• Publications

    40. Wang, C., Zhou, Y., Wang, Y.J., Guha, T.K., Luo, Z., McIntyre, T.I., Schwab, M.E., Davidson, B.R., Reeder, G.C., Wong, R.J., England, S., Gonzalez, J.M., Blelloch, R., Combes, A.J., Guidice, L.C., Erlebacher, A., MacKenzie, T.C., Stevenson, D.K., Shaw, G., Snyder, M., Fisher, S.J., Winn, V.D., Li, J. A Multiomics, Spatiotemporal, and Single Cell Atlas for Mapping Cell-Type-Specific Dysregulation at the Maternal-Fetal Interface. BioRxiv 2004, doi: https://doi.org/10.1101/2024.01.18.576324


    39. Wang, C., Wang, Y.J., Ying, L., Wong, R.J., Quaintance, C.C., Hong, X., Neff, N., Wang, X., Biggio, J.R., Mesiano, S., Quake, S.R., Alvira, C.M., Cornfield, D.N., Stevenson, D.K., Shaw, G.M., Li, J.# Integrative analysis of noncoding mutations identifies the druggable genome in preterm birth. Science Advances 2024, 10(3).

    # Press release from UCSF News  - Genetic Discovery Reveals Who Can Benefit from Preterm Birth Therapy.

    Also see reports from March of Dimes (link), Stanford University (link),   Precision Medicine Online (link), and  Science Daily (link).


    38. Wang, L., Pang, K., Zhou, L., Cebrián-Silla, A., González-Granero, S., Wang, S., Bi, Q., White, M.L., Ho, B., Li, J., Li, T., Perez, Y., Huang, E.J., Winkler, E.A., Paredes, M.F., Kovner, R., Sestan, N., Pollen, A.A., Liu, P., Li, J., Piao, X., Verdugo, J.M.G., Alvarez-Buylla, A., Liu, Z., Kriegstein, A.R. A cross-species proteomic map of synapse development reveals neoteny during human postsynaptic density maturation. Nature 2023, 622(7981):112-119.


    37. Wang, Y.J., Zhang, X., Lam, C.K., Guo, H., Wang, C., Zhang, S., Wu, J.C., Snyder, M.#, and Li, J.# Systems analysis of de novo mutations in congenital heart diseases identified a protein network in hypoplastic left heart syndrome. Cell Systems 2022, 13:1-16.


    36. Li, J.*,#, Yang, W.*, Wang, Y.*, ..., Shaw, G.M.#, and the National Birth Defects Prevention Study. Exome sequencing identifies genetic variants in anophthalmia and microphthalmia. American Journal of Medical Genetics (A) 2022, 188(8):2376-2388.


    35. Zhang, S., Cooper-Knock, J., et al., Genome-wide identification of the genetic basis of amyotrophic lateral sclerosis. Neuron 2022, 11:S0896-6273(21)01036-9.


    34. Zilocchi, M., Wang, C., Babu, M.#, and Li, J.# A panoramic view of proteomics and multiomics in precision health. iScience 2021, 24(8):102925.


    33. Wang, C. and Li, J. A deep learning framework identifies pathogenic noncoding somatic mutations from personal prostate cancer genomes. Cancer Research 2020, 80:4644–54.


    32. Li, J., Li, X., Zhang, S., Snyder, M. Gene-environment interaction in the era of precision medicine. Cell 2019, 177(1):38-44.


    31. Spiegel, A.M., Li, J., Oehlert, J.W., Mayo, J.A., Quaintance, C.C., Girsen, A.I., Druzin, M.L., El-Sayed, Y.Y., Shaw, G.M., Stevenson, D.K., Gibbs, R.S. A genome-wide analysis of clinical chorioamnionitis among preterm infants. American Journal of Perinatology 2019, 36(14):1453-1458.


    30. Stevenson, D.K., Wong, R.J., Shaw, G.M., Li, J., Wise, P.H., and Davis, J.M. The contributions of genetics to premature birth. Pediatric Research 2019, 85:416-417.


    29. Stevenson, D.K., Wong, R.J., Aghaeepour, N., Angst, M.S., Darmstadt, G.L., DiGiulio, D.B., Druzin, M.L., Gaudilliere, B., Gibbs, R.S., Gould, J.B., Katz, M., Li, J., Moufarrej, M.N., Quaintance, C.C., Quake, S.R., Relman, D.A., Shaw, G.M., Snyder, M., Wang, X., Wise, P.H. Understanding health disparities. Journal of Perinatology 2019,39(3):354-358.


