Chris Bailey-Kellogg

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Identifying residue coupling relationships within a protein family can provide important insights into the family's evolutionary record, and has significant applications in analyzing and optimizing sequence-structure-function relationships. We present the first algorithm to infer an undirected graphical model representing residue coupling in protein(More)
Active data mining is becoming prevalent in applications requiring focused sampling of data relevant to a high-level mining objective. It is especially pertinent in scientific and engineering applications where we seek to characterize a configuration space or design space in terms of spatial aggregates, and where data collection can become costly. Examples(More)
High-throughput, data-directed computational protocols for <i>Structural Genomics</i> (or <i>Proteomics</i>) are required in order to evaluate the protein products of genes for structure and function at rates comparable to current gene-sequencing technology. This paper presents the JIGSAW algorithm, a novel high-throughput, automated approach to protein(More)
Spatial aggregation is a framework for organizing computations around image-like, analogue representations of physical processes in data interpretation and control tasks. It conceptualizes common computational structures in a class of implemented problem solvers for difficult scientific and engineering problems. It comprises a mechanism, a language, and a(More)
Reasoning about spatial data is a key task in many applications , including geographic information systems, meteorological and fluid flow analysis, computer-aided design, and protein structure databases. Such applications often require the identification and manipulation of qualitative spatial representations , for example, to detect whether one " object "(More)
Nuclear magnetic resonance (NMR) spectroscopy allows scientists to study protein structure, dynamics, and interactions in solution. A necessary first step for such applications is determining the resonance assignment, mapping spectral data to atoms and residues in the primary sequence. Automated resonance assignment algorithms rely on information regarding(More)
This paper develops an approach for designing protein variants by sampling sequences that satisfy residue constraints encoded in an undirected probabilistic graphical model. Due to evolutionary pressures on proteins to maintain structure and function, the sequence record of a protein family contains valuable information regarding position-specific residue(More)
Therapeutic proteins continue to yield revolutionary new treatments for a growing spectrum of human disease, but the development of these powerful drugs requires solving a unique set of challenges. For instance, it is increasingly apparent that mitigating potential anti-therapeutic immune responses, driven by molecular recognition of a therapeutic protein's(More)
Many important science and engineering applications, such as regulating the temperature distribution over a semiconductor wafer and controlling the noise from a photocopy machine, require interpreting distributed data and designing decentralized controllers for spatially distributed systems. Developing effective computational techniques for representing and(More)