Extracting transcription factor targets from ChIP-Seq data (2009)
Tuteja, Geetu, White, Peter, Schug, Jonathan, Kaestner, Klaus H.
ChIP-Seq technology, which combines chromatin immunoprecipitation (ChIP) with massively parallel sequencing, is rapidly replacing ChIP-on-chip for the genome-wide identification of transcription...
Lefterova, Martina I., Zhang, Yong, Steger, David J., Schupp, Michael, Schug, Jonathan, Cristancho, Ana, ...
Peroxisome proliferator-activated receptor γ(PPARγ), a nuclear receptor and the target of anti-diabetic thiazolinedione drugs, is known as the master regulator of adipocyte biology. Although it...
of luminescence in the marine bacterium (2007)
Calin Belta, Jonathan Schug, Paul Dunlap
and reachability analysis of a hybrid model
of luminescence in the marine bacterium (2007)
Calin Belta, Jonathan Schug, Thao Dang, Paul Dunlap
and reachability analysis of a hybrid model
Hybrid Modeling and Simulation of Biomolecular Networks (2007)
Abstract. In a biological cell, cellular functions and the genetic regulatory apparatus are implemented and controlled by a network of chemical reactions in which regulatory proteins can control...
MODELING AND ANALYZING BIOMOLECULAR NETWORKS (2007)
George J. Pappas, Harvey Rubin, Jonathan Schug
The authors argue for the need to model and analyze biological networks at molecular and cellular levels. They propose a computational toolbox for biologists. Central to their approach is the...
Mazzarelli, Joan M., Brestelli, John, Gorski, Regina K., Liu, Junmin, Manduchi, Elisabetta, Pinney, Deborah F., ...
EPConDB (http://www.cbil.upenn.edu/EPConDB) is a public web site that supports research in diabetes, pancreatic development and beta-cell function by providing information about genes expressed in...
Mazzarelli, Joan M., Brestelli, John, Gorski, Regina K., Liu, Junmin, Manduchi, Elisabetta, Pinney, Deborah F., ...
EPConDB (http://www.cbil.upenn.edu/EPConDB ) is a public web site that supports research in diabetes, pancreatic development and beta-cell function by providing information about genes expressed in...
Mazzarelli, Joan M., Brestelli, John, Gorski, Regina K., Liu, Junmin, Manduchi, Elisabetta, Pinney, Deborah F., ...
EPConDB (http://www.cbil.upenn.edu/EPConDB ) is a public web site that supports research in diabetes, pancreatic development and beta-cell function by providing information about genes expressed in...
Mazzarelli, Joan M., Brestelli, John, Gorski, Regina K., Liu, Junmin, Manduchi, Elisabetta, Pinney, Deborah F., ...
EPConDB (http://www.cbil.upenn.edu/EPConDB ) is a public web site that supports research in diabetes, pancreatic development and beta-cell function by providing information about genes expressed in...
Mazzarelli, Joan M., Brestelli, John, Gorski, Regina K., Liu, Junmin, Manduchi, Elisabetta, Pinney, Deborah F., ...
EPConDB (http://www.cbil.upenn.edu/EPConDB ) is a public web site that supports research in diabetes, pancreatic development and beta-cell function by providing information about genes expressed in...
Glucocorticoid Receptor-Dependent Gene Regulatory Networks (2005)
Phillip Phuc Le, Joshua R. Friedman, Jonathan Schug, John E. Brestelli, J. Brandon Parker, Irina M. Bochkis, ...
While the molecular mechanisms of glucocorticoid regulation of transcription have been studied in detail, the global networks regulated by the glucocorticoid receptor (GR) remain unknown. To address...
Promoter features related to tissue specificity as measured by Shannon entropy (2005)
Schug, Jonathan, Schuller, Winfried-Paul, Kappen, Claudia, Salbaum, J Michael, Bucan, Maja, Stoeckert, Christian J
Abstract Background The regulatory mechanisms underlying tissue specificity are a crucial part of the development and maintenance of multicellular organisms. A genome-wide analysis of promoters in...
Integrating gene expression signals with bounded collection grammars (2005)
Tissue-specific expression is one of the most obvious and important patterns of gene expression in complex eukaryotes. Every cell in an organism has the same set of genes, yet only a subset of the...
Jonathan Schug, C. Pierce, Jonathan Schug, G. Christian Overton
Though his name does not appear on the title page as my advisor, without Chris Overton, who sadly passed away June 1, 2000, this dissertation would not be what it is. My interest in transcription...
Bahl, Amit, Brunk, Brian, Crabtree, Jonathan, Fraunholz, Martin J., Gajria, Bindu, Grant, Gregory R., ...
PlasmoDB (http://PlasmoDB.org) is the official database of the Plasmodium falciparum genome sequencing consortium. This resource incorporates the recently completed P. falciparum genome sequence and...
Visual Programming for Modeling and Simulation of Biomolecular Regulatory Networks (2002)
Alur, Rajeev, Belta, Calin, Ivancic, Franjo, Kumar, R. Vijay, Rubin, Harvey, Schug, Jonathan, ...
In this paper we introduce our new tool BIOSKETCHPAD that allows visual programming and modeling of biological regulatory networks. The tool allows biologists to create dynamic models of networks...
Visual Programming for Modeling and Simulation of Biomolecular Regulatory Networks (2002)
Alur, Rajeev, Belta, Calin, Ivancic, Franjo, Kumar, Vijay, Rubin, Harvey, Schug, Jonathan, ...
In this paper we introduce our new tool BIOSKETCHPAD that allows visual progamming and modeling of biological regulatory networks. The tool allows biologists to create dynamic models of networks...
Modeling and Analyzing Biomolecular Networks (2002)
Alur, Rajeev, Belta, Calin, Kumar, R. Vijay, Mintz, Max L, Pappas, George J, Rubin, Harvey, ...
The authors argue for the need to model and analyze biological networks at molecular and cellular levels. They propose a computational toolbox for biologists. Central to their approach is the...
Bahl, Amit, Brunk, Brian, Coppel, Ross L., Crabtree, Jonathan, Diskin, Sharon J., Fraunholz, Martin J., ...
PlasmoDB (http://PlasmoDB.org) is the official database of the Plasmodium falciparum genome sequencing consortium. This resource incorporates finished and draft genome sequence data and...
Belta, Calin, Schug, Jonathan, Dang, Thao, Kumar, R. Vijay, Pappas, George J, Rubin, Harvey, ...
This paper addresses the mathematical modeling and analysis of the quorum sensing system found in unicellular bacteria that exhibit bioluminescence. The luminescence is governed by the expression of...
K2/Kleisli and GUS: Experiments in Integrated Access to Genomic Data Sources (2001)
Davidson, Susan B, Crabtree, Jonathan, Brunk, Brian P., Schug, Jonathan, Tannen, Val, Overton, Chris, ...
The integration of heterogeneous data sources and software systems is a major issue in the biomed ical community and several approaches have been explored: linking databases, "on-the- fly"...
Hybrid modeling and simulation of biomolecular networks (2001)
Rajeev Alur, Calin Belta, Franjo Ivančić, Vijay Kumar, Max Mintz, Harvey Rubin, ...
Abstract. In a biological cell, cellular functions and the genetic regulatory apparatus are implemented and controlled by a network of chemical reactions in which regulatory proteins can control...
Hybrid modeling and simulation of biomolecular networks (2001)
Rajeev Alur, Calin Belta, Franjo Ivanifi, Vijay Kumar, Max Mintz, Harvey Rubin, ...
Abstract. In a biological cell, cellular functions and the genetic regulatory apparatus are implemented and controlled by a network of chemical reactions in which regulatory proteins can control...
K2/Kleisli and GUS: Experiments in Integrated Access to Genomic Data Sources (2001)
Susan B. Davidson, Jonathan Crabtree, Brian Brunk, Jonathan Schug, Val Tannen, Chris Overton, ...
