Welcome to our Research Group's webpage!
We are a group of human geneticists and computational biologists. We utilize cutting-edge analytic tools to address questions at the intersection of human medical and population genetics. These insights will be critical for future medical genetics studies and in practicing personalized medicine.
For new and current members of the group, please check out Lab Expectations and Resources here
4.2021: Our lab is represented at PROBGEN 2021 conference (Probabilistic Modeling in Genomics at CSHL) by Caoqi Fan, who is presenting his project on a novel estimator of genetic relationship matrix based on inferred genome-wide genealogical tree sequences (Abstract #80). Poster can also be accessed here.
4.2021: Ying-Chu Lo has joined our group as a postdoctoral fellow. Ying-Chu is funded by the USC-Taiwan postdoctoral fellowship, and will immediately jump into multiple ongoing projects in the lab. Welcome Ying-Chu!
2.2021: The paper on impact of genetic ancestry on risk of complex traits in Native Hawaiian is now published in PLoS Genetics! The paper is co-led by former M.S. student Hanxiao and former postdoc Meng Lin, with contributions also from Tsz Fung and Bryan. There is a press release from USC and some media coverage. We learned quite a bit (and are continuing to learn) on how to work with an understudied indigenous population in a respectable and sensitive way, including having the Native Hawaiian Community Advisory Board established by University of Hawaii Cancer Center to review our research proposal and to provide feedback on the manuscript. We look forward to continue this research journey and look forward to more engagement with the community once we are out of this covid pandemic. Any trainee from the community who might be interested in working with us either at the pre- or post-doctoral level please reach out!
1.2021: New semester, we welcome new members joining the lab: Echo Tang, an undergraduate student in Quantitative Biology at USC Dornsife College of Arts and Sciences with a minor in Health Policy, and Jordan Cahoon, an undergraduate student in Computer Science at USC Viterbi School of Engineering. Welcome Echo and Jordan!
12.2020: We are looking for a postdoc to join us! This is a 2 year position with possibility to extend for a 3rd year. Remote working is expected at start, and negotiable after "life is back to normal." Interested applicant please see our Join.Us tab for detail. Official ad is here but the easiest way to apply is to email Charleston with application material or questions. (This is different from the postdoc position we are also looking to hire through the T32 fellowship!)
10.2020: Our group is well-represented at ASHG 2020, including two Reviewer's Choice Abstracts! We have posted full size poster and/or lightning talks here, in case you wish to review for details. Specifically, we have:
Caoqi (Abstract #2975) "A genealogical estimate of genetic relationship." PPT
Minhui (Abstract #3013) "Polygenic adaptation at height-associated loci among continental populations." PDF
Feel free to reach out to each presenter directly with any questions or comments on the specific project or research in general!
10.2020: Minhui published a new preprint on frequency differentiation of height-associated SNPs among global continental populations. In this manuscript we showed that by using height-associated SNPs ascertained from biobank GWAS we can be protected from any confounding due to residual stratification in GWAS summary statistics. We found that these height-associated SNPs exhibit significantly higher level of differentiation among African, European, and East Asian populations, consistent with a signature of polygenic adaptation. Any question or comment are welcomed!
9.2020: The consortium paper on trans-ethnic GWAS of blood cell traits in >700,000 individuals is out in Cell!. It was a fun collaboration where we contributed population genetic analyses to demonstrate the power of GWAS in diverse populations.
9.2020: Camellia was awarded the 2020 Provost Fellowship to conduct research in the lab for this school year. Congrats Camellia!
7.2020: Soyoung gave a lightning talk on her multi-ethnic GWAS on acute lymphoblastic leukemia (ALL) in the International Genetic Epidemiology Society (IGES) 2020 annual meeting. Her lightning talk and poster won one of the three Best Poster Awards. Congratulations Soyoung!
7.2020: Minhui's paper on using Biobank Japan GWAS to investigate polygenic adaptation in Sardinia and Europe is officially out in the July issue of American Journal of Human Genetics (free PDF through link available until 8.21.2020)!
Read our older news here.
The overarching theme of our research group is to use genetic approaches to understand how evolutionary forces shaped the genetic architecture of complex traits within and between populations. To this end, we have been involved in a number of past and ongoing medical genetics studies in mapping genetic loci underlying human complex traits. We are also continually interested in investigating the evolutionary forces, namely demography and selection, that shaped the pattern of genetic variability and phenotypic distribution. We are particularly interested in diverse, global human populations and our successes result from collaborating with innovative colleagues and thriving in resourceful consortiums. Read a more detailed description of our work here.
