Rong Chen

Summary

Affiliation: Stanford University
Country: USA

Publications

  1. pmc Sequencing and analysis of a South Asian-Indian personal genome
    Ravi Gupta
    SciGenom Labs Pvt Ltd, Kakkanad, Cochin, Kerala, India
    BMC Genomics 13:440. 2012
  2. pmc Non-synonymous and synonymous coding SNPs show similar likelihood and effect size of human disease association
    Rong Chen
    Department of Pediatrics, Stanford University School of Medicine, Stanford, California, United States of America
    PLoS ONE 5:e13574. 2010
  3. pmc FitSNPs: highly differentially expressed genes are more likely to have variants associated with disease
    Rong Chen
    Stanford Center for Biomedical Informatics Research, 251 Cmpus Drive, Stanford, CA 94305, USA
    Genome Biol 9:R170. 2008
  4. pmc GeneChaser: identifying all biological and clinical conditions in which genes of interest are differentially expressed
    Rong Chen
    Stanford Center for Biomedical Informatics Research, Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
    BMC Bioinformatics 9:548. 2008
  5. pmc Differentially expressed RNA from public microarray data identifies serum protein biomarkers for cross-organ transplant rejection and other conditions
    Rong Chen
    Department of Pediatrics, Stanford University School of Medicine, Stanford, California, United States of America
    PLoS Comput Biol 6:. 2010
  6. doi request reprint Progressive histological damage in renal allografts is associated with expression of innate and adaptive immunity genes
    Maarten Naesens
    Division of Nephrology, Department of Pediatrics, Stanford University School of Medicine, Stanford, California, USA
    Kidney Int 80:1364-76. 2011
  7. pmc ProfileChaser: searching microarray repositories based on genome-wide patterns of differential expression
    Jesse M Engreitz
    Division of Systems Medicine, Department of Pediatrics, Stanford University School of Medicine, Stanford, CA 94305, USA
    Bioinformatics 27:3317-8. 2011
  8. pmc Compartmental localization and clinical relevance of MICA antibodies after renal transplantation
    Li Li
    Department of Pediatrics, Stanford University, Stanford, CA, USA 2 Department of Pathology, Stanford University, Stanford, CA 94304, USA
    Transplantation 89:312-9. 2010
  9. pmc Systematic identification of DNA variants associated with ultraviolet radiation using a novel Geographic-Wide Association Study (GeoWAS)
    Irving Hsu
    Division of Systems Medicine, Department of Pediatrics, Stanford University School of Medicine, 1265 Welch Road, MS 5415, Stanford, CA 94305, USA
    BMC Med Genet 14:62. 2013
  10. pmc Analysis of the genetic basis of disease in the context of worldwide human relationships and migration
    Erik Corona
    Division of Systems Medicine, Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, USA
    PLoS Genet 9:e1003447. 2013

