• March 27 - 30, 2017, San Francisco

    2017 Joint Summits

2017 Joint Summits Podium Presentations

Monday, March 27

10:30 a.m. – 12:00 p.m.

S04: Podium Presentations – Informatics Signatures of Disease

Biological Activity Biomarkers in a Biobank Cohort: An Evaluation of Metabolomic and Clinical Biomarkers in Metformin and Type 2 Diabetes 
M. Breitenstein, A. Clay, K. Nair, Mayo Clinic; R. Kaddurah-Daouk, Duke University ; R. Weinshilboum, L. Wang, Mayo Clinic

Biomarker Discovery, Ranking and Mechanistic Annotation for Severe Malarial Anemia in Children 
S. Mani, D. Cannon, P. Kempaiah, C. Bologa, D. Perkins, University of New Mexico

Dysregulated Innate Immune Response is a Robust Marker of Allograft Injury and Survival Across All Transplanted Organs
M. Donato, T. Azad, Stanford University; L. Heylen, University of Leuven; S. Shen-Orr, Technion-Israel Institute of Technology; T. Sweeney, P. Khatri, Stanford University; M. Naesens, University of Leuven

Multi-cohort Analysis of Systemic Sclerosis Identifies Robust Transcriptional Signature of Disease Severity 
S. Lofgren, Stanford University; M. Hinchcliff, M. Carns, Northwestern University; T. Wood, Dartmouth University; K. Aren, E. Arroyo, Northwestern University; P. Cheung, A. Kuo, A. Valenzuela, L. Chung, D. Fiorentino, P. Utz, P. Khatri, Stanford University; A. Haemel, P. Wolters, F. Boin, University of California, San Francisco; J. Gordon, R. Spiera, Hospital for Special Surgery; S. Assassi, University of Texas Houston; M. Whitfield, Dartmouth College

Sex Differences in Immune System Gene Expression 
E. Bongen, F. Vallania, P. Utz, P. Khatri, Stanford University

Understanding Human Disease Relationships Through Integrated Molecular and Clinical Analysis 
W. Haynes, R. Vashisht, F. Vallania, C. Liu, G. Gaskin, E. Bongen, S. Lofgren, T. Sweeney, P. Utz, N. Shah, P. Khatri, Stanford University

1:30 p.m. – 3:00 p.m.

S07: Podium Presentations – Data-driven Precision Medicine

repoDB: A New Standard for Drug Repositioning Validation 
A. Brown, C. Patel, Harvard Medical School

A Multi-omics Approach for Identifying Therapeutically Important Pathways in Cancer 
H. Frost, C. Amos, Dartmouth College

Patient-specific Variations in Periodontitis Revealed by Integrated Biomarker Profiling and Ensemble Classification 
R. Nagarajan, J. Ebersole, University of Kentucky

Reversal of Disease Gene Expression Correlates with Drug Efficacy in Cancers 
B. Chen, University of California, San Francisco; L. Ma, Stanford University; H. Paik, M. Sirota, M. Chua, S. So, Stanford University; A. Butte, University of California, San Francisco

A Human Factors Approach to Making Complex Cancer Precision Medicine Data Clinically Actionable 
V. Sharma, R. Beckman, S. Rao, Georgetown University Medical Center; A. Fong, A. Hettinger, MedStar Health; S. Boca, P. McGarvey, S. Madhavan, Georgetown University Medical Center; R. Ratwani, MedStar Health

Repurposing Drugs for Precision Medicine: Haplotype-specific Modular Assembly of Drug Safety Subnetworks (hapMADSS) 
T. Lorberbaum, A. Yahi, N. Tatonetti, Columbia University

3:30 p.m. – 5:00 p.m.

S09: Podium Presentations – Data Integration and Interoperability

Devleopment of a Novel Ontology for Biobanking (OBIB) Through a Cross Disciplinary and Multi-institutional Collaboration 
C. Stoeckert, D. Birtwell, University of Pennsylvania; M. Brochhausen, University of Arkansas; H. Ellis, A. Masci, Duke University ; P. Guan, H. Moore, National Cancer Institute; F. Manion, University of Michigan; J. Obeid, Medical University of South Carolina; L. Schick, Samvit Solutions; H. Williams, J. Zheng, University of Pennsylvania

Effect of Evolution of the Gene Ontology on Interpretation of Experiments: Implications for Reproducibility 
A. Tomczak, J. Mortensen, R. Winnenburg, W. Haynes, C. Liu, D. Alessi, F. Vallania, S. Lofgren, V. Swamy, N. Shah, M. Musen, P. Khatri, Stanford University

immunoStates: A New Strategy to Remove Platform and Disease Bias In Cell-mixture Deconvolution 
F. Vallania, A. Tam, S. Lofgren, M. Alonso, E. Engleman, P. Khatri, Stanford University

Linking Data in dbGaP Using PhenX Measures 
H. Pan, W. Huggins, S. Hwang, J. levy, Y. Qin, J. Guo, RTI International; M. Kimura, M. Feolo, National Center for Biotechnology Information; C. Hamilton, RTI International

Making Phenotypic Data Computable and Discoverable 
C. Mungall, Lawrence Berkeley Labs; J. Jacobsen, Sanger Instittute; J. Balhoff, RTI International; J. Nguyen–Xuan, S. Lewis, Lawrence Berkeley Labs; K. Shefchek, D. Keith, J. McMurry, S. Bhattamishra, M. Haendel, Oregon Health & Science University; H. Hochheiser, University of Pittsburgh; S. Köhler, Charité – Universitätsmedizin; P. Robinson, The Jackson Laboratory for Genomic Medicine; T. Groza, Garvan Institute

Utilizing Integrative Multi-omic Data Analysis Methods Within an Automated Workflow System 
A. Srivastava, The Ohio State University; R. Adusumilli, Stanford University; V. Ratnakar, R. Mayani, Y. Gil, University of Southern California; P. Mallick, Stanford University; K. Huang, R. Machiraju, The Ohio State University

S10: Podium Presentations – Deep Phenotyping of Disease

A Network Approach for the Identification of Transcriptional Modules in Chronic Leukemia from – Omics Data Integration 
E. Sauta, A. Demartini, F. Vitali, University of Pavia; A. Riva, Interdisciplinary Center for Biotechnology Research/University of Florida; M. Della Porta, Humanitas Cancer Center and Research Hospital; R. Bellazzi, University of Pavia

Bayesian Network Discovery of Differences in Breast Cancer Gene Expression Between Pre- and Post-menopausal Women 
Y. Liu, V. Gopalakrishnan, University of Pittsburgh

Characterizing the Temporal Patterns of Diseases and Deaths at Scale Using Healthcare Records from Over 2.1 Million Patients
H. Paik, K. Kodama, D. Hadley, M. Sirota, A. Butte, University of California, San Francisco

Deep Phenotyping to Aid Coding and Non-coding Rare Disease Variants 
D. Smedley, QMUL; M. Schubach, Charite; J. Jacobsen, QMUL; G. Valentini, University of Milan; C. Mungall, LBNL; S. Köhler, Charite; S. Lewis, LBNL; M. Haendel, Oregon Health & Sciences University; P. Robinson, Jackson Laboratory

High-sensitivity EHR Phenotyping Using Recurrent Neural Networks 
J. Romano, P. Thangaraj, A. Yahi, T. Lorberbaum, K. Quinnies, R. Vanguri, B. Kummer, C. Esenwa, J. Luna, M. Elkind, N. Tatonetti, Columbia University

Learning to De-identify Clinical Text with Existing Hybrid Tools 
A. Khalifa, University of Utah; S. Meystre, Medical University of South Carolina

Tuesday, March 28

10:30 a.m. – 12:00 p.m.

S12: Podium Presentations – NLP for Discovery

Biomarker-driven Patient Stratification and Discovery from Clinical Narratives Using NLP Systems 
J. Lin, W. Chan, S. Hmwe, W. Zhu, City of Hope

Targeted Natural Language Processing Improves the Accuracy of Identifying Dialysis Status of Patients from Clinical Narratives 
M. Scheitel, R. Komandur Elayavilli, H. Liu, M. Kessler, J. Shellum, R. Chaudhry, Mayo Clinic

Representation of Occupation Information in Clinical Texts: An Analysis of Free-text Clinical Documentation in Multiple Sources 
E. Lindemann, University of Minnesota; E. Chen, Brown University; S. Rajamani, University of Minnesota; N. Manohar, West Side Community Health Services; Y. Wang, G. Melton, University of Minnesota

Natural Language Processing in NIH Biomedical Translational Research Information System (BTRIS) 
J. Galvez, E. Ayres, A. Beri, K. Rai, S. Rath, NIH

3:30 p.m. – 5:00 p.m.

S21: Podium Presentations – Data Sharing and Governance

A Method for Adjudicating De-identification of Free-text Notes that Provides Auditability and Collaboration with Health Systems 
T. McMahon, M. Hoag, R. Gyore, G. Ator, University of Kansas Medical Center; R. Spaniol, University of Kansas Hospital; R. Waitman, University of Kansas Medical Center

Developing a Method of Transferring Healthcare Research Data from Data Broker to Researcher: Interactive Secure Institutional Data Release Overseer (ISIDRO) 
P. Eads, C. Ganoe, R. Jacobson, T. Onega, Dartmouth College

Count Everything: Secure Count Query Framework Across Big Data Centers 
X. Jiang, C. Farcas, University of California, San Diego; B. Paten, M. Diekhans, University of California, Santa Cruz; P. Avillach, Harvard Medical School; W. Wadge, Overlap Health, Inc.; D. Haussler, University of California, Santa Cruz; L. Ohno-Machado, University of California, San Diego; I. Sim, University of California, San Francisco

Creating a Patient Information Commons from Multiple Research Informatics Platforms 
S. Murphy, Massachusetts General Hospital; C. Herrick, M. Mendis, L. Phillips, A. Porter, Partners Healthcare; G. Weber, S. Churchill, I. Kohane, Harvard Medical School; W. Chan, Partners Healthcare

Making Aggregate Content of ClinicalTrials.gov Freely Available to Everyone 
S. Tibbs, K. Chiswell, Duke Clinical Research Institute; S. Calvert, Clinical Trials Transformation Initiative

Early Successes with Reference Data Governance at an Academic Medical Center 
R. Chandras, J. Xu, S. Nukala, C. DaSilva, NYU Langone Health System; J. Weider, M. Radford, NYU Langone Health System/NYU School of Medicine

Wednesday, March 29

8:30 a.m. – 10:00 a.m.

S23: Podium Presentations – Clinical Predictive Modeling

Mortality Prognostic Model for Peripheral Arterial Disease 
A. Arruda-Olson, N. Afzal, H. Moussa Pacha, A. Said, B. Lewis, C. Scott, K. Bailey, H. Liu, I. Kullo, Mayo Clinic

A Real-time Predictive Model for Identifying High Need, High Cost Patients for Population Health Management 
C. Monsen, University of Washington/Atrius Health; Y. Dvorkis, S. Pal, C. Larish, Atrius Health

Improving Predictive Models with Clustered Sequences: An Application on Heart Failure Risk Prediction 
K. Lin, P. Zhang, G. Yuen-Reed, Y. Li, J. Hu, IBM

Leveraging Machine Learning Based Approaches to Assess Human Papillomavirus Vaccination Sentiment Trends with Twitter 
J. Du, J. Xu, H. Song, C. Tao, The University of Texas Health Science Center at Houston

Prediction of Organ Space Colorectal Surgical Site Infections Using Prognostic Bayesian Network 
Y. Zhou, D. Larson, E. Habermann, J. Naessens, H. Liu, S. Sohn, Mayo Clinic

Using Ensembles of NLP Engines without a Common Type System to Improve Abbreviation Disambiguation 
G. Finley, B. Knoll, University of Minnesota; H. Liu, Mayo Clinic; H. Xu, The University of Texas Health Science Center at Houston; G. Melton, S. Pakhomov, University of Minnesota

10:30 a.m. – 12:00 p.m.

S27: Podium Presentations – Phenotyping Methods

A Study on Phenotyping and Visualizing Black Box Warnings of Antineoplastic Breast Cancer Medications 
D. Sun, G. Sarda, S. Skube, A. Blaes, R. Zhang, G. Melton, University of Minnesota

Developing Computable Phenotypes for Pediatric Chronic Conditions in PEDSnet
L. Utidjian, R. Khare, H. Razzaghi, The Children's Hospital of Philadelphia; A. Dempsey, Children's Hospital Colorado; M. Denburg, C. Forrest, C. Bailey, The Children's Hospital of Philadelphia

Automated Identification of Families in Electronic Health Records to Support Clinical Research

F. Polubriaginof, K. Quinnies, R. Vanguri, A. Yahi, Columbia University; M. Simmerling, Cornell University; I. Ionita–Laza, Columbia University; H. Salmasian, NewYork-Presbyterian Hospital/ Columbia University; S. Bakken, G. Hripcsak, K. Kiryluk, D. Goldstein, N. Tatonetti, Columbia University; D. Vawdrey, NewYork–Presbyterian Hospital/Columbia University

SNOMED CT for Structured, Computable Cancer Synoptic Reporting 
W. Campbell, University of Nebraska Medical Center; D. Karlsson, Linkoping University; A. Lazenby, G. Talmon, J. Campbell, University of Nebraska Medical Center

An Evolving Ecosystem for Natural Language Processing in Department of Veterans Affairs 
J. Garvin, M. Kalsy, Department of Veterans Affairs/University of Utah; C. Brandt, S. Luther, Department of Veterans Affairs; G. Divita, G. Coronado, D. Redd, Q. Zeng, Department of Veterans Affairs/George Washington University

Graph-based Clustering of ICD-10 Codes with Alternative Semantic Contexts 
J. Fan, J. Li, Y. Lussier, The University of Arizona

1:30 p.m. – 3:00 p.m.

S30: Podium Presentations – Genome, Phenome, and Actionability

Genomic Resources with Clinical Actionable Knowledge: A Preliminary Review
X. Jing, Ohio University; M. Sun, Soochow University

Applying Protein Functional Annotation to Clinical Interpretation of Genomic Variants
P. McGarvey, Georgetown Medical Center; A. Nightingale, EMBL–EBI; H. Huang, University of Delaware; M. Martin, EMBL–EBI; C. Wu, University of Delaware/Georgetown Medical Center; S. Madhavan, Georgetown University Medical Center

Comprehensive Analysis of Disease-associated Variants Identifies Shared Genetic Architecture Between Human Autoimmune Diseases 
W. Sikora-Wohlfeld, Stanford University; A. Sengupta, Harker School/University of California, San Francisco; R. Chen, Personalis; A. Butte, M. Sirota, University of California, San Francisco

Integrative Analysis of ExomeSeq and Gene Expression Data for Identification of Novel Non-HLA Variants Associated with Antibody Mediated Rejection in Kidney Transplant 
S. Pineda, T. Sigdel, University of California, San Francisco; A. Jackson, Johns Hopkins Medicine; M. Sirota, M. Sarwal, University of California, San Francisco

Sharing Clinical Pharmacogenomic Test Results via Mobile Devices
R. Rostami, University of Wisconsin; S. Hofer, K. Blagec, H. Xu, Medical University of Vienna; R. Kiefer, Mayo Clinic; M. Samwald, Medical University of Vienna; R. Freimuth, Mayo Clinic

The Genetic Underpinning of Complex Clinical Phenomic Profiles
C. Bauer, Geisinger Health System

S32: Podium Presentations – Data Quality

Informed Presence Bias in the Analysis of Electronic Health Records
B. Goldstein, Duke University/Duke Clinical Research Institute; M. Phelan, Duke Clinical Research Institute; N. Bhavsar, Duke University

Exploring Factors that Contribute to Missing Values in Observational Huntington’s Disease Study Data 
Z. Sun, Y. Li, S. Ghosh, Y. Cheng, IBM T.J. Watson Research Center; A. Mohan, C. Sampaio, CHDI Management/CHDI Foundation; J. Hu, IBM T.J. Watson Research Center

