Polygenic risk alters the penetrance of monogenic kidney disease.Nature communications,
2023Atlas Khan, Ning Shang, Jordan G Nestor, Chunhua Weng, George Hripcsak, Peter C Harris, Ali G Gharavi, Krzysztof Kiryluk
Polygenic Risk Score
Monogenic Kidney Disease
Autosomal Dominant Polycystic Kidney Disease
Col4a1-Associated Nephropathy
Risk Stratification
Phenotype-Driven Molecular Genetic Test Recommendation for Diagnosing Pediatric Rare Disorders.Research square,
2023Fangyi Chen, Priyanka Ahimaz, Kai Wang, Wendy K Chung, Casey Ta, Chunhua Weng, Cong Liu
Phenotype-Based Test Recommendation
Rare Pediatric Genetics
EHR Phenotype Integration
Machine Learning Classifier
Learning Health System
Strong protective effect of the APOL1 p.N264K variant against G2-associated focal segmental glomerulosclerosis and kidney disease.Nature communications,
2023Yask Gupta, David J Friedman, Michelle T McNulty, Atlas Khan, Brandon Lane, Chen Wang, Juntao Ke, Gina Jin, Benjamin Wooden, Andrea L Knob, Tze Y Lim, Gerald B Appel, Kinsie Huggins, Lili Liu, Adele Mitrotti, Megan C Stangl, Andrew Bomback, Rik Westland, Monica Bodria, Maddalena Marasa, Ning Shang, David J Cohen, Russell J Crew, William Morello, Pietro Canetta, Jai Radhakrishnan, Jeremiah Martino, Qingxue Liu, Wendy K Chung, Angelica Espinoza, Yuan Luo, Wei-Qi Wei, Qiping Feng, Chunhua Weng, Yilu Fang, Iftikhar J Kullo, Mohammadreza Naderian, Nita Limdi, Marguerite R Irvin, Hemant Tiwari, Sumit Mohan, Maya Rao, Geoffrey K Dube, Ninad S Chaudhary, Orlando M Gutiérrez, Suzanne E Judd, Mary Cushman, Leslie A Lange, Ethan M Lange, Daniel L Bivona, Miguel Verbitsky, Cheryl A Winkler, Jeffrey B Kopp, Dominick Santoriello, Ibrahim Batal, Sérgio Veloso Brant Pinheiro, Eduardo Araújo Oliveira, Ana Cristina Simoes E Silva, Isabella Pisani, Enrico Fiaccadori, Fangming Lin, Loreto Gesualdo, Antonio Amoroso, Gian Marco Ghiggeri, Vivette D D'Agati, Riccardo Magistroni, Eimear E Kenny, Ruth J F Loos, Giovanni Montini, Friedhelm Hildebrandt, Dirk S Paul, Slavé Petrovski, David B Goldstein, Matthias Kretzler, Rasheed Gbadegesin, Ali G Gharavi, Krzysztof Kiryluk, Matthew G Sampson, Martin R Pollak, Simone Sanna-Cherchi
Apol1 G2 Variant
P.n264k Protective Variant
Focal Segmental Glomerulosclerosis
African American CKD Risk
Apol1 Nephropathy Modifiers
Clusters, crop dusters, and myth busters: a scoping review of environmental exposures and cutaneous T-cell lymphoma.Italian journal of dermatology and venereology,
2023Emily R Gordon, Oluwaseyi Adeuyan, Celine M Schreidah, Caroline Chen, Megan H Trager, Brigit A Lapolla, Lauren M Fahmy, Chunhua Weng, Larisa J Geskin
Cutaneous T-Cell Lymphoma
Environmental Risk Factors
Geographic Exposure
Chemical Exposure
Occupational Exposure
Enhancing Phenotype Recognition in Clinical Notes Using Large Language Models: PhenoBCBERT and PhenoGPT.ArXiv,
2023Jingye Yang, Cong Liu, Wendy Deng, Da Wu, Chunhua Weng, Yunyun Zhou, Kai Wang
Phenotype Extraction
Clinical Text NLP
Large Language Models
Human Phenotype Ontology
BERT vs GPT
Prospective, multi-site study of healthcare utilization after actionable monogenic findings from clinical sequencing.American journal of human genetics,
2023Jodell E Linder, Ran Tao, Wendy K Chung, Krzysztof Kiryluk, Cong Liu, Chunhua Weng, John J Connolly, Hakon Hakonarson, Margaret Harr, Kathleen A Leppig, Gail P Jarvik, David L Veenstra, Sharon Aufox, Rex L Chisholm, Adam S Gordon, Christin Hoell, Laura J Rasmussen-Torvik, Maureen E Smith, Ingrid A Holm, Erin M Miller, Cynthia A Prows, Omar Elskeally, Iftikhar J Kullo, Christopher Lee, Sheethal Jose, Teri A Manolio, Robb Rowley, Nana Addo Padi-Adjirackor, Ni Ketut Wilmayani, Brittany City, Wei-Qi Wei, Georgia L Wiesner, Alanna Kulchak Rahm, Janet L Williams, Marc S Williams, Josh F Peterson
Actionable Monogenic Screening
Healthcare Utilization
Genomic Sequencing Outcomes
Cost Analysis
Emerge Study
Uncovering key clinical trial features influencing recruitment.Journal of clinical and translational science,
2023Betina Idnay, Yilu Fang, Alex Butler, Joyce Moran, Ziran Li, Junghwan Lee, Casey Ta, Cong Liu, Chi Yuan, Huanyao Chen, Edward Stanley, George Hripcsak, Elaine Larson, Karen Marder, Wendy Chung, Brenda Ruotolo, Chunhua Weng
Clinical Trial Recruitment
Accrual Prediction
Machine Learning Models
Funding Impact
Participant Compensation
Evaluating large language models on medical evidence summarization.NPJ digital medicine,
