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 broader 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.

Mooney Lab group photo, 2026

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.

Local ancestry and runs of homozygosity diagram

Broadly, our lab uses empirical data analysis, simulation frameworks, and methods development to: (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!

We are an inclusive lab. I support my students and believe they all deserve an opportunity to be in computational biology. The Mooney lab is a space where lab members not only learn the science but also are excited about the future of science. There are no required prerequisites 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.

Mooney Lab, December 2024

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. Please also list 2–3 professional references and include any recent work you'd like to share.


PhD students

Feel free to contact me — 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 complete coursework and 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, email me with either "Undergraduate student position" or "Master's student position" in the subject line at jazlynmo@usc.edu. Please include a CV, relevant course history, and a statement of interest.

Experience with command line, Python, R, or C/C++ is beneficial but not 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 and Directions


Our Publications


& indicates co-first authorship  ·  + indicates co-corresponding authorship

2026
Sweetalana&, Nataneli S&, Huang S, Mooney JA+, Szpiech ZA+. Genotypic and phenotypic consequences of domestication in dogs. G3 (Bethesda). 2026 Sep 2;16(9):jkag195. doi: 10.1093/g3journal/jkag195.
Oleksyk TK, Wolfsberger WW, Chhugani K, et al., Mooney JA, et al. Challenges and recommendations in establishing national human diversity genomic projects. Nat Methods. 2026 Jul;23(7):1261–1266. doi: 10.1038/s41592-026-03131-9.
Nataneli S, Karatas AL, Ferrari T, Patel RA, Mooney JA. Analytical expectations for ancestry junction accumulation in admixed genomes. Genetics. 2026 Jun 3;233(2):iyag062. doi: 10.1093/genetics/iyag062.
Agranat-Tamir L, Agwamba KD, Mooney JA, & Rosenberg NA. Shared ancestors and the birthday problem. The American Statistician. 2026 Feb 10;1–10. doi: 10.1080/00031305.2025.2595972.

2025
Akopyan M, Genchev M, Armstrong EE, Mooney JA. Reference genome choice compromises population genetic analyses. Cell. 2025 Nov 26;188(24):6939–6952.e11. doi: 10.1016/j.cell.2025.08.034. PDF
Sherman CA&, Nataneli S&, Claw KG, Mooney JA. Echoes of eugenics: confronting its effects in indigenous genomics. Genetics. 2025 Oct 8;231(2):iyaf127. doi: 10.1093/genetics/iyaf127.
Ferrari T, Feng S, Zhang X+, Mooney J+. Parameter scaling in population genetics simulations may introduce unintended background selection: considerations for scaled simulation design. Genome Biol Evol. 2025 May 30;17(6):evaf097. doi: 10.1093/gbe/evaf097.

2024
Kreger J, Mooney JA, Shibata D, & MacLean AL. Developmental hematopoietic stem cell variation explains clonal hematopoiesis later in life. Nat Commun. 2024 Nov 26;15(1):10268. doi: 10.1038/s41467-024-54711-2.
Armstrong EE&, Li C&, Campana MG, Ferrari T, et al., Mooney JA. A pipeline and recommendations for population and individual diagnostic SNP selection in non-model species. Mol Ecol Resour. 2025 Apr;25(3):e14048. doi: 10.1111/1755-0998.14048.
Armstrong EE+,&, Mooney JA+,&, Solari KA, et al., Hadly EA+. Unraveling the genomic diversity and admixture history of captive tigers in the United States. Proc Natl Acad Sci USA. 2024 Sep 24;121(39):e2402924121. doi: 10.1073/pnas.2402924121.
Armstrong EE, Bissell KL, Fatima HS, et al., Mooney JA+ & Mychajliw AM+. Chromosome-level assembly of the gray fox (Urocyon cinereoargenteus) confirms the basal loss of PRDM9 in Canidae. G3 (Bethesda). 2024 Apr 3;14(4):jkae034. doi: 10.1093/g3journal/jkae034.
Agranat-Tamir L, Mooney JA, Rosenberg NA. Counting the genetic ancestors from source populations in members of an admixed population. Genetics. 2024 Apr 3;226(4):iyae011. doi: 10.1093/genetics/iyae011.

2023
Mooney JA, Agranat-Tamir L, Pritchard JK, Rosenberg NA. On the number of genealogical ancestors tracing to the source groups of an admixed population. Genetics. 2023 Jul 6;224(3):iyad079. doi: 10.1093/genetics/iyad079.
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. 2023 Jan 4;40(1):msac277. doi: 10.1093/molbev/msac277.

2021
Mooney JA, Yohannes A, Lohmueller KE. The impact of identity by descent on fitness and disease in dogs. Proc Natl Acad Sci USA. 2021 Apr 20;118(16):e2019116118. doi: 10.1073/pnas.2019116118.

