Cong Liu, Ph.D.

Columbia University, Department of Biomedical Informatics, New York, NY, 2019-present
Associate Research Scientist

University of Illinois, Chicago, IL, 2011-2017
Ph.D. in Bioinformatics, 2017
Thesis: Investigation of Feature Selection Methods in High-Throughput Omics Data Analysis (advisor: Dr. Hui Lu)

University of Illinois, Chicago, IL, 2011-2015
M.S. in Mathematics, 2015

Fudan University, Shanghai, China, 2007-2011
B.S. in Biological Science, 2011

Columbia University, New York, NY
Postdoc Research Scientist, Biomedical Informatics, 2018-2019

Memberships and Positions: American Medical Informatics Association (2018-present); American Society of Human Genetics (2014-present); Institute of Electrical and Electronics Engineers (2016-2017);

Journal Editor: Frontier in Genetics: Guest Editor

Journal Reviewer (selected): Journal of Biomedical Informatics, Journal of the American Medical Informatics Association, American Journal of Human Genetics, Genetics in Medicine, Frontiers in Genetics, Human Genetics and Genomics Advances, American Journal of Translational Research, Journal of Medical Internet Research, BMC Medical Informatics and Decision Making, Trends in Artificial Intelligence, International Journal of Epidemiology, etc.

Guest Editor: Frontiers in Genetics, 2022

Session Chair: International Conference on Intelligent Biology and Medicine 2021

Consultative: Scientific advisor at EPN, Inc., Shanghai, China, 2016-2017

R01HG012655
RESCUE: Rare Disease Detection and Escalation Support via a Learning Health System
Status of Support: Active
Role: PI
Source of Support: NHGRI
07/01/2022 - 06/30/2027

U01HG008680
EHR-based Genomic Risk Assessment and Management for Diverse Populations
Status of Support: Active
Role: Scientist
PD/PI: Weng, Chung, Hripcsak, Kiryluk
Source of Support: NHGRI
7/1/2020 - 4/30/2025

R01LM012895
Deep Phenotyping in EHR for Genomic Medicine
Status of Support: Active
Role: Scientist
PD/PI: Weng, Wang
Source of Support: NHGRI/NLM
09/17/2018 - 05/31/2023

PTC CU21-0036
AADC deficiency project AADC retrospective screening
Status of Support: Past
Role: Scientist
PD/PI: Chung
Source of Support: PTC
10/17/2020 - 10/16/2021

Faculty Award-Clinical Program award. Department of Pediatrics, Columbia University 2023

Guest Lecturer, Biomedical Informatics Colloquium class CityTech CUNY, Summer 2022

Guest Lecturer, Symbolic Methods (G4003), Columbia University, Fall 2019, Spring 2020, Fall 2021 & Fall 2022

Teaching Assistant, Introduction to Bioinformatics (BIOE480), University of Illinois, Fall 2011, Fall 2012, Fall 2013 & Fall 2014

Guest Lecture and Teaching Assistant, Data mining in Bioinformatics (BIOE594), University of Illinois, Spring 2013, Spring 2014, Spring 2015 & Spring 2016

Teaching Assistant, Biodatabase (BIOE594), University of Illinois, Fall 2015, Fall 2016, Spring 2017, Fall 2017 & Spring 2015

Linder, J. E., ..., Liu, C., ..., & Lange, C. (2023). Returning integrated genomic risk and clinical recommendations: The eMERGE study. Genetics in Medicine, 25(4), 100006.

Namjou, B., ..., Liu, C., ..., & eMERGE Network, T. (2022). Multiancestral polygenic risk score for pediatric asthma. Journal of Allergy and Clinical Immunology, 150(5), 1086-1096.

Sherafati, ..., Liu, C., ..., & & Kullo, I. J. (2022). Pathogenic variants in arteriopathy genes detected in a targeted sequencing study: Penetrance and 1-year outcomes after return of results. Genetics in Medicine.

Liu, C. Ta, C. N., Havrilla, J. M., Nestor, J. G., Spotnitz, M. E., Geneslaw, A. S., ... & Weng, C. (2022). OARD: Open annotations for rare diseases and their phenotypes based on real-world data. The American Journal of Human Genetics.

Khan, A., ..., Liu, C., ..., & Kiryluk, K. (2022). Genome-wide polygenic score to predict chronic kidney disease across ancestries. Nature Medicine, 1-9.

Namjou, B., ..., Liu, C., ..., & eMERGE Network, T. (2022). Multiancestral polygenic risk score for pediatric asthma. Journal of Allergy and Clinical Immunology.

Liu, C., Lee, J., Ta, C., Soroush, A., Rogers, J., Kim, J. H., ... & Weng, C. (2022). A Retrospective Analysis of Risk Factors Associated with the SARS-CoV-2 Breakthrough in Fully mRNA Vaccinated Individuals. JMIR Public Health and Surveillance.

Glazer, A. M., ..., Liu, C., ..., & Roden, D. M. (2022). Arrhythmia variant associations and reclassifications in the eMERGE-III sequencing study. Circulation, 145(12), 877-891.

Rogers, J. R., Pavisic, J., Ta, C. N., Liu, C., Soroush, A., Cheung, Y. K., ... & Weng, C. (2022). Leveraging electronic health record data for clinical trial planning by assessing eligibility criteria’s impact on patient count and safety. Journal of Biomedical Informatics, 127, 104032.

Havrilla, J. M., Liu, C., Dong, X., Weng, C., & Wang, K. (2021). PhenCards: a data resource linking human phenotype information to biomedical knowledge. Genome medicine, 13(1), 1-9.

Lee, J., Kim, J. H., Liu, C., Hripcsak, G., Natarajan, K., Ta, C., & Weng, C. (2021). Columbia Open Health Data for COVID-19 Research: Database Analysis. Journal of Medical Internet Research, 23(9), e31122.

Liu, C., Zeinomar, N., Chung, W. K., Kiryluk, K., Gharavi, A. G., Hripcsak, G., ... & Weng, C. (2021). Generalizability of Polygenic Risk Scores for Breast Cancer Among Women With European, African, and Latinx Ancestry. JAMA Network Open, 4(8), e2119084-e2119084.

Havrilla, J. M., Zhao, M., Liu, C., Weng, C., Helbig, I., Bhoj, E., & Wang, K. (2021). Clinical Phenotypic Spectrum of 4095 Individuals with Down Syndrome from Text Mining of Electronic Health Records. Genes, 12(8), 1159.

Fan, X., Wynn, J., Shang, N.,Liu, C., Fedotov, A., Hallquist, M. L., ... & Chung, W. K. (2021). Penetrance of Breast Cancer Susceptibility Genes from the eMERGE III Network. JNCI Cancer Spectrum.

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Fang, Y., ... Liu, C. & Weng, C. (2021). Participatory Design of a Clinical Trial Eligibility Criteria Simplification Method. Studies in Health Technology and Informatics, 281, 984-988.

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Lee, J., Liu, C., Kim, J. H., Butler, A., Shang, N., Pang, C., ... & Weng, C. (2021). Comparative effectiveness of medical concept embedding for feature engineering in phenotyping. JAMIA open, 4(2), ooab028.

Kim, J. H., Ta, C. N., Liu, C., Sung, C., Butler, A. M., Stewart, L. A., ... & Weng, C. (2021). Towards clinical data-driven eligibility criteria optimization for interventional COVID-19 clinical trials. Journal of the American Medical Informatics Association, 28(1), 14-22.

Lee, J., Ta, C., Kim, J. H., Liu, C., & Weng, C. (2021). Severity Prediction for COVID-19 Patients via Recurrent Neural Networks. In AMIA Annual Symposium Proceedings (Vol. 2021, p. 374). American Medical Informatics Association.

Peng, J., Zhao, M., Havrilla, J., Liu, C., Weng, C., Guthrie, W., ... & Zhou, Y. (2020). 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, 20(11), 1-9.

Sun, Y., Butler, A., Lin, F., Liu, H., Stewart, L. A., Kim, J. H., Liu, C.,... & Weng, C. (2021). The COVID-19 Trial Finder. Journal of the American Medical Informatics Association.