2023Liyan Tang, Zhaoyi Sun, Betina Idnay, Jordan G Nestor, Ali Soroush, Pierre A Elias, Ziyang Xu, Ying Ding, Greg Durrett, Justin F Rousseau, Chunhua Weng, Yifan Peng
Large Language Models
Medical Evidence Summarization
Zero-Shot Evaluation
Factual Consistency
Clinical Domain Summaries
The suitability of UMLS and SNOMED-CT for encoding outcome concepts.Journal of the American Medical Informatics Association : JAMIA,
2023Abigail Newbury, Hao Liu, Betina Idnay, Chunhua Weng
Outcome Concept Mapping
Umls Coverage
SNOMED-CT Coverage
Metamap Evaluation
RCT Abstract Annotation
Strong protective effect of the.medRxiv : the preprint server for health sciences,
2023Yask Gupta, David J Friedman, Michelle McNulty, Atlas Khan, Brandon Lane, Chen Wang, Juntao Ke, Gina Jin, Benjamin Wooden, Andrea L Knob, Tze Y Lim, Gerald B Appel, Kinsie Huggins, Lili Liu, Adele Mitrotti, Megan C Stangl, Andrew Bomback, Rik Westland, Monica Bodria, Maddalena Marasa, Ning Shang, David J Cohen, Russell J Crew, William Morello, Pietro Canetta, Jai Radhakrishnan, Jeremiah Martino, Qingxue Liu, Wendy K Chung, Angelica Espinoza, Yuan Luo, Wei-Qi Wei, Qiping Feng, Chunhua Weng, Yilu Fang, Iftikhar J Kullo, Mohammadreza Naderian, Nita Limdi, Marguerite R Irvin, Hemant Tiwari, Sumit Mohan, Maya Rao, Geoffrey Dube, Ninad S Chaudhary, Orlando M Gutiérrez, Suzanne E Judd, Mary Cushman, Leslie A Lange, Ethan M Lange, Daniel L Bivona, Miguel Verbitsky, Cheryl A Winkler, Jeffrey B Kopp, Dominick Santoriello, Ibrahim Batal, Sérgio Veloso Brant Pinheiro, Eduardo Araújo Oliveira, Ana Cristina Simoes E Silva, Isabella Pisani, Enrico Fiaccadori, Fangming Lin, Loreto Gesualdo, Antonio Amoroso, Gian Marco Ghiggeri, Vivette D D'Agati, Riccardo Magistroni, Eimear E Kenny, Ruth J F Loos, Giovanni Montini, Friedhelm Hildebrandt, Dirk S Paul, Slavé Petrovski, David B Goldstein, Matthias Kretzler, Rasheed Gbadegesin, Ali G Gharavi, Krzysztof Kiryluk, Matthew G Sampson, Martin R Pollak, Simone Sanna-Cherchi
CKD Risk Disparities
FSGS Genetic Link
G1 G2 Variant Effects
Black Americans CKD Risk
Natural Language Processing Can Automate Extraction of Barrett's Esophagus Endoscopy Quality Metrics.medRxiv : the preprint server for health sciences,
2023Ali Soroush, Courtney J Diamond, Haley M Zylberberg, Benjamin May, Nicholas Tatonetti, Julian A Abrams, Chunhua Weng
Barrett's Esophagus
Endoscopy Quality Metrics
NLP Extraction
EHR Data Mining
Endoscopic Eradication Therapy
Principal Investigators' Perceptions on Factors Associated with Successful Recruitment in Clinical Trials.AMIA Joint Summits on Translational Science proceedings. AMIA Joint Summits on Translational Science,
2023Betina Idnay, Alex Butler, Yilu Fang, Ziran Li, Junghwan Lee, Casey Ta, Cong Liu, Brenda Ruotolo, Chi Yuan, Huanyao Chen, George Hripcsak, Elaine Larson, Chunhua Weng
Clinical Trial Recruitment
Principal Investigator Perspective
Informatics-Driven Recruitment
Study Design Impact
Staff Support Strategies
Hierarchical Concept Relations Improve Detection of Off-Label Drug Use in Electronic Health Records Data.AMIA Joint Summits on Translational Science proceedings. AMIA Joint Summits on Translational Science,
2023Kayla Schiffer, Yoolim A Choi, Chunhua Weng
Off-Label Drug Detection
Electronic Health Records
Hierarchical Concept Mapping
Medication-Indication Knowledge Base
Real-World Evidence
Can Race-sensitive Biomedical Embeddings Improve Healthcare Predictive Models?.AMIA Joint Summits on Translational Science proceedings. AMIA Joint Summits on Translational Science,
2023Hao Liu, Nour Moustafa-Fahmy, Casey Ta, Chunhua Weng
Race-Sensitive Embeddings
Clinical Trial Weighting
Length of Stay Prediction
ICU Readmission Modeling
EHR Embedding Evaluation
Selection, optimization, and validation of ten chronic disease polygenic risk scores for clinical implementation in diverse populations.medRxiv : the preprint server for health sciences,
2023Niall J Lennon, Leah C Kottyan, Christopher Kachulis, Noura Abul-Husn, Josh Arias, Gillian Belbin, Jennifer E Below, Sonja Berndt, Wendy Chung, James J Cimino, Ellen Wright Clayton, John J Connolly, David Crosslin, Ozan Dikilitas, Digna R Velez Edwards, QiPing Feng, Marissa Fisher, Robert Freimuth, Tian Ge, GIANT Consortium, All of Us Research Program, Joseph T Glessner, Adam Gordon, Candace Guiducci, Hakon Hakonarson, Maegan Harden, Margaret Harr, Joel Hirschhorn, Clive Hoggart, Li Hsu, Ryan Irvin, Gail P Jarvik, Elizabeth W Karlson, Atlas Khan, Amit Khera, Krzysztof Kiryluk, Iftikhar Kullo, Katie Larkin, Nita Limdi, Jodell E Linder, Ruth Loos, Yuan Luo, Edyta Malolepsza, Teri Manolio, Lisa J Martin, Li McCarthy, James B Meigs, Tesfaye B Mersha, Jonathan Mosley, Bahram Namjou, Nihal Pai, Lorenzo L Pesce, Ulrike Peters, Josh Peterson, Cynthia A Prows, Megan J Puckelwartz, Heidi Rehm, Dan Roden, Elisabeth A Rosenthal, Robb Rowley, Konrad Teodor Sawicki, Dan Schaid, Tara Schmidlen, Roelof Smit, Johanna Smith, Jordan W Smoller, Minta Thomas, Hemant Tiwari, Diana Toledo, Nataraja Sarma Vaitinadin, David Veenstra, Theresa Walunas, Zhe Wang, Wei-Qi Wei, Chunhua Weng, Georgia Wiesner, Yin Xianyong, Eimear Kenny
Polygenic Risk Scores
Chronic Disease
Population Diversity
Genetic Ancestry Calibration
Clinical Implementation
AI-generated text may have a role in evidence-based medicine.Nature medicine,
2023Yifan Peng, Justin F Rousseau, Edward H Shortliffe, Chunhua Weng
AI-Generated Text
Evidence-Based Medicine
Literature Retrieval
Epistemological Ranking
Social Media Evidence
Polygenic risk affects the penetrance of monogenic kidney disease.medRxiv : the preprint server for health sciences,
2023Atlas Khan, Ning Shang, Jordan G Nestor, Chunhua Weng, George Hripcsak, Peter C Harris, Ali G Gharavi, Krzysztof Kiryluk
Polygenic Risk Score
Monogenic Kidney Disease
Adpkd
Col4a Nephropathy
Penetrance Variability
A Model for Multi-Institutional Clinical Data Repository.Studies in health technology and informatics,
2023Karthik Natarajan, Chunhua Weng, Soumitra Sengupta
Clinical Data Repository
Fair Data Principles
Data Governance
Sustainable Infrastructure
Multi-Institutional Collaboration
How Good Is ChatGPT for Medication Evidence Synthesis?.Studies in health technology and informatics,
2023Hao Liu, Yifan Peng, Chunhua Weng
Chatgpt
Medication Evidence Synthesis
Hybrid Summarization
Drugbank
AI Clinical Review
A metadata framework for computational phenotypes.JAMIA open,
2023Matthew Spotnitz, Nripendra Acharya, James J Cimino, Shawn Murphy, Bahram Namjou, Nancy Crimmins, Theresa Walunas, Cong Liu, David Crosslin, Barbara Benoit, Elisabeth Rosenthal, Jennifer A Pacheco, Anna Ostropolets, Harry Reyes Nieva, Jason S Patterson, Lauren R Richter, Tiffany J Callahan, Ahmed Elhussein, Chao Pang, Krzysztof Kiryluk, Jordan Nestor, Atlas Khan, Sumit Mohan, Evan Minty, Wendy Chung, Wei-Qi Wei, Karthik Natarajan, Chunhua Weng
Computational Phenotyping
Metadata Framework
Phenotype Retrieval
Validation Metrics
Data Standards Compliance
Evaluating Large Language Models on Medical Evidence Summarization.medRxiv : the preprint server for health sciences,
2023Liyan Tang, Zhaoyi Sun, Betina Idnay, Jordan G Nestor, Ali Soroush, Pierre A Elias, Ziyang Xu, Ying Ding, Greg Durrett, Justin Rousseau, Chunhua Weng, Yifan Peng
Large Language Models
Medical Evidence Summarization
Zero-Shot Evaluation
Factually Inconsistent Errors
Clinical Domain Summaries
A data-driven approach to optimizing clinical study eligibility criteria.Journal of biomedical informatics,
2023Yilu Fang, Hao Liu, Betina Idnay, Casey Ta, Karen Marder, Chunhua Weng
Clinical Trial Eligibility
Data-Driven Criteria Optimization
Multi-Attribute Decision Making
Mimic-Iii Dataset
Algorithmic Cohort Selection
Evidence of epistasis in regions of long-range linkage disequilibrium across five complex diseases in the UK Biobank and eMERGE datasets.American journal of human genetics,
2023Pankhuri Singhal, Yogasudha Veturi, Scott M Dudek, Anastasia Lucas, Alex Frase, Kristel van Steen, Steven J Schrodi, David Fasel, Chunhua Weng, Rion Pendergrass, Daniel J Schaid, Iftikhar J Kullo, Ozan Dikilitas, Patrick M A Sleiman, Hakon Hakonarson, Jason H Moore, Scott M Williams, Marylyn D Ritchie, Shefali S Verma
Epistasis Detection
Long-Range Ld
Complex Disease GWAS
Pleiotropy
Conserved Gene Families
EvidenceMap: a three-level knowledge representation for medical evidence computation and comprehension.Journal of the American Medical Informatics Association : JAMIA,
2023Tian Kang, Yingcheng Sun, Jae Hyun Kim, Casey Ta, Adler Perotte, Kayla Schiffer, Mutong Wu, Yang Zhao, Nour Moustafa-Fahmy, Yifan Peng, Chunhua Weng
Computable Medical Evidence
RCT Abstract Annotation
NLP Clinical Trials
Evidence Mapping Framework
Interoperable Evidence Representation
Inference of Causal Relationships Between Genetic Risk Factors for Cardiometabolic Phenotypes and Female-Specific Health Conditions.Journal of the American Heart Association,
