Publications

Last Updated: 09/2022

2022


OARD: Open annotations for rare diseases and their phenotypes based on real-world data
The American Journal of Human Genetics, 2022
Cong Liu, Casey N. Ta, Jim M. Havrilla, Jordan G. Nestor, Matthew E. Spotnitz, Andrew S. Geneslaw, Yu Hu, Wendy K. Chung, Kai Wang, Chunhua Weng

Harmonization of Measurement Codes for Concept-Oriented Lab Data Retrieval
MEDINFO 2021, 2022
Matthew Spotnitz; Jason Patterson; Vojtech Huser; Chunhua Weng; Karthik Natarajan

Evaluation of Criteria2Query: Towards Augmented Intelligence for Cohort Identification
Studies in health technology and informatics, 2022
Cong Liu; Hao Liu; Casey Ta; James Roger; Alex Butler; Junghwan Lee; Jaehyun Kim; Ning Shang; Chunhua Weng

Biolink Model: A universal schema for knowledge graphs in clinical, biomedical, and translational science
Clinical and translational science, 2022
Deepak R. Unni; Sierra A. T. Moxon; Michael Bada; Matthew Brush; Richard Bruskiewich; J. Harry Caufield; Paul A. Clemons; Vlado Dancik; Michel Dumontier; Karamarie Fecho; Gustavo Glusman; Jennifer J. Hadlock; Nomi L. Harris; Arpita Joshi; Tim Putman; Guangrong Qin; Stephen A. Ramsey; Kent A. Shefchek; Harold Solbrig; Karthik Soman; Anne E. Thessen; Melissa A. Haendel; Chris Bizon; Christopher J. Mungall; Liliana Acevedo; Stanley C. Ahalt; John Alden; Ahmed Alkanaq; Nada Amin; Ricardo Avila; Jim Balhoff; Sergio E. Baranzini; Andrew Baumgartner; William Baumgartner; Basazin Belhu; MacKenzie Brandes; Namdi Brandon; Noel Burtt; William Byrd; Jackson Callaghan; Marco Alvarado Cano; Steven Carrell; Remzi Celebi; James Champion; Zhehuan Chen; Mei‐Jan Chen; Lawrence Chung; Kevin Cohen; Tom Conlin; Dan Corkill; Maria Costanzo; Steven Cox; Andrew Crouse; Camerron Crowder; Mary E. Crumbley; Cheng Dai; Vlado Dančík; Ricardo De Miranda Azevedo; Eric Deutsch; Jennifer Dougherty; Marc P. Duby; Venkata Duvvuri; Stephen Edwards; Vincent Emonet; Nathaniel Fehrmann; Jason Flannick; Aleksandra M. Foksinska; Vicki Gardner; Edgar Gatica; Amy Glen; Prateek Goel; Joseph Gormley; Alon Greyber; Perry Haaland; Kristina Hanspers; Kaiwen He; Kaiwen He; Jeff Henrickson; Eugene W. Hinderer; Maureen Hoatlin; Andrew Hoffman; Sui Huang; Conrad Huang; Robert Hubal; Kenneth Huellas‐Bruskiewicz; Forest B. Huls; Lawrence Hunter; Greg Hyde; Tursynay Issabekova; Matthew Jarrell; Lindsay Jenkins; Adam Johs; Jimin Kang; Richa Kanwar; Yaphet Kebede; Keum Joo Kim; Alexandria Kluge; Michael Knowles; Ryan Koesterer; Daniel Korn; David Koslicki; Ashok Krishnamurthy; Lindsey Kvarfordt; Jay Lee; Margaret Leigh; Jason Lin; Zheng Liu; Shaopeng Liu; Chunyu Ma; Andrew Magis; Tarun Mamidi; Meisha Mandal; Michelle Mantilla; Jeffrey Massung; Denise Mauldin; Jason McClelland; Julie McMurry; Philip Mease; Luis Mendoza; Marian Mersmann; Abrar Mesbah; Matthew Might; Kenny Morton; Sandrine Muller; Arun Teja Muluka; John Osborne; Phil Owen; Michael Patton; David B. Peden; R. Carter Peene; Bria Persaud; Emily Pfaff; Alexander Pico; Elizabeth Pollard; Guthrie Price; Shruti Raj; Jason Reilly; Anders Riutta; Jared Roach; Ryan T. Roper; Greg Rosenblatt; Irit Rubin; Sienna Rucka; Nathaniel Rudavsky‐Brody; Rayn Sakaguchi; Eugene Santos; Kevin Schaper; Charles P. Schmitt; Shepherd Schurman; Erik Scott; Sarah Seitanakis; Priya Sharma; Ilya Shmulevich; Manil Shrestha; Shalki Shrivastava; Meghamala Sinha; Brett Smith; Noel Southall; Nicholas Southern; Lisa Stillwell; Michael " Michi" Strasser; Andrew I. Su; Casey Ta; Anne E. Thessen; Jillian Tinglin; Lucas Tonstad; Thi Tran‐Nguyen; Alexander Tropsha; Gaurav Vaidya; Luke Veenhuis; Adam Viola; Marcin Grotthuss; Max Wang; Patrick Wang; Paul B. Watkins; Rosina Weber; Qi Wei; Chunhua Weng; Jordan Whitlock; Mark D. Williams; Andrew Williams; Finn Womack; Erica Wood; Chunlei Wu; Jiwen Kevin Xin; Hao Xu; Colleen Xu; Chase Yakaboski; Yao Yao; Hong Yi; Arif Yilmaz; Marissa Zheng; Xinghua Zhou; Eric Zhou; Qian Zhu; Tom Zisk; The Biomedical Data Translator Consortium

Towards Better Diagnosis Prediction Using Bidirectional Recurrent Neural Networks
Studies in health technology and informatics, 2022
Junghwan Lee; Cong Liu; Casey Ta; Chunhua Weng

Extending PICO with Observation Normalization for Evidence Computing
Studies in health technology and informatics, 2022
Ali Turfah; Hao Liu; Latoya A Stewart; Tian Kang; Chunhua Weng

Representation and Normalization of Complex Interventions for Evidence Computing
Studies in health technology and informatics, 2022
Zhehuan Chen; Hao Liu; Stan Liao; Marguerite Bernard; Tian Kang; Latoya A Stewart; Chunhua Weng

A Sample Size Extractor for RCT Reports
Studies in health technology and informatics, 2022
Fengyang Lin; Hao Liu; Paul Moon; Chunhua Weng

Interactive Similarity-Based Search of Clinical Trials
Studies in health technology and informatics, 2022
Yingcheng Sun; Jiaqi Tang; Alex Butler; Cong Liu; Yilu Fang; Chunhua Weng

Large-scale genomic analyses reveal insights into pleiotropy across circulatory system diseases and nervous system disorders
Nature Communications, 2022
Xinyuan Zhang; Anastasia M. Lucas; Yogasudha Veturi; Theodore G. Drivas, William P. Bone; Anurag Verma; Wendy K. Chung; David Crosslin; Joshua C. Denny; Scott Hebbring; Gail P. Jarvik; Iftikhar Kullo; Eric B. Larson; Laura J. Rasmussen-Torvik; Daniel J. Schaid; Jordan W. Smoller; Ian B. Stanaway; Wei-Qi Wei; Chunhua Weng; Marylyn D. Ritchie

Psychiatric manifestations of rare variation in medically actionable genes: a PheWAS approach
BMC genomics, 2022
Yen-Chen A Feng; Ian B Stanaway; John J Connolly; Joshua C Denny; Yuan Luo; Chunhua Weng; Wei-Qi Wei; Scott T Weiss; Elizabeth W Karlson; Jordan W Smoller

A systematic review on natural language processing systems for eligibility prescreening in clinical research
Journal of the American Medical Informatics Association, 2022
Betina Idnay; Caitlin Dreisbach; Chunhua Weng; Rebecca Schnall

Assessing socioeconomic bias in machine learning algorithms in health care: a case study of the HOUSES index
Journal of the American Medical Informatics Association, 2022
Young J Juhn; Euijung Ryu; Chung-Il Wi; Katherine S King; Momin Malik; Santiago Romero-Brufau; Chunhua Weng; Sunghwan Sohn; Richard R Sharp; John D Halamka

A research agenda to support the development and implementation of genomics-based clinical informatics tools and resources
Journal of the American Medical Informatics Association, 2022
Ken Wiley; Laura Findley; Madison Goldrich; Tejinder K Rakhra-Burris; Ana Stevens; Pamela Williams; Carol J Bult; Rex Chisholm; Patricia Deverka; Geoffrey S Ginsburg; Eric D Green; Gail Jarvik; George A Mensah; Erin Ramos; Mary V Relling; Dan M Roden; Robb Rowley; Gil Alterovitz; Samuel Aronson; Lisa Bastarache; James J Cimino; Erin L Crowgey; Guilherme Del Fiol; Robert R Freimuth; Mark A Hoffman; Janina Jeff; Kevin Johnson; Kensaku Kawamoto; Subha Madhavan; Eneida A Mendonca; Lucila Ohno-Machado; Siddharth Pratap; Casey Overby Taylor; Marylyn D Ritchie; Nephi Walton; Chunhua Weng; Teresa Zayas-Cabán; Teri A Manolio; Marc S Williams

A Retrospective Analysis of Risk Factors Associated with the SARS-CoV-2 Breakthrough in Fully mRNA Vaccinated Individuals.
JMIR Public Health and Surveillance, 2022
Cong Liu; Junghwan Lee; Casey Ta; Ali Soroush; James Rogers; Jae Hyun Kim; Karthik Natarajan; Jason Zucker; Yehoshua Perl; Chunhua Weng

Risk Factors Associated With SARS-CoV-2 Breakthrough Infections in Fully mRNA-Vaccinated Individuals: Retrospective Analysis
JMIR public health and surveillance, 2022
Cong Liu; Junghwan Lee; Casey Ta; Ali Soroush; James R Rogers; Jae Hyun Kim; Karthik Natarajan; Jason Zucker; Yehoshua Perl; Chunhua Weng

Association of Pathogenic Variants in Hereditary Cancer Genes With Multiple Diseases
JAMA oncology, 2022
Chenjie Zeng; Lisa A Bastarache; Ran Tao; Eric Venner; Scott Hebbring; Justin D Andujar; Sarah T Bland; David R Crosslin; Siddharth Pratap; Ayorinde Cooley; Jennifer A Pacheco; Kurt D Christensen; Emma Perez; Carrie L Blout Zawatsky; Leora Witkowski; Hana Zouk; Chunhua Weng; Kathleen A Leppig; Patrick M A Sleiman; Hakon Hakonarson; Marc S Williams; Yuan Luo; Gail P Jarvik; Robert C Green; Wendy K Chung; Ali G Gharavi; Niall J Lennon; Heidi L Rehm; Richard A Gibbs; Josh F Peterson; Dan M Roden; Georgia L Wiesner; Joshua C Denny

Combining human and machine intelligence for clinical trial eligibility querying
Journal of the American Medical Informatics Association, 2022
Yilu Fang; Betina Idnay; Yingcheng Sun; Hao Liu; Zhehuan Chen; Karen Marder; Hua Xu; Rebecca Schnall; Chunhua Weng

Under-specification as the source of ambiguity and vagueness in narrative phenotype algorithm definitions
BMC Medical Informatics and Decision Making, 2022
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 Mentch; Shawn N Murphy; Peggy L Peissig; Andrea H Ramirez; Nephi Walton; Wei-Qi Wei; Luke V Rasmussen

Polygenic risk vectors (PRV) improve genetic risk stratification for cardio-metabolic diseases
medRxiv, 2022
Ruowang Li; Xinyuan Zhang; Binglan Li; Qiping Feng; Leah Kottyan; Yuan Luo; Konrad Teodor Sawicki; Atlas Khan; Nita Limdi; Megan Puckelwartz; Wei-Qi Wei; Chunhua Weng; Yong Chen; Marylyn D. Ritchie; Jason H. Moore

