A novel scoring estimator to screening for oncogenic chimeric transcripts in cancer transcriptome sequencing. - Jianlei Gu; Yao Lu; Shi-Yi Liu; Cong Liu 020; Hui Lu 004 (BIBM, 2016)

High-dimensional omics data analysis using a variable screening protocol with prior knowledge integration (SKI). - Cong Liu 020; Jianping Jiang; Jianlei Gu; Zhangsheng Yu; Tao Wang 067; Hui Lu 004 (BMC Syst. Biol., 2016)

Meta-analysis of sex differences in gene expression in schizophrenia. - Wenyi Qin; Cong Liu 020; Monsheel Sodhi; Hui Lu 004 (BMC Syst. Biol., 2016)

DQueST: dynamic questionnaire for search of clinical trials. - Cong Liu 020; Chi Yuan; Alex M. Butler; Richard D. Carvajal; Ziran Ryan Li; Casey N. Ta; Chunhua Weng (J. Am. Medical Informatics Assoc., 2019)

Facilitating phenotype transfer using a common data model. - George Hripcsak; Ning Shang; Peggy L. Peissig; Luke V. Rasmussen; Cong Liu 020; Barbara Benoit; Robert J. Carroll; David S. Carrell; Joshua C. Denny; Ozan Dikilitas; Vivian S. Gainer; Kayla Marie Howell; et al. (J. Biomed. Informatics, 2019)

Ensembles of natural language processing systems for portable phenotyping solutions. - Cong Liu 020; Casey N. Ta; James R. Rogers; Ziran Li; Junghwan Lee; Alex M. Butler; Ning Shang; Fabricio Sampaio Peres Kury; Liwei Wang 010; Feichen Shen; Hongfang Liu; Lyudmila Ena; et al. (J. Biomed. Informatics, 2019)

Making work visible for electronic phenotype implementation: Lessons learned from the eMERGE network. - Ning Shang; Cong Liu 020; Luke V. Rasmussen; Casey N. Ta; Robert J. Carroll; Barbara Benoit; Todd Lingren; Ozan Dikilitas; Frank D. Mentch; David S. Carrell; Wei-Qi Wei; Yuan Luo 001; et al. (J. Biomed. Informatics, 2019)

Doc2Hpo: a web application for efficient and accurate HPO concept curation. - Cong Liu 020; Fabricio Sampaio Peres Kury; Ziran Li; Casey N. Ta; Kai Wang 049; Chunhua Weng (Nucleic Acids Res., 2019)

Natural language processing (NLP) tools in extracting biomedical concepts from research articles: a case study on autism spectrum disorder. - Jacqueline Peng; Mengge Zhao; James M. Havrilla; Cong Liu 020; Chunhua Weng; Whitney Guthrie; Robert T. Schultz; Kai Wang 049; Yunyun Zhou (BMC Medical Informatics Decis. Mak., 2020)

Evaluation of the Portability of Natural Language Processing-based Computable Phenotypes in the eMERGE Network. - Jennifer A. Pacheco; Luke V. Rasmussen; Ken Wiley; Thomas N. Person; David J. Cronkite; Sunghwan Sohn; Shawn N. Murphy; Justin H. Gundelach; Vivian S. Gainer; Victor M. Castro; Cong Liu 020; Todd Lingren; et al. (AMIA, 2021)

Towards Better Diagnosis Prediction Using Bidirectional Recurrent Neural Networks. - Junghwan Lee; Cong Liu 020; Casey N. Ta; Chunhua Weng (MedInfo, 2021)

Evaluation of Criteria2Query: Towards Augmented Intelligence for Cohort Identification. - Cong Liu 020; Hao Liu 054; Casey N. Ta; James Roger; Alex Butler; Junghwan Lee; Jaehyun Kim; Ning Shang; Chunhua Weng (MedInfo, 2021)

Interactive Similarity-Based Search of Clinical Trials. - Yingcheng Sun; Jiaqi Tang 008; Alex Butler; Cong Liu 020; Yilu Fang; Chunhua Weng (MedInfo, 2021)

Participatory Design of a Clinical Trial Eligibility Criteria Simplification Method. - Yilu Fang; Jae Hyun Kim; Betina Ross S. Idnay; Rebeca Aragon Garcia; Carmen E. Castillo; Yingcheng Sun; Hao Liu 054; Cong Liu 020; Chi Yuan; Chunhua Weng (MIE, 2021)

