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Displaying 1-35 out of 35 total
Peptide Sequence Tag-Based Blind Identification-based SVM Model
Found in: Machine Learning and Applications, Fourth International Conference on
By Hui Li, Chunmei Liu, Xumin Liu, Macire Diakite, Legand Burge, Abdul-Aziz Yakubu, William Southerland
Issue Date:December 2010
pp. 979-984
Identifying the ion types for a mass spectrum is essential for interpreting the spectrum and deriving its peptide sequence. In this paper, we proposed a novel method for identifying ion types and deriving matched peptide sequences for tandem mass spectra. ...
 
A rapid 3D protein Structural Classification using Pseudo 2D HMMs
Found in: 2012 IEEE International Conference on Granular Computing (GrC-2012)
By Hui Li,Jean-Claude Tounkara,Legand Burge,Chunmei Liu
Issue Date:August 2012
pp. 742-745
In this paper, we introduce a rapid method to classify protein structures. Instead of using the 3D structures of proteins directly, we used 2D inner-distance matrices converted from the 3D protein structures and extracted feature vectors from the 2D inner-...
 
Rapid identification of multi-PTMs peptide sequence tags with a graph search approach
Found in: Bioinformatics and Biomedicine Workshop, IEEE International Conference on
By Hui Li,Chunmei Liu,Mugizi Rwebangira,Legand Burge,William Southerland
Issue Date:November 2011
pp. 247-250
Identifying post-translational modifications (PTMs) is a big challenge for proteomics. Mass spectrometry is a popular tool for the identification of peptide sequence. Here we present a method for rapid identification of PTMs by mass spectrometry based on g...
 
The development of a proteomic analyzing pipeline to identify proteins with multiple RRMs and predict their domain boundaries
Found in: Bioinformatics and Biomedicine Workshop, IEEE International Conference on
By Kyung Dae Ko,Chunmei Liu,Mugizi Robert Rwebangira,Legand Burge,William Southerland
Issue Date:November 2011
pp. 374-381
The RNA-recognition motif (RRM) is the most abundant RNA-binding domain involved in many post-transcriptional processes. Since RRM-containing proteins have different functions with similar domain architecture, it is challenging to implement an automated an...
 
A Heuristic Algorithm for Finding the Longest Pathways in a Biochemical Network
Found in: Machine Learning and Applications, Fourth International Conference on
By Chunmei Liu, Hui Li, Alison Leonce, Legand Burge, John Trimble, Peter Keiller, Abdul-Aziz Yakubu
Issue Date:December 2010
pp. 515-522
Finding the longest cycle is a novel concept in biochemical feedback loop analysis in systems biology. Biochemical networks are often represented as directed graphs in which vertices represent chemical compounds and edges represent chemical reactions betwe...
 
Learning parameters for non-coding RNA sequence-structure alignment
Found in: Bioinformatics and Biomedicine Workshop, IEEE International Conference on
By Yinglei Song, Chunmei Liu, Junfeng Qu
Issue Date:November 2009
pp. 73-77
Sequence-structure alignment is the most important part for an algorithm that can search genomes and identify non-coding RNAs. A model that can accurately describe the secondary structure of a noncoding RNA family is crucial to the search accuracy of genom...
 
A graph algorithm for extracting features from transcription factor binding sites
Found in: Bioinformatics and Biomedicine Workshop, IEEE International Conference on
By Chunmei Liu, Junfeng Qu, Yinglei Song, A.U. Andy
Issue Date:November 2009
pp. 68-72
Transcription factors play important roles in gene regulation. An accurate model that can describe the binding site of a transcription factor in the promoter region of a gene is thus the key for understanding the regulation of the gene. In this paper, we d...
 
Clustering for DNA Microarray Data Analysis with a Graph Cut Based Algorithm
Found in: Machine Learning and Applications, Fourth International Conference on
By Jia Song, Chunmei Liu, Yinglei Song, Junfeng Qu
Issue Date:December 2008
pp. 595-598
Clustering is an important approach to the analysis of DNA microarray data. In this paper, we develop a new algorithm that can cluster DNA microarray data with a graph cut based algorithm. The algorithm can generate a list of clustering results with statis...
 
