Source: Interfolio F180

Chunlei Wu

Department of Integrative Structural and Computational Biology


Scripps Research Joint Appointments

Molecular Medicine
Skaggs Graduate School of Chemical and Biological Sciences

Research Focus

We are currently focusing on applying data science methodology and cloud computing technologies to facilitate biomedical discovery, through the large-scale biological data integration.

Research areas
? Biomedical knowledgebase infrastructure and inference engine
? Semantic knowledge presentation and integration
? Biomedical resource discovery
? Clinical informatics
? Crowdsourcing in biological research
? Scientific data management
? Gene network and pathway analysis
? Large-scale genomic data analysis

Scientific applications developed
? (Gene-centric resource portal)
? (Gene-centric API, ~30M hits per month)
? (Genetic Variant API, ~7M hits per month)
? (Chemical/drug-centric API)
? (Disease-centric API)
? (Generic SDK to power APIs above)
? (Biomedical API registry and semantic integration)
? (Biomedical resource discovery)


Ph.D. (Biomathematics and Biostatistics), The University of Texas Health Science Center at Houston, 2006
B.S. (Biochemistry), Nanjing University, 1997
M.S. (Biochemistry), Nanjing University, 2000

Professional Experience

2021-Present  Associate Professor with Tenure, Integrative Structural and Computational Biology, Scripps Research
2017-2021  Associate Professor, Integrative Structural and Computational Biology, Scripps Research
2017-2017 Associate Professor of Molecular Medicine, Molecular Medicine, Scripps Research

2011-2017 Associate Professor of Molecular Medicine, Molecular and Experimental Medicine (MEM), Scripps Research
2010-2011 Research Investigator II, Genomics Institute of the Novartis Research Foundation (GNF)
2007-2010 Research Investigator I, Genomics Institute of the Novartis Research Foundation (GNF)

Awards & Professional Activities

2017 Best In-Use Paper Award, ESWC
2015 2nd-place, BD2K Hackathon
2014 1st Place, Network of BioThings Hackathon
2005 GSBS Student Travel Award, University of Texas at Houston
2003 Co-Author for Best Presentation Award, CAMSA

Selected Publications

Xin, Jiwen; Afrasiabi, C.; Lelong, S.; Adesara, J.; Tsueng, G.; Su, Andrew; Wu, Chunlei Cross-linking BioThings APIs through JSON-LD to facilitate knowledge exploration. BMC Bioinformatics 2018, 19.

Xin, Jiwen; Mark, A.; Afrasiabi, C.; Tsueng, G.; Juchler, M.; Gopal, N.; Stupp, G. S.; Putman, T. E.; Ainscough, B. J.; Griffith, O. L.; Torkamani, Ali; Whetzel, P. L.; Mungall, C. J.; Mooney, S. D.; Su, Andrew; Wu, Chunlei High-performance web services for querying gene and variant annotation. Genome Biology 2016, 17.

Liu, X.; Wu, Chunlei; Li, C.; Boerwinkle, E. dbNSFP v3.0: A one-stop database of functional predictions and annotations for human nonsynonymous and splice-site SNVs. Human Mutation 2016, 37, 235-241.

Wu, Chunlei; Jin, Xuefeng; Tsueng, Ginger; Afrasiabi, Cyrus; Su, Andrew I. BioGPS: Building your own mash-up of gene annotations and expression profiles. Nucleic Acids Research 2016, 44, D313-D316.

Wu, Chunlei; Macleod, Ian; Su, Andrew I. BioGPS and Organizing online, gene-centric information. Nucleic Acids Research 2013, 41, D561-D565.

Wu, Chunlei; Orozco, Camilo; Boyer, Jason; Leglise, Marc; Goodale, James; Batalov, Serge; Hodge, Christopher L.; Haase, James; Janes, Jeff; Huss III, Jon W.; Su, Andrew I. BioGPS: an extensible and customizable portal for queryingand organizing gene annotation resources. Genome Biology 2009, 10, R130.