Publications

Molecular Biology of the Cell

Davidson, George S.

Abstract not provided.

Davidson, George S.; Schoenwald, David A.

A multi-laboratory ontology construction effort during the summer and fall of 2009 prototyped an ontology for counterfeit semiconductor manufacturing. This effort included an ontology development team and an ontology validation methods team. Here the third team of the Ontology Project, the Data Analysis (DA) team reports on their approaches, the tools they used, and results for mining literature for terminology pertinent to counterfeit semiconductor manufacturing. A discussion of the value of ontology-based analysis is presented, with insights drawn from other ontology-based methods regularly used in the analysis of genomic experiments. Finally, suggestions for future work are offered.

Davidson, George S.

Abstract not provided.

Davidson, George S.

Realistic cell models could greatly accelerate our ability to engineer biochemical pathways and the production of valuable organic products, which would be of great use in the development of biofuels, pharmaceuticals, and the crops for the next green revolution. However, this level of engineering will require a great deal more knowledge about the mechanisms of life than is currently available. In particular, we need to understand the interactome (which proteins interact) as it is situated in the three dimensional geometry of the cell (i.e., a situated interactome), and the regulation/dynamics of these interactions. Methods for optical proteomics have become available that allow the monitoring and even disruption/control of interacting proteins in living cells. Here, a range of these methods is reviewed with respect to their role in elucidating the interactome and the relevant spatial localizations. Development of these technologies and their integration into the core competencies of research organizations can position whole institutions and teams of researchers to lead in both the fundamental science and the engineering applications of cellular biology. That leadership could be particularly important with respect to problems of national urgency centered around security, biofuels, and healthcare.

Human Factors

Dornburg, Courtney S.; Hendrickson, Stacey M.; Davidson, George S.

Abstract not provided.

Dornburg, Courtney S.; Adams, Susan S.; Hendrickson, Stacey M.; Davidson, George S.

An experiment was conducted comparing the effectiveness of individual versus group electronic brainstorming in order to address difficult, real world challenges. While industrial reliance on electronic communications has become ubiquitous, empirical and theoretical understanding of the bounds of its effectiveness have been limited. Previous research using short-term, laboratory experiments have engaged small groups of students in answering questions irrelevant to an industrial setting. The present experiment extends current findings beyond the laboratory to larger groups of real-world employees addressing organization-relevant challenges over the course of four days. Employees and contractors at a national security laboratory participated, either in a group setting or individually, in an electronic brainstorm to pose solutions to a 'wickedly' difficult problem. The data demonstrate that (for this design) individuals perform at least as well as groups in producing quantity of electronic ideas, regardless of brainstorming duration. However, when judged with respect to quality along three dimensions (originality, feasibility, and effectiveness), the individuals significantly (p<0.05) out-performed the group working together. When idea quality is used as the benchmark of success, these data indicate that work-relevant challenges are better solved by aggregating electronic individual responses, rather than electronically convening a group. This research suggests that industrial reliance upon electronic problem solving groups should be tempered, and large nominal groups might be the more appropriate vehicle for solving wicked corporate issues.

Dornburg, Courtney S.; Hendrickson, Stacey M.; Davidson, George S.

Abstract not provided.

Dornburg, Courtney S.; Hendrickson, Stacey M.; Forsythe, James C.; Bauer, Travis L.; Davidson, George S.

Abstract not provided.

Dornburg, Courtney S.; Hendrickson, Stacey M.; Davidson, George S.

An experiment was conducted comparing the effectiveness of individual versus group electronic brainstorming in addressing real-world 'wickedly difficult' challenges. Previous laboratory research has engaged small groups of students in answering questions irrelevant to an industrial setting. The current experiment extended this research to larger, real-world employee groups engaged in addressing organization-relevant challenges. Within the present experiment, the data demonstrated that individuals performed at least as well as groups in terms of number of ideas produced and significantly (p < .02) outperformed groups in terms of the quality of those ideas (as measured along the dimensions of originality, feasibility, and effectiveness).

Adams, Susan S.; Hendrickson, Stacey M.; Dornburg, Courtney S.; Davidson, George S.

Abstract not provided.

Dornburg, Courtney S.; Adams, Susan S.; Forsythe, James C.; Davidson, George S.

The present paper explores group dynamics and electronic communication, two components of wicked problem solving that are inherent to the national security environment (as well as many other business environments). First, because there can be no ''right'' answer or solution without first having agreement about the definition of the problem and the social meaning of a ''right solution'', these problems (often) fundamentally relate to the social aspects of groups, an area with much empirical research and application still needed. Second, as computer networks have been increasingly used to conduct business with decreased costs, increased information accessibility, and rapid document, database, and message exchange, electronic communication enables a new form of problem solving group that has yet to be well understood, especially as it relates to solving wicked problems.

Adams, Susan S.; Davidson, George S.; Dornburg, Courtney S.; Forsythe, James C.

An experiment is proposed which will compare the effectiveness of individual versus group brainstorming in addressing difficult, real world challenges. Previous research into electronic brainstorming has largely been limited to laboratory experiments using small groups of students answering questions irrelevant to an industrial setting. The proposed experiment attempts to extend current findings to real-world employees and organization-relevant challenges. Our employees will brainstorm ideas over the course of several days, echoing the real-world scenario in an industrial setting. The methodology and hypotheses to be tested are presented along with two questions for the experimental brainstorming sessions. One question has been used in prior work and will allow calibration of the new results with existing work. The second question qualifies as a complicated, perhaps even wickedly hard, question, with relevance to modern management practices.

Davidson, George S.; Dornburg, Courtney S.; Adams, Susan S.; Hendrickson, Stacey M.; Bauer, Travis L.; Forsythe, James C.