Alignment of Multiple Proteins with an Ensemble of Hidden Markov Models
Found in: Machine Learning and Applications, Fourth International Conference on
By Jia Song, Chunmei Liu, Yinglei Song, Junfeng Qu, Gurdeep S. Hura
Issue Date:December 2007
pp. 594-599
The alignment of multiple protein sequences is a problem of fundamental importance in bioinformatics. In general, the optimal alignment can be obtained through the optimization of an objective function. However, such an optimization task is often computati...
 
The Security Threat Posed by Steganographic Content on the Internet
Found in: Information Technology: New Generations, Third International Conference on
By Rajni Goel, Moses Garuba, Chunmei Liu, Trang Nguyen
Issue Date:April 2007
pp. 794-798
After the September 11, 2001 terrorist attack, the United States declared war on terrorism. The Patriot Act (H.R. 3162) authorizes law enforcement agencies to monitor and intercept the electronic communications of suspected terrorists. Telephone communicat...
 
Tree Decomposition Based Fast Search of RNA Structures Including Pseudoknots in Genomes
Found in: Computational Systems Bioinformatics Conference, International IEEE Computer Society
By Yinglei Song, Chunmei Liu, Russell Malmberg, Fangfang Pan, Liming Cai
Issue Date:August 2005
pp. 223-234
<p>Searching genomes for RNA secondary structure with computational methods has become an important approach to the annotation of non-coding RNAs. However, due to the lack of efficient algorithms for accurate RNA structure-sequence alignment, compute...
 
Semantic Support for Adaptive Long Term Composed Services
Found in: Web Services, IEEE International Conference on
By Xumin Liu, Chunmei Liu, Manjeet Rege, Athman Bouguettaya
Issue Date:July 2010
pp. 267-274
We propose an integrated framework that manages changes in long term composed services. The main procedure of change reaction is presented. One of the most challenging research issues of change management is how to automate the process of change reaction. ...
 
Measure the Thickness of the Thin-Film Single-Slice-Capacitor
Found in: International Symposiums on Information Processing
By Liu Changhui, Xu Chunmei, Liu Le, He Huahui
Issue Date:May 2008
pp. 770-773
According to wave-absorbing material's electricity characteristic, this text created a kind of new high-performance, low-cost capacitance type absorbing-wave coat's thickness measuring system. Carry out a research of thin film measurement which from nm-lev...
 
Intensity-Based Skeletonization of CryoEM Gray-Scale Images Using a True Segmentation-Free Algorithm
Found in: IEEE/ACM Transactions on Computational Biology and Bioinformatics
By Kamal Al Nasr,Chunmei Liu,Mugizi Rwebangira,Legand Burge,Jing He
Issue Date:September 2013
pp. 1289-1298
Cryo-electron microscopy is an experimental technique that is able to produce 3D gray-scale images of protein molecules. In contrast to other experimental techniques, cryo-electron microscopy is capable of visualizing large molecular complexes such as viru...
 
Predicting protein-protein interactions using full Bayesian network
Found in: 2012 IEEE International Conference on Bioinformatics and Biomedicine Workshops (BIBMW)
By Hui Li,Chunmei Liu,Legand Burge,Kyung Dae Ko,William Southerland
Issue Date:October 2012
pp. 544-550
Protein-protein interactions (PPIs) are central to the most cellular processes. Although PPIs have been generated exponentially from experimental methods ranging from high throughput protein sequences to the crystallized structures of complexes, only a fra...
 
Spatial index and visualization of protein structure
Found in: 2012 IEEE International Conference on Bioinformatics and Biomedicine Workshops (BIBMW)
By Hui Li,Chunmei Liu,Legand Burge,William Southerland
Issue Date:October 2012
pp. 540-543
The generation of protein data is increasing exponentially with the rapid development of experimental technology. It is becoming a major issue for bioinformatics scientists to find an efficient method for retrieving and visualizing the protein structures. ...
 
Rapid generation of peptide sequence tags with a graph search algorithm
Found in: Bioinformatics and Biomedicine Workshop, IEEE International Conference on
By Hui Li,Chunmei Liu,Mugizi Rwebangira,Legand Burge,William Southerland
Issue Date:November 2011
pp. 251-254
Tandem mass spectrometry is a popular tool for the identification of peptide sequences. In this paper, we present a method for rapid generation of short peptide sequences via tandem mass spectrometry based on a graph search. The approach takes advantage of...
 