2019
Sura SA, Smith LL, Ambrose MR, et al., Mooney JA, et al. Ten simple rules for giving an effective academic job talk. PLoS Comput Biol. 2019 Jul 25;15(7):e1007163. doi: 10.1371/journal.pcbi.1007163.

2018
Mooney JA&, Huber CD&, Service S, et al. Understanding the hidden complexity of Latin American population isolates. Am J Hum Genet. 2018 Nov 1;103(5):707–726. doi: 10.1016/j.ajhg.2018.09.013.

The Team


Jazlyn Mooney

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. CV

Jazlyn completed her undergraduate degree at the University of New Mexico studying human evolution with Jeffrey Long in Anthropology. She completed her PhD in Human Genetics at UCLA in 2020 under the advisement of Kirk Lohmueller, studying 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.

When I am not in lab, I enjoy record collecting and going to concerts.

Postdoctoral Fellows

Hayden Davis

Hayden Davis (he/him)

Postdoctoral Fellow

Hayden recently completed a joint postdoctoral appointment at the University of Washington and NOAA, where he studied the genetic basis of disease resistance and life-history traits in salmonids and developed computational approaches for modeling temporal effective population size. He completed his PhD at the University of Washington, using population genetics and phylogenetic methods to investigate gene flow, species boundaries, and population structure in non-model species. Currently, he is working on inferring the demography of Channel Island foxes using ancestral recombination graphs.

I plan to visit all US national parks in my lifetime — currently at 25/63.
Matt Beaumont

Matt Beaumont (he/him)

Postdoctoral Fellow

Matt completed his MSc in Biotechnology at Nottingham Trent University and his PhD at the Institute of Population Genetics at Veterinärmedizinische Universität Wien, where he studied transposable elements and their invasion dynamics in Drosophila. He specializes in pipeline development and bridging the gap between experimental and computational biology. Matt is interested in better understanding complex non-additive trait architecture in human genetics.

I have lived on three different continents.

Graduate Students

Shirin Nataneli

Shirin Nataneli (she/her)

Graduate student, CBB Program

Shirin is broadly interested in population genetics and evolution. Currently, she is exploring how we can better model complex admixture scenarios and infer demography using local ancestry information.

I've collected snow globes from every place I've traveled and my favorite animal is a sheep.
Aydin Loid Karatas

Aydin Loid Karatas (he/him)

Graduate student, CBB Program

Aydin is excited about the intersection of modeling human disease and large-scale simulation frameworks. His work addresses how admixture affects the distribution of identity-by-descent segments, and he is building a detailed demographic model of admixed populations from North America.

I own (and use) several film cameras and older digicams.
Shengmiao Huang

Shengmiao (Morgan) Huang (she/her)

Graduate student, CBB Program

Shengmiao is interested in developing mathematical models for conservation biology. Her work focuses on extending mathematical models to better understand the genealogical and demographic history of admixed populations.

Water is my natural habitat. And I have the best cat in the world.
Tessa Ferrari

Tessa Ferrari (she/her)

Graduate student, CBB Program · Simons Graduate Fellow

Tessa graduated from the Quantitative Biology undergraduate program, had a stint as our lab Research Technician, and is now in our CBB PhD program. She is interested in building and using large-scale simulation frameworks to infer demography, and developing methods to quantify recessive mutational load while controlling for structure.

In my free time I'm a competitive hip hop and open style dancer!

Postbac Researcher

Matthew Genchev

Matthew Genchev

Postbac Researcher

Matthew was an undergraduate in the Quantitative Biology program with an interest in modeling recombination and demography in non-human populations. He is currently reconstructing the demographic history of Channel Island foxes. Matthew was a Provost Undergraduate Research Fellow, SURF, and URAP Fellow.

I won $20 from a scratch off ticket one time.

Alumni

Tina Lasisi

Tina Lasisi (she/her)

Former Postdoctoral Fellow → Assistant Professor, University of Michigan (Anthropology)

Tina's background and interests fall within Biological Anthropology and complex trait genetics, specifically the evolution of human variation in pigmentation and scalp hair. Check out her website and PBS mini-series Why Am I Like This?

I have a standard poodle.
Maria Akopyan

Maria Akopyan (she/her)

Former Postdoctoral Fellow → Assistant Professor, Rice University (BioSciences)

Maria completed her PhD at Cornell studying gene flow and adaptation in Atlantic silversides. While in our group, she explored how reference bias affects demographic inference in Canidae using whole genome sequence data from Mainland foxes. She was also an NSF PRFB postdoc in the Samuk and Armstrong labs at UCR.

I like to paint and dance!
Mengdi Chai

Mengdi (Kim) Chai

Former Undergraduate → Harvard Master's → Eli Lilly

Mengdi graduated with honors from the Quantitative Biology program. As a WiSE Undergraduate Fellow, she used identity-by-descent segments to identify genes associated with coat color in tigers and track their ancestral origins.

I have one hamster and he is cute!
Anika Shrivastava

Anika Shrivastava

Former Undergraduate → Software Engineer, Capital One

Anika worked on quantifying regions of the genome that harbor potential recessive lethal mutations by layering information from multiple types of genomic annotations. She was a Provost Undergraduate Research Fellow.

I have been playing the piano for 15 years and have a minor in musical studies at USC.
Chenyang Li

Chenyang (Julie) Li

Former Undergraduate → PhD student, Emory (Population Biology, Ecology, and Evolution)

Julie created the population assignment algorithm for mPCRselect. She was a WiSE Undergraduate Fellow, graduated with honors, and received the USC Discovery Scholar Distinction.

I've never dyed my hair. My reddish/brown hair color is my natural hair color.
Mahija Mogalipuvvu

Mahija Mogalipuvvu

Former Undergraduate → preparing for medical school

Mahija co-led our QBIO 490 section on Multi-Omic Data Analysis. In the lab, she worked on better understanding the allele frequency spectra of cancer-associated variants.

I love chocolate milk.
Peyton Hall

Peyton Hall

Former Undergraduate → Medical student, Howard University

Peyton's project layered information from multiple types of genomic annotations to explore whether there were differences in annotation distributions across ancestries, extending our work on captive tigers.

I am a volunteer birth doula.
Joseph Caluya

Joseph Caluya

Former Undergraduate → continuing research

Joseph worked on data from TCGA, seeking to understand shared and population-specific differential expression in variants associated with breast cancer.

In my free time I like to needle felt animals, write/read poetry, and try out different skincare products.
Aiko Abo Dominguez

Aiko Abo Dominguez

Former Undergraduate → PhD student, University of Maryland (MEES Program)

Co-advised with Dr. Regina Wetzer at LA NHM, Aiko studied the Los Angeles population of Ligia using macroevolutionary and population genetic analyses. She was a URAP Fellow and recipient of both the NSF GRFP and a Fulbright Research Award in Argentina.

I pick up a new hobby every winter break — this year it was beading jewelry!
Sydney Bruce

Sydney Bruce

Former Undergraduate → EMT

Sydney worked on creating a recombination map for captive tigers in North America. She was a WiSE Undergraduate Fellow and a URAP Fellow.

I work as an EMT during the summers!
Bruk Tefera

Bruk Tefera

Former Undergraduate

Bruk is interested in bioinformatics, cancer genomics, and machine learning.

I've worked more than 7 different jobs in my lifetime so far.

Classes Taught


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

Fall 2020

Fiat Lux seminar 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 taught at SFSU. Students' scientific curiosity was 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 co-taught with Dr. Remo Rohs at USC. The introductory seminar for students taking the QBIO major — ideally taken as a freshman or after transferring into the 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, 2023, 2024, 2025, 2026

QBIO capstone course co-taught with Dr. Doc Edge at USC. An upper-division course introducing quantitative biologists to central ideas in the mathematical modeling and statistical analysis of genetic variation. Topics from evolutionary genetics and medical genetics are explored using a mix of math, simulation, and data analysis — including genetic drift, natural selection, mutation, migration, population structure, and study designs for learning about genotype-phenotype relationships. Syllabus


QBIO 115w flyer

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

Spring 2024 & Spring 2025

Dornsife GE course created and taught at USC. Biology, medicine, and statistics are each deeply rooted in 19th-century eugenics. This course critically reflects on the origins of each field and explores modern research practices that offer hope for an equitable future, using a mixture of readings, presentations, and discussions. Syllabus


Outreach and Science Communication


UCLA Association for Multi-Ethnic Bioscientists Advancement (AMEBA)

Co-founder

During graduate school I co-founded AMEBA alongside 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, 2020 and 2022

Workshops covering basic statistics and plotting using Tidyverse for computational biology. Presentation (2022)


Ethics in Genetics and Genomics — Paradigm Podcast

Interviewed by former QBIO student Wade Boohar for the Paradigm Podcast (Shift SC, USC). We explored ethical considerations when dealing with population genetics and large-scale genomic studies.

Genetics, Ethics, and the Responsibility of Science

What are the origins of genetics and what are the ethical considerations of large-scale genomic studies?


Elephant in the Room — Natural History Museum of Los Angeles

Panel discussion for NHM's public series exploring bold and sometimes controversial topics. Our panel explored both established facts and emerging mysteries about dire wolves, addressing misconceptions and exciting developments in biotechnology, sequencing, and de-extinction.

Dire Wolves: Still Extinct?

What do we know about dire wolves? Are they still extinct?


Lab in the News


Reference genome choice compromises population genetic analyses

News about our work on using non-species-matched reference genomes, led by former postdoc Dr. Maria Akopyan.


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

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


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 with Dr. Noah Rosenberg.