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Jennifer A. Pacheco
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- affiliation: Northwestern University Feinberg School of Medicine, Chicago, IL, USA
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2020 – today
- 2023
- [j20]Pascal S. Brandt
, Abel N. Kho, Yuan Luo
Characterizing variability of electronic health record-driven phenotype definitions. J. Am. Medical Informatics Assoc. 30(3): 427-437 (2023) - [j19]Chengsheng Mao, Jie Xu, Luke V. Rasmussen, Yikuan Li, Prakash Adekkanattu, Jennifer A. Pacheco, Borna Bonakdarpour, Robert Vassar, Li Shen, Guoqian Jiang, Fei Wang, Jyotishman Pathak, Yuan Luo:
AD-BERT: Using pre-trained language model to predict the progression from mild cognitive impairment to Alzheimer's disease. J. Biomed. Informatics 144: 104442 (2023) - 2022
- [j18]Pascal S. Brandt
Design and validation of a FHIR-based EHR-driven phenotyping toolbox. J. Am. Medical Informatics Assoc. 29(9): 1449-1460 (2022) - [j17]Jingzhi Yu, Jennifer A. Pacheco, Anika S. Ghosh, Yuan Luo, Chunhua Weng, Ning Shang, Barbara Benoit, David S. Carrell, Robert J. Carroll, Ozan Dikilitas, Robert R. Freimuth, Vivian S. Gainer, Hakon Hakonarson, George Hripcsak, Iftikhar J. Kullo, Frank D. Mentch, Shawn N. Murphy, Peggy L. Peissig, Andrea H. Ramirez, Nephi Walton, Wei-Qi Wei, Luke V. Rasmussen:
Under-specification as the source of ambiguity and vagueness in narrative phenotype algorithm definitions. BMC Medical Informatics Decis. Mak. 22(1): 23 (2022) - [j16]Yu Deng, Jennifer A. Pacheco, Anika S. Ghosh, Anh H. Chung, Chengsheng Mao, Joshua C. Smith, Juan Zhao, Wei-Qi Wei, April Barnado, Chad Dorn, Chunhua Weng, Cong Liu, Adam Cordon, Jingzhi Yu, Yacob Tedla, Abel Kho, Rosalind Ramsey-Goldman, Theresa Walunas, Yuan Luo
Natural language processing to identify lupus nephritis phenotype in electronic health records. BMC Medical Informatics Decis. Mak. 22-S(2): 348 (2022) - [i5]Chengsheng Mao, Jie Xu, Luke V. Rasmussen, Yikuan Li, Prakash Adekkanattu, Jennifer A. Pacheco, Borna Bonakdarpour, Robert Vassar, Guoqian Jiang, Fei Wang, Jyotishman Pathak, Yuan Luo:
AD-BERT: Using Pre-trained contextualized embeddings to Predict the Progression from Mild Cognitive Impairment to Alzheimer's Disease. CoRR abs/2212.06042 (2022) - 2021
- [c36]Prakash Adekkanattu, Jennifer A. Pacheco, Joseph Kabariti, Daniel J. Stone, Yue Yu, Parag Goyal, Faraz S. Ahmad, Guoqian Jiang, Yuan Luo, Luke V. Rasmussen, Pascal S. Brandt, Zhenxing Xu, Jie Xu, Fei Wang, Natalie C. Benda, Thomas R. Campion Jr., Jyotishman Pathak:
Multi-site Evaluation of Longitudinal Changes in Ejection Fraction in Heart Failure Patients Through Data-driven Phenotyping. AMIA 2021 - [c35]Natalie C. Benda, Pascal S. Brandt, Jessica S. Ancker, Jennifer A. Pacheco, Prakash Adekkanattu, Guoqian Jiang, Jyotishman Pathak, Luke V. Rasmussen:
Supporting EHR-based Cohort Discovery Through User-centered Design: Results of an Early Formative Usability Study. AMIA 2021 - [c34]Chengsheng Mao, Jie Xu, Luke V. Rasmussen, Jennifer A. Pacheco, Guoqian Jiang, Fei Wang, Richard Isaacson, Jyotishman Pathak, Yuan Luo:
