfarjam A, Sarker A, O’Connor K, Ginn R, Gonzalez G. Pharmacovigilance from social media: mining adverse drug reaction mentions using sequence labeling with word embedding cluster features. Journal of the American Medical Informatics Association. 2015; 22(3):671—681.

Sarker A, Gonzalez G. Portable automatic text classification for adverse drug reaction detection via multi-corpus training. Journal of Biomedical Informatics. 2015; Vol. 53: 196—207.


Emadzadeh E, Nikfarjam A,  Ginn RE,  Gonzalez G; Unsupervised gene function extraction using semantic vectors, Oxford University Press, Database (2014) Sep 10;2014. pii: bau084.

Mao Y, Van Auken K, Li D, Arighi CN, McQuilton P, Hayman GT, Tweedie S, Schaeffer ML, Laulederkind SJF, Wang S, Gobeill J, Ruch P, Tuan Luu A, Kim J, Chiang J, Chen Y, Yang C, Liu H, Zhu D, Li Y, Yu H, Emadzadeh E, Gonzalez G, Chen J, Dai H, Lu Z; Overview of the gene ontology task at BioCreative IV, Oxford University Press, Database (2014) July 2014 : bau086.


Nikfarjam A, Emadzadeh E, Gonzalez G; Towards generating a patient’s timeline: Extracting temporal relationships from clinical notes, Journal of Biomedical Informatics, 2013.

Jonnalagadda SR, Cohen T, Wu S, Liu H, Gonzalez G; Using empirically constructed Lexical Resources for named entity Recognition, Journal of Biomedical Informatics Insights, 2013:6 (Suppl. 1) 17-27.

Nikfarjam A, Emadzadeh E, Gonzalez G; A Hybrid system for Emotion Extraction from Suicide Notes, Journal of Biomedical Informatics Insights, 2012:5 (Suppl. 1) 165-174.

Jonnalagadda SR, Cohen T, Wu S, Gonzalez G; Enhancing clinical concept extraction with distributional semantics, Journal of Biomedical Informatics, 2012 Feb; 45(1):129-40. Epub 2011 Nov 7 (PMID 22085698; PMC3272090).