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Jingjing Li, PhD

Photo of Jingjing Li, PhD
Title(s)Associate Professor, Neurology
SchoolSchool of Medicine
Emailjingjing.li@ucsf.edu
PronounsHe/Him/His
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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 Featured Publications

    Collapse Bibliographic 
    Collapse selected 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. to make corrections and additions.
    Newest   |   Oldest   |   Most Cited   |   Most Discussed   |   Timeline   |   Field Summary   |   Plain Text
    Altmetrics Details PMC Citations indicate the number of times the publication was cited by articles in PubMed Central, and the Altmetric score represents citations in news articles and social media. (Note that publications are often cited in additional ways that are not shown here.) Fields are based on how the National Library of Medicine (NLM) classifies the publication's journal and might not represent the specific topic of the publication. Translation tags are based on the publication type and the MeSH terms NLM assigns to the publication. Some publications (especially newer ones and publications not in PubMed) might not yet be assigned Field or Translation tags.) Click a Field or Translation tag to filter the publications.
    1. Single-cell proteomic landscape of the developing human brain. Nat Biotechnol. 2026 Jan 27. Wu T, Jiang L, Mukhtar T, Wang L, Jian R, Wang C, Trinh T, Kriegstein AR, Snyder M, Li J. PMID: 41593231.
      View in: PubMed   Mentions:    Fields:    
    2. Landscape of allele-specific expression in prostate cancer reveals recurrent, stage-specific events in AR signaling and resistance pathways. Mol Cancer Res. 2026 Jan 16. Tsui M, Hu K, Song H, Hsu SC, Chen YA, Nuniz L, Pham JH, Chang CH, Hui KSF, Quigley DA, Li J, Huang FW. PMID: 41543497.
      View in: PubMed   Mentions:
    3. Anticlustering for sample allocation to minimize batch effects. Cell Rep Methods. 2025 Aug 18; 5(8):101137. Papenberg M, Wang C, Diop M, Bukhari SH, Oskotsky B, Davidson BR, Vo KC, Liu B, Irwin JC, Combes AJ, Gaudilliere B, Li J, Stevenson DK, Klau GW, Giudice LC, Sirota M, Oskotsky TT. PMID: 40829575; PMCID: PMC12461633.
      View in: PubMed   Mentions:    Fields:    Translation:Humans
    4. Molecular and cellular dynamics of the developing human neocortex. Nature. 2025 Nov; 647(8088):169-178. Wang L, Wang C, Moriano JA, Chen S, Zuo G, Cebrián-Silla A, Zhang S, Mukhtar T, Wang S, Song M, de Oliveira LG, Bi Q, Augustin JJ, Ge X, Paredes MF, Huang EJ, Alvarez-Buylla A, Duan X, Li J, Kriegstein AR. PMID: 39779846; PMCID: PMC12589127.
      View in: PubMed   Mentions: 34     Fields:    Translation:HumansCells
    5. Systems analysis of de novo mutations in congenital heart diseases identified a protein network in the hypoplastic left heart syndrome. Cell Syst. 2022 11 16; 13(11):895-910.e4. Wang YJ, Zhang X, Lam CK, Guo H, Wang C, Zhang S, Wu JC, Snyder M, Li J. PMID: 36167075; PMCID: PMC9671831.
      View in: PubMed   Mentions: 7     Fields:    Translation:HumansCells
    6. A Deep Learning Framework Identifies Pathogenic Noncoding Somatic Mutations from Personal Prostate Cancer Genomes. Cancer Res. 2020 11 01; 80(21):4644-4654. Wang C, Li J. PMID: 32907840.
      View in: PubMed   Mentions: 9     Fields:    Translation:Humans
    7. Gene-Environment Interaction in the Era of Precision Medicine. Cell. 2019 03 21; 177(1):38-44. Li J, Li X, Zhang S, Snyder M. PMID: 30901546; PMCID: PMC8108774.
      View in: PubMed   Mentions: 47     Fields:    Translation:Humans
    8. A Genome-Wide Analysis of Clinical Chorioamnionitis among Preterm Infants. Am J Perinatol. 2019 12; 36(14):1453-1458. Spiegel AM, Li J, Oehlert JW, Mayo JA, Quaintance CC, Girsen AI, Druzin ML, El-Sayed YY, Shaw GM, Stevenson DK, Gibbs RS. PMID: 30674050; PMCID: PMC11182631.
