Principal Investigator. CV
Jim received his undergraduate degree in Biology and English Literature (Honors) from Binghamton University in upstate New York. He carried out his graduate work with Dr. Richard Myers in the Department of Genetics at Stanford University, where he contributed to the Human Genome Project and characterized the evolutionary history of protocadherin cluster genes in vertebrates. He received his Ph.D. in 2004. He did his postdoctoral work in Dr. Edward Rubin's lab at the Lawrence Berkeley National Laboratory and the U.S. Department of Energy Joint Genome Institute. At Berkeley, Jim developed methods to sequence and analyze ancient genomic DNA, providing the first insight into the Neanderthal genome. He also pioneered the discovery and analysis of uniquely human genetic changes that altered developmental gene regulation during human evolution. Jim joined the Yale Genetics faculty in 2007. He is currently the Albert E. Kent Professor of Genetics, with secondary appointments in Ecology and Evolutionary Biology and Neuroscience. He is also a member of the Kavli Institute for Neuroscience, the Yale Stem Cell Center, and Executive Director for Genome Sciences at the Yale Center for Genome Analysis. Jim was also named a NOMIS Foundation researcher in 2020.
Lab Manager
Ryan received his bachelor’s degree in chemistry from Western New England University and a master’s degree in biochemistry from the University of Connecticut (UCONN). Ryan has over a decade of experience in lab management, first working as a technician at the Yale Child Health Research Center in the Department of Pediatrics and later managing a multi-PI lab at the University of Florida. Upon returning to Connecticut, Ryan joined the Noonan lab as a lab manager in spring 2024.
Postdoctoral researcher
Marybeth is interested in the genetic underpinnings of brain evolution, neurodevelopment, and cell type specification. As a postdoctoral fellow in the Noonan lab, she has focused on parsing the genetics of cortical expansion in human evolution by utilizing multiple experimental fronts. She has developed humanized mouse models to study the impact of regulatory elements with uniquely human activity on gene expression and cortical development. In parallel, she has leveraged mouse models of neurodevelopmental conditions, such as autism spectrum disorder, and single-cell transcriptome analyses to establish how disrupting specific genes impacts individual cell types over time and contributes to these conditions. She is also designing complementary screens in 2D neural stem cells, the major proliferating cell type in the developing brain, to inform target selection for humanized mouse generation.
Marybeth completed her undergraduate studies at Mount Holyoke College and earned a PhD in physiology and neurobiology from the University of Connecticut in 2019. She joined the Noonan lab in 2020 and is supported by an F32 fellowship from NICHD.
Yu Ji
Postdoctoral researcher
Yu is interested in how human-specific cis-regulatory elements regulate gene expression during development, contributing to the evolution of uniquely human traits such as face and limb morphology. One such element, HACNS1, functions as a human-specific enhancer in the developing limb bud and pharyngeal arches. Using a humanized mouse model, Yu studies how HACNS1 regulates chondrogenic differentiation in human evolution.
Yu earned his Ph.D. in Biochemistry, Molecular Biology, and Cell and Developmental Biology from the University of California, Davis in 2021. During his graduate studies, he explored the role of Wnt signaling in determining the fate of neural crest cells.
Je Won Yang
Graduate student
Je Won joined the lab in 2022 and is investigating how post-transcriptional regulation, such as m6A RNA modifications, may play a role in differential gene expression during human and chimpanzee neurodevelopment. After graduating from Seoul National University in 2020, she developed an interest in RNA biology during her research internship at the Korea Advanced Institute of Science & Technology. Alongside her work in RNA biology, she recently initiated a project generating chimeric in vitro 3D somitogenesis models (somitoids) to tackle the question of heterochrony.
Aside from the lab, Je Won enjoys baking or playing the oboe in the orchestra.
Claudia Mimoso
YSM Science Fellow
Claudia is a YSM Science Fellow in the Department of Genetics, under the joint mentorship of the Noonan and Reinke Labs. At Yale, Claudia is developing an independent research program at the intersection of RNA biology, neurodevelopment, and human health.
Claudia first worked at NYU Langone Medical Center and The Rockefeller University where she studied gene expression changes in psoriasis. She went on to earn a B.S. in Biological Sciences at Cornell University, where she also studied the role of an RNA-binding protein in modulating allele-specific gene expression in the Soloway Lab. Claudia then completed her PhD in Karen Adelman’s Lab at Harvard Medical School, where she studied mechanisms of metazoan transcription. Now, as a YSM Science Fellow, she is interested in fundamental principles of gene expression during neurodevelopment and how disruptions in this process contribute to neurological diseases.
Reem Abu-Shamma
Graduate student
Reem joined the lab in 2023. She combines human and chimpanzee cortical organoids with genetic screening to investigate genomic regions and mechanisms involved in unique human brain development.
Reem received her bachelor’s degree from UCLA where she began research in the Sagasti Lab, studying skin morphogenesis in zebrafish with confocal microscopy. She later joined the Pathogen Genomics lab at KAUST, Saudi Arabia as a postgraduate intern, generating CRISPR knock-in lines in the malaria parasite. In 2023, she graduated with an M.S. in Bioinformatics from Johns Hopkins University, where she also worked as a research assistant in the lab of Tatiana Larman, and used 3D intestinal organoids to study colorectal cancer.
Reem is a member of the Yale Journal of Biology and Medicine (YJBM) editorial board and enjoys science writing for a general audience. Outside of the lab, she frequently travels, practices yoga, and plays tennis.
Graduate Student
Matheo is a Ph.D candidate in the Noonan Lab using neural organoid models to study gene regulatory differences between human and chimpanzee neurodevelopment. Matheo joined the Noonan Lab in 2020 after receiving a dual M.S. in Genetics and Computational Mathematical Sciences at Arizona State University. His dissertation work focuses on exploring the underlying gene regulatory mechanisms that contribute to uniquely human features of the thalamus and cortex by modeling their development using neural organoids derived from human and chimpanzee induced pluripotent stem cells (iPSCs). His work blends computational and experimental techniques, with a focus on high-dimensional analysis of single-cell sequencing data.
Outside his research, Matheo is involved in the Yale BBS Diversity and Inclusion Collective (YBDIC)
Lab Lab
Sophie is a Labrador Retriever/Vizsla mix (mostly Vizsla) who visits the Noonan Lab when the team needs a break from their hard work (or when Jim’s wife Laura is out of town). She was born in Houston, TX and adopted as a rescue dog in 2012. When she is not at the lab, she is helping kids with anxiety issues, learning differences and developmental disorders. And chasing squirrels.
Alumni
Postdocs and Associate Research Scientists
Sunghee Oh, Ph.D. Postdoctoral Associate, 2009-2011
Research project: Developing statistical methods for differential gene expression analysis using RNA-seq data
Current position: Instructor, Jeju National University, South Korea
Justin Cotney, Ph.D. Postdoctoral Associate, 2009-2013; Associate Research Scientist, 2013-2015
Research project: Identifying enhancers with human-specific function during limb development using comparative chromatin state mapping
Awards and honors: Rudolph J. Anderson postdoctoral fellowship; NIH K99 Pathway to Independence Award
Current position: Associate Professor of Genomic Science, Center for Craniofacial Innovation, Children’s Hospital of Philadelphia and the University of Pennsylvania
Jun Yin, Ph.D. Postdoctoral Associate, 2012-2015
Research project: Integrated computational analysis of gene expression and chromatin state in human development, evolution and disease
Awards and honors: Brown-Coxe Postdoctoral Fellowship, Yale University
Current position: Director, Bioinformatics Shared Resource at Sanford Burnham Prebys Medical Discovery Institute
Deena Emera, Ph.D. 2012-2017. Postdoctoral Associate, 2012-2017
Research project: Origin and evolution of developmental enhancers in the cortex
Awards and honors: NIH NRSA Postdoctoral Fellowship
Current position: Senior Scientist, Center for Reproductive Longevity and Equality, Buck Institute for Aging
Wei Niu, Ph.D. Associate Research Scientist, 2013-2016
Research project: Genome editing tools to elucidate neurodevelopmental gene regulatory networks associated with autism risk
Current position: Research Scientist, University of Michigan
Rebecca Muhle, M.D., Ph.D. Resident, Albert J. Solnit Integrated Adult and Child & Adolescent Psychiatry Program, Yale Child Study Center, 2011-2017; Instructor, Child Study Center, 2017-2019
Research project: The role of chromatin modifiers in autism spectrum disorder
Awards and honors: American Academy of Child and Adolescent Psychiatry Pilot Research Award; NIH K08 Mentored Clinical Scientist Research Career Award; Simons Foundation Bridge to Independence Award
Current position: Assistant Professor, Columbia University Department of Psychiatry and the New York State Psychiatric Institute
Martina Krenzer, M.D. Postdoctoral Fellow & Associate Research Scientist, 2016-2021
Awards: Postdoctoral Fellowship from the German Research Foundation
Current Position: Geriatrics/Neuropsychiatry/Behavioral Neurology Fellow. Mt. Sinai Hospital, New York
Severin Uebbing, Ph.D. Postdoctoral Fellow, Associate Research Scientist, 2016-2023
Awards: Postdoctoral Fellowship from the German Research Foundation
Current Position: Assistant Professor, Division of Genome Biology and Epigenetics, Utrecht University.
Graduate Students
Laura DeMare, PhD. 2008-2013
Thesis title: “A cohesin-mediated chromatin interactome during embryonic limb development.”
Awards and Honors: Carolyn Slayman Prize for Outstanding Ph.D. Thesis in Genetics
Current position: Product Manager, Single Cell Epigenomics, 10X Genomics
Jing Leng, Ph.D. 2009-2014.
Thesis title: “Studying the evolution of gene regulation using next-generation sequencing: computational methods and data integration.”
Joint with Mark Gerstein, Computational Biology and Bioinformatics
Current position: Bioinformatics Scientist, Illumina Inc.
Steven K. Reilly, Ph.D. 2010-2015.
Thesis title: “Evolutionary changes in promoter and enhancer activity during human corticogenesis.”
Awards and Honors: NSF Graduate Research Fellowship; Carolyn Slayman Prize for Outstanding Ph.D. Thesis in Genetics
Current position: Assistant Professor, Department of Genetics, Yale University
Richard Sarro, Ph.D. 2012-2017.
Thesis title: “Topologically directed disruption of a developmental enhancer through genome engineering.”
Current position: Corporate Development, Jazz Pharmaceuticals
Jake Gockley, Ph.D. 2013-2017.
Thesis title: “Investigations into the genetic foundations of sex bias in Autism Spectrum Disorders and evolution of non-coding regulatory elements.”
Current Position: Principal Data Scientist, Regeneron Pharmaceuticals
Evan Geller, Ph.D. 2014-2019
Thesis title: “Massively parallel genetic disruption of enhancers active during human corticogenesis.”
Awards and Honors: Autism Speaks Weatherstone Fellowship
Current Position: Research Scientist, Immunai Inc.
Emily Dutrow, Ph.D. 2015-2019
Thesis title: “Using humanized mouse models to study human evolution.”
Current Position: Principal Scientist, Zoetis
Acadia Kocher, Ph.D. 2016-2022
Thesis title: “CpG island turnover predicts evolutionary change in enhancer activity.”
Awards and Honors: NSF Graduate Research Fellowship
Current Position: Postdoctoral Fellow, Bas van Steensel group, Netherlands Cancer Institute
Kristina Yim, Ph.D. 2016-2022; temporary postdoc, 2023
Thesis title: “Metagene analysis reveals convergence of autism risk gene trajectories in the developing human and mouse cortex.”
Awards and Honors: NSF Graduate Research Fellowship
Mark Noble, Ph.D. 2018-2024
Thesis title: “Single-cell perturbation of Human Accelerated Regions in neural stem cells.”
Awards and Honors: NSF Graduate Research Fellowship
Current Position: Postdoctoral Fellow, Jürgen Knoblich group, Institute of Molecular Biotechnology, Vienna
Atreyo Pal, Ph.D. 2021-2025
Thesis title: “Resolving the three-dimensional interactome of Human Accelerated Regions during human and chimpanzee neurodevelopment.”
Awards and Honors: Lo Graduate Fellowship for Excellence in Stem Cell Research, Yale Stem Cell Center, 2024; Carolyn Slayman Prize for Outstanding Ph.D. Thesis in Genetics
Current Position: Senior Scientist, Illumina AI Lab
Postgraduate and Undergraduate Students
Sarah Abdallah, Honors thesis student, 2013-2014
Thesis title: “Identifying target genes of the autism-implicated transcription factor NFIA.”
Awards and Honors: HHMI-ASHG Medical Research Fellows Award
Current position: Resident, Albert J. Solnit Integrated Adult and Child & Adolescent Psychiatry Program, Yale Child Study Center (Tom Fernandez, Research Mentor)
Britt Bistis, Undergraduate Research Student, 2018-2020; Honors thesis student, 2020-2021
Awards and Honors: Yale College Dean’s Research Fellowship, 2020
Current position: PhD graduate student, Columbia University