UCLA faculty members who have microbiome related funding (extra-or intramural)



Photo of Eran Halperin, PhD
Eran Halperin, PhD
Professor, Departments of Computer Science, Computational Medicine, Anesthesiology, Human Genetics, UCLA; Associate Director of Informatics, Institute of Precision Health, UCLA; Co-Director, Computation Genomics Summer Institute, UCLA

Dr. Eran Halperin is a professor in the departments of Computer Science, Computational Medicine, Anesthesiology, and Human Genetics. He is also the associate director of informatics in the Institute of Precision Health at UCLA and the co-director of the Computation Genomics Summer Institute at UCLA. Dr. Halperin received his Ph.D. in computer science from Tel-Aviv University. Prior to his current position, he held research and postdoctoral positions at the University of California, Berkeley, the International Computer Science Institute in Berkeley, Princeton University, and Tel-Aviv University. Dr. Halperin is a computational biologist who develops statistical and computational methods for the analysis of genomic and medical data in the context of human diseases. His group has developed methods and software that have been used by hundreds of researchers worldwide in a range of genomic applications including genetics, epigenetics, and microbiome. He has published over 100 peer-reviewed articles across different disciplines such as human genetics, computational biology, and theoretical computer science. He received various honors for academic achievements, including the Rothschild Fellowship, the Technion-Juludan prize, and the Krill prize.

Relevant Recent Publications

  1. Sankararaman, S., Sridhar, S., Kimmel, G., & Halperin, E. (2008). Estimating local ancestry in admixed populations. The American Journal of Human Genetics, 82(2), 290-303.
  2. Sankararaman, S., Obozinski, G., Jordan, M. I., & Halperin, E. (2009). Genomic privacy and limits of individual detection in a pool. Nature genetics, 41(9), 965
  3. Yang, W. Y., Novembre, J., Eskin, E., & Halperin, E. (2012). A model-based approach for analysis of spatial structure in genetic data. Nature genetics, 44(6), 725.
  4. Rahmani, Elior, et al. “Sparse PCA corrects for cell type heterogeneity in epigenome-wide association studies.” Nature methods 13.5 (2016): 443
  5. Shenhav, L., Furman, O., Briscoe, L., Thompson, M., Silverman, J. D., Mizrahi, I., & Halperin, E. (2019). Modeling the temporal dynamics of the gut microbial community in adults and infants. PLOS Computational Biology, 15(6), e1006960
  6. Shenhav, L., Thompson, M., Joseph, T. A., Briscoe, L., Furman, O., Bogumil, D., … & Halperin, E. (2019). FEAST: fast expectation-maximization for microbial source tracking. Nature methods, 1
  7. Baran, Yael, and Eran Halperin. “Joint analysis of multiple metagenomic samples.” PLoS computational biology 8.2 (2012): e1002373.
Photo of Xuesong He, DDS., PhD
Xuesong He, DDS., PhD
Assistant Adjunct Professor, UCLA School of Dentistry

Dr. Xuesong He is an Adjunct Assistant Professor in School of Dentistry at UCLA. Dr. He received his D.D.S. from Peking University Health Science Center in 1999, and his PhD in Microbiology from Indiana University in USA in 2006. Dr. He’s research interest includes: 1) Interspecies interaction between oral microbes; 2) culturing and studying “yet-to-be” cultivated oral microbes; and 3) studying the oral microbial ecology and its impact on human oral health and diseases. He is currently the co-principle investigator of a NIH RO1 grant on studying the unique epibiotic parasitic relationship between two oral commensal bacteria that could be involved in oral mucosal infectious disease. The international impact of his research can be proved by his over 30 well-cited publications in peer-reviewed leading scientific journals including: PNAS, ISME Journal, Advance in Dental Research, Microbiology and Molecular Biology Reviews, Journal of dental research, Journal of Endodontics, Molecular Microbiology, Microbiome Journal, Scientific Reports, Frontiers in Microbiology, Molecular Oral Microbiology, Microbial Ecology, Plos One, International Journal of Oral Science, FEMS Microbiology Letter and Journal of Bacteriology, etc.