Inference of causal relationships based on the genetics of cardiometabolic traits and conditions unique to females in> 50,000 participants
MedRxiv, 2022
Brenda Xiao; Digna R. Velez Edwards; Anastasia Lucas; Theodore Drivas; Kathryn Gray; Brendan Keating; Chunhua Weng; Gail P. Jarvik; Hakon Hakonarson; Leah Kottyan; Noemie Elhadad; Regeneron Genetics Center; Wei-Qi Wei; Yuan Luo; Dokyoon Kim; Marylyn Ritchie; Shefali Setia Verma

EHR-based cohort assessment for multicenter RCTs: a fast and flexible model for identifying potential study sites
Journal of the American Medical Informatics Association, 2022
Sarah J Nelson; Bethany Drury; Daniel Hood; Jeremy Harper; Tiffany Bernard; Chunhua Weng; Nan Kennedy; Bernie LaSalle; Ramkiran Gouripeddi; Consuelo H Wilkins; Paul Harris

Leveraging electronic health record data for clinical trial planning by assessing eligibility criteria’s impact on patient count and safety
Journal of Biomedical Informatics, 2022
James R Rogers; Jovana Pavisic; Casey N Ta; Cong Liu; Ali Soroush; Ying Kuen Cheung; George Hripcsak; Chunhua Weng

A machine learning approach to identifying delirium from electronic health records
JAMIA Open, 2022
Jae Hyun Kim; May Hua; Robert A Whittington; Junghwan Lee; Cong Liu; Casey N Ta; Edward R Marcantonio; Terry E Goldberg; Chunhua Weng

Inference of causal relationships between genetic risk factors for cardiometabolic phenotypes and female-specific health conditions
Preprint, 2022
Brenda 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

Data-Driven Modeling of Randomized Controlled Trial Outcomes
Studies in Health Technology and Informatics, 2022
Zhehuan Chen; Yilu Fang; Hao Liu; Chunhua Weng

Arrhythmia variant associations and reclassifications in the eMERGE-III sequencing study
Circulation, 2022
Andrew M Glazer; Giovanni Davogustto; Christian M Shaffer; Carlos G Vanoye; Reshma R Desai; Eric H Farber-Eger; Ozan Dikilitas; Ning Shang; Jennifer A Pacheco; Tao Yang; Ayesha Muhammad; Jonathan D Mosley; Sara L Van Driest; Quinn S Wells; Lauren Lee Shaffer; Olivia R Kalash; Yuko Wada; Sarah Bland; Zachary T Yoneda; Devyn W Mitchell; Brett M Kroncke; Iftikhar J Kullo; Gail P Jarvik; Adam S Gordon; Eric B Larson; Teri A Manolio; Tooraj Mirshahi; Jonathan Z Luo; Daniel Schaid; Bahram Namjou; Tarek Alsaied; Rajbir Singh; Ashutosh Singhal; Cong Liu; Chunhua Weng; George Hripcsak; James D Ralston; Elizabeth M McNally; Wendy K Chung; David S Carrell; Kathleen A Leppig; Hakon Hakonarson; Patrick Sleiman; Sunghwan Sohn; Joseph Glessner; eMERGE Network; Joshua Denny; Wei-Qi Wei; Alfred L George Jr; M Benjamin Shoemaker; Dan M Roden

2021


Genetic regulation of serum IgA levels and susceptibility to common immune, infectious, kidney, and cardio-metabolic traits
medRxiv, 2021
Lili 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

Generalizability of polygenic risk scores for breast cancer among women with European, African, and Latinx ancestry
JAMA Network Open, 2021
Cong Liu; Nur Zeinomar; Wendy K Chung; Krzysztof Kiryluk; Ali G Gharavi; George Hripcsak; Katherine D Crew; Ning Shang; Atlas Khan; David Fasel; Teri A Manolio; Gail P Jarvik; Robb Rowley; Ann E Justice; Alanna K Rahm; Stephanie M Fullerton; Jordan W Smoller; Eric B Larson; Paul K Crane; Ozan Dikilitas; Georgia L Wiesner; Alexander G Bick; Mary Beth Terry; Chunhua Weng

From clinical trials to clinical practice: How long are drugs tested and then used by patients?
Journal of the American Medical Informatics Association, 2021
Chi Yuan; Patrick B Ryan; Casey N Ta; Jae Hyun Kim; Ziran Li; Chunhua Weng

A Comparison between Human and NLP-based Annotation of Clinical Trial Eligibility Criteria Text Using The OMOP Common Data Model
AMIA Annual Symposium Proceedings, 2021
Xinhang Li; Hao Liu; Fabrício Kury; Chi Yuan; Alex Butler; Yingcheng Sun; Anna Ostropolets; Hua Xu; Chunhua Weng

A framework for systematic assessment of clinical trial population representativeness using electronic health records data
Applied Clinical Informatics, 2021
Yingcheng Sun; Alex Butler; Ibrahim Diallo; Jae Hyun Kim; Casey Ta; James R Rogers; Hao Liu; Chunhua Weng

Natural language processing to identify lupus nephritis phenotype in electronic health records
arXiv preprint arXiv:2112.10821, 2021
Yu Deng; Jennifer A. Pacheco; Anh Chung; Chengsheng Mao; Joshua C. Smith; Juan Zhao; Wei-Qi Wei; April Barnado; Chunhua Weng; Cong Liu; Adam Cordon; Jingzhi Yu; Yacob Tedla; Abel Kho; Rosalind Ramsey-Goldman; Theresa Walunas; Yuan Luo

An individual-level socioeconomic measure for assessing algorithmic bias in health care settings: A case for HOUSES index
medRxiv, 2021
Young J. Juhn; Euijung Ryu; Chung-Il Wi; Katherine S. King; Santiago Romero Brufau; Chunhua Weng; Sunghwan Sohn; Richard Sharp; John D. Halamka

Columbia Open Health Data for COVID-19 Research: Database Analysis
Journal of Medical Internet Research, 2021
Junghwan Lee; Jae Hyun Kim; Cong Liu; George Hripcsak; Karthik Natarajan; Casey Ta; Chunhua Weng

Genome-wide polygenic score with APOL1 risk genotypes predicts chronic kidney disease across major continental ancestries
medRxiv, 2021
Atlas Khan; Michael C. Turchin; Amit Patki; Vinodh Srinivasasainagendra; Ning Shang; Rajiv Nadukuru; Alana C. Jones; Edyta Malolepsza; Ozan Dikilitas; Iftikhar J. Kullo; Daniel J. Schaid; Elizabeth Karlson; Tian Ge; James B. Meigs; Jordan W. Smoller; Christoph Lange; David R. Crosslin; Gail Jarvik; Pavan Bhatraju; Jacklyn N. Hellwege; Paulette Chandler; Laura Rasmussen Torvik; Alex Fedotov; Cong Liu; Christopher Kachulis; Noura S. Abul-Husn; Judy H. Cho; Iuliana Ionita-Laza; Ali G. Gharavi; Wendy K. Chung; George Hripcsak; Chunhua Weng; Girish Nadkarni; Marguerite R. Irvin; Hemant K. Tiwari; Eimear E. Kenny; Nita A. Limdi; Krzysztof Kiryluk

Study of Pre-trained Language Models for Named Entity Recognition in Clinical Trial Eligibility Criteria from Multiple Corpora
2021 IEEE 9th International Conference on Healthcare Informatics (ICHI), 2021
Jianfu Li; Qiang Wei; Omid Ghiasvand; Miao Chen; Victor Lobanov; Chunhua Weng; Hua Xu

A retrospective analysis of COVID-19 mRNA vaccine breakthrough infections-risk factors and vaccine effectiveness
medRxiv, 2021
Cong Liu; Junghwan Lee; Casey Ta; Ali Soroush; James R Rogers; Jae Hyun Kim; Karthik Natarajan; Jason Zucker; Chunhua Weng

Clinical Phenotypic Spectrum of 4095 Individuals with Down Syndrome from Text Mining of Electronic Health Records
Genes, 2021
James Margolin Havrilla; Mengge Zhao; Cong Liu; Chunhua Weng; Ingo Helbig; Elizabeth Bhoj; Kai Wang

The potential role of EHR data in optimizing eligibility criteria definition for cardiovascular outcome trials
International journal of medical informatics, 2021
Jae Hyun Kim; Alex M Butler; Casey N Ta; Yingcheng Sun; Mathew S Maurer; Chunhua Weng

Medical records-based genetic studies of the complement system
Journal of the American Society of Nephrology, 2021
Atlas Khan; Ning Shang; Lynn Petukhova; Jun Zhang; Yufeng Shen; Scott J Hebbring; Halima Moncrieffe; Leah C Kottyan; Bahram Namjou-Khales; Rachel Knevel; Soumya Raychaudhuri; Elizabeth W Karlson; John B Harley; Ian B Stanaway; David Crosslin; Joshua C Denny; Mitchell S V Elkind; Ali G Gharavi; George Hripcsak; Chunhua Weng; Krzysztof Kiryluk

A deep database of medical abbreviations and acronyms for natural language processing
Scientific Data, 2021
Lisa Grossman Liu; Raymond H Grossman; Elliot G Mitchell; Chunhua Weng; Karthik Natarajan; George Hripcsak; David K Vawdrey

An AI tool to make clinical trials more inclusive
Nature, 2021
Chunhua Weng; James R. Rogers


PhenCards: a data resource linking human phenotype information to biomedical knowledge
Genome medicine, 2021
James M Havrilla; Cong Liu; Xiangchen Dong; Chunhua Weng; Kai Wang

A conceptual framework for external validity
Journal of Biomedical Informatics, 2021
Amelia J Averitt; Patrick B Ryan; Chunhua Weng; Adler Perotte

Loci identified by a genome‐wide association study of carotid artery stenosis in the eMERGE network
Genetic epidemiology, 2021
Melody R Palmer; Daniel S Kim; David R Crosslin; Ian B Stanaway; Elisabeth A Rosenthal; David S Carrell; David J Cronkite; Adam Gordon; Xiaomeng Du; Yatong K Li; Marc S Williams; Chunhua Weng; Qiping Feng; Rongling Li; Sarah A Pendergrass; Hakon Hakonarson; David Fasel; Sunghwan Sohn; Patrick Sleiman; Samuel K Handelman; Elizabeth Speliotes; Iftikhar J Kullo; Eric B Larson; eMERGE Consortium; Gail P Jarvik

Potential Role of Clinical Trial Eligibility Criteria in Electronic Phenotyping
Public Health and Informatics: Proceedings of MIE 2021, 2021
Zhehuan Chen; Hao Liu; Alex Butler; Anna Ostropolets; Chunhua Weng

Participatory Design of a Clinical Trial Eligibility Criteria Simplification Method
Studies in Health Technology and Informatics, 2021
Yilu Fang; Jae Hyun Kim; Betina Ross Idnay; Rebeca Aragon Garcia; Carmen E Castillo; Yingcheng Sun; Hao Liu; Cong Liu; Chi Yuan; Chunhua Weng

Cognitive Function Characterization Using Electronic Health Records Notes
AMIA Annual Symposium Proceedings, 2021
Adrienne Pichon; Betina Idnay; Karen Marder; Rebecca Schnall; Chunhua Weng

A mendelian randomization approach using 3-HMG-coenzyme-A reductase gene variation to evaluate the association of statin-induced low-density lipoprotein cholesterol lowering with noncardiovascular disease phenotypes
JAMA network open, 2021
Ge Liu; Mingjian Shi; Jonathan D Mosley; Chunhua Weng; Yanfei Zhang; Ming Ta Michael Lee; Gail P Jarvik; Hakon Hakonarson; Bahram Namjou-Khales; Patrick Sleiman; Yuan Luo; Frank Mentch; Joshua C Denny; MacRae F Linton; Wei-Qi Wei; C Michael Stein; QiPing Feng

Neptune: an environment for the delivery of genomic medicine
Genetics in Medicine, 2021
Venner Eric; Victoria Yi; David Murdock; Sara E Kalla; Tsung-Jung Wu; Aniko Sabo; Shoudong Li; Qingchang Meng; Xia Tian; Mullai Murugan; Michelle Cohen; Christie Kovar; Wei-Qi Wei; Wendy K Chung; Chunhua Weng; Georgia L Wiesner; Gail P Jarvik; Donna Muzny; Richard A Gibbs; eMERGE Consortium