Collaborators

Detail Information

Publications35

  1. pmc Sequencing and analysis of a South Asian-Indian personal genome
    Ravi Gupta
    SciGenom Labs Pvt Ltd, Kakkanad, Cochin, Kerala, India
    BMC Genomics 13:440. 2012
    ..In this study we have sequenced and analyzed the genome of a South Asian Indian female (SAIF) from the Indian state of Kerala...
  2. pmc Non-synonymous and synonymous coding SNPs show similar likelihood and effect size of human disease association
    Rong Chen
    Department of Pediatrics, Stanford University School of Medicine, Stanford, California, United States of America
    PLoS ONE 5:e13574. 2010
    ..Our results suggest that sSNPs are just as likely to be involved in disease mechanisms, so we recommend that sSNPs discovered from GWAS should also be examined with functional studies...
  3. pmc FitSNPs: highly differentially expressed genes are more likely to have variants associated with disease
    Rong Chen
    Stanford Center for Biomedical Informatics Research, 251 Cmpus Drive, Stanford, CA 94305, USA
    Genome Biol 9:R170. 2008
    ..We propose to use the more than 200,000 microarray studies in the Gene Expression Omnibus to systematically prioritize candidate SNPs from GWASs...
  4. pmc GeneChaser: identifying all biological and clinical conditions in which genes of interest are differentially expressed
    Rong Chen
    Stanford Center for Biomedical Informatics Research, Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
    BMC Bioinformatics 9:548. 2008
    ....
  5. pmc Differentially expressed RNA from public microarray data identifies serum protein biomarkers for cross-organ transplant rejection and other conditions
    Rong Chen
    Department of Pediatrics, Stanford University School of Medicine, Stanford, California, United States of America
    PLoS Comput Biol 6:. 2010
    ....
  6. doi request reprint Progressive histological damage in renal allografts is associated with expression of innate and adaptive immunity genes
    Maarten Naesens
    Division of Nephrology, Department of Pediatrics, Stanford University School of Medicine, Stanford, California, USA
    Kidney Int 80:1364-76. 2011
    ..Thus, measurement of specific immune gene expression in protocol biopsies may be warranted to predict the development of subsequent chronic injury in histologically quiescent grafts and as a means to titrate immunosuppressive therapy...
  7. pmc ProfileChaser: searching microarray repositories based on genome-wide patterns of differential expression
    Jesse M Engreitz
    Division of Systems Medicine, Department of Pediatrics, Stanford University School of Medicine, Stanford, CA 94305, USA
    Bioinformatics 27:3317-8. 2011
    ..This analysis identifies statistical links to similar expression experiments from the vast array of publicly available data on diseases, drugs, phenotypes and other experimental conditions...
  8. pmc Compartmental localization and clinical relevance of MICA antibodies after renal transplantation
    Li Li
    Department of Pediatrics, Stanford University, Stanford, CA, USA 2 Department of Pathology, Stanford University, Stanford, CA 94304, USA
    Transplantation 89:312-9. 2010
    ..Antibodies (Ab) responses to major and minor human leukocyte antigen loci may impact graft survival after organ transplantation...
  9. pmc Systematic identification of DNA variants associated with ultraviolet radiation using a novel Geographic-Wide Association Study (GeoWAS)
    Irving Hsu
    Division of Systems Medicine, Department of Pediatrics, Stanford University School of Medicine, 1265 Welch Road, MS 5415, Stanford, CA 94305, USA
    BMC Med Genet 14:62. 2013
    ..A systematic approach utilizing bioinformatics to identify associations among environmental variables, genetic variation, and diseases across various geographical locations is needed but has been lacking...
  10. pmc Analysis of the genetic basis of disease in the context of worldwide human relationships and migration
    Erik Corona
    Division of Systems Medicine, Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, USA
    PLoS Genet 9:e1003447. 2013
    ..We anticipate that our findings will enable detailed analysis pertaining to the driving forces behind genetic risk differentiation...
  11. pmc Systematic functional regulatory assessment of disease-associated variants
    Konrad J Karczewski
    Biomedical Informatics Training Program, Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
    Proc Natl Acad Sci U S A 110:9607-12. 2013
    ..Thus, using this integrative approach, we provide a unique means to assign putative function to many disease-associated SNPs...
  12. pmc Systematic identification of interaction effects between genome- and environment-wide associations in type 2 diabetes mellitus