Wang, L., Wang, Q., Bai, H., Liu, C., Liu, W., Zhang, Y., ... & Zhou, Y. (2020). EHR2Vec: Representation Learning of Medical Concepts From Temporal Patterns of Clinical Notes Based on Self-Attention Mechanism. Frontiers in genetics, 11, 630.

Zhao, M., Havrilla, J. M., Fang, L., Chen, Y., Peng, J., Liu, C., ... & Wang, K. (2020). Phen2Gene: rapid phenotype-driven gene prioritization for rare diseases. NAR genomics and bioinformatics, 2(2), lqaa032.

Liu, C., Yuan, C., Li, Z., Ta, C., & Weng, C. (2019). Ensembles of Natural Language Processing Systems for Portable Phenotyping Solutions. Journal of biomedical informatics, 103318.

Wang, X., Zhang, Z., Qing, W., Liu, S., Liu, C.; Genchev, G.; Hui, L., Zhao, H., & Lu, H. (2019) RePhine: A Regression based Pharmacogenomic and ChIP-seq data integration method for identification of novel transcriptional regulators associated with response to cancer drug therapy. Genomics Proteomics and Bioinformatics, accepted.

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Shang, N., Liu, C., Rasmussen, L. V., Ta, C. N., Caroll, R. J., Benoit, B., ... & Wei, W. Q. (2019). Making work visible for electronic phenotype implementation: lessons learned from the eMERGE network. Journal of biomedical informatics, 103293.

Zouk, H., ...,Liu, C. & Mukherjee, S. (2019). Harmonizing clinical sequencing and interpretation for the eMERGE III network. The American Journal of Human Genetics, 105(3), 588-605.

Liu, C., Yuan, C., Butler, A. M., Carvajal, R. D., Li, Z. R., Ta, C. N., & Weng, C. (2019). DQueST: dynamic questionnaire for search of clinical trials. Journal of the American Medical Informatics Association, 26(11), 1333-1343.

Hripcsak, G., Shang, N., Peissig, P. L., Rasmussen, L. V., Liu, C., Benoit, B., ... & Gainer, V. S. (2019). Facilitating phenotype transfer using a common data model. Journal of biomedical informatics, 103253.

Liu, C., Kury, P., Sampaio, F., Li, Z., Ta, C., Wang, K., & Weng, C. (2019). Doc2Hpo: a web application for efficient and accurate HPO concept curation. Nucleic acids research.

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Liu, C., Yuan, C., Pua, E., Harris, P., & Weng, C. (2018). Dynamic Questionnaire Generation for Efficient Patient Search of Trials. AMIA annual symposium.

Liu, C., Wang, X., Genchev, G. Z., & Lu, H. (2017). Multi-omics facilitated variable selection in Cox-regression model for cancer prognosis prediction. Methods, 124, 100-107.

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Bergau, D., Liu, C., & Lu, H. (2017). Prediction of human QT prolongation liability based on pre- clinical RNA expression profiles, IEEE International Conference on Bioinformatics and Biomedicine (BIBM)

Carson, M. B., Liu, C., Lu, Y., Jia, C., & Lu, H. (2017). A disease similarity matrix based on the uniqueness of shared genes. BMC medical genomics, 10(1), 26.

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Szilágyi, K. L., Liu, C., Zhang, X., Wang, T., Fortman, J. D., Zhang, W., & Garcia, J. G. (2017). Epigenetic contribution of the myosin light chain kinase gene to the risk for acute respiratory distress syndrome. Translational Research, 180, 12-21.

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Gu J., Lu Y., Liu S., Liu, C., & Lu H. (2016). A novel scoring estimator to screening for oncogenic chimeric transcripts in cancer transcriptome sequencing, IEEE International Conference on Bioinformatics and Biomedicine (BIBM).

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Liu, C., Chen, W., & Zhang, W. (2016). Essential Pharmacogenomic Biomarkers in Clinical Practice (Chapter 3). In Applying Pharmacogenomics in Therapeutics (pp. 51-74). CRC Press.

Liu, C., Jiang, J., Gu, J., Yu, Z., Wang, T., & Lu, H. (2016). High-dimensional omics data analysis using a variable screening protocol with prior knowledge integration (SKI). BMC Systems Biology, 10(4), 457.

