Božidar Vujičić, In The, Božidar Vujičić, Božidar Vujičić, Dr. Jie Liang, Senior Supervisor
and characterization of traffic in a public safety wireless network Examining Committee: Chair:
Jin, Guangfu, Xu, Lin, Shu, Yongqian, Tian, Tian, Liang, Jie, Xu, Yan, ...
Chromosome 5p15.33, containing TERT and CLPTM1L genes, was recently identified as one of the susceptible regions for lung cancer in Caucasian populations. We hypothesized that single-nucleotide...
Ji, Guixiang, Gu, Aihua, Hu, Fan, Wang, Shoulin, Liang, Jie, Xia, Yankai, ...
BACKGROUNDThe FAS/FASLG system has been proposed to play a key role in germ cell apoptosis. To elucidate the role of the genetic variants of cell death pathway genes in male infertility, we genotyped...
Changyu Hu, Xiang Li, Jie Liang
Motivation. Protein design aims to identify sequences compatible with a given protein fold but incompatible to any alternative folds. To select the correct sequences and to guide the search process,...
Integrating Specification and Documentation in an Object-Oriented Language (2008)
This paper reports on the integration of specification and documentation features into an object-oriented programming language and its compiler. The goal of this integration is to improve software...
Sridhar Srinivasan, Pohsiang (john Hsu, Kunal Mukerjee, Shankar L. Regunathan, Bruce Lin, Jie Liang, ...
by matching local surfaces: a Bayesian Monte Carlo (2008)
Evolutionary model for predicting protein function
Abstract Background Stochasticity plays important roles in many molecular networks when molecular concentrations are in the range of 0.1 μ M to 10 n M (about 100 to 10 copies in a cell). The...
Ronald Jackups, Sarah Cheng, Jie Liang
Integral membrane proteins can be categorized into two structural classes: α-helical proteins and βbarrel proteins. The structural properties of helical membrane proteins are well characterized,...
Optimal Block Boundary Pre/Postfiltering for Wavelet-Based Image and Video Compression (2008)
Jie Liang, Chengjie Tu, Trac D. Tran
Abstract—This paper presents a pre/postfiltering framework to reduce the reconstruction errors near block boundaries in waveletbased image and video compression. Two algorithms are developed to...
Jie Liang, Larisa Adamian, Ronald Jackups
Membrane proteins have important roles in many cellular processes. Computational analysis of their sequences and structures has provided much insight into the organizing principles of transmembrane...
Larisa Adamian, Zheng Ouyang, Yan Yuan Tseng, Jie Liang
patterns of retinal-binding pockets of type I rhodopsins and
Liang J: Order independent structural alignment of circularly permuted proteins (2008)
T. Andrew Binkowski, Bhaskar Dasgupta, Jie Liang
Abstract–Circular permutation connects the N and C termini of a protein and concurrently cleaves elsewhere in the chain, providing an important mechanism for generating novel protein fold and...
Topology Independent Protein Structural Alignment (2008)
Joe Dundas, T. A. Binkowski, Bhaskar Dasgupta, Jie Liang
Abstract. Protein structural alignment is an indispensable tool used for many different studies in bioinformatics. Most structural alignment algorithms assume that the structural units of two similar...
Monte Carlo Sampling of Near-Native Structures of Proteins With Applications (2008)
Aq Jinfeng Zhang, Ming Lin, Rong Chen, Jie Liang, Jun S Liu
ABSTRACT Since a protein’s dynamic fluctuation inside cells affects the protein’s biological properties, we present a novel method to study the ensemble of near-native structures (NNS) of...
SHORT COMMUNICATION Prediction of Buried Helices in Multispan Alpha helical Membrane Proteins (2008)
ABSTRACT Analysis of a database of structures of membrane proteins shows that membrane proteins composed of 10 or more transmembrane (TM) helices often contain buried helices that are inaccessible to...
Integral membrane proteins can be categorized into two structural classes: a-helical proteins and b-barrel proteins. b-Barrel proteins are found in the outer membrane of Gram-negative bacteria,...
The sulfated glycosaminoglycan heparin is an important anticoagulant, widely used to treat and to prevent arterial thrombosis. Heparin triggers conformational changes in, and the functional...
Xiang Li, Ozlem Keskin, Buyong Ma, Ruth Nussinov, Jie Liang, Human Genetics
*Corresponding authors
Protein folding dynamics in lattice model with physical movement (2008)
Sëma Kachalo, Hsiao-mei Lu, Jie Liang
Abstract — We study folding dynamcis of protein-like sequences on square lattice by constructing a physically realizable move set that exhausts all possible conformational changes for a structure....