    Chirag J Patel
    Division of Systems Medicine, Department of Pediatrics, Stanford University School of Medicine, 1265 Welch Road, Room X 163 MS 5415, Stanford, CA 94305, USA
    Hum Genet 132:495-508. 2013
    ..Unbiased consideration of environmental and genetic factors may help identify larger and more relevant effect sizes for disease associations...
  13. pmc Integrative approach to pain genetics identifies pain sensitivity loci across diseases
    David Ruau
    Department of Anesthesia, Stanford University School of Medicine, Stanford, California, United States of America
    PLoS Comput Biol 8:e1002538. 2012
    ..This data-derived list of pain gene candidates enables additional focused and efficient biological studies validating additional candidates...
  14. pmc Phased whole-genome genetic risk in a family quartet using a major allele reference sequence
    Frederick E Dewey
    Center for Inherited Cardiovascular Disease, Division of Cardiovascular Medicine, Stanford University, Stanford, California, USA
    PLoS Genet 7:e1002280. 2011
    ..These ethnicity-specific, family-based approaches to interpretation of genetic variation are emblematic of the next generation of genetic risk assessment using whole-genome sequencing...
  15. pmc Network-based elucidation of human disease similarities reveals common functional modules enriched for pluripotent drug targets
    Silpa Suthram
    Stanford Center for Biomedical Informatics Research, Stanford University, Stanford, California, USA
    PLoS Comput Biol 6:e1000662. 2010
    ....
  16. pmc Performance comparison of whole-genome sequencing platforms
    Hugo Y K Lam
    Department of Genetics, Stanford University, Stanford, California, USA
    Nat Biotechnol 30:78-82. 2012
    ..Our results have important implications for understanding the accuracy and completeness of the genome sequencing platforms...
  17. pmc Personal omics profiling reveals dynamic molecular and medical phenotypes
    Rui Chen
    Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
    Cell 148:1293-307. 2012
    ..This study demonstrates that longitudinal iPOP can be used to interpret healthy and diseased states by connecting genomic information with additional dynamic omics activity...
  18. pmc Content-based microarray search using differential expression profiles
    Jesse M Engreitz
    Department of Bioengineering, Stanford University School of Medicine, CA, USA
    BMC Bioinformatics 11:603. 2010
    ....
  19. pmc Ontology-driven indexing of public datasets for translational bioinformatics
    Nigam H Shah
    Centre for Biomedical Informatics, School of Medicine, Stanford University, Stanford, CA 94305, USA
    BMC Bioinformatics 10:S1. 2009
    ..The key functionality of this system is to enable users to locate biomedical data resources related to particular ontology concepts...
  20. pmc Clinical utility of sequence-based genotype compared with that derivable from genotyping arrays
    Alexander A Morgan
    Department of Biochemistry, Stanford Genome Technology Center, Stanford University, Stanford, California, USA
    J Am Med Inform Assoc 19:e21-7. 2012
    ..We investigated the common-disease relevant information obtained from sequencing compared with that reported from genotyping arrays...
  21. pmc Human genomic disease variants: a neutral evolutionary explanation
    Joel T Dudley
    Program in Biomedical Informatics, Stanford University School of Medicine, Stanford, California 94305, USA
    Genome Res 22:1383-94. 2012
    ....
  22. pmc Expression-based genome-wide association study links the receptor CD44 in adipose tissue with type 2 diabetes
    Keiichi Kodama
    Division of Systems Medicine, Department of Pediatrics, Stanford University School of Medicine, Stanford, CA 94305, USA
    Proc Natl Acad Sci U S A 109:7049-54. 2012
    ..Genes repeatedly implicated in publicly available experimental data may have unique functionally important roles in T2D and other complex diseases...
  23. pmc Identifying compartment-specific non-HLA targets after renal transplantation by integrating transcriptome and "antibodyome" measures
    Li Li
    Department of Pediatrics, Blood and Marrow Transplantation Division, Stanford University, 300 Pasteur Drive, Stanford, CA 94304, USA
    Proc Natl Acad Sci U S A 106:4148-53. 2009
    ..Correlation of the most significant non-HLA antibody responses with transplant health and dysfunction are currently underway...
  24. pmc Clinical assessment incorporating a personal genome
    Euan A Ashley
    Center for Inherited Cardiovascular Disease, Division of Cardiovascular Medicine, Stanford University School of Medicine, Stanford, CA, USA
    Lancet 375:1525-35. 2010
