Honors & Awards

  • Stanford Graduate Fellowship, Stanford University

Education & Certifications

  • BSE, Princeton University, Computer Science (2017)

All Publications

  • Childhood environment influences epigenetic age and methylation concordance of a CpG clock locus in British-Bangladeshi migrants. Epigenetics Stoger, R., Choi, M., Begum, K., Leeman, G., Emes, R. D., Melamed, P., Bentley, G. R. 2022: 1-10


    Migration from one location to another often comes with a change in environmental conditions. Here, we analysed features of DNA methylation in young, adult British-Bangladeshi women who experienced different environments during their childhoods: a) migrants, who grew up in Bangladesh with exposure to comparatively higher pathogen loads and poorer health care, and b) second-generation British-Bangladeshis, born to Bangladeshi parents, who grew up in the UK. We used buccal DNA to estimate DNA methylation-based age (DNAm age) from 14 migrants and 11 second-generation migrants, aged 18-35years. 'AgeAccel,' a measure of DNAm age, independent of chronological age, showed that the group of women who spent their childhood in Bangladesh had higher AgeAccel (P=0.028), compared to their UK peers. Since epigenetic clocks have been proposed to be associated with maintenance processes of epigenetic systems, we evaluated the preference for concordant DNA methylation at the luteinizing hormone/choriogonadotropin receptor (LHCGR/LHR) locus, which harbours one of the CpGs contributing to Horvath's epigenetic clock. Measurements on both strands of individual, double-stranded DNA molecules indicate higher stability of DNA methylation states at this LHCGR/LHR locus in samples of women who grew up in Bangladesh. Together, our two independent analytical approaches imply that childhood environments may induce subtle changes that are detectable long after exposure occurred, which might reflect altered activity of the epigenetic maintenance system or a difference in the proportion of cell types in buccal tissue. This exploratory work supports our earlier findings that adverse childhood environments lead to phenotypic life history trade-offs.

    View details for DOI 10.1080/15592294.2022.2153511

    View details for PubMedID 36495138

  • Mechanosensory input during circuit formation shapes Drosophila motor behavior through patterned spontaneous network activity. Current biology : CB Carreira-Rosario, A., York, R. A., Choi, M., Doe, C. Q., Clandinin, T. R. 2021


    Neural activity sculpts circuit wiring in many animals. In vertebrates, patterned spontaneous network activity (PaSNA) generates sensory maps and establishes local circuits.1-3 However, it remains unclear how PaSNA might shape neuronal circuits and behavior in invertebrates. Previous work in the developing Drosophila embryo discovered intrinsic muscle activity that did not require synaptic transmission, and hence was myogenic, preceding PaSNA.4-6 These studies, however, monitored muscle movement, not neural activity, and were therefore unable to observe how myogenic activity might relate to subsequent neural network engagement. Here we use calcium imaging to directly record neural activity and characterize the emergence of PaSNA. We demonstrate that the spatiotemporal properties of PaSNA are highly stereotyped across embryos, arguing for genetic programming. Neural activity begins well before it becomes patterned, emerging during the myogenic stage. Remarkably, inhibition of mechanosensory input, as well as inhibition of muscle contractions, results in premature and excessive PaSNA, demonstrating that muscle movement serves as a brake on this process. Finally, transient mechanosensory inhibition during PaSNA, followed by quantitative modeling of larval behavior, shows that mechanosensory modulation during development is required for proper larval foraging. This work provides a foundation for using the Drosophila embryo to study the role of PaSNA in circuit formation, provides mechanistic insight into how PaSNA is entrained by motor activity, and demonstrates that spontaneous network activity is essential for locomotor behavior. These studies argue that sensory feedback during the earliest stages of circuit formation can sculpt locomotor behaviors through innate motor learning.

    View details for DOI 10.1016/j.cub.2021.08.022

    View details for PubMedID 34478644

  • Accelerated epigenetic ageing and altered stability of DNA methylation detected in adult British-Bangladeshi women exposed to elevated infectious disease loads in childhood Stager, R., Leeman, G., Choi, M., Emes, R. D., Begum, K., Melamed, P., Bentley, G. R. WILEY. 2020: 277
  • Cortical Observation by Synchronous Multifocal Optical Sampling Reveals Widespread Population Encoding of Actions. Neuron Kauvar, I. V., Machado, T. A., Yuen, E. n., Kochalka, J. n., Choi, M. n., Allen, W. E., Wetzstein, G. n., Deisseroth, K. n. 2020


    To advance the measurement of distributed neuronal population representations of targeted motor actions on single trials, we developed an optical method (COSMOS) for tracking neural activity in a largely uncharacterized spatiotemporal regime. COSMOS allowed simultaneous recording of neural dynamics at ∼30 Hz from over a thousand near-cellular resolution neuronal sources spread across the entire dorsal neocortex of awake, behaving mice during a three-option lick-to-target task. We identified spatially distributed neuronal population representations spanning the dorsal cortex that precisely encoded ongoing motor actions on single trials. Neuronal correlations measured at video rate using unaveraged, whole-session data had localized spatial structure, whereas trial-averaged data exhibited widespread correlations. Separable modes of neural activity encoded history-guided motor plans, with similar population dynamics in individual areas throughout cortex. These initial experiments illustrate how COSMOS enables investigation of large-scale cortical dynamics and that information about motor actions is widely shared between areas, potentially underlying distributed computations.

    View details for DOI 10.1016/j.neuron.2020.04.023

    View details for PubMedID 32433908

  • Epigenetic memory via concordant DNA methylation is inversely correlated to developmental potential of mammalian cells PLOS GENETICS Choi, M., Genereux, D. P., Goodson, J., Al-Azzawi, H., Allain, S. Q., Simon, N., Palasek, S., Ware, C. B., Cavanaugh, C., Miller, D. G., Johnson, W. C., Sinclair, K. D., Stoger, R., Laird, C. D. 2017; 13 (11): e1007060


    In storing and transmitting epigenetic information, organisms must balance the need to maintain information about past conditions with the capacity to respond to information in their current and future environments. Some of this information is encoded by DNA methylation, which can be transmitted with variable fidelity from parent to daughter strand. High fidelity confers strong pattern matching between the strands of individual DNA molecules and thus pattern stability over rounds of DNA replication; lower fidelity confers reduced pattern matching, and thus greater flexibility. Here, we present a new conceptual framework, Ratio of Concordance Preference (RCP), that uses double-stranded methylation data to quantify the flexibility and stability of the system that gave rise to a given set of patterns. We find that differentiated mammalian cells operate with high DNA methylation stability, consistent with earlier reports. Stem cells in culture and in embryos, in contrast, operate with reduced, albeit significant, methylation stability. We conclude that preference for concordant DNA methylation is a consistent mode of information transfer, and thus provides epigenetic stability across cell divisions, even in stem cells and those undergoing developmental transitions. Broader application of our RCP framework will permit comparison of epigenetic-information systems across cells, developmental stages, and organisms whose methylation machineries differ substantially or are not yet well understood.

    View details for DOI 10.1371/journal.pgen.1007060

    View details for Web of Science ID 000416836900008

    View details for PubMedID 29107996

    View details for PubMedCentralID PMC5690686