A Deep Learning Framework Using a Pre-trained BERT Model to Predict the Risk of Progression from Mild Cognitive Impairment to Alzheimer's Disease. AMIA 2021 - [c33]Jennifer A. Pacheco, Luke V. Rasmussen, Ken Wiley, Thomas N. Person, David J. Cronkite, Sunghwan Sohn, Shawn N. Murphy, Justin H. Gundelach, Vivian S. Gainer, Victor M. Castro, Cong Liu, Todd Lingren, Frank D. Mentch, Agnes S. Sundaresan, Garrett Eickelberg, Valerie Willis, Al'ona Furmanchuk, Roshan Patel, David S. Carrell, Marc S. Williams, Elizabeth W. Karlson, Jodell E. Linder, Yuan Luo, Chunhua Weng, Wei-Qi Wei:
Evaluation of the Portability of Natural Language Processing-based Computable Phenotypes in the eMERGE Network. AMIA 2021 - [c32]Daniel J. Stone, Sijia Liu, Yuan Luo, Andrew Wen, Nansu Zong, Luke V. Rasmussen, Prakash Adekkanattu, Pascal S. Brandt, Jennifer A. Pacheco, Fei Wang, Cui Tao, Jyotishman Pathak, Hongfang Liu, Guoqian Jiang:
FHIRTime: Standardizing Temporal Patterns Identified from Clinical Narratives Using HL7 FHIR. AMIA 2021 - [c31]Andrew Wen, Luke V. Rasmussen, Daniel J. Stone, Sijia Liu, Prakash Adekkanattu, Pascal S. Brandt, Jennifer A. Pacheco, Yuan Luo, Fei Wang, Jyotishman Pathak, Hongfang Liu, Guoqian Jiang:
On Constraints and Considerations for Extending Support for Natural Language Processing-Based FHIR Resource Generation. AMIA 2021 - [i4]Yu Deng, Jennifer A. Pacheco, Anh H. Chung, Chengsheng Mao, Joshua C. Smith, Juan Zhao, Wei-Qi Wei, April Barnado, Chunhua Weng, Cong Liu, Adam Cordon, Jingzhi Yu, Yacob Tedla, Abel N. Kho, Rosalind Ramsey-Goldman, Theresa Walunas, Yuan Luo:
Natural language processing to identify lupus nephritis phenotype in electronic health records. CoRR abs/2112.10821 (2021) - 2020
- [j15]Zhenxing Xu, Jingyuan Chou, Xi Sheryl Zhang, Yuan Luo
Identifying sub-phenotypes of acute kidney injury using structured and unstructured electronic health record data with memory networks. J. Biomed. Informatics 102: 103361 (2020) - [c30]Pascal S. Brandt, Richard C. Kiefer, Jennifer A. Pacheco, Prakash Adekkanattu, Evan Sholle, Faraz S. Ahmad, Jie Xu, Zhenxing Xu, Jessica S. Ancker, Fei Wang, Yuan Luo, Guoqian Jiang, Jyotishman Pathak, Luke V. Rasmussen:
Feasibility of Cross-Platform EHR-Driven Phenotyping Using Clinical Quality Language. AMIA 2020 - [c29]Jie Xu, Fei Wang, Zhenxing Xu, Prakash Adekkanattu, Pascal S. Brandt, Guoqian Jiang, Richard C. Kiefer, Yuan Luo, Chengsheng Mao, Jennifer A. Pacheco, Luke V. Rasmussen, Yiye Zhang, Richard Isaacson, Jyotishman Pathak:
Identification of Alzheimer's Disease Subtypes from Electronic Health Records Using a Data-Driven Approach. AMIA 2020
2010 – 2019
- 2019
- [j14]Luke V. Rasmussen
An ancillary genomics system to support the return of pharmacogenomic results. J. Am. Medical Informatics Assoc. 26(4): 306-310 (2019) - [j13]Na Hong, Andrew Wen, Daniel J. Stone, Shintaro Tsuji, Paul R. Kingsbury, Luke V. Rasmussen
Developing a FHIR-based EHR phenotyping framework: A case study for identification of patients with obesity and multiple comorbidities from discharge summaries. J. Biomed. Informatics 99 (2019) - [j12]Ning Shang
Making work visible for electronic phenotype implementation: Lessons learned from the eMERGE network. J. Biomed. Informatics 99 (2019) - [c28]Prakash Adekkanattu, Guoqian Jiang, Yuan Luo, Paul R. Kingsbury, Zhenxing Xu, Luke V. Rasmussen, Jennifer A. Pacheco, Richard C. Kiefer, Daniel J. Stone, Pascal S. Brandt, Liang Yao, Yizhen Zhong, Yu Deng, Fei Wang, Jessica S. Ancker, Thomas R. Campion Jr., Jyotishman Pathak:
Evaluating the Portability of an NLP System for Processing Echocardiograms: A Retrospective, Multi-site Observational Study. AMIA 2019 - [c27]Luke V. Rasmussen, Pascal S. Brandt, Guoqian Jiang, Richard C. Kiefer, Jennifer A. Pacheco, Prakash Adekkanattu, Jessica S. Ancker, Fei Wang, Zhenxing Xu, Jyotishman Pathak, Yuan Luo:
Considerations for Improving the Portability of Electronic Health Record-Based Phenotype Algorithms. AMIA 2019 - [c26]Zhenxing Xu, Yuan Luo
Stratified Mortality Prediction of Patients with Acute Kidney Injury in Critical Care. MedInfo 2019: 462-466 - [c25]Theresa L. Walunas
Assessing the Concordance of Clinical Classification Criteria for Lupus Between Electronic Health Records and a Physician Curated Registry. MedInfo 2019: 1466-1467 - [i3]Zhenxing Xu, Jingyuan Chou, Xi Sheryl Zhang, Yuan Luo, Tamara Isakova, Prakash Adekkanattu, Jessica S. Ancker, Guoqian Jiang, Richard C. Kiefer, Jennifer A. Pacheco, Luke V. Rasmussen, Jyotishman Pathak, Fei Wang:
Identification of Predictive Sub-Phenotypes of Acute Kidney Injury using Structured and Unstructured Electronic Health Record Data with Memory Networks. CoRR abs/1904.04990 (2019) - [i2]Prakash Adekkanattu, Guoqian Jiang, Yuan Luo, Paul R. Kingsbury, Zhenxing Xu, Luke V. Rasmussen, Jennifer A. Pacheco, Richard C. Kiefer, Daniel J. Stone, Pascal S. Brandt, Liang Yao, Yizhen Zhong, Yu Deng, Fei Wang, Jessica S. Ancker, Thomas R. Campion Jr., Jyotishman Pathak:
Evaluating the Portability of an NLP System for Processing Echocardiograms: A Retrospective, Multi-site Observational Study. CoRR abs/1905.01961 (2019) - 2018
- [j11]Jennifer A. Pacheco
A case study evaluating the portability of an executable computable phenotype algorithm across multiple institutions and electronic health record environments. J. Am. Medical Informatics Assoc. 25(11): 1540-1546 (2018) - [c24]Yizhen Zhong, Luke V. Rasmussen
Characterizing Design Patterns of EHR-Driven Phenotype Extraction Algorithms. BIBM 2018: 1143-1146 - [i1]Yizhen Zhong, Luke V. Rasmussen, Yu Deng, Jennifer A. Pacheco, Maureen E. Smith, Justin Starren, Wei-Qi Wei, Peter Speltz, Joshua C. Denny, Nephi Walton, George Hripcsak, Christopher G. Chute, Yuan Luo:
Characterizing Design Patterns of EHR-Driven Phenotype Extraction Algorithms. CoRR abs/1811.06183 (2018) - 2017
- [c23]Erin N. Gustafson, Al'ona Furmanchuk, Jennifer A. Pacheco, Firas H. Wehbe, Kathryn L. Jackson, Abel N. Kho, William K. Thompson, Jonathan Silverberg:
A Machine Learning-Based Approach for Identifying Atopic Dermatitis in Adults from Electronic Health Records. AMIA 2017 - [c22]Richard C. Kiefer, Luke V. Rasmussen, Jennifer A. Pacheco, Peter Speltz, Joshua C. Denny, William K. Thompson, Jyotishman Pathak, Guoqian Jiang:
Leveraging Value Sets from the Value Set Authority Center (VSAC) in a Standards-Based Clinical Data Repository. AMIA 2017 - [c21]Jennifer A. Pacheco, Agnes S. Sundaresan, Kenneth M. Borthwick, Sergio E. Chiarella, David T. Coleman, Andy Yizhou Wu, Abel N. Kho, M. Geoffrey Hayes, Marc S. Williams:
Portable Precision Phenotype Algorithm for Chronic Rhinosinusitis. AMIA 2017 - [c20]Angela Smith, Ada Ng, Eleanor R. Burgess, Jennifer A. Pacheco, Noah D. Weingarten:
Sensi-steps: Using Patient-Generated Data to Prevent Post-stroke Falls. AMIA 2017 - [c19]Peter Speltz, Luke V. Rasmussen, Richard C. Kiefer, Jennifer A. Pacheco, William K. Thompson, Guoqian Jiang, Jyotishman Pathak, Joshua C. Denny:
The Phenotype Execution and Modeling Architecture: A Roadmap Towards Next-generation Phenotyping Using EHRs. AMIA 2017 - [c18]Erin N. Gustafson, Jennifer A. Pacheco