    ..The cost of genomic information has fallen steeply, but the clinical translation of genetic risk estimates remains unclear. We aimed to undertake an integrated analysis of a complete human genome in a clinical context...
  25. ncbi request reprint Disease risk factors identified through shared genetic architecture and electronic medical records
    Li Li
    Division of Systems Medicine, Department of Pediatrics, Stanford University School of Medicine, 1265 Welch Road, Stanford, CA 94305, USA
    Sci Transl Med 6:234ra57. 2014
    ..Disease-trait associations identify traits that could serve as future prognostics, if validated through EMR and subsequent prospective trials. ..
  26. pmc Type 2 diabetes risk alleles demonstrate extreme directional differentiation among human populations, compared to other diseases
    Rong Chen
    Division of Systems Medicine, Department of Pediatrics, Stanford University School of Medicine, Stanford, California, United States of America
    PLoS Genet 8:e1002621. 2012
    ..Our results indicate that the differential frequencies of T2D risk alleles may contribute to the observed disparity in T2D incidence rates across ethnic populations...
  27. pmc Data-driven integration of epidemiological and toxicological data to select candidate interacting genes and environmental factors in association with disease
    Chirag J Patel
    Division of Systems Medicine, Department of Pediatrics, Stanford University School of Medicine, Stanford, CA 94305, USA
    Bioinformatics 28:i121-6. 2012
    ..Next, we search for evidence of toxicological relationships between these genetic and environmental factors that may have an etiological role in the disease. We illustrate our method by selecting candidate interacting factors for T2D...
  28. pmc Quantifying multi-ethnic representation in genetic studies of high mortality diseases
    Rong Chen
    Division of Systems Medicine, Department of Pediatrics, Stanford University School of Medicine, Stanford, CA
    AMIA Summits Transl Sci Proc 2012:11-8. 2012
    ..Our results demonstrate that diseases killing most Americans are still lacking genetic studies across ethnicities...
  29. pmc Translational bioinformatics in the cloud: an affordable alternative
    Joel T Dudley
    Program in Biomedical Informatics, Stanford University School of Medicine, 251 Campus Drive, Stanford, CA 94305, USA
    Genome Med 2:51. 2010
    ....
  30. pmc Population genetic inference from personal genome data: impact of ancestry and admixture on human genomic variation
    Jeffrey M Kidd
    Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
    Am J Hum Genet 91:660-71. 2012
    ....
  31. pmc Coanalysis of GWAS with eQTLs reveals disease-tissue associations
    Hyunseok Peter Kang
    Division of Systems Medicine, Department of Pediatrics, Stanford University School of Medicine, Stanford, CA
    AMIA Summits Transl Sci Proc 2012:35-41. 2012
    ..This suggests that eQTL data sets can be used to determine tissues that play a role in the pathogenesis of a disease, thereby highlighting these tissue types for further post-GWAS functional studies...
  32. pmc Likelihood ratios for genome medicine
    Alexander A Morgan
    Department of Pediatrics and the Department of Medicine, Stanford University School of Medicine, 251 Campus Drive, MS 5415, Stanford, CA 94305 5479, USA
    Genome Med 2:30. 2010
    ..By using well-established methods of evidence based medicine, these very many parallel tests may be combined using likelihood ratios to report a post-test probability of disease for use in patient assessment...
  33. doi request reprint Performance comparison of exome DNA sequencing technologies
    Michael J Clark
    Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
    Nat Biotechnol 29:908-14. 2011
    ..We also compare exome sequencing and whole genome sequencing (WGS) of the same sample, demonstrating that exome sequencing can detect additional small variants missed by WGS...
  34. ncbi request reprint Interference of globin genes with biomarker discovery for allograft rejection in peripheral blood samples
    Li Li
    Pediatrics Department, Stanford University, Stanford, CA, USA
    Physiol Genomics 32:190-7. 2008
    ..Similar applications may exist for array-based biomarker discovery for other diseases associated with changes in leukocyte trafficking, activation, or function...
  35. pmc Family history of prostate and breast cancer and the risk of prostate cancer in the PSA era
    Yen Ching Chen
    Department of Medicine, Channing Laboratory, Brigham and Women s Hospital, Harvard Medical School, Boston, Massachusetts 02115, USA
    Prostate 68:1582-91. 2008
    ..A family history of prostate cancer (PCa) or breast cancer (BCa) has been associated with the risk of PCa, but the risks were inconsistent in terms of the affected family members, and data in the PSA era are limited...