Rong Chen, Ph.D. is a bioinformatics scientist in the Butte lab. Rong received his undergradute degree in Chemical Physics from the University of Science and Technology of China in 1994, his M.S. degree in Protein Crystallography and Organic Chemistry from Shanghai Institute of Organic Chemistry of Chinese Academy of Science in 1997, and his Ph.D. degree in bioinformatics from Boston University in 2003. After graduation, he worked as a Scientist at Accelrys (on the Discovery Studio team), a senior computational Biologist at Amgen/Abgenix (on the Antibody Discovery team), and a principal software engineer at Quest Diagnostics Nichols Institute (on the development of novel diagnostic assays).

Rong joined the Butte lab in Nov 2005, has been developing bioinformatics methods to integrate and translate genomic, genetic, phenotypic, and clinic data into diagnostic and personalized medicine. His research focuses on three directions. First, he has been developing databases and tools to make medical assessment such as disease risk on personal genome sequences. An example of this was a work on published in The Lancet (2010). Second, he has been working on the identification and validation of biomarkers for the early diagnosis of disease. An example of this was a work on the identification of new test for transplant rejection published in The PLoS Computational Biology (2010), and reported in the GenomeWeb. Another example of this was a work on annotating gene expression data published in Nature Methods (2007). Last, he has been working on the discovery of causal variants, pathway, and mechanism to illustrate human disease through integrative genomics. An example of this was a work on prioritizing disease SNPs using gene expression data published in the Genome Biology (2008), and interviewed by GenomeWeb (2008).

Rong's publications have been cited 2,669 times with an h-index of 23 and i10-index of 33 as shown in Google Citations.

• Personal website
• Google Citations
• Research Profile from BiomedExperts
• Twitter
• Z/RDOCK: a tool to predict 3-dimentional atomic structure for protein-protein interaction complexes
  • Commercial software
  • Academic web server

• Personalized Genetics: Automatically assess disease risks across nosology for personal genome sequences
• GeneChaser: Identify all conditions in which a gene or set of genes was differentially expressed
• FitSNPs: Prioritize disease-associated SNPs from GWAS and predict SNPs for 597 syndromes with unknown molecule mechanism
• Cancer Systems
• AILUN: Annotate all microarray platforms across all species

26. Clinical assessment incorporating a personal genome – Authors' reply
    Morgan AA, Chen R, Butte AJ, Ashley EA
    Lancet 102 p869-70 (2010 Sep 11)
40. Ontology-driven Indexing of Public Datasets for Translational Bioinformatics
    Shah NH, Chiang AP, Butte AJ, Chen R, Musen MA
    American Medical Informatics Association Symposium on Translational Bioinformatics (2008)(PDF)
54. Theoretical Studies on Electrocompression of Electrodeposited Halid Monolayer on Au(111) Surface
    Wang XQ, Chen R, Wang YL, He TJ, Liu FC
    J Phys Chem B 102 p7568-76 (1998 Sep 9)(PDF)

1. System to assess disease risks through personal genome sequences
2. Software to identify differentially expressed genes for a gene or set of genes
3. Methods and composition for monitoring an allograft recipient for a rejection response (61/152,199)
4. Self organizing map in clinical diagnostics (20080221395)
5. Software to predict the 3-dimentional structure of protein-protein interaction (ZDOCKpro)

1. Interview by Science on Diabetes genes decline out of Africa
2. Media reports on disease risk from a family's whole genomes
3. Interview by GenomeWeb on synonymous and 3' SNPs for disease association
4. Media report on identifying new test for the diagnosis of organ transplant rejection
5. More media report on new test for the diagnosis of organ transplant rejection
6. Media report on clinical assessment of a personal genome
7. More media report on clinical assessment of personal genomes
8. Media report on the prioritization of SNPs from GWAS
9. Interview by ebiotrade from China
10. Interview by GenomeWeb on curating a disease SNP database
11. Interview by Genome Technology on prioritizing disease SNPs

• Invited lectures in BMI 205, Dept. of Biomedical Informatics, Stanford University
  • Fall 2010, Disease risk assessment of personal genome sequences
  • Fall, 2009, Biomarker Discovery from Public Gene Expression Data
• Invited lectures in BE703 , Dept. of Biomedical Engineering, Boston University
  • Fall 2002, Protein-protein Docking

