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Jingjing Li, PhD

Title(s)Assistant Professor, Neurology, Neurology
SchoolSchool of Medicine
Phone415-502-2572
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    Other Positions
    Title(s)UCSF Weill Institute for Neurosciences


    Collapse Biography 
    Collapse Education and Training
    University of TorontoPh.D.2011Molecular Genetics
    Stanford UniversityPostdoc (Banting Fellow)2016Human Genomics
    Stanford UniversityInstructor2019Pediatrics

    Collapse Overview 
    Collapse Overview
    Dr. Li works on human genomics. The main theme of his research is large-scale analysis of disease genomes by integrating multi-omics data, evolutionary insights, electronic health records, as well as digitized clinical traits from imaging and wearable sensor readouts. The ultimate goal is to build a data-driven framework to detect diseases before symptoms emerge and to achieve precision health management.

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    Collapse In The News

    Collapse Bibliographic 
    Collapse Publications
    Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Researchers can login to make corrections and additions, or contact us for help.
    List All   |   Timeline
    1. Li J, Li X, Zhang S, Snyder M. Gene-Environment Interaction in the Era of Precision Medicine. Cell. 2019 Mar 21; 177(1):38-44. PMID: 30901546.
      View in: PubMed
    2. Spiegel AM, Li J, Oehlert JW, Mayo JA, Quaintance CC, Girsen AI, Druzin ML, El-Sayed YY, Shaw GM, Stevenson DK, Gibbs RS. A Genome-Wide Analysis of Clinical Chorioamnionitis among Preterm Infants. Am J Perinatol. 2019 Jan 23. PMID: 30674050.
      View in: PubMed
    3. Stevenson DK, Wong RJ, Shaw GM, Li J, Wise PH, Davis JM. The contributions of genetics to premature birth. Pediatr Res. 2019 03; 85(4):416-417. PMID: 30644444.
      View in: PubMed
    4. Stevenson DK, Wong RJ, Aghaeepour N, Angst MS, Darmstadt GL, DiGiulio DB, Druzin ML, Gaudilliere B, Gibbs RS, B Gould J, Katz M, Li J, Moufarrej MN, Quaintance CC, Quake SR, Relman DA, Shaw GM, Snyder MP, Wang X, Wise PH. Understanding health disparities. J Perinatol. 2019 03; 39(3):354-358. PMID: 30560947.
      View in: PubMed
    5. Li J, Pan C, Zhang S, Spin JM, Deng A, Leung LLK, Dalman RL, Tsao PS, Snyder M. Decoding the Genomics of Abdominal Aortic Aneurysm. Cell. 2018 09 06; 174(6):1361-1372.e10. PMID: 30193110.
      View in: PubMed
    6. Li J, Hong X, Mesiano S, Muglia LJ, Wang X, Snyder M, Stevenson DK, Shaw GM. Natural Selection Has Differentiated the Progesterone Receptor among Human Populations. Am J Hum Genet. 2018 07 05; 103(1):45-57. PMID: 29937092.
      View in: PubMed
    7. Li J, Oehlert J, Snyder M, Stevenson DK, Shaw GM. Fetal de novo mutations and preterm birth. PLoS Genet. 2017 04; 13(4):e1006689. PMID: 28388617.
      View in: PubMed
    8. Yu KH, Li J, Snyder M, Shaw GM, O'Brodovich HM. The genetic predisposition to bronchopulmonary dysplasia. Curr Opin Pediatr. 2016 06; 28(3):318-23. PMID: 26963946.
      View in: PubMed