2023Brenda Xiao, Digna R Velez Edwards, Anastasia Lucas, Theodore Drivas, Kathryn Gray, Brendan Keating, Chunhua Weng, Gail P Jarvik, Hakon Hakonarson, Leah Kottyan, Noemie Elhadad, Wei-Qi Wei, Yuan Luo, Dokyoon Kim, Marylyn Ritchie, Shefali Setia Verma, Regeneron Genetics Center *
Polygenic Risk Scores
Mendelian Randomization
Cardiometabolic Genetics
Female-Specific Health
Genetic Correlation
Author Correction: Genetic regulation of serum IgA levels and susceptibility to common immune, infectious, kidney, and cardio-metabolic traits.Nature communications,
2023Lili Liu, Atlas Khan, Elena Sanchez-Rodriguez, Francesca Zanoni, Yifu Li, Nicholas Steers, Olivia Balderes, Junying Zhang, Priya Krithivasan, Robert A LeDesma, Clara Fischman, Scott J Hebbring, John B Harley, Halima Moncrieffe, Leah C Kottyan, Bahram Namjou-Khales, Theresa L Walunas, Rachel Knevel, Soumya Raychaudhuri, Elizabeth W Karlson, Joshua C Denny, Ian B Stanaway, David Crosslin, Thomas Rauen, Jürgen Floege, Frank Eitner, Zina Moldoveanu, Colin Reily, Barbora Knoppova, Stacy Hall, Justin T Sheff, Bruce A Julian, Robert J Wyatt, Hitoshi Suzuki, Jingyuan Xie, Nan Chen, Xujie Zhou, Hong Zhang, Lennart Hammarström, Alexander Viktorin, Patrik K E Magnusson, Ning Shang, George Hripcsak, Chunhua Weng, Tatjana Rundek, Mitchell S V Elkind, Elizabeth C Oelsner, R Graham Barr, Iuliana Ionita-Laza, Jan Novak, Ali G Gharavi, Krzysztof Kiryluk
Serum IGA
Genetic Regulation
GWAS
Kidney Disease
Cardio-Metabolic Risk
Evaluation of the portability of computable phenotypes with natural language processing in the eMERGE network.Scientific reports,
2023Jennifer A Pacheco, Luke V Rasmussen, Ken Wiley, Thomas Nate Person, David J Cronkite, Sunghwan Sohn, Shawn Murphy, Justin H Gundelach, Vivian Gainer, Victor M Castro, Cong Liu, Frank Mentch, Todd Lingren, Agnes S Sundaresan, Garrett Eickelberg, Valerie Willis, Al'ona Furmanchuk, Roshan Patel, David S Carrell, Yu Deng, Nephi Walton, Benjamin A Satterfield, Iftikhar J Kullo, Ozan Dikilitas, Joshua C Smith, Josh F Peterson, Ning Shang, Krzysztof Kiryluk, Yizhao Ni, Yikuan Li, Girish N Nadkarni, Elisabeth A Rosenthal, Theresa L Walunas, Marc S Williams, Elizabeth W Karlson, Jodell E Linder, Yuan Luo, Chunhua Weng, WeiQi Wei
NLP-Enhanced Phenotyping
Electronic Health Records
Algorithm Portability
Emerge Network
Clinical Document Heterogeneity
Clinical research staff perceptions on a natural language processing-driven tool for eligibility prescreening: An iterative usability assessment.International journal of medical informatics,
2023Betina Idnay, Yilu Fang, Caitlin Dreisbach, Karen Marder, Chunhua Weng, Rebecca Schnall
Natural Language Processing
Eligibility Prescreening
Clinical Research Recruitment
Usability Evaluation
Iterative Design
Returning integrated genomic risk and clinical recommendations: The eMERGE study.Genetics in medicine : official journal of the American College of Medical Genetics,
2023Jodell E Linder, Aimee Allworth, Harris T Bland, Pedro J Caraballo, Rex L Chisholm, Ellen Wright Clayton, David R Crosslin, Ozan Dikilitas, Alanna DiVietro, Edward D Esplin, Sophie Forman, Robert R Freimuth, Adam S Gordon, Richard Green, Maegan V Harden, Ingrid A Holm, Gail P Jarvik, Elizabeth W Karlson, Sofia Labrecque, Niall J Lennon, Nita A Limdi, Kathleen F Mittendorf, Shawn N Murphy, Lori Orlando, Cynthia A Prows, Luke V Rasmussen, Laura Rasmussen-Torvik, Robb Rowley, Konrad Teodor Sawicki, Tara Schmidlen, Shannon Terek, David Veenstra, Digna R Velez Edwards, Devin Absher, Noura S Abul-Husn, Jorge Alsip, Hana Bangash, Mark Beasley, Jennifer E Below, Eta S Berner, James Booth, Wendy K Chung, James J Cimino, John Connolly, Patrick Davis, Beth Devine, Stephanie M Fullerton, Candace Guiducci, Melissa L Habrat, Heather Hain, Hakon Hakonarson, Margaret Harr, Eden Haverfield, Valentina Hernandez, Christin Hoell, Martha Horike-Pyne, George Hripcsak, Marguerite R Irvin, Christopher Kachulis, Dean Karavite, Eimear E Kenny, Atlas Khan, Krzysztof Kiryluk, Bruce Korf, Leah Kottyan, Iftikhar J Kullo, Katie Larkin, Cong Liu, Edyta Malolepsza, Teri A Manolio, Thomas May, Elizabeth M McNally, Frank Mentch, Alexandra Miller, Sean D Mooney, Priyanka Murali, Brenda Mutai, Naveen Muthu, Bahram Namjou, Emma F Perez, Megan J Puckelwartz, Tejinder Rakhra-Burris, Dan M Roden, Elisabeth A Rosenthal, Seyedmohammad Saadatagah, Maya Sabatello, Dan J Schaid, Baergen Schultz, Lynn Seabolt, Gabriel Q Shaibi, Richard R Sharp, Brian Shirts, Maureen E Smith, Jordan W Smoller, Rene Sterling, Sabrina A Suckiel, Jeritt Thayer, Hemant K Tiwari, Susan B Trinidad, Theresa Walunas, Wei-Qi Wei, Quinn S Wells, Chunhua Weng, Georgia L Wiesner, Ken Wiley, eMERGE Consortium, Josh F Peterson
