Semi-supervised protein subcellular localization (2009)
Xu, Qian, Hu, Derek, Xue, Hong, Yu, Weichuan, Yang, Qiang
Abstract Background Protein subcellular localization is concerned with predicting the location of a protein within a cell using computational method. The location information can indicate key...
Wan, Xiang, Yang, Can, Yang, Qiang, Xue, Hong, Tang, Nelson LS, Yu, Weichuan
Abstract Background The interactions of multiple single nucleotide polymorphisms (SNPs) are highly hypothesized to affect an individual's susceptibility to complex diseases. Although many works have...
Comparison of public peak detection algorithms for MALDI mass spectrometry data analysis (2009)
Yang, Chao, He, Zengyou, Yu, Weichuan
Abstract Background In mass spectrometry (MS) based proteomic data analysis, peak detection is an essential step for subsequent analysis. Recently, there has been significant progress in the...
Yang, Can, He, Zengyou, Wan, Xiang, Yang, Qiang, Xue, Hong, Yu, Weichuan
Motivation: Hundreds of thousands of single nucleotide polymorphisms (SNPs) are available for genome-wide association (GWA) studies nowadays. The epistatic interactions of SNPs are believed to be...
The Seventh Asia Pacific Bioinformatics Conference (APBC 2009) (2009)
Bmc Bioinformatics, Qian Xu, Derek Hao Hu, Hong Xue, Weichuan Yu, Qiang Yang, ...
endoplasmic reticulum, cell nucleus and Golgi apparatus. These compartments play different roles, for instance, mitochondria supply chemical energy ATP for cell survive; chloroplasts transform light...
Improving peptide identification with single-stage mass spectrum peaks (2009)
Motivation: Database searching is the major peptide identification method in shotgun proteomics. It searches tandem mass spectrometry (MS/MS) spectra against a protein database to identify target...
BMC Bioinformatics BioMed Central Methodology article (2009)
Xiang Wan, Can Yang, Qiang Yang, Hong Xue, Nelson Ls Tang, Weichuan Yu
MegaSNPHunter: a learning approach to detect disease predisposition SNPs and high level interactions in genome wide association study
Optimization-Based Peptide Mass Fingerprinting for Protein Mixture Identification (2008)
Zengyou He, Chao Yang, Can Yang, Robert Z Qi, Weichuan Yu
*Motivation:* In current proteome research, peptide sequencing is probably the most widely used method for protein mixture identification. However, this peptide-centric method has its own...
Ultrasound Imaging: A Linear Model (2008)
Weichuan Yu, Ning Lin, Ping Yan, Kailasnath Purushothaman, Albert Sinusas, Karl Thiele, ...
• Study the relation between feature and tissue motion from the ultrasound imaging perspective • Look for feature robust against de-correlation • Validate the theory with the newest 3D...
Aligning Peaks Across Multiple Mass Spectrometry Data Sets Using A Scale-Space Based Approach (2008)
Weichuan Yu, Xiaoye Li, Hongyu Zhao
Introduction. In mass spectrometry (MS) based proteomics research, only the spectral peaks are biologically relevant in analysis applications such as biomarker discovery and disease classification....
Motion Analysis of 3D Ultrasound Texture Patterns (2008)
Weichuan Yu, Ning Lin, Ping Yan, Kailasnath Purushothaman, Albert Sinusas, Karl Thiele, ...
We model the process of imaging soft tissues with a 3D ultrasound probe using a linear convolution model, and obtain analytical expressions of both the ultrasound image and its spectrum. We use this...
Local 3D Orientation Analysis and Its Applications (2008)
Weichuan Yu, Kostas Daniilidis, Gerald Sommer
In this paper we present a new method for approximation of local 3D orientation based on Gaussian functions. Compared with current 3D steerability approaches our method achieves higher orientation...
Is Subcellular Localization Informative for Modeling Protein-Protein Interaction Signal? (2008)
Junfeng Liu, Hongyu Zhao, Jun Tan, Dajie Luo, Weichuan Yu, E. James Harner, ...
Statistical methods have been intensively applied in genomic signal processing (Dougherty et al. 2005). For budding yeast Saccharomyces cerevisiae with around 6000 proteins, genome-wide...
Bayesian Mass Spectra Peak Alignment from Mass Charge Ratios (2008)
Junfeng Liu, Weichuan Yu, Baolin Wu, Hongyu Zhao
Proteomics studies based on mass spectrometry (MS) are gaining popular applications in biomedical research for protein identification/quantification and biomarker discovery, especially for potential...
Bayesian Mass Spectra Peak Alignment from Mass Charge Ratios (2008)
Junfeng Liu, Weichuan Yu, Baolin Wu, Hongyu Zhao
Proteomics studies based on mass spectrometry (MS) are gaining popular applications in biomedical research for protein identification/quantification and biomarker discovery, especially for potential...
Is Subcellular Localization Informative for Modeling Protein-Protein Interaction Signal? (2008)
Junfeng Liu, Hongyu Zhao, Jun Tan, Dajie Luo, Weichuan Yu, E. James Harner, ...
Statistical methods have been intensively applied in genomic signal processing (Dougherty et al. 2005). For budding yeast Saccharomyces cerevisiae with around 6000 proteins, genome-wide...
Peak bagging for peptide mass fingerprinting (2008)
He, Zengyou, Yang, Can, Yu, Weichuan
Motivation: Mass Spectrometry (MS)-based protein identification via peptide mass fingerprinting (PMF) is a key component in high-throughput proteome research. While PMF was the first commonly used...
Arnd Gebhard, Weichuan Yu, Gerald Sommer
Abstract. A novel approach for the analysis of facial features is presented. Instead of analyzing facial features with global models (such as the popular deformable templates) we perform a local...
Junction Characterization Using Polar Pyramid (2007)
Weichuan Yu, Kostas Daniilidis, Gerald Sommer
Abstract. In this paper we present a new approach in characterizing gray-value junctions. Due to the multiple intrinsic orientations present in junctions the response of a filter is needed at every...
Weichuan Yu, Kostas Daniilidis, Steven Beauchemin, Gerald Sommer
The computation of optical flow is a well studied topic in biological and computational vision. However, the existence of multiple motions in dynamic imagery due to occlusion or even transparency...
Weichuan Yu, Kostas Daniilidis, Gerald Sommer
Abstract. In this paper we present a new lter based on Gaussian functions for the extraction of local 3D orientation information. Compared with current 3D steerability approaches our method achieves...
Correcting the Skewness of Gaborwavelets (2007)
Weichuan Yu, Gerald Sommer, Kostas Daniilidis
The positive skewness of Gaborwavelets in the parameter space aects the identication of source signals. In this paper, we present a new lter to correct the skewness and describe the result in the...
Weichuan Yu, Gerald Sommer, Kostas Daniilidis
In this paper, we address multiple motion analysis from the standpoint of orientation analysis. Using the fact that multiple motions are equivalent to multiple planes in the derivative space or in...
Eliminating outliers in motion occlusion analysis (2007)
Weichuan Yu, Kostas Daniilidis, Gerald Sommer
Abstract. Occlusion boundaries are considered either as outliers or as noise in most optical ow algorithms. In order to treat the boundary problem, many probabilistic algorithms like maximum...
Multiple peak alignment in sequential data analysis : a scale-space-based approach (2006)
Yu, Weichuan, Li, Xiaoye, Liu, Junfeng, Wu, Baolin, Williams, Kenneth R., Zhao, Hongyu
In this paper, we address the multiple peak alignment problem in sequential data analysis with an approach based on the Gaussian scale-space theory. We assume that multiple sets of detected peaks are...
Weichuan Yu, Baolin Wu, Tao Huang, Xiaoye Li, Kenneth Williams, Hongyu Zhao
Proteomics technologies are rapidly evolving and attracting great attention in the post-genome era. In this chapter, we review two key applications of proteomics techniques: disease biomarker...
Weichuan Yu, Gerald Sommer, Kostas Daniilidis
Responses of Gabor wavelets in the mid-frequency space build a local spectral representation scheme with optimal properties regarding the time-frequency uncertainty principle. However, when using...
Oriented Structure of the Occlusion Distortion: Is It Reliable? (2002)
Yu, Weichuan, Sommer, Gerald, Beauchemin, Steven, Daniilidis, Kostas
In the energy spectrum of an occlusion sequence, the distortion term has the same orientation as the velocity of the occluding signal. Recent works claimed that this oriented structure can be used to...
Oriented structure of the occlusion distortion: Is it reliable (2002)
Weichuan Yu, Gerald Sommer, Steven Beauchemin, Kostas Daniilidis
In the energy spectrum of an occlusion sequence, the distortion term has the same orientation as the velocity of the occluding signal. Recent works claimed that this oriented structure can be used to...
Oriented structure of the occlusion distortion: Is it reliable (2002)
Weichuan Yu, Gerald Sommer, Steven Beauchemin, Kostas Daniilidis
In the energy spectrum of an occlusion sequence, the distortion term has the same orientation as the velocity of the occluding signal. Recent works claimed that this oriented structure can be used to...
Oriented structure of the occlusion distortion: Is it reliable (2002)
Weichuan Yu, Gerald Sommer, Steven Beauchemin, Kostas Daniilidis
Abstract—In the energy spectrum of an occlusion sequence, the distortion term has the same orientation as the velocity of the occluding signal. Recent works claimed that this oriented structure can...
Combinative Multi-Scale Level Set Framework for Echocardiographic Image Segmentation (2002)
Ning Lin, Weichuan Yu, James S. Duncan
In the automatic segmentation of echocardiographic images, a priori shape knowledge is used to compensate poor features in ultrasound images. The shape knowledge is often learned via off-line...
Oriented structure of the occlusion distortion: Is it reliable (2002)
Weichuan Yu, Gerald Sommer, Steven Beauchemin, Kostas Daniilidis
Abstract—In the energy spectrum of an occlusion sequence, the distortion term has the same orientation as the velocity of the occluding signal. Recent works claimed that this oriented structure can...
3D-Orientation Signatures with Conic Kernel Filtering for Multiple Motion Analysis (2001)
Yu, Weichuan, Sommer, Gerald, Daniilidis, Kostas
In this paper we propose a new 3D kernel for the recovery of 3D-orientation signatures. The kernel is a Gaussian function defined in local spherical coordinates and its Cartesian support has the...
Local orientation analysis in images and image sequences using steerable filters / (2001)
Zugl.: Kiel, University, Diss., 2001.
Approximate orientation steerability based on angular gaussians (2001)
Weichuan Yu, Kostas Daniilidis, Gerald Sommer
Junctions are signicant features in images with an intensity variation that exhibits multiple orientations. This makes the detection and characterization of junctions a challenging problem. In this...
Approximate orientation steerability based on angular gaussians (2001)
Weichuan Yu, Kostas Daniilidis, Gerald Sommer
Junctions are signicant features in images with intensity variation that exhibits multiple orientations. This makes the detection and characterization of junctions a challenging problem. The...
Skewness of Gabor wavelets and source signal separation. submitted to (2001)
Weichuan Yu, Gerald Sommer, Kostas Daniilidis
Responses of Gabor wavelets in the mid-frequency space build a local spectral representation scheme with optimal properties regarding the time-frequency uncertainty principle. However, when using...
Approximate orientation steerability based on angular gaussians (2001)
Bericht Nr, Weichuan Yu, Weichuan Yu, Weichuan Yu, Kostas Daniilidis, Kostas Daniilidis, ...