Relevant Recent Publications

  1. Guo, L., JS. McLean, Y.Yang, R. Eckert, C.W. Kaplan, P.Kyme, O. Sheikh, B. Varnum, R. Lux, W. Shi and X. He*. 2015 A precision guided antimicrobial peptide as a targeted modulator of human microbial ecology. Proc Natl Acad Sci USA 112(24): 7569-7574
  2. He, X., JS. McLean, A. Edlund, S. Yooseph, A.P. Hall, SY. Liu, P. Dorrestein, E. Esquenazi, R. Hunter, G. Cheng, KE. Nelson, R. Lux and W. Shi. 2015. Domestication of a human-associated TM7 reveals a reduced genome and parasitic lifestyle. Proc Natl Acad Sci USA 112(1):244-9. PMCID:PMC4291631
  3. Wu, T., L. Cen, C. Kaplan, X. Zhou, R. Lux, W. Shi and X. He*. 2015. Cellular components mediating co-aggregation of Candida albican and Fusobacterium nucleatum. Journal of Dental Research. DOI:10.1177/0022034515593706

Active Funding in Microbiome-Related Research

Funding Agency/Grant Number:NIH NIDCR 1R01DE023810
Title:“Domestication and characterization of TM7-the most elusive oral phylum”
Photo of Elaine Y. Hsiao, PhD
Elaine Y. Hsiao, PhD
Assistant Professor, Department of Integrative Biology and Physiology, De Logi Chair in Biological Sciences, Division of Digestive Diseases, Department of Medicine, David Geffen School of Medicine at UCLA

Dr. Elaine Y. Hsiao is an Assistant Professor in the Department of Integrative Biology & Physiology at UCLA, where she leads a laboratory studying fundamental interactions between the microbiome, brain and behavior, and their applications to neurological disorders. Her studies on the relationships between the microbiota, immune system and nervous system led her to discover that the microbiota can regulate behavioral, metabolic and gastrointestinal abnormalities relevant to autism spectrum disorder (ASD). Her work in this area, and on neuroimmune interactions in autism, has led to several honors, including the National Institutes of Health Director’s Early Independence Award, distinction as Forbes’ 30 Under 30 in Science and Healthcare, National Geographic’s Emerging Explorer Award and fellowships from the National Institute of Mental Health and Autism Speaks. Inspired by this interplay between the microbiota and nervous system, the Hsiao laboratory is mining the human microbiota for microbial modulators of host neuroactive molecules, investigating the impact of microbiota-immune system interactions on neurodevelopment and examining the microbiome as an interface between gene-environment interactions in neurological diseases.

Relevant Recent Publications

  1. Yano JM, Yu K, Donaldson G, Shastri G, Ma L, Ann P, Nagler C, Ismagilov RF, Mazmanian SK, Hsiao EY (2015) Indigenous bacteria from the gut microbiota regulate host serotonin biosynthesis. Cell, 161:264-76.
  2. Hsiao EY, McBride SW, Hsien S, Sharon G, Hyde ER, McCue T, Codelli JA, Chow J, Reisman SE, Petrosino JF, Patterson PH*, Mazmanian SK* (2013) The microbiota modulates behavioral and physiological abnormalities associated with neurodevelopmental disorders. Cell, 155:1451-1463.
  3. Hsiao EY, McBride SW, Chow J, Mazmanian SK, Patterson PH (2012) Modeling an autism risk factor in mice leads to permanent immune dysregulation. PNAS 109:12776-81
Photo of Yu Huang, PhD
Yu Huang, PhD
Associate Professor, Materials Science and Engineering; Member, California NanoSystems Institute, JCCC Cancer and Stem Cell Biology Program Area

Dr. Huang is a Professor in the department of Materials Science and Engineering at UCLA. She received her Ph.D. and M.A degrees in physical chemistry from Harvard University and her B.S. degree from University of Science and Technology of China. Following her Ph.D. studies, Dr. Huang received the Lawrence Postdoctoral Fellowship and conducted her postdoctoral research at MIT and Lawrence Livermore National Labs concurrently. Dr. Huang’s research interest focuses around two intertwined goals: creating complex materials structures with nanoscale precision using chemical and biological approaches; and studying the new physical properties (optical, magnetic, electrical, and even catalytic properties) that arise in these new nanoscale architectures. The overall goal is to create functional nanostructures through rational design, and to systematically determine the fundamental structure-property relationship at the nanometer scale; and in doing so, to understand and to explore the new dimension of applications that these well-defined nanostructures can bring. In order to achieve this goal, we set out to tackle the most challenging and critical problem of understanding the fundamental mechanism governing material/molecular assembly process, and apply the knowledge gleaned from these studies in biomimetic materials, quantum electronics and biomedical applications.

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