Integrated Genomic Risk Assessment
Polygenic Risk Scores
Monogenic Disease Risk
Emerge Study
Clinical Decision Support
Characterizing variability of electronic health record-driven phenotype definitions.Journal of the American Medical Informatics Association : JAMIA,
2023Pascal S Brandt, Abel Kho, Yuan Luo, Jennifer A Pacheco, Theresa L Walunas, Hakon Hakonarson, George Hripcsak, Cong Liu, Ning Shang, Chunhua Weng, Nephi Walton, David S Carrell, Paul K Crane, Eric B Larson, Christopher G Chute, Iftikhar J Kullo, Robert Carroll, Josh Denny, Andrea Ramirez, Wei-Qi Wei, Jyoti Pathak, Laura K Wiley, Rachel Richesson, Justin B Starren, Luke V Rasmussen
Electronic Health Record Phenotypes
FHIR Cql
Logical Expression Variability
Computable Phenotype Representation
Standard Terminology Usage
Genomic Disorders in CKD across the Lifespan.Journal of the American Society of Nephrology : JASN,
2023Miguel Verbitsky, Sarathbabu Krishnamurthy, Priya Krithivasan, Daniel Hughes, Atlas Khan, Maddalena Marasà, Natalie Vena, Pavan Khosla, Junying Zhang, Tze Y Lim, Joseph T Glessner, Chunhua Weng, Ning Shang, Yufeng Shen, George Hripcsak, Hakon Hakonarson, Iuliana Ionita-Laza, Brynn Levy, Eimear E Kenny, Ruth J F Loos, Krzysztof Kiryluk, Simone Sanna-Cherchi, David R Crosslin, Susan Furth, Bradley A Warady, Robert P Igo, Sudha K Iyengar, Craig S Wong, Afshin Parsa, Harold I Feldman, Ali G Gharavi
Genomic Disorders
Chronic Kidney Disease
Phenome-Wide Association
Structural Variants
Neuropsychiatric Comorbidity
Clinical and temporal characterization of COVID-19 subgroups using patient vector embeddings of electronic health records.Journal of the American Medical Informatics Association : JAMIA,
2023Casey N Ta, Jason E Zucker, Po-Hsiang Chiu, Yilu Fang, Karthik Natarajan, Chunhua Weng
COVID-19 Subphenotypes
EHR Vector Embeddings
Temporal Disease Trajectory
K-Means Clustering
Clinical Phenotyping
Multimodal Machine Learning Combining Facial Images and Clinical Texts Improves Diagnosis of Rare Genetic Diseases.arXiv,
2023Da Wu, Jingye Yang, Steven Klein, Cong Liu, Tzung-Chien Hsieh, Peter Krawitz, Chunhua Weng, Gholson J. Lyon, Jennifer M. Kalish, Kai Wang
Multimodal ML For Rare Diseases
NLP Clinical Texts
Facial Image Analysis
Genetic Disease Diagnosis
Polygenic risk alters the penetrance of monogenic kidney disease.Nature Communications,
2023Atlas Khan, Ning Shang, Jordan G. Nestor, Chunhua Weng, George Hripcsak, Peter C. Harris, Ali G. Gharavi & Krzysztof Kiryluk
Polygenic Risk Score
Penetrance Modifier Genes
Monogenic Kidney Disease
Genotype Phenotype Interaction
The suitability of UMLS and SNOMED-CT for encoding outcome concepts.Journal of the American Medical Informatics Association,
2023Abigail Newbury, Hao Liu, Betina Idnay, Chunhua Weng
UMLS And SNOMED-CT Suitability
Encoding Outcome Concepts
Clinical Ontology Mapping
Standardized Medical Terminologies
Strong protective effect of the APOL1 p.N264K variant against G2-associated focal segmental glomerulosclerosis and kidney disease.Nature Communications,
2023Yask Gupta, David J. Friedman, Michelle T. McNulty, Atlas Khan, Brandon Lane, Chen Wang, Juntao Ke, Gina Jin, Benjamin Wooden, Andrea L. Knob, Tze Y. Lim, Gerald B. Appel, Kinsie Huggins, Lili Liu, Adele Mitrotti, Megan C. Stangl, Andrew Bomback, Rik Westland, Monica Bodria, Maddalena Marasa, Ning Shang, David J. Cohen, Russell J. Crew, William Morello, Pietro Canetta, Jai Radhakrishnan, Jeremiah Martino, Qingxue Liu, Wendy K. Chung, Angelica Espinoza, Yuan Luo, Wei-Qi Wei, Qiping Feng, Chunhua Weng, Yilu Fang, Iftikhar J. Kullo, Mohammadreza Naderian, Nita Limdi, Marguerite R. Irvin, Hemant Tiwari, Sumit Mohan, Maya Rao, Geoffrey K. Dube, Ninad S. Chaudhary, Orlando M. Gutiérrez, Suzanne E. Judd, Mary Cushman, Leslie A. Lange, Ethan M. Lange, Daniel L. Bivona, Miguel Verbitsky, Cheryl A. Winkler, Jeffrey B. Kopp, Dominick Santoriello, Ibrahim Batal, Sérgio Veloso Brant Pinheiro, Eduardo Araújo Oliveira, Ana Cristina Simoes e Silva, Isabella Pisani, Enrico Fiaccadori, Fangming Lin, Loreto Gesualdo, Antonio Amoroso, Gian Marco Ghiggeri, Vivette D. D’Agati, Riccardo Magistroni, Eimear E. Kenny, Ruth J. F. Loos, Giovanni Montini, Friedhelm Hildebrandt, Dirk S. Paul, Slavé Petrovski, David B. Goldstein, Matthias Kretzler, Rasheed Gbadegesin, Ali G. Gharavi, Krzysztof Kiryluk, Matthew G. Sampson, Martin R. Pollak & Simone Sanna-Cherchi