Quantitative disease risk scores from EHR with applications to clinical risk stratification and genetic studies
NPJ Digital Medicine, 2021
Danqing Xu; Chen Wang; Atlas Khan; Ning Shang; Zihuai He; Adam Gordon; Iftikhar J Kullo; Shawn Murphy; Yizhao Ni; Wei-Qi Wei; Ali Gharavi; Krzysztof Kiryluk; Chunhua Weng; Iuliana Ionita-Laza

Identifying Data Quality Dimensions for Person-Generated Wearable Device Data: Multi-Method Study
JMIR mHealth and uHealth, 2021
Sylvia Cho; Chunhua Weng; Michael G Kahn; Karthik Natarajan

The COVID-19 trial finder
Journal of the American Medical Informatics Association, 2021
Yingcheng Sun; Alex Butler; Fengyang Lin; Hao Liu; Latoya A Stewart; Jae Hyun Kim; Betina Ross S Idnay; Qingyin Ge; Xinyi Wei; Cong Liu; Chi Yuan; Chunhua Weng

Comparative effectiveness of medical concept embedding for feature engineering in phenotyping
JAMIA open, 2021
Junghwan Lee; Cong Liu; Jae Hyun Kim; Alex Butler; Ning Shang; Chao Pang; Karthik Natarajan; Patrick Ryan; Casey Ta; Chunhua Weng

Preferences for updates on general research results: A survey of participants in genomic research from two institutions
Journal of personalized medicine, 2021
Casey Overby Taylor; Natalie Flaks Manov; Katherine D Crew; Chunhua Weng; John J Connolly; Christopher G Chute; Daniel E Ford; Harold Lehmann; Alanna Kulchak Rahm; Iftikhar J Kullo; Pedro J Caraballo; Ingrid A Holm; Debra Mathews

Evaluating Patient Count Vs Hospitalization Risk for Common Clinical Trial Eligibility Criteria: A Case Study for Relapsed/Refractory Lymphoma/Leukemia
OHDSI Global Symposium, 2021
James Rogers; Casey N. Ta; Cong Liu; Ali Soroush; Ying Kuen Cheung; George Hripcsak; Chunhua Weng

Severity Prediction for COVID-19 Patients via Recurrent Neural Networks
AMIA Annual Symposium Proceedings, 2021
Junghwan Lee; Casey Ta; Jae Hyun Kim; Cong Liu; Chunhua Weng

UMLS-based data augmentation for natural language processing of clinical research literature
Journal of the American Medical Informatics Association, 2021
Tian Kang; Adler Perotte; Youlan Tang; Casey Ta; Chunhua Weng

Charting the life course: Emerging opportunities to advance scientific approaches using life course research
Journal of clinical and translational science, 2021
Heidi A Hanson; Claire L Leiser; Gretchen Bandoli; Brad H Pollock; Margaret R Karagas; Daniel Armstrong; Ann Dozier; Nicole G Weiskopf; Maureen Monaghan; Ann M Davis; Elizabeth Eckstrom; Chunhua Weng; Jonathan N Tobin; Frederick Kaskel; Mark R Schleiss; Peter Szilagyi; Carrie Dykes; Dan Cooper; Shari L Barkin

Penetrance of breast cancer susceptibility genes from the eMERGE III Network
JNCI Cancer Spectrum, 2021
Xiao Fan; Julia Wynn; Ning Shang; Cong Liu; Alexander Fedotov; Miranda L G Hallquist; Adam H Buchanan; Marc S Williams; Maureen E Smith; Christin Hoell; Laura J Rasmussen-Torvik; Josh F Peterson; Georgia L Wiesner; Andrea M Murad; Gail P Jarvik; Adam S Gordon; Elisabeth A Rosenthal; Ian B Stanaway; David R Crosslin; Eric B Larson; Kathleen A Leppig; Nora B Henrikson; Janet L Williams; Rongling Li; Scott Hebbring; Chunhua Weng; Yufeng Shen; Katherine D Crew; Wendy K Chung

Misalignment between COVID-19 hotspots and clinical trial sites
Journal of the American Medical Informatics Association, 2021
Lauren Franks; Hao Liu; Mitchell S V Elkind; Muredach P Reilly; Chunhua Weng; Shing M Lee

Contemporary use of real-world data for clinical trial conduct in the United States: a scoping review
Journal of the American Medical Informatics Association, 2021
James R Rogers; Junghwan Lee; Ziheng Zhou; Ying Kuen Cheung; George Hripcsak; Chunhua Weng

Medical records-based chronic kidney disease phenotype for clinical care and “big data” observational and genetic studies
NPJ digital medicine, 2021
Ning Shang; Atlas Khan; Fernanda Polubriaginof; Francesca Zanoni; Karla Mehl; David Fasel; Paul E Drawz; Robert J Carrol; Joshua C Denny; Matthew A Hathcock; Adelaide M Arruda-Olson; Peggy L Peissig; Richard A Dart; Murray H Brilliant; Eric B Larson; David S Carrell; Sarah Pendergrass; Shefali Setia Verma; Marylyn D Ritchie; Barbara Benoit; Vivian S Gainer; Elizabeth W Karlson; Adam S Gordon; Gail P Jarvik; Ian B Stanaway; David R Crosslin; Sumit Mohan; Iuliana Ionita-Laza; Nicholas P Tatonetti; Ali G Gharavi; George Hripcsak; Chunhua Weng; Krzysztof Kiryluk

A knowledge base of clinical trial eligibility criteria
Journal of Biomedical Informatics, 2021
Hao Liu; Yuan Chi; Alex Butler; Yingcheng Sun; Chunhua Weng


Comparison of clinical characteristics between clinical trial participants and nonparticipants using electronic health record data
JAMA network open, 2021
James R Rogers; Cong Liu; George Hripcsak; Ying Kuen Cheung; Chunhua Weng

Penetrance of breast cancer genes from the eMERGE III Network
medRxiv, 2021
Xiao Fan; Julia Wynn; Ning Shang; Cong Liu; Alexander Fedotov; Miranda L G Hallquist; Adam H Buchanan; Marc S Williams; Maureen E Smith; Christin Hoell; Laura J Rasmussen-Torvik; Josh F Peterson; Georgia L Wiesner; Andrea M Murad; Gail P Jarvik; Adam S Gordon; Elisabeth A Rosenthal; Ian B Stanaway; David R Crosslin; Eric B Larson; Kathleen A Leppig; Nora B Henrikson; Janet L Williams; Rongling Li; Scott Hebbring; Chunhua Weng; Yufeng Shen; Katherine D Crew; Wendy K Chung

Building an OMOP common data model-compliant annotated corpus for COVID-19 clinical trials
Journal of biomedical informatics, 2021
Yingcheng Sun; Alex Butler; Latoya A Stewart; Hao Liu; Chi Yuan; Christopher T Southard; Jae Hyun Kim; Chunhua Weng

Data Quality of Chemotherapy-Induced Nausea and Vomiting Documentation
Applied Clinical Informatics, 2021
Melissa Beauchemin; Chunhua Weng; Lillian Sung; Adrienne Pichon; Maura Abbott; Dawn L Hershman; Rebecca Schnall

GeneLiFT: A novel test to facilitate rapid screening of genetic literacy in a diverse population undergoing genetic testing
Journal of genetic counseling, 2021
Hila Milo Rasouly; Nicole Cuneo; Maddalena Marasa; Natalia DeMaria; Debanjana Chatterjee; Jacqueline J. Thompson; David A. Fasel; Julia Wynn; Wendy K. Chung; Paul Appelbaum; Chunhua Weng; Suzanne Bakken; Ali G. Gharavi

A scalable EHR-based approach for phenotype discovery and variant interpretation for hereditary cancer genes
medRxiv, 2021
Chenjie Zeng; Lisa A. Bastarache; Ran Tao; Eric Venner; Scott Hebbring; Justin D. Andujar; Sarah T. Bland; ProfileDavid R. Crosslin; Siddharth Pratap; Ayorinde Cooley; Jennifer A. Pacheco; Kurt D. Christensen; Emma Perez; Carrie L. Blout Zawatsky; Leora Witkowski; Hana Zouk; Chunhua Weng; Kathleen A. Leppig; Patrick M. A. Sleiman; Hakon Hakonarson; Marc. S. Williams; Yuan Luo; Gail P. Jarvik; Robert C. Green; Wendy K. Chung; Ali G. Gharavi; Niall J. Lennon; Heidi L. Rehm; Richard A. Gibbs; Josh F. Peterson; Dan M. Roden; Georgia L. Wiesner; Joshua C. Denny

Factors affecting the quality of person-generated wearable device data and associated challenges: rapid systematic review
JMIR mHealth and uHealth, 2021
Sylvia Cho; Ipek Ensari; Chunhua Weng; Michael G Kahn; Karthik Natarajan

An electronic health record (EHR) log analysis shows limited clinician engagement with unsolicited genetic test results
JAMIA open, 2021
Jordan G Nestor; Alexander Fedotov; David Fasel; Maddalena Marasa; Hila Milo-Rasouly; Julia Wynn; Wendy K Chung; Ali Gharavi; George Hripcsak; Suzanne Bakken; Soumitra Sengupta; Chunhua Weng

Similarity-based health risk prediction using Domain Fusion and electronic health records data
Journal of Biomedical Informatics, 2021
Jia Guo; Chi Yuan; Ning Shang; Tian Zheng; Natalie A Bello; Krzysztof Kiryluk; Chunhua Weng; Shuang Wang

A neuro-symbolic method for understanding free-text medical evidence
Journal of the American Medical Informatics Association, 2021
Tian Kang; Ali Turfah; Jaehyun Kim; Adler Perotte; Chunhua Weng

Towards clinical data-driven eligibility criteria optimization for interventional COVID-19 clinical trials
Journal of the American Medical Informatics Association, 2021
Jae Hyun Kim; Casey N Ta; Cong Liu; Cynthia Sung; Alex M Butler; Latoya A Stewart; Lyudmila Ena; James R Rogers; Junghwan Lee; Anna Ostropolets; Patrick B Ryan; Hao Liu; Shing M Lee; Mitchell S V Elkind; Chunhua Weng

A framework (SOCRATex) for hierarchical annotation of unstructured electronic health records and integration into a standardized medical database: development and usability study
JMIR medical informatics, 2021
Jimyung Park; Seng Chan You; Eugene Jeong; Chunhua Weng; Dongsu Park; Jin Roh; Dong Yun Lee; Jae Youn Cheong; Jin Wook Choi; Mira Kang; Rae Woong Park

2020


Modelling kidney disease using ontology: insights from the Kidney Precision Medicine Project
Nature Reviews Nephrology, 2020
Edison Ong; Lucy L Wang; Jennifer Schaub; John F O'Toole; Becky Steck; Avi Z Rosenberg; Frederick Dowd; Jens Hansen; Laura Barisoni; Sanjay Jain; Ian H de Boer; M Todd Valerius; Sushrut S Waikar; Christopher Park; Dana C Crawford; Theodore Alexandrov; Christopher R Anderton; Christian Stoeckert; Chunhua Weng; Alexander D Diehl; Christopher J Mungall; Melissa Haendel; Peter N Robinson; Jonathan Himmelfarb; Ravi Iyengar; Matthias Kretzler; Sean Mooney; Yongqun He; Kidney Precision Medicine Project

How have experimental cancer interventions evolved over time?
Studies in health technology and informatics, 2020
Ziran Li; Huanyao Chen; Chi Yuan; Chunhua Weng

Generalizability of Polygenic Risk Scores for Breast Cancer in the Multiethnic eMERGE Study
medRxiv, 2020
Cong Liu; Nur Zeinomar; Wendy K. Chung; Krzysztof Kiryluk; Ali G. Gharavi; George Hripcsak; Katherine D. Crew; Ning Shang; Atlas Khan; David Fasel; Teri A. Manolio; Gail P. Jarvik; Robb Rowley; Ann E. Justice; Alanna K. Rahm; Stephanie M. Fullerton; Jordan W. Smoller; Eric B. Larson; Paul K. Crane; Ozan Dikilitas; Georgia L. Wiesner; Alexander G. Bick; Mary Beth Terry; Chunhua Weng