    9. Li J, Ma Z, Shi M, Malty RH, Aoki H, Minic Z, Phanse S, Jin K, Wall DP, Zhang Z, Urban AE, Hallmayer J, Babu M, Snyder M. Identification of Human Neuronal Protein Complexes Reveals Biochemical Activities and Convergent Mechanisms of Action in Autism Spectrum Disorders. Cell Syst. 2015 Nov 25; 1(5):361-374. PMID: 26949739.
      View in: PubMed
    10. Li J, Yu KH, Oehlert J, Jeliffe-Pawlowski LL, Gould JB, Stevenson DK, Snyder M, Shaw GM, O'Brodovich HM. Exome Sequencing of Neonatal Blood Spots and the Identification of Genes Implicated in Bronchopulmonary Dysplasia. Am J Respir Crit Care Med. 2015 Sep 01; 192(5):589-96. PMID: 26030808.
      View in: PubMed
    11. Li J, Shi M, Ma Z, Zhao S, Euskirchen G, Ziskin J, Urban A, Hallmayer J, Snyder M. Integrated systems analysis reveals a molecular network underlying autism spectrum disorders. Mol Syst Biol. 2014 Dec 30; 10:774. PMID: 25549968.
      View in: PubMed
    12. Cheng Y, Ma Z, Kim BH, Wu W, Cayting P, Boyle AP, Sundaram V, Xing X, Dogan N, Li J, Euskirchen G, Lin S, Lin Y, Visel A, Kawli T, Yang X, Patacsil D, Keller CA, Giardine B, Kundaje A, Wang T, Pennacchio LA, Weng Z, Hardison RC, Snyder MP. Principles of regulatory information conservation between mouse and human. Nature. 2014 Nov 20; 515(7527):371-375. PMID: 25409826.
      View in: PubMed
    13. Li J, Kim T, Nutiu R, Ray D, Hughes TR, Zhang Z. Identifying mRNA sequence elements for target recognition by human Argonaute proteins. Genome Res. 2014 May; 24(5):775-85. PMID: 24663241.
      View in: PubMed
    14. Kasowski M, Kyriazopoulou-Panagiotopoulou S, Grubert F, Zaugg JB, Kundaje A, Liu Y, Boyle AP, Zhang QC, Zakharia F, Spacek DV, Li J, Xie D, Olarerin-George A, Steinmetz LM, Hogenesch JB, Kellis M, Batzoglou S, Snyder M. Extensive variation in chromatin states across humans. Science. 2013 Nov 08; 342(6159):750-2. PMID: 24136358.
      View in: PubMed
    15. Xin X, Gfeller D, Cheng J, Tonikian R, Sun L, Guo A, Lopez L, Pavlenco A, Akintobi A, Zhang Y, Rual JF, Currell B, Seshagiri S, Hao T, Yang X, Shen YA, Salehi-Ashtiani K, Li J, Cheng AT, Bouamalay D, Lugari A, Hill DE, Grimes ML, Drubin DG, Grant BD, Vidal M, Boone C, Sidhu SS, Bader GD. SH3 interactome conserves general function over specific form. Mol Syst Biol. 2013; 9:652. PMID: 23549480.
      View in: PubMed
    16. Li J, Zhang Z. miRNA regulatory variation in human evolution. Trends Genet. 2013 Feb; 29(2):116-24. PMID: 23128010.
      View in: PubMed
    17. Li J, Liu Y, Xin X, Kim TS, Cabeza EA, Ren J, Nielsen R, Wrana JL, Zhang Z. Evidence for positive selection on a number of MicroRNA regulatory interactions during recent human evolution. PLoS Genet. 2012; 8(3):e1002578. PMID: 22457636.
      View in: PubMed
    18. Jin K, Li J, Vizeacoumar FS, Li Z, Min R, Zamparo L, Vizeacoumar FJ, Datti A, Andrews B, Boone C, Zhang Z. PhenoM: a database of morphological phenotypes caused by mutation of essential genes in Saccharomyces cerevisiae. Nucleic Acids Res. 2012 Jan; 40(Database issue):D687-94. PMID: 22009677.
      View in: PubMed
    19. Li Z, Vizeacoumar FJ, Bahr S, Li J, Warringer J, Vizeacoumar FS, Min R, Vandersluis B, Bellay J, Devit M, Fleming JA, Stephens A, Haase J, Lin ZY, Baryshnikova A, Lu H, Yan Z, Jin K, Barker S, Datti A, Giaever G, Nislow C, Bulawa C, Myers CL, Costanzo M, Gingras AC, Zhang Z, Blomberg A, Bloom K, Andrews B, Boone C. Systematic exploration of essential yeast gene function with temperature-sensitive mutants. Nat Biotechnol. 2011 Apr; 29(4):361-7. PMID: 21441928.