A New Image Interpolation Algorithm Based on Pulse-Coupled Neural Networks
Found in: Computational and Information Sciences, International Conference on
By Chunmei Liu,Lei Xu,Wen Cao
Issue Date:October 2011
pp. 71-74
To reduce the edge saw tooth and blur of image during the digital image interpolation, a new image interpolation method base on Pulse-Coupled Neural Networks (PCNN) is proposed. Firstly, the clusters and the propagation paths of pulse are obtained by using...
 
Degraded Character Recognition by Image Quality Evaluation
Found in: Pattern Recognition, International Conference on
By Chunmei Liu
Issue Date:August 2010
pp. 1908-1911
The character image quality plays an important role in degraded character recognition which could tell the recognition difficulty. This paper proposed a novel approach to degraded character recognition by three kinds of independent degradation sources. It ...
 
Analysis of Detection and Track on Partially Occluded Face
Found in: Information Technology and Applications, International Forum on
By Xingjing Du, Chunmei Liu, Yongxia Yu
Issue Date:May 2009
pp. 158-161
As a new field of information technology, biometrics recognition consists of the recognition of face, iris, retina, pronunciation etc. In recent years, Static face detection algorithms concerning the categories of detection technology have been raised, but...
 
IRCDB: A Database of Inter-residues Contacts in Protein Chains
Found in: Advances in Databases, First International Conference on
By Peng Chen, Chunmei Liu, Legand Burge, Mahmood Mohammad, Bill Southerland, Clay Gloster, Bing Wang
Issue Date:March 2009
pp. 1-6
In protein structure prediction, identifying the inter-residue contacts is a very important task to understand the mechanism of complicated protein folding and therefore to predict three-dimensional structures of proteins. So far, many methods were develop...
 
Study on Vulnerability Model of Spacecraft Impacting by Orbital Debris
Found in: Advanced Computer Theory and Engineering, International Conference on
By Chunmei Liu, Shunshan Feng, Xurong Zhang
Issue Date:December 2008
pp. 1067-1070
The spacecraft was studied. Spacecraft vulnerability was analyzed in some aspects as environment, representative structure, aviation theory, damage principle and existence speciality. Then the destruction types were advanced on debris against double plates...
 
Prediction of Inter-residue Contact Clusters from Hydrophobic Cores
Found in: Machine Learning and Applications, Fourth International Conference on
By Peng Chen, Chunmei Liu, Legand Burge, Mahmood Mohammad, Bill Southerland, Clay Gloster
Issue Date:December 2008
pp. 703-708
Motivation: Contact map is a key factor to represent a specific protein structure. As previous work reported, even a corrupted contact map can be used to reconstruct its corresponding protein structure. Thus we can predict the structure of a protein partia...
 
A Comparative Analysis of Anti-Malware Software, Patch Management, and Host-Based Firewalls in Preventing Malware Infections on Client Computers
Found in: Information Technology: New Generations, Third International Conference on
By Moses Garuba, Chunmei Liu, Nicki Washington
Issue Date:April 2008
pp. 628-632
This purpose of this paper is to provide a comparative analysis of three methods used by organizations to prevent malware on client computers. These methods include anti-malware software, patch management, and host-based firewalls.??Each method will be bri...
 
Intrusion Techniques: Comparative Study of Network Intrusion Detection Systems
Found in: Information Technology: New Generations, Third International Conference on
By Moses Garuba, Chunmei Liu, Duane Fraites
Issue Date:April 2008
pp. 592-598
Organizations require security systems that are flexible and adaptable in order to combat increasing threats from software vulnerabilities, virus attacks and other malicious code, in addition to internal attacks. Network intrusion detection systems, which ...
 
Efficient Parameterized Algorithms for Biopolymer Structure-Sequence Alignment
Found in: IEEE/ACM Transactions on Computational Biology and Bioinformatics
By Yinglei Song, Chunmei Liu, Xiuzhen Huang, Russell L. Malmberg, Ying Xu, Liming Cai
Issue Date:October 2006
pp. 423-432
Computational alignment of a biopolymer sequence (e.g., an RNA or a protein) to a structure is an effective approach to predict and search for the structure of new sequences. To identify the structure of remote homologs, the structure-sequence alignment ha...
 