The characteristics of lung cancer cases in 1996-2005 in Nanjing, China (2008)
Yi ZENG, Jie LIANG, Hongbing SHEN
Background and objective Epidemiology of lung cancer has changed along with the time. The aim of this study is to analyze the distribution of sex, age, pathology and smoking in the lung cancer cases...
Predicting protein folding rates from geometric contact and amino acid sequence (2008)
Protein folding speeds are known to vary over more than eight orders of magnitude. Plaxco, Simons, and Baker (see References) first showed a correlation of folding speed with the topology of the...
Wang, Yan, Hu, Zhibin, Liang, Jie, Wang, Zhanwei, Tang, Jinhai, Wang, Shui, ...
Telomerase reactivation, which prevents telomere shortening and maintains cell viability, is crucial for the continued growth or progression of cancer cells. A minisatellite tandem repeat, MNS16A,...
Expression of 15-PGDH is downregulated by COX-2 in gastric cancer (2008)
Liu, Zhenxiong, Wang, Xin, Lu, Yuanyuan, Han, Shuang, Zhang, Faming, Zhai, Huihong, ...
To explore the proteins regulated by cyclooxygenase-2 (COX-2) in gastric cancer, the expression plasmid of COX-2siRNA was constructed and transfected into gastric cancer cell line SGC7901. Then,...
Liang, Jie, Chen, Peizhan, Hu, Zhibin, Zhou, Xiaoyi, Chen, Lu, Li, Mian, ...
Fibroblast growth factor receptor 2 (FGFR2) belongs to the FGFR family, which plays an important role in cell growth, invasiveness, motility and angiogenesis. In human breast cancer, expression of...
A Universal Robust Low Frequency Watermarking Scheme (2007)
Jie Liang, Peng Xu, Trac D. Tran
| A novel robust low frequency digital watermarking scheme is proposed, in which the watermark is embedded in the DFT magnitude of the low frequency subband of an image. This lowpass subband can be...
Changyu Hu, Xiang Li, Jie Liang
Motivation. Protein design aims to identify sequences compatible with a given protein fold but incompatible to any alternative folds. To select the correct sequences and to guide the search process,...
Potential function plays critica... (2007)
Potential functions are critical for computational studies of protein structure prediction, folding, and sequence design. A class of widely used potentials for coarse grained models of proteins are...
Ignatius Gomes, Tiffany T. Sharma, Nadim Mahmud, Seby Edassery, Noreen Fulton, Jie Liang, ...
Highly abundant genes in the transcriptosome of human and baboon
Hydration Effects of Heparin on Antithrombin Probed by Osmotic Stress (2007)
Maria P. Mcgee, Jie Liang, James Luba
ABSTRACT Antithrombin is a key inhibitor of blood coagulation proteases and a prototype metastable protein. Heparin binding to antithrombin induces conformational transitions distal to the binding...
Chloride Binding Regulates the Schiff Base pK in Gecko P521 Cone-Type Visual Pigment † (2007)
Ching Yuan, Osamu Kuwata, Jie Liang, Saurav Misra, Sergei P. Balashov, Thomas G. Ebrey
ABSTRACT: The binding of chloride is known to shift the absorption spectrum of most long-wavelengthabsorbing cone-type visual pigments roughly 30 nm to the red. We determined that the chloride...
ASSESSING EFFECT OF CROSS- HYBRIDIZATION ON OLIGONUCLEOTIDE MICROARRAYS (2007)
Seman Kachalo, Zarema Arbieva, Jie Liang
Abstract: We introduce computational method, which allows estimating the input of non-specific binding into hybridization signal intensities on the oligonucleotide-based Affymetrix GeneChip arrays....
Ca 2+-transporting ATPase of sarcoplasmic reticulum couples ATP hydrolysis with ion transport. Phosphorylation of the cytosolic region of the calcium-bound conformation (E1) of the protein leads to...
Jie Liang, Herbert Edelsbrunner, Ping Fu, Pamidighantam V. Sudhakar, Shankar Subramaniam
ABSTRACT The size and shape of macromolecules such as proteins and nucleic acids play an important role in their functions. Prior efforts to quantify these properties have been based on various...
Error Resilient Pre-/Post-Filtering for DCT-based Block Coding Systems (2007)
Chengjie Tu, Trac D. Tran, Jie Liang, Student Member, Student Member
Block coding based on the Discrete Cosine Transform (DCT) is very popular in image and video compression. Pre-/post-filtering can be attached to a DCT-based block coding system to improve coding...
COMMUNICATION Are Residues in a Protein Folding Nucleus (2007)
Evolutionarily Conserved, Yan Yuan Tseng, Jie Liang
Are amino acid residues important for rapid folding preferentially conserved during evolution? Does natural selection optimize proteins for folding kinetics? If protein folding involves initially the...
T. Andrew Binkowski, Patrick Freeman, Jie Liang
Detecting similar protein surfaces provides an important route for discovering unrecognized or novel functional relationship between proteins. The webserver pvSOAR (pocket and void Surfaces Of Amino...
Topology independent protein structural alignment (2007)
Dundas, Joe, Binkowski, TA, DasGupta, Bhaskar, Liang, Jie
Abstract Background Identifying structurally similar proteins with different chain topologies can aid studies in homology modeling, protein folding, protein design, and protein evolution. These...
Risk factors of inflammatory bowel disease in the North-Western Chinese population. (2007)
Yahong Li; PLA 323 Hospital, Datong , China., Shengjun Wu; Department Of Psychology, Faculty Of Aerospace Of Medicine, Fourth Military Medical University , Xi،¯an , China., Jie Liang; State Key Laboratory Of Cancer Biology, XiJing Hospital , Fourth Military Medical University , Xi،¯an , China., Xia Zhu; Department Of Psychology, Faculty Of Aerospace Of Medicine, Fourth Military Medical University , Xi،¯an , China., Xin Zhang; Central Hospital Of Xi،¯an , China., Kaichun Wu; State Key Laboratory Of Cancer Biology, XiJing Hospital , Fourth Military Medical University , Xi،¯an , China., ...
BACKGROUND: The aim of study was to screen the risk factors of inflammatory bowel disease (IBD) in north-western Chinese population by case investigation.METHODS: 72 determined IBD patients and 72...
Risk factors of inflammatory bowel disease in the North-Western Chinese population. (2007)
Yahong Li; PLA 323 Hospital, Datong , China., Shengjun Wu; Department Of Psychology, Faculty Of Aerospace Of Medicine, Fourth Military Medical University , Xi،¯an , China., Jie Liang; State Key Laboratory Of Cancer Biology, XiJing Hospital , Fourth Military Medical University , Xi،¯an , China., Xia Zhu; Department Of Psychology, Faculty Of Aerospace Of Medicine, Fourth Military Medical University , Xi،¯an , China., Xin Zhang; Central Hospital Of Xi،¯an , China., Kaichun Wu; State Key Laboratory Of Cancer Biology, XiJing Hospital , Fourth Military Medical University , Xi،¯an , China., ...
BACKGROUND: The aim of study was to screen the risk factors of inflammatory bowel disease (IBD) in north-western Chinese population by case investigation.METHODS: 72 determined IBD patients and 72...
Research article Topology independent protein structural alignment (2007)
Joe Dundas, Ta Binkowski, Bhaskar Dasgupta, Jie Liang, Jie Liang
© 2007 Dundas et al.; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License
To study protein nascent chain folding during biosynthesis, we investigate the folding behavior of models of hydrophobic and polar (HP) chains at growing length using both two-dimensional square...
Filter banks for prediction-compensated multiple description coding (2007)
This paper investigates the design and application of the optimal filter banks for a predictioncompensated multiple description coding (PC-MDC) scheme, where the coefficients in each subband are...
Prediction of transmembrane helix orientation in polytopic membrane proteins (2006)
Abstract Background Membrane proteins compose up to 30% of coding sequences within genomes. However, their structure determination is lagging behind compared with soluble proteins due to the...
Experiments on the modular nature of word and sentence phonology in Chinese Broca's patients (2006)
Promotor: V.J.J.P. van Heuven
Experiments on the modular nature of word and sentence phonology in Chinese Broca's patients (2006)
This book investigates the effects of brain lesions in the left hemisphere (Broca’s area) on the production and perception of vowels, word tones and the linguistic use of sentence melody. We aimed...
Knowledge-based energy functions for computational studies of proteins (2006)
This chapter discusses theoretical framework and methods for developing knowledge-based potential functions essential for protein structure prediction, protein-protein interaction, and protein...
$\beta$-barrel membrane proteins are found in the outer membrane of gram-negative bacteria, mitochondria, and chloroplasts. We have developed probabilistic models to quantify propensities of residues...
Zhang, Jinfeng, Chen, Rong, Liang, Jie
An effective potential function is critical for protein structure prediction and folding simulation. Simplified protein models such as those requiring only $C_\alpha$ or backbone atoms are attractive...
Computation of protein geometry and its applications: Packing and function prediction (2006)
This chapter discusses geometric models of biomolecules and geometric constructs, including the union of ball model, the weigthed Voronoi diagram, the weighted Delaunay triangulation, and the alpha...
The amino acid sequences of proteins provide rich information for inferring distant phylogenetic relationships and for predicting protein functions. Estimating the rate matrix of residue...
Protein folding dynamics via quantification of kinematic energy landscape (2006)
Kachalo, Sëma, Lu, Hsiao-Mei, Liang, Jie
We study folding dynamics of protein-like sequences on square lattice using physical move set that exhausts all possible conformational changes. By analytically solving the master equation, we follow...
Membrane Proteins, Larisa Adamian, Jie Liang, Larisa Adamian, Jie Liang
Background: Membrane proteins compose up to 30 % of coding sequences within genomes. However, their structure determination is lagging behind compared with soluble proteins due to the experimental...
Proefschrift Universiteit Leiden.
Dundas, Joe, Ouyang, Zheng, Tseng, Jeffery, Binkowski, Andrew, Turpaz, Yaron, Liang, Jie
Cavities on a proteins surface as well as specific amino acid positioning within it create the physicochemical properties needed for a protein to perform its function. CASTp...
The amino acid sequences of proteins provide rich information for inferring distant phylogenetic relationships and for predicting protein functions. Estimating the rate matrix of residue...
T. Andrew Binkowski, Andrzej Joachimiak, Jie Liang
surface analysis for function annotation
models: Combining contact and local (2005)
Jinfeng Zhang, Rong Chen, Jie Liang
Empirical potential function for simplified protein
Geometric cooperativity and anticooperativity of three-body interactions in native proteins (2005)
Abstract Characterizing multibody interactions of hydrophobic, polar, and ionizable residues in protein is important for understanding the stability of protein structures. We introduce a geometric...
Screening phage-displayed combinatorial peptide library is an effective approach for discovery of peptide modulators for protein-protein interactions. However, as peptide length increases, the chance...
Larisa Adamian, Vikas N, William F. Degrado, Jie Liang
ABSTRACT Characterizing the interactions between amino acid residues and lipid molecules is important for understanding the assembly of transmembrane helices and for studying membrane protein...
Improved Collision Attack on Hash Function MD5. Cryptology ePrint Archive (2005)
Abstract. In this paper, we present a fast attack algorithm to find two-block collision of hash function MD5. The algorithm is based on the two-block collision differential path of MD5 that was...
The amino acid sequences of proteins provide rich information for inferring distant phylogenetic relationships and for predicting protein functions. Estimating the rate matrix of residue...
The amino acid sequences of proteins provide rich information for inferring distant phylogenetic relationships and for predicting protein functions. Estimating the rate matrix of residue...
Order independent structural alignment of circularly permuted proteins (2004)
Binkowski, T. Andrew, DasGupta, Bhaskar, Liang, Jie
Circular permutation connects the N and C termini of a protein and concurrently cleaves elsewhere in the chain, providing an important mechanism for generating novel protein fold and functions....
Developing optimal nonlinear scoring function for protein design (2004)
Hu, Changyu, Li, Xiang, Liang, Jie
Motivation. Protein design aims to identify sequences compatible with a given protein fold but incompatible to any alternative folds. To select the correct sequences and to guide the search process,...
Zhang, Jinfeng, Chen, Rong, Liang, Jie
An effective potential function is critical for protein structure prediction and folding simulation. For simplified models of proteins where coordinates of only $C_\alpha$ atoms need to be specified,...
Zhang, Jinfeng, Chen, Yu, Chen, Rong, Liang, Jie
In simple models side chains are often represented implicitly (e.g., by spin-states) or simplified as one atom. We study side chain effects using square lattice and tetrahedral lattice models, with...
Inheritance, specification and documentation support for and object-oriented language / (2004)
Thesis (M.Sc.) -- McMaster University, 2004.
Nathan O. Stitziel, T. Andrew Binkowski, Yan Yuan Tseng, Jie Liang, Simon Kasif
The database of topographic mapping of Single Nucleotide Polymorphism (topoSNP) provides an online resource for analyzing non-synonymous SNPs (nsSNPs) that can be mapped onto known 3D structures of...
Potential Function Of Simplified Protein Models For Discriminating (2004)
Native Proteins From, Jinfeng Zhang, Rong Chen, Jie Liang
An effective potential function is critical for protein structure prediction and folding simulation. For simplified models of proteins where coordinates of only atoms need to be specified, an...
T. Andrew Binkowski, Patrick Freeman, Jie Liang
Detecting similar protein surfaces provides an important route for discovering unrecognized or novel functional relationship between proteins. The web server pvSOAR (pocket and void Surfaces Of Amino...
The DNA architectural protein HMGB1 facilitates RTA- (2004)
Moon Jung Song, Seungmin Hwang, Wendy Wong, June Round, Deeann Martinez, Yaron Turpaz, ...
Song et al. page 1
Developing optimal nonlinear scoring function for protein design (2004)
Hu, Changyu, Li, Xiang, Liang, Jie
Motivation: Protein design aims to identify sequences compatible with a given protein fold but incompatible to any alternative folds. To select the correct sequences and to guide the search process,...
Binkowski, T. Andrew, Freeman, Patrick, Liang, Jie
Detecting similar protein surfaces provides an important route for discovering unrecognized or novel functional relationship between proteins. The web server pvSOAR (pocket and void Surfaces Of Amino...
Developing optimal non-linear scoring function for protein design (2004)
Hu, Changyu, Li, Xiang, Liang, Jie
Motivation. Protein design aims to identify sequences compatible with a given protein fold but incompatible to any alternative folds. To select the correct sequences and to guide the search process,...
Stitziel, Nathan O., Binkowski, T. Andrew, Tseng, Yan Yuan, Kasif, Simon, Liang, Jie
The database of topographic mapping of Single Nucleotide Polymorphism (topoSNP) provides an online resource for analyzing non‐synonymous SNPs (nsSNPs) that can be mapped onto known 3D structures...
Developing optimal nonlinear scoring function for protein design (2004)
Hu, Changyu, Li, Xiang, Liang, Jie
Motivation: Protein design aims to identify sequences compatible with a given protein fold but incompatible to any alternative folds. To select the correct sequences and to guide the search process,...
Are residues in a protein folding nucleus evolutionarily conserved? (2003)
It is important to understand how protein folding and evolution influences each other. Several studies based on entropy calculation correlating experimental measurement of residue participation in...
Li, Xiang, Hu, Changyu, Liang, Jie
Protein representation and potential function are essential ingredients for studying proteins folding and protein prediction. We introduce a novel geometric representation of contact interactions...
Hu, Changyu, Li, Xiang, Liang, Jie
Potential functions are critical for computational studies of protein structure prediction, folding, and sequence design. A class of widely used potentials for coarse grained models of proteins are...
Zhang, Jinfeng, Chen, Rong, Tang, Chao, Liang, Jie
Single domain proteins are thought to be tightly packed. The introduction of voids by mutations is often regarded as destabilizing. In this study we show that packing density for single domain...
Filter bank design for image/video compression and digital communications [microform] / (2003)
Vita.
Xiang Li, Changyu Hu, Jie Liang
ABSTRACT Protein representation and potential function are two important ingredients for studying protein folding, equilibrium thermodynamics, and sequence design. We introduce a novel geometric...
CASTp: Computed atlas of surface topography of proteins (2003)
T. Andrew Binkowski, Shapor Naghibzadeh, Jie Liang
Computed atlas of surface topography of proteins (CASTp) provides an online resource for locating, delineating, and measuring concave surface regions on three-dimensional structures of proteins....
Higher-order interhelical spatial interactions in membrane proteins (2003)
Larisa Adamian, Ronald Jackups, T. Andrew Binkowski, Jie Liang
Membrane proteins play essential cellular roles, including signal transduction, proton pumping, ion transport, and light harvesting. Although transmembrane (TM) helices can be predicted
James D. Lear, Holly Gratkowski, Larisa Adamian, Jie Liang, William F. DeGrado
Recent studies with model peptides and statistical analyses of the crystal structures of membrane proteins have shown that buried polar interactions contribute significantly to the stabilization of...
T. Andrew Binkowski, Larisa Adamian, Jie Liang
es, and for further inquiries on evolutionary origins of structural elements important for protein function. q 2003 Elsevier Ltd. All rights reserved. Keywords: protein surface; surface pattern;...
Adaptive Runlength Coding (2003)
Chengjie Tu, Jie Liang, Student Member, Student Member, Trac D. Tran
Runlength coding is the standard coding technique for block transform-based image/video compression. A block of quantized transform coefficients is first represented as a sequence of RUN/LEVEL pairs...
Lapped Transform via Time-Domain Pre- And Post-Filtering (2003)
Trac D. Tran, Jie Liang, Chengjie Tu, Student Member, Student Member
This paper presents a general framework of constructing a large family of lapped transforms with symmetric basis functions by adding simple time-domain pre- and post-processing modules onto existing...
Error resilient pre-/post-filtering for DCT-based block coding systems (2003)
Chengjie Tu, Trac D. Tran, Jie Liang
Abstract—Block coding based on the discrete cosine transform (DCT) is very popular in image and video compression. Pre/post-filtering can be attached to a DCT-based block coding system to improve...
