BeoBLAST: distributed BLAST and PSI-BLAST on a Beowulf cluster. - Jeffrey D. Grant; Roland L. Dunbrack Jr.; Frank J. Manion; Michael F. Ochs (Bioinform., 2002)

Application of Bayesian Decomposition for analysing microarray data. - Thomas D. Moloshok; R. R. Klevecz; Jeffrey D. Grant; Frank J. Manion; W. F. Speier IV; Michael F. Ochs (Bioinform., 2002)

ASAP: automated sequence annotation pipeline for web-based updating of sequence information with a local dynamic database. - Andrew V. Kossenkov; Frank J. Manion; Eugene V. Korotkov; Thomas D. Moloshok; Michael F. Ochs (Bioinform., 2003)

FGDP: functional genomics data pipeline for automated, multiple microarray data analyses. - Jeffrey D. Grant; Luke A. Somers; Yue Zhang; Frank J. Manion; Ghislain Bidaut; Michael F. Ochs (Bioinform., 2004)

WaveRead: Automatic measurement of relative gene expression levels from microarrays using wavelet analysis. - Ghislain Bidaut; Frank J. Manion; Christophe Garcia; Michael F. Ochs (J. Biomed. Informatics, 2006)

FuGEFlow: data model and markup language for flow cytometry. - Yu Qian; Olga Tchuvatkina; Josef Spidlen; Peter Wilkinson; Maura Gasparetto; Andrew R. Jones; Frank J. Manion; Richard H. Scheuermann; Rafick-Pierre Sekaly; Ryan Remy Brinkman (BMC Bioinform., 2009)

Integration of prostate cancer clinical data using an ontology. - Hua Min; Frank J. Manion; Elizabeth Goralczyk; Yu-Ning Wong; Eric A. Ross; J. Robert Beck (J. Biomed. Informatics, 2009)

Security and privacy requirements for a multi-institutional cancer research data grid: an interview-based study. - Frank J. Manion; Robert J. Robbins; William A. Weems; Rebecca S. Crowley (BMC Medical Informatics Decis. Mak., 2009)

Data visualization of teen birth rate data using freely available rapid prototyping tools. - Risa B. Myers; James W. Lomax III; Frank J. Manion; Nancy M. Wood; Todd R. Johnson (IHI, 2010)

Extending OpenClinica using Web 2.0 Technologies. - Anjali Bhandari; Wei Shi; John Harju; Frank J. Manion; Becky Marshall; Andrew Chang; Rebecca M. Minter (AMIA, 2012)

Hedging their Mets: The Use of Uncertainty Terms in Clinical Documents and its Potential Implications when Sharing the Documents with Patients. - David A. Hanauer; Yang Liu 019; Qiaozhu Mei; Frank J. Manion; Ulysses J. Balis; Kai Zheng 002 (AMIA, 2012)

Development of an Informed Consent Ontology to Support Biobanking. - Alla Karnovsky; Frank J. Manion; Terry E. Weymouth; V. Glenn Tarcea; Lisa Powell; Blake Roessler; Nicholas Steneck (AMIA, 2012)

tranSMART Supports a Post-GWAS Data Coordinating Center. - Dan Stuart; John Harju; Wei Shi; David A. Hanauer; Dina Aronzon; Jinlei Liu; Raveen Sharma; Frank J. Manion; Haiping Xia; Carolyn Hutter; Stephen Gruber (AMIA, 2012)

Analysis of Content Coverage for Informed Consent Concepts. - Frank J. Manion; Elizabeth Eisenhauer; Alla Karnovsky; Yongqun He; Yu Lin; Marcelline R. Harris (AMIA, 2014)

Development of a BFO-Based Informed Consent Ontology (ICO). - Yu Lin; Marcelline R. Harris; Frank J. Manion; Elizabeth Eisenhauer; Bin Zhao; Wei Shi; Alla Karnovsky; Yongqun He (ICBO, 2014)

A Research Capability Framework. - Airong Luo; Marcelline R. Harris; Frank J. Manion; Barbara Mirel (AMIA, 2016)

From Scoping Review to Metadata: An Evidence-Based Approach to Identifying Informed Consent Metadata for Biorepositories. - Marcelline R. Harris; Frank J. Manion; Hsing-yi Song; Yongqun He; Muhamamd F. Amith; Cui Tao (AMIA, 2017)

Evaluation of the Surveillance, Epidemiology, and End Results Data Management System (SEER*DMS) to support the efforts in enhancing U.S cancer surveillance. - Marina Z. Matatova; Paul Fearn; Eric B. Durbin; Gary Levin; Frank J. Manion; Patrick Mergler (AMIA, 2017)

