People



Current Lab members

Yin Shen, Ph.D.

Principal Investigator

Dr. Yin Shen has been a member of the Institute for Human Genetics and the Department of Neurology at UCSF since 2015. Yin obtained a B.S. degree in Biological Sciences and Technologies from Nanjing University in China and a Ph.D. degree in Human Genetics in 2008 from UCLA, studying epigenetic regulation in stem cells. For postdoc training, she joined Dr. Bing Ren’s laboratory at UCSD, studying cis-regulatory elements in the mammalian genome. 

Xingjie Ren, Ph.D.

Postdoctoral Fellow

As the saying goes, "Interest is the best teacher." I found myself that I had fallen in love with biomedical research when I was a graduate student. Many interesting biomedical questions that needed to be uncovered triggered me in achieving my Ph.D. degree at Tsinghua University. During my graduate years at THU, I entered the field of CRISPR, a powerful biotechnology. Transitioning from THU to UCSF, I joined the Shen lab where I believe I could contribute to understanding human diseases with my background knowledge in CRISPR and drosophila genetics. Here in the Shen lab, I will shift my focus from Drosophila genetics to human genetics. In my spare time, I like photography and playing sports.

 

Xiaoyu Yang, Ph.D.

Postdoctoral Fellow

Human brain is the most amazing system in the world. I chose to study in the field of neurological disorders in my Ph.D. work, in Shanghai Institute of Materials Medica. My thesis focuses on the modulation of histone modifications involved in stroke and Parkinson’s Disease, and seeking for potential drug targets in the HDAC family. Now I’m extending my study in Shen Lab, investigating how noncoding risk variants within cis-regulatory element act in gene regulatory in neurological disorders, further annotating the function of putative enhancers in temporal and cell specific manners. Scientific research is a course into the unknown. The beauty in this journey depends on your knowledge, and how much you enjoy and love it!

Xiekui Cui, Ph.D.

Postdoctoral Fellow

I obtained my Ph.D. at Institute of Genetics and Developmental Biology Chinese Academy of Sciences, where I studied silencing of transposable elements in plants. Then I spent a couple years studying Piwi/piRNA in Haifan Lin's Lab at Yale, and developed interest in the functional studies of non-coding elements in the genome. My goal in the Shen lab is to illustrate the function of those 'dark matter' in human genome and how they can serve as regulatory elements to turn the genes on and off under different situations. During spare time, I enjoy traveling and cooking.

Han Yang, Ph.D.

Postdoctoral Fellow

I received a B.S. degree in Biological Sciences at CAU and a Ph.D. degree in Pathology at Peking University in China. During my Ph.D. study, I mainly focused on elucidating the relationship between the genetic factor and breast cancer risk, and became interested in disease-related functional genomics and gene regulation, especially in how susceptible variants could contribute to human complex diseases. After ten years in Beijing, I join Shen lab at UCSF as a postdoctoral fellow to further explore the causal non-coding variants and gene regulation in disease occurrence and development. My long-term goal is to provide novel ideas for the early prevention, diagnosis and treatment of diseases. In my spare time, I am fond of hiking, traveling and photographing.

Sean Ganther

DDS/Ph.D program

After graduating from high school, Sean was sure that his career choice in music was what he was destined to do. However, his career trajectory shifted towards the sciences after transferring to California State University, San Bernardino (CSUSB) where he graduated with his B.A. in Biology and minor in chemistry. Sean began to establish himself as a scientist in the laboratory of Dr. Nicole Bournias-Vardiabasis, whose lab largely focuses on aging and Alzheimer’s disease using Drosophila melanogaster. Through a series of influential experiences, large exposure in the clinic and an innate passion to innovate the dental field, Sean has set his long-term goal of becoming a dental clinician attending the University of California, San Francisco’s Advanced Dual-Degree DDS/Ph.D program.
 
As a graduate student, his motivation is to develop alternative drug and/or gene therapies that focus on patients who suffer from more advanced or chronic forms of periodontal disease (PD), ~8.5% of the U.S. population. These patients do not respond to conventional treatment methods compared to patients who present with more moderate forms of the disease, largely due to a tissue-destructive transcriptional profile which is driven by oral pathogens such as the gram- negative spirochete, Treponema denticola (T. denticola). He is particularly interested in better understanding oral microbial-host interactions and how these interactions lead to the progression of oral pathogenesis through the modulation of cellular and tissue processes at the transcriptional and epigenetic levels.
 
The last arm of his dissertation research is focused on better understanding how T. denticola, modulates the epigenetic landscape in human periodontal ligament fibroblasts using next generation and high-throughput sequencing methods such as ATAC-Seq and CUT&RUN (Modified ChIP-Seq). Thus, by investigating into the cell populations, pathways, and gene regulatory network involved in periodontal pathogenesis, he strives to develop the most efficacious strategies for better patient outcome. As a dental clinician, he hopes to make molecular connections underpinning similar chronic diseases such as osteoarthritis and gut dysbiosis, in an effort to bridge the gap between oral pathology and systemic health.