Structural location of disease-associated singlenucleotide polymorphisms (2003)
Nathan O. Stitziel, Yan Yuan Tseng, Dimitri Pervouchine, David Goddeau, Simon Kasif, Jie Liang
Single-nucleotide polymorphisms (SNPs) are the most common form of human genetic variation. The coding regions of the human genome contain about 500,000 SNPs. 1 Among these, the nonsynonymous
FILTER BANK DESIGN FOR IMAGE/VIDEO COMPRESSION AND DIGITAL COMMUNICATIONS (2003)
The growing demands for delivering multimedia services over Internet and wireless networks call for high-performance and low-complexity data compression and transmission algorithms. Various such...
CASTp: Computed Atlas of Surface Topography of proteins (2003)
Binkowski, T. Andrew, Naghibzadeh, Shapor, Liang, Jie
Computed Atlas of Surface Topography of proteins (CASTp) provides an online resource for locating, delineating and measuring concave surface regions on three-dimensional structures of proteins. These...
STUDY OF THE EFFECTIVENESS OF A WEB-BASED INTERACTIVE HOMEWORK (2002)
With increased use of the web in teaching there is growing interest in the effectiveness of web-based tools in facilitating student learning. I have conducted a case study on the effectiveness of...
STUDY OF THE EFFECTIVENESS OF A WEB-BASED INTERACTIVE HOMEWORK (2002)
With increased use of the web in teaching there is growing interest in the effectiveness of web-based tools in facilitating student learning. I have conducted a case study on the effectiveness of...
Liang, Jie, Zhang, Jinfeng, Chen, Rong
Voids exist in proteins as packing defects and are often associated with protein functions. We study the statistical geometry of voids in two-dimensional lattice chain polymers. We define voids as...
Study of the effectiveness of a web-based interactive homework (2002)
Thesis (M.S.)--Mississippi State University. Department of Physics and Astronomy.
Study of the effectiveness of a web-based interactive homework [electronic resource] / (2002)
With increased use of the web in teaching there is growing interest in the effectiveness of web-based tools in facilitating student learning. I have conducted a case study on the effectiveness of...
Study of the effectiveness of a web-based interactive homework (2002)
Thesis (M.S.)--Mississippi State University. Department of Physics and Astronomy.
DCT-based general structure for linear phase paraunitary filter banks (2002)
Paraunitary Filterbanks, Jie Liang, Student Member, Trac D. Tran, Senior Member
Abstract—In this paper, we present a general structure for linear phase paraunitary filterbanks (LPPUFB) via both time-domain pre-processing and frequency-domain post-processing of the discrete...
Further results on DCT-based linear phase paraunitary filter banks (2002)
A DCT-based simplified general structure for linear phase paraunitary filter bank (LPPUFB) is developed recently by the pre- and post-processing of the DCT in the time domain. The new structure can...
Helix-helix packing and interfacial pairwise interactions of residues in membrane proteins (2001)
Integral membrane proteins play essential cellular roles, including signal transduction, proton pumping, ion transport, and light harvesting. They are abundantly found and account for about 20-
Are proteins well-packed (2001)
ABSTRACT The average packing density inside proteins is as high as in crystalline solids. Does this mean proteins are well-packed? We go beyond average densities, and look at the full distribution...
Fast Multiplierless Approximations of the DCT with the Lifting Scheme (2001)
Abstract|In this paper, we present the design, implementation and application of several families of fast multiplierless approximations of the discrete cosine transform (DCT) with the lifting scheme,...
Fast Multiplierless Approximations of the DCT with the Lifting Scheme (2001)
Jie Liang, Student Member, Trac D. Tran
In this paper, we present the design, implementation, and application of several families of fast multiplierless approximations of the discrete cosine transform (DCT) with the lifting scheme called...
Fast Multiplierless Approximation of the DCT with the Lifting Scheme (2000)
In this paper, we present a systematic approach to design two families of fast multiplierless approximations of the DCT with the lifting scheme, based on two kinds of factorizations of the DCT matrix...
1 Digital Photography Market Overview Contents (2000)
Wissam Rabadi, Raj Talluri, Klaus Illgner, Jie Liang, Youngjun Yoo
Digital Still Camera Business Unit This article presents a programmable digital signal processor (DSP) platform for digital still cameras based on the Texas Instruments TMS320C54x family. One major...
New Trends in Multimedia Standards: MPEG4 and JPEG2000 (1999)
The dramatic increase in both computational power, brought on by the introduction of increasingly powerful chips, and the communications bandwidth, unleashed by the introduction of cable modem and...
