Marbach, Daniel, Prill, Robert J., Schaffter, Thomas, Mattiussi, Claudio, Floreano, Dario, Stolovitzky, Gustavo
Over the past decade, numerous methods have been developed for inferring the structure of gene regulatory networks from gene expression data, yet their comparative performance remains poorly...
Ramakrishna Ramaswamy, Gyan Bhanot, Jorge Lepre, Gustavo Stolovitzky, Babu Venkataraghavan, Arnold J Levine
One of the major challenges in cancer diagnosis from microarray data is to develop robust classification models which are independent of the analysis techniques used and can combine data from...
Reece K. Hart, Ajay K. Royyuru, Gustavo Stolovitzky, Andrea Califano
We present an efficient algorithm to systematically and automatically identify patterns in protein sequence families. The procedure is based on the Splash deterministic pattern discovery algorithm...
[6] L Avery and S Wasserman. Ordering gene function: the interpretation of (2008)
Alfred V. Aho, M. R. Garey, Tatsuya Akutsu, Satoru Kuhara, Osamu Maruyama, Satoru Miyano Identification, ...
of gene regulatory networks by strategic gene disruptions and gene
Dash, Ranjan K., Li, Yanjun, Kim, Jaeyeon, Beard, Daniel A., Saidel, Gerald M., Cabrera, Marco E., ...
Control mechanisms of cellular metabolism and energetics in skeletal muscle that may become evident in response to physiological stresses such as reduction in blood flow and oxygen supply to...
A noise model for mass spectrometry based proteomics (2008)
Du, Peicheng, Stolovitzky, Gustavo, Horvatovich, Peter, Bischoff, Rainer, Lim, Jihyeon, Suits, Frank
Motivation: Mass spectrometry data are subjected to considerable noise. Good noise models are required for proper detection and quantification of peptides. We have characterized noise in both...
Reece K. Hart, Gustavo Stolovitzky, Andrea Califano
We present an efficient algorithm to systematically and automatically identify patterns in protein sequence families. The procedure is based on the Splash deterministic pattern discovery algorithm...
ChIP-on-chip significance analysis reveals ubiquitous transcription factor binding (2007)
Margolin, Adam A, Palomero, Teresa, Ferrando, Adolfo A, Califano, Andrea, Stolovitzky, Gustavo
No abstract available.
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...
Margolin, Adam A, Nemenman, Ilya, Basso, Katia, Wiggins, Chris, Stolovitzky, Gustavo, Favera, Riccardo, ...
Abstract Background Elucidating gene regulatory networks is crucial for understanding normal cell physiology and complex pathologic phenotypes. Existing computational methods for the genome-wide...
Reconstructing biological networks using conditional correlation analysis (2005)
Rice, John Jeremy, Tu, Yuhai, Stolovitzky, Gustavo
Motivation: One of the present challenges in biological research is the organization of the data originating from high-throughput technologies. One way in which this information can be organized is...
On The Reconstruction of Interaction Networks with Applications to Transcriptional Regulation (2004)
Margolin, Adam A., Nemenman, Ilya, Wiggins, Chris, Stolovitzky, Gustavo, Califano, Andrea
A novel information-theoretic method for reconstruction of interaction networks is introduced. We prove that the method is exact for some class of networks. Performance tests on large synthetic...
Margolin, Adam A., Nemenman, Ilya, Basso, Katia, Klein, Ulf, Wiggins, Chris, Stolovitzky, Gustavo, ...
Background: Elucidating gene regulatory networks is crucial for understanding normal cell physiology and complex pathologic phenotypes. Existing computational methods for the genome-wide ``reverse...
Lepre, Jorge, Rice, J. Jeremy, Tu, Yuhai, Stolovitzky, Gustavo
Motivation: Despite the growing literature devoted to finding differentially expressed genes in assays probing different tissues types, little attention has been paid to the combinatorial nature of...
Reconstructing biological networks using conditional correlation analysis (2004)
Rice, John Jeremy, Tu, Yuhai, Stolovitzky, Gustavo
Motivation: One of the present challenges in biological research is the organization of the data originating from high throughput technologies. One way in which this information can be organized is...
Lepre, Jorge, Rice, J. Jeremy, Tu, Yuhai, Stolovitzky, Gustavo
Motivation: Despite the growing literature devoted to finding differentially expressed genes in assays probing different tissues types, little attention has been paid to the combinatorial nature of...
Reconstructing biological networks using conditional correlation analysis (2004)
Rice, John Jeremy, Tu, Yuhai, Stolovitzky, Gustavo
Motivation: One of the present challenges in biological research is the organization of the data originating from high throughput technologies. One way in which this information can be organized is...
Efficiency of DNA replication in the Polymerase Chain Reactio (2001)
Cecchi, Guillermo A., Stolovitzky, Gustavo
We present a detailed kinetic model for the Polymerase Chain Reaction, and model the probability of replication in terms of the physical parameters of the problem. Applying the theory of branching...
Analysis of gene expression microarrays for phenotype classification (2000)
Andrea Califano, Gustavo Stolovitzky, Yuhai Tu
Several microarray technologies that monitor the level of expression of a large number of genes have recently emerged. Given DNA-microarray data for a set of cells characterized by a given phenotype...
Systematic and automated discovery of patterns in PROSITE families (2000)
Reece Hart, Ajay K. Royyuru, Gustavo Stolovitzky, Andrea Califano
PROSITE is a method for protein classification which relies on a database of biologically significant sites and patterns in protein sequences. Most patterns in PROSITE have been gathered by a a labor...
Wentian Li, Gustavo Stolovitzky, Pedro Bernaola-galván, José L. Oliver
The heterogeneity within, and similarities between, yeast chromosomes are studied. For the former, we show by the size distribution of domains, coding density, size distribution of open reading...
Califano A: Statistical significance of patterns in biosequences (1998)
Gustavo Stolovitzky, Andrea Califano
Several algorithms for pattern discovery in sequences have recently emerged, such as Pratt, Teiresias, Splash, and Meme. These are proving useful in biological sequences analysis, as the presence of...
Catalytic tempering: A method for sampling rough energy landscapes by Monte Carlo
Stolovitzky, Gustavo, Berne, B. J.
A new Monte Carlo algorithm is presented for the efficient sampling of the Boltzmann distribution of configurations of systems with rough energy landscapes. The method is based on the introduction of...
Efficiency of DNA replication in the polymerase chain reaction
Stolovitzky, Gustavo, Cecchi, Guillermo
A detailed quantitative kinetic model for the polymerase chain reaction (PCR) is developed, which allows us to predict the probability of replication of a DNA molecule in terms of the physical...
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...
Ising Model of Cardiac Thin Filament Activation with Nearest-Neighbor Cooperative Interactions
Rice, John Jeremy, Stolovitzky, Gustavo, Tu, Yuhai, De Tombe, Pieter P.
We have developed a model of cardiac thin filament activation using an Ising model approach from equilibrium statistical physics. This model explicitly represents nearest-neighbor interactions...
Catalytic tempering: A method for sampling rough energy landscapes by Monte Carlo
Stolovitzky, Gustavo, Berne, B. J.
A new Monte Carlo algorithm is presented for the efficient sampling of the Boltzmann distribution of configurations of systems with rough energy landscapes. The method is based on the introduction of...
Efficiency of DNA replication in the polymerase chain reaction
Stolovitzky, Gustavo, Cecchi, Guillermo
A detailed quantitative kinetic model for the polymerase chain reaction (PCR) is developed, which allows us to predict the probability of replication of a DNA molecule in terms of the physical...
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...
Ising Model of Cardiac Thin Filament Activation with Nearest-Neighbor Cooperative Interactions
Rice, John Jeremy, Stolovitzky, Gustavo, Tu, Yuhai, De Tombe, Pieter P.
We have developed a model of cardiac thin filament activation using an Ising model approach from equilibrium statistical physics. This model explicitly represents nearest-neighbor interactions...
Margolin, Adam A, Nemenman, Ilya, Basso, Katia, Wiggins, Chris, Stolovitzky, Gustavo, Favera, Riccardo Dalla, ...
Margolin, Adam A., Palomero, Teresa, Sumazin, Pavel, Califano, Andrea, Ferrando, Adolfo A., Stolovitzky, Gustavo
ChIP-on-chip has emerged as a powerful tool to dissect the complex network of regulatory interactions between transcription factors and their targets. However, most ChIP-on-chip analysis methods use...
Ordered cyclic motifs contribute to dynamic stability in biological and engineered networks
Ma'ayan, Avi, Cecchi, Guillermo A., Wagner, John, Rao, A. Ravi, Iyengar, Ravi, Stolovitzky, Gustavo
Representation and analysis of complex biological and engineered systems as directed networks is useful for understanding their global structure/function organization. Enrichment of network motifs,...