A Machine Learning Algorithm for Identifying Atopic Dermatitis in Adults from Electronic Health Records. ICHI 2017: 83-90 - 2016
- [j10]Jacqueline Kirby, Peter Speltz, Luke V. Rasmussen
PheKB: a catalog and workflow for creating electronic phenotype algorithms for transportability. J. Am. Medical Informatics Assoc. 23(6): 1046-1052 (2016) - [j9]Raymond Heatherly, Luke V. Rasmussen
A multi-institution evaluation of clinical profile anonymization. J. Am. Medical Informatics Assoc. 23(e1): e131-e137 (2016) - [j8]Guoqian Jiang, Richard C. Kiefer, Luke V. Rasmussen
Developing a data element repository to support EHR-driven phenotype algorithm authoring and execution. J. Biomed. Informatics 62: 232-242 (2016) - [c17]Raja Arul Cholan, Jennifer A. Pacheco, Gene Ren, Laura Hickerson:
Personalized Heart Disease Risk Manager: A Tool for Patients and Clinicians to Manage Cardiovascular Risk. AMIA 2016 - [c16]Guoqian Jiang, William K. Thompson, Luke V. Rasmussen, Richard C. Kiefer, Jennifer A. Pacheco, Huan Mo, Peter Speltz, Joshua C. Denny, Jyotishman Pathak:
An NLP Extension to the Quality Data Model for EHR-Driven Phenotype Algorithm Authoring and Execution. AMIA 2016 - [c15]Luke V. Rasmussen, Maureen E. Smith, Federico Almaraz, Stephen D. Persell, Laura Rasmussen-Torvik, Jennifer A. Pacheco, Carl Christensen, Timothy M. Herr, Firas H. Wehbe, Justin Starren:
Design and Implementation of an Ancillary Genomics System for the Return of Pharmacogenetic Results. AMIA 2016 - [c14]Huan Mo, Guoqian Jiang, Jennifer A. Pacheco, Richard C. Kiefer, Luke V. Rasmussen, Jyotishman Pathak, Joshua C. Denny, William K. Thompson:
A Decompositional Approach to Executing Quality Data Model Algorithms on the i2b2 Platform. CRI 2016 - 2015
- [j7]Rishika De, Shefali S. Verma, Fotios Drenos
Identifying gene-gene interactions that are highly associated with Body Mass Index using Quantitative Multifactor Dimensionality Reduction (QMDR). BioData Min. 8: 41 (2015) - [j6]Huan Mo
Desiderata for computable representations of electronic health records-driven phenotype algorithms. J. Am. Medical Informatics Assoc. 22(6): 1220-1230 (2015) - [j5]Jie Xu, Luke V. Rasmussen
Review and evaluation of electronic health records-driven phenotype algorithm authoring tools for clinical and translational research. J. Am. Medical Informatics Assoc. 22(6): 1251-1260 (2015) - [c13]Guoqian Jiang, Harold R. Solbrig, Richard C. Kiefer, Luke V. Rasmussen, Huan Mo, Jennifer A. Pacheco, Enid N. H. Montague, Jie Xu, Peter Speltz, William K. Thompson, Joshua C. Denny, Christopher G. Chute, Jyotishman Pathak:
Harmonization of Quality Data Model with HL7 FHIR to Support EHR-driven Phenotype Authoring and Execution: A Pilot Study. AMIA 2015 - [c12]Yoonjung Y. Joo, Jennifer A. Pacheco, Loren L. Armstrong, William K. Thompson, Robert J. Carroll, Joshua C. Denny, Peggy L. Peissig, James G. Linneman, Jyotishman Pathak, Girish N. Nadkarni, Laura Rasmussen-Torvik, M. Geoffrey Hayes, Abel N. Kho:
A Genome- and Phenome- Wide Study of Diverticulosis. AMIA 2015 - [c11]Huan Mo, Jennifer A. Pacheco, Richard C. Kiefer, Luke V. Rasmussen, Jyotishman Pathak, Joshua C. Denny, William K. Thompson:
Translating Electronic Clinical Quality Measures to Executable, Portable, and Customizable Workflows in KNIME. AMIA 2015 - [c10]Enid N. H. Montague, Jie Xu, Luke V. Rasmussen, Joshua C. Denny, Guoqian Jiang, Richard C. Kiefer, Jennifer A. Pacheco, Peter Speltz, William K. Thompson, Jyotishman Pathak:
