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2020  2019    2018    2017    2016    2015    2014    2013

2020

Pregnancy and health in the age of the Internet: A content analysis of online “birth club” forums. Wexler A, Davoudi A, Weissenbacher D, Choi R, O’Connor K, Cummings H, et al. PLoS ONE. 2020;15(4): e0230947. https://doi.org/10.1371/journal.pone.0230947

Promoting Reproducible Research for Characterizing Nonmedical Use of Medications Through Data Annotation: Description of a Twitter Corpus and Guidelines. O’Connor, Karen ; Sarker, Abeed; Perrone Jeanmarie; Gonzalez-Hernandez, Graciela. Journal of medical Internet research. 2020;22(2):e15861.

Under Review:

Effective buprenorphine use and tapering strategies: Endorsements and insights by people in recovery from opioid use disorder on a Reddit forum. Graves, Rachel L; Sarker, Abeed; Al-Garadi, Mohammed Ali; Yang, Yuan-chi; Love, Jennifer S; O’Connor, Karen; Gonzalez-Hernandez, Graciela; Perrone, Jeanmarie;JAMA Network Open

A natural language processing pipeline to advance the use of Twitter data for digital epidemiology of adverse pregnancy outcomes. Klein, Ari Z; Cai, Haitao; Weissenbacher, Davy; Levine, Lisa; Gonzalez-Hernandez, Graciela. Journal of Biomedical Informatics

A chronological and geographical analysis of personal reports of COVID-19 on Twitter. Klein, Ari Z; Magge, Arjun; O’Connor, Karen; Cai, Haitao; Weissenbacher, Davy; Gonzalez-Hernandez, Graciela. npj Digital Medicine

Evaluating Annotation tools for Twitter Data. Weissenbacher D., O’Connor K., Hiraki A. T., Gonzalez-Hernandez G., Genomics and Informatics.

2019

Disease associations depend on visit type: results from a visit-wide association study. Boland MR, Alur-Gupta S, Levine L, Gabriel P, Gonzalez-Hernandez G. BioData mining 12.1 (2019): 15.

Towards scaling Twitter for digital epidemiology of birth defects. Klein AZ, Sarker A, Weissenbacher D, Gonzalez-Hernandez G. NPJ digital medicine. 2019 Oct 1;2(1):1-9

Deep neural networks ensemble for detecting medication mentions in tweets. Weissenbacher D, Sarker A, Klein A, O’Connor K, Magge A, Gonzalez-Hernandez G. Journal of the American Medical Informatics Association 26.12 (2019): 1618-1626.

Machine Learning and Natural Language Processing for Geolocation-Centric Monitoring and Characterization of Opioid-Related Social Media Chatter. Sarker A, Gonzalez-Hernandez G, Ruan Y, Perrone J. JAMA network open 2.11 (2019): e1914672-e1914672.

Towards Automatic Bot Detection in Twitter for Health-related Tasks. Davoudi A, Klein AZ, Sarker A, Gonzalez-Hernandez G. arXiv preprint arXiv:1909.13184 (2019).

Towards automating location-specific opioid toxicosurveillance from Twitter via data science methods. Studies in health technology and informatics. Sarker A, Gonzalez-Hernandez G, Perrone J. Studies in health technology and informatics 264 (2019): 333.

Automatically Identifying Comparator Groups on Twitter for Digital Epidemiology of Pregnancy Outcomes. Klein AZ, Gebreyesus A, Gonzalez-Hernandez G. arXiv preprint arXiv:1908.06015 (2019).

# Science: The potential and the challenges of utilizing social media and other electronic communication platforms in health care. Gijsen V, Maddux M, Lavertu A, Gonzalez‐Hernandez G, Ram N, Reeves B, Robinson T, Ziesenitz V, Shakhnovich V, Altman R. Clinical and Translational Science (2019).

Comment on:“Deep learning for pharmacovigilance: recurrent neural network architectures for labeling adverse drug reactions in Twitter posts”. Magge A, Sarker A, Nikfarjam A, Gonzalez-Hernandez G. Journal of the American Medical Informatics Association 26.6 (2019): 577-579.

Pharmacoepidemiologic evaluation of birth defects from health-related postings in social media during pregnancy. Golder S, Chiuve S, Weissenbacher D, Klein A, O’Connor K, Bland M, Malin M, Bhattacharya M, Scarazzini LJ, Gonzalez-Hernandez G. Drug safety 42.3 (2019): 389-400.

Incorporating sampling uncertainty in the geospatial assignment of taxa for virus phylogeography. Scotch M, Tahsin T, Weissenbacher D, O’Connor K, Magge A, Vaiente M, Suchard MA, Gonzalez-Hernandez G. Virus evolution 5.1 (2019): vey043.

Preparing next-generation scientists for biomedical big data: artificial intelligence approaches. Moore JH, Boland MR, Camara PG, Chervitz H, Gonzalez G, Himes BE, Kim D, Mowery DL, Ritchie MD, Shen L, Urbanowicz RJ. Personalized medicine 16.3 (2019): 247-257.

Effective buprenorphine use and tapering strategies: Endorsements and insights by people in recovery from opioid use disorder on a Reddit forum. Graves RL, Sarker A, Al-Garadi MA, Yang YC, Love JS, O’Connor K, Gonzalez-Hernandez G, Perrone J. bioRxiv (2019): 871608.

An Analysis of a Twitter Corpus for Training a Medication Intake Classifier. Klein AZ, Sarker A, O’Connor K, Gonzalez-Hernandez G. AMIA Summits on Translational Science Proceedings 2019 (2019): 102.

2018

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

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

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. 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. Journal of the American Medical Informatics Association, ocy114. doi: 10.1093/jamia/ocy114.

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

2017

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

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

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

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

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

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

2016

Analysis of the effect of sentiment analysis on extracting adverse drug reactions from tweets and forum posts. Korkontzelos I, Nikfarjam A, Shardlow M, Sarker A, Ananidou S, Gonzalez G. Journal of Biomedical Informatics. 2016; Vol. 62. 148—158.

A high-precision rule-based extraction system for expanding geospatial metadata in GenBank records. Journal of the American Medical Informatics Association. Tahsin T, Weissenbacher D, Rivera R, Firago M, Wallstrom G, Scotch M, Gonzalez G. 2016 Sep;23(5):934-41. doi: 10.1093/jamia/ocv172. Epub 2016 Jan 17.

2015

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

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

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

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

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

2014

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

Overview of the gene ontology task at BioCreative IV. 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; Oxford University Press, Database (2014) July 2014 : bau086.

2013

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

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

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

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