    28. Li, J.*, Pan, C.*, Zhang, S*, Spin, J.M., Deng, A., Dalman, R.L., Tsao, P.S., Snyder, M. Decoding the genomics of abdominal aortic aneurysm.Cell 2018, 174: 1361-1372 (Research Article).

    # Featured in Nature: How to warn of a pulsating artery that could burst any time

    # Press release from Stanford Medicine, Cell Press, Science Daily, etc.


    27. Li, J., Hong, X., Mesiano, S., Muglia, L.J., Wang, X. Snyder, M. Stevenson, D.K., Shaw, G.M. Natural selection has differentiated the progesterone receptor among human populations. American Journal of Human Genetics (AJHG) 2018,103:1-13.

    # Featured by Nature: Gene important in pregnancy shows evolution in action

    # Press Release by Stanford Medicine: Genetic variation in progesterone receptor tied to prematurity risk


    26. Li, J., Oehlert, J., Snyder M., Stevenson, D.K., and Shaw, G.M. Fetal de novo mutations and preterm birth. PLoS Genetics 2017 13(4): e1006689.


    25. Yu, K*, Li, J.*, Snyder M., Shaw, G.M., and O’Brodvich, H.M.The genetic predisposition to bronchopulmonary dysplasia. Current Opinion in Pediatrics 2016, 28(3):318-323 (*co-first author).


    24.Li, J., Ma, Z., Shi, M., Malty, R.H., Aoki, H.A., Minic, Z., Phanse, S., Jin, K., Wall, D.P., Zhang, Z., Urban, A.E., Hallmayer, J., Babu, M., and Snyder, M. Identification of human neuronal protein complexes reveals biochemical activities and convergent mechanisms of action in autism spectrum disorders. Cell Systems 2015, 1(5): 361-374.

    # Also see the preview article by Dr. Haiyuan Yu and colleagues: Study Autism in Context. Cell Systems, 2015, 1(5):312-313.


    23. Li, J.*, Yu, K.H.*, Oehlert, J., Jeliffe-Pawlowski, L.L., Gould, J.B., Stevenson, D.K., Snyder, M., Shaw, G.M., and O’Brodvich, H.M. Exome sequencing of neonatal blood spots identifies genes implicated in bronchopulmonary dysplasia. American Journal of Respiratory and Critical Care Medicine (AJRCCM) 2015, 192:589-596 (the Blue Journal).

    # Also see the editorial by Dr. Steven Abman et al.: Genomic Insights into Respiratory Outcomes after Preterm Birth, American Journal of Respiratory and Critical Care Medicine 2015, 192:530-532.


    22. Li, J.*, Shi, M.*, Ma, Z.*, Zhao, S., Euskirchen, G., Ziskin, J., Urban, A., Hallmayer, J., and Snyder, M. Integrated systems analysis reveals a molecular network underlying autism spectrum disorders. Molecular Systems Biology 2014, 10:774.

    # Also see the News & Views by Dr. Charles Auffray: Autism cornered: network analyses reveal mechanisms of autism spectrum disorders. Molecular Systems Biology 2014, 10:778.

    # Highlighted by Nature Genetics, 2015, 47:105.

    # Media coverage by EMBO Press, Los Angeles Times, FOX News, Science Daily, GenomeWeb.


    21. Li, J.*, Kim, T.*, Nutiu, R., Ray, D., Hughes, T.R., and Zhang, Z. Identifying mRNA sequence elements for target recognition by human Argonaute proteins. Genome Research 2014, 24(5):775-785.

    # Interviewed by BioTechniQues: Argonaute Protein Preferences


    20. Cheng, Y., Ma, Z., Kim, B.H., Wu, W., Cayting, P., ..., Dogan, N., Li, J., Euskirchen, G., ..., Snyder, M. Principles of regulatory information conservation between mouse and human. Nature 2014, 515: 371–375.


    19. Kasowski, M.,...,Li, J., Xie, D., .., Snyder, M. Extensive variation in chromatin states across humans. Science 2013, 342(6159):750-752.


    18. Li, J. and Zhang, Z. microRNA regulatory variation in human evolution. Trends in Genetics 2013, 29(2): 116-124.


    17. Xin, X., Gfeller, D., ..., Li, J., Cheng, A.T., ..., Vidal, M., Boone, C., Sidhu, S.S., and Bader, G.D. SH3 interactome conserves general function over specific form. Molecular Systems Biology 2013, 9:652.


