Mooney Lab @ University of Southern California



Welcome! We are the Mooney Lab. Our goal is to use patterns of variation in the genome to understand the evolutionary and population histories of both humans and other species. We do this by implementing and developing computational and statistical methods to study the genome.

We are also interested in more broad population genetics questions such as: the genomic consequences of deleterious (non-neutral) mutations, where deleterious mutations tend to aggregate in the genome, and understanding patterns of genomic sharing through identity-by-descent segments and runs of homozygosity.

We are located at the University of Southern California (USC) in the Department of Quantitative and Computational Biology (QCB).



Our Research



For the last decade, population genetics has rapidly accelerated to new heights with the availability of sequence data. These data sets have provided valuable insights about population history, phenotypes, disease architecture, evolution, and genomic diversity.


Broadly, our lab uses empirical data analysis, simulation frameworks, and methods development to do the following: 1) infer demography, 2) understand the fitness impact of recessive variation, and 3) investigate complex trait architecture.

We focus primarily on integrating data from both human and non-human populations to develop a more complete picture of mechanisms that shape patterns of genomic sharing (in the form of identity-by-descent segments and runs of homozygosity) and deleterious variation. We are also interested in developing methods for conservation biology, inference of the genealogical histories of admixed populations, and the equitable inclusion of underrepresented populations in genomics.

Jazlyn's talk at CGSI

On-going research in the Mooney Lab on uncovering the history of African Americans.


Join the Mooney Lab



We are glad you are interested in joining us!

I make every effort to create an inclusive lab environment where lab members not only learn the science but also are excited about the future of science. There are no required pre-requisites for joining the lab and lab members may come from any background. In the Mooney lab, most projects will include coding for genetic data analysis, some mathematics, simulation, and data visualization. Most of all, I want students to learn relevant skills for the next step in their career, in a lab where they feel like science is a place where they can grow and thrive.


Postdoctoral researchers

To inquire about postdoctoral positions, please write to Jazlyn at jazlynmo@usc.edu. Interest areas that would fit particularly well in the lab include the population genetics of runs of homozygosity, identity-by-descent segments, complex traits, and demographic inference.

Please include a CV and a short description (1-2 pages) of your research experience, interests, and ideas for work in the lab. Please put “Postdoc position” in the subject line of your email to jazlynmo@usc.edu. Please also list 2-3 professional references and include any recent work you’d like to share.


PhD students

Feel free to contact me and put “Graduate student position” in the subject line of your email to jazlynmo@usc.edu. We can talk about potential research interests and relevant projects in the lab.

Students should apply to USC’s Computational Biology and Bioinformatics (CBB) program. Our graduate program will give you experience in algorithms, statistics, and biology. During the first year, students will complete coursework as well as rotate in up to three CBB-affiliated labs. Students interested in completing a PhD in the lab should arrange to do one of their rotations with us. CBB admissions are handled by the admissions committee and not by individual labs.


Undergraduates, Master’s students, and others

We are looking to include USC undergraduates and Master's students on research projects. If you are interested in joining the lab, email me with the relevant header of either “Undergraduate student position” or " Master’s student position" in the subject line of your email to jazlynmo@usc.edu. Please include a CV, relevant course history, and statement of interest.

Experience with command line, Python, R, C/C++, would be beneficial but are not necessarily required.



Contact Us



Email: jazlynmo@usc.edu

We are located on the 4th floor of Ray R. Irani Hall (RRI) at the University of Southern California, in the University Park neighborhood of Los Angeles.
The closest parking structure is the Downey Way Structure.
USC Maps



Our Publications


2024
Armstrong EE*,&, Mooney JA*,&, Solari KA ... Hadly, EA*. Unraveling the genomic diversity and admixture history of captive tigers in the United States, Proc Natl Acad Sci U S A. 2024 Sep 24;121(39):e2402924121. doi: 10.1073/pnas.2402924121. * indicates co-corresponding & indicates co-first authorship

Armstrong EE, Bissell KL, Fatima HS, ... Mooney JA & Mychajliw, AM. Chromosome-level assembly of the gray fox (Urocyon cinereoargenteus) confirms the basal loss of PRDM9 in Canidae, G3 Genes|Genomes|Genetics,, 2024 15 February; https://doi.org/10.1093/g3journal/jkae034.


Agranat-Tamir L, Mooney JA, and Rosenberg NA. Counting the genetic ancestors from source populations in members of an admixed population, GENETICS, 2024 30 January; https://doi.org/10.1093/genetics/iyae011.


2023
Mooney JA, Agranat-Tamir L, Pritchard JK, and Rosenberg NA. On the number of genealogical ancestors tracing to the source groups of an admixed population, GENETICS, 2023 6 July; https://doi.org/10.1093/genetics/iyad079.