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Morrison, G., Liu, C., Wing, C., Delaney, S. M., Zhang, W., & Dolan, M. E. (2016). Evaluation of inter-batch differences in stem-cell derived neurons. Stem cell research, 16(1), 140- 148.

Qin, W., Liu, C., Sodhi, M., & Lu, H. (2016). Meta-analysis of sex differences in gene expression in schizophrenia. BMC systems biology, 10(1), S9.

Liu, C., Xu, J., Chen, Y., Guo, X., Zheng, Y., Wang, Q., ... & Baccarelli, A. (2015). Characterization of genome-wide H3K27ac profiles reveals a distinct PM 2.5-associated histone modification signature. Environmental Health, 14(1), 65.

Zhang, W., Gamazon, E. R., Zhang, X., Konkashbaev, A., Liu, C.,... & Cox, N. J. (2015). SCAN database: facilitating integrative analyses of cytosine modification and expression QTL. Database, bav025.

Gu, J. L., Lu, Y., Liu, C., & Lu, H. (2014). Multiclass classification of sarcomas using pathway based feature selection method. Journal of theoretical biology, 362, 3-8.

Zhang, X., Moen, E. L., Liu, C., Mu, W., Gamazon, E. R., ... & Zhang, W. (2014). Linking the genetic architecture of cytosine modifications with human complex traits. Human molecular genetics, 23(22), 5893-5905.

Zhang, X., Mu, W., Liu, C., & Zhang, W. (2014). Ancestry-informative markers for African Americans based on the Affymetrix Pan-African genotyping array. PeerJ, 2, e660.

Carson, M.B., Liu, C., & Lu, H. (2012). Knowledge Mining of Disease Network can Provide New Insights in Cancer Research through Analysis of Other Diseases. Journal of Carcinogenesis & Mutagenesis, Vol 3(1): e103.

Xu, J., Dou, T., Liu, C., Fu, M., Huang, Y., Gu, S., ... & Xie, Y. (2011). The evolution of alternative splicing exons in vascular endothelial growth factor A. Gene, 487(2), 143-150.

AMIA Informatics Summit, Panel presentation, Virtual. Mar 14, 2023

NHGRI AGMR Annual Grantee Meeting, Oral presentation, Virtual, Mar 1, 2023

Columbia DBMI Specifal Seminar, Oral presetnation, Virtual. May 02, 2022

American Society of Human Genetics, Annual Meeting, Poster presetnation, Virtual. October 18, 2021

International Medical Informatics Association, MedInfo, Oral presetnation, Virtual, Oct 2, 2021

COVID-19 Virtual Symposium, Oral presetnation, Virtual. October 7, 2020

eMERGE Network Steering Committee Meeting, Oral presetnation, Bethesda, MD. February 19, 2020

American Society of Human Genetics, Annual Meeting, Poster presetnation, Houston, TX. October 18, 2019

Observational Health Data Sciences and Informatics Annual Symposium, Cohort definition workshop. North Bethesda, Sep.14th, 2019

American Medical Informatics Association Annual Symposium, Oral presentation. San Francisco, Nov.6th, 2018

American Medical Informatics Association Annual Symposium, Oral presentation. San Francisco, Nov.7th, 2018

Observational Health Data Sciences and Informatics Annual Symposium, Software demonstration. North Bethesda, Oct.12th, 2018

Data Science Day at Columbia, Software demonstration. New York, Mar.28th, 2018.

Department of Biomedical Informatics, Columbia University, Seminar talk. New York, Dec. 17th, 2017

Department of System Biology, Columbia University, Seminar talk. New York, Oct 27th, 2017

Department of Oncology Biotherapeutic Discovery, Invited talk. Pfizer, Pearl River, Oct. 18, 2017

Department of Computer Science, Hunter College, Seminar talk. CUNY, New York, Oct. 5th, 2017

IEEE International Conference on Bioinformatics and Biomedicine (BIBM), Oral presentation. Shenzheng, Nov.13th, 2016

International Conference on Genome Informatics, Oral presentation. Shanghai, Oct.5th, 2016

American Society of Human Genetics, Annual Meeting, Poster presetnation, San Diego, CA. October 20, 2014