Low Resolution Character Recognition by Image Quality Evaluation
Found in: Pattern Recognition, International Conference on
By Chunmei Liu, Chunheng Wang, Ruwei Dai
Issue Date:August 2006
pp. 864-867
The character image database plays an important role for the evaluation of a character recognition system. But there is no measure which tells the level of recognition difficulty of a given database. This paper proposes a novel approach for the low resolut...
 
Text Detection in Images Based on Unsupervised Classification of Edge-based Features
Found in: Document Analysis and Recognition, International Conference on
By Chunmei Liu, Chunheng Wang, Ruwei Dai
Issue Date:September 2005
pp. 610-614
In this paper, an algorithm is proposed for detecting texts in images and video frames. It is performed by three steps: edge detection, text candidate detection and text refinement detection. Firstly, it applies edge detection to get four edge maps in hori...
 
Incorporating Service-Oriented Programming techniques into undergraduate CS and SE curricula
Found in: 2013 IEEE Frontiers in Education Conference (FIE)
By Xumin Liu,Rajendra Raj,Tom Reichlmayr, Chunmei Liu,Alex Pantaleev
Issue Date:October 2013
pp. 1369-1371
Service-Oriented Programming (SOP) has emerged as a new programming paradigm that allows the wrapping of existing software as web services, thus permitting the development of new software applications by using existing web services as building blocks. SOP ...
   
Teaching Service-Oriented Programming to CS and SE undergraduate students
Found in: 2013 IEEE Frontiers in Education Conference (FIE)
By Xumin Liu,Rajendra K. Raj,Thomas J. Reichlmayr, Chunmei Liu,Alex Pantaleev
Issue Date:October 2013
pp. 15-16
Service-Oriented Programming (SOP) is a relatively new programming paradigm that supports the development of new software applications using existing services as building blocks. SOP has gained significant popularity in industry as it increases software re...
   
A Machine Learning Approach for Accurate Annotation of Noncoding RNAs
Found in: IEEE/ACM Transactions on Computational Biology and Bioinformatics
By Yinglei Song,Chunmei Liu,Zhi Wang
Issue Date:February 2015
pp. 1
Searching genomes to locate noncoding RNA genes with known secondary structure is an important problem in bioinformatics. In general, the secondary structure of a searched noncoding RNA is defined with a structure model constructed from the structural alig...
 
Prediction of protein structures using a map-reduce Hadoop framework based simulated annealing algorithm
Found in: 2013 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)
By Hui Li,Chunmei Liu
Issue Date:December 2013
pp. 6-10
The accomplishment of molecular functions depends on protein tertiary structures. The development of protein structure prediction algorithms and tools is essential for proteomics study. Among the existing developed prediction algorithms, simulated annealin...
   
Teaching service-oriented programming to CS and SE undergraduate students (abstract only)
Found in: Proceedings of the 45th ACM technical symposium on Computer science education (SIGCSE '14)
By Alex Pantaleev, Chunmei Liu, Rajendra K. Raj, Thomas J. Reichlmayr, Xumin Liu
Issue Date:March 2014
pp. 740-740
The Blackbox project, launched in 2013, collects large amounts of data about beginner student behaviour in the BlueJ IDE. In this this workshop, we will introduce researchers to the Blackbox data and show them how to get started with analyzing it to answer...
     
Intensity-Based Skeletonization of CryoEM Gray-Scale Images Using a True Segmentation-Free Algorithm
Found in: IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
By Chunmei Liu, Jing He, Kamal Al Nasr, Legand Burge, Mugizi Rwebangira
Issue Date:September 2013
pp. 1289-1298
Cryo-electron microscopy is an experimental technique that is able to produce 3D gray-scale images of protein molecules. In contrast to other experimental techniques, cryo-electron microscopy is capable of visualizing large molecular complexes such as viru...
     
Efficient Parameterized Algorithms for Biopolymer Structure-Sequence Alignment
Found in: IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
By Chunmei Liu, Liming Cai, Russell L. Malmberg, Xiuzhen Huang, Ying Xu, Yinglei Song
Issue Date:October 2006
pp. 423-432
Computational alignment of a biopolymer sequence (e.g., an RNA or a protein) to a structure is an effective approach to predict and search for the structure of new sequences. To identify the structure of remote homologs, the structure-sequence alignment ha...
     
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