Natural language processing (NLP) tools in extracting biomedical concepts from research articles: a case study on autism spectrum disorder
BMC Medical Informatics and Decision Making, 2020
Jacqueline Peng; Mengge Zhao; James Havrilla; Cong Liu; Chunhua Weng; Whitney Guthrie; Robert Schultz; Kai Wang; Yunyun Zhou

COHD-COVID: Columbia Open Health Data for COVID-19 Research
medRxiv, 2020
Junghwan Lee; Jae Hyun Kim; Cong Liu; George Hripcsak; Casey Ta; Chunhua Weng

4429 Powering precision medicine research with the efficient construction of large diverse cohorts
Journal of Clinical and Translational Science, 2020
Lynn Petukhova; Nana Ekua Adenu-Mensah; Ning Shang; Lyudmila Ena; Carol Friedman; Chunhua Weng; Eric W Schrimshaw

Impact of IMPACT: Longitudinal Analysis of an Integrated Participant Scheduling System in a Clinical Research Setting
AMIA Annual Symposium Proceedings, 2020
Alex Butler; Junghwan Lee; Yat So; Linda Busacca; Karen Marder; Henry N Ginsberg; Dianne Frederick; Ismael Castaneda; Elizabeth Guerridoi; Chunhua Weng

Chia, a large annotated corpus of clinical trial eligibility criteria
Scientific data, 2020
Fabrício Kury; Alex Butler; Chi Yuan; Li-Heng Fu; Yingcheng Sun; Hao Liu; Ida Sim; Simona Carini; Chunhua Weng

Comparative effectiveness of knowledge graphs-and EHR data-based medical concept embedding for phenotyping
Preprint, 2020
Junghwan Lee; Cong Liu; Jae Hyun Kim; Alex Butler; Ning Shang; Chao Pang; Karthik Natarajan; Patrick Ryan; Casey Ta; Chunhua Weng

A graph-based method for reconstructing entities from coordination ellipsis in medical text
Journal of the American Medical Informatics Association, 2020
Chi Yuan; Yongli Wang; Ning Shang; Ziran Li; Ruxin Zhao; Chunhua Weng

Adapting electronic health records-derived phenotypes to claims data: Lessons learned in using limited clinical data for phenotyping
Journal of biomedical informatics, 2020
Anna Ostropolets; Christian Reich; Patrick Ryan; Ning Shang; George Hripcsak; Chunhua Weng

Rapid exome sequencing in PICU patients with new-onset metabolic or neurological disorders
Pediatric research, 2020
Abigail S Carey; John P Schacht; Christine Umandap; David Fasel; Chunhua Weng; Joshua Cappell; Wendy K Chung; Steven G Kernie

Missense variants in TAF1 and developmental phenotypes: challenges of determining pathogenicity
Human mutation, 2020
Hanyin Cheng; Simona Capponi; Emma Wakeling; Elaine Marchi; Quan Li; Mengge Zhao; Chunhua Weng; Stefan G. Piatek; Helena Ahlfors; Robert Kleyner; Alan Rope; Aimé Lumaka; Prosper Lukusa; Koenraad Devriendt; Joris Vermeesch; Jennifer E. Posey; Elizabeth E. Palmer; Lucinda Murray; Eyby Leon; Jullianne Diaz; Lisa Worgan; Amali Mallawaarachchi; Julie Vogt; Sonja A. Munnik; Lauren Dreyer; Gareth Baynam; Lisa Ewans; Zornitza Stark; Sebastian Lunke; Ana R. Gonçalves; Gabriela Soares; Jorge Oliveira; Emily Fassi; Marcia Willing; Jeff L. Waugh; Laurence Faivre; Jean-Baptiste Riviere; Sebastien Moutton; Shehla Mohammed; Katelyn Payne; Laurence Walsh; Amber Begtrup; Maria J. Guillen Sacoto; Ganka Douglas; Nora Alexander; Michael F. Buckley; Paul R. Mark; Lesley C. Adès; Sarah A. Sandaradura; James R. Lupski; Tony Roscioli; Pankaj B. Agrawal; Antonie D. Kline; Kai Wang; H. T. Marc Timmers; Gholson J. Lyon

Association of genetic risk of obesity with postoperative complications using Mendelian randomization
World journal of surgery, 2020
Jamie R Robinson; Robert J Carroll; Lisa Bastarache; Qingxia Chen; Zongyang Mou; Wei-Qi Wei; John J Connolly; Frank Mentch; Patrick Sleiman; Paul K Crane; Scott J Hebbring; Ian B Stanaway; David R Crosslin; Adam S Gordon; Elisabeth A Rosenthal; David Carrell; M Geoffrey Hayes; Wei Wei; Lynn Petukhova; Bahram Namjou; Ge Zhang; Maya S Safarova; Nephi A Walton; Christopher Still; Erwin P Bottinger; Ruth J F Loos; Shawn N Murphy; Gretchen P Jackson; Iftikhar J Kullo; Hakon Hakonarson; Gail P Jarvik; Eric B Larson; Chunhua Weng; Dan M Roden; Joshua C Denny

A new approach to integrating patient-generated data with expert knowledge for personalized goal setting: A pilot study
International journal of medical informatics, 2020
Marissa Burgermaster; Jung H Son; Patricia G Davidson; Arlene M Smaldone; Gilad Kuperman; Daniel J Feller; Katherine Gardner Burt; Matthew E Levine; David J Albers; Chunhua Weng; Lena Mamykina

Harmonizing outcomes for genomic medicine: comparison of eMERGE outcomes to ClinGen outcome/intervention pairs
The Road from Nanomedicine to Precision Medicine, 2020
Janet L Williams; Wendy K Chung; Alex Fedotov; Krzysztof Kiryluk; Chunhua Weng; John J Connolly; Margaret Harr; Hakon Hakonarson; Kathleen A Leppig; Eric B Larson; Gail P Jarvik; David L Veenstra; Christin Hoell; Maureen E Smith; Ingrid A Holm; Josh F Peterson; Marc S Williams

Clinical Characterization of Trial Participants Using Electronic Health Record Data
OHDSI Global Symposium, 2020
James Rogers; Cong Liu; Ying Kuen Cheung; Chunhua Weng

Guideline concordant care for prevention of acute chemotherapy-induced nausea and vomiting in children, adolescents, and young adults
Supportive Care in Cancer, 2020
Melissa Beauchemin; Lillian Sung; Dawn L Hershman; Chunhua Weng; L Lee Dupuis; Rebecca Schnall

Choices, attitudes, and experiences of genetic screening in Latino/a and Ashkenazi Jewish individuals
Journal of community genetics, 2020
Anne E Reed-Weston; Aileen Espinal; Bianca Hasar; Codruta Chiuzan; Gabriel Lazarin; Chunhua Weng; Paul S Appelbaum; Wendy K Chung; Julia Wynn


Deep phenotyping: embracing complexity and temporality-towards scalability, portability, and interoperability
Journal of biomedical informatics, 2020
Chunhua Weng; Nigam H Shah; George Hripcsak

Characterizing database granularity using SNOMED-CT hierarchy
AMIA Annual Symposium Proceedings, 2020
Anna Ostropolets; Christian Reich; Patrick Ryan; Chunhua Weng; Anthony Molinaro; Frank DeFalco; Jitendra Jonnagaddala; Siaw-Teng Liaw; Hokyun Jeon; Rae Woong Park; Matthew E Spotnitz; Karthik Natarajan; George Argyriou; Kristin Kostka; Robert Miller; Andrew Williams; Evan Minty; Jose Posada; George Hripcsak

Understanding the nature and scope of clinical research commentaries in PubMed
Journal of the American Medical Informatics Association, 2020
James R Rogers; Hollis Mills; Lisa V Grossman; Andrew Goldstein; Chunhua Weng

Clinical data quality: a data life cycle perspective
Biostatistics & epidemiology, 2020
Chunhua Weng

Phen2Gene: rapid phenotype-driven gene prioritization for rare diseases
NAR genomics and bioinformatics, 2020
Mengge Zhao; James M Havrilla; Li Fang; Ying Chen; Jacqueline Peng; Cong Liu; Chao Wu; Mahdi Sarmady; Pablo Botas; Julián Isla; Gholson J Lyon; Chunhua Weng; Kai Wang

2019


Combining Clinical Data and Domain Knowledge for Analyzing Mental Disorder Concept Relatedness and Usage
2019 IEEE International Conference on Healthcare Informatics (ICHI), 2019
Duo Helen Wei; Casey Ta; Harold Alan Pincus; Chunhua Weng

Pathway analysis of genomic pathology tests for prognostic cancer subtyping
Journal of biomedical informatics, 2019
Olga Lyudovyk; Yufeng Shen; Nicholas P Tatonetti; Susan J Hsiao; Mahesh M Mansukhani; Chunhua Weng

Dialogue Analysis for Clinical Data Query Mediation
Studies in health technology and informatics, 2019
Chunhua Weng; Amy K Mir; David Hanauer; James Cimino

Detecting systemic data quality issues in electronic health records
Studies in health technology and informatics, 2019
Casey N Ta; Chunhua Weng

User engagement with web-based genomics education videos and implications for designing scalable patient education materials
AMIA Annual Symposium Proceedings, 2019
Julia Wynn; Wei Wei; Xinhang Li; Yat S So; Suzanne Bakken; Chunhua Weng; Wendy K Chung

Finding Success in Clinical Trial Recruitment: A Trial Registry Analysis
Preprint, 2019
Alex Butler; Ziran Li; Cong Liu; Casey Ta; Chi Yuan; Huanyao Chen; Bruce Levin; George Hripcsak; Chunhua Weng

Evaluation of the cost and effectiveness of diverse recruitment methods for a genetic screening study
Genetics in Medicine, 2019
Hila Milo Rasouly; Julia Wynn; Maddalena Marasa; Rachel Reingold; Debanjana Chatterjee; Sheena Kapoor; Stacy Piva; Byum Hee Kil; Xueru Mu; Maria Alvarez; Jordan Nestor; Karla Mehl; Anya Revah-Politi; Natalie Lippa; Michelle E Ernst; Louise Bier; Aileen Espinal; Bianca Haser; Anoushka Sinha; Ian Halim; David Fasel; Nicole Cuneo; Jacqueline J Thompson; Miguel Verbitsky; Elizabeth G Cohn; Jill Goldman; Karen Marder; Robert L Klitzman; Manuela A Orjuela; Yat S So; Alex Fedotov; Katherine D Crew; Krzysztof Kiryluk; Paul S Appelbaum; Chunhua Weng; Karolynn Siegel; Ali G Gharavi; Wendy K Chung

Ensembles of natural language processing systems for portable phenotyping solutions
Journal of biomedical informatics, 2019
Cong Liu; Casey N Ta; James R Rogers; Ziran Li; Junghwan Lee; Alex M Butler; Ning Shang; Fabricio Sampaio Peres Kury; Liwei Wang; Feichen Shen; Hongfang Liu; Lyudmila Ena; Carol Friedman; Chunhua Weng

Construction of disease similarity networks using concept embedding and ontology
Studies in health technology and informatics, 2019
Duo Helen Wei; Tian Kang; Harold Alan Pincus; Chunhua Weng

Generate the concept representation using OMOP ontology graph
OHDSI US Symposium, 2019
Junghwan Lee; Cong Liu; Ning Shang; Xinzhuo Jiang; Kai Chen; Krishna Sai Dheeraj Kalluri; Chao Pang; Karthik Natarajan; Patrick Ryan; Chunhua Weng

Pretraining to recognize PICO elements from randomized controlled trial literature
Studies in health technology and informatics, 2019
Tian Kang; Shirui Zou; Chunhua Weng

Crowdsourcing Public Opinion for Sharing Medical Records for the Advancement of Science
Studies in health technology and informatics, 2019
Chunhua Weng; Tianyong Hao; Carol Friedman; John Hurdle

SNOMEDtxt: Natural Language Generation from SNOMED Ontology
Studies in health technology and informatics, 2019
Olga Lyudovyk; Chunhua Weng