Charleston Chiang is the principal investigator of the group. He is a tenure-track Assistant Professor in the Department of Preventive Medicine at USC Keck School of Medicine and Department of Biological Sciences at USC Dornsife College of Letters, Arts, and Sciences. He is broadly interested in using genetic approaches to understand how natural selection and demographic history shaped the variations in complex traits within and between diverse human populations.
Previously, he was an NRSA postdoctoral fellow with Nelson Freimer and John Novembre at UCLA. Charleston received his Ph.D. in Genetics from Harvard University where he worked with Joel Hirschhorn.
Soyoung (Elizabeth) Jeon is a Ph.D student in the group (co-advised by Dr. Joe Wiemels). She is pursuing her Ph.D. in the Cancer Biology and Genomics track through PIBBS at Keck School of Medicine. Her project investigates the correlation between ancestry and the risk of Childhood Leukemia in a number of multiethnic U.S. cohorts. She is interested in understanding how human population history contributes to variations in susceptibility to disease and response to therapy. Before joining the group, she received her Bachelor of Science in Molecular and Cell Biology, with Medical Biology and Physiology track from University of California, Berkeley in 2017.
Caoqi (Ephraim) Fan is a Ph.D student in the group since 2019. He is pursuing his Ph.D. in the Computational Biology and Bioinformatics program in the Department of Biological Sciences. Working closely also with Dr. Nicholas Mancuso in the Center for Genetic Epidemiology, Caoqi's current research focus is on incorporating genealogies and ancestral recombination graphs into estimating the genetic relationship matrix to improve heritability estimates and complex phenotypes imputations. Before joining the group, he received his Bachelor of Science in Biology on Bioinformatics track from Peking University (Beijing, China) in 2018.
Tsz Fung Chan is a Ph.D student in the group since 2019. He is pursuing his Ph.D. in Epidemiology in the Department of Preventive Medicine. Co-advised by both Dr. Chiang and Dr. Nicholas Mancuso in the Center for Genetic Epidemiology, he is interested in developing methods for analyzing genomic data of admixed populations. Before joining the group, Tsz Fung studied the genetics of Epstein-Barr virus under the guidance of Alan Chiang and Wanling Yang at the University of Hong Kong. He received his Bachelor of Biomedical Sciences (with a minor in Computer Sciences) and M.Phil in Bioinformatics from University of Hong Kong in 2017 and 2019, respectively.
Sydney Rashid is an undergraduate student in the group since 2020. She is pursuing a B.S. degree in Quantitative Biology at the USC Dornsife College of Letters, Arts and Sciences. She is studying to bridge the gap between computer science and genomics. Her research interests include investigating the underlying evolutionary forces driving genetic variation and disease susceptibility in understudied populations. Currently, she is working on calculating polygenic risk scores for children with Acute Lymphoblastic Leukemia using known loci from GWAS.
Bryan Dinh is a Ph.D. student in the group since 2020. He is pursuing his Ph.D. in the Computational Biology and Bioinformatics program in the Department of Biological Sciences. Bryan is interested in algorithms and their applications to biology, genetics, and diverse populations. Before joining the group, Bryan received a Master of Science in Computer Science and a Bachelor of Science in Mathematics and Economics from UCSD.
Camellia Rui is an undergraduate student in the group since 2020. She is pursuing a B.A. degree in Mathematics at the USC Dornsife College of Letters, Arts, and Sciences, as well as a progressive M.S. degree in Biostatistics at Keck School of Medicine. Before joining the group, she has completed coursework in human biology, biochemistry, and mathematics. Previous to joining the lab, she had worked as an undergraduate research assistant and research intern in primate neurobiology. Currently, she is rapidly learning about coding and human genetics.
Personal Website: http://camelliarui.github.io/
Echo Tang is an undergraduate student in the group since 2021. She is pursuing a B.S. degree in Quantitative Biology from USC Dornsife College of Letters, Arts and Sciences and a minor in Health Policy. Before joining the group, she worked as a research assistant studying the genetics of aging and sex-specific effects of mutations. Currently, she is quickly learning about imputation in population genetics and coding in data analysis.
Jordan Cahoon is an undergraduate student in the group since 2021. She is pursuing a B.S. degree in Computer Science at the USC Viterbi School of Engineering with a minor in Computational Biology and Bioinformatics. Jordan is interested in analyzing and visualizing genetic disease factors in diverse populations. Prior to joining the lab, she worked as an undergraduate research assistant in single-cell transcriptomics research. Currently, she is working to deepen her understanding of computational population genetics.
