Jun Li, Ph.D.

Associate Professor, Department of Human Genetics
Associate Professor and Associate Chair for Research, Department of Computational Medicine and Bioinformatics
Faculty, Center for Statistical Genetics
Faculty Member, Comprehensive Cancer Center
Member, Depression Center, Michigan Diabetes Research Center, Michigan Metabolomics and Obesity Center,

5940A Buhl
1241 E. Catherine St. SPC 5618
Ann Arbor
Staff Support: 
Sue Kellogg
Research Interests: 

The Li lab studies the genetic basis of complex human diseases using genomic approaches. Currently our interests include analyses of gene expression patterns in postmortem brain tissues associated with major depression, bipolar disorder, and schizophrenia, sequencing-based variant discovery and analysis in rare Mendelian disorders and the bipolar disorder, integrated analysis of cancer genome alterations, intratumor heterogeneity in breast and esophageal cancers, and spontaneous mutation patterns in the human genome.

Honors and Awards: 
2009-2011 NARSAD Young Investigator Award
2011-2014 Ellison Medical Foundation New Scholar in Aging
2011-2014 IMHRO – Johnson & Johnson Rising Star Translational Research Award
2014 Dean's Basic Science Research Award
2015 Endowment for the Basic Sciences Recognition Award
1985- 1989 B.Sc., Department of Physics, Beijing University. Thesis: Computation of the Characteristic Inversion Rates of Semiconductor Lasers
1991- 1998 Ph.D., Division of Biology, California Institute of Technology. Thesis: Structure-function relationship and single-channel behavior of cyclic nucleotide-gated channels
1998- 2001 Postdoctoral fellow, Department of Genetics, Stanford University School of Medicine.
2001- 2007 Senior Scientist and project leader, Stanford Human Genome Center, Stanford University
Selected Publications: 

Also see Google Scholar page:


Q. Song, S.D.Merajver, J.Z. Li (2015) Cancer classification in the genomic era: five contemporary problems. Hum Genomics. 9:27. PMCID: 4612488

E.L. Aurbach, E.G. Inui, C.A. Turner, M.H. Hagenauer, K. E. Prater, J.Z. Li, D. Absher, N. Shah, P. Blandino Jr., W. E. Bunney, R. M. Myers, J. D. Barchas, A. F. Schatzberg, S. J. Watson, Jr., H. Akil (2015) Fibroblast Growth Factor 9 is a Novel Modulator of Negative Affect, PNAS, 112(38):11953-8. PMCID: 4586860

E. Sandford E, J.Z. Li, M. Burmeister (2015) Evaluation of exome sequencing variation in undiagnosed ataxias. Brain. 138(Pt 10):e383. PMCID: 4671475

J. Higgins, M. Brogley, N. Palanisamy, R. Mehra, M.M. Ittmann, J.Z. Li, S.A. Tomlins, D.M. Robins (2015) Interaction of the Androgen Receptor, ETV1, and PTEN Pathways in Mouse Prostate Varies with Pathological Stage and Predicts Cancer Progression. Hum Cancer. 6(2-3):67-86. PMCID: 4414739

Gene, Environment Association Studies (GENEVA) Consortium (including J. Li). (2015) Characterization of large structural genetic mosaicism in human autosomes, AJHG, 96(3):487-97. PMCID: 4375431

Psychiatric Genomics Consortium (including J. Li as a collaborator). (2015) Joint Analysis of Psychiatric Disorders Increases Accuracy of Risk Prediction for Schizophrenia, Bipolar Disorder, and Major Depressive Disorder, AJHG 96(2):283-94. PMCID: In Process

Y. Ren, L.G. Koch, S.L. Britton, N.R. Qi, M.K. Treutelaar, C.F. Burant, J.Z. Li. (2015) Selection-, age-, and exercise-dependence of skeletal muscle gene expression patterns in a rat model of metabolic fitness. bioRxiv doi: http://dx.doi.org/10.1101/013706

B. G. Bunney, J. Z. Li, D. M. Walsh, R. Stein, M. P. Vawter, P. Cartagena, J. D. Barchas, A. F. Schatzberg, R. M. Myers, S. J. Watson, Jr., H. Akil, W. E. Bunney. (2015) Circadian dysregulation of clock genes: clues to rapid treatments in Major Depressive Disorder. Molecular Psychiatry. 20(1):48-55. PMCID: In Process


B. Li, J.Z. Li. (2014) A general framework for analyzing tumor subclonality using SNP array and DNA sequencing data. Genome Biology. 15(9):473. PMCID: 4203890.

R. Burns, K. Majczenko, J. Xu, W. Peng, Z. Yapici, J. J. Dowling, J. Z. Li, M. Burmeister. (2014) Homozygous splice mutation in CWF19L1 in a Turkish family with recessive ataxia syndrome. Neurology. 83(23):2175-82. PMCID: 4276403.

