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
We are part of the Center for Genetic Epidemiology, in the Department of Population and Public Health Sciences at USC Keck School of Medicine, and jointly affiliated with the Department of Quantitative and Computational Biology at USC Dornsife College of Letters, Arts, and Sciences.
2.2023: Jalen Langie presented her project of admixture mapping in a Latino cohort to identify loci associated with childhood leukemia as a poster in the Quantitative Genetics and Genomics Gordon Research Conference! You can find the PDF of the poster here. Any questions or comments are welcomed!
1.13.2023: The first PhD student from our group, Soyoung Jeon, successfully defended her PhD dissertation titled "Understanding Acute Lymphoblastic Leukemia in different ethnic groups in the United States." Congrats Dr. Jeon!
1.2023: The triple-liftOver manuscript was highlighted in this month's HGG Advances with a short interview. It is amazing this paper materialized from a tenacious deep dive into a QC anomaly, which could easily have been ignored.
12.2022: Tsz Fung Chan, co-advised by Nick Mancuso, passed his qualifying exam with flying color! His dissertation will focus on "Inferring Genetic Architecture of Complex Traits in Admixed Populations." Congrats Tsz Fung!
11.2022: Our manuscript reporting a bioinformatic error when converting the genomic coordinates of variants in regions inverted between genome build is now published in Human Genetics and Genomics Advances! The manuscript is led by Xin Sheng with the Multiethnic Cohort, with additional help from Jordan Cahoon. We also devised a light-weight tool called triple-liftOver to identify these variants and correct for the errors!
10.2022: Our lab is well represented in the 2022 American Society of Human Genetics meeting here at LA! This includes 6 posters, which are all available online for anyone interested (see this tweet, this tweet, and this tweet, for pictures and links to posters), and culminated in a platform talk by Soyoung Jeon on her work identifying a Latino-specific variant associated with childhood leukemia that may exhibit signature of positive selection!
8.2022: Our lab has been awarded a R01 grant from NIH/NHGRI (R01HG011646), where we will leverage the evolutionary history to improve trait mapping studies and risk stratification models for Native Hawaiians and other Polynesian-anecstry populations! Any motivated and interested postdocs and students please reach out!
6.2022: A number of our lab members are undertaking internships this summer! Jordan Cahoon is a Cloud Infrastructure Software Engineering intern with Oracle. Echo Tang is a Clinical Operations intern with Arthrosi Therapeutics. Soyoung Jeon is a Translational Research intern in the Therapeutics team at 23andMe. Here's hope for a safe and productive summer!
5.2022: Earlier this semester, Camellia Rui successfully completed her M.S. in Biostatistics thesis titled "A Global View of Disparity in Imputation Resources for Conducting Genetic Studies in Diverse Populations." She graduated this Spring term and will be starting in the Biostatistics Ph.D. program at USC this Fall working with Nick Mancuso and Steven Gazal.
4.2022: Caoqi Fan's first author paper, a genealogical estimate of genetic relationships is now published online at American Journal of Human Genetics! The reviewers loved the paper, calling it "a very important contribution highlighting the power of ARG-based inference for detecting population structure." Congrats Caoqi! You can download a copy of the paper for free using this link (until 6/1/2022), and a tl;dr twitter thread here.
3.2022: Dorcus Kholofelo Malomane has joined our group as a postdoctoral fellow. Dorcus obtained her Ph.D. from University of Goettingen, Germany, working on the population and evolutionary genomics of global chicken populations. She will move into human genetics starting with examining the population structure and patterns of genetic variation in Saudi Arabian populations in collaboration with the Mangul Lab. Welcome Dorcus!
2.2022: We have posted a new preprint demonstrating an error that can occur when imputing variants found within regions that are inverted between genome builds. We also provided a simple tool that can identify variants susceptible to this error from plink files.
12.2021: Caoqi Fan successfully defended his qualifying exam proposal and has now officially advanced to candidacy. Congrats Caoqi!
11.2021: Soyoung Jeon's first author paper, a GWAS for childhood acute lymphoblastic leukemia (ALL) across multiple populations, is now published in Leukemia! The paper also received contributions from Minhui Chen and Tsz Fung Chan from our lab. Congrats Soyoung!
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 Population and Public Health Sciences at USC Keck School of Medicine and Department of Quantitative and Computational Biology 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.
Prior to setting up his lab in 2018, he was an NRSA postdoctoral fellow working with Nelson Freimer and John Novembre at UCLA. Charleston received his Ph.D. in Genetics from Harvard University where he worked with Joel Hirschhorn.
