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2017

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.

2016

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.

2015

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.

2014

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.

2013

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).