New Trends in Multimedia Standards: MPEG4 and JPEG2000 (1999)
The dramatic increase in both computational power, brought on by the introduction of increasingly powerful chips, and the communications bandwidth, unleashed by the introduction of cable modem and...
Jie Liang, Herbert Edelsbrunner, Ping Fu, Pamidighantam V. Sudhakar, Shankar Subramaniam
ABSTRACT The structures of proteins are well-packed, yet they contain numerous cavities which play key roles in accommodating small molecules, or enabling conformational changes. From high-resolution...
ABSTRACT The serine protease inhibitor antithrombin undergoes extensive conformational changes during functional interaction with its target proteases. Changes include insertion of the reactive loop...
Analytical shape computing of macromolecules I: Molecular area and volume through alpha-shape (1998)
Jie Liang, Herbert Edelsbrunner, Ping Fu, Pamidighantam V. Sudhakar, Shankar Subramaniam
ABSTRACT The structures of proteins are well-packed, yet they contain numerous cavities which play key roles in accommodating small molecules, or enabling conformational changes. From high-resolution...
Computation of molecular electrostatics with boundary element methods (1997)
Jie Liang, Shankar Subramaniam
ABSTRACT In continuum approaches to molecular electrostatics, the boundary element method (BEM) can provide accurate solutions to the Poisson-Boltzmann equation. However, the numerical aspects of...
Early Photolysis Intermediates of Gecko and Bovine Artificial Visual Pigments † (1997)
James W. Lewis, Jie Liang, Thomas G. Ebrey, Mordechai Sheves, Nurit Livnah, Osamu Kuwata, ...
pigments prepared from the cone-type visual pigment, P521, of the Tokay gecko (Gekko gekko) retina. Artificial pigments were prepared by regeneration of bleached gecko photoreceptor membranes with...
Numerical Computing of Molecular Electrostatics through Boundary Integral Equations (1996)
Jie Liang, Shankar Subramaniam
this paper, we apply accurate methods to compute molecular shapes for use in BEM electrostatics calculations. We also determine the desired formulation of BEM which has the advantage of numerical...
Typescript.
Measuring proteins and voids in proteins (1995)
Herbert Edelsbrunner, Michael Face, Ping Fu, Jie Liang
Common geometric models for proteins and other molecules are the space filling diagram, the solvent ac-cessible surface, and the molecular surface. We descnbe software that compules metric properties...
On the Definition and the Construction of Pockets in Macromolecules (1995)
Herbert Edelsbrunner, Michael Facello, Jie Liang
The shape of a protein is important for its functions. This includes the location and size of identifiable regions in its complement space. We formally define pockets as regions in the complement...
Chloride Effect on the Early Photolysis Intermediates of a Gecko Cone-Type Visual Pigment+ (1994)
James W. Lewis, Jie Liang, Thomas G. Ebrey, Mordechai Sheves, David S. Kliger
ABSTRACT: Nanosecond laser photolysis measurements were conducted on the cone-type visual pigment P521 in digitonin extracts of Tokay gecko (Gekko gekko) retina containing physiological chloride ion...
Metarhodopsin Intermediates of the Gecko Cone Pigment P521t (1993)
Jie Liang, Rajni Govindjee, Thomas G. Ebrey
ABSTRACT: Cone visual pigments are responsible for color vision. Using low-temperature spectroscopy and linear/logarithmic time scale flash photolysis, we studied the photochemistry of the cone...
Equidistant binary arithmetic codes (1986)
Jie Liang, Range Cdf, J. Liang, J. Liang, J. Liang, J. Liang, ...
� Arithmetic coding is slow in general: To decode a symbol, we need a series of decisions and multiplications: While (Tag> LOW + RANGE * Sum(n) / N- 1) { n++; � The complexity is greatly...
Chemical complementation identifies a proton acceptor for redox-active tyrosine D in photosystem II
Kim, Sunyoung, Liang, Jie, Barry, Bridgette A.
Through the use of site-directed mutagenesis and chemical rescue, we have identified the proton acceptor for redox-active tyrosine D in photosystem II (PSII). Effects of chemical rescue on the...
CASTp: Computed Atlas of Surface Topography of proteins
Binkowski, T. Andrew, Naghibzadeh, Shapor, Liang, Jie
Computed Atlas of Surface Topography of proteins (CASTp) provides an online resource for locating, delineating and measuring concave surface regions on three-dimensional structures of proteins. These...
Stitziel, Nathan O., Binkowski, T. Andrew, Tseng, Yan Yuan, Kasif, Simon, Liang, Jie
The database of topographic mapping of Single Nucleotide Polymorphism (topoSNP) provides an online resource for analyzing non-synonymous SNPs (nsSNPs) that can be mapped onto known 3D structures of...
Binkowski, T. Andrew, Freeman, Patrick, Liang, Jie
Detecting similar protein surfaces provides an important route for discovering unrecognized or novel functional relationship between proteins. The web server pvSOAR (pocket and void Surfaces Of Amino...
Jung Song, Moon, Hwang, Seungmin, Wong, Wendy, Round, June, Martinez-Guzman, DeeAnn, Turpaz, Yaron, ...
Replication and transcription activator (RTA), an immediate-early gene product of gamma-2 herpesviruses including Kaposi's sarcoma-associated herpesvirus (KSHV) and murine gamma herpesvirus 68...
Hydration effects of heparin on antithrombin probed by osmotic stress.
McGee, Maria P, Liang, Jie, Luba, James
Antithrombin is a key inhibitor of blood coagulation proteases and a prototype metastable protein. Heparin binding to antithrombin induces conformational transitions distal to the binding site. We...
Dundas, Joe, Ouyang, Zheng, Tseng, Jeffery, Binkowski, Andrew, Turpaz, Yaron, Liang, Jie
Cavities on a proteins surface as well as specific amino acid positioning within it create the physicochemical properties needed for a protein to perform its function. CASTp () is an online tool that...
Chemical complementation identifies a proton acceptor for redox-active tyrosine D in photosystem II
Kim, Sunyoung, Liang, Jie, Barry, Bridgette A.
Through the use of site-directed mutagenesis and chemical rescue, we have identified the proton acceptor for redox-active tyrosine D in photosystem II (PSII). Effects of chemical rescue on the...
CASTp: Computed Atlas of Surface Topography of proteins
Binkowski, T. Andrew, Naghibzadeh, Shapor, Liang, Jie
Computed Atlas of Surface Topography of proteins (CASTp) provides an online resource for locating, delineating and measuring concave surface regions on three-dimensional structures of proteins. These...
Stitziel, Nathan O., Binkowski, T. Andrew, Tseng, Yan Yuan, Kasif, Simon, Liang, Jie
The database of topographic mapping of Single Nucleotide Polymorphism (topoSNP) provides an online resource for analyzing non-synonymous SNPs (nsSNPs) that can be mapped onto known 3D structures of...
Binkowski, T. Andrew, Freeman, Patrick, Liang, Jie
Detecting similar protein surfaces provides an important route for discovering unrecognized or novel functional relationship between proteins. The web server pvSOAR (pocket and void Surfaces Of Amino...
Jung Song, Moon, Hwang, Seungmin, Wong, Wendy, Round, June, Martinez-Guzman, DeeAnn, Turpaz, Yaron, ...
Replication and transcription activator (RTA), an immediate-early gene product of gamma-2 herpesviruses including Kaposi's sarcoma-associated herpesvirus (KSHV) and murine gamma herpesvirus 68...
Hydration effects of heparin on antithrombin probed by osmotic stress.
McGee, Maria P, Liang, Jie, Luba, James
Antithrombin is a key inhibitor of blood coagulation proteases and a prototype metastable protein. Heparin binding to antithrombin induces conformational transitions distal to the binding site. We...
Dundas, Joe, Ouyang, Zheng, Tseng, Jeffery, Binkowski, Andrew, Turpaz, Yaron, Liang, Jie
Cavities on a proteins surface as well as specific amino acid positioning within it create the physicochemical properties needed for a protein to perform its function. CASTp () is an online tool that...
Protein surface analysis for function annotation in high-throughput structural genomics pipeline
Binkowski, T. Andrew, Joachimiak, Andrzej, Liang, Jie
Structural genomics (SG) initiatives are expanding the universe of protein fold space by rapidly determining structures of proteins that were intentionally selected on the basis of low sequence...
Nathan O. Stitziel, Yan Yuan Tseng, Dimitri Pervouchine, David Goddeau, Simon Kasif, Jie Liang
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Predicting protein folding rates from geometric contact and amino acid sequence
Protein folding speeds are known to vary over more than eight orders of magnitude. Plaxco, Simons, and Baker (see References) first showed a correlation of folding speed with the topology of the...
Lin, Ming, Lu, Hsiao-Mei, Chen, Rong, Liang, Jie
Inferring three-dimensional structural information of biomacromolecules such as proteins from limited experimental data is an important and challenging task. Nuclear Overhauser effect measurements...
Large macromolecular assemblies are often important for biological processes in cells. Allosteric communications between different parts of these molecular machines play critical roles in cellular...