Li Li, MD
- ASSISTANT PROFESSOR | Genetics and Genomic Sciences
Research Topics:Bioinformatics, Computational Biology, Drug Design and Discovery, Fibrosis, Genetics, Genomics, Microarray, Tolerance, Transplantation
Dr. Li is an assistant professor and has over 15 years experience in clinical informatics, precision medicine, and bioinformatics involving genetic and clinical risk factor identification, diagnostic assay development, and new therapeutic targets discovery. Her expertise is in translational research by integrating high-throughput genomics, genetics, various molecular measurements, and electronic medical records data with over 50 peer-reviewed publications including Science Translational Medicine, PNAS, Nature Methods, Nature Biotechnology, and JASN.
Her studies on identifying T2D sub populations through EMR has been recently featured by NIH director http://directorsblog.nih.gov/2015/11/10/big-data-reveals-possible-subtypes-of-type-2-diabetes/ and identifying risk factors through genetic architecture was highlighted by NIH director http://directorsblog.nih.gov/2014/05/06/mining-the-big-data-mountain/.
Her previous studies on developing novel diagnostic biomarker for tolerance, rejection post-transplantation cross-organ and steroid-avoidance treatment clinical studies have been awarded The Young Investigator Award in 2008, 2009, and 2010 in American Society of Transplantation, the distinguished research fellow in 2009, and The Transplantation Society (TTS) Astellas Young Investigators Award in 2010.
MD, Dalian Medical University
MS, Boston University
PostDoc, University of California, San Diego
The Transplantation Society (TTS) Astellas Young Investigators Award
Young Investigator Award, American Society of Transplantation (AST)
Distinguished Follow of American society of Transplantation (AST)
Young Investigator Award, American Society of Transplantation (AST)
Outstanding Achievement Award
precision medicine, EMR, genetics risk factor, GWAS, machine learning, meta-clinical trials, genomics meta-analysis, diagnostic and prognostic biomarker assay development, drug target discovery
To view a complete list of publications, please click here.
Li L, Lee NJ, Glicksberg BS, Radbill BD, Dudley JT. Data-Driven Identification of Risk Factors of Patient Satisfaction at a Large Urban Academic Medical Center. PloS one 2016; 11(5).
Miotto R, Li L, Kidd BA, Dudley JT. Deep Patient: An Unsupervised Representation to Predict the Future of Patients from the Electronic Health Records. Scientific reports 2016; 6.
Yadav KK, Khader S, Readhead B, Yadav SS, Li L, Kasarksis A, Tewari AK, Dudley JT. Systems Medicine approaches to improving understanding, treatment, and clinical management of Neuroendocrine Prostate Cancer. Current pharmaceutical design 2016 May;.
Kidd BA, Hoffman G, Zimmerman N, Li L, Morgan JW, Glowe PK, Botwin GJ, Parekh S, Babic N, Doust MW, Stock GB, Schadt EE, Dudley JT. Evaluation of direct-to-consumer low-volume lab tests in healthy adults. The Journal of clinical investigation 2016 May; 126(5).
Li L, Cheng WY, Glicksberg BS, Gottesman O, Tamler R, Chen R, Bottinger EP, Dudley JT. Identification of type 2 diabetes subgroups through topological analysis of patient similarity. Science translational medicine 2015 Oct; 7(311).
Brohl AS, Li L, Andikyan V, Običan SG, Cioffi A, Hao K, Dudley JT, Ascher-Walsh C, Kasarskis A, Maki RG. Age-stratified risk of unexpected uterine sarcoma following surgery for presumed benign leiomyoma. The oncologist 2015 Apr; 20(4).
Glicksberg BS, Li L, Cheng WY, Shameer K, Hakenberg J, Castellanos R, Ma M, Shi L, Shah H, Dudley JT, Chen R. An integrative pipeline for multi-modal discovery of disease relationships. Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing 2015;.
Menon MC, Chuang PY, Li Z, Wei C, Zhang W, Luan Y, Yi Z, Xiong H, Woytovich C, Greene I, Overbey J, Rosales I, Bagiella E, Chen R, Ma M, Li L, Ding W, Djamali A, Saminego M, O'Connell PJ, Gallon L, Colvin R, Schroppel B, He JC, Murphy B. Intronic locus determines SHROOM3 expression and potentiates renal allograft fibrosis. The Journal of clinical investigation 2015 Jan; 125(1).