Natural language processing to identify lupus nephritis phenotype in electronic health records. - Yu Deng; Jennifer A. Pacheco; Anh H. Chung; Chengsheng Mao; Joshua C. Smith; Juan Zhao 003; Wei-Qi Wei; April Barnado; Chunhua Weng; Cong Liu 020; Adam Cordon; Jingzhi Yu; et al. (CoRR, 2021)

RePhine: An Integrative Method for Identification of Drug Response-related Transcriptional Regulators. - Xujun Wang; Zhengtao Zhang; Wenyi Qin; Shiyi Liu; Cong Liu 020; Georgi Z. Genchev; Lijian Hui; Hongyu Zhao 003; Hui Lu 004 (Genom. Proteom. Bioinform., 2021)

Towards clinical data-driven eligibility criteria optimization for interventional COVID-19 clinical trials. - Jae Hyun Kim; Casey N. Ta; Cong Liu 020; Cynthia Sung 002; Alex M. Butler; Latoya A. Stewart; Lyudmila Ena; James R. Rogers; Junghwan Lee; Anna Ostropolets; Patrick B. Ryan; Hao Liu 054; et al. (J. Am. Medical Informatics Assoc., 2021)

The COVID-19 Trial Finder. - Yingcheng Sun; Alex M. Butler; Fengyang Lin; Hao Liu 054; Latoya A. Stewart; Jae Hyun Kim; Betina Ross S. Idnay; Qingyin Ge; Xinyi Wei; Cong Liu 020; Chi Yuan; Chunhua Weng (J. Am. Medical Informatics Assoc., 2021)

Deep learning for rare disease: A scoping review. - Junghwan Lee; Cong Liu 020; Junyoung Kim; Zhehuan Chen; Yingcheng Sun; James R. Rogers; Wendy K. Chung; Chunhua Weng (J. Biomed. Informatics, 2022)

Leveraging electronic health record data for clinical trial planning by assessing eligibility criteria's impact on patient count and safety. - James R. Rogers; Jovana Pavisic; Casey N. Ta; Cong Liu 020; Ali Soroush; Ying Kuen Cheung; George Hripcsak; Chunhua Weng (J. Biomed. Informatics, 2022)

Natural language processing to identify lupus nephritis phenotype in electronic health records. - Yu Deng; Jennifer A. Pacheco; Anika S. Ghosh; Anh H. Chung; Chengsheng Mao; Joshua C. Smith; Juan Zhao 003; Wei-Qi Wei; April Barnado; Chad Dorn; Chunhua Weng; Cong Liu 020; et al. (BMC Medical Informatics Decis. Mak., 2022)

Multimodal Machine Learning Combining Facial Images and Clinical Texts Improves Diagnosis of Rare Genetic Diseases. - Da Wu; Jingye Yang; Steven Klein; Cong Liu 020; Tzung-Chien Hsieh; Peter M. Krawitz; Chunhua Weng; Gholson J. Lyon; Jennifer M. Kalish; Kai Wang 049 (CoRR, 2023)

Characterizing variability of electronic health record-driven phenotype definitions. - Pascal S. Brandt; Abel N. Kho; Yuan Luo 001; Jennifer A. Pacheco; Theresa L. Walunas; Hakon Hakonarson; George Hripcsak; Cong Liu 020; Ning Shang; Chunhua Weng; Nephi Walton; David S. Carrell; et al. (J. Am. Medical Informatics Assoc., 2023)

Fine-tuning large language models for rare disease concept normalization. - Andy Wang; Cong Liu 020; Jingye Yang; Chunhua Weng (J. Am. Medical Informatics Assoc., 2024)

Converting OMOP CDM to phenopackets: A model alignment and patient data representation evaluation. - Kayla Schiffer-Kane; Cong Liu 020; Tiffany J. Callahan; Casey N. Ta; Jordan G. Nestor; Chunhua Weng (J. Biomed. Informatics, 2024)

Phenotype driven molecular genetic test recommendation for diagnosing pediatric rare disorders. - Fangyi Chen; Priyanka Ahimaz; Quan M. Nguyen; Rachel Lewis; Wendy K. Chung; Casey N. Ta; Katherine M. Szigety; Sarah E. Sheppard; Ian M. Campbell; Kai Wang 049; Chunhua Weng; Cong Liu 020 (npj Digit. Medicine, 2024)

Enhancing phenotype recognition in clinical notes using large language models: PhenoBCBERT and PhenoGPT. - Jingye Yang; Cong Liu 020; Wendy Deng; Da Wu; Chunhua Weng; Yunyun Zhou; Kai Wang 049 (Patterns, 2024)