Junctions are significant features in images with an intensity variation that exhibits multiple orientations. This makes the detection and characterization of junctions a challenging problem. In this...
Skewness of Gabor wavelets and source signal separation. submitted to (2001)
Weichuan Yu, Gerald Sommer, Kostas Daniilidis
Responses of Gabor wavelets in the mid-frequency space build a local spectral representation scheme with optimal properties regarding the time-frequency uncertainty principle. However, when using...
Approximate orientation steerability based on angular gaussians (2001)
Weichuan Yu, Kostas Daniilidis, Gerald Sommer
Abstract Junctions are significant features in images with intensity variation that exhibits multiple orientations. This makes the detection and characterization of junctions a challenging problem....
Local orientation analysis in images and image sequences using steerable filters / (2000)
Zugl.: Kiel., Univ., Diss., 2000.
Multiple motion analysis using 3d orientation steerable filters (2000)
Bericht Nr, Bericht Nr, Weichuan Yu, Weichuan Yu, Weichuan Yu, Gerald Sommer, ...
In this paper, we study the characterization of multiple motions from the standpoint of orientation in spatiotemporal volume. Using the fact that multiple motions are equivalent to multiple planes in...
Multiple motion analysis using 3d orientation steerable filters (2000)
Weichuan Yu, Gerald Sommer, Kostas Daniilidis
In this paper we address multiple motion analysis from the standpoint of orientation analysis. After pointing out that multiple motions are equivalent to multiple planes in the derivative space or in...
Local Orientation Analysis in Images and Image Sequences Using Steerable Filters (2000)
In this thesis, we address the issue of local orientation analysis using steerable filters. From the standpoint of the sampling theory, current orientation steerable filters sample the spectrum of...
Multiple Motion Analysis Using 3D Orientation Steerable Filters (2000)
Weichuan Yu, Kostas Daniilidis, Gerald Sommer
In this paper we address multiple motion analysis from the standpoint of orientation analysis.
Multiple motion analysis using 3d orientation steerable filters (2000)
Weichuan Yu, Gerald Sommer, Kostas Daniilidis
In this paper, we address multiple motion analysis from the standpoint of orientation analysis. Using the fact that multiple motions are equivalent to multiple planes in the derivative space or in...
Detection and Characterization of Multiple Motion Points (1999)
Weichuan Yu, Kostas Daniilidis, Steven Beauchemin, Gerald Sommer
The computation of optical flow is a well studied topic in biological and computational vision. However, the existence of multiple motions in dynamic imagery due to occlusion or even transparency...
Approximate Orientation Steerability Based on Angular Gaussians (1999)
Weichuan Yu, Kostas Daniilidis, Gerald Sommer
Junctions are significant features in images with an intensity variation that exhibits multiple orientations.
Rotated wedge averaging method for junction characterization (1998)
Weichuan Yu, Kostas Daniilidis, Gerald Sommer
The computational cost of conventional filter methods for junction characterization is very high. This burden can be attenuated by using steerable filters. However, in order to achieve a high...
Low-cost junction characterization using polar averaging filters (1998)
Weichuan Yu, Kostas Daniilidis, Gerald Sommer
Junction characterization is a very costly task since junctions are multi-scalar and multi-oriented structures. Besides, high directional selectivity is also required to deal with complex junctions....
Weichuan Yu, Gerald Sommer, Kostas Daniilidis
In this paper we propose a new 3D kernel for the recovery of 3Dorientation signatures. The kernel is a Gaussian function defined in local spherical coordinates and its Cartesian support has the shape...
Bayesian Mass Spectra Peak Alignment from Mass Charge Ratios
Liu, Junfeng, Yu, Weichuan, Wu, Baolin, Zhao, Hongyu
Proteomics studies based on mass spectrometry (MS) are gaining popular applications in biomedical research for protein identification/quantification and biomarker discovery, especially for potential...