Finding local communities in protein networks (2009)
Voevodski, Konstantin, Teng, Shang-Hua, Xia, Yu
Abstract Background Protein-protein interactions (PPIs) play fundamental roles in nearly all biological processes, and provide major insights into the inner workings of cells. A vast amount of PPI...
Linghu, Bolan, Snitkin, Evan S, Hu, Zhenjun, Xia, Yu, DeLisi, Charles
Abstract We integrate 16 genomic features to construct an evidence-weighted functional-linkage network comprising 21,657 human genes. The functional-linkage network is used to prioritize candidate...
Ram Samudrala A, Yu Xia, Michael Levitt, Enoch S Huang
An approach to construct low resolution models of protein structure from sequence information using a combination of di erent methodologies is described. All possible compact self-avoiding C...
Liu, Qiji, Xia, Yu, Zhang, Wenjing, Li, Jisheng, Wang, Pin, Li, Huaichen, ...
Abstract Background Mutation in SPINK5 causes Netherton syndrome, a rare recessive skin disease that is accompanied by severe atopic manifestations including atopic dermatitis, allergic rhinitis,...
Two-dimensional Second-Order Cone Programming (2009)
We show that the primal and dual 2-dimensional second-order cone programs in standard form are equivalent to the standard-form primal and dual linear programs via a linear transformation. We show how...
Two-dimensional Second-Order Cone Programming (2009)
We show that the primal and dual 2-dimensional second-order cone programs in standard form are equivalent to the standard-form primal and dual linear programs via a linear transformation. We show how...
Lean Implementations of Software Testing Tools Using XML Representations of Source Codes (2009)
Abstract—By utilizing XML representations of source programs under test, a new approach is proposed to concisely implement some prototypes for TACCLE, a software testing methodology. The...
Collins Brian, Vahdat Saloomeh, Erickson Kelly, Collins Sean, Suy Simeng, Yu Xia, ...
Abstract Objective Curative surgery is not an option for many patients with clinical stage I non-small-cell lung carcinoma (NSCLC), but radical radiosurgery may be effective. Methods Inoperable...
Wang, Yong, Zhang, Xiang-Sun, Xia, Yu
Transcriptional cooperativity among several transcription factors (TFs) is believed to be the main mechanism of complexity and precision in transcriptional regulatory programs. Here, we present a...
alpha-associated zinc- nger protein using (2008)
Ram Samudrala A, Yu Xia, Michael Levitt, Naomi J Cotton, Enoch S Huang, Ralph Davis
Probing structure-function relationships of the DNA polymerase
Ram Samudrala A, Yu Xia, Michael Levitt, Enoch S Huang
An approach to construct low resolution models of protein structure from sequence information using a combination of di erent methodologies is described. All possible compact self-avoiding C...
High-precision high-coverage functional inference from integrated data sources (2008)
Linghu, Bolan, Snitkin, Evan S, Holloway, Dustin T, Gustafson, Adam M, Xia, Yu, DeLisi, Charles
Abstract Background Information obtained from diverse data sources can be combined in a principled manner using various machine learning methods to increase the reliability and range of knowledge...
Selection and Characterization of Small Random (2008)
Transmembrane Proteins That, Ann M. Dixon, Jennifer B. Frank, Yu Xia, Lara Ely, ...
this article can be found at doi: 10.1016/j.jmb.2004.03.044 E-mail address of the corresponding author: daniel.dimaio@yale.edu Abbreviations used: PDGF, platelet-derived growth factor; CAT,...
A Combined Approach For Ab Initio Construction Of Low Resolution Protein Tertiary Structures (2008)
From Sequence Ram, Ram Samudrala B, Yu Xia, Michael Levitt, Enoch S Huang
Introduction The prediction of protein three dimensional structure from sequence alone with accuracy rivalling that of experiment is an unsolved problem. However, for certain classes of small...
Annotation Transfer Between Genomes: (2008)
Protein–protein Interologs, Haiyuan Yu, Nicholas M. Luscombe, Hao Xin Lu, Xiaowei Zhu, ...
this paper, we present results from both approaches
Bmc Bioinformatics, Bolan Linghu, Evan S Snitkin, Dustin T Holloway, Adam M Gustafson, Yu Xia, ...
Research article High-precision high-coverage functional inference from integrated data sources
Liang, Xiaorong, Han, Hongling, Xia, Yu, McLuckey, Scott A.