Making work visible for electronic phenotype implementation: Lessons learned from the eMERGE network
Journal of biomedical informatics, 2019
Ning Shang; Cong Liu; Luke V Rasmussen; Casey N Ta; Robert J Caroll; Barbara Benoit; Todd Lingren; Ozan Dikilitas; Frank D Mentch; David S Carrell; Wei-Qi Wei; Yuan Luo; Vivian S Gainer; Iftikhar J Kullo; Jennifer A Pacheco; Hakon Hakonarson; Theresa L Walunas; Joshua C Denny; Ken Wiley; Shawn N Murphy; George Hripcsak; Chunhua Weng

Analysis of evidence appraisals for interventional studies in family medicine using an informatics approach
Primary health care research & development, 2019
Alain Nathan Sahin; Andrew Goldstein; Chunhua Weng

A two-site survey of medical center personnel’s willingness to share clinical data for research: implications for reproducible health NLP research
BMC Medical Informatics and Decision Making, 2019
Chunhua Weng; Carol Friedman; Casey A Rommel; John F Hurdle

Diagnostic utility of exome sequencing for kidney disease
New England Journal of Medicine, 2019
Emily E. Groopman; Maddalena Marasa; Sophia Cameron-Christie; Slavé Petrovski; Vimla S. Aggarwal; Hila Milo-Rasouly; Yifu Li; Junying Zhang; Jordan Nestor; Priya Krithivasan; Wan Yee Lam; Adele Mitrotti; Stacy Piva; Byum H. Kil; Debanjana Chatterjee; Rachel Reingold; Drew Bradbury; Michael DiVecchia; Holly Snyder; Xueru Mu; Karla Mehl; Olivia Balderes; David A. Fasel; Chunhua Weng; Jai Radhakrishnan; Pietro Canetta; Gerald B. Appel; Andrew S. Bomback; Wooin Ahn; Natalie S. Uy; Shumyle Alam; David J. Cohen; Russell J. Crew; Geoffrey K. Dube; Maya K. Rao; Sitharthan Kamalakaran; Brett Copeland; Zhong Ren; Joshua Bridgers; Colin D. Malone; Caroline M. Mebane; Neha Dagaonkar; Bengt C. Fellström; Carolina Haefliger; Sumit Mohan; Simone Sanna-Cherchi; Krzysztof Kiryluk; an Fleckner; Ruth March; Adam Platt; David B. Goldstein; Ali G. Gharavi

Informatics approaches to participant recruitment
Clinical Research Informatics, 2019
Chunhua Weng; Peter J Embi

DQueST: dynamic questionnaire for search of clinical trials
Journal of the American Medical Informatics Association, 2019
Cong Liu; Chi Yuan; Alex M Butler; Richard D Carvajal; Ziran Ryan Li; Casey N Ta; Chunhua Weng

The burden of candidate pathogenic variants for kidney and genitourinary disorders emerging from exome sequencing
Annals of internal medicine, 2019
Hila Milo Rasouly; Emily E Groopman; Reuben Heyman-Kantor; David A Fasel; Adele Mitrotti; Rik Westland; Louise Bier; Chunhua Weng; Zhong Ren; Brett Copeland; Priya Krithivasan; Wendy K Chung; Simone Sanna-Cherchi; David B Goldstein; Ali G Gharavi

Facilitating phenotype transfer using a common data model
Journal of biomedical informatics, 2019
George Hripcsak; Ning Shang; Peggy L Peissig; Luke V Rasmussen; Cong Liu; Barbara Benoit; Robert J Carroll; David S Carrell; Joshua C Denny; Ozan Dikilitas; Vivian S Gainer; Kayla Marie Howell; Jeffrey G Klann; Iftikhar J Kullo; Todd Lingren; Frank D Mentch; Shawn N Murphy; Karthik Natarajan; Jennifer A Pacheco; Wei-Qi Wei; Ken Wiley; Chunhua Weng

Genomic information for clinicians in the electronic health record: lessons learned from the clinical genome resource project and the electronic medical records and genomics network
Frontiers in genetics, 2019
Marc S Williams; Casey Overby Taylor; Nephi A Walton; Scott R Goehringer; Samuel Aronson; Robert R Freimuth; Luke V Rasmussen; Eric S Hall; Cynthia A Prows; Wendy K Chung; Alexander Fedotov; Jordan Nestor; Chunhua Weng; Robb K Rowley; Georgia L Wiesner; Gail P Jarvik; Guilherme Del Fiol

Clinical decision support for therapeutic decision-making in cancer: A systematic review
International journal of medical informatics, 2019
Melissa Beauchemin; Meghan T Murray; Lillian Sung; Dawn L Hershman; Chunhua Weng; Rebecca Schnall

Doc2Hpo: a web application for efficient and accurate HPO concept curation
Nucleic acids research, 2019
Cong Liu; Fabricio Sampaio Peres Kury; Ziran Li; Casey Ta; Kai Wang; Chunhua Weng

Clinical data: sources and types, regulatory constraints, applications
Clinical and translational science, 2019
Stanley C Ahalt; Christopher G Chute; Karamarie Fecho; Gustavo Glusman; Jennifer Hadlock; Casey Overby Taylor; Emily R Pfaff; Peter N Robinson; Harold Solbrig; Casey Ta; Nicholas Tatonetti; Chunhua Weng; Biomedical Data Translator Consortium

A data element-function conceptual model for data quality checks
eGEMs, 2019
James R Rogers; Tiffany J Callahan; Tian Kang; Alan Bauck; Ritu Khare; Jeffrey S Brown; Michael G Kahn; Chunhua Weng

Complexities, variations, and errors of numbering within clinical notes: the potential impact on information extraction and cohort-identification
BMC Medical Informatics and Decision Making, 2019
David A Hanauer; Qiaozhu Mei; V G Vinod Vydiswaran; Karandeep Singh; Zach Landis-Lewis; Chunhua Weng

Association of thyroid function genetic predictors with atrial fibrillation: a phenome-wide association study and inverse-variance weighted average meta-analysis
JAMA cardiology, 2019
Joe-Elie Salem; M Benjamin Shoemaker; Lisa Bastarache; Christian M Shaffer; Andrew M Glazer; Brett Kroncke; Quinn S Wells; Mingjian Shi; Peter Straub; Gail P Jarvik; Eric B Larson; Digna R Velez Edwards; Todd L Edwards; Lea K Davis; Hakon Hakonarson; Chunhua Weng; David Fasel; Bjorn C Knollmann; Thomas J Wang; Joshua C Denny; Patrick T Ellinor; Dan M Roden; Jonathan D Mosley

Harmonizing clinical sequencing and interpretation for the eMERGE III network
The American Journal of Human Genetics, 2019
eMERGE Consortium; Hana Zouk; Eric Venner; Niall J Lennon; Donna M Muzny; Debra Abrams; Samuel Adunyah; Ladia Albertson-Junkans; Darren C Ames; Paul Appelbaum; Samuel Aronson; Sharon Aufox; Lawrence J Babb; Adithya Balasubramanian; Hana Bangash; Melissa Basford; Lisa Bastarache; Samantha Baxter; Meckenzie Behr; Barbara Benoit; Elizabeth Bhoj; Suzette J Bielinski; Sarah T Bland; Carrie Blout; Kenneth Borthwick; Erwin P Bottinger; Mark Bowser; Harrison Brand; Murray Brilliant; Wendy Brodeur; Pedro Caraballo; David Carrell; Andrew Carroll; Berta Almoguera; Lisa Castillo; Victor Castro; Gauthami Chandanavelli; Theodore Chiang; Rex L Chisholm; Kurt D Christensen; Wendy Chung; Christopher G Chute; Brittany City; Beth L Cobb; John J Connolly; Paul Crane; Katherine Crew; David Crosslin; Mariza De Andrade; Jessica De la Cruz; Shawn Denson; Josh Denny; Tim DeSmet; Ozan Dikilitas; Christopher Friedrich; Stephanie M Fullerton; Birgit Funke; Stacey Gabriel; Vivian Gainer; Ali Gharavi; Andrew M Glazer; Joseph T Glessner; Jessica Goehringer; Adam S Gordon; Chet Graham; Robert C Green; Justin H Gundelach; Jyoti Dayal; Heather S Hain; Hakon Hakonarson; Maegan V Harden; John Harley; Margaret Harr; Andrea Hartzler; M Geoffrey Hayes; Scott Hebbring; Nora Henrikson; Andrew Hershey; Christin Hoell; Ingrid Holm; Kayla M Howell; George Hripcsak; Jianhong Hu; Gail P Jarvik; Joy C Jayaseelan; Yunyun Jiang; Yoonjung Yoonie Joo; Sheethal Jose; Navya Shilpa Josyula; Anne E Justice; Sara E Kalla; Divya Kalra; Elizabeth Karlson; Melissa A Kelly; Brendan J Keating; Eimear E Kenny; Dustin Key; Krzysztof Kiryluk; Terrie Kitchner; Barbara Klanderman; Eric Klee; David C Kochan; Viktoriya Korchina; Leah Kottyan; Christie Kovar; Emily Kudalkar; Iftikhar J Kullo; Philip Lammers; Eric B Larson; Matthew S Lebo; Magalie Leduc; Ming Ta Michael Lee; Kathleen A Leppig; Nancy D Leslie; Rongling Li; Wayne H Liang; Chiao-Feng Lin; Jodell Linder; Noralane M Lindor; Todd Lingren; James G Linneman; Cong Liu; Wen Liu; Xiuping Liu; John Lynch; Hayley Lyon; Alyssa Macbeth; Harshad Mahadeshwar; Lisa Mahanta; Brad Malin; Teri Manolio; Maddalena Marasa; Keith Marsolo; Michael J Dinsmore; Sheila Dodge; Elizabeth Duffy Hynes; Phil Dunlea; Todd L Edwards; Christine M Eng; David Fasel; Alex Fedotov; Qiping Feng; Mark Fleharty; Andrea Foster; Robert Freimuth; Michelle L McGowan; Elizabeth McNally; Jim Meldrim; Frank Mentch; Jonathan Mosley; Shubhabrata Mukherjee; Thomas E Mullen; Jesse Muniz; David R Murdock; Shawn Murphy; Mullai Murugan; Melanie F Myers; Bahram Namjou; Yizhao Ni; Aniwaa Owusu Obeng; Robert C Onofrio; Casey Overby Taylor; Thomas N Person; Josh F Peterson; Lynn Petukhova; Cassandra J Pisieczko; Siddharth Pratap; Cynthia A Prows; Megan J Puckelwartz; Alanna Kulchak Rahm; Ritika Raj; James D Ralston; Arvind Ramaprasan; Andrea Ramirez; Luke Rasmussen; Laura Rasmussen-Torvik; Hila Milo Rasouly; Soumya Raychaudhuri; Marylyn D Ritchie; Catherine Rives; Beenish Riza; Dan Roden; Elisabeth A Rosenthal; Avni Santani; Dan Schaid; Steven Scherer; Stuart Scott; Aaron Scrol; Soumitra Sengupta; Ning Shang; Himanshu Sharma; Richard R Sharp; Rajbir Singh; Patrick M A Sleiman; Kara Slowik; Joshua C Smith; Maureen E Smith; Jordan W Smoller; Sunghwan Sohn; Ian B Stanaway; Justin Starren; Mary Stroud; Jessica Su; Kasia Tolwinski; Sara L Van Driest; Sean M Vargas; Matthew Varugheese; David Veenstra; Miguel Verbitsky; Gina Vicente; Michael Wagner; Kimberly Walker; Theresa Walunas; Liwen Wang; Qiaoyan Wang; Wei-Qi Wei; Scott T Weiss; Georgia L Wiesner; Quinn Wells; Chunhua Weng; Peter S White; Ken L Wiley Jr; Janet L Williams; Marc S Williams; Michael W Wilson; Leora Witkowski; Laura Allison Woods; Betty Woolf; Tsung-Jung Wu; Julia Wynn; Yaping Yang; Victoria Yi; Ge Zhang; Lan Zhang; Heidi L Rehm; Richard A Gibbs

Criteria2Query: a natural language interface to clinical databases for cohort definition
Journal of the American Medical Informatics Association, 2019
Chi Yuan; Patrick B Ryan; Casey Ta; Yixuan Guo; Ziran Li; Jill Hardin; Rupa Makadia; Peng Jin; Ning Shang; Tian Kang; Chunhua Weng