Q. Ma, A. B. Ozel, S. Ramdas, B. McGee, R. Khoriaty, D. Siemieniak, H. Li, Y. Guan, L. C. Brody, J. L. Mills, A. M. Molloy, D. Ginsburg, J. Z. Li, K. C. Desch. (2014) Genetic variants in PLG, LPA and SIGLEC 14 as well as smoking contribute to plasma plasminogen levels. Blood. 124(20):3155-64. PMCID: 4231423.

P. Hysi, C-Y Cheng, et al. (including J. Li) (2014) Genome-wide analysis of multiethnic cohorts identifies new loci influencing intraocular pressure and susceptibility to glaucoma. Nature Genetics, 46(10):1126-30. PMCID: 4177225.

Y. Şenbabaoğlu, G. Michailidis, J. Z. Li. (2014) Critical limitations of consensus clustering in class discovery. Scientific Reports, 4:6207. PMCID: 4145288.

M. J. Kiel, T. Velusamy, D. Rolland, A. Sahasrabuddhe, F. Chung, N. Bailey, A. Schrader, B. Li, J. Li, A. Ozel, D. Bahler, B. Betz, D. Huebner-Chan, R. Miranda, L. J. Medeiros, M. Herling, M. S. Lim, K. S.J. Elenitoba-Johnson. Integrated Genomic Sequencing Reveals Mutational Landscape of T-cell Prolymphocytic Leukemia, Blood, 124(9):1460-72. PMCID: 4148768.

J.Z. Li. (2014) Circadian rhythms and mood: opportunities for multi-level analyses in genomics and neuroscience. BioEssays 36: 305–315. PMCID: 4033528

C.M. Theriot, M. Koenigsknecht, P.E. Carlson, G. Hatton, A. Nelson, B. Li, G. Huffnagle, J.Z. Li, V. Young. (2014) Antibiotic-mediated Shifts in the Murine Gut Microbiome and Metabolome Leads to Susceptibility to Clostridium difficile Infection. Nature Communications. 5:3114. PMCID: 3950275


Y. Ren, K. A. Overmyer, N. R. Qi, M. K. Treutelaar, L. Heckenkamp, M. Kalahar, L. G. Koch, S. L. Britton, C. F. Burant, J. Z. Li. (2013) Genetic Analysis of a Rat Model of Aerobic Capacity and Metabolic Fitness. PLoS ONE 8(10):e77588..

V. M. Schaibley, M. Zawistowski, D. Wegmann, M. G. Ehm, M. R. Nelson, P. L. St. Jean, G. Abecasis, J. Novembre, S. Zöllner, J. Z. Li. (2013) The Influence of Genomic Context on Mutation Patterns Inferred from Rare Variants. Genome Research. 23(12):1974-84.

Psychiatric Genomics Consortium (including J. Li) (2013) Genetic relationship between five psychiatric disorders estimated from genome-wide SNPs. Nature Genetics. 45(9):984-94.

N.A. Rosenberg, T.J. Pemberton, J.Z. Li, J.W. Belmont (2013) Runs of homozygosity and parental relatedness. Genetics in Medicine, 15: 753-754.

A. B. Ozel, S. E. Moroi, D. M. Reed, M. Nika, C. M. Schmidt, S. Akbari, K. Scott, F. Rozsa, H. Pawar, D. C. Musch, P. R. Lichter, D. Gaasterland, K. Branham, J. Gilbert, S. J. Garnai, W. Chen, M. Othman, J. Heckenlively, A. Swaroop, G. Abecasis, D. S. Friedman, D. Zack, A. E. Ashley-Koch, M. Ulmer, J. H. Kang, NEIGHBOR Consortium, Y. Liu, B. L. Yaspan, J. Haines, R. R. Allingham, M. A. Hauser, L. Pasquale, J. Wiggs, J. E. Richards, J Z. Li. (2013) Genome-wide Association Study and Meta-analysis of Intraocular Pressure. Human Genetics. Published online September 4, 2013.

Z. A Szpiech, J. Xu, T. J Pemberton, W. Peng, S. Zollner, N. A Rosenberg, J. Z Li. (2013) Long runs of homozygosity are enriched for deleterious variation. (2013) AJHG. 93(1): 90-102.

J. Z. Li,* B. G. Bunney, F. Meng, M. H. Hagenauer, D. M. Walsh, M. P. Vawter, S. J. Evans, P. V. Choudary, J. D. Barchas, A. F. Schatzberg, E. G. Jones, R. M. Myers, S. J. Watson, H. Akil, W. E. Bunney. Circadian patterns of gene expression in the human brain and disruption in major depressive disorder. (2013) PNAS. 110(24): 9950-9955.

