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
10.2020: We are looking for a postdoc to join us through the T32 postdoctoral training fellowship shared between USC and University of Hawaii. This is a 2 year position with possibility to extend for a 3rd year. Interested applicant please see our posting on jobRxiv and reach out to Charleston for more details!
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)!
6.2020: Sam and Sydney were funded on a Undergraduate Research Associates Program (URAP) over the summer to conduct research in constructing and analyzing polygenic risk scores for ALL!
6.2020: As we began the summer, two more students joined our group: Bryan Dinh, a Ph.D. student from CBB who just finished a rotation in the lab this Spring, and Camellia Rui, an undergraduate student from Mathematics at USC who will also be completing a progressive M.S. thesis in Biostats with us. Welcome Bryan and Camellia!
5.2020: We are looking for a postdoctoral fellow through the Taiwan-USC Postdoctoral Fellowship Program. Please see their website for eligibility and application process. If you are interested, contact Charleston to discuss about submitting an application.
5.2020: A preprint co-led by Hanxiao and Meng are posted on bioRxiv. This was the bulk of Hanxiao's M.S. thesis, where we investigated the impact of genetic ancestry on risk of complex traits in Native Hawaiians. It is important to note that while we estimated genetic ancestry, these estimates are not without errors at the individual levels, and are correlated with non-genetic factors such as culture, life-style, etc. So please see these tweets to interpret the results with caution!
5.2020: Caoqi presented a poster at Biology of Genomes (virtual) conference on his project a genealogical estimate of genetic relationships. Despite the challenges of not being able to see each other face to face, there were still good discussion!
4-5.2020: To keep the Center of Genetic Epidemiology cohesive during COVID-19, we are organizing a virtual seminar series via zoom with an amazing line-up of speakers from statistical, medical, and population geneticists. Please contact Charleston if you're interested to listen in.
1.2020: Charleston was invited to give a seminar at Department of Genetics, University of Georgia in Athens, GA. It is a department strong in evolutionary biology and filled with exciting research from its faculty and students!
1.2020: Sydney Rashid, an undergraduate student from Quantitative Biology has joined our group as a research assistant! Welcome Sydney!
10-11.2019: Minhui gave a short talk at Bay Area Population Genetics meeting (BAPG XVIII) on his preprint on polygenic adaptation and height. Meng also presented a poster on her preprint about CREBRF locus in Native Hawaiians at ASHG 2019 in Houston!
10.2019: A pair of preprints from the lab is posted on bioRxiv! These are the first two research papers from the group. One led by Minhui on polygenic adaptation of height associated loci in Europe and Sardinia, the other led by Meng on the CREBRF locus in Native Hawaiians in the Multiethnic Cohort. Feel free to get in contact if you have any comments or questions!
9.2019: As we start the new semester, the lab is also growing! This term we welcome three new members joining the lab: Caoqi (Ephraim) Fan (PhD student, CBB), Tsz Fung Chan (PhD student, Epidemiology, co-advised with Nick Mancuso), and Sam Sommerer (Undergraduate student, Quantitative Biology). Welcome Caoqi, Tsz Fung, and Sam!
9.2019: Charleston was invited to give a seminar at International Laboratory for Human Genome Research (LIIGH) in Queretaro, Mexico. It was an enjoyable visit to see an up and coming institute with a core of young and energetic faculty!
8.2019: Our manuscript on leveraging Finnish population history to improve power of rare variant association and to detect novel associations to quantitative cardiometabolic traits is published in Nature! This paper really exemplifies the utility to leverage populations of special population history in human medical genetics, which is the central theme of our research group moving forward!
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.
Minhui Chen is a postdoctoral scholar in the group. His research utilizes genomic data to study the evolutionary and demographic processes that shaped the genetic architecture of complex traits in Finland. He is interested in population genetics and statistical methodologies. Before joining the group, Minhui received his Ph.D. from China Agricultural University and Aarhus University in Denmark, working on selective sweeps, population admixture and adaptive introgression in domesticated animals.
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 with Dr. Chiang and 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. Working closely with 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/
All of the wonderful trainees, visitors, and colleagues that have contributed to our work!
Samuel Sommerer, B.S. Quantitative Biology 2019-2020. Last known location: B.S. student in Computer Science at USC
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
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 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! ~16Mb)
T32 Postdoctoral Fellowship: We currently have one opening for a postdoctoral fellow in genetic epidemiology and population genetics. 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.
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