    16. Li, J., Liu, Y., Xin, X., Kim, T., Cabeza, E.A., Ren, J., Nielsen, R., Wrana, J. and Zhang, Z. Evidence for positive selection on a number of microRNA regulatory interactions during recent human evolution. PLoS Genetics 2012, 8(3): e1002578.


    15. Li, Z.*, Vizeacoumar, F.J.*, Bahr, S., Li, J., Warringer, J., Vizeacoumar, F.S., VanderSluis, B., Bellay, J., DeVit, M., Fleming, J.A., Stephens, A., Haase, J., Lin, Z.-Y., Baryshnikova, A., Min, R., Lu, H., Yan, Z., Jin, K., Datti, A., Nislow, C., Costanzo, M., Bulawa, C., Myers, C.L., Gingras, A., Zhang, Z., Blomberg, A., Bloom, K., Andrews, B., and Boone, C. Systematic exploration of essential yeast gene function with temperature-sensitive mutants. Nature Biotechnology 2011, 29: 361-367.


    14. Jin, K., Li, J., Vizeacoumar, F.S., Li, Z., Min, R. Zamparo, L., Vizeacoumar, F.J., Datti, A., Andrews, B., Boone, C., and Zhang, Z. PhenoM: a morphological database of essential genes in Saccharomyces cerevisiae. Nucleic Acids Research 2011, 40(D1): D687-D694.


    13. Li, J., Min, R., Vizeacoumar, F.J., Jin, K., Xin, X. and Zhang, Z. Exploiting the determinants of stochastic gene expression in S. cerevisiae for genome-wide prediction of expression noise. PNAS 2010, 107(23): 10472-10477.


    12. Li, J., Liu, Y., Kim, T., Min, R., and Zhang, Z. Gene expression variability within and between human populations and implications toward disease susceptibility. PLoS Computational Biology 2010, 6(8): e1000910.


    11. Li, J., Yuan, Z. and Zhang, Z. The cellular robustness by genetic redundancy in budding yeast. PLoS Genetics 2010, 6(11): e1001187.


    10. Li, J., Yuan, Z. and Zhang, Z. Revisiting the contribution of cis elements to expression divergence between duplicated genes: the role of chromatin structure. Molecular Biology and Evolution 2010, 27(7): 1461-1466.


    9. Li, J., Liu, Y., Dong, D. and Zhang, Z. Evolution of an X-linked primate-specific microRNA cluster. Molecular Biology and Evolution 2010, 27(3): 671-683.


    8. Vizeacoumar, F.J., van Dyk, N., Vizeacoumar, F.S., Cheung, V., Li, J., Sydorsky, Y., Case, N., Li, Z., Datti, A., Nislow, C., Raught, B., Zhang, Z., Frey, B., Bloom, K., Boone, C. and Andrews, B.J. Integrating high-throughput genetic interaction mapping and high-content screening to explore yeast spindle morphogenesis. Journal of Cell Biology 2010, 188: 69-81.


    7. Li J., Min R., Bonner A., and Zhang Z. A probabilistic framework to improve microRNA target prediction by incorporating proteomics data. Journal of Bioinformatics and Computational Biology 2009, 7(6): 955-972.


    6. Min, R., Bonner, A., Li, J.and Zhang, Z. Learned random-walk kernels and empirical-map kernels for protein sequence classification. Journal of Computational Biology 2009, 16(3): 457-474.


    5. Li, J., Musso, G., and Zhang, Z. Preferential regulation of duplicated genes by microRNAs in mammals. Genome Biology 2008, 9:R132.

    # Highlighted Research in Nature Review Genetics 2008, 9:734.


    4. Li, J., Huang,D.S., Wang, B. and Chen, P. Identifying protein-protein interfacial residues in heterocomplexes using residue conservation scores. International Journal of Biological Macromolecules 2006, 38(3-5): 241-247.


    3. Li, J., Huang, D.S., Lok, T.-M., Lyu, M.R., Li, Y.-X., and Zhu, Y.-P. Network analysis of the protein chain tertiary structures of heterocomplexes. Protein and Peptide Letters 2006, 13(4): 391-396.


    2. Wang, B., Chen, P., Huang, D.S., Li, J., Lok, T.M., and Lyu, M.R. Predicting protein interaction sites from residue spatial sequence profile and evolution rate. FEBS Letters 2006, 580 (2):380-384.


    1. 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.