      View in: PubMed   Mentions: 3     Fields:    Translation:Humans
    9. The contributions of genetics to premature birth. Pediatr Res. 2019 03; 85(4):416-417. Stevenson DK, Wong RJ, Shaw GM, Li J, Wise PH, Davis JM. PMID: 30644444.
      View in: PubMed   Mentions: 5     Fields:    Translation:Humans
    10. Understanding health disparities. J Perinatol. 2019 03; 39(3):354-358. 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. PMID: 30560947.
      View in: PubMed   Mentions: 9     Fields:    Translation:HumansPHPublic Health
    11. Decoding the Genomics of Abdominal Aortic Aneurysm. Cell. 2018 09 06; 174(6):1361-1372.e10. Li J, Pan C, Zhang S, Spin JM, Deng A, Leung LLK, Dalman RL, Tsao PS, Snyder M. PMID: 30193110.
      View in: PubMed   Mentions: 40     Fields:    Translation:HumansAnimals
    12. Natural Selection Has Differentiated the Progesterone Receptor among Human Populations. Am J Hum Genet. 2018 07 05; 103(1):45-57. Li J, Hong X, Mesiano S, Muglia LJ, Wang X, Snyder M, Stevenson DK, Shaw GM. PMID: 29937092; PMCID: PMC6035283.
      View in: PubMed   Mentions: 21     Fields:    Translation:HumansAnimals
    13. Fetal de novo mutations and preterm birth. PLoS Genet. 2017 04; 13(4):e1006689. Li J, Oehlert J, Snyder M, Stevenson DK, Shaw GM. PMID: 28388617; PMCID: PMC5384656.
      View in: PubMed   Mentions: 22     Fields:    Translation:HumansAnimals
    14. The genetic predisposition to bronchopulmonary dysplasia. Curr Opin Pediatr. 2016 06; 28(3):318-23. Yu KH, Li J, Snyder M, Shaw GM, O'Brodovich HM. PMID: 26963946; PMCID: PMC4853271.
      View in: PubMed   Mentions: 24     Fields:    Translation:Humans
    15. 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. 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. PMID: 26949739; PMCID: PMC4776331.
      View in: PubMed   Mentions: 30     Fields:    
    16. 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. Li J, Yu KH, Oehlert J, Jeliffe-Pawlowski LL, Gould JB, Stevenson DK, Snyder M, Shaw GM, O'Brodovich HM. PMID: 26030808; PMCID: PMC4595691.
      View in: PubMed   Mentions: 45     Fields:    Translation:HumansAnimalsCellsPHPublic Health
    17. Integrated systems analysis reveals a molecular network underlying autism spectrum disorders. Mol Syst Biol. 2014 Dec 30; 10:774. Li J, Shi M, Ma Z, Zhao S, Euskirchen G, Ziskin J, Urban A, Hallmayer J, Snyder M. PMID: 25549968; PMCID: PMC4300495.
      View in: PubMed   Mentions: 79     Fields:    Translation:HumansAnimalsCells
    18. Principles of regulatory information conservation between mouse and human. Nature. 2014 Nov 20; 515(7527):371-375. 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, mouse ENCODE Consortium, Kundaje A, Wang T, Pennacchio LA, Weng Z, Hardison RC, Snyder MP. PMID: 25409826; PMCID: PMC4343047.
      View in: PubMed   Mentions: 183     Fields:    Translation:HumansAnimalsCells
    19. Identifying mRNA sequence elements for target recognition by human Argonaute proteins. Genome Res. 2014 May; 24(5):775-85. Li J, Kim T, Nutiu R, Ray D, Hughes TR, Zhang Z. PMID: 24663241; PMCID: PMC4009607.
      View in: PubMed   Mentions: 23     Fields:    Translation:HumansCells
    20. Extensive variation in chromatin states across humans. Science. 2013 Nov 08; 342(6159):750-2. 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. PMID: 24136358; PMCID: PMC4075767.
      View in: PubMed   Mentions: 210     Fields:    Translation:HumansCells
    21. SH3 interactome conserves general function over specific form. Mol Syst Biol. 2013; 9:652. 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. PMID: 23549480; PMCID: PMC3658277.
      View in: PubMed   Mentions: 42     Fields:    Translation:AnimalsCells
    22. miRNA regulatory variation in human evolution. Trends Genet. 2013 Feb; 29(2):116-24. Li J, Zhang Z. PMID: 23128010.
      View in: PubMed   Mentions: 19     Fields:    Translation:HumansCells
    23. Evidence for positive selection on a number of MicroRNA regulatory interactions during recent human evolution. PLoS Genet. 2012; 8(3):e1002578. Li J, Liu Y, Xin X, Kim TS, Cabeza EA, Ren J, Nielsen R, Wrana JL, Zhang Z. PMID: 22457636; PMCID: PMC3310733.