      View in: PubMed
    20. Li J, Yuan Z, Zhang Z. The cellular robustness by genetic redundancy in budding yeast. PLoS Genet. 2010 Nov 04; 6(11):e1001187. PMID: 21079672.
      View in: PubMed
    21. Li J, Liu Y, Kim T, Min R, Zhang Z. Gene expression variability within and between human populations and implications toward disease susceptibility. PLoS Comput Biol. 2010 Aug 26; 6(8). PMID: 20865155.
      View in: PubMed
    22. Li J, Min R, Vizeacoumar FJ, Jin K, Xin X, Zhang Z. Exploiting the determinants of stochastic gene expression in Saccharomyces cerevisiae for genome-wide prediction of expression noise. Proc Natl Acad Sci U S A. 2010 Jun 08; 107(23):10472-7. PMID: 20489180.
      View in: PubMed
    23. Li J, Yuan Z, Zhang Z. Revisiting the contribution of cis-elements to expression divergence between duplicated genes: the role of chromatin structure. Mol Biol Evol. 2010 Jul; 27(7):1461-6. PMID: 20139146.
      View in: PubMed
    24. Vizeacoumar FJ, van Dyk N, S Vizeacoumar F, Cheung V, Li J, Sydorskyy Y, Case N, Li Z, Datti A, Nislow C, Raught B, Zhang Z, Frey B, Bloom K, Boone C, Andrews BJ. Integrating high-throughput genetic interaction mapping and high-content screening to explore yeast spindle morphogenesis. J Cell Biol. 2010 Jan 11; 188(1):69-81. PMID: 20065090.
      View in: PubMed
    25. Li J, Min R, Bonner A, Zhang Z. A probabilistic framework to improve microrna target prediction by incorporating proteomics data. J Bioinform Comput Biol. 2009 Dec; 7(6):955-72. PMID: 20014473.
      View in: PubMed
    26. Li J, Liu Y, Dong D, Zhang Z. Evolution of an X-linked primate-specific micro RNA cluster. Mol Biol Evol. 2010 Mar; 27(3):671-83. PMID: 19933172.
      View in: PubMed
    27. Min R, Bonner A, Li J, Zhang Z. Learned random-walk kernels and empirical-map kernels for protein sequence classification. J Comput Biol. 2009 Mar; 16(3):457-74. PMID: 19254184.
      View in: PubMed
    28. Li J, Musso G, Zhang Z. Preferential regulation of duplicated genes by microRNAs in mammals. Genome Biol. 2008; 9(8):R132. PMID: 18727826.
      View in: PubMed
    29. Li JJ, Huang DS, Wang B, Chen P. Identifying protein-protein interfacial residues in heterocomplexes using residue conservation scores. Int J Biol Macromol. 2006 May 30; 38(3-5):241-7. PMID: 16600360.
      View in: PubMed
    30. Li JJ, Huang DS, Lok TM, Lyu MR, Li YX, Zhu YP. Network analysis of the protein chain tertiary structures of heterocomplexes. Protein Pept Lett. 2006; 13(4):391-6. PMID: 16712516.
      View in: PubMed
    31. Wang B, Chen P, Huang DS, Li JJ, Lok TM, Lyu MR. Predicting protein interaction sites from residue spatial sequence profile and evolution rate. FEBS Lett. 2006 Jan 23; 580(2):380-4. PMID: 16376878.
      View in: PubMed
    32. Li, J., Huang, D., MacCallum, R., and Wu, X.-R.Characterizing human gene splice sites using evolved regular expressions. Proceedings of IEEE International Joint Conference on Neural Networks. 2005; 1:493-498.