A pulsed triple ionization source, using a common atmosphere/vacuum interface and ion path, has been developed to generate different types of ions for sequential ion/ion reaction experiments in a...
Design principles of molecular networks revealed by global comparisons and composite motifs (2006)
Yu, Haiyuan, Xia, Yu, Trifonov, Valery, Gerstein, Mark
Abstract Background Molecular networks are of current interest, particularly with the publication of many large-scale datasets. Previous analyses have focused on topologic structures of individual...
Ion/ion reactions in a linear ion trap (LIT) are of great interest because LITs provide significantly higher trapping efficiency and trapping capacity for externally injected ions than...
Printable electronics: patterning of conductive materials for novel applications (2005)
Karwa, Anupama, Xia, Yu, Clark, Daniel, Smith, Thomas, Kahn, Bruce
Article may be found at: http://www.mrs.org/s_mrs/sec_subscribe.asp?CID=2684&DID=114329&action=detail
Printable electronics: patterning of conductive materials for novel applications (2005)
Karwa, Anupama, Xia, Yu, Clark, Daniel, Smith, Thomas, Kahn, Bruce
Article may be found at: http://www.mrs.org/s_mrs/sec_subscribe.asp?CID=2684&DID=114329&action=detail
Fabrication of electronic devices using high volume printing techniques / (2005)
This thesis studies the possibility of using high volume offset lithographic and flexographic printing to fabricate single and multiple layer electronic devices, and discusses the performance and...
A new theoretical framework for K-means-type clustering (2005)
One of the fundamental clustering problems is to assign n points into k clusters based on the minimal sum-of-squares(MSSC), which is known to be NP-hard. In this paper, by using matrix arguments, we...
Balasubramanian, Suganthi, Xia, Yu, Freinkman, Elizaveta, Gerstein, Mark
We assessed the disease-causing potential of single nucleotide polymorphisms (SNPs) based on a simple set of sequence-based features. We focused on SNPs from the dbSNP database in G-protein-coupled...
Assessing the limits of genomic data integration for predicting protein networks (2005)
Lu, Long J., Xia, Yu, Paccanaro, Alberto, Yu, Haiyuan, Gerstein, Mark
Genomic data integration—the process of statistically combining diverse sources of information from functional genomics experiments to make large-scale predictions—is becoming increasingly...
Analyzing cellular biochemistry in terms of molecular networks (2004)
Yu Xia, Haiyuan Yu, Ronald Jansen, Michael Seringhaus, Sarah Baxter, Dov Greenbaum, ...
Key Words genome-wide high-throughput experiments, protein-protein interaction networks, regulatory networks, integration and prediction, network topology f Abstract One way to understand cells and...
To understand the physical and evolutionary determinants of protein folding, we map out the complete organization of thermodynamic and kinetic properties for protein sequences that share the same...
Sequence variation in G-protein-coupled receptors: (2004)
Suganthi Balasubramanian, Yu Xia, Elizaveta Freinkman, Mark Gerstein
analysis of single nucleotide polymorphisms
Annotation Transfer Between Genomes: Protein-Protein Interologs and Protein-DNA Regulogs (2004)
Yu, Haiyuan, Luscombe, Nicholas M., Lu, Hao Xin, Zhu, Xiaowei, Xia, Yu, Han, Jing-Dong J., ...
Proteins function mainly through interactions, especially with DNA and other proteins. While some large-scale interaction networks are now available for a number of model organisms, their...
Thesis (Ph. D.)--University of Virginia, 2003.
Thesis (Ph. D.)--University of Virginia, 2003.
Thesis (Ph. D.)--University of Virginia, 2003.
Thesis (M.S.)--Ohio University, March, 2003.
Xia, Yu., Levitt, Michael Advisor
Submitted to the Department of Chemistry.
Design of an optimal Chebyshev-expanded discrimination function for globular proteins (2002)
Boris Fain, Yu Xia, Michael Levitt
We describe the construction of a scoring function designed to model the free energy of protein folding. An optimization technique is used to determine the best functional forms of the hydrophobic,...
Design of an optimal Chebyshev-expanded discrimination function for globular proteins (2002)
Fain, Boris, Xia, Yu, Levitt, Michael
We describe the construction of a scoring function designed to model the free energy of protein folding. An optimization technique is used to determine the best functional forms of the hydrophobic,...
