Structured clustering representations and methods

Rather than designing focused experiments to test individual hypotheses, scientists now commonly acquire measurements using massively parallel techniques, for post hoc interrogation. The resulting data is both high-dimensional and structured, in that observed variables are grouped and ordered into related subspaces, reflecting both natural physical organization and factorial experimental designs. Such structure encodes critical constraints and clues to interpretation, but typical unsupervised learning methods assume exchangeability and fail to account adequately for the structure of data in a flexible and interpretable way. In this thesis, I develop computational methods for exploratory analysis of structured high-dimensional data, and apply them to study gene expression regulation in Parkinson’s (PD) and Huntington’s diseases (HD). BOMBASTIC (Block-Organized, Model-Based, Tree-Indexed Clustering) is a methodology to cluster and visualize data organized in pre-specified subspaces, by combining independent clusterings of blocks into hierarchies. BOMBASTIC provides a formal specification of the block-clustering problem and a modular implementation that facilitates integration, visualization, and comparison of diverse datasets and rapid exploration of alternative analyses. These tools, along with standard methods, were applied to study gene expression in mouse models of neurodegenerative diseases, in collaboration with Dr. Myriam Heiman and Dr. Robert Fenster. In PD, I analyzed cell-type-specific expression following levodopa treatment to study mechanisms underlying levodopa-induced dyskinesia (LID). I identified likely regulators of the transcriptional changes leading to LID and implicated signaling pathways amenable to pharmacological modulation (Heiman, Heilbut et al, 2014). In HD, I analyzed multiple mouse models (Kuhn, 2007), cell-type specific profiles of medium spiny neurons (Fenster, 2011), and an RNA-Seq dataset profiling multiple tissue types over time and across an mHTT allelic series (CHDI, 2015). I found evidence suggesting that altered activity of the PRC2 complex significantly contributes to the transcriptional dysregulation observed in striatal neurons in HD

Sexo en las Márgenes : Troubling Sexuality Education in Colombia and Embracing a Critical Sexuality Education Framework towards Social Justice.

La presente tesis provee una crítica al Programa de Educación para la Sexualidad y Construcción de Ciudadanía en Colombia y examina contribuciones teóricas de pedagogías feministas, Queer y pedagogías críticas con el fin de crear alternativas para la práctica de una educación sexual fundamentada en la justicia social. El desarrollo de currículo y las ideologías que soportan prácticas educativas son explorados desde una perspectiva oposicional; la transformación curricular se posiciona como una alternativa para desarrollar una educación sexual inclusiva que centra en sus temáticas a las poblaciones LGBTI y a las mujeres. La educación sexual crítica conecta los aspectos individuales de la sexualidad con problemáticas sociales más amplias que nacen de la construcción social de la sexualidad. Finalmente, centrar discursos sobre el erotismo y el deseo grueso en educación sexual es crucial para crear espacios pedagógicos que fomenten la resistencia, la esperanza y la transformación personal y social.This thesis provides a critique of the Colombian Program for Sexuality Education and Construction of Citizenship, and examines theoretical contributions of feminist, queer, and critical pedagogies, in order to create alternatives for practicing a social justice-based sexuality education. Curriculum development and education ideologies are explored from an oppositional perspective, and curriculum transformation is provided as an alternative to develop an inclusive sexuality education that centers LGBTQ young adults and women. Critical sexuality education bridges the individual aspects of sexuality with larger social issues rooted in the social construction of sexuality. Finally, centering discourses of pleasure and thick desire in sexuality education put forth as crucial to build pedagogical spaces that foster resistance, hope, personal and social transformation

Chemical combination effects predict connectivity in biological systems

Efforts to construct therapeutically useful models of biological systems require large and diverse sets of data on functional connections between their components. Here we show that cellular responses to combinations of chemicals reveal how their biological targets are connected. Simulations of pathways with pairs of inhibitors at varying doses predict distinct response surface shapes that are reproduced in a yeast experiment, with further support from a larger screen using human tumour cells. The response morphology yields detailed connectivity constraints between nearby targets, and synergy profiles across many combinations show relatedness between targets in the whole network. Constraints from chemical combinations complement genetic studies, because they probe different cellular components and can be applied to disease models that are not amenable to mutagenesis. Chemical probes also offer increased flexibility, as they can be continuously dosed, temporally controlled, and readily combined. After extending this initial study to cover a wider range of combination effects and pathway topologies, chemical combinations may be used to refine network models or to identify novel targets. This response surface methodology may even apply to non-biological systems where responses to targeted perturbations can be measured

Large-scale mapping of human protein–protein interactions by mass spectrometry

Mapping protein–protein interactions is an invaluable tool for understanding protein function. Here, we report the first large-scale study of protein–protein interactions in human cells using a mass spectrometry-based approach. The study maps protein interactions for 338 bait proteins that were selected based on known or suspected disease and functional associations. Large-scale immunoprecipitation of Flag-tagged versions of these proteins followed by LC-ESI-MS/MS analysis resulted in the identification of 24 540 potential protein interactions. False positives and redundant hits were filtered out using empirical criteria and a calculated interaction confidence score, producing a data set of 6463 interactions between 2235 distinct proteins. This data set was further cross-validated using previously published and predicted human protein interactions. In-depth mining of the data set shows that it represents a valuable source of novel protein–protein interactions with relevance to human diseases. In addition, via our preliminary analysis, we report many novel protein interactions and pathway associations

Complex Reorganization and Predominant Non-Homologous Repair Following Chromosomal Breakage in Karyotypically Balanced Germline Rearrangements and Transgenic Integration

We defined the genetic landscape of balanced chromosomal rearrangements at nucleotide resolution by sequencing 141 breakpoints from cytogenetically-interpreted translocations and inversions. We confirm that the recently described phenomenon of “chromothripsis” (massive chromosomal shattering and reorganization) is not unique to cancer cells but also occurs in the germline where it can resolve to a karyotypically balanced state with frequent inversions. We detected a high incidence of complex rearrangements (19.2%) and substantially less reliance on microhomology (31%) than previously observed in benign CNVs. We compared these results to experimentally-generated DNA breakage-repair by sequencing seven transgenic animals, and revealed extensive rearrangement of the transgene and host genome with similar complexity to human germline alterations. Inversion is the most common rearrangement, suggesting that a combined mechanism involving template switching and non-homologous repair mediates the formation of balanced complex rearrangements that are viable, stably replicated and transmitted unaltered to subsequent generations