Usability of a phenotype builder prototype and lessons learned for the design of phenotyping tools. AMIA 2015 - [c9]Jennifer A. Pacheco, Abel N. Kho, Jyotishman Pathak, Joshua C. Denny, Shawn N. Murphy:
(Authoring) Rules, (Distributed Query) Tools, and Drools: The challenging new world of high throughput phenotyping. AMIA 2015 - 2014
- [j4]Luke V. Rasmussen
Design patterns for the development of electronic health record-driven phenotype extraction algorithms. J. Biomed. Informatics 51: 280-286 (2014) - [c8]Jennifer A. Pacheco, William K. Thompson, Kathryn L. Jackson, Abel N. Kho:
Automating Extraction and Calculation of Daily Dose and Duration for Medications in EHRs. AMIA 2014 - [c7]Luke V. Rasmussen, Jie Xu, Ruijue Liu, Qian Zhu, Jennifer A. Pacheco, Jyotishman Pathak, William K. Thompson, Joshua C. Denny, Huan Mo, Richard C. Kiefer, Peter Speltz, Enid N. H. Montague:
Evaluation of Existing Phenotype Authoring Tools for Clinical Research. AMIA 2014 - [c6]Qian Zhu, Huan Mo, Luke V. Rasmussen, Andrew R. Post, Jennifer A. Pacheco, Jie Xu, Richard C. Kiefer, Peter Speltz, Enid N. H. Montague, William K. Thompson, Joshua C. Denny, Jyotishman Pathak:
Qualitative evaluation of three phenotype information models to find methotrexate liver injury. AMIA 2014 - [c5]Janina M. Jeff, Kristin Brown-Gentry, Robert J. Goodloe, Marylyn D. Ritchie, Joshua C. Denny
Replication of SCN5A Associations with Electrocardiographic Traits in African Americans from Clinical and Epidemiologic Studies. EvoApplications 2014: 939-951 - 2012
- [j3]Abel N. Kho, M. Geoffrey Hayes
Use of diverse electronic medical record systems to identify genetic risk for type 2 diabetes within a genome-wide association study. J. Am. Medical Informatics Assoc. 19(2): 212-218 (2012) - [j2]Wei-Qi Wei, Cynthia L. Leibson, Jeanine E. Ransom, Abel N. Kho, Pedro J. Caraballo, High Seng Chai, Barbara P. Yawn, Jennifer A. Pacheco
Impact of data fragmentation across healthcare centers on the accuracy of a high-throughput clinical phenotyping algorithm for specifying subjects with type 2 diabetes mellitus. J. Am. Medical Informatics Assoc. 19(2): 219-224 (2012) - [j1]Robert J. Carroll, William K. Thompson, Anne E. Eyler, Arthur M. Mandelin, Tianxi Cai, Raquel M. Zink, Jennifer A. Pacheco
Portability of an algorithm to identify rheumatoid arthritis in electronic health records. J. Am. Medical Informatics Assoc. 19(e1) (2012) - [c4]Anna Roberts, Arun Muthalagu, Jennifer A. Pacheco, William K. Thompson, Andrew Gawron, Abel N. Kho:
A Geographic Exploration of Colon Polyps. AMIA 2012 - [c3]William K. Thompson, Luke V. Rasmussen, Jennifer A. Pacheco, Peggy L. Peissig, Joshua C. Denny, Abel N. Kho, Aaron W. Miller, Jyotishman Pathak:
An Evaluation of the NQF Quality Data Model for Representing Electronic Health Record Driven Phenotyping Algorithms. AMIA 2012 - [c2]William K. Thompson, Luke V. Rasmussen, Jennifer A. Pacheco, Anna Roberts, Arun Muthalagu, Abel N. Kho:
Open Source Workflow Tools for Electronic Health Record Based Phenotyping Algorithms. AMIA 2012
2000 – 2009
- 2009
- [c1]Jennifer A. Pacheco, Pedro C. Avila, Jason A. Thompson, May Law, Jihan A. Quraishi, Alyssa K. Greiman, Eric M. Just, Abel N. Kho:
A Highly Specific Algorithm for Identifying Asthma Cases and Controls for Genome-Wide Association Studies. AMIA 2009
Coauthor Index
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