2022
Tidyverse Session at SACNAS

Mooney JA,Marsden CD, Yohannes A, Wayne RK, Lohmueller KE. Long-term small population size, deleterious variation, and altitude adaptation in the Ethiopian wolf, a severely endangered canid, Mol Biol Evol, 2022; msac277, https://doi.org/10.1093/molbev/msac277



2021
Mooney JA, Yohannes A, and Lohmueller KE. The impact of identity by descent on fitness and disease in dogs, Proc Natl Acad Sci U S A. 2021 Apr 20;118(16)



2019
Sura SA, Smith LL, Ambrose MR, Amorim CEG, Beichman AC, Gomez ACR, Juhn M, Kandlikar GS, Miller JS, Mooney JA, Mummah RO, Lohmueller KE, Lloyd-Smith JO. Ten simple rules for giving an effective academic job talk. PLoS Comput Biol, 2019; 15:e1007163.



2018
Mooney JA, Huber CD, Service S, Sul JH, Marsden CD, Zhang Z, Sabatti C, Ruiz-Linares A, Bedoy G, Costa Rica/Colombia Consortium for Genetic Investigation of Bipolar Endophenotypes, Freimer N, Lohmueller KE. Understanding the hidden complexity of Latin American population isolates. Am J Hum Genet.2018 Nov 1;103(5):707-726.



The Team



Jazlyn Mooney (she/her)

Principal Investigator (jazlynmo@usc.edu)

Jazlyn is a Gabilan Assistant Professor in the Quantitative and Computational Biology (QCB) Department within the Dornsife College of Letters, Arts and Sciences at USC. Her research combines computational approaches with population genetics theory to better understand genetic variation, medical genetics, and human evolution. Jazlyn's CV

Jazlyn completed her undergraduate degree at the University of New Mexico where she studied human evolution with Jeffrey Long in the department of Anthropology. She completed her PhD in Human Genetics at UCLA in 2020 under the advisement of Kirk Lohmueller. At UCLA, Jazlyn studied genetic variation in admixed populations, complex traits in dogs, and conservation genomics. Afterward, she moved to Stanford’s Biology department for postdoctoral research with Noah Rosenberg; where she continued to study admixed populations with a focus on inference method development.

Fun fact from Jazlyn: When I am not in lab, I enjoy record collecting and going to concerts.


Maria Akopyan (she/her)

Postdoctoral Fellow

Dr. Maria Akopyan is a postdoc in the Mooney lab, she completed her PhD at Cornell where she studied gene flow and adaptation in Atlantic silversides. Dr. Akopyan also holds an M.S. which she completed at CSUN where she studied variation in Red-eyed Tree frogs. Currently, she is exploring how reference bias can affect demographic inference in Canidae by using whole genome sequence data from Mainland foxes and Channel Island foxes.

Fun fact from Maria: I like to paint and dance!


Shirin Nataneli (she/her)

Graduate student

Shirin is a graduate student in the Computational Biology and Bioinformatics program and is broadly interested population genetics and evolution. Currently, she is exploring how we can better model complex admixture scenarios to infer demography in humans and populations of conservation concern.

Fun fact from Shirin: I've collected snow globes from every place I've traveled and my favorite animal is a sheep.


Tessa Ferrari

Lab Technician

Tessa just graduated from the Quantitative Biology undergraduate program and is now a lab Research Technician. While in the Mooney Lab, Tessa will be building and using large-scale simulation frameworks to infer demography and model mutational load.

Fun fact from Tessa: In my free time I’m a competitive hip hop and open style dancer!


Matthew Genchev

Undergraduate student

Matthew is an undergraduate in the Quantitative Biology program with an interest in modeling recombination and demography in non-human populations. Matthew is currently exploring recombination and demography in Canidae, specifically foxes. Matthew is also a Provost Undergraduate Research Fellow.

Fun fact from Matthew: I won $20 from a scratch off ticket one time.


Sydney Bruce

Undergraduate student

Sydney is an undergraduate in the Quantitative Biology program with an interest in population genetics and systems biology. Currently, Sydney is working to create a recombination map for captive tigers in the U.S. and will be exploring the relationship between genetic diversity and the recombination landscape in tigers.

Fun fact from Sydney: I work as an EMT during the summers!


Tina Lasisi (she/her)

Former Postdoctoral Fellow

Dr. Tina Lasisi is now an Assistant Professor at the University of Michigan in the Anthropology department, and a former Postdoctoral Researcher in the Mooney and Edge labs. Tina's background and interests fall within the realm of Biological Anthropology and complex trait genetics. Specifically, her research area includes understanding the evolution of human variation in 1) pigmentation and 2) scalp hair. Tina is also active in science communication. Check out Tina's website and her amazing PBS mini-series Why Am I Like This?.

Fun fact from Tina: I have a standard poodle.


Mengdi (Kim) Chai

Former Undergraduate student

Mengdi is an alumni of the Mooney Lab and graduated with honors from the Quantitative Biology undergraduate program. While in the lab, Mengdi was a WiSE undergraduate fellow and used identity-by-descent segments to identify genes associated with coat color in tigers and tracking their ancestral origins. She is currently pursuing a Master's Degree at Harvard in Computational Biology and Quantitative Genetics.