APOL1 p.N264K Variant
G2 Associated FSGS
Kidney Disease Genomics
Nephrology Genetic Insight
Phenotype-Driven Molecular Genetic Test Recommendation for Diagnosing Pediatric Rare Disorders.Preprint,
2023Fangyi Chen, Priyanka Ahimaz, Kai Wang, Wendy K. Chung, Casey Ta, Chunhua Weng, and Cong Liu
Phenotype Driven Genetic Testing
Pediatric Rare Disorder Diagnosis
Molecular Genetic Test Recommendations
Diagnostic Precision Medicine
Genotype Phenotype Correlation
Prospective, multi-site study of healthcare utilization after actionable monogenic findings from clinical sequencing.The American Journal of Human Genetics,
2023Jodell E. Linder, Ran Tao, Wendy K. Chung, Krzysztof Kiryluk, Cong Liu, Chunhua Weng, John J. Connolly, Hakon Hakonarson, Margaret Harr, Kathleen A. Leppig, Gail P. Jarvik, David L. Veenstra, Sharon Aufox, Rex L. Chisholm, Adam S. Gordon, Christin Hoell, Laura J. Rasmussen-Torvik, Maureen E. Smith, Ingrid A. Holm, Erin M. Miller, Cynthia A. Prows, Omar Elskeally, Iftikhar J. Kullo, Christopher Lee, Sheethal Jose, Teri A. Manolio, Robb Rowley, Nana Addo Padi-Adjirackor, Ni Ketut Wilmayani, Brittany City, Wei-Qi Wei, Georgia L. Wiesner, Alanna Kulchak Rahm, Janet L. Williams, Marc S. Williams, Josh F. Peterson
Actionable Monogenic Findings
Multi-Site Prospective Study
Genomic Medicine In Healthcare
Healthcare Utilization After Genomic Findings
Evaluating large language models on medical evidence summarization.npj Digital Medicine,
2023Liyan Tang, Zhaoyi Sun, Betina Idnay, Jordan G. Nestor, Ali Soroush, Pierre A. Elias, Ziyang Xu, Ying Ding, Greg Durrett, Justin F. Rousseau, Chunhua Weng, Yifan Peng
Evaluating Large Language Models
Medical Evidence Summarization
Clinical NLP Evaluation
Healthcare AI Assessment
Large Language Models for Granularized Barrett's Esophagus Diagnosis Classification.arXiv,
2023Jenna Kefeli, Ali Soroush, Courtney J. Diamond, Haley M. Zylberberg, Benjamin May, Julian A. Abrams, Chunhua Weng, Nicholas Tatonetti
LLM Based Barrett's Diagnosis
Barrett's Esophagus Classification
Granularized Diagnosis Classification
NLP For EHR Insights
Natural Language Processing Can Automate Extraction of Barrett’s Esophagus Endoscopy Quality Metrics.medRxiv,
2023Ali Soroush, Courtney J Diamond, Haley M Zylberberg, Benjamin May, Nicholas Tatonetti, Julian A Abrams, Chunhua Weng
NLP For Barrett's Esophagus
Automated Extraction Of Endoscopy Metrics
Endoscopy Quality Metrics
Clinical NLP In GI
AI-generated text may have a role in evidence-based medicine.Nature medicine,
2023Yifan Peng, Justin F Rousseau, Edward H Shortliffe, Chunhua Weng
AI Generated Text
Evidence Based Medicine
Role Of AI In EBM
NLP For Evidence Synthesis
A metadata framework for computational phenotypes.JAMIA open,
2023Matthew Spotnitz, Nripendra Acharya, James J Cimino, Shawn Murphy, Bahram Namjou, Nancy Crimmins, Theresa Walunas, Cong Liu, David Crosslin, Barbara Benoit, Elisabeth Rosenthal, Jennifer A Pacheco, Anna Ostropolets, Harry Reyes Nieva, Jason S Patterson, Lauren R Richter, Tiffany J Callahan, Ahmed Elhussein, Chao Pang, Krzysztof Kiryluk, Jordan Nestor, Atlas Khan, Sumit Mohan, Evan Minty, Wendy Chung, Wei-Qi Wei, Karthik Natarajan, Chunhua Weng
Computational Phenotypes Metadata
Metadata Framework For Phenotypes
Phenotype Algorithm Metadata
EHR Data Integration
Informatics approaches to participant recruitment.Clinical Research Informatics,
2023Chunhua Weng, Peter J Embi
NLP Assisted Recruitment
EHR Based Recruitment
AI Driven Recruitment
Participant Recruitment Informatics
A data-driven approach to optimizing clinical study eligibility criteria.Journal of Biomedical Informatics,
2023Yilu Fang, Hao Liu, Betina Idnay, Casey Ta, Karen Marder, Chunhua Weng
Clinical Trial Eligibility
Eligibility Criteria Optimization
Data Driven Optimization
Data Driven Study Design
EvidenceMap: a three-level knowledge representation for medical evidence computation and comprehension.Journal of the American Medical Informatics Association,
2023Tian Kang, Yingcheng Sun, Jae Hyun Kim, Casey Ta, Adler Perotte, Kayla Schiffer, Mutong Wu, Yang Zhao, Nour Moustafa-Fahmy, Yifan Peng, Chunhua Weng
Evidence Map
Three Level Knowledge Representation
Medical Evidence Computation
Knowledge Representation In Medicine
Polygenic risk affects the penetrance of monogenic kidney disease.medRxiv,