An experiment was conducted comparing the effectiveness of individual versus group electronic brainstorming in order to address difficult, real world challenges. While industrial reliance on electronic communications has become ubiquitous, empirical and theoretical understanding of the bounds of its effectiveness have been limited. Previous research using short-term, laboratory experiments have engaged small groups of students in answering questions irrelevant to an industrial setting. The current experiment extends current findings beyond the laboratory to larger groups of real-world employees addressing organization-relevant challenges over the course of four days. Findings are twofold. First, the data demonstrate that (for this design) individuals perform at least as well as groups in producing quantity of electronic ideas, regardless of brainstorming duration. However, when judged with respect to quality along three dimensions (originality, feasibility, and effectiveness), the individuals significantly (p<0.05) out performed the group working together. The theoretical and applied (e.g., cost effectiveness) implications of this finding are discussed. Second, the current experiment yielded several viable solutions to the wickedly difficult problem that was posed.

Dornburg, Courtney S.; Davidson, George S.; Forsythe, James C.

A web-based brainstorm was conducted in the summer of 2007 within the Sandia Restricted Network. This brainstorming experiment was modeled around the 'yellow sticky' brainstorms that are used in many face-to-face meetings at Sandia National Laboratories. This document discusses the implementation and makes suggestions for future implementations.

Davidson, George S.; Brown, William M.

Techniques for high throughput determinations of interactomes, together with high resolution protein collocalizations maps within organelles and through membranes will soon create a vast resource. With these data, biological descriptions, akin to the high dimensional phase spaces familiar to physicists, will become possible. These descriptions will capture sufficient information to make possible realistic, system-level models of cells. The descriptions and the computational models they enable will require powerful computing techniques. This report is offered as a call to the computational biology community to begin thinking at this scale and as a challenge to develop the required algorithms and codes to make use of the new data.3

Sale, Kenneth L.; Williams, Pamela J.; Davidson, George S.

Abstract not provided.

Haaland, David M.; Sinclair, Michael B.; Jones, Howland D.; Timlin, Jerilyn A.; Bachand, George B.; Sasaki, Darryl Y.; Davidson, George S.; Van Benthem, Mark V.

A novel hyperspectral fluorescence microscope for high-resolution 3D optical sectioning of cells and other structures has been designed, constructed, and used to investigate a number of different problems. We have significantly extended new multivariate curve resolution (MCR) data analysis methods to deconvolve the hyperspectral image data and to rapidly extract quantitative 3D concentration distribution maps of all emitting species. The imaging system has many advantages over current confocal imaging systems including simultaneous monitoring of numerous highly overlapped fluorophores, immunity to autofluorescence or impurity fluorescence, enhanced sensitivity, and dramatically improved accuracy, reliability, and dynamic range. Efficient data compression in the spectral dimension has allowed personal computers to perform quantitative analysis of hyperspectral images of large size without loss of image quality. We have also developed and tested software to perform analysis of time resolved hyperspectral images using trilinear multivariate analysis methods. The new imaging system is an enabling technology for numerous applications including (1) 3D composition mapping analysis of multicomponent processes occurring during host-pathogen interactions, (2) monitoring microfluidic processes, (3) imaging of molecular motors and (4) understanding photosynthetic processes in wild type and mutant Synechocystis cyanobacteria.

Leukemia

Martin, S.B.; Mosquera-Caro, M.P.; Potter, J.W.; Davidson, George S.; Andries, E.; Kang, H.; Helman, P.; Veroff, R.L.; Atlas, S.R.; Murphy, M.; Wang, X.; Ar, K.; Xu, Y.; Chen, I.M.; Schultz, F.A.; Wilson, C.S.; Harvey, R.; Bedrick, E.; Shuster, J.; Carroll, A.J.; Camitta, B.; Willman, C.L.

Abstract not provided.

Proposed for publication in Gene.

Davidson, George S.

Abstract not provided.

Faulon, Jean-Loup M.; Zhang, Zhaoduo Z.; Martino, Anthony M.; Timlin, Jerilyn A.; Haaland, David M.; Davidson, George S.; May, Elebeoba E.; Slepoy, Alexander S.

Our aim is to determine the network of events, or the regulatory network, that defines an immune response to a bio-toxin. As a model system, we are studying T cell regulatory network triggered through tyrosine kinase receptor activation using a combination of pathway stimulation and time-series microarray experiments. Our approach is composed of five steps (1) microarray experiments and data error analysis, (2) data clustering, (3) data smoothing and discretization, (4) network reverse engineering, and (5) network dynamics analysis and fingerprint identification. The technological outcome of this study is a suite of experimental protocols and computational tools that reverse engineer regulatory networks provided gene expression data. The practical biological outcome of this work is an immune response fingerprint in terms of gene expression levels. Inferring regulatory networks from microarray data is a new field of investigation that is no more than five years old. To the best of our knowledge, this work is the first attempt that integrates experiments, error analyses, data clustering, inference, and network analysis to solve a practical problem. Our systematic approach of counting, enumeration, and sampling networks matching experimental data is new to the field of network reverse engineering. The resulting mathematical analyses and computational tools lead to new results on their own and should be useful to others who analyze and infer networks.

Davidson, George S.; Boyack, Kevin W.

Abstract not provided.

Thompson, Aidan P.; Slepoy, Alexander S.; Davidson, George S.; Peters, Michael D.

Abstract not provided.

Nature Methods

Davidson, George S.

Abstract not provided.

Blood

Davidson, George S.

Abstract not provided.

Proposed for publication in New England Journal of Medicine.

Davidson, George S.

Abstract not provided.