Berg, Bart, Thanthiriwatte, Chamali, Manda, Prashanti, Bridges, Susan M
Abstract The widespread availability of microarray technology has driven functional genomics to the forefront as scientists seek to draw meaningful biological conclusions from their microarray...
Exploratory visual analysis of conserved domains on multiple sequence alignments (2009)
Jankun-Kelly, TJ, Lindeman, Andrew D, Bridges, Susan M
Abstract Background Multiple alignment of protein sequences can provide insight into sequence conservation across many species and thus allow identification of those sections of the sequence most...
Integrating phenotype and gene expression data for predicting gene function (2009)
Malone, Brandon M, Perkins, Andy D, Bridges, Susan M
Abstract Background This paper presents a framework for integrating disparate data sets to predict gene function. The algorithm constructs a graph, called an integrated similarity graph, by computing...
Introduction to the Proceedings of the Avian Genomics and Gene Ontology Annotation Workshop (2009)
Bridges, Susan M, Burgess, Shane C, McCarthy, Fiona M
Abstract The Avian Genomics Conference and Gene Ontology Annotation Workshop brought together researchers and students from around the world to present their latest research addressing the delivery...
Bmc Bioinformatics, William S S, Susan M Bridges, Fiona M Mccarthy, Bindu N, Shane C Burgess, ...
Proceedings Prediction of peptides observable by mass spectrometry applied at the experimental set level
INTERACTIVE CLUSTERING FOR EXPLORATION OF GENOMIC DATA (2008)
Xiufeng Wan, John A. Boyle, Susan M. Bridges, Alan P. Boyle
The complete genomic sequences for many organisms, particularly primitive organisms with relatively small genomes (prokaryotes), are now available. We describe an approach that supports interactive...
Accelerating String Set Matching in FPGA Hardware for Bioinformatics Research (2008)
Dandass, Yoginder S, Burgess, Shane C, Lawrence, Mark, Bridges, Susan M
Abstract Background This paper describes techniques for accelerating the performance of the string set matching problem with particular emphasis on applications in computational proteomics. The...
Ambareen Siraj, Rayford B. Vaughn, Susan M. Bridges
This paper describes the use of artificial intelligence techniques in the creation of a network-based decision engine for decision support in an Intelligent Intrusion Detection System (IIDS). In...
Gene Ontology annotation quality analysis in model eukaryotes (2008)
Buza, Teresia J., McCarthy, Fiona M., Wang, Nan, Bridges, Susan M., Burgess, Shane C.
Functional analysis using the Gene Ontology (GO) is crucial for array analysis, but it is often difficult for researchers to assess the amount and quality of GO annotations associated with different...
A Java Implementation Of (2007)
Leding Wu Project, Leding Wu, Leding Wu, Donna S. Reese, Susan M. Bridges, Name Leding Wu
This paper presents a re-implemented GUI tool and demonstrates how it can be used to evaluate an MPI program's performance. The DQoS tool provides a method of observing the effect of QoS levels...
Near-Critical Path Analysis Of Parallel Program Performance: The Statistical Perspective (2007)
Ronald Brian Brightwell, Ronald Brian Brightwell, Donna S. Reese, R. Rainey Little, Susan M. Bridges, Lois C. Boggess, ...
evaluation of the effectiveness of the Maximum Benefit metric. ii ACKNOWLEDGEMENTS First, I would like to extend sincere thanks and appreciation to Dr. Donna Reese and Dr. Cedell Alexander for their...
Fuzzy Frequent Episodes for Real-Time Intrusion Detection (2007)
Jianxiong Luo, Susan M. Bridges, Rayford B. Vaughn
Data mining methods including association rule mining and frequent episode mining have been applied to the intrusion detection problem. In other work, we have introduced modifications of these...
Xiufeng Wan, John A. Boyle, Susan M. Bridges, Alan P. Boyle
The complete genomic sequences for many organisms, particularly primitive organisms with relatively small genomes (prokaryotes), are now available. We describe an approach that supports interactive...
Parallel genetic algorithms for tuning a fuzzy data mining system (2007)
In previous work, we have described methods that we have developed for tuning a fuzzy data mining system for intrusion detection using a hierarchical genetic algorithm. Unfortunately, the genetic...
Prediction of peptides observable by mass spectrometry applied at the experimental set level (2007)
Sanders, William S, Bridges, Susan M, McCarthy, Fiona M, Nanduri, Bindu, Burgess, Shane C
Abstract Background When proteins are subjected to proteolytic digestion and analyzed by mass spectrometry using a method such as 2D LC MS/MS, only a portion of the proteotypic peptides associated...
