Jiang Qian, Marisa Dolled-filhart, Jimmy Lin, Haiyuan Yu, Mark Gerstein
The complexity of biological systems provides for a great diversity of relationships between genes. The current analysis of whole-genome expression data focuses on relationships based on global...
An empirical framework for binary interactome mapping (2009)
Venkatesan, Kavitha, Rual, Jean-Francois, Vazquez, Alexei, Stelzl, Ulrich, Lemmens, Irma, Hirozane-Kishikawa, Tomoko, ...
Several attempts have been made to systematically map protein-protein interaction, or 'interactome', networks. However, it remains difficult to assess the quality and coverage of existing data sets....
An experimentally derived confidence score for binary protein-protein interactions (2009)
Braun, Pascal, Tasan, Murat, Dreze, Matija, Barrios-Rodiles, Miriam, Lemmens, Irma, Yu, Haiyuan, ...
Information on protein-protein interactions is of central importance for many areas of biomedical research. At present no method exists to systematically and experimentally assess the quality of...
Simonis, Nicolas, Rual, Jean-Francois, Carvunis, Anne-Ruxandra, Tasan, Murat, Lemmens, Irma, Hirozane-Kishikawa, Tomoko, ...
Abstract: To provide accurate biological hypotheses and elucidate global properties of cellular networks, systematic identification of protein-protein interactions must meet high quality standards....
Inferring Protein-Protein Interactions Using Interaction Network Topologies (2008)
Alberto Paccanaro, Valery Trifonov, Haiyuan Yu, Mark Gerstein
[ ∗ these authors contributed equally to this work] Abstract — We describe two novel methods for predicting protein interactions, using only the topology of an observed protein interaction...
BIOINFORMATICS ORIGINAL PAPER Systems biology (2008)
Haiyuan Yu, Alberto Paccanaro, Valery Trifonov, Mark Gerstein
Vol. 22 no. 7 2006, pages 823–829 doi:10.1093/bioinformatics/btl014 Predicting interactions in protein networks by completing defective cliques
Kevin Y. Yip, Haiyuan Yu, Philip M. Kim, Martin Schultz, Mark Gerstein
Biological processes involve complex networks of interactions between molecules. Various large-scale experiments and curation efforts have led to preliminary versions of complete cellular networks...
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
Revisiting the Saccharomyces cerevisiae predicted ORFeome (2008)
Li, Qian-Ru, Carvunis, Anne-Ruxandra, Yu, Haiyuan, Han, Jing-Dong J., Zhong, Quan, Simonis, Nicolas, ...
Accurately defining the coding potential of an organism, i.e., all protein-encoding open reading frames (ORFs) or “ORFeome,” is a prerequisite to fully understand its biology. ORFeome annotation...
Yu, Haiyuan, Jansen, Ronald, Stolovitzky, Gustavo, Gerstein, Mark
Motivation: Many classifications of protein function such as Gene Ontology (GO) are organized in directed acyclic graph (DAG) structures. In these classifications, the proteins are terminal leaf...
Haiyuan Yu, Philip M. Kim, Emmett Sprecher, Valery Trifonov, Mark Gerstein
It has been a long-standing goal in systems biology to find relations between the topological properties and functional features of protein networks. However, most of the focus in network studies has...
Haiyuan Yu, Philip M. Kim, Emmett Sprecher, Valery Trifinov, Mark Gerstein
It has been a long-standing goal in systems biology to find relations between the topological properties and functional features of protein networks. However, most of the focus in network studies has...
Yu, Haiyuan, Nguyen, Katherine, Royce, Tom, Qian, Jiang, Nelson, Kenneth, Snyder, Michael, ...
Microarray technology is currently one of the most widely-used technologies in biology. Many studies focus on inferring the function of an unknown gene from its co-expressed genes. Here, we are able...
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...