Semi-supervised learning to improve generalizability of risk prediction models
Journal of Biomedical Informatics, 2019
Shengqiang Chi; Xinhang Li; Yu Tian; Jun Li; Xiangxing Kong; Kefeng Ding; Chunhua Weng; Jingsong Li

Evaluation of the cost and effectiveness of diverse recruitment methods for a genetic screening study
Genetics in Medicine, 2019
Hila Milo Rasouly; Julia Wynn; Maddalena Marasa; Rachel Reingold; Debanjana Chatterjee; Sheena Kapoor; Stacy Piva; Byum Hee Kil; Xueru Mu; Maria Alvarez; Jordan Nestor; Karla Mehl; Anya Revah-Politi; Natalie Lippa; Michelle E Ernst; Louise Bier; Aileen Espinal; Bianca Haser; Anoushka Sinha; Ian Halim; David Fasel; Nicole Cuneo; Jacqueline J Thompson; Miguel Verbitsky; Elizabeth G Cohn; Jill Goldman; Karen Marder; Robert L Klitzman; Manuela A Orjuela; Yat S So; Alex Fedotov; Katherine D Crew; Krzysztof Kiryluk; Paul S Appelbaum; Chunhua Weng; Karolynn Siegel; Ali G Gharavi; Wendy K Chung

2018


The representativeness of eligible patients in type 2 diabetes trials: a case study using GIST 2.0
Journal of the American Medical Informatics Association, 2018
Anando Sen; Andrew Goldstein; Shreya Chakrabarti; Ning Shang; Tian Kang; Anil Yaman; Patrick B Ryan; Chunhua Weng

A method for harmonization of clinical abbreviation and acronym sense inventories
Journal of biomedical informatics, 2018
Lisa V Grossman; Elliot G Mitchell; George Hripcsak; Chunhua Weng; David K Vawdrey

An exploration of the terminology of clinical cognition and reasoning
AMIA Annual Symposium Proceedings, 2018
James J Cimino; Ziran Li; Chunhua Weng

Call for papers: deep phenotyping for precision medicine
Journal of biomedical informatics, 2018
Chunhua Weng; Nigam Shah; George Hripcsak

The data gap in the EHR for clinical research eligibility screening
AMIA Summits on Translational Science Proceedings, 2018
Alex Butler; Wei Wei; Chi Yuan; Tian Kang; Yuqi Si; Chunhua Weng

Post-publication peer review and evidence appraisals in primary care
The Lancet, 2018
Alain Nathan Sahin; Andrew Goldstein; Chunhua Weng

Numerical Age Variations within Clinical Notes: The Potential Impact on De-Identification and Information Extraction
2018 IEEE International Conference on Healthcare Informatics Workshop (ICHI-W), 2018
David Hanauer; Qiaozhu Mei; VG Vinod Vydiswaran; Karandeep Singh; Zach Landis-Lewis; Chunhua Weng

The ranking of scientists.
Journal of Biomedical Informatics, 2018
Chunhua Weng; Andrew Goldstein; Chi Yuan; Zhiping Zhou

Empowering genomic medicine by establishing critical sequencing result data flows: the eMERGE example
Journal of the American Medical Informatics Association, 2018
Samuel Aronson; Lawrence Babb; Darren Ames; Richard A Gibbs; Eric Venner; John J Connelly; Keith Marsolo; Chunhua Weng; Marc S Williams; Andrea L Hartzler; Wayne H Liang; James D Ralston; Emily Beth Devine; Shawn Murphy; Christopher G Chute; Pedro J Caraballo; Iftikhar J Kullo; Robert R Freimuth; Luke V Rasmussen; Firas H Wehbe; Josh F Peterson; Jamie R Robinson; Ken Wiley; Casey Overby Taylor; eMERGE Network EHRI Working Group

Deep phenotyping on electronic health records facilitates genetic diagnosis by clinical exomes
The American Journal of Human Genetics, 2018
Jung Hoon Son; Gangcai Xie; Chi Yuan; Lyudmila Ena; Ziran Li; Andrew Goldstein; Lulin Huang; Liwei Wang; Feichen Shen; Hongfang Liu; Karla Mehl; Emily E Groopman; Maddalena Marasa; Krzysztof Kiryluk; Ali G Gharavi; Wendy K Chung; George Hripcsak; Carol Friedman; Chunhua Weng; Kai Wang


A conceptual framework for evaluating data suitability for observational studies
Journal of the American Medical Informatics Association, 2018
Ning Shang; Chunhua Weng; George Hripcsak

Clinical concept value sets and interoperability in health data analytics
AMIA Annual Symposium Proceedings, 2018
Sigfried Gold; Andrea Batch; Robert McClure; Guoqian Jiang; Hadi Kharrazi; Rishi Saripalle; Vojtech Huser; Chunhua Weng; Nancy Roderer; Ana Szarfman; Niklas Elmqvist; David Gotz

Columbia Open Health Data, clinical concept prevalence and co-occurrence from electronic health records
Scientific data, 2018
Casey N Ta; Michel Dumontier; George Hripcsak; Nicholas P Tatonetti; Chunhua Weng

Detecting potential pleiotropy across cardiovascular and neurological diseases using univariate, bivariate, and multivariate methods on 43,870 individuals from the eMERGE network
BIOCOMPUTING 2019: Proceedings of the Pacific Symposium, 2018
Xinyuan Zhang; Yogasudha Veturi; Shefali Verma; William Bone; Anurag Verma; Anastasia Lucas; Scott Hebbring; Joshua C Denny; Ian B Stanaway; Gail P Jarvik; David Crosslin; Eric B Larson; Laura Rasmussen-Torvik; Sarah A Pendergrass; Jordan W Smoller; Hakon Hakonarson; Patrick Sleiman; Chunhua Weng; David Fasel; Wei-Qi Wei; Iftikhar Kullo; Daniel Schaid; Wendy K Chung; Marylyn D Ritchie

Methods for quality assessment in secondary use of EHR data
For Medical Informatics Initiative Germany, 2018
Nicole Weiskopf; Chunhua Weng

2017


Systematic data ingratiation of clinical trial recruitment locations for geographic-based query and visualization
International journal of medical informatics, 2017
Jake Luo; Weiheng Chen; Min Wu; Chunhua Weng


An OMOP CDM-based relational database of clinical research eligibility criteria
Studies in health technology and informatics, 2017
Yuqi Si; Chunhua Weng

A survey of practices for the use of electronic health records to support research recruitment
Journal of clinical and translational science, 2017
Jihad S Obeid; Laura M Beskow; Marie Rape; Ramkiran Gouripeddi; R Anthony Black; James J Cimino; Peter J Embi; Chunhua Weng; Rebecca Marnocha; John B Buse

A data quality assessment guideline for electronic health record data reuse
Egems, 2017
Nicole G Weiskopf; Suzanne Bakken; George Hripcsak; Chunhua Weng

Correlating eligibility criteria generalizability and adverse events using Big Data for patients and clinical trials
Annals of the New York Academy of Sciences, 2017
Anando Sen; Patrick B Ryan; Andrew Goldstein; Shreya Chakrabarti; Shuang Wang; Eileen Koski; Chunhua Weng

Correlating lab test results in clinical notes with structured lab data: a case study in hba1c and glucose
AMIA Summits on Translational Science Proceedings, 2017
Sijia Liu; Liwei Wang; Donna Ihrke; Vipin Chaudhary; Cui Tao; Chunhua Weng; Hongfang Liu

An interoperable similarity-based cohort identification method using the omop common data model version 5.0
Journal of healthcare informatics research, 2017
Shreya Chakrabarti; Anando Sen; Vojtech Huser; Gregory W Hruby; Alexander Rusanov; David J Albers; Chunhua Weng

Building a semantic web-based metadata repository for facilitating detailed clinical modeling in cancer genome studies
Journal of biomedical semantics, 2017
Deepak K Sharma; Harold R Solbrig; Cui Tao; Chunhua Weng; Christopher G Chute; Guoqian Jiang

Evidence appraisal: a scoping review, conceptual framework, and research agenda
Journal of the American Medical Informatics Association, 2017
Andrew Goldstein; Eric Venker; Chunhua Weng

EliIE: An open-source information extraction system for clinical trial eligibility criteria
Journal of the American Medical Informatics Association, 2017
Tian Kang; Shaodian Zhang; Youlan Tang; Gregory W Hruby; Alexander Rusanov; Noémie Elhadad; Chunhua Weng

2016


A multi-site cognitive task analysis for biomedical query mediation
International journal of medical informatics, 2016
Gregory W Hruby; Luke V Rasmussen; David Hanauer; Vimla L Patel; James J Cimino; Chunhua Weng

Assessing eligibility criteria generalizability and their correlations with adverse events using big data for ehrs and clinical trials
Proceedings of the Data Science Learning and Applications to Biomedical and Health Sciences Conference (Big Data Workshop organized by New York Academy of Sciences), 2016
Anando Sen; Patrick Ryan; Andrew Goldstein; Shreya Chakrabarti; Shuang Wang; Chunhua Weng

Learning optimal individualized treatment rules from electronic health record data
2016 IEEE International Conference on Healthcare Informatics (ICHI), 2016
Yuanjia Wang; Peng Wu; Ying Liu; Chunhua Weng; Donglin Zeng

Data-driven and expert-based informatics approaches to identifying HIV-associated common data elements (CDE) in empirically generated and knowledge-based resources
APHA 2016 Annual Meeting & Expo (Oct. 29-Nov. 2, 2016), 2016
William Brown III; Timothy Frasca; Chunhua Weng; David Vawdrey; Alex Carballo-Diéguez; Suzanne Bakken


Expert-based and data-driven informatics methods for characterizing semantic heterogeneity among HIV-associated datasets
APHA 2016 Annual Meeting & Expo (Oct. 29-Nov. 2, 2016), 2016
William Brown III; Timothy Frasca; Chunhua Weng; David Vawdrey; Alex Carballo-Diéguez; Suzanne Bakken

SMASH: A Data-driven Informatics Method to Assist Experts in Characterizing Semantic Heterogeneity among Data Elements
AMIA Annual Symposium Proceedings, 2016
William Brown III; Chunhua Weng; David K Vawdrey; Alex Carballo-Diéguez; Suzanne Bakken

Unsupervised time-series clustering over lab data for automatic identification of uncontrolled diabetes
2016 IEEE International Conference on Healthcare Informatics (ICHI), 2016
Alexander Rusanov; Patric V Prado; Chunhua Weng

Pathogenic mutations in cancer-predisposing genes: A survey of 300 patients with whole-genome sequencing and lifetime electronic health records
Plos one, 2016
Karen Y He; Yiqing Zhao; Elizabeth W McPherson; Quan Li; Fan Xia; Chunhua Weng; Kai Wang; Max M He

A harmonized data quality assessment terminology and framework for the secondary use of electronic health record data
Egems, 2016
Michael G Kahn; Tiffany J Callahan; Juliana Barnard; Alan E Bauck; Jeff Brown; Bruce N Davidson; Hossein Estiri; Carsten Goerg; Erin Holve; Steven G Johnson; Siaw-Teng Liaw; Marianne Hamilton-Lopez; Daniella Meeker; Toan C Ong; Patrick Ryan; Ning Shang; Nicole G Weiskopf; Chunhua Weng; Meredith N Zozus; Lisa Schilling

Identification of questionable exclusion criteria in mental disorder clinical trials using a medical encyclopedia
Biocomputing 2016: Proceedings of the Pacific Symposium, 2016
Handong Ma; Chunhua Weng

Automated learning of domain taxonomies from text using background knowledge
Journal of biomedical informatics, 2016
Julia Hoxha; Guoqian Jiang; Chunhua Weng

DREAM: Classification scheme for dialog acts in clinical research query mediation
Journal of biomedical informatics, 2016
Julia Hoxha; Praveen Chandar; Zhe He; James Cimino; David Hanauer; Chunhua Weng

How have cancer clinical trial eligibility criteria evolved over time?
AMIA Summits on Translational Science Proceedings, 2016
Anil Yaman; Shreya Chakrabarti; Anando Sen; Chunhua Weng


A data-driven concept schema for defining clinical research data needs
International journal of medical informatics, 2016
Gregory W Hruby; Julia Hoxha; Praveen Chandar Ravichandran; Eneida A Mendonça; David A Hanauer; Chunhua Weng

Multivariate analysis of the population representativeness of related clinical studies
Journal of biomedical informatics, 2016
Zhe He; Patrick Ryan; Julia Hoxha; Shuang Wang; Simona Carini; Ida Sim; Chunhua Weng


Facilitating biomedical researchers’ interrogation of electronic health record data: Ideas from outside of biomedical informatics
Journal of biomedical informatics, 2016
Gregory W Hruby; Konstantina Matsoukas; James J Cimino; Chunhua Weng

GIST 2.0: A scalable multi-trait metric for quantifying population representativeness of individual clinical studies
Journal of biomedical informatics, 2016
Anando Sen; Shreya Chakrabarti; Andrew Goldstein; Shuang Wang; Patrick B Ryan; Chunhua Weng

Bacterial clinical infectious diseases ontology (BCIDO) dataset
Data Brief, 2016
Claire L Gordon; Chunhua Weng

Valx: a system for extracting and structuring numeric lab test comparison statements from text
Methods of information in medicine, 2016
Tianyong Hao; Hongfang Liu; Chunhua Weng

2015


Case-based reasoning using electronic health records efficiently identifies eligible patients for clinical trials
Journal of the American Medical Informatics Association, 2015
Riccardo Miotto; Chunhua Weng

Structuring clinical trial eligibility criteria with the common data model
CiteSeerX, 2015
Gal Levy-fix; Anil Yaman; Chunhua Weng

Exploration of temporal icd coding bias related to acute diabetic conditions
AMIA Annual Symposium Proceedings, 2015
Mollie McKillop; Fernanda Polubriaginof; Chunhua Weng

What Are Frequent Data Requests from Researchers? A Conceptual Model of Researchers' EHR Data Needs for Comparative Effectiveness Research.
AMIA, 2015
Gregory William Hruby; Praveen Chandar Ravichandran; Julia Hoxha; Eneida A Mendonça; David A Hanauer; Chunhua Weng

Clinical Trial Eligibility Criteria and the Burden of Generalizability
OHDSI Talk, 2015
Amelia J Averitt; Chunhua Weng; Adler J Perotte

Assessing the collective population representativeness of related type 2 diabetes trials by combining public data from ClinicalTrials. gov and NHANES
Studies in health technology and informatics, 2015
Zhe He; Shuang Wang; Elhaam Borhanian; Chunhua Weng

Examination of Temporal ICD Coding Bias Related to Acute Diseases
CiteSeerX, 2015
Mollie McKillop; Fernanda Polubriaginof; Chunhua Weng

Optimizing clinical research participant selection with informatics
Trends in pharmacological sciences, 2015
Chunhua Weng

Quality assurance of cancer study common data elements using a post-coordination approach
AMIA Annual Symposium Proceedings, 2015
Guoqian Jiang; Harold R Solbrig; Eric Prud'hommeaux; Cui Tao; Chunhua Weng; Christopher G Chute

Simulation-based evaluation of the generalizability index for study traits
AMIA Annual Symposium Proceedings, 2015
Zhe He; Praveen Chandar; Patrick Ryan; Chunhua Weng

Practical considerations in genomic decision support: The eMERGE experience
Journal of pathology informatics, 2015
Timothy M Herr; Suzette J Bielinski; Erwin Bottinger; Ariel Brautbar; Murray Brilliant; Christopher G Chute; Beth L Cobb; Joshua C Denny; Hakon Hakonarson; Andrea L Hartzler; George Hripcsak; Joseph Kannry; Isaac S Kohane; Iftikhar J Kullo; Simon Lin; Shannon Manzi; Keith Marsolo; Casey Lynnette Overby; Jyotishman Pathak; Peggy Peissig; Jill Pulley; James Ralston; Luke Rasmussen; Dan M Roden; Gerard Tromp; Timothy Uphoff; Chunhua Weng; Wendy Wolf; Marc S Williams; Justin Starren


Visual aggregate analysis of eligibility features of clinical trials
Journal of biomedical informatics, 2015
Zhe He; Simona Carini; Ida Sim; Chunhua Weng

Adaptive semantic tag mining from heterogeneous clinical research texts
Methods of information in medicine, 2015
Tianyong Hao; Chunhua Weng

Biomedical Data Management and Graph Online Querying
Book, 2015
Fusheng Wang; Gang Luo; Chunhua Weng; Arijit Khan; Prasenjit Mitra; Cong Yu

Initial readability assessment of clinical trial eligibility criteria
AMIA Annual Symposium Proceedings, 2015
Tian Kang; Noémie Elhadad; Chunhua Weng

Similarity-based recommendation of new concepts to a terminology
AMIA annual symposium proceedings, 2015
Praveen Chandar; Anil Yaman; Julia Hoxha; Zhe He; Chunhua Weng

Use of self-service query tools varies by experience and research knowledge
MEDINFO 2015: eHealth-enabled Health, 2015
Gregory W Hruby; Jessica Ancker; Chunhua Weng


Desiderata for Major Eligibility Criteria in Breast Cancer Clinical Trials
AMIA Annual Symposium Proceedings, 2015
Matthew L Paulson; Chunhua Weng

Research Data Explorer: Lessons Learned in Design and Development of Context-based Cohort Definition and Selection
AMIA Summits on Translational Science Proceedings, 2015
Adam Wilcox; David Vawdrey; Chunhua Weng; Mark Velez; Suzanne Bakken

2014


Development and validation of an electronic phenotyping algorithm for chronic kidney disease
AMIA Annual Symposium Proceedings, 2014
Girish N Nadkarni; Omri Gottesman; James G Linneman; Herbert Chase; Richard L Berg; Samira Farouk; Rajiv Nadukuru; Vaneet Lotay; Steve Ellis; George Hripcsak; Peggy Peissig; Chunhua Weng; Erwin P Bottinger

Using software to elicit user needs for clinical research visit scheduling
AMIA Summits on Translational Science Proceedings, 2014
Chunhua Weng; Mary Regina Boland; Yat So; Alexander Rusanov; Carlos Lopez; Richard Steinman; Linda Busacca; Suzanne Bakken; J Thomas Bigger

Cross-system evaluation of clinical trial search engines
AMIA Summits on Translational Science Proceedings, 2014
Silis Y Jiang; Chunhua Weng

What is asked in clinical data request forms? A multi-site thematic analysis of forms towards better data access support
AMIA Annual Symposium Proceedings, 2014
David A Hanauer; Gregory W Hruby; Daniel G Fort; Luke V Rasmussen; Eneida A Mendonça; Chunhua Weng


Temporal analysis of the usage log of a research networking system
AMIA Summits on Translational Science Proceedings, 2014
Sunmoo Yoon; Sylvia Trembowelski; Richard C Steinman; Suzanne Bakken; Chunhua Weng

Enhancing electronic health records to support clinical research
AMIA Summits on Translational Science Proceedings, 2014
David K. Vawdrey; Chunhua Weng; David Herion; James J. Cimino

A method for analyzing commonalities in clinical trial target populations
AMIA Annual Symposium Proceedings, 2014
Zhe He; Simona Carini; Tianyong Hao; Ida Sim; Chunhua Weng

Could patient self-reported health data complement EHR for phenotyping?
AMIA Annual Symposium Proceedings, 2014
Daniel Fort; Adam B Wilcox; Chunhua Weng

Toward a cognitive task analysis for biomedical query mediation
AMIA Summits on Translational Science Proceedings, 2014
Gregory W. Hruby; James J. Cimino; Vimla Patel; and Chunhua Weng

Towards symbiosis in knowledge representation and natural language processing for structuring clinical practice guidelines
Studies in health technology and informatics, 2014
Chunhua Weng; Philip R O Payne; Mark Velez; Stephen B Johnson; Suzanne Bakken

Clustering clinical trials with similar eligibility criteria features
Journal of biomedical informatics, 2014
Tianyong Hao; Alexander Rusanov; Mary Regina Boland; Chunhua Weng

Automatic generation of investigator bibliographies for institutional research networking systems
Journal of biomedical informatics, 2014
Stephen B Johnson; Michael E Bales; Daniel Dine; Suzanne Bakken; Paul J Albert; Chunhua Weng


Hidden in plain sight: bias towards sick patients when sampling patients with sufficient electronic health record data for research
BMC medical informatics and decision making, 2014
Alexander Rusanov; Nicole G Weiskopf; Shuang Wang; Chunhua Weng


From expert-derived user needs to user-perceived ease of use and usefulness: a two-phase mixed-methods evaluation framework
Journal of biomedical informatics, 2014
Mary Regina Boland; Alexander Rusanov; Yat So; Carlos Lopez-Jimenez; Linda Busacca; Richard C Steinman; Suzanne Bakken; J Thomas Bigger; Chunhua Weng

Considerations for using research data to verify clinical data accuracy
AMIA Summits on Translational Science Proceedings, 2014
Daniel Fort; Chunhua Weng; Suzanne Bakken; Adam B. Wilcox

Absence of Pancreatic Intraepithelial Neoplasia (PanIN) Predicts Poor Survival Following Resection of Pancreatic Cancer
Pancreas, 2014
Benjamin G. Hassid; Aimee L. Lucas; Marcela Salomao; Chunhua Weng; Feng Liu; Lauren G. Khanna; Sheila Kumar; Caroline Hwang; John A. Chabot; Harold Frucht

Impact of cervical effacement and fetal station on progress during the first stage of labor: A biexponential model
American journal of perinatology, 2014
Maria M E Quincy; Chunhua Weng; Steven L Shafer; Richard M Smiley; Pamela D Flood; Fadi G Mirza

Building a semantic web-based metadata repository for facilitating detailed clinical modeling in cancer genome studies
SWAT4LS, 2014
Deepak K Sharma; Harold R Solbrig; Cui Tao; Chunhua Weng; Christopher G Chute; Guoqian Jiang

Associating co-authorship patterns with publications in high-impact journals
Journal of biomedical informatics, 2014
Michael E Bales; Daniel C Dine; Jacqueline A Merrill; Stephen B Johnson; Suzanne Bakken; Chunhua Weng

Trend and network analysis of common eligibility features for cancer trials in ClinicalTrials. gov
International Conference on Smart Health, 2014
Chunhua Weng; Anil Yaman; Kuo Lin; Zhe He

2013


Unsupervised mining of frequent tags for clinical eligibility text indexing
Journal of biomedical informatics, 2013
Riccardo Miotto; Chunhua Weng

Sick patients have more data: the non-random completeness of electronic health records
AMIA Annual Symposium Proceedings, 2013
Nicole G Weiskopf; Alex Rusanov; Chunhua Weng

Design and evaluation of a bacterial clinical infectious diseases ontology
AMIA Annual Symposium Proceedings, 2013
Claire L Gordon; Stephanie Pouch; Lindsay G Cowell; Mary Regina Boland; Heather L Platt; Albert Goldfain; Chunhua Weng

Towards dynamic and interactive retrieval of clinical trials using common eligibility features.
AMIA Joint Summits on Translational Science proceedings. AMIA Joint Summits on Translational Science, 2013
Riccardo Miotto; Chunhua Weng

Evaluation considerations for EHR-based phenotyping algorithms: A case study for drug-induced liver injury
AMIA Summits on Translational Science Proceedings, 2013
Casey Lynnette Overby; Chunhua Weng; Krystl Haerian; Adler Perotte; Carol Friedman; George Hripcsak

Characterization of the biomedical query mediation process
AMIA Summits on Translational Science Proceedings, 2013
Gregory W. Hruby; Mary Regina Boland; James J. Cimino; Junfeng Gao; Adam B. Wilcox; Julia Hirschberg; Chunhua Weng

Opportunities for genomic clinical decision support interventions
Genetics in Medicine, 2013
Casey Lynnette Overby; Isaac Kohane; Joseph L Kannry; Marc S Williams; Justin Starren; Erwin Bottinger; Omri Gottesman; Joshua C Denny; Chunhua Weng; Peter Tarczy-Hornoch; George Hripcsak