Ab initio construction of protein tertiary structures using a hierarchical approach (2000)
Yu Xia, Enoch S. Huang, Michael Levitt, Ram Samudrala
*Corresponding authors
Ram Samudrala, Yu Xia, Michael Levitt, Naomi J. Cotton, Enoch S Huang, Ralph Davis
this paper is on one protein, we have applied this approach using a combination of theoretical and experimental data, guided by intuition, to attempt to predict structure/function relationships of...
Ram Samudrala, Yu Xia, Michael Levitt, Enoch S. Huang
Introduction The prediction of protein three dimensional structure from sequence alone with accuracy rivalling that of experiment is an unsolved problem. However, for certain classes of small...
Ab initio protein structure prediction using a combined hierarchical approach (1999)
Ram Samudrala, Yu Xia, Enoch Huang, Michael Levitt
predict the three-dimensional structures for 13 proteins using a hierarchical approach. First, all possible compact conformations of a protein sequence are enumerated using a highly simplified...
A Sparse Image Method for BEM Capacitance Extraction (1996)
Abstract—Boundary element methods (BEM) are often used for complex 3-D capacitance extraction because of their efficiency, ease of data preparation, and automatic handling of open regions. BEM...
Molecular Modeling and Design of Invariant Chain Peptides with Altered (1996)
Dissociation Kinetics From, Michael N. Liang, Christopher Lee, Yu Xia, Harden M. Mcconnell
We have used molecular modeling to design substitutions in an invariant chain-derived peptide (CLIP), so as to alter the stability of its complex with class II major histocompatibility complex (MHC)...
BEM capacitance extraction using shift and truncate electrostatic potentials / (1995)
Report (M.S.)--University of Texas at Austin, 1995.
Phylogenetic analysis of the genus Azospirillum /--by Yu Xia. (1994)
Thesis (Ph. D.)--University of Newcastle upon Tyne, 1994.
Phlogenetic analysis of the genus Azospirillum. (1994)
Thesis (Ph. D.)--University of Newcastle upon Tyne, 1994.
McSharry, Charles, Xia, Yu, Holland, Celia V., Kennedy, Malcolm W.
Children putatively immune to the large roundworm Ascaris lumbricoides were identified in an area of Nigeria where infection is hyperendemic. Immunity was associated with higher levels of serum...
Roles of mutation and recombination in the evolution of protein thermodynamics
We present a comprehensive study of the evolutionary origin of the thermodynamic behavior of proteins. With the use of a simplified model, we exhaustively enumerate the space of all sequences and the...
Annotation Transfer Between Genomes: Protein–Protein Interologs and Protein–DNA Regulogs
Yu, Haiyuan, Luscombe, Nicholas M., Lu, Hao Xin, Zhu, Xiaowei, Xia, Yu, Han, Jing-Dong J., ...
Proteins function mainly through interactions, especially with DNA and other proteins. While some large-scale interaction networks are now available for a number of model organisms, their...
Sequence variation in G-protein-coupled receptors: analysis of single nucleotide polymorphisms
Balasubramanian, Suganthi, Xia, Yu, Freinkman, Elizaveta, Gerstein, Mark
We assessed the disease-causing potential of single nucleotide polymorphisms (SNPs) based on a simple set of sequence-based features. We focused on SNPs from the dbSNP database in G-protein-coupled...
Huber, Damon, Boyd, Dana, Xia, Yu, Olma, Michael H., Gerstein, Mark, Beckwith, Jon
We have previously reported that the DsbA signal sequence promotes efficient, cotranslational translocation of the cytoplasmic protein thioredoxin-1 via the bacterial signal recognition particle...
Assessing the limits of genomic data integration for predicting protein networks
Lu, Long J., Xia, Yu, Paccanaro, Alberto, Yu, Haiyuan, Gerstein, Mark
Genomic data integration—the process of statistically combining diverse sources of information from functional genomics experiments to make large-scale predictions—is becoming increasingly...
McSharry, Charles, Xia, Yu, Holland, Celia V., Kennedy, Malcolm W.
Children putatively immune to the large roundworm Ascaris lumbricoides were identified in an area of Nigeria where infection is hyperendemic. Immunity was associated with higher levels of serum...
Roles of mutation and recombination in the evolution of protein thermodynamics
We present a comprehensive study of the evolutionary origin of the thermodynamic behavior of proteins. With the use of a simplified model, we exhaustively enumerate the space of all sequences and the...