      View in: PubMed   Mentions: 35     Fields:    Translation:HumansCells
    24. 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. Jin K, Li J, Vizeacoumar FS, Li Z, Min R, Zamparo L, Vizeacoumar FJ, Datti A, Andrews B, Boone C, Zhang Z. PMID: 22009677; PMCID: PMC3245137.
      View in: PubMed   Mentions: 9     Fields:    Translation:Animals
    25. Systematic exploration of essential yeast gene function with temperature-sensitive mutants. Nat Biotechnol. 2011 Apr; 29(4):361-7. 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. PMID: 21441928; PMCID: PMC3286520.
      View in: PubMed   Mentions: 248     Fields:    Translation:Animals
    26. The cellular robustness by genetic redundancy in budding yeast. PLoS Genet. 2010 Nov 04; 6(11):e1001187. Li J, Yuan Z, Zhang Z. PMID: 21079672; PMCID: PMC2973813.
      View in: PubMed   Mentions: 37     Fields:    Translation:Animals
    27. Gene expression variability within and between human populations and implications toward disease susceptibility. PLoS Comput Biol. 2010 Aug 26; 6(8). Li J, Liu Y, Kim T, Min R, Zhang Z. PMID: 20865155; PMCID: PMC2928754.
      View in: PubMed   Mentions: 55     Fields:    Translation:HumansCells
    28. 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. Li J, Min R, Vizeacoumar FJ, Jin K, Xin X, Zhang Z. PMID: 20489180; PMCID: PMC2890810.
      View in: PubMed   Mentions: 21     Fields:    Translation:Animals
    29. 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. Li J, Yuan Z, Zhang Z. PMID: 20139146.
      View in: PubMed   Mentions: 6     Fields:    Translation:AnimalsCells
    30. 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. 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. PMID: 20065090; PMCID: PMC2812844.
      View in: PubMed   Mentions: 52     Fields:    Translation:AnimalsCells
    31. A probabilistic framework to improve microrna target prediction by incorporating proteomics data. J Bioinform Comput Biol. 2009 Dec; 7(6):955-72. Li J, Min R, Bonner A, Zhang Z. PMID: 20014473.
      View in: PubMed   Mentions: 8     Fields:    Translation:Cells
    32. Evolution of an X-linked primate-specific micro RNA cluster. Mol Biol Evol. 2010 Mar; 27(3):671-83. Li J, Liu Y, Dong D, Zhang Z. PMID: 19933172.
      View in: PubMed   Mentions: 41     Fields:    Translation:HumansAnimalsCells
    33. Learned random-walk kernels and empirical-map kernels for protein sequence classification. J Comput Biol. 2009 Mar; 16(3):457-74. Min R, Bonner A, Li J, Zhang Z. PMID: 19254184.
      View in: PubMed   Mentions: 1     Fields:    Translation:Cells
    34. Preferential regulation of duplicated genes by microRNAs in mammals. Genome Biol. 2008; 9(8):R132. Li J, Musso G, Zhang Z. PMID: 18727826; PMCID: PMC2575522.
      View in: PubMed   Mentions: 17     Fields:    Translation:HumansAnimalsCells
    35. Identifying protein-protein interfacial residues in heterocomplexes using residue conservation scores. Int J Biol Macromol. 2006 May 30; 38(3-5):241-7. Li JJ, Huang DS, Wang B, Chen P. PMID: 16600360.
      View in: PubMed   Mentions: 8     Fields:    Translation:Cells
    36. Network analysis of the protein chain tertiary structures of heterocomplexes. Protein Pept Lett. 2006; 13(4):391-6. Li JJ, Huang DS, Lok TM, Lyu MR, Li YX, Zhu YP. PMID: 16712516.
      View in: PubMed   Mentions:    Fields:    Translation:Cells
    37. Predicting protein interaction sites from residue spatial sequence profile and evolution rate. FEBS Lett. 2006 Jan 23; 580(2):380-4. Wang B, Chen P, Huang DS, Li JJ, Lok TM, Lyu MR. PMID: 16376878.
      View in: PubMed   Mentions: 59     Fields:    Translation:Cells
    38. Characterizing human gene splice sites using evolved regular expressions. Proceedings of IEEE International Joint Conference on Neural Networks. 2005; 1:493-498. Li, J., Huang, D., MacCallum, R., and Wu, X.-R.
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