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Using Multi-Trait Genome-Wide Association Summary Statistics to Understand Genetic Architecture and Pleiotropy: Novel Methods and Translational Applications to Cancer
No full textGenetic epidemiology is a subject that studies how genetic factors impact the health and
disease status among populations. With the development of modern statistics and data science,
statistical and big-data techniques are increasingly used to study genetic epidemiology.
In this thesis, I developed multiple statistical methods to tackle the challenges in the
field. These challenges include understanding the genetic architectures of complex traits for a
better study design in the future, prioritizing genetic variants and genes that are potentially
associated with one trait or multiple traits (i.e., pleiotropic), and exploring the shared biological
pathways across multiple genetically correlated traits. These methods are built upon multi-trait
genome-wide association summary statistics and leverage the concept of cross-trait meta-
analysis. The methods are also computationally efficient and can be applied to a wide range of
polygenic phenotypes.
I applied these novel methods to study the genetic profiles of twelve cancer types and
have made a series of consequential discoveries including but not limited to novel pleiotropic
variants and regions, novel cancer-associated genes, and shared cancer-related biological
pathways. Among them, some have already been validated through molecular genetics
experiments, and others offer an opportunity for further study in the field of genetic research.Biostatistic
Towards Multimodal Foundation Models in Molecular Cell Biology
No full textThe rapid advent of high-throughput omics technologies has created an exponential growth in biological data, often outpacing our ability to derive molecular insights. Large-language models have shown a way out of this data deluge in natural language processing by integrating massive data sets into a joint model with manifold downstream use cases. Here, we envision developing multimodal foundation models, pretrained on diverse omics datasets, including genomics, transcriptomics, epigenomics, proteomics, metabolomics, and spatial profiling. These models are expected to exhibit unprecedented potential for characterizing the molecular states of cells across a broad continuum, thereby facilitating the creation of holistic maps of cells, genes, and tissues. Context-specific transfer learning of the foundation models can empower diverse applications from novel cell type recognition, biomarker discovery, gene regulation inference, to in silico perturbations. This new paradigm could launch an era of AI-empowered analyses, one that promises to unravel the intricate complexities of molecular cell biology, to support experimental design, and, more broadly, to profoundly extend our understanding of life sciences.Stem Cell and Regenerative BiologyProo
Kathryn Schwartz, Book Historian of the Modern Middle East
No full textThis article presents the contributions of Dr. Kathryn Schwartz (1984-2022), book historian of the modern Middle East. Her study of the origins and impact of the printing press in late Ottoman Egypt has challenged some long-standing assumptions in the historiography. She has also put into question the long-held belief that Ottomans banned printing. More broadly, her work has challenged Eurocentric approaches to this topic and has innovated by combining material and intellectual history.Near Eastern Languages and CivilizationsCommittee on the Study of ReligionAccepted Manuscrip
Insurgent Geology: Dismantling Alaska’s Petrostate
No full textSet in Alaska in 2051, Insurgent Geology is a post-oil speculative fiction about hydrocarbons, fossils, power and people. The story blows up pipelines and takes care of the soil and, shifting from deep time to a speculative near future, it calls for Arctic insurrection, environmental geopoetics and social justice. The project critiques geology as an extractive and neocolonial discipline and activity through alternative geosocial practices, mineral kinships, and geoaesthetics in a series of design interventions along the infamous Trans-Alaska Pipeline System.Accepted Manuscrip
Timed chromatin invasion during mitosis governs prototype foamy virus integration site selection and infectivity
No full textSelection of a suitable chromatin environment during retroviral integration is a tightly regulated process. Most retroviruses, including spumaretroviruses, require mitosis for nuclear entry. However, whether intrinsic chromatin dynamics during mitosis modulates retroviral genome invasion is unknown. Previous work uncovered critical interactions of prototype foamy virus (PFV) Gag with nucleosomes via a highly conserved arginine anchor residue. Yet, the regulation of Gag-chromatin interaction and its functional consequences for spumaretrovirus biology remain obscure. Here, we investigated the kinetics of chromatin binding by Gag during mitosis and proviral integration in synchronized cells. We showed that alteration of Gag affinity for nucleosome binding induced untimely chromatin tethering during mitosis, decreased infectivity, and redistributed viral integration sites to markers associated with late replication timing of chromosomes. Mutant Gag proteins were, moreover, defective in their ability to displace the histone H4 tail from the nucleosome acidic patch of highly condensed chromatin. These data indicate that the chromatin landscape during Gag-nucleosome interactions is important for PFV integration site selection and that spumaretroviruses evolved high-affinity chromatin binding to overcome early mitosis chromatin condensation.Version of Recor
How the SO(5) k=1 WZW near-CFT3 explains the underdoped regime of the cuprate high temperature superconductors
No full textPhysicsAuthor's Origina
FL* theory of the pseudogap, d-wave superconductivity, and charge order in the cuprates
No full textPhysicsAuthor's Origina
12 Million and Two Black Voices: The Ethnographic Convergence of Richard Wright and Kendrick Lamar
No full text12 Million and Two Black Voices: The Ethnographic Convergence of Richard Wright and Kendrick Lamar investigates how two Black artists, separated by generations and working in different media, converge in their roles as cultural ethnographers. Through a comparative analysis of Wright’s prose and photography and Lamar’s lyrical narratives, this study interrogates the representation of systemic racism, historical trauma, urban confinement, and the formation of Black masculinity. Drawing on ethnographic theory, literary criticism, and cultural studies, the thesis examines the formal strategies—linguistic, visual, and sonic—by which both artists articulate the lived realities of Black America. Each chapter traces thematic and methodological recursions between Wright’s mid-twentieth-century portraits of racial oppression and Lamar’s twenty-first-century sonic geographies of resistance. Ultimately, the research argues that their works not only document enduring structures of racial inequality but also mobilize expressive culture as a form of critique, reclamation, and cultural survival. This analysis contributes to broader conversations on race, representation, and resistance, demonstrating the capacity of art across time and form to challenge ethnographic instability and assert agency.Extension Studie