L. A. Carmody, J. Zhao, P. D. Schloss, J. F. Petrosino, S. Murray, V. B. Young, J. Z. Li, J. J. LiPuma. (2013) Changes in Cystic Fibrosis Airway Microbiota at Pulmonary Exacerbation. Annals of the American Thoracic Society. 10(3):179-87.

Lu Y, Vitart V, Burdon KP, Khor CC, Bykhovskaya Y, Mirshahi A, et al. (2013) Genome-wide association analyses identify multiple loci associated with central corneal thickness and keratoconus. Nat Genet.;45(2):155-63.

K. Desch, A. B. Ozel, D. Siemieniak, Y. Kalish, C. Thornburg, A. Sharathkumar, C. McHugh, C. Laurie, A. Crenshaw, D. Mirel, Y. Kim, C. Cropp, A. Molloy, P. Kirke, J. Bailey-Wilson, A. Wilson, J. Mills, J. Scott, L. Brody, J.Z. Li* and D. Ginsburg*. (2013) Linkage Analysis Identifies a Locus for Plasma von Willebrand Factor Undetected by Genome-Wide Association. PNAS. 110(2): 588-93.

A. E. Davidson, F. M. Siddiqui, M. Lopez, P. Lunt, H. A. Carlson, B. E. Moore, S. Love, D. E. Born, H. Roper, A. Majumdar, S. Jayadev, H. R. Underhill, C. O. Smith, M. von der Hagen, A. Hubner, P. Jardine, A. Merrison, E. Curtis1, T. Cullup, H. Jungbluth, M. O. Cox, T. L. Winder, H. Abdel Salam, J. Z. Li, S. A. Moore, J. J. Dowling. (2013) Novel deletion of lysine 7 expands the clinical, histopathologic and genetic spectrum of TPM2-related myopathies. Brain. 136 (Pt 2): 508-21.


S. Candille, D. M. Absher, S. Beleza, M. Bauchet, B. McEvoy, N. Garrison, J.Z. Li, R.M. Myers, G. S. Barsh, H. Tang, M.D. Shriver. (2012) Genome-wide Association Studies of Quantitatively Measured Skin, Hair, and Eye Pigmentation in Four European Populations, PLoSONE. 7(10): e48294.

B. Li, Y. Senbabaoglu, W. Peng, M. Yang, J. Xu, J. Z. Li. (2012) Genomic estimates of aneuploid content in Glioblastoma Multiforme and proposal of a new integrated classification, Clinical Cancer Research. 18:5595-5605.

Y. Lee, et al. (including J. Li) (2012) Mutations in KCND3 cause spinocerebellar ataxia type 22. Annals of Neurology. 72(6): 859-69

T. J. Pemberton, D. Absher, M. W. Feldman, R. M. Myers, N. A. Rosenberg, J. Z. Li. (2012) Genomic patterns of homozygosity in worldwide human populations, AJHG, 91: 275-292.

K. Majczenko, A. E. Davidson, S. Camelo-Piragua, X. Li, S. Joshi, J. Xu, W. Peng, J. Z. Li, M. Burmeister, J. J. Dowling. (2012) Dominant mutation in CCDC78 in a Unique Congenital Myopathy with Prominent Internal Nuclei and Atypical Cores, AJHG, 91(2):365-71.

M. Ulmer, J. Li, B. Yaspan, A. B. Ozel, J. Richards, S. E. Moroi, J. S. Schuman, D. S. Friedman, R. Lee, D. Budenz, M. Pericak-Vance, NEIGHBOR Consortium Investigators, J. L. Wiggs, A. Ashley-Koch, M.l A. Hauser. (2012) Genome-wide Analysis Of Central Corneal Thickness In POAG Cases From The NEIGHBOR Consortium, Investigative Ophthalmology & Visual Science, 53(8):4468-74

M. R. Nelson et al. (including J. Li). (2012) An abundance of rare functional variants in 202 drug target genes sequenced in 14002 people. Science, 337: 100-104.

C. C. Laurie et al. (including J. Li). (2012) Chromosomal mosaicism from birth to old age and its relationship to cancer. Nature Genetics, 44: 642-650.

Sequeira A, Morgan L, Walsh DM, Cartagena PM, Choudary P, Li J, Schatzberg AF, Watson SJ, Akil H, Myers RM, Jones EG, Bunney WE, Vawter MP (2012) Gene expression changes in the prefrontal cortex, anterior cingulate cortex and nucleus accumbens of mood disorders subjects that committed suicide.. PLoS One. 7(4):e35367. Epub 2012 Apr 30

J. K. Bedoyan, V. M. Schaibley, W. Peng, Y. Bai, K. Mondal, A. Shetty, M. Durham, A. Dhiraaj, J. M. Skidmore, J. Kaplan, C. Skinner, R. Stevenson, C. Schwartz, A. Antonellis, M. Zwick, J. Cavalcoli, J. Z. Li, D. M. Martin. (2012) Disruption of RAB40AL function leads to Martin-Probst Syndrome, a rare X-linked multisystem neurodevelopmental human disorder. Journal of Medical Genetics, 49:332-340.