Roedder S, Li L, Alonso MN, Hsieh SC, Vu MT, Dai H, Sigdel TK, Bostock I, Macedo C, Metes D, Zeevi A, Shapiro R, Salvatierra O, Scandling J, Alberu J, Engleman E, Sarwal MM. A Three-Gene Assay for Monitoring Immune Quiescence in Kidney Transplantation. Journal of the American Society of Nephrology : JASN 2014 Nov;.
A comprehensive assessment of RNA-seq accuracy, reproducibility and information content by the Sequencing Quality Control Consortium. Nature biotechnology 2014 Sep; 32(9).
Sansanwal P, Li L, Sarwal MM. Inhibition of intracellular clusterin attenuates cell death in nephropathic cystinosis. Journal of the American Society of Nephrology : JASN 2015 Mar; 26(3).
Li L, Ruau DJ, Patel CJ, Weber SC, Chen R, Tatonetti NP, Dudley JT, Butte AJ. Disease risk factors identified through shared genetic architecture and electronic medical records. Science translational medicine 2014 Apr; 6(234).
Li L, Ruau D, Chen R, Weber S, Butte AJ. Systematic identification of risk factors for Alzheimer's disease through shared genetic architecture and electronic medical records. Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing 2013;.
Li L, Khatri P, Sigdel TK, Tran T, Ying L, Vitalone MJ, Chen A, Hsieh S, Dai H, Zhang M, Naesens M, Zarkhin V, Sansanwal P, Chen R, Mindrinos M, Xiao W, Benfield M, Ettenger RB, Dharnidharka V, Mathias R, Portale A, McDonald R, Harmon W, Kershaw D, Vehaskari VM, Kamil E, Baluarte HJ, Warady B, Davis R, Butte AJ, Salvatierra O, Sarwal MM. A peripheral blood diagnostic test for acute rejection in renal transplantation. American journal of transplantation : official journal of the American Society of Transplantation and the American Society of Transplant Surgeons 2012 Oct; 12(10).
Kohrt HE, Tian L, Li L, Alizadeh AA, Hsieh S, Tibshirani RJ, Strober S, Sarwal M, Lowsky R. Identification of gene microarray expression profiles in patients with chronic graft-versus-host disease following allogeneic hematopoietic cell transplantation. Clinical immunology (Orlando, Fla.) 2013 Jul; 148(1).
Sarwal MM, Ettenger RB, Dharnidharka V, Benfield M, Mathias R, Portale A, McDonald R, Harmon W, Kershaw D, Vehaskari VM, Kamil E, Baluarte HJ, Warady B, Tang L, Liu J, Li L, Naesens M, Sigdel T, Waskerwitz J, Salvatierra O. Complete steroid avoidance is effective and safe in children with renal transplants: a multicenter randomized trial with three-year follow-up. American journal of transplantation : official journal of the American Society of Transplantation and the American Society of Transplant Surgeons 2012 Oct; 12(10).
Sigdel TK, Li L, Tran TQ, Khatri P, Naesens M, Sansanwal P, Dai H, Hsieh SC, Sarwal MM. Non-HLA antibodies to immunogenic epitopes predict the evolution of chronic renal allograft injury. Journal of the American Society of Nephrology : JASN 2012 Apr; 23(4).
Li L, Wozniak LJ, Rodder S, Heish S, Talisetti A, Wang Q, Esquivel C, Cox K, Chen R, McDiarmid SV, Sarwal MM. A common peripheral blood gene set for diagnosis of operational tolerance in pediatric and adult liver transplantation. American journal of transplantation : official journal of the American Society of Transplantation and the American Society of Transplant Surgeons 2012 May; 12(5).
Lee S, Naesens M, Li L, Sarwal M. Stanniocalcin supports the functional adaptation of adult-sized kidneys transplanted into the pediatric recipients. Transplantation 2012 Jun; 93(11).
Sigdel TK, Woo SH, Dai H, Khatri P, Li L, Myers B, Sarwal MM, Lafayette RA. Profiling of autoantibodies in IgA nephropathy, an integrative antibiomics approach. Clinical journal of the American Society of Nephrology : CJASN 2011 Dec; 6(12).
Vitalone MJ, Naesens M, Sigdel T, Li L, Hseih S, Sarwal MM. The dual role of epithelial-to-mesenchymal transition in chronic allograft injury in pediatric renal transplantation. Transplantation 2011 Oct; 92(7).
