Rui Feng, Ph.D.

My methodology research has focused on developing genetic and genomic models in diverse study designs. My recent research interests include Mendelian randomization, machine learning, and big data.

My long-term projects span from genomic studies in cardiovascular and pulmonary diseases to multi-center clinical trials.

Current genetic, neurological, and clinical studies

  1. Lung Transplantation Outcomes Group (LTOG)
  2. Prematurity and Respiratory Outcomes Program (PROP)
  3. Pulmonary Arterial Hypertension and Anastrozole Study (PHANTOM)
  4. Regional versus General Anesthesia for promoting Independence after hip fracture (REGAIN)
  5. Neural Mechanisms Underlying the Antidepressant Effects of Sleep Deprivation (NASD)
  6. Reducing Proviral HIV DNA With Interferon-a Immunotherapy (BEAT-HIV)

International Visiting Students and Scholars

Graduate students and scholars from internationally renowned universities are welcome to apply for visiting positions at my lab. Please follow the links for the university policy and process: https://www.med.upenn.edu/bgs/visiting_policies.shtml . For anyone who is interested, please send your current CV, official school transcript (for students only), research proposal, and two letters of recommendation to ruifeng@upenn.edu .

Selected Publications

  • Genetic models for ordinal phenotypes
    • Zhang H., Feng R., Zhu H.: A Latent Variable Model of Segregation Analysis for Ordinal Traits. Journal of the American Statistical Association 98: 1023-1034, 2003.
    • Feng R., Leckman J., Zhang H.: Linkage Analysis of Ordinal Traits for Pedigree Data. Proceedings of the National Academy of Sciences 101(48): 16739-16744, 2004.
    • Feng R., Zhang H.: A Score Test for Linkage Analysis of Ordinal Traits Based on IBD Sharing. Biostatistics 9(1): 114-127, 2008.
    • Zhang M., Feng R., Chen X., Hu B., Zhang H.: LOT: a Tool for Linkage Analysis of Ordinal Traits for Pedigree Data. Bioinformatics 24(15): 1737-1739, June 2008.
  • Haplotype-based methods in genetics studies
    • Jang G.H., Christie J.D., Feng R.: A method for calling copy number polymorphism using haplotypes. Frontiers in Genetics 4(165), Sep 2013.
    • Wang F., Meyer N.,Walley KR, Russell JA, Feng R.: Causal Genetic Inference Using Haplotypes as Instrumental Variables. Genetic Epidemiology 40(1): 35-44, Jan 2016.
  • Methods and designs for testing parent-of-origin effects
    • Feng R., Zhang H.: A Genomic Imprinting Test for Ordinal Traits in Pedigree Data. Genetic Epidemiology 32(2): 132-142, 2008.
    • Feng R., Wu Y., Jang G., Ordovas M. J., Donna A. A Powerful Test of Imprinting for Quantitative Traits Using Haplotypes. PloS ONE. 2011;6(12):e28909.
    • Lin D., Weinberg C.R., Feng R., Hochner H., Chen J.: A Multi-Locus Likelihood Method for Assessing Parent-of-Origin Effects Using Case-Control Mother-Child Pairs. Genetic Epidemiology 37(2): 152-162, February 2013.
    • Yu X., Chen G., Feng R. : An Efficient Study Design to Test Parent-of-Origin Effect in Family Trios. Genetic epidemiology. Genetic Epidemiology. In print, 2017.
  • Twin studies
    • Bizzarro M.J., Hussain N., Jonsson B., Feng R., Ment L.R., Gruen J.R., Zhang H., Bhandari V.: The Genetic Susceptibility to Retinopathy of Prematurity. Pediatrics 118(5): 1858-1863, 2006.
    • Feng R., Zhou G., Zhang M., Zhang H.: Analysis of Twin Data Using SAS. Biometrics 65(2): 584-589, June 2009.
    • Segal N., Feng R., McGuire S.A., Allison D.B., Miller S.: Genetic and Environmental Contributions to Body Mass Index: Analysis of Monozygotic Twins, Dizygotic Twins and Same-age Unrelated Siblings. International Journal of Obesity 33(1): 37-41, 2009.
  • Family disease history in survival data
    • Feng R., McClure L., Tiwari H.K., Howard G.: A new estimate of family disease history providing improved prediction of disease risks. Statistics in Medicine, 28(8): 1269-1283, 2009. Epub, January 2009.