Predicting interactions in protein networks by completing defective cliques (2006)
Haiyuan Yu, Alberto Paccanaro, Valery Trifonov, Mark Gerstein
defective cliques
Yip, Kevin Y., Yu, Haiyuan, Kim, Philip M., Schultz, Martin, Gerstein, Mark
Summary: Biological processes involve complex networks of interactions between molecules. Various large-scale experiments and curation efforts have led to preliminary versions of complete cellular...
Predicting interactions in protein networks by completing defective cliques (2006)
Yu, Haiyuan, Paccanaro, Alberto, Trifonov, Valery, Gerstein, Mark
Datasets obtained by large-scale, high-throughput methods for detecting protein–protein interactions typically suffer from a relatively high level of noise. We describe a novel method for improving...
Yu, Haiyuan, Nguyen, Katherine, Royce, Tom, Qian, Jiang, Nelson, Kenneth, Snyder, Michael, ...
Microarray technology is currently one of the most widely-used technologies in biology. Many studies focus on inferring the function of an unknown gene from its co-expressed genes. Here, we are able...
Target hub proteins serve as master regulators of development in yeast (2006)
Borneman, Anthony R., Leigh-Bell, Justine A., Yu, Haiyuan, Bertone, Paul, Gerstein, Mark, Snyder, Michael
To understand the organization of the transcriptional networks that govern cell differentiation, we have investigated the transcriptional circuitry controlling pseudohyphal development in...
Yu, Haiyuan, Nguyen, Katherine, Royce, Tom, Qian, Jiang, Nelson, Kenneth, Snyder, Michael, ...
Microarray technology is currently one of the most widely-used technologies in biology. Many studies focus on inferring the function of an unknown gene from its co-expressed genes. Here, we are able...
Genomics analysis of large-scale biological networks and their relationships [microform] / (2005)
Thesis (Ph. D.)--Yale University, 2005.
Genomics analysis of large-scale biological networks and their relationships / (2005)
Thesis (Ph. D.)--Yale University, 2005.
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...
Biochemical and genetic analysis of the yeast proteome with a movable ORF collection (2005)
Gelperin, Daniel M., White, Michael A., Wilkinson, Martha L., Kon, Yoshiko, Kung, Li A., Wise, Kevin J., ...
Functional analysis of the proteome is an essential part of genomic research. To facilitate different proteomic approaches, a MORF (moveable ORF) library of 5854 yeast expression plasmids was...
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...
Yu, Haiyuan, Zhu, Xiaowei, Greenbaum, Dov, Karro, John, Gerstein, Mark
Biological networks are a topic of great current interest, particularly with the publication of a number of large genome‐wide interaction datasets. They are globally characterized by a variety...
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...
Relationship between gene co-expression and probe localization on microarray slides (2003)
Kluger, Yuval, Yu, Haiyuan, Qian, Jiang, Gerstein, Mark
Abstract Background Microarray technology allows simultaneous measurement of thousands of genes in a single experiment. This is a potentially useful tool for evaluating co-expression of genes and...
Qian, Jiang, Lin, Jimmy, Luscombe, Nicholas M., Yu, Haiyuan, Gerstein, Mark
Motivation: Defining regulatory networks, linking transcription factors (TFs) to their targets, is a central problem in post-genomic biology. One might imagine one could readily determine these...
Qian, Jiang, Stenger, Brad, Wilson, Cyrus A., Lin, Jimmy, Jansen, Ronald, Teichmann, Sarah A., ...
As the number of protein folds is quite limited, a mode of analysis that will be increasingly common in the future, especially with the advent of structural genomics, is to survey and re-survey the...
Jiao, Yuling, Yang, Hongjuan, Ma, Ligeng, Sun, Ning, Yu, Haiyuan, Liu, Tie, ...
A microarray based on PCR amplicons of 1,864 confirmed and predicted Arabidopsis transcription factor genes was produced and used to profile the global expression pattern in seedlings, specifically...
Yu, Haiyuan, Zhu, Xiaowei, Greenbaum, Dov, Karro, John, Gerstein, Mark
Biological networks are a topic of great current interest, particularly with the publication of a number of large genome-wide interaction datasets. They are globally characterized by a variety of...
