Dov Greenbaum, Nicholas M. Luscombe, Ronald Jansen, Jiang Qian, Mark Gerstein
With the completion of genome sequences, the current challenge for biology is to determine the functions of all gene products and to understand how they contribute in making an organism viable. For...
DRAFT 2 Functions of the Arabidopsis microRNA and siRNA Systems (2008)
Michael Snyder, Heng Zhu, Christine Horak, Anuj Kumar, Ghia Euskirchen, Rebecca Goetsch, ...
The genomes of a wide variety of organisms have now been sequenced; a major challenge ahead is to identify genes and their encoded projects and to understand their function and regulation. For the...
Mark Gerstein, Ronald Jansen, Ted Johnson, Jerry Tsai, Werner Krebs
We describe database approaches taken in our lab to the study of protein and nucleic acid motions. We have developed a database of macromolecular motions, which is accessible on the World Wide Web...
Letter Relating Whole-Genome Expression Data with Protein-Protein Interactions (2007)
Ronald Jansen, Dov Greenbaum, Mark Gerstein
We investigate the relationship of protein-protein interactions with mRNA expression levels, by integrating a variety of data sources for yeast. We focus on known protein complexes that have clearly...
Ronald Jansen, Mark Gerstein T, Whitney Avenue
Genom.e-wide a.nalysis relating expression level wth proten subcellular localization
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...
Signal Processing in the TGF-β Superfamily Ligand-Receptor Network (2006)
The TGF-β pathway plays a central role in tissue homeostasis and morphogenesis. It transduces a variety of extracellular signals into intracellular transcriptional responses that control a plethora...
Signal processing in the TGF-β superfamily ligand-receptor network (2005)
The TGF-β pathway plays a central role in tissue homeostasis and morphogenesis. It transduces a variety of extracellular signals into intracellular transcriptional responses that control a plethora...
Signal processing in the TGF-beta superfamily ligand-receptor network (2005)
Vilar, Jose M. G., Jansen, Ronald, Sander, Chris
The TGF-beta pathway plays a central role in tissue homeostasis and morphogenesis. It transduces a variety of extracellular signals into intracellular transcriptional responses that control a...
Information assessment on predicting protein-protein interactions (2004)
Lin, Nan, Wu, Baolin, Jansen, Ronald, Gerstein, Mark, Zhao, Hongyu
Abstract Background Identifying protein-protein interactions is fundamental for understanding the molecular machinery of the cell. Proteome-wide studies of protein-protein interactions are of...
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...
Information assessment on predicting protein-protein interactions (2004)
Bmc Bioinformatics, Nan Lin, Baolin Wu, Ronald Jansen, Mark Gerstein, Hongyu Zhao, ...
Research article
Jansen, Ronald, Bussemaker, Harmen J., Gerstein, Mark
Highly expressed genes in many bacteria and small eukaryotes often have a strong compositional bias, in terms of codon usage. Two widely used numerical indices, the codon adaptation index (CAI) and...
Thesis (Ph. D.)--Yale University, 2002.
Computational proteomics : integrating expression data with genome-wide information / (2002)
Thesis (Ph. D.)--Yale University, 2002.
Greenbaum, Dov, Jansen, Ronald, Gerstein, Mark
Motivation: Protein abundance is related to mRNA expression through many different cellular processes. Up to now, there have been conflicting results on how correlated the levels of these two...
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...
Jansen, Ronald, Gerstein, Mark
We analyzed 10 genome expression data sets by large-scale cross-referencing against broad structural and functional categories. The data sets, generated by different techniques (e.g. SAGE and gene...
Studying Macromolecular Motions in a Database Framework: From Structure to Sequence (1999)
Mark Gerstein, Ronald Jansen, Ted Johnson, Jerry Tsai, Werner Krebs
We describe database approaches taken in our lab to the study of protein and nucleic acid motions. We have developed a database of macromolecular motions, which is accessible on the World Wide Web...
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...
Jansen, Ronald, Gerstein, Mark
We analyzed 10 genome expression data sets by large-scale cross-referencing against broad structural and functional categories. The data sets, generated by different techniques (e.g. SAGE and gene...
Jansen, Ronald, Bussemaker, Harmen J., Gerstein, Mark
Highly expressed genes in many bacteria and small eukaryotes often have a strong compositional bias, in terms of codon usage. Two widely used numerical indices, the codon adaptation index (CAI) and...
Mateos, Alvaro, Dopazo, Joaquín, Jansen, Ronald, Tu, Yuhai, Gerstein, Mark, Stolovitzky, Gustavo
Recent advances in microarray technology have opened new ways for functional annotation of previously uncharacterised genes on a genomic scale. This has been demonstrated by unsupervised clustering...
Information assessment on predicting protein-protein interactions
Lin, Nan, Wu, Baolin, Jansen, Ronald, Gerstein, Mark, Zhao, Hongyu
Signal Processing in the TGF-β Superfamily Ligand-Receptor Network
Vilar, Jose M. G, Jansen, Ronald, Sander, Chris
The TGF-β pathway plays a central role in tissue homeostasis and morphogenesis. It transduces a variety of extracellular signals into intracellular transcriptional responses that control a plethora...
Relating Whole-Genome Expression Data with Protein-Protein Interactions
Jansen, Ronald, Greenbaum, Dov, Gerstein, Mark
We investigate the relationship of protein-protein interactions with mRNA expression levels, by integrating a variety of data sources for yeast. We focus on known protein complexes that have clearly...
Subcellular localization of the yeast proteome
Kumar, Anuj, Agarwal, Seema, Heyman, John A., Matson, Sandra, Heidtman, Matthew, Piccirillo, Stacy, ...
Protein localization data are a valuable information resource helpful in elucidating eukaryotic protein function. Here, we report the first proteome-scale analysis of protein localization within any...
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...
Jansen, Ronald, Gerstein, Mark
We analyzed 10 genome expression data sets by large-scale cross-referencing against broad structural and functional categories. The data sets, generated by different techniques (e.g. SAGE and gene...
Jansen, Ronald, Bussemaker, Harmen J., Gerstein, Mark
Highly expressed genes in many bacteria and small eukaryotes often have a strong compositional bias, in terms of codon usage. Two widely used numerical indices, the codon adaptation index (CAI) and...
Relating Whole-Genome Expression Data with Protein-Protein Interactions
Jansen, Ronald, Greenbaum, Dov, Gerstein, Mark
We investigate the relationship of protein-protein interactions with mRNA expression levels, by integrating a variety of data sources for yeast. We focus on known protein complexes that have clearly...
Subcellular localization of the yeast proteome
Kumar, Anuj, Agarwal, Seema, Heyman, John A., Matson, Sandra, Heidtman, Matthew, Piccirillo, Stacy, ...
Protein localization data are a valuable information resource helpful in elucidating eukaryotic protein function. Here, we report the first proteome-scale analysis of protein localization within any...
Mateos, Alvaro, Dopazo, Joaquín, Jansen, Ronald, Tu, Yuhai, Gerstein, Mark, Stolovitzky, Gustavo
Recent advances in microarray technology have opened new ways for functional annotation of previously uncharacterised genes on a genomic scale. This has been demonstrated by unsupervised clustering...
Information assessment on predicting protein-protein interactions
Lin, Nan, Wu, Baolin, Jansen, Ronald, Gerstein, Mark, Zhao, Hongyu
Signal Processing in the TGF-β Superfamily Ligand-Receptor Network
Vilar, Jose M. G, Jansen, Ronald, Sander, Chris
The TGF-β pathway plays a central role in tissue homeostasis and morphogenesis. It transduces a variety of extracellular signals into intracellular transcriptional responses that control a plethora...
Objective: To compare the costs and effectiveness of 2 oral antifungal treatment regimens in patients with dermatophyte toenail onychomycosis. Design and methods: A cost-effectiveness analysis using...