Annotation Transfer Between Genomes: Protein–Protein Interologs and Protein–DNA Regulogs
Yu, Haiyuan, Luscombe, Nicholas M., Lu, Hao Xin, Zhu, Xiaowei, Xia, Yu, Han, Jing-Dong J., ...
Proteins function mainly through interactions, especially with DNA and other proteins. While some large-scale interaction networks are now available for a number of model organisms, their...
Sequence variation in G-protein-coupled receptors: analysis of single nucleotide polymorphisms
Balasubramanian, Suganthi, Xia, Yu, Freinkman, Elizaveta, Gerstein, Mark
We assessed the disease-causing potential of single nucleotide polymorphisms (SNPs) based on a simple set of sequence-based features. We focused on SNPs from the dbSNP database in G-protein-coupled...
Huber, Damon, Boyd, Dana, Xia, Yu, Olma, Michael H., Gerstein, Mark, Beckwith, Jon
We have previously reported that the DsbA signal sequence promotes efficient, cotranslational translocation of the cytoplasmic protein thioredoxin-1 via the bacterial signal recognition particle...
Assessing the limits of genomic data integration for predicting protein networks
Lu, Long J., Xia, Yu, Paccanaro, Alberto, Yu, Haiyuan, Gerstein, Mark
Genomic data integration—the process of statistically combining diverse sources of information from functional genomics experiments to make large-scale predictions—is becoming increasingly...
Design principles of molecular networks revealed by global comparisons and composite motifs
Yu, Haiyuan, Xia, Yu, Trifonov, Valery, Gerstein, Mark
A global comparison of the four basic molecular networks in yeast - regulatory, co-expression, interaction and metabolic - reveals general design principles.
The role of disorder in interaction networks: a structural analysis
Kim, Philip M, Sboner, Andrea, Xia, Yu, Gerstein, Mark
Recent studies have emphasized the value of including structural information into the topological analysis of protein networks. Here, we utilized structural information to investigate the role of...
High-precision high-coverage functional inference from integrated data sources
Linghu, Bolan, Snitkin, Evan S, Holloway, Dustin T, Gustafson, Adam M, Xia, Yu, DeLisi, Charles
Design of an optimal Chebyshev-expanded discrimination function for globular proteins
Fain, Boris, Xia, Yu, Levitt, Michael
We describe the construction of a scoring function designed to model the free energy of protein folding. An optimization technique is used to determine the best functional forms of the hydrophobic,...
Ab Initio Protein Structure Prediction Using a Combined Hierarchical Approach
Ram Samudrala, Yu Xia, Enoch Huang, Michael Levitt
As part of the third Critical Assessment of Structure Prediction meeting (CASP3), we predict the three-dimensional structures for 13 proteins using a hierarchical approach. First, all possible...
Integrated Assessment of Genomic Correlates of Protein Evolutionary Rate
Xia, Yu, Franzosa, Eric A., Gerstein, Mark B.
Rates of evolution differ widely among proteins, but the causes and consequences of such differences remain under debate. With the advent of high-throughput functional genomics, it is now possible to...
A functional polymorphism in the SPINK5 gene is associated with asthma in a Chinese Han Population
Liu, Qiji, Xia, Yu, Zhang, Wenjing, Li, Jisheng, Wang, Pin, Li, Huaichen, ...
Blasius, Amanda L., Brandl, Katharina, Crozat, Karine, Xia, Yu, Khovananth, Kevin, Krebs, Philippe, ...
The classical recessive coat color mutation misty (m) arose spontaneously on the DBA/J background and causes generalized hypopigmentation and localized white-spotting in mice, with a lack of pigment...
Wang, Yong, Zhang, Xiang-Sun, Xia, Yu
Transcriptional cooperativity among several transcription factors (TFs) is believed to be the main mechanism of complexity and precision in transcriptional regulatory programs. Here, we present a...
Linghu, Bolan, Snitkin, Evan S, Hu, Zhenjun, Xia, Yu, DeLisi, Charles
An evidence-weighted functional-linkage network of human genes reveals associations among diseases that share no known disease genes and have dissimilar phenotypes
Wang, Zhi-Qiang, Si, Lizhen, Tang, Quan, Lin, Debao, Fu, Zhangjie, Zhang, Jing, ...
Familial progressive hyperpigmentation (FPH) is an autosomal-dominantly inherited disorder characterized by hyperpigmented patches in the skin, present in early infancy and increasing in size and...