Exploring Completeness in Clinical Data Research Networks with DQe–c 
H. Estiri, Harvard Medical School; K. Stephens, University of Washington; J. Klann, S. Murphy, Harvard Medical School

Understanding the Gaps between Data Quality Checks and Research Capabilities in a Pediatric Data Research Network 
R. Khare, H. Razzaghi, L. Utidjian, M. Miller, C. Bailey, CHOP

Needs–Driven Data Quality Assessment for Clinical Research 
J. Klann, Massachusetts General Hospital/Harvard Medical School/Partners Healthcare System; V. Raghavan, C. Weng, Columbia University; S. Weiler, Harvard Medical School; K. Mandl, Boston Children's Hospital/Harvard Medical School; S. Murphy, Partners Healthcare System/ Massachusetts General Hospital/Harvard Medical School

Heart Failure Data for Patient Treatment Goals at the Point of Care: Automated Data Extraction and Consistent Reference Standard Importance 
S. Meystre, Medical University of South Carolina; Y. Kim, University of Utah; G. Gobbel, M. Matheny, Vanderbilt University; A. Redd, Salt Lake City VA Healthcare System; B. Bray, J. Garvin, University of Utah

Thursday, March 30

10:30 a.m. – 12:00 p.m.

S38: Podium Presentations – Translation in Clinical Practice

Standardized Communications of Quantitative Image Analysis Results Using DICOM: Establishing Interoperability Through Outreach and Community Engagement
A. Fedorov, Brigham and Women's Hospital/Harvard Medical School; D. Rubin, Stanford University; D. Clunie, PixelMed Publishing, LLC; S. Pieper, Isomics Inc.; R. Kikinis, Brigham and Women's Hospital/Harvard Medical School/Fraunhofer MEVIS

Supplementing Electronic Health Records with Census Data to support Clinical Research Informatics 
K. Lenoir, M. Horvath, B. Ostasiewski, W. Futrell, B. Wells, Wake Forest School of Medicine

On Combining Clinical and Cost Pathways for Multimorbid Patients Using Electronic Health Record Data 
Y. Zhang, Weill Cornell Medical College/Cornell University; R. Padman, Carnegie Mellon University

How Do Hospital Patients Engage with a Tablet–based Health Portal? 
B. Ryan, NewYork–Presbyterian Hospital/Columbia University Medical Center; L. Grossman, F. Polubriaginof, Columbia University Medical Center; D. Vawdrey, Columbia University Medical Center/NewYork-Presbyterian Hospital

Problem Based Charting: A Method for Improving Problem List Utilization and Completeness 
R. Li, L. Shieh, G. Krishnan, D. Fang, J. Chen, Stanford University

Usability Testing of a Clinical Document Search Engine for Researchers 
G. Hultman, R. McEwan, S. Pakhomov, S. Skube, G. Melton, University of Minnesota

S39: Podium Presentations – Clinical Visualization and Modeling

Visualizing Healthcare System Dynamics in Biomedical Big Data 
N. Benik, Harvard Medical School; K. Borner, Indiana University; N. Brown, Harvard Medical School; D. Halsey, D. O'Donnell, Indiana University; G. Weber, Harvard Medical School

Decaying Relevance of Clinical Data when Predicting Future Decisions 
M. Alagappan, Beth Israel Deaconess Medical Center; M. Goldstein, S. Asch, Stanford University/Palo Alto Veterans Affairs; R. Altman, J. Chen, Stanford University

Network Abstractions of Prescription Patterns in a Medicaid Population 
R. Nagarajan, J. Talbert, University of Kentucky

Automated Mapping of Concomitant Medication Verbatims to WHO Drug Dictionary Drug Codes with Naïve Bayes Classification 
A. Howland, P. Beineke, P. Allen, Medidata Solutions

A Novel Propensity Modeling Approach to Estimate the Causal Impact of Acute Organ Dysfunction on Long-term Survival In Sepsis 
A. Schuler, Stanford University; D. Wulf, Y. Lu, J. Baker, G. Escobar, Kaiser Permanente Northern California; N. Shah, Stanford University; V. Liu, Kaiser Permanente Northern California

A Deeper Exploration of Contagious Risk and the Neighborhood Effect 
A. Mayampurath, D. Edelson, M. Howell, M. Churpek, S. Volchenboum, University of Chicago

1:30 p.m. – 3:00 p.m.

S41: Podium Presentations – Interoperability and Knowledge Representation

ShEx, RDF and FHIR
E. Prud’hommeaux, W3C/MIT; H. Solbrig, G. Jiang, Mayo Clinic

Research Data Repositories: A Tailored Approach to Secondary Use of Electronic Health Record Data 
E. Sholle, Weill Cornell Medicine; R. Bollapragada, Cornell University; T. Campion, Weill Cornell Medicine

Investigating the Coverage of Diseases across Biomedical Research and Clinical Ontologies 
S. Raje, O. Bodenreider, National Library of Medicine

Strategic Assessment and Planning for the PCORnet Common Data Model 
A. Berchuck, Duke Clinical Research Institute; M. Kahn, University of Colorado; S. Rusincovitch, Duke Clinical and Translational Research Institute; D. Meeker, University of Southern California Keck School of Medicine; S. Murphy, Massachusetts General Hospital; R. Bhosale, University of Florida; K. Marsolo, Cincinnati Children’s Hospital Medical Center; M. Matheny, Vanderbilt University Medical Center; R. Waitman, University of Kansas Medical Center; R. Hess, University of Utah

Deployment of ONC Standard Terminologies within an i2b2 Data Warehouse 
J. Pedersen, B. Gardner, W. Campbell, J. Campbell; J. McClay, University of Nebraska Medical Center

FloMap: A Collaborative Tool for Mapping Local EHR Flowsheet Data to Information Models 
S. Johnson, University of Minnesota, School of Nursing; L. Pruinelli, University of Minnesota, School of Nursing; B. Christie, Fairview Health Services; C. Delaney, University of Minnesota, School of Nursing/University of Minnesota/Institute for Health Informatics; G. Gao, J. Park, University of Minnesota, School of Nursing; A. LaFlamme, S. Sherman, Fairview Health Services; B. Westra, University of Minnesota, School of Nursing/University of Minnesota/Institute for Health Informatics

S43: Podium Presentations – Grand Challenges in Clinical Research Informatics

The Design and Implementation of StudyBudget: A Module for Preparing and Tracking Clinical Research Budgets and Costs 
Y. Bushmanova; J. Patel, L. Wimbiscus Yoon, K. Richey, A. Huskin, M. Baumann, P. Friedman, M. Gurley, S. Sharba, A. Cosentino-Boehm, J. Starren, F. Wehbe, Northwestern University Feinberg School of Medicine

Development and Testing of Participant Provided Information Modules for the Precision Medicine Initiative 
R. Cronin, R. Jerome, B. Mapes, K. Goggins, K. Wallston, K. Donato, Vanderbilt University; M. Couper, M. Elliott, University of Michigan; C. Mouton, K. Bonnet, E. Benaim, J. Sinclair, P. Speltz, E. Fielstein, J. Pulley, S. Kripalani, D. Schlundt, J. Denny, Vanderbilt University

Prioritizing Quality & Patient Safety Interventions: A Decision Model Approach 
T. Tsai, Johns Hopkins University; M. Gerst, University of Maryland; C. Engineer, Towson University; H. Lehmann, Johns Hopkins University

Engage: An Open Source, Automated Clinical Trial Awareness Tool 
W. Haslett, C. Ganoe, S. Andrews, R. Faill, Geisel School of Medicine at Dartmouth

Current Challenges in Clinical Research Informatics: A Survey of AMIA Clinical Research Informatics Work Group (CRI-WG) 
C. Weng, Columbia University; M. Ahuja, Weill Cornell Medicine; K. Fultz Hollis, Oregon Health & Sciences University; B. LaSalle, University of Utah; S. Fischer, Rand Institute; A. Solomonides, NorthShore University HealthSystem; J. Logan, Oregon Health & Sciences University

A Web-based Platform for Evaluating and Disseminating Predictive Models 
W. Hsu, F. Meng, P. Petousis, W. Yu, A. Bui, University of California, Los Angeles