Ameet Soni

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Uch37 is a de-ubiquitylating enzyme that is functionally linked with the 26S proteasome via Rpn13, and is essential for metazoan development. Here, we report the X-ray crystal structure of full-length human Uch37 at 2.95 Å resolution. Uch37's catalytic domain is similar to those of all UCH enzymes characterized to date. The C-terminal extension is(More)
MOTIVATION One bottleneck in high-throughput protein crystallography is interpreting an electron-density map, that is, fitting a molecular model to the 3D picture crystallography produces. Previously, we developed ACMI (Automatic Crystallographic Map Interpreter), an algorithm that uses a probabilistic model to infer an accurate protein backbone layout.(More)
i For my parents, who nurtured my curiosity, and for Natalie, who now piques it. ii ABSTRACT Supervised machine learning is a branch of artificial intelligence concerned with automatically inducing predictive models from labeled data. Such learning approaches are useful for many interesting real-world applications, but particularly shine for tasks involving(More)
In line with institutions across the United States, the Computer Science Department at Swarthmore College has faced the challenge of maintaining a demographic composition of students that matches the student body as a whole. To combat this trend, our department has made a concerted effort to revamp our introductory course sequence to both attract and retain(More)
An important problem in high-throughput protein crystallography is constructing a protein model from an electron-density map. Previous work by some of this pa-per's authors [1] describes an automated approach to this otherwise time-consuming process. An important step in the previous method requires searching the density map for many small template(More)
Several methods for automatically constructing a protein model from an electron-density map require searching for many small protein-fragment templates in the density. We propose to use the spherical-harmonic decomposition of the template and the maps density to speed this matching. Unlike other template-matching approaches, this allows us to eliminate(More)
Peak-to-average power ratio (PAPR) is a major drawback in most multi-carrier communication techniques such as orthogonal frequency division multiplex system (OFDM). OFDM consists of lots of independent modulated subcarriers, as a result the amplitude of such a signal can have very large values. These large peaks increase the amount of inter-modulation(More)
ACKNOWLEDGMENTS First I would like to acknowledge my advisor, Jude Shavlik, for his patient guidance throughout. His careful attention and rigorous approach have not only helped to develop my work, but have also set the ideal example of how to perform meaningful professional research. Next, I would like to thank the other members of my thesis committee:(More)
We present a comparison of weak and distant supervision methods for producing proxy examples for supervised relation extraction. We find that knowledge-based weak supervision tends to outperform popular distance supervision techniques, providing a higher yield of positive examples and more accurate models.
A major bottleneck in high-throughput protein crystallography is producing protein-structure models from an electron-density map. In previous work, we developed Acmi, a probabilistic framework for sampling all-atom protein-structure models. Acmi uses a fully connected, pairwise Markov random field to model the 3D location of each non-hydrogen atom in a(More)