Naesens M, Khatri P, Li L, Sigdel TK, Vitalone MJ, Chen R, Butte AJ, Salvatierra O, Sarwal MM. Progressive histological damage in renal allografts is associated with expression of innate and adaptive immunity genes. Kidney international 2011 Dec; 80(12).
Zarkhin V, Bezchinsky M, Li L, Sarwal MM. Soluble human leukocyte antigen-G in pediatric renal transplantation. Transplantation 2011 Jul; 92(1).
Zarkhin V, Lovelace PA, Li L, Hsieh SC, Sarwal MM. Phenotypic evaluation of B-cell subsets after rituximab for treatment of acute renal allograft rejection in pediatric recipients. Transplantation 2011 May; 91(9).
Li L, Chaudhuri A, Chen A, Zhao X, Bezchinsky M, Concepcion W, Salvatierra O, Sarwal MM. Efficacy and safety of thymoglobulin induction as an alternative approach for steroid-free maintenance immunosuppression in pediatric renal transplantation. Transplantation 2010 Dec; 90(12).
Li L, Sigdel T, Vitalone M, Lee SH, Sarwal M. Differential immunogenicity and clinical relevance of kidney compartment specific antigens after renal transplantation. Journal of proteome research 2010 Dec; 9(12).
Sansanwal P, Li L, Hsieh SC, Sarwal MM. Insights into novel cellular injury mechanisms by gene expression profiling in nephropathic cystinosis. Journal of inherited metabolic disease 2010 Dec; 33(6).
Zarkhin V, Talisetti A, Li L, Wozniak LJ, McDiarmid SV, Cox K, Esquivel C, Sarwal MM. Expression of soluble HLA-G identifies favorable outcomes in liver transplant recipients. Transplantation 2010 Nov; 90(9).
Chen R, Sigdel TK, Li L, Kambham N, Dudley JT, Hsieh SC, Klassen RB, Chen A, Caohuu T, Morgan AA, Valantine HA, Khush KK, Sarwal MM, Butte AJ. Three non-invasive protein biomarkers for solid-organ transplant rejection found through integrative genomics. PLoS computational biology 2010; 6(9).
The MicroArray Quality Control (MAQC)-II study of common practices for the development and validation of microarray-based predictive models. reproducibility and information content by the Microarray Quality Control Consortium. Nature Biotechnology 2010 Aug; 28(8).
Li L, Chen A, Chaudhuri A, Kambham N, Sigdel T, Chen R, Sarwal MM. Compartmental localization and clinical relevance of MICA antibodies after renal transplantation. Transplantation 2010 Feb; 89(3).
Sutherland SM, Li L, Sigdel TK, Wadia PP, Miklos DB, Butte AJ, Sarwal MM. Protein microarrays identify antibodies to protein kinase Czeta that are associated with a greater risk of allograft loss in pediatric renal transplant recipients. Kidney international 2009 Dec; 76(12).
Zarkhin V, Li L, Sarwal MM. BAFF may modulate the rate of B-cell repopulation after rituximab therapy for acute renal transplant rejection. Transplantation 2009 Nov; 88(10).
Sigdel T, Ling X, Lau K, Li L, Schilling J, Sarwal M. Urinary peptidomic analysis identifies potential biomarkers for acute rejection of renal transplantation. . Clinical Proteomics 2009; 5.
Naesens M, Li L, Ying L, Sansanwal P, Sigdel TK, Hsieh SC, Kambham N, Lerut E, Salvatierra O, Butte AJ, Sarwal MM. Gene expression differences between living and deceased donor kidneys in human transplantation . Journal of the American Society of Nephrology : JASN 2009 Aug; 20(8).
Li L, Chang A, Naesens M, Kambham N, Waskerwitz J, Martin J, Wong C, Alexander S, Grimm P, Concepcion W, Salvatierra O, Sarwal MM. Steroid-free immunosuppression since 1999: 129 pediatric renal transplants with sustained graft and patient benefits. American journal of transplantation : official journal of the American Society of Transplantation and the American Society of Transplant Surgeons 2009 Jun; 9(6).
Sutherland S, Li L, Concepcion W, Salvatierra O, Sarwal MM. Steroid-free immunosuppression in pediatric renal transplantation: rationale for and [corrected] outcomes following conversion to steroid based therapy. Transplantation 2009 Jun; 87(11).
