Jingjing Li, PhD
Associate Professor
Neurology
School of Medicine

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.

Education & Training

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• Instructor Pediatrics Stanford University 2019
• Postdoc (Banting Fellow) Human Genomics Stanford University 2016
• Ph.D. Molecular Genetics University of Toronto 2011

Websites

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• From Big Data to Big Mind (complexdisease.org)

Publications (32)

Top publication keywords:
Evolution, MolecularArgonaute ProteinsGenes, DuplicateBronchopulmonary DysplasiaTwins, DizygoticGenome, HumanReceptors, ProgesteroneGene Regulatory NetworksSelection, GeneticModels, GeneticFetal DevelopmentGene Expression Regulation, FungalGene DuplicationMicroRNAsWearable Electronic Devices

• Gene-Environment Interaction in the Era of Precision Medicine.
  Cell 2019 Li J, Li X, Zhang S, Snyder M
• Decoding the Genomics of Abdominal Aortic Aneurysm.
  Cell 2018 Li J, Pan C, Zhang S, Spin JM, Deng A, Leung LLK, Dalman RL, Tsao PS, Snyder M
• Natural Selection Has Differentiated the Progesterone Receptor among Human Populations.
  American journal of human genetics 2018 Li J, Hong X, Mesiano S, Muglia LJ, Wang X, Snyder M, Stevenson DK, Shaw GM
• Integrated systems analysis reveals a molecular network underlying autism spectrum disorders.
  Molecular systems biology 2014 Li J, Shi M, Ma Z, Zhao S, Euskirchen G, Ziskin J, Urban A, Hallmayer J, Snyder M
• A Genome-Wide Analysis of Clinical Chorioamnionitis among Preterm Infants.
  American journal of perinatology 2019 Spiegel AM, Li J, Oehlert JW, Mayo JA, Quaintance CC, Girsen AI, Druzin ML, El-Sayed YY, Shaw GM, Stevenson DK, Gibbs RS

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• The contributions of genetics to premature birth.
  Pediatric research 2019 Stevenson DK, Wong RJ, Shaw GM, Li J, Wise PH, Davis JM
• Understanding health disparities.
  Journal of perinatology : official journal of the California Perinatal Association 2018 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…
• Fetal de novo mutations and preterm birth.
  PLoS genetics 2017 Li J, Oehlert J, Snyder M, Stevenson DK, Shaw GM
• The genetic predisposition to bronchopulmonary dysplasia.
  Current opinion in pediatrics 2016 Yu KH, Li J, Snyder M, Shaw GM, O'Brodovich HM
• Identification of Human Neuronal Protein Complexes Reveals Biochemical Activities and Convergent Mechanisms of Action in Autism Spectrum Disorders.
  Cell systems 2015 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
• Exome Sequencing of Neonatal Blood Spots and the Identification of Genes Implicated in Bronchopulmonary Dysplasia.
  American journal of respiratory and critical care medicine 2015 Li J, Yu KH, Oehlert J, Jeliffe-Pawlowski LL, Gould JB, Stevenson DK, Snyder M, Shaw GM, O'Brodovich HM
• Principles of regulatory information conservation between mouse and human.
  Nature 2014 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, …
• Identifying mRNA sequence elements for target recognition by human Argonaute proteins.
  Genome research 2014 Li J, Kim T, Nutiu R, Ray D, Hughes TR, Zhang Z
• Extensive variation in chromatin states across humans.
  Science (New York, N.Y.) 2013 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, …
• SH3 interactome conserves general function over specific form.
  Molecular systems biology 2013 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, …
• miRNA regulatory variation in human evolution.
  Trends in genetics : TIG 2012 Li J, Zhang Z
• Evidence for positive selection on a number of MicroRNA regulatory interactions during recent human evolution.
  PLoS genetics 2012 Li J, Liu Y, Xin X, Kim TS, Cabeza EA, Ren J, Nielsen R, Wrana JL, Zhang Z
• PhenoM: a database of morphological phenotypes caused by mutation of essential genes in Saccharomyces cerevisiae.
  Nucleic acids research 2011 Jin K, Li J, Vizeacoumar FS, Li Z, Min R, Zamparo L, Vizeacoumar FJ, Datti A, Andrews B, Boone C, Zhang Z
• Systematic exploration of essential yeast gene function with temperature-sensitive mutants.
  Nature biotechnology 2011 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…
• The cellular robustness by genetic redundancy in budding yeast.
  PLoS genetics 2010 Li J, Yuan Z, Zhang Z
• Gene expression variability within and between human populations and implications toward disease susceptibility.
  PLoS computational biology 2010 Li J, Liu Y, Kim T, Min R, Zhang Z
• Exploiting the determinants of stochastic gene expression in Saccharomyces cerevisiae for genome-wide prediction of expression noise.
  Proceedings of the National Academy of Sciences of the United States of America 2010 Li J, Min R, Vizeacoumar FJ, Jin K, Xin X, Zhang Z
• Revisiting the contribution of cis-elements to expression divergence between duplicated genes: the role of chromatin structure.
  Molecular biology and evolution 2010 Li J, Yuan Z, Zhang Z
• Integrating high-throughput genetic interaction mapping and high-content screening to explore yeast spindle morphogenesis.
  The Journal of cell biology 2010 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
• A probabilistic framework to improve microrna target prediction by incorporating proteomics data.
  Journal of bioinformatics and computational biology 2009 Li J, Min R, Bonner A, Zhang Z
• Evolution of an X-linked primate-specific micro RNA cluster.
  Molecular biology and evolution 2009 Li J, Liu Y, Dong D, Zhang Z
• Learned random-walk kernels and empirical-map kernels for protein sequence classification.
  Journal of computational biology : a journal of computational molecular cell biology 2009 Min R, Bonner A, Li J, Zhang Z
• Preferential regulation of duplicated genes by microRNAs in mammals.
  Genome biology 2008 Li J, Musso G, Zhang Z
• Identifying protein-protein interfacial residues in heterocomplexes using residue conservation scores.
  International journal of biological macromolecules 2006 Li JJ, Huang DS, Wang B, Chen P
• Network analysis of the protein chain tertiary structures of heterocomplexes.
  Protein and peptide letters 2006 Li JJ, Huang DS, Lok TM, Lyu MR, Li YX, Zhu YP
• Predicting protein interaction sites from residue spatial sequence profile and evolution rate.
  FEBS letters 2005 Wang B, Chen P, Huang DS, Li JJ, Lok TM, Lyu MR
• Characterizing human gene splice sites using evolved regular expressions
  Proceedings of IEEE International Joint Conference on Neural Networks 2005 Li, J., Huang, D., MacCallum, R., and Wu, X.-R.