Terry E. Weymouth

University of Michigan | U-M · Department of Computational Medicine and Bioinformatics

Motivation: Capabilities in the field of metabolomics have grown tremendously in recent years. Many existing resources contain the chemical properties and classifications of commonly identified metabolites. However, the annotation of small molecules (both endogenous and synthetic) to meaningful biological pathways and concepts still lags behind th...

Motivation: Functional enrichment testing facilitates the interpretation of Chromatin immunoprecipitation followed by high-throughput sequencing (ChIP-seq) data in terms of pathways and other biological contexts. Previous methods developed and used to test for key gene sets affected in ChIP-seq experiments treat peaks as points, and are based on th...

Gene set enrichment testing can enhance the biological interpretation of ChIP-seq data. Here, we develop a method, ChIP-Enrich, for this analysis which empirically adjusts for gene locus length (the length of the gene body and its surrounding non-coding sequence). Adjustment for gene locus length is necessary because it is often positively associat...

In recent years, metabolomics has emerged as an approach to perform large-scale characterization of small molecules in biological systems. Metabolomics posed a number of bioinformatics challenges associated in data analysis and interpretation. Genome-based metabolic reconstructions have established a powerful framework for connecting metabolites to...

Background The relative contribution of epigenetic mechanisms to carcinogenesis is not well understood, including the extent to which epigenetic dysregulation and somatic mutations target similar genes and pathways. We hypothesize that during carcinogenesis, certain pathways or biological gene sets are commonly dysregulated via DNA methylation acro...

Figure S1. Waterfall plots showing the methylation change in significant genes between normal and tumor samples involved in neurogenesis and epidermis development (GO terms). Positive values indicate hypermethylation in cancer, while negative values indicate hypomethylation in cancer. A. Neurogenesis. B. Epidermis Development. Figure S2. Change in...

Table S1. Significance of overlap in the specific differentially methylated genes in significant GO terms between pairs of studies using Fisher’s exact test (p-value<0.05 is indicated with red text)GO term - Immune Response GO term - Epidermis Development GO term – Neurogenesis.

Metabolomics is a rapidly evolving field that holds promise to provide insights into genotype-phenotype relationships in cancers, diabetes and other complex diseases. One of the major informatics challenges is providing tools that link metabolite data with other types of high-throughput molecular data (e.g. transcriptomics, proteomics), and incorpo...

Background / Purpose: Our goal is to improve support that visualization applications offer scientists for generating novel biological meanings and insights from molecular interaction networks. We have empirically modeled scientists' higher order cognition for a specific workflow and mapped their cognitive tasks to user requirements for network vi...

Metscape is a plug-in for Cytoscape, used to visualize and interpret metabolomic data in the context of human metabolic networks. We have developed a metabolite database by extracting and integrating information from several public sources. By querying this database, Metscape allows users to trace the connections between metabolites and genes, visu...

Motivation: The elucidation of biological concepts enriched with differentially expressed genes has become an integral part of the analysis and interpretation of genomic data. Of additional importance is the ability to explore networks of relationships among previously defined biological concepts from diverse information sources, and to explore res...

Molecular interaction data exists in a number of repositories, each with its own data format, molecule identifier and information coverage. Michigan molecular interactions (MiMI) assists scientists searching through this profusion of molecular interaction data. The original release of MiMI gathered data from well-known protein interaction databases...

Unlabelled: The MiMI molecular interaction repository integrates data from multiple sources, resolves interactions to standard gene names and symbols, links to annotation data from GO, MeSH and PubMed and normalizes the descriptions of interaction type. Here, we describe a Cytoscape plugin that retrieves interaction and annotation data from MiMI a...

The Upper Atmospheric Research Collaboratory was actively used over a period of six years to study space weather phenomena such as magnetic storms and solar winds. The UARC software was designed as a modular system of independent services that work over a wide area network and support a complex array of data suppliers, transformation modules that p...

An abstract is not available.

Upper atmospheric physics focuses on the study of the earth’s ionosphere, looking particularly at the interactions of the solar wind, the earth’s magnetic field, and the characteristics of the upper atmosphere. Observations of these phenomena are made with ground-based instruments, satellites, and rockets. In recent years, a series of computational...

Organ definition in computed tomography (CT) is of interest for treatment planning and response monitoring. We present a method for organ definition using a priori information about shape encoded in a set of biometric organ models--specifically for the liver and kidney--that accurately represents patient population shape information. Each model is...