Fun fact from Kim: I have one hamster and he is cute! I decide to have two dogs, one cat, and two hamsters when I have my own apartment!

Anika Shrivastava

Former Undergraduate student

Anika was an undergraduate in the Quantitative Biology program and is interested in human genetics and disease. While in the lab, she worked on quantifying regions of the genome that harbor potential recessive lethal mutations by layering information from multiple types of genomic annotations. Anika was also a Provost Undergraduate Research Fellow and has recently completed an internship at Expedia.

Fun fact from Anika: I have been playing the piano for 15 years and have a minor in musical studies at USC.

Chenyang (Julie) Li

Former Undergraduate student

Julie was an undergraduate in Applied and Computational Mathematics & the Quantitative Biology program with an interest in conservation and disease. She created the population assignment algorithm for mPCRselect, which allows users to construct informative marker panels in populations of conservation concern. She was a WiSE Undergraduate Fellow, graduated with honors and received the USC Discovery Scholar Distinction. Julie will be heading to Emory to join the Population Biology, Ecology, and Evolution PhD program.

Fun fact from Julie: I've never dyed my hair. My reddish/brown hair color is my natural hair color.



Classes Taught



HUMGEN 19: How Genetics has Contributed to Racial Injustice in America and the World

Fall 2020

Fiat Lux seminar I co-taught with Dr. Nelson Freimer at UCLA. We used a mixture of readings, presentations, and discussions to navigate the history of Genetics and its ties to Eugenics. Syllabus


BIOL 870: Biology Colloquium

Fall 2020

Seminar based course I taught at SFSU. In this course students’ scientific curiosity was be piqued as they heard and interacted with biologists from a range of subfields. Syllabus


QBIO 105: Introduction to Quantitative Biology Seminar

Spring 2023

Seminar based course I co-taught with Dr. Remo Rohs at USC. This course is the introductory seminar for students taking the QBIO major. It is ideally taken as freshman but it can be taken after a student‘s transfer into the QBIO program. The instructors introduce the general field of Quantitative Biology, its definition and role within the Biological Sciences, and its relationship with Chemistry, Computer Science, Engineering, Mathematics, Medicine, and Physics. Syllabus


QBIO 475: Statistical and Evolutionary Genetics

Fall 2022, Fall 2024, and Fall 2024

QBIO capstone course I co-teach with Dr. Doc Edge at USC. This is an upper-division course designed to introduce quantitative biologists to some central ideas in the mathematical modeling and statistical analysis of genetic variation. Topics from evolutionary genetics and medical genetics will be explored using a mix of math, simulation, and data analysis. Topics may include genetic drift, natural selection, mutation, migration, population structure, and study designs for learning about genotype-phenotype relationships, such as family-based studies, analyses of gene-expression variation, and genome-wide association studies. Syllabus


QBIO 115w: Ethics in Biology, Medicine, and Statistics

Spring 2024 & Spring 2025

Dornsife General Education (GE) course I created and teach at USC. Biology, medicine, and statistics have each made a large impact on understanding life sciences and human disease. This impact has been bolstered over the last 20 years with the integration of information from all three fields and the advancement of genetics and computation. However, these fields are also deeply rooted in 19th century eugenics. Unfortunately, these ties percolated into foundational scientific data and were used to establish biased public policies with rise of eugenics movement. This course will critically reflect on the origins of each field through a scientific perspective and explore modern research practices that offer hope for an equitable future. We will use a mixture of readings, presentations, and discussions to navigate these topics. Syllabus



Outreach



UCLA Association for Multi-Ethnic Bioscientists Advancement (AMEBA)

Co-founder

During graduate school I co-founded AMEBA algonside of Drs. Andrew Lopez, Jessica Ochoa and Christopher Robles. The goal of AMEBA is to create a community and support the academic development of underrepresented students across Biosciences. AMEBA has now grown to 40+ students spanning Life Sciences, Physical Sciences, and Graduate Programs in Biosciences.



Introduction to Tidyverse for Computational Biology

SACNAS Workshops

Attended SACNAS in 2020 and 2022 to conduct workshops that cover the basic statistics and plotting using tidyverse for computational biology.
Presentation 2022



Lab in the news



Unraveling the genomic diversity and admixture history of captive tigers in the United States

News about our work on Tigers with Dr. Ellie Armstrong .


DNA Reveals the Origin Stories of America's Captive Tigers
The genetic secrets of the United States’s privately owned tigers
How captive tigers can help the wild ones: Q&A with USC’s Jazlyn Mooney




On the number of genealogical ancestors tracing to the source groups of an admixed population

News about our work on uncovering lost ancestors of African Americans

Study sheds light on Black Americans' ancestral links
A new approach to genetic genealogy sheds light on African American ancestry
New study offers African American genealogical information unrecoverable from written record
Researchers illuminate centuries of identity lost because of slavery
Breaking down the ‘brick wall’ of African American genealogy