Expressing Biomedical Ontologies in Natural Language for Expert Evaluation. - Muhammad Amith; Frank J. Manion; Marcelline R. Harris; Yaoyun Zhang; Hua Xu 001; Cui Tao (MedInfo, 2017)

Development and Validation of an Ontological Representation of the US Common Rule. - Frank J. Manion; Marcelline R. Harris; Muhamamd F. Amith; Cui Tao (AMIA, 2018)

OntoKeeper: Semiotic-driven Ontology Evaluation Tool For Biomedical Ontologists. - Muhammad Amith; Frank J. Manion; Chen Liang 005; Marcelline R. Harris; Dennis Wang; Yongqun He; Cui Tao (BIBM, 2018)

Coordinated Evolution of Ontologies of Informed Consent. - J. Neil Otte; Cooper Stansbury; Jonathan Vajda; Frank J. Manion; Elizabeth Umberfield; Yongqun He; Marcelline R. Harris; Jihad S. Obeid; Mathias Brochhausen; William D. Duncan; Cui Tao (ICBO, 2018)

A Scoping Review to Identify Biobank Classification and Permissions to Share Metadata. - Marcelline R. Harris; Frank J. Manion; Madhuri Sankaranarayanapillai; Hsing-yi Song; Marisa Conte; Cui Tao (AMIA, 2019)

Refactoring and Expanding the Informed Consent Ontology (ICO). - Jonathan M. Vajda; J. Neil Otte; Cooper Stansbury; Marcelline R. Harris; Frank J. Manion; Cui Tao (AMIA, 2019)

Expanding the Representation of Permissions and Deontic Roles in the Informed Consent Ontology (ICO). - Jonathan M. Vajda; J. Neil Otte; Cooper Stansbury; Marcelline R. Harris; Elizabeth Umberfield; Frank J. Manion; Cui Tao (AMIA, 2019)

Using Stases to Enrich Queries for When and Where Regulations Are in Force. - Jonathan M. Vajda; J. Neil Otte; Cooper Stansbury; Frank J. Manion; Marcelline R. Harris; Cui Tao (ICBO, 2019)

Architecture and usability of OntoKeeper, an ontology evaluation tool. - Muhammad Amith; Frank J. Manion; Chen Liang 005; Marcelline R. Harris; Dennis Wang; Yongqun He; Cui Tao (BMC Medical Informatics Decis. Mak., 2019)

COVID-19 SignSym: A fast adaptation of general clinical NLP tools to identify and normalize COVID-19 signs and symptoms to OMOP common data model. - Jingqi Wang; Huy Anh Pham; Frank J. Manion; Masoud Rouhizadeh; Yaoyun Zhang (CoRR, 2020)

Expressing and Executing Informed Consent Permissions using SWRL: The All of Us Use Case. - Muhammad Amith; Marcelline R. Harris; Cooper Stansbury; Kathleen Ford; Frank J. Manion; Cui Tao (AMIA, 2021)

COVID-19 SignSym: a fast adaptation of a general clinical NLP tool to identify and normalize COVID-19 signs and symptoms to OMOP common data model. - Jingqi Wang; Noor Abu-El-Rub; Josh Gray; Huy Anh Pham; Yujia Zhou 003; Frank J. Manion; Mei Liu; Xing Song; Hua Xu 001; Masoud Rouhizadeh; Yaoyun Zhang (J. Am. Medical Informatics Assoc., 2021)

LANN: an Integrated Online Annotation Tool for Information Extraction. - Jingqi Wang; Yaoyun Zhang; Bin Lin; Huy Anh Pham; Long He; Jingcheng Du; Frank J. Manion (ICHI, 2022)

Machine learning-based donor permission extraction from informed consent documents. - Meng Zhang; Madhuri Sankaranarayanapillai; Jingcheng Du; Yang Xiang 003; Frank J. Manion; Marcelline R. Harris; Cooper Stansbury; Huy Anh Pham; Cui Tao (BMC Bioinform., 2023)

AutoCriteria: a generalizable clinical trial eligibility criteria extraction system powered by large language models. - Surabhi Datta; Kyeryoung Lee; Hunki Paek; Frank J. Manion; Nneka Ofoegbu; Jingcheng Du; Ying Li; Liang-Chin Huang; Jingqi Wang; Bin Lin; Hua Xu; Xiaoyan Wang (J. Am. Medical Informatics Assoc., 2024)