
Multicellular organisms consist of cells of many different types that are established during development. Each type of cell is characterized by the unique combination of expressed gene products as a result of spatiotemporal gene regulation. Currently, a fundamental challenge in regulatory biology is to elucidate the gene expression controls that generate the complex body plans during development. Recent advances in high-throughput biotechnologies have generated spatiotemporal expression patterns for thousands of genes in the model organism fruit fly Drosophila melanogaster. Existing qualitative methods enhanced by a quantitative analysis based on computational tools we present in this paper would provide promising ways for addressing key scientific questions.
Results
We develop a set of computational methods and open source tools for identifying co-expressed embryonic domains and the associated genes simultaneously. To map the expression patterns of many genes into the same coordinate space and account for the embryonic shape variations, we develop a mesh generation method to deform a meshed generic ellipse to each individual embryo. We then develop a co-clustering formulation to cluster the genes and the mesh elements, thereby identifying co-expressed embryonic domains and the associated genes simultaneously. Experimental results indicate that the gene and mesh co-clusters can be correlated to key developmental events during the stages of embryogenesis we study. The open source software tool has been made available at http://compbio.cs.odu.edu/fly/.
Conclusions
Our mesh generation and machine learning methods and tools improve upon the flexibility, ease-of-use and accuracy of existing methods.

Learning Sparse Representations for Fruit-Fly Gene Expression Pattern Image Annotation and Retrieval
Fruit fly embryogenesis is one of the best understood animal development systems, and the spatiotemporal gene expression dynamics in this process are captured by digital images. Analysis of these high-throughput images will provide novel insights into the functions, interactions, and networks of animal genes governing development. To facilitate comparative analysis, web-based interfaces have been developed to conduct image retrieval based on body part keywords and images. Currently, the keyword annotation of spatiotemporal gene expression patterns is conducted manually. However, this manual practice does not scale with the continuously expanding collection of images. In addition, existing image retrieval systems based on the expression patterns may be made more accurate using keywords.
Results
In this article, we adapt advanced data mining and computer vision techniques to address the key challenges in annotating and retrieving fruit fly gene expression pattern images. To boost the performance of image annotation and retrieval, we propose representations integrating spatial information and sparse features, overcoming the limitations of prior schemes.
Conclusions
We perform systematic experimental studies to evaluate the proposed schemes in comparison with current methods. Experimental results indicate that the integration of spatial information and sparse features lead to consistent performance improvement in image annotation, while for the task of retrieval, sparse features alone yields better results.

Drosophila melanogaster has been established as a model organism for investigating the developmental gene interactions. The spatio-temporal gene expression patterns of Drosophila melanogaster can be visualized by in situ hybridization and documented as digital images. Automated and efficient tools for analyzing these expression images will provide biological insights into the gene functions, interactions, and networks. To facilitate pattern recognition and comparison, many web-based resources have been created to conduct comparative analysis based on the body part keywords and the associated images. With the fast accumulation of images from high-throughput techniques, manual inspection of images will impose a serious impediment on the pace of biological discovery. It is thus imperative to design an automated system for efficient image annotation and comparison.
Results
We present a computational framework to perform anatomical keywords annotation for Drosophila gene expression images. The spatial sparse coding approach is used to represent local patches of images in comparison with the well-known bag-of-words (BoW) method. Three pooling functions including max pooling, average pooling and Sqrt (square root of mean squared statistics) pooling are employed to transform the sparse codes to image features. Based on the constructed features, we develop both an image-level scheme and a group-level scheme to tackle the key challenges in annotating Drosophila gene expression pattern images automatically. To deal with the imbalanced data distribution inherent in image annotation tasks, the undersampling method is applied together with majority vote. Results on Drosophila embryonic expression pattern images verify the efficacy of our approach.
Conclusion
In our experiment, the three pooling functions perform comparably well in feature dimension reduction. The undersampling with majority vote is shown to be effective in tackling the problem of imbalanced data. Moreover, combining sparse coding and image-level scheme leads to consistent performance improvement in keywords annotation.
In this essay, I set out to explore and analyze how Shirley Jackson’s The Haunting of Hill House, and the character of Eleanor Vance in particular, disrupts and redefines the traditional conventions of the Female Gothic within the context of the 20th century. I utilize Tania Modleski's gendering of Freud's theory of psychoanalysis in her exploration of the ‘Female Uncanny,’ arguing that the source of the Uncanny in the Female Gothic can be found in the "fear of being lost in the mother." I argue that Jackson's complex personal life, including her fraught relationship with her mother and her difficult marriage with literary critic Edgar Hyman, color her fiction and the primary motivations of her protagonist, Eleanor Vance. I also outline the traditional structure of the Gothic novel and the heroine's journey. With the necessary context provided, I then explain how Eleanor Vance’s character rejects these Gothic traditions and ushers in a new era of Female Gothic fiction.
This paper explores the intersection of female madness and Gothic space in four pieces of Gothic media: Jane Eyre written By Charlotte Brontë, "The Yellow Wallpaper" written by Charlotte Perkins Gilman, Carrie (1976) directed by Brian De Palma, and Midsommar (2016) directed by Ari Aster. In these texts, female characters find themselves driven “mad,” either by their own design or from outside influences. While the madness presents itself differently in each text, they all share common elements, especially in terms of Gothic space. Each text sees its madwoman affected by the environment around them whether it is explicitly stated in-text or not. Gothic space acts as both a metanarrative on the characters’ lives and emotions, and as literal, physical spaces that the characters inhabit and interact with. Oftentimes, what the character cannot express is told through the environment around her. Feelings of suffocation, misery, entrapment, and repression are represented in and through haunted homes, quasi-asylums, closets, schools, attics, and sun-lit fields. In analyzing all four texts individually and in relation to one another, this paper also argues for the presence of a paradox inherent in the cultural formation of female madness. In each text, all written/created across 200+ years, a common theme emerges. Though the expression of madness for the women in each text is a freeing and liberating experience, they also meet tragic and often violent ends. The madness exhibited in each text is both a response to and an expression of trauma - resulting in either victimization or villainization for the women who succumb to it. The end result depicts women who have been physically, mentally, and emotionally destroyed from their own madness. In freeing themselves, they unknowingly and unintentionally subject themselves to further pain and misery.