Ying-Chu Lo is a postdoctoral scholar in the group. She has had experience studying both fungal and plant models, exploring the genetic variation between populations. She obtained her Ph.D. in genetics and evolutionary biology in 2019 from the University of Paris-Saclay (University Paris XI) in Paris, France. In her Ph.D. she focused on using population genetics and comparative genomic methods to study fungi domestication and adaptation. After her PhD, she was a postdoc at ABRC Academia Sinica in Taiwan as a bioinformatic scientist, where she investigated the genes or gene clusters correlated to plant homeostasis under heavy metal stress. Currently, Ying-Chu is funded by a USC-Taiwan postdoctoral fellowship. She is focusing on understanding the genetic and non-genetic factors contributing to the poor transferability of polygenic risk score (PRS) risk prediction models between human populations.
All of the wonderful trainees, visitors, and colleagues that have contributed to our work!
Hanxiao Sun, M.S. Biostatistics 2018-2019. Last known location: Ph.D. student at UT Health School of Public Health
Meng Lin, postdoc 2018-2020. Last known location: postdoc at University of Colorado
Samuel Sommerer, B.S. Quantitative Biology 2019-2020. Last known location: B.S. student in Computer Science at USC
Minhui Chen, postdoc 2018-2021. Last known location: postdoc at University of Chicago
Image credit: modified from "Graduation" by Wilson Joseph / CC
We are always interested in talented and highly motivated individuals to join our team! We currently have space and funding for a postdoctoral fellow in genetic epidemiology and population genetics to join our group. Please check out this page for expectations and resources for lab members. See below for how to apply:
Postdoctoral Fellows: Highly motivated individuals are encouraged to contact Charleston Chiang for inquiries. In particular, there are openings for postdocs either interested in population genetics or in genetic epidemiology. Funding could be through unrestricteed funds or through the USC-UH Multiethnic Cohort T32 Postdoctoral Training Program. Applicants ideally should have extensive exposure and experience in human medical and/or population genetics research and have analyzed large genetic datasets. Programming skills (e.g. python, perl, C, R, etc.) and proficiency in Unix-based computing environments are very desirable. Successful candidates may also develop projects broadly within the scope of the group's research interests.
Informal inquiries or applications (cover letter, CV, and contact information to at least two references) should be emailed to Charleston Chiang.
Graduate Students: The research group is recruiting prospective PhD students. Generally, doctoral students are enrolled through Program in Biological and Biomedical Sciences (PIBBS), Computational Biology and Bioinformatics (CBB) or one of the Public Health Sciences programs (such as Biostatistics or Epidemiology) at USC. Email Charleston Chiang for inquiries.
Image credit: "Unknown" by Bybzee / CC BY
Charleston can be reached via email at:
charleston [dot] chiang [at] med [dot] usc [dot] edu
We are located in the Harlyne J. Norris Research Tower (NRT) on the Health Science Campus at USC
1450 Biggy Street
Los Angeles, CA 90033
BISC577: Computational Biology Laboratory
"Genetics and Evolution": slides (2020.09.15)
(This is a huge slide deck! ~17Mb)
Postdoctoral Fellows: We currently have one opening for a postdoctoral fellow in population genetics. Highly motivated individuals are encouraged to contact Charleston Chiang for inquiries. Applicants ideally should have extensive exposure and experience in human medical and/or population genetics research and have analyzed large genetic datasets. Programming skills (e.g. python, perl, C, R, etc.) and proficiency in Unix-based computing environments are very desirable. Successful candidates may also develop projects broadly within the scope of the group's research interests.
The official ad can be found here. Informal inquiries or applications (cover letter, CV, and contact information to at least two references) should be emailed to Charleston Chiang.
T32 Postdoctoral Fellowship: We currently have one opening for a postdoctoral fellow in genetic epidemiology. Applicants ideally should have extensive exposure and experience in human medical and/or population genetics research and have analyzed large genetic datasets. Programming skills (e.g. python, perl, C, R, etc.) and proficiency in Unix-based computing environments are very desirable. The position is funded for 2 years with possibility to extend for a 3rd year. Successful candidates may also develop projects broadly within the scope of the group's research interests using the Multiethnic Cohort, which consists of genotyping and sequencing data on up to 70K individuals from African American, Latino American, Japanese American, European American, and Native Hawaiian individuals.
In felis turpis, tincidunt a odio interdum, ornare interdum magna. Proin leo tortor, adipiscing et volutpat tincidunt, imperdiet sit amet purus.