J. Zhao, P. D. Schloss, L. M. Kalikin, L. A. Carmody, B. K. Foster, J. F. Petrosino, J. D. Cavalcoli, D. R. VanDevanter, S. Murray, J. Z. Li, V. B. Young, J. J. LiPuma. (2012) Decade-long bacterial community dynamics in cystic fibrosis airways, PNAS. 109(15):5809-14,

J. Zhao, L. A. Carmody, L. M. Kalikin, J. Li, J. F. Petrosino, P. D. Schloss, V. B. Young, J. J. LiPuma. (2012) Impact of Enhanced Staphylococcus DNA Extraction on Microbial Community Measures in Cystic Fibrosis Sputum. PLoS ONE 7(3): e33127. doi:10.1371


K. Desch, J. Li, S. Kim, N. Laventhal, K. Metzger, D. Siemieniak, D. Ginsburg. (2011) Analysis of informed consent document utilization in a minimal-risk genetic study. Ann Intern Med. 155(5):316-22.

The Psychiatric GWAS Consortium (including J. Li). (2011) Large-scale genome-wide association analysis of bipolar disorder identifies a new susceptibility locus near ODZ4. Nature Genetics, 43: 977–983.

The Cancer Genome Atlas Research Network (including J. Li). (2011) Integrated Genomic Analyses of Ovarian Carcinoma. Nature, 474:609-15.

T. Pemberton, C. Wang, J. Z. Li, N. A. Rosenberg. (2010) Inference of unexpected genetic relatedness among individuals in HapMap Phase III. American Journal of Human Genetics. 87(4): 457-464.

Casto AM, Li JZ, Absher D, Myers R, Ramachandran S, Feldman MW. (2010) Characterization of X-linked SNP genotypic variation in globally distributed human populations. Genome Biol. 11(1):R10. PMID: 20109212

N. Zhang, Y. Senbabaoglu, and J. Z. Li, (2010). Joint Estimation of DNA Copy Number from Multiple Platforms. Bioinformatics, 26(2):153-60.

N. Zhang, D. Siegmund, H. Ji, and J. Z. Li, (2009). Detecting simultaneous change points in multiple sequences. Biometrika, 97(3):631-645

L. J. Scott, P. Muglia, X. Kong, W. Guan, M. Flickinger, R.i Upmanyu, F. Tozzi, J. Li, M. Burmeister, D. Absher, R. C. Thompson, C. Francks, F. Meng, A. Antoniades, A. M. Southwick, A. Schatzberg, W. Bunney, J. Barchas, E. Jones, R. Day, K. Matthews, P. McGuffin, J. S. Strauss, J. L. Kennedy, L. Middleton, A. Roses, S. J. Watson, J. B. Vincent, R. M. Myers, A. E. Farmer, H. Akil, D. K. Burns, M. Boehnke. (2009). Genome-wide association and meta-analysis of bipolar disorder in individuals of European ancestry. Proc Natl Acad Sci U S A. 106(18):7501-7506

J. K. Pickrell, G. Coop, J. Novembre, S.r Kudaravalli, J. Li, D. Absher, B.S. Srinivasan, G. S. Barsh, R. M. Myers, M. W. Feldman, J. K. Pritchard. (2009). Signals of recent positive selection in a worldwide sample of human populations. Genome Res. 19(5):826-37

K. A. McGowan, J. Z. Li, C. Y. Park, V. Beaudry, H. K. Tabor, A. J. Sabnis, W. Zhang, H. Fuchs, M. H. de Angelis, R. M. Myers, L. D. Attardi G. S. Barsh. (2008) Genetics of dark skin: ribosomal protein mutations act through p53. Nat Genet. 40(8):963-70.

The Cancer Genome Atlas Research Network (including J. Li). (2008) Comprehensive genomic characterization defines human glioblastoma genes and core pathways. Nature. 255:1061-8.

J. Z. Li*, D. M. Absher*, H. Tang, A. M. Southwick, A. M. Casto, S. Ramachandran, H. M. Cann, G. S. Barsh, M. Feldman, L. L. Cavalli-Sforza, R. M. Myers. (2008). Worldwide human relationships inferred from genome-wide patterns of variation. Science, 319:1100-1104.

J. Z. Li, F. Meng, L. Tsavaler, S. J. Evans, P. V. Choudary, H. Tomita, M. P. Vawter, D. Walsh, V. Shokoohi, T. Chung, W. E. Bunney Jr., E. G. Jones, H. Akil, S. J. Watson, R. M. Myers (2007). Sample matching by inferred agonal stress in gene expression analyses of the brain. BMC Genomics, 8:336