2023Atlas Khan, Ning Shang, Jordan G Nestor, Chunhua Weng, George Hripcsak, Peter C Harris, Ali G Gharavi, Krzysztof Kiryluk
Polygenic Risk And Penetrance
Monogenic Kidney Disease
Genetic Architecture Of Kidney Disease
Genetic Modifiers In Kidney Disease
How Good Is ChatGPT for Medication Evidence Synthesis?.MIE,
2023Hao Liu, Yifan Peng, Chunhua Weng
ChatGPT For Medication Evidence Synthesis
AI Enhanced Evidence Synthesis
NLP For Medication Evidence
LLM In Healthcare Evidence
A Model for Multi-Institutional Clinical Data Repository.MIE,
2023Karthik Natarajan, Chunhua Weng, Soumitra Sengupta
Multi-Institutional Data Repository
EHR Data Sharing
Health Data Interoperability
FHIR Based Integration
Clinical Data Standardization
Returning integrated genomic risk and clinical recommendations: The eMERGE study.Genetics in Medicine,
2023Jodell E Linder, Aimee Allworth, Harris T Bland, Pedro J Caraballo, Rex L Chisholm, Ellen Wright Clayton, David R Crosslin, Ozan Dikilitas, Alanna DiVietro, Edward D Esplin, Sophie Forman, Robert R Freimuth, Adam S Gordon, Richard Green, Maegan V Harden, Ingrid A Holm, Gail P Jarvik, Elizabeth W Karlson, Sofia Labrecque, Niall J Lennon, Nita A Limdi, Kathleen F Mittendorf, Shawn N Murphy, Lori Orlando, Cynthia A Prows, Luke V Rasmussen, Laura Rasmussen-Torvik, Robb Rowley, Konrad Teodor Sawicki, Tara Schmidlen, Shannon Terek, David Veenstra, Digna R Velez Edwards, Devin Absher, Noura S Abul-Husn, Jorge Alsip, Hana Bangash, Mark Beasley, Jennifer E Below, Eta S Berner, James Booth, Wendy K Chung, James J Cimino, John Connolly, Patrick Davis, Beth Devine, Stephanie M Fullerton, Candace Guiducci, Melissa L Habrat, Heather Hain, Hakon Hakonarson, Margaret Harr, Eden Haverfield, Valentina Hernandez, Christin Hoell, Martha Horike-Pyne, George Hripcsak, Marguerite R Irvin, Christopher Kachulis, Dean Karavite, Eimear E Kenny, Atlas Khan, Krzysztof Kiryluk, Bruce Korf, Leah Kottyan, Iftikhar J Kullo, Katie Larkin, Cong Liu, Edyta Malolepsza, Teri A Manolio, Thomas May, Elizabeth M McNally, Frank Mentch, Alexandra Miller, Sean D Mooney, Priyanka Murali, Brenda Mutai, Naveen Muthu, Bahram Namjou, Emma F Perez, Megan J Puckelwartz, Tejinder Rakhra-Burris, Dan M Roden, Elisabeth A Rosenthal, Seyedmohammad Saadatagah, Maya Sabatello, Dan J Schaid, Baergen Schultz, Lynn Seabolt, Gabriel Q Shaibi, Richard R Sharp, Brian Shirts, Maureen E Smith, Jordan W Smoller, Rene Sterling, Sabrina A Suckiel, Jeritt Thayer, Hemant K Tiwari, Susan B Trinidad, Theresa Walunas, Wei-Qi Wei, Quinn S Wells, Chunhua Weng, Georgia L Wiesner, Ken Wiley, Adam Gordon, Agboade Sobowale, Akshar Patel, Alanna Strong, Alborz Sherafati, Alborz Sherfati, Alex Bick, Alka Chandel, Alyssa Rosenthal, Amit Khera, Amy Kontorovich, Andrew Beck, Andy Beck, Angelica Espinoza, Anna Lewis, Anya Prince, Ayuko Iverson, Bahram Namjou Khales, Barbara Benoit, Becca Hernan, Ben Kallman, Ben Kerman, Ben Shoemaker, Benjamin Satterfield, Bethany Etheridge, Blake Goff, Bob Freimuth, Bob Grundmeier, Brenae Collier, Brett Harnett, Brian Chang, Brian Piening, Brittney Davis, Candace Patterson, Carmen Demetriou, Casey Ta, Catherine Hammack, Catrina Nelson, Caytie Gascoigne, Chad Dorn, Chad Moretz, Chris Kachulis, Christie Hoell, Christine Cowles, Christoph Lange
Integrated Genomic Risk
Clinical Genomic Recommendations
eMERGE Study
EHR Based Genomic Integration
Precision Medicine Implementation
Characterizing variability of electronic health record-driven phenotype definitions.Journal of the American Medical Informatics Association,
2023Pascal S Brandt, Abel Kho, Yuan Luo, Jennifer A Pacheco, Theresa L Walunas, Hakon Hakonarson, George Hripcsak, Cong Liu, Ning Shang, Chunhua Weng, Nephi Walton, David S Carrell, Paul K Crane, Eric B Larson, Christopher G Chute, Iftikhar J Kullo, Robert Carroll, Josh Denny, Andrea Ramirez, Wei-Qi Wei, Jyoti Pathak, Laura K Wiley, Rachel Richesson, Justin B Starren, Luke V Rasmussen
EHR Driven Phenotype Definitions
Phenotype Definition Variability
Electronic Health Records
FHIR Based Phenotyping
Clinical research staff perceptions on a natural language processing-driven tool for eligibility prescreening: An iterative usability assessment.International journal of medical informatics,
2023Betina Idnay, Yilu Fang, Caitlin Dreisbach, Karen Marder, Chunhua Weng, Rebecca Schnall
NLP Driven Eligibility
Eligibility Prescreening Usability
Clinical Research Staff
Iterative Usability Assessment