 

Ian Jones

PSPG Graduate student

I graduated from the University of California, Berkeley with a B.A. degree in Molecular and Cellular Biology with an emphasis in Genetics. While at UC Berkeley, I worked in the Glass Lab to identify the roles of the functional domains of zinc binuclear cluster transcription factors involved in plant cell wall degradation in N. crassa. Currently, I am excited to study the impact non-coding regulatory elements have on disease. In my free time I like to play basketball and grow bonsai.

Cooper Beaman

Junior Specialist

I graduated from the University of California, San Diego with a dual B.S. in Molecular Biology and Cognitive Neuroscience. After graduating, I volunteered in Dr. Joshi's immuno-oncology lab at UC San Diego where I employed molecular assays, in vitro and in vivo models to test the efficacy and determine the mechanisms of macrophage targeting immunotherapeutic cancer drugs. I find the application of genomic and other -omic methods to the study of neurodevelopmental psychiatric disorders fascinating; I'm hopeful the results of such research will inform a more personalized and quantified approach to psychiatry. I'm excited to be studying the functional role of cis-regulatory element variants in neurodevelopment. Outside of lab, I enjoy gardening, hiking and podcasts.

JJ Vivek

Junior Specialist

Born and raised in the Bay Area, I attended City College of San Francisco, where I pursued political activism and collaborated with my community to make tuition free. I then transferred to UC Berkeley (B.A. Molecular/Cell Biology and Integrative Biology, 2019) and worked at the Shapira Lab. There, I studied how a complex intestinal microbiota mediates heat stress tolerance in C. elegans hosts, and characterized patterns of gut colonization by functionally-significant bacterial strains. At the Shen Lab, I am thrilled to be studying the role of cis-regulatory elements and epigenetic modifications in neural development and pathology. 

Briana Li

UC Berkeley Undergraduate Student

I am a 3rd year undergraduate student at the University of California, Berkeley majoring in Molecular and Cell Biology and minoring in Global Public Health. I am particularly interested in neurodegenerative diseases and hope to contribute to a deeper understanding of such diseases, its causes, and potential treatments. At the Shen Lab, I am excited to investigate the role that non-coding genetic variants play in neurological diseases through the use of genomic and genetic tools. In my free time, I enjoy baking, cooking, sewing/embroidery, and playing the piano.

 

Former Lab members

Year Left Name Position at Shen Lab Current Position  
2015 Yien-Ming Kuo, Ph.D. Specialist Morphology Core Director at Ophthalmology Department, UCSF
2016 Jean Badroos Work Study Undergraduate from UC Berkeley Undergraduate at UC Berkeley
2016 Seokho Kim, Ph.D. Post-Doctoral Scholar Scientist at National Institute of Animal Science, Republic of Korea
2016 Gabrielle Kleyner Summer Intern Undergraduate at Rutgers University
2016 Vasco Morais CIRM Intern Undergraduate at UC Davis
2016 Yuan Wang (Simon), Ph.D. Post-Doctoral Scholar Postdoc at Harvard University
2017 Lydia Liu Lowell High School Summer Intern Undergraduate at John Hopkins University
2017 Jonghoon (John) Chang Junior Specialist Graduate Student at Georgetown University
2019 Tsz Wai (David) Tam Junior Specialist Graudate student at the University of Hong Kong
2019 Seth Bergenholtz Junior Specialist Medical School Student at Boston University
2019 Ian Jones Junior Specialist Graduate Student at UCSF
2019 Brianna Li Lowell High School Summer Intern 2018 & 2019 Undergraduate at UC Berkeley
2019 Brian Tong Woodbridge High School Summer Intern High School Student at Woodbridge High School
2019 Lenka Maliskova Research Associate Associate Specialist at Functional Genomics Lab, UCSF
2020 Jerry Lee Junior Specialist Graduate Student at University of Chicago
2020 Asami Takagi Junior Specialist Medical School Student at Central Michigan
2020 Michael Song PSPG Graduate Student Scientist at Monte Rosa Therapeutics
2020 Niko Eng Master Student    
2021 Kirsty Jamieson Post-Doctoral Scholar Research Scientist at Invitae
2021 Bingkun (Alex) Li Junior Specialist Master student, The Erasmus+ International Master in Innovative Medicine (IMIM)
2021 Michael Yu Lincoln High School Intern  
2022 Lazaros Lataniotis Post-Doctoral Scholar Sr. Scientist at Sana Biotechnology, South San Francisco.
2022 Hongjiang Liu Visiting Undergraduate Student  
2022 Charles Cai Junior Specialist  
2022 Hao Liu Visiting Undergraduate Student Junior Specialist at UCSF
2022 Cady Chen High School Volunteer Undergraduate at Columbia University
2022 Zachary Amador UCSF Summer Research Training Program (SRTP) Undergraduate at UC Riverside