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...
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...
Biochemical and genetic analysis of the yeast proteome with a movable ORF collection
Gelperin, Daniel M., White, Michael A., Wilkinson, Martha L., Kon, Yoshiko, Kung, Li A., Wise, Kevin J., ...
Functional analysis of the proteome is an essential part of genomic research. To facilitate different proteomic approaches, a MORF (moveable ORF) library of 5854 yeast expression plasmids was...
Target hub proteins serve as master regulators of development in yeast
Borneman, Anthony R., Leigh-Bell, Justine A., Yu, Haiyuan, Bertone, Paul, Gerstein, Mark, Snyder, Michael
To understand the organization of the transcriptional networks that govern cell differentiation, we have investigated the transcriptional circuitry controlling pseudohyphal development in...
Qian, Jiang, Stenger, Brad, Wilson, Cyrus A., Lin, Jimmy, Jansen, Ronald, Teichmann, Sarah A., ...
As the number of protein folds is quite limited, a mode of analysis that will be increasingly common in the future, especially with the advent of structural genomics, is to survey and re-survey the...
Jiao, Yuling, Yang, Hongjuan, Ma, Ligeng, Sun, Ning, Yu, Haiyuan, Liu, Tie, ...
A microarray based on PCR amplicons of 1,864 confirmed and predicted Arabidopsis transcription factor genes was produced and used to profile the global expression pattern in seedlings, specifically...
Yu, Haiyuan, Zhu, Xiaowei, Greenbaum, Dov, Karro, John, Gerstein, Mark
Biological networks are a topic of great current interest, particularly with the publication of a number of large genome-wide interaction datasets. They are globally characterized by a variety of...
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...
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...
Biochemical and genetic analysis of the yeast proteome with a movable ORF collection
Gelperin, Daniel M., White, Michael A., Wilkinson, Martha L., Kon, Yoshiko, Kung, Li A., Wise, Kevin J., ...
Functional analysis of the proteome is an essential part of genomic research. To facilitate different proteomic approaches, a MORF (moveable ORF) library of 5854 yeast expression plasmids was...
Target hub proteins serve as master regulators of development in yeast
Borneman, Anthony R., Leigh-Bell, Justine A., Yu, Haiyuan, Bertone, Paul, Gerstein, Mark, Snyder, Michael
To understand the organization of the transcriptional networks that govern cell differentiation, we have investigated the transcriptional circuitry controlling pseudohyphal development in...
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.
Yu, Haiyuan, Nguyen, Katherine, Royce, Tom, Qian, Jiang, Nelson, Kenneth, Snyder, Michael, ...
Microarray technology is currently one of the most widely-used technologies in biology. Many studies focus on inferring the function of an unknown gene from its co-expressed genes. Here, we are able...
Genomic analysis of the hierarchical structure of regulatory networks
A fundamental question in biology is how the cell uses transcription factors (TFs) to coordinate the expression of thousands of genes in response to various stimuli. The relationships between TFs and...
Yu, Haiyuan, Kim, Philip M, Sprecher, Emmett, Trifonov, Valery, Gerstein, Mark
It has been a long-standing goal in systems biology to find relations between the topological properties and functional features of protein networks. However, most of the focus in network studies has...
Revisiting the Saccharomyces cerevisiae predicted ORFeome
Li, Qian-Ru, Carvunis, Anne-Ruxandra, Yu, Haiyuan, Han, Jing-Dong J., Zhong, Quan, Simonis, Nicolas, ...
Accurately defining the coding potential of an organism, i.e., all protein-encoding open reading frames (ORFs) or “ORFeome,” is a prerequisite to fully understand its biology. ORFeome annotation...
Tonikian, Raffi, Xin, Xiaofeng, Toret, Christopher P., Gfeller, David, Landgraf, Christiane, Panni, Simona, ...
A genome-scale specificity and interaction map for yeast SH3 domain-containing proteins reveal how family members show selective binding to target proteins and predicts the dynamic localization of...