1. Feb. 23, 2012, Molecular Med Tri-Con 2012, San Francisco, CA. Session chair on Integrated R&D Informatics & Knowledge Management, Talk title “Type 2 diabetes risk alleles show extreme directional differentiation among human populations, compared to other diseases”
2. Feb. 22, 2012, Molecular Med Tri-Con 2012, San Francisco, CA. Talk title “Use public molecular measurements to drive the discovery of diagnostic protein biomarkers”.
3. Feb. 16, 2012, 13th annual Advances in Genome Biology and Technology (AGBT), Marco Island, FL. Plenary Talk Title: “Type 2 diabetes risk alleles show extreme directional differentiation among human populations, compared to other diseases”
4. Oct. 13, 2011, 12th International Congress of Human Genetics / American Society of Human Genetics 61th annual meeting, Montreal, Canada. Talk Title: “Type 2 diabetes risk alleles show extreme directional differentiation among human populations, compared to other diseases”
5. Sep. 14, 2011, Clinical Sequencing Standards Symposium in HL7, San Diego, CA. Talk Title: “Standardizing Genetic Reports for Medical Assessment of Personal Genome Sequences”
6. Sep. 8, 2011, ADAPT Accelerating Development & advancing personalized medicine, Philadelphia, PA. Session chair in Biomarker Discovery Informatics. Talk Title: “Using Public Molecular Measurements to Drive Biomarker Discovery”
7. Apr. 14, 2011, BioIT World Conference, Boston, MA. session chair on Data Modeling & Computational Integrative Tools, Talk Title: “Using Public Molecular Measurements to Drive Discovery of Diagnostic Biomarkers”
8. Mar. 18, 2011, Third NIH/Scripps Genomics for Transplantation Symposium, San Diego, CA. Title: “Using public molecular measurements to drive discovery of biomarkers for cross-organ transplant rejection”.
9. Mar. 15, 2011, 2nd International Conference on Transplantomics and Biomarkers in Organ Transplantation, Barcelona, Spain. Title: “The clinical utility of whole genome sequencing”, “Differentially Expressed RNA from Public Microarray Data Identifies Serum Protein Biomarkers for Cross-organ Transplant Rejection and Other Conditions”.
10. Mar. 8, 2011, 2011 AMIA Summit on Translational Bioinformatics, San Francisco, CA. Title: “Non-synonymous and Synonymous Coding SNPs Show Similar Likelihood and Effect Size of Human Disease Association”.
11. Feb. 27, 2011, Biomarkers for Brain Disorders: Challenges and Opportunities, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK Title: “Using Public Molecular Measurements to Drive Discovery of Diagnostic Biomarkers”
12. Feb. 3, 2011, 12th annual Advances in Genome Biology and Technology (AGBT), Marco Island, FL. Title: “Genetics explains the ethnic disparity of incidence rate of Melanoma and Pancreatic cancer”.
13. Jan. 20, 2011, International workshop on Bioinformatics: Advanced course on High Throughput Sequencing Data with R and Bioconductor, The University of The West Indies, Trinidad and Tobago. Title: “Medical assessment of personal genome sequences”.
14. Jan. 4, 2011, Pacific Symposium on Biocomputing (PSB), Big Island of Hawaii. Title: “Is the reference human genome a good representation of a healthy control and consensus?”.
15. Jun. 11, 2010, 13th Annual International Toronto Heart Summit, Toronto, Ontario, Canada. Title: “Bioinformatics Approaches Yielding Biomarkers for Personalized Medicine”.
16. Aug. 11, 2010, Xiameng University, Xiameng, China. Title: “Translating publically-available molecular data into diagnostics and personalized medicine”.
17. Mar. 9, 2009, FDA / National Center for Toxicological Research, Jefferson, AR. Title: “Biomarker Discovery from Public Gene Expression Data”.
18. May. 12 2008, Indiana University School of Medicine, Indianapolis, IN. Title: “Differentially Expressed Genes are Most Likely to have Variants Associated With Disease”.
19. Jun. 12, 2004, Biogeometry workshop, ACM Symposium on Computational Geometry, New York, NY. Title: “An Integrated Approach to Protein-Protein Docking”.
20. Sep. 19, 2002, First CAPRI Evaluation Meeting, Agelonde, La Londe-des-Maures, France. Title: “ZDOCK Predictions for the CAPRI Challenge”.
21. Jul. 25, 2002, Boston University-Humboldt University Workshop, Boston, MA. Title: “A Novel Shape Complementarity Scoring Function for Protein Docking”.
22. Dec. 1, 2001, Computational Genomics Conference, Baltimore, Maryland. Title: “An Integrated Approach to Predictive Protein-protein Docking”.