ProtQuant: a tool for the label-free quantification of MudPIT proteomics data (2007)
Bridges, Susan M, Magee, G Bryce, Wang, Nan, Williams, W Paul, Burgess, Shane C, Nanduri, Bindu
Abstract Background Effective and economical methods for quantitative analysis of high throughput mass spectrometry data are essential to meet the goals of directly identifying, characterizing, and...
AgBase: a unified resource for functional analysis in agriculture (2007)
McCarthy, Fiona M., Bridges, Susan M., Wang, Nan, Magee, G. Bryce, Williams, W. Paul, Luthe, Dawn S., ...
Analysis of functional genomics (transcriptomics and proteomics) datasets is hindered in agricultural species because agricultural genome sequences have relatively poor structural and functional...
AgBase: a functional genomics resource for agriculture (2006)
McCarthy, Fiona M, Wang, Nan, Magee, G Bryce, Nanduri, Bindu, Lawrence, Mark L, Camon, Evelyn B, ...
Abstract Background Many agricultural species and their pathogens have sequenced genomes and more are in progress. Agricultural species provide food, fiber, xenotransplant tissues, biopharmaceuticals...
BMC Genomics BioMed Central Database AgBase: a functional genomics resource for agriculture (2006)
Fiona M Mccarthy, Nan Wang, G Bryce Magee, Bindu N, Mark L Lawrence, Evelyn B Camon, ...
© 2006 McCarthy et al; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License
Intrusion Sensor Data Fusion in an Intelligent Intrusion Detection System Architecture (2004)
Ambareen Siraj, Rayford B. Vaughn, Susan M. Bridges
Most modern intrusion detection systems employ multiple intrusion sensors to maximize their trustworthiness. The overall security view of the multisensor intrusion detection system can serve as an...
Edward B. Allen, Edward B. Allen, Julia E. Hodges, Susan M. Bridges, Edward B. Allen, A. Wayne Bennett, ...
dissertation or thesis in empiri-cal software engineering. This document is in the form of a hypothetical master’s thesis with a hypothetical Graduate Committee. Limit the length of the abstract:...
Attacking a high performance computer cluster (2003)
Miguel Torres, Rayford B. Vaughn, German Florez, Zhen Liu, Susan M. Bridges
Abstract – This paper describes several scenarios that could potentially be used to implement attacks against a Linux high performance cluster, resulting in actions that corrupt information in the...
Ambareen Siraj, Rayford B. Vaughn, Susan M. Bridges
This paper describes the use of artificial intelligence techniques in the creation of a network-based decision engine for decision support in an Intelligent Intrusion Detection System (IIDS). In...
A comparison of input representations in neural networks: A case study in intrusion detection (2002)
Zhen Liu, German Florez, Susan M. Bridges
Abstract- Recently intrusion detection techniques have shifted from user-based and connection-based to processbased intrusion detection. Forrest et al. [2] presented one of the first papers analyzing...
AI techniques applied to high performance computing intrusion detection (2002)
Susan M. Bridges, Rayford B. Vaughn, Ambareen Siraj
This paper describes a prototype intelligent intrusion detection system (IIDS) that is being developed to demonstrate the effectiveness of specific artificial intelligence approaches to intrusion...
Ambareen Siraj, Susan M. Bridges, Rayford B. Vaughn
The "health " of a computer network needs to be assessed and protected in much the same manner as the health of a person. The task of an intrusion detection system is to protect a...
A framework for an adaptive intrusion detection system with data mining (2001)
Mahmood Hossain, Susan M. Bridges
The goal of a network-based intrusion detection system (IDS) is to identify patterns of known intrusions (misuse detection) or to differentiate anomalous network activity from normal network traffic...
Fuzzy data mining and genetic algorithms applied to intrusion detection (2000)
Susan M. Bridges, Rayford B. Vaughn, Associate Professor, Associate Professor
We are developing a prototype intelligent intrusion detection system (IIDS) to demonstrate the effectiveness of data mining techniques that utilize fuzzy logic and genetic algorithms. This system...
Fuzzy Data Mining And Genetic (2000)
Algorithms Applied To, Susan M. Bridges, Rayford B. Vaughn, Associate Professor, Associate Professor
We are developing a prototype intelligent intrusion detection system (IIDS) to demonstrate the effectiveness of data mining techniques that utilize fuzzy logic and genetic algorithms. This system...
August Mining Fuzzy, Jianxiong Luo, Susan M. Bridges
have previously reported the use of association rules and frequency episodes for mining audit data to gain knowledge for intrusion detection. The integration of association rules and frequency...