Genetic regulation of serum IgA levels and susceptibility to common immune, infectious, kidney, and cardio-metabolic traits.Nature Communications,
2023Lili Liu, Atlas Khan, Elena Sanchez-Rodriguez, Francesca Zanoni, Yifu Li, Nicholas Steers, Olivia Balderes, Junying Zhang, Priya Krithivasan, Robert A LeDesma, Clara Fischman, Scott J Hebbring, John B Harley, Halima Moncrieffe, Leah C Kottyan, Bahram Namjou-Khales, Theresa L Walunas, Rachel Knevel, Soumya Raychaudhuri, Elizabeth W Karlson, Joshua C Denny, Ian B Stanaway, David Crosslin, Thomas Rauen, Juergen Floege, Frank Eitner, Zina Moldoveanu, Colin Reily, Barbora Knoppova, Stacy Hall, Justin T Sheff, Bruce A Julian, Robert J Wyatt, Hitoshi Suzuki, Jingyuan Xie, Nan Chen, Xujie Zhou, Hong Zhang, Lennart Hammarstroem, Alexander Viktorin, Patrik KE Magnusson, Ning Shang, George Hripcsak, Chunhua Weng, Tatjana Rundek, Mitchell SV Elkind, Elizabeth C Oelsner, R Graham Barr, Iuliana Ionita-Laza, Jan Novak, Ali G Gharavi, Krzysztof Kiryluk
IgA Serum Levels
GWAS Of IgA Regulation
Immune And Kidney Traits
Cardio Metabolic Susceptibility
Evaluation of the portability of computable phenotypes with natural language processing in the eMERGE network.Scientific reports,
2023Jennifer A Pacheco, Luke V Rasmussen, Ken Wiley Jr, Thomas Nate Person, David J Cronkite, Sunghwan Sohn, Shawn Murphy, Justin H Gundelach, Vivian Gainer, Victor M Castro, Cong Liu, Frank Mentch, Todd Lingren, Agnes S Sundaresan, Garrett Eickelberg, Valerie Willis, Al’ona Furmanchuk, Roshan Patel, David S Carrell, Yu Deng, Nephi Walton, Benjamin A Satterfield, Iftikhar J Kullo, Ozan Dikilitas, Joshua C Smith, Josh F Peterson, Ning Shang, Krzysztof Kiryluk, Yizhao Ni, Yikuan Li, Girish N Nadkarni, Elisabeth A Rosenthal, Theresa L Walunas, Marc S Williams, Elizabeth W Karlson, Jodell E Linder, Yuan Luo, Chunhua Weng, WeiQi Wei
Computable Phenotypes Portability
NLP In EHR Phenotyping
eMERGE Network Evaluation
Interoperability With EHR Data
Clinical and temporal characterization of COVID-19 subgroups using patient vector embeddings of electronic health records.Journal of the American Medical Informatics Association,
2023Casey N Ta, Jason E Zucker, Po-Hsiang Chiu, Yilu Fang, Karthik Natarajan, Chunhua Weng
COVID-19 Subgroups
EHR Based Embeddings
Temporal Analysis
Clinical Phenotyping
Fine-tuning Large Language Models for Rare Disease Concept Normalization.bioRxiv,
2023Andy Wang, Cong Liu, Jingye Yang, Chunhua Weng
LLM Fine-Tuning For Rare Diseases
Rare Disease Concept Normalization
Biomedical NLP For Rare Diseases
EHR Based Normalization
Uncovering key clinical trial features influencing recruitment.Journal of Clinical and Translational Science,
2023Betina Idnay, Yilu Fang, Alex Butler, Joyce Moran, Ziran Li, Junghwan Lee, Casey Ta, Cong Liu, Chi Yuan, Huanyao Chen, Edward Stanley, George Hripcsak, Elaine Larson, Karen Marder, Wendy Chung, Brenda Ruotolo, Chunhua Weng
Clinical Trial Recruitment
Key Features Influencing Recruitment
Trial Enrollment Factors
Recruitment Determinants
Principal Investigators’ Perceptions on Factors Associated with Successful Recruitment in Clinical Trials.AMIA Summits,
2023Betina Idnay, Alex Butler, Yilu Fang, Ziran Li, Junghwan Lee, Casey Ta, Cong Liu, Brenda Ruotolo, Chi Yuan, Huanyao Chen, George Hripcsak, Elaine Larson, Chunhua Weng
Clinical Trial Recruitment Factors
Investigators Perceptions On Recruitment
Enrollment Barriers In Trials
Strategies For Participant Enrollment
Hierarchical Concept Relations Improve Detection of Off-Label Drug Use in Electronic Health Records Data.AMIA Summits,
2023Kayla Schiffer, Yoolim A Choi, Chunhua Weng
Hierarchical Concept Relations
Off Label Drug Use
EHR Data Mining
Clinical NLP Approaches
Can Race-sensitive Biomedical Embeddings Improve Healthcare Predictive Models?.AMIA Summits,
2023Hao Liu, Nour Moustafa-Fahmy, Casey Ta, Chunhua Weng
Race Sensitive Biomedical Embeddings
Fairness In Healthcare AI
Clinical NLP For Prediction
EHR Based Predictive Modeling
Risk factors affecting polygenic score performance across diverse cohorts.medRxiv,
2023Daniel Hui, Scott Dudek, Krzysztof Kiryluk, Theresa L Walunas, Iftikhar J Kullo, Wei-Qi Wei, Hemant Tiwari, Josh F Peterson, Wendy K Chung, Brittney H Davis, Atlas Khan, Leah C Kottyan, Nita A Limdi, Qiping Feng, Megan J Puckelwartz, Chunhua Weng, Johanna L Smith, Elizabeth W Karlson, Gail Jarvik, Marylyn D Ritchie
Polygenic Score Performance
Diverse Cohort Representation
Cross-Ancestry GWAS Insights
Risk Factors Across Populations