A method for probing disease relatedness using common clinical eligibility criteria
Studies in health technology and informatics, 2013
Mary Regina Boland; Riccardo Miotto; Chunhua Weng

Methods and dimensions of electronic health record data quality assessment: enabling reuse for clinical research
Journal of the American Medical Informatics Association, 2013
Nicole Gray Weiskopf; Chunhua Weng


eTACTS: a method for dynamically filtering clinical trial search results
Journal of biomedical informatics, 2013
Riccardo Miotto; Silis Jiang; Chunhua Weng

Extracting and normalizing temporal expressions in clinical data requests from researchers
International Conference on Smart Health, 2013
Tianyong Hao; Alex Rusanov; Chunhua Weng

Defining and measuring completeness of electronic health records for secondary use
Journal of biomedical informatics, 2013
Nicole G. Weiskopf; George Hripcsak; Sushmita Swaminathan; Chunhua Weng


An Integrated Model for Patient Care and Clinical Trials (IMPACT) to support clinical research visit scheduling workflow for future learning health systems
Journal of biomedical informatics, 2013
Chunhua Weng; Yu Li; Solomon Berhe; Mary Regina Boland; Junfeng Gao; Gregory W Hruby; Richard C Steinman; Carlos Lopez-Jimenez; Linda Busacca; George Hripcsak; Suzanne Bakken; J Thomas Bigger

Discovering medical conditions associated with periodontitis using linked electronic health records
Journal of clinical periodontology, 2013
Mary Regina Boland; George Hripcsak; David J Albers; Ying Wei; Adam B Wilcox; Jin Wei; Jianhua Li; Steven Lin; Michael Breene; Ronnie Myers; John Zimmerman; Panos N Papapanou; Chunhua Weng

A centralized research data repository enhances retrospective outcomes research capacity: a case report
Journal of the American Medical Informatics Association, 2013
Gregory William Hruby; James McKiernan; Suzanne Bakken; Chunhua Weng

A human-computer collaborative approach to identifying common data elements in clinical trial eligibility criteria
Journal of biomedical informatics, 2013
Zhihui Luo; Riccardo Miotto; Chunhua Weng

Defining a comprehensive verotype using electronic health records for personalized medicine
Journal of the American Medical Informatics Association, 2013
Mary Regina Boland; George Hripcsak; Yufeng Shen; Wendy K Chung; Chunhua Weng

A collaborative approach to developing an electronic health record phenotyping algorithm for drug-induced liver injury
Journal of the American Medical Informatics Association, 2013
Casey Lynnette Overby; Jyotishman Pathak; Omri Gottesman; Krystl Haerian; Adler Perotte; Sean Murphy; Kevin Bruce; Stephanie Johnson; Jayant Talwalkar; Yufeng Shen; Steve Ellis; Iftikhar Kullo; Christopher Chute; Carol Friedman; Erwin Bottinger; George Hripcsak; Chunhua Weng

2012


An Initial Log-based Usage Analysis of Research Networking Systems
AMIA Summits on Translational Science Proceedings 2012, 2012
Mary Regina Boland; SB Johnson; S Trembowelski; DC Dine; RC Steinman; S Bakken; C Weng

Clinical research informatics: a conceptual perspective
Journal of the American Medical Informatics Association, 2012
Michael G Kahn; Chunhua Weng

Using EHRs to integrate research with patient care: promises and challenges
Journal of the American Medical Informatics Association, 2012
Chunhua Weng; Paul Appelbaum; George Hripcsak; Ian Kronish; Linda Busacca; Karina W Davidson; J Thomas Bigger

An initial log analysis of usage patterns on a research networking system
Clinical and translational science, 2012
Mary Regina Boland; Sylvia Trembowelski; Suzanne Bakken; Chunhua Weng

Natural language processing, electronic health records, and clinical research
Clinical Research Informatics, 2012
Feifan Liu; Chunhua Weng; Hong Yu

EliXR-TIME: a temporal knowledge representation for clinical research eligibility criteria
AMIA summits on translational science proceedings, 2012
Mary Regina Boland; Samson W Tu; Simona Carini; Ida Sim; Chunhua Weng

2011


Similarity-based Disease Risk Assessment for Personal Genomes: Proof of Concept
AMIA Annual Symposium Proceedings, 2011
Jung Hoon Woo; Albert M Lai; Wendy K Chung; Chunhua Weng

317: Validation of a bi-exponential model for labor progress in a cohort of mixed parity with quantification of the impact of cervical effacement and fetal station
American Journal of Obstetrics & Gynecology, 2011
Maria Quincy; Fadi Mirza; Chunhua Weng; Richard Smiley; Pamela Flood

A real-time screening alert improves patient recruitment efficiency
AMIA Annual Symposium Proceedings, 2011
Chunhua Weng; Candido Batres; Tomas Borda; Nicole G Weiskopf; Adam B Wilcox; J Thomas Bigger; Karina W Davidson

EliXR: an approach to eligibility criteria extraction and representation
Journal of the American Medical Informatics Association, 2011
Chunhua Weng; Xiaoying Wu; Zhihui Luo; Mary Regina Boland; Dimitri Theodoratos; Stephen B Johnson

Extracting temporal constraints from clinical research eligibility criteria using conditional random fields
AMIA annual symposium proceedings, 2011
Zhihui Luo; Stephen B Johnson; Albert M Lai; Chunhua Weng

Beta-2 adrenoceptor genotype and progress in term and late preterm active labor
American journal of obstetrics and gynecology, 2011
Russell S Miller; Richard M Smiley; Danette Daniel; Chunhua Weng; Charles W Emala; Jean-Louis Blouin; Pamela D Flood

Dynamic categorization of clinical research eligibility criteria by hierarchical clustering
Journal of biomedical informatics, 2011
Zhihui Luo; Meliha Yetisgen-Yildiz; Chunhua Weng


2010


Comparing the effectiveness of a clinical registry and a clinical data warehouse for supporting clinical trial recruitment: a case study
AMIA Annual Symposium Proceedings, 2010
Chunhua Weng; J Thomas Bigger; Linda Busacca; Adam Wilcox; Asqual Getaneh


Corpus-based approach to creating a semantic lexicon for clinical research eligibility criteria from UMLS
Summit on Translational Bioinformatics, 2010
Zhihui Luo; Robert Duffy; Stephen Johnson; Chunhua Weng

Aligning structured and unstructured medical problems using UMLS
AMIA Annual Symposium Proceedings, 2010
Lorena Carlo; Herbert S Chase; Chunhua Weng

Secondary use of EHR: data quality issues and informatics opportunities
Summit on Translational Bioinformatics, 2010
Taxiarchis Botsis; Gunnar Hartvigsen; Fei Chen; Chunhua Weng

Developing a multivariable prognostic model for pancreatic endocrine tumors using the clinical data warehouse resources of a single institution
Applied clinical informatics, 2010
Taxiarchis Botsis; Valsamo K Anagnostou; Gunnar Hartvigsen; George Hripcsak; Chunhua Weng

Formal representation of eligibility criteria: a literature review
Journal of biomedical informatics, 2010
Chunhua Weng; Samson W Tu; Ida Sim; Rachel Richesson

Special report: Identifying interdisciplinary research priorities to prevent and treat pediatric obesity in New York City
Clinical and translational science, 2010
Dympna Gallagher; Elaine L. Larson; Yun-Hsin Claire Wang; Boyd Richards; Chunhua Weng; Patricia Hametz; Melissa D. Begg; Wendy K. Chung; Bernadette Boden-Albala; Sharon R. Akabas

2009


A Phenome-Wide Association Study Through Secondary Uses of Clinical and Research Data
, 2009
Chunhua Weng; Richard Smiley; Pamela Flood; Bin Cheng; Carol Friedman; George Hripcsak

Electronic screening improves efficiency in clinical trial recruitment
Journal of the American Medical Informatics Association, 2009
Samir R. Thadani; Chunhua Weng; J. Thomas Bigger; John F. Ennever; David Wajngurt

Graphic analysis of population structure on genome-wide rheumatoid arthritis data
BMC proceedings, 2009
Jun Zhang; Chunhua Weng; Partha Niyogi

Development, Selection, and Adoption of Clinical Research Eligibility Representation Standards and Screening Methods: Current and Future Directions
Fall AMIA 2009 Panel, 2009
Joyce C Niland; MD Gilan El Saadawi; Chunhua Weng; Vojtech Huser; Jason P Jones; Rachel Richesson

Using personal health records for automated clinical trials recruitment: the ePaIRing Model
Summit on translational bioinformatics, 2009
Adam Wilcox; Karthik Natarajan; Chunhua Weng

Modeling prognostic factors in resectable pancreatic adenocarcinomas
Cancer Informatics, 2009
Taxiarchis Botsis; Valsamo K. Anagnostou; Gunnar Hartvigsen; George Hripcsak; Chunhua Weng

A review of auditing methods applied to the content of controlled biomedical terminologies
Journal of biomedical informatics, 2009
Xinxin Zhu; Jung-Wei Fan; David M. Baorto; Chunhua Weng; James J. Cimino

2008


Informatics tools for meeting information and communication needs related to interdisciplinary research competency development
AMIA... Annual Symposium proceedings. AMIA Symposium, 2008
Suzanne Bakken; Po-Yin Yen; Chunhua Weng

Social network analysis of interdisciplinarity in obesity research
AMIA Annu Symp Proc, 2008
Michael Bales; Stephen B Johnson; Chunhua Weng

ECRL: an eligibility criteria representation language based on the UMLS Semantic Network
AMIA... Annual Symposium proceedings. AMIA Symposium, 2008
Chintan O Patel; Chunhua Weng

Comparing ICD9-encoded diagnoses and NLP-processed discharge summaries for clinical trials pre-screening: a case study
AMIA Annual Symposium Proceedings, 2008
Li Li; Herbert S Chase; Chintan O Patel; Carol Friedman; Chunhua Weng

Understanding interdisciplinary health sciences collaborations: a campus-wide survey of obesity experts
AMIA Annual Symposium Proceedings, 2008
Chunhua Weng; Dympna Gallagher; Michael E Bales; Suzanne Bakken; Henry N Ginsberg

2007


Collective Domain Modeling across Clinical Trials Standards: Needs, Challenges, and Design Implications
Information Technology and Communications in Health (ITCH), 2007
Chunhua Weng; Michael Becich; Douglas Fridsma

User-centered semantic harmonization: a case study
Journal of biomedical informatics, 2007
Chunhua Weng; John H Gennari; Douglas B Fridsma

Participatory design of a collaborative clinical trial protocol writing system
International Journal of Medical Informatics, 2007
Chunhua Weng; David W. McDonald; Dana Sparks; Jason McCoy; John H.Gennari

2006


A call for collaborative semantic harmonization
AMIA Annual Symposium Proceedings, 2006
Chunhua Weng; Douglas B. Fridsma

2005




Asynchronous communication among clinical researchers: A study for systems design
International journal of medical informatics, 2005
John H.Gennari; ChunhuaWeng; JacquelineBenedetti; David W.McDonald

2004


Annotation and Asynchronous Collaborative Writing
Proc of CSCW'04, 2004
Chunhua Weng; J.H. Gennari

A collaborative clinical trial protocol writing system
MEDINFO 2004, 2004
Chunhua Weng; John H Gennari; David W McDonald

Asynchronous collaborative writing through annotations
Proceedings of the 2004 ACM conference on Computer supported cooperative work, 2004
Chunhua Weng; John H. Gennari.

The multiple views of inter-organizational authoring
Proceedings of the 2004 ACM conference on Computer supported cooperative work, 2004
David W. McDonald; Chunhua Weng; John H. Gennari

An ethnographic study of collaborative clinical trial protocol writing
MEDINFO 2004, 2004
John H Gennari; Chunhua Weng; David W McDonald; Jacqueline Benedetti; Stephanie Green

2003


Scenario-based participatory design of a collaborative clinical trial protocol authoring system
AMIA Annual Symposium Proceedings, 2003
Chunhua Weng; John H Gennari; David W McDonald

2002


Temporal knowledge representation for scheduling tasks in clinical trial protocols
Proceedings of the AMIA Symposium, 2002
Chunhua Weng; Michael Kahn; John Gennari