Intrusion Detection via fuzzy data mining (2000)
Susan M. Bridges, Rayford B. Vaughn, Associate Professor, Associate Professor
This paper describes a prototype intelligent intrusion detection system (IIDS) that is being developed to demonstrate the effectiveness of data mining techniques that utilize fuzzy logic. This system...
Integrating Fuzzy Logic With Data Mining Methods For Intrusion Detection (1999)
Jianxiong Luo, Jianxiong Luo, Susan M. Bridges, Julia E. Hodges, Major Professor, Dr. Susan Bridges
This report explores integrating fuzzy logic with two data mining methods (association rules and frequency episodes) for intrusion detection. Data mining methods are capable of extracting patterns...
Adam Gaither, Adam Gaither, Donna S. Reese, David L. Marcum, Bradley D. Carter, Susan M. Bridges, ...
The purpose of this thesis is to develop a topology data structure that supports both structured and unstructured grid generation methods. This topology data structure directly supports the method of...
Jin Li, Jin Li, Anthony Skjellum, Ioana Banicescu, Donna S. Reese, Susan M. Bridges, ...
this document with L aT
Chemiluminescence in Wounded Root Tissue 12: EVIDENCE FOR PEROXIDASE INVOLVEMENT
Salin, Marvin L., Bridges, Susan M.
Root and stem segments from soybean (Merrill cv. `Bragg') showed an enhanced chemiluminescence upon mechanical injury. Roots emitted more light than did stems. Light emission was diminished by CN−...
Salin, Marvin L., Bridges, Susan M.
A cyanide-insensitive superoxide dismutase (EC 1.15.1.1) was purified from leaves of the water lily Nuphar luteum (L.) Sibth. and Smith Subsp. macrophyllum (Small) Beal. The enzyme had a molecular...
Distribution of Iron-Containing Superoxide Dismutase in Vascular Plants 12
Bridges, Susan M., Salin, Marvin L.
Superoxide dismutases (EC 1.15.1.1) in vascular plants representing different evolutionary levels were characterized using polyacrylamide gel electrophoresis. The three forms of the enzyme were...
AgBase: a functional genomics resource for agriculture
McCarthy, Fiona M, Wang, Nan, Magee, G Bryce, Nanduri, Bindu, Lawrence, Mark L, Camon, Evelyn B, ...
Chemiluminescence in Wounded Root Tissue 12: EVIDENCE FOR PEROXIDASE INVOLVEMENT
Salin, Marvin L., Bridges, Susan M.
Root and stem segments from soybean (Merrill cv. `Bragg') showed an enhanced chemiluminescence upon mechanical injury. Roots emitted more light than did stems. Light emission was diminished by CN−...
Salin, Marvin L., Bridges, Susan M.
A cyanide-insensitive superoxide dismutase (EC 1.15.1.1) was purified from leaves of the water lily Nuphar luteum (L.) Sibth. and Smith Subsp. macrophyllum (Small) Beal. The enzyme had a molecular...
Distribution of Iron-Containing Superoxide Dismutase in Vascular Plants 12
Bridges, Susan M., Salin, Marvin L.
Superoxide dismutases (EC 1.15.1.1) in vascular plants representing different evolutionary levels were characterized using polyacrylamide gel electrophoresis. The three forms of the enzyme were...
AgBase: a functional genomics resource for agriculture
McCarthy, Fiona M, Wang, Nan, Magee, G Bryce, Nanduri, Bindu, Lawrence, Mark L, Camon, Evelyn B, ...
AgBase: a unified resource for functional analysis in agriculture
McCarthy, Fiona M., Bridges, Susan M., Wang, Nan, Magee, G. Bryce, Williams, W. Paul, Luthe, Dawn S., ...
Analysis of functional genomics (transcriptomics and proteomics) datasets is hindered in agricultural species because agricultural genome sequences have relatively poor structural and functional...
Prediction of peptides observable by mass spectrometry applied at the experimental set level
Sanders, William S, Bridges, Susan M, McCarthy, Fiona M, Nanduri, Bindu, Burgess, Shane C
ProtQuant: a tool for the label-free quantification of MudPIT proteomics data
Bridges, Susan M, Magee, G Bryce, Wang, Nan, Williams, W Paul, Burgess, Shane C, Nanduri, Bindu
Gene Ontology annotation quality analysis in model eukaryotes
Buza, Teresia J., McCarthy, Fiona M., Wang, Nan, Bridges, Susan M., Burgess, Shane C.
Functional analysis using the Gene Ontology (GO) is crucial for array analysis, but it is often difficult for researchers to assess the amount and quality of GO annotations associated with different...