The integration of heterogeneous data sources and software systems is a major issue in the biomedical community and several approaches have been explored: linking databases, \on-the- y "...
High-Resolution BAC-Based Map of the Central Portion of Mouse Chromosome 5 (2001)
Crabtree, Jonathan, Wiltshire, Tim, Brunk, Brian, Zhao, Shaying, Schug, Jonathan, Stoeckert, Christian J., ...
The GAIA software framework for genome annotation (1998)
G. Christian Overton, Charles Bailey, Jonathan Crabtree, Mark Gibson, Stephen Fischer, Jonathan Schug
We describe a software framework, GAIA, that supports semiautomated annotation of uncharacterized sequence data. The annotation framework incorporates annotation by data source integration, data...
GAIA: Framework Annotation of Genomic Sequence (1998)
Bailey, L. Charles, Fischer, Stephen, Schug, Jonathan, Crabtree, Jonathan, Gibson, Mark, Overton, G. Christian
Tess: Transcription element search software on the www (1997)
Jonathan Schug, G. Christian Overton
TESS, Transcription Element Search Software, is a web-based software tool for locating possible transcription factor binding sites in DNA sequence and for browsing the TRANSFAC database. It provides...
Bahl, Amit, Brunk, Brian, Coppel, Ross L., Crabtree, Jonathan, Diskin, Sharon J., Fraunholz, Martin J., ...
PlasmoDB (http://PlasmoDB.org) is the official database of the Plasmodium falciparum genome sequencing consortium. This resource incorporates finished and draft genome sequence data and annotation...
PlasmoDB: the Plasmodium genome resource. A database integrating experimental and computational data
Bahl, Amit, Brunk, Brian, Crabtree, Jonathan, Fraunholz, Martin J., Gajria, Bindu, Grant, Gregory R., ...
PlasmoDB (http://PlasmoDB.org) is the official database of the Plasmodium falciparum genome sequencing consortium. This resource incorporates the recently completed P. falciparum genome sequence and...
Predicting Gene Ontology Functions from ProDom and CDD Protein Domains
Schug, Jonathan, Diskin, Sharon, Mazzarelli, Joan, Brunk, Brian P., Stoeckert, Christian J.
A heuristic algorithm for associating Gene Ontology (GO) defined molecular functions to protein domains as listed in the ProDom and CDD databases is described. The algorithm generates rules for...
High-Resolution BAC-Based Map of the Central Portion of Mouse Chromosome 5
Crabtree, Jonathan, Wiltshire, Tim, Brunk, Brian, Zhao, Shaying, Schug, Jonathan, Stoeckert, Christian J., ...
The current strategy for sequencing the mouse genome involves the combination of a whole-genome shotgun approach with clone-based sequencing. High-resolution physical maps will provide a foundation...
Orthogonal analysis of C/EBPβ targets in vivo during liver proliferation
Friedman, Joshua R., Larris, Brian, Le, Phillip P., Peiris, T. Harshani, Arsenlis, Athanasios, Schug, Jonathan, ...
CCAAT enhancer-binding protein β (C/EBPβ), a basic-leucine zipper transcription factor, is an important effector of signals in physiologic growth and cancer. The identification of direct C/EBPβ...
Promoter features related to tissue specificity as measured by Shannon entropy
Schug, Jonathan, Schuller, Winfried-Paul, Kappen, Claudia, Salbaum, J Michael, Bucan, Maja, Stoeckert, Christian J
A genome-wide analysis of promoters was carried out in the context of gene expression patterns in tissue surveys using human microarray and EST-based expression data. The study revealed that most...
Glucocorticoid Receptor-Dependent Gene Regulatory Networks
Phuc Le, Phillip, Friedman, Joshua R, Schug, Jonathan, Brestelli, John E, Parker, J. Brandon, Bochkis, Irina M, ...
While the molecular mechanisms of glucocorticoid regulation of transcription have been studied in detail, the global networks regulated by the glucocorticoid receptor (GR) remain unknown. To address...
Bahl, Amit, Brunk, Brian, Coppel, Ross L., Crabtree, Jonathan, Diskin, Sharon J., Fraunholz, Martin J., ...
PlasmoDB (http://PlasmoDB.org) is the official database of the Plasmodium falciparum genome sequencing consortium. This resource incorporates finished and draft genome sequence data and annotation...
PlasmoDB: the Plasmodium genome resource. A database integrating experimental and computational data
Bahl, Amit, Brunk, Brian, Crabtree, Jonathan, Fraunholz, Martin J., Gajria, Bindu, Grant, Gregory R., ...
PlasmoDB (http://PlasmoDB.org) is the official database of the Plasmodium falciparum genome sequencing consortium. This resource incorporates the recently completed P. falciparum genome sequence and...
Predicting Gene Ontology Functions from ProDom and CDD Protein Domains
Schug, Jonathan, Diskin, Sharon, Mazzarelli, Joan, Brunk, Brian P., Stoeckert, Christian J.
A heuristic algorithm for associating Gene Ontology (GO) defined molecular functions to protein domains as listed in the ProDom and CDD databases is described. The algorithm generates rules for...
High-Resolution BAC-Based Map of the Central Portion of Mouse Chromosome 5
Crabtree, Jonathan, Wiltshire, Tim, Brunk, Brian, Zhao, Shaying, Schug, Jonathan, Stoeckert, Christian J., ...
The current strategy for sequencing the mouse genome involves the combination of a whole-genome shotgun approach with clone-based sequencing. High-resolution physical maps will provide a foundation...
Orthogonal analysis of C/EBPβ targets in vivo during liver proliferation
Friedman, Joshua R., Larris, Brian, Le, Phillip P., Peiris, T. Harshani, Arsenlis, Athanasios, Schug, Jonathan, ...
CCAAT enhancer-binding protein β (C/EBPβ), a basic-leucine zipper transcription factor, is an important effector of signals in physiologic growth and cancer. The identification of direct C/EBPβ...
Promoter features related to tissue specificity as measured by Shannon entropy
Schug, Jonathan, Schuller, Winfried-Paul, Kappen, Claudia, Salbaum, J Michael, Bucan, Maja, Stoeckert, Christian J
A genome-wide analysis of promoters was carried out in the context of gene expression patterns in tissue surveys using human microarray and EST-based expression data. The study revealed that most...
Glucocorticoid Receptor-Dependent Gene Regulatory Networks
Phuc Le, Phillip, Friedman, Joshua R, Schug, Jonathan, Brestelli, John E, Parker, J. Brandon, Bochkis, Irina M, ...
While the molecular mechanisms of glucocorticoid regulation of transcription have been studied in detail, the global networks regulated by the glucocorticoid receptor (GR) remain unknown. To address...
Mazzarelli, Joan M., Brestelli, John, Gorski, Regina K., Liu, Junmin, Manduchi, Elisabetta, Pinney, Deborah F., ...
EPConDB () is a public web site that supports research in diabetes, pancreatic development and beta-cell function by providing information about genes expressed in cells of the pancreas. EPConDB...
PPARγ and C/EBP factors orchestrate adipocyte biology via adjacent binding on a genome-wide scale
Lefterova, Martina I., Zhang, Yong, Steger, David J., Schupp, Michael, Schug, Jonathan, Cristancho, Ana, ...
Peroxisome proliferator-activated receptor γ(PPARγ), a nuclear receptor and the target of anti-diabetic thiazolinedione drugs, is known as the master regulator of adipocyte biology. Although it...
Extracting transcription factor targets from ChIP-Seq data
Tuteja, Geetu, White, Peter, Schug, Jonathan, Kaestner, Klaus H.
ChIP-Seq technology, which combines chromatin immunoprecipitation (ChIP) with massively parallel sequencing, is rapidly replacing ChIP-on-chip for the genome-wide identification of transcription...