Windows to the Universe is a World Wide Web site that presents information about the Earth and Space sciences as well as related historical and cultural topics to the general public in an attractive and user-friendly way. The site makes extensive use of graphically annotated button panels to allow intuitive navigation through the site. The site is...

Mobile robots operate in a wide variety of environments, and the tasks they are being designed to perform vary from the simplest pick-and-place factory jobs to space station construction, maintenance, and repair. Vision systems for mobile robots are used to help locate goal objects or locations, plan paths to the goal, avoid obstacles along the cho...

This paper is intended to compare the two architectures, focusing on abilities exhibited in the robot competition and the underlying approaches used by the two teams. A shorter version of this paper appeared originally in [6].

A video database provides content based access to video. This is achieved by organizing or indexing video data based on some set of features. This paper defines the problem of video indexing based on video data models. The procedure required to index video data is outlined. The use of semi-automatic techniques to speed up the indexing processes are...

Effective and efficient tools for segmenting and content-based indexing of digital video are essential to allow easy access to video-based information. Most existing segmentation techniques do not use explicit models of video. The approach proposed here is inspired and influenced by well established video production processes. Computational models...

The National Collaboratory concept has great potential for enabling 'critical mass' working groups and highly interdisciplinary research projects. We report here on a new program to build a prototype collaboratory using the Sondrestrom Upper Atmospheric Research Facility in Kangerlussuaq, Greenland and a group of associated scientists. The Upper At...

Indexing video data is essential for providing content based access. Indexing has typically been viewed either from a manual annotation perspective or from an image sequence processing perspective. This work proposes a methodology for designing video indexing schemes which use low level machine derivable indices to map into the set of application s...

A video database provides content based access to video. This is achieved by organizing or indexing video data based on some set of features. This paper defines the problem of video indexing based on video data models. The procedure required to index video data is outlined. The use of semi-automatic techniques to speed up the indexing processes are...

Organ definition in computed tomography (CT) is of interest for treatment planning and response monitoring. We present a method for organ definition using a priori information about shape encoded in a biometric organ model-specifically a liver model-that accurately represents patient population shape information. This model is generated by averagin...

The goal of ARPA's Unmanned Ground Vehicle project is to demonstrate the use of small teams of cooperating autonomous robots (2 - 4 vehicles) to carry out military tasks in an outdoor environment. The role of the University of Michigan within the project focuses on aspects of mission planning, assimilation of information provided by multiple agents...

Researchers at the University of Michigan's AI Lab are working to produce mobile robot systems capa-ble of intelligently reacting to events and objects in a real world environment. A system has been built which integrates a reactive planner with perception and navigation capabilities in order to generate ble, responsive vehicle behavior. The system...

A new multidisciplinary effort is linking research in the upper atmospheric and space, computer, and behavioral sciences to develop a prototype electronic environment for conducting team science worldwide. A real-world electronic collaboration testbed has been established to support scientific work centered around the experimental operations being...

Autonomous robot navigation requires the solution of several problems like obstacle avoidance and road following. Traditionally, the problem of obstacle avoidance has been solved by using range information acquired through some form of range measurements like laser range cameras or vision based range estimation. This paper presents a novel approach...

Automated liver surface determination in abdominal computed tomography scans, currently difficult to achieve, is of interest to determine liver location and size for various medical applications, including radiation therapy treatment planning, surgical planning, and oncologic monitoring. The authors propose to facilitate automation by the addition...

We present an approach to control information flow in object-oriented systems. The decision of whether an informatin flow is permitted or denied depends on both the authorizations specified on the objects and the process by which information is obtained ...

The data driven, bottom up approach to video segmentation has ignored the inherent structure that exists in video. This work uses the model driven approach to digital video segmentation. Mathematical models of video based on video production techniques are formulated. These models are used to classify the edit effects used in video and film product...

Topological maps represent the world as a network of nodes and arcs: the nodes are distinctive places in the environment and the arcs represent paths between places. A significant issue in building topological maps is defining distinctive places. Most previous work in topological mapping has concentrated on using sonar sensors to define distinctive...

The Carmel project (computer-aided robotics for maintenance, emergency, and life support) which won the AAAI 1992 Robot Competition, is discussed. Carmel's design philosophy and architecture, obstacle avoidance, global path planning, vision sensing, landmark triangulation, and supervisory planning system are described. The Carmel project shows that...

An abstraction-based paradigm that makes explicit the process of imposing assumptions on data is discussed. The units of abstraction are models in which levels of abstraction are determined by the degree of assumption necessary for their application. A general-to-specific refinement process provides a mechanism to proceed gracefully through the abs...

This paper describes the design and implementation of an integrated system for combining obstacle avoidance, path planning, landmark detection and position triangulation. Such an integrated system allows the robot to move from place to place in an environment, avoiding obstacles and planning its way out of traps, while maintaining its position and...

This paper describes the design and implementation of an integrated system for combining obstacle avoidance, path planning, landmark detection and position triangulation. Such an integrated system allows the robot to move from place to place in an environment, avoiding obstacles and planning its way out of traps, while maintaining its position and...

In this paper we discuss the implementation and uses of the object recognition system used for CARMEL, the University of Michigan's winning entry in the AAAI-92 Autonomous Robot Competition. Following the rules of the competition, the robot was required to navigate within a large, unstructured environment performing exploration, and then a directed...

Last summer, AAAI sponsored a mobile robot competition in conjunction with the AAAI-92 conference in San Jose, California. Ten robots from across the country competed in the competition, with CARMEL from the University of Michigan finishing first. CARMEL is a Cybermotion K2A mobile platform with a ring of 24 sonar sensors and a single black and whi...

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The authors present a novel approach to the problem of constructing a depth map from a sequence of monocular images. The approach requires knowledge only of the axial translation component of the moving camera. When the configuration of the camera is known with respect to the mobile platform, this information can be readily obtained by projecting d...

Pose determination for robot navigation is discussed. The problem is to maintain the system's instantaneous precept of its position and orientation in space for performing various tasks. The authors describe a system in which models were used to guide the sensory interpretation and to correct expectations. In this system, simulated images were used...

An approach to developing more capable mobile robots through integrating robotics R&D with advanced reactor design is presented. The GE ALMR (Advanced Liquid Metal Reactor) design is used as the focus for defining the mobile robotic R&D being performed in the areas of locomotion, sensing, manipulation, navigation, machine intelligence, and man-mach...

This paper presents an object-oriented data model for an image database. The formal presentation of the model stems from an analysis of the domain of remotely sensed radar images of the Arctic ice. The data model maintains the distinction between generic spatial attributes and representation dependent spatial attributes. This results in a four-laye...

This paper describes an algorithm used for the navigation of a vehicle in intelligent vehicle highway systems (IVHS). An internal map is constructed in the computer main memory to reflect a relevant road network which can be updated by the Traffic Management Center (TMC) or other resources on line. The network information is simply decomposed hiera...

The authors show how stereo-based range data, obtained over time by a moving vehicle can be integrated without the explicit knowledge or computation of camera motion. A unique aspect of the approach is the transformation of range information into relative distances and encoding these distances in image registered maps. Results of experiments on dyn...

Recently, the problem of automatic left ventricular boundary detection has yielded to methods that rely on the matching of the image data to a model of the heart. The problem of matching such a model to data is further complicated by the fact that heart position, orientation and size can vary widely for various patient studies. In this paper, we pr...

Quantitative regional curvature analysis, a method for measuring the shape of the left ventricle at end-diastole and end-systole, was further developed to allow determination of systolic and diastolic ventricular function by measuring shape on a frame-by-frame basis. A two-dimensional, color-modulated parametric display was created that coded the t...

An autonomous mobile robot must be able to combine uncertain sensory information with prior knowledge of the world. Moreover these operations have to be performed fast enough to be able to react to the changes in the world. This paper presents a model-driven system for a real-time indoor mobile robot. As the robot is constantly in motion informatio...

It is shown how a contour can be estimated from a few edge positions. The technique fits a cubic spline to edges using the position and orientations of edges (tangent slopes) and computes tangent magnitudes by a minimization based on the second derivatives. Cubic splines (piecewise third-order polynomials) are used because they are the lowest-order...

Most of the depth from image flow algorithms has to rely on either good initial guesses, or some assumptions about the object surfaces to achieve solutions that agree with the physical world. Waxman and Sinha point out that those restrictions can be relaxed if depth is computed from a relative image flow field. Since image flow determination is rel...

Dynamic programming is discussed as an approach to solving variational problems in vision. Dynamic programming ensures global optimality of the solution, is numerically stable, and allows for hard constraints to be enforced on the behavior of the solution within a natural and straightforward structure. As a specific example of the approach's effica...

Fusion of 3-D spatial information obtained by a dynamic vision system is addressed. The representation of information is seen to be critical in forming a solution. An object-centered representation that encodes, in image registered maps, the relative distances of objects to a set of scene referents is proposed. This representation facilitates fusio...