    • Kennedy R.E., Howard G., Go R.C., Rothwell P.M., Tiwari H.K., Feng R., McClure L.A., Prineas R.J., Banerjee A., Arnett D.K.: Association Between Family Risk of Stroke and Myocardial Infarction with Prevalent Risk Factors and Coexisting Diseases. Stroke 43(4): 974-9, February 2012.
    • Feng R., Hersh P., Howard G.: Quantifying Maternal and Paternal Disease History Using Log-Rank Score with an Application to a National Cohort Study. International Journal of Statistics in Medical Research 3: 21-31, 2014.
    • Xu E., DeMauro S., Feng R.: The Impact of Parental History on Children's Risk of Asthma: a Study Based on the National Health and Nutrition Examination Survey-III. Journal of Asthma and Allergy 8: 51-61, May 2015.
  • High-dimensional genetics
    • Lin W., Feng R., Li H.: Regularization Methods for High-Dimensional Instrumental Variables Regression with an Application to Genetical Genomics. Journal of the American Statistical Association 110(509): 270-288, Apr 2015.
    • Lin W., Shi P., Feng R., Li H.: Variable Selection in Regression with Compositional Covariates. Biometrika 101(4): 785-797, Aug 2014.
    • Sun H., Lin W., Feng R., Li H.: Network-Regularized High-Dimensional Cox Regression for Analysis of Genomic Data. Statistica Sinica 24: 1433-1459, 2014.
  • Genetics in lung diseases
    • Meyer N.J., Li M., Feng R., Gallop R., Localio A.R., Bellamy S., Bradfield J., Hakonarson H., Fuchs B.F., Lanken P.N., Albelda S.M., Aplenc R., Ware L.D., Calfe C.S., O'Keefe G.E., Wurfe M.M., Christiani D.C., Christie J.D.: ANGPT2 Genetic Variant is Associated with Trauma-Associated Acute Lung Injury and Altered Plasma Angiopoietin-2 Isoform Ratio. American Journal of Respiratory and Critical Care Medicine 183(10): 1344-53, May 2011.
    • Rushefski M., Aplenc R., Meyer N., Li M., Feng R., Lanken PN., Gallop R., Bellamy S., Localio A.R., Feinstein S.I., Fisher A.B., Albelda S.M., Christie J.D.: Novel Variants in the PRDX6 Gene and the Risk of Acute Lung Injury Following Major Trauma. BMC Medical Genetics 12: 77, May 2011.
    • Christie J., Wurfel M., Feng R., O'Keefe G., Bradfield J., Ware L., Christiani D., Calfee C., Meyer N., Kim C., Li M., Akey J., Barnes K., Sevransky J., Lanken P.N., Aplenc R., Maloney J., Hakonarson H.: Genome Wide Association Identifies PPFIA1 as a Candidate Gene for Acute Lung Injury Risk Following Major Trauma. PLoS ONE 7(1): e28268, Jan 2012.
    • Meyer N.J., Daye Z.J., Rushefski M., Aplenc R., Lanken P.N., Shashaty M.G., Christie J.D., Feng R.: SNP-Set Analysis Replicates Acute Lung Injury Genetic Risk Factors. BMC Medical Genetics 13: 52, Jun 2012.
    • Diamond J.M., Meyer N.J., Feng R., Rushefski M., Lederer D.J., Kawut S.M., Lee J.C., Cantu E., Shah R.J., Lama V.N., Bhorade S., Crespo M., Demissie E., Sonett J., Wille K., Orens J., Weinacker A., Weill D., Arcasoy S., Shah P.D., Belperio J.A., Wilkes D., Ware L.B., Palmer S.M.,Christie J.D.: Variation in PTX3 is Associated with Primary Graft Dysfunction after Lung Transplantation. American Journal of Respiratory and Critical Care Medicine 186(6): 546-552, Sep 2012.
    • Tejera P., Meyer N.J., Chen F., Feng R., Zhao Y., O'Mahony D.S., Li L., Sheu C.C., Zhai R., Wang Z., Su L., Bajwa E., Ahasic A.M., Clardy P.F., Gong M.N., Frank A.J., Lanken P.N., Thompson B.T., Christie J.D., Wurfel M.M., O'Keefe G.E., Christiani D.C.: Distinct and Replicable Genetic Risk Factors for Acute Respiratory Distress Syndrome of Pulmonary or Extrapulmonary Origin. Journal of Medical Genetics 49(11): 671-680, Nov 2012.
    • Meyer N.J., Feng R., Li M., Zhao Y., Sheu C.C., Tejera P., Gallop R., Bellamy S., Rushefski M., Lanken P.N., Aplenc R., O'Keefe G.E., Wurfel M.M., Christiani D.C., Christie J.D.: IL1RN Coding Variant is Associated with Lower Risk of Acute Respiratory Distress Syndrome and Increased Plasma IL-1 Receptor Antagonist. American Journal of Respiratory and Critical Care Medicine 187(9): 950-959, May 2013
    • Reilly J.P., Meyer N.J., Shashaty M.G., Feng R., Lanken P.N., Gallop R., Kaplan S., Herlim M., Oz N.L., Hiciano I., Campbell A., Holena D.N., Reilly M.P., Christie J.D.: ABO Blood Type A is Associated with Increased Risk of ARDS in Whites Following both Major Trauma and Severe Sepsis. Chest 145(4): 753-61, Apr 2014.
    • Diamond J.M., Akimova T., Kazi A., Shah R.J., Cantu E., Feng R., Levine M.H., Kawut S.M., Meyer N.J., Lee J.C., Hancock W.W., Aplenc R., Ware L.B., Palmer S.M., Bhorade S., Lama V.N., Weinacker A., Orens J., Wille K., Crespo M., Lederer D.J., Arcasoy S., Demissie E., Christie J.D., Lung Transplant Outcomes Group : Genetic Variation in the Prostaglandin E2 Pathway is Associated with Primary Graft Dysfunction. American Journal of Respiratory and Critical Care Medicine 189(5): 567-575, Mar 2014.
    • Christie J., Wurfel M., Feng R., O'Keefe G., Bradfield J., Ware L., Christiani D., Calfee C., Meyer N., Kim C., Li M., Akey J., Barnes K., Sevransky J., Lanken P.N., Aplenc R., Maloney J., Hakonarson H.: Genome Wide Association Identifies Candidate Susceptibility Loci for Acute Lung Injury Following Major Trauma PLoS ONE 7(1), January 2012.
    • Meyer N.J., Ferguson J.F., Feng R., Wang F., Patel P.N., Li M., Xue C., Qu L., Liu Y., Boyd J.H., Russell J.A., Christie J.D., Walley K.R., Reilly M.P.: A Functional Synonymous Coding Variant in the IL1RN Gene is Associated with Survival in Septic Shock. American Journal of Respiratory and Critical Care Medicine 190(6): 656-664, Sep 2014.
    • Cantu E., Shah R.J., Lin W., Daye Z.J., Diamond J.M., Suzuki Y., Ellis J.H., Borders C.F., Andah G.A., Beduhn B., Meyer N.J., Ruschefski M., Aplenc R., Feng R., Christie J.D.; Lung Transplant Outcomes Group Investigators.: Oxidant Stress Regulatory Genetic Variation in Recipients and Donors Contributes to Risk of Primary Graft Dysfunction after Lung Transplantation. Journal of Thoracic and Cardiovascular Surgery. Epub 2014 Sep 28, 149(2): 596-602, Feb 2015.
  • Prospective studies in pediatric pulmonology
    • Healy F., Lin W., Feng R., Hanna B.D., Hedrick H., Panitch H.B.: An Association between Pulmonary Hypertension and Impaired Lung Function in Infants with Congenital Diaphragmatic Hernia. Pediatric Pulmonology Mar 2014.
    • Panitch H.B., Weiner D.J., Feng R., Perez M.R., Healy F., McDonough J.M., Rintoul N., Hedrick H.L.: Lung Function over the First 3 Years of Life in Children with Congenital Diaphragmatic Hernia. Pediatric Pulmonology Jul 2014.
    • Poindexter B.B., Feng R., Schmidt B., Aschner ¬J.L., Ballard R.A., Hamvas A., Reynolds A.M., Shaw P.A., Jobe A.H. Limitations of Current Definitions of Bronchopulmonary Dysplasia Outcomes of the PROP Cohort at 36 Weeks PMA. Annals of the American Thoracic Society. 12(12): 1822-1830, Dec 2015.
    • Keller R., Feng R., Shaw P., Bellamy S., Ferkol T., Rogers E., Stevens T., Voynow J., Hardie B., DeMauro S., and Moore P.: Respiratory Outcome of PROP Premature Infants after Hospital Discharge. Journal of Pediatrics. In print, 2017

    Resources for Trainees

    Previous Students/Fellows and their Current Positions

    • Xiaobo Yu, Zhejiang University
    • Edward Cantu, University of Pennsylvania
    • Erik Jensen, University of Pennsylvania
    • Fan Wang, The Cleveland Clinic
    • Emily Xu, University of Pennsylvania
    • Jessica Palakshappa, University of Pennsylvania
    • Andrew Costarino, University of Pennsylvania
    • Wei Lin, Peking University
    • Gun Ho Jang, University of Toronto
    • Scott Weiss, University of Pennsylvania
    • John Reilly, University of Pennsylvania
    • Matthew P Kronman, Seattle Children’s South Clinic
    • D'Jahna Akinyemi, Johns Hopkins University
    • Joshua Diamond, University of Pennsylvania
    • Lu Chen, University of Pennsylvania
    • Hersh Patel, TowerBrook
    • Rupal Shah, University of Pennsylvania
    • Liyan Gao, University of Alabama at Birmingham