Charleston's CV and
Google Scholar profile
Email: charleston [dot] chiang [at] med [dot] usc [dot] edu
Follow him on twitter: @CharlestonCWKC
Soyoung (Elizabeth) Jeon is a postdoc in the group. She received her Ph.D. in the Cancer Biology and Genomics track through PIBBS at Keck School of Medicine in 2023. Her dissertation investigated the genetic architecture of childhood leukemia in a multi-ethnic cohort, examines the correlation between ancestry and the risk of childhood Leukemia, and construct and evaluates polygenic risk stratification models for leukemia. Generally, she is interested in understanding how human population history contributes to variations in susceptibility to disease and response to therapy. She is pursuing these avenues of research in the Multiethnic Cohort, particularly focusing on the Native Hawaiian cohort. Prior to her Ph.D., 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 to re-define the genetic relationship matrix and to infer demographic parameters for human populations. 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 currently developing methods to estimate heritability of complex traits explained by local ancestry and to evaluate stratification bias in admixture mapping studies. 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.
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. Supported by a F31 predoctoral fellowship from NHGRI, Bryan's dissertation focuses on constructing and evaluating genomic resources for Native Hawaiian community, with the goal to empower cutting edge genomic studies in this understudied population. Before joining the group, Bryan received a Master of Science in Computer Science and a Bachelor of Science in Mathematics and Economics from UCSD.
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 part of a team of researchers evaluating the current efficacy for imputing populations around the globe.
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. Supported by the Viterbi Merit Scholarship, she is leading a team of undergraduate researchers to evaluate the current efficacy for imputing populations around the globe, supporting algorithm development in the lab, and exploring the application of machine learning methods for population genetic inference using the ancestral recombination graph.
Ying-Chu Lo is a postdoctoral scholar in the group since 2021. 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.
Christopher Simons is an undergraduate student joining the group in 2021. He is pursuing a B.S. and M.S. in Quantitative Biology at USC. He enjoys learning about genetics, and hopes to improve upon current methods for data analysis using biological information. Prior to joining the lab, he participated in a student group which analyzed publicly available cancer datasets. He is currently leveraging sequencing data from diverse populations to directly assess the precision of imputation methods.
Jalen Langie is a Ph.D. student in the group since 2021. She is pursuing a Ph.D. in Epidemiology (Genetic Track) in the Department of Population and Public Health Sciences. Overall, she aims to investigate genetic contributions to disease through the lens of evolutionary history. Her interests include admixture mapping, fine mapping, and SNP-to-gene annotations in multiethnic populations. Prior to joining the lab, she received her Bachelor of Science in Microbiology from California State University Los Angeles in 2019. During undergraduate, she worked as a research assistant for three years studying fungal pathogenesis and regulatory pathways and completed an internship studying viral kinetics and chemokine expression at Johns Hopkins University.
Dorcus Kholofelo Malomane is a postdoctoral research scholar in the group since 2022. She is interested in exploring patterns of genetic variation in diverse human populations and their relation to complex traits. Dorcus has a background in population and evolutionary genomics. She obtained her PhD in 2019 from the University of Goettingen, Germany. In her PhD work she studied how different geographic distributions, management and breeding practices have shaped genetic diversity in a wide variety of globally collected chicken populations. Furthermore, she investigated the genetic patterns of different genomic regions, pathways and genes in the chicken to explore their subjection to different evolutionary dynamics. Prior to joining the group, she was shortly a postdoctoral research associate at the University of Goettingen and her work was aimed at developing genetic markers for ash dieback disease. Her current project utilizes the genome-wide array data, whole exome and genome sequencing data to understand the impact of population structure and history on patterns of variation in a Saudi population.
Covid certainly made it hard for us to do a lot of fun things together, but click here for some pictures of the lab over the years!
Image credit: modified from "Group" by Nawicon / CC
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
Sydney Rashid, B.S. Quantitative Biology 2019-2020. Last known location: B.S. student in Quantitative Biology at USC
Minhui Chen, postdoc 2018-2021. Last known location: postdoc at University of Chicago
Camellia Xinyue Rui, M.S. Biostatistics 2020-2022. Last known location: Ph.D. student at USC
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 one or more postdoctoral fellows 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 a R35 grant, an anticipated R01, unrestricted 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
PM534: Statistical Genetics (Fall 2021, 2022)
Introduction to Medical Population Genetics
syllabus (Fall 2021)
BISC577: Computational Biology Laboratory (Fall 2019, Fall 2020, Fall 2021)
"Genetics and Evolution": slides (2020.09.15)
(This is a huge slide deck! ~17Mb)
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
Postdoctoral Fellows: We are always looking for talented and motivated individuals to join our group! Interested individuals are encouraged to contact Charleston Chiang for inquiries. There are multiple ways a postdoctoral fellow can be funded, through NIH grants in the lab, collaborative funds, or unrestricted funds. This means you have the stability as well as the flexibility to explore topics broadly of interest to the lab. Positions are generally for at least 2 years, with salary commensurate with experience and adjusted for cost of living in LA (definitely higher than NIH scale!). Applicants ideally should have extensive exposure and experience in human medical and/or population genetics research and have analyzed large genetic datasets. Programming skills (in at least one of, 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.
Inquiries or applications (cover letter, CV, and contact information to at least two references) should be emailed to Charleston Chiang.
Graduate Students:We are open to accepting doctoral and master students. Generally, doctoral students are enrolled through Program in Biomedical and Biological 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.
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