This paper describes a novel computational model for dynamic vision which promises to be both powerful and robust. Furthermore the paradigm is ideal for an active vision system where camera vergence changes dynamically. Its basis is the retinotopically indexed object-centered encoding of the early visual information. Specifically, the relative dist...

An autonomous mobile robot must be able to combine un- certain sensory information with prior knowledge of the world. Moreover, these operations have to be performed fast enough for the robot to be able to react to the changes in the world. This pa- per presents a model-driven system for a real-time indoor mobile robot. As the robot is constantly i...

Extraction of two-dimensional object locations using current techniques is a computationally intensive process. In this paper a parallel algorithm is presented that can specify the location of objects from edge streaks produced by an edge operator. Best-first searches are carried out in a number of non-interacting and localized edge streak spaces....

Growth in the intelligence of space systems requires the use and integration of data from multiple sensors. Generic tools are being developed for extracting and integrating information obtained from multiple sources. The full spectrum is addressed for issues ranging from data acquisition, to characterization of sensor data, to adaptive systems for...

A novel depth computation algorithm is described. Based on linear equations derived from the consideration of relative normal velocity, this algorithm determines depth values locally and uniquely from normal velocities. Multiple independently moving objects present no problem for the algorithm. A velocity constraint is implemented to estimate norma...

Interpolation of X-ray motion pictures of the heart (cineventiculograms of the left ventricle) is complicated by the low contrast of the images and the elastic motion of the heart. Here, the problem of placing the heart boundary in each frame of the motion sequence is described by a framework for the application of knowledge in the form of diagnost...

Advances in the field of knowledge-guided computer vision require the development of large scale projects and experimentation with them. One factor which impedes such development is the lack of software environments which combine standard image processing and graphics abilities with the ability to perform symbolic processing. In this paper, we desc...

Interpretation of X-ray motion pictures of the heart (cineventiculograms of the left ventricle) is complicated by the low contrast of the images and the elastic motion of the heart. We describe a framework for the application of knowledge in the form of diagnostically relevant models of the heart in motion to the problem of placing the heart bounda...

Stereo algorithms using a wide baseline must cope with a large search space on top of the problems due to noise. A single pair of images is not a reliable source of depth information. One solution is to integrate the information from several image pairs. By incrementally refining estimates of the depth as the camera changes position, it is possible...

An algorithm is presented for minimizing the energy of active contour models. The result of M. Kass and D. Terzopolous (1987) is generalized by allowing hard constraints to become an integral part of the minimization process. The optimization problem is set up as a discrete multistage decision process and is solved by a time-delayed discrete dynami...

ABSTRACT Among the sources of information,that ,can ,be used,to guide,the ,processing,of visual ,sensory,data are the constraints implied ,by the,geometry,of the objects,being ,viewed. ,Experiments ,have ,been performed,using,representations ,of this ,type ,of knowledge,to control ,image,processing. ,They show how such geometric knowledge can be us...

Machine vision systems are often confronted with images of great complexity. Preprocessing, region growing, and edge extraction algorithms must rely on their underlying image models in order to make effective use of the data. This study presents an alternate approach to the definition of an image model. It also discusses an algorithm, based on this...

Described in this paper is a small, modular operating system which was written for an Interdata-70 machine. The total operating system is memory resident and occupies 5K bytes. The primary motivation in redesigning the operating system was to structure it so that students and general system users could easily expand or modify the basic services of...

This paper describes the use of the Chief Programmer Team method in an operating systems class to implement a subset of a multiprogramming operating system. The operating system consisted of elements of Job Management, Task Management, and Data Management functions. The students were divided into four groups. One of these, called the Steering Commi...

Mobile robot navigation using visual sensors requires that a robot be able to detect landmarks and obtain pose information from a camera image. This paper presents a vision system for finding man made markers of known size and calculating the pose of these markers. The algorithm detects and identifies the markers using a weighted pattern matching t...

Among the sources

MetScape is a Cytoscape <http://cytoscape.org> plugin which is used to visualize and analyze metabolomic data. A number of public sources contain information about human metabolic networks consisting of compounds, chemical reactions, pathways, enzymes and genes like KEGG, and EHMN. In MetScape, we use EHMN, a high-quality human metabolic network ma...

Topological maps represent the world as a network of nodes and arcs: the nodes are distinctive places in the environment and the arcs represent paths be-tween places. A significant issue in building topologi-cal maps is defining distinctive places. Most previous work in topological mapping has concentrated on us-ing sonar sensors to define distinct...