Li L, Wadia P, Chen R, Kambham N, Naesens M, Sigdel TK, Miklos DB, Sarwal MM, Butte AJ. Identifying compartment-specific non-HLA targets after renal transplantation by integrating transcriptome and . Proceedings of the National Academy of Sciences of the United States of America 2009 Mar; 106(11).
Zarkhin V, Li L, Kambham N, Sigdel T, Salvatierra O, Sarwal MM. A randomized, prospective trial of rituximab for acute rejection in pediatric renal transplantation. American journal of transplantation : official journal of the American Society of Transplantation and the American Society of Transplant Surgeons 2008 Dec; 8(12).
Zarkhin V, Li L, Sarwal M. . Transplantation 2008 Jun; 85(12).
Chen R, Morgan AA, Dudley J, Deshpande T, Li L, Kodama K, Chiang AP, Butte AJ. FitSNPs: highly differentially expressed genes are more likely to have variants associated with disease. Genome biology 2008; 9(12).
Li L, Weintraub L, Concepcion W, Martin JP, Miller K, Salvatierra O, Sarwal MM. Potential influence of tacrolimus and steroid avoidance on early graft function in pediatric renal transplantation. Pediatric transplantation 2008 Sep; 12(6).
Naesens M, Salvatierra O, Li L, Kambham N, Concepcion W, Sarwal M. Maturation of dose-corrected tacrolimus predose trough levels in pediatric kidney allograft recipients. Transplantation 2008 Apr; 85(8).
Li L, Ying L, Naesens M, Xiao W, Sigdel T, Hsieh S, Martin J, Chen R, Liu K, Mindrinos M, Davis R, Sarwal M. Interference of globin genes with biomarker discovery for allograft rejection in peripheral blood samples. Physiological genomics 2008 Jan; 32(2).
Weintraub L, Li L, Kambham N, Alexander S, Concepcion W, Miller K, Wong C, Salvatierra O, Sarwal M. Patient selection critical for calcineurin inhibitor withdrawal in pediatric kidney transplantation. Pediatric transplantation 2008 Aug; 12(5).
Chen R, Li L, Butte AJ. AILUN: reannotating gene expression data automatically. Nature methods 2007 Nov; 4(11).
Brouard S, Mansfield E, Braud C, Li L, Giral M, Hsieh SC, Baeten D, Zhang M, Ashton-Chess J, Braudeau C, Hsieh F, Dupont A, Pallier A, Moreau A, Louis S, Ruiz C, Salvatierra O, Soulillou JP, Sarwal M. Identification of a peripheral blood transcriptional biomarker panel associated with operational renal allograft tolerance. Proceedings of the National Academy of Sciences of the United States of America 2007 Sep; 104(39).
Nagarajan S, Mansfield E, Hsieh S, Liu R, Hsieh F, Li L, Salvatierra O, Sarwal MM. Transplant reno-vascular stenoses associated with early erythropoietin use. Clinical transplantation 2007; 21(5).
Beaunoyer M, Snehal M, Li L, Concepcion W, Salvatierra O, Sarwal M. Optimizing outcomes for neonatal ARPKD. Pediatric transplantation 2007 May; 11(3).
Li L, Chaudhuri A, Weintraub LA, Hsieh F, Shah S, Alexander S, Salvatierra O, Sarwal MM. Subclinical cytomegalovirus and Epstein-Barr virus viremia are associated with adverse outcomes in pediatric renal transplantation. Pediatric transplantation 2007 Mar; 11(2).
Kambham N, Nagarajan S, Shah S, Li L, Salvatierra O, Sarwal MM. A novel, semiquantitative, clinically correlated calcineurin inhibitor toxicity score for renal allograft biopsies. Clinical journal of the American Society of Nephrology : CJASN 2007 Jan; 2(1).
Sarwal MM, Li L. Designer genes: Filling the gap in transplantation. Transplantation 2006 Nov; 82(10).
Li L, Chen R, Weng Z. RDOCK: refinement of rigid-body protein docking predictions. Proteins 2003 Nov; 53(3).
Chen R, Li L, Weng Z. ZDOCK: an initial-stage protein-docking algorithm. Proteins 2003 Jul; 52(1).
Chen R, Tong W, Mintseris J, Li L, Weng Z. ZDOCK predictions for the CAPRI challenge. Proteins 2003 Jul; 52(1).