Aurrecoechea, Cristina, Brestelli, John, Brunk, Brian P., Carlton, Jane M., Dommer, Jennifer, Fischer, Steve, ...
GiardiaDB (http://GiardiaDB.org) and TrichDB (http://TrichDB.org) house the genome databases for Giardia lamblia and Trichomonas vaginalis, respectively, and represent the latest additions to the...
PlasmoDB: a functional genomic database for malaria parasites (2009)
Aurrecoechea, Cristina, Brestelli, John, Brunk, Brian P., Dommer, Jennifer, Fischer, Steve, Gajria, Bindu, ...
PlasmoDB (http://PlasmoDB.org) is a functional genomic database for Plasmodium spp. that provides a resource for data analysis and visualization in a gene-by-gene or genome-wide scale. PlasmoDB...
Aurrecoechea, Cristina, Brestelli, John, Brunk, Brian P., Carlton, Jane M., Dommer, Jennifer, Fischer, Steve, ...
© 2008 The Authors. This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License. The definitive version was published in Nucleic Acids...
Taylor, Chris F., Field, Dawn, Sansone, Susanna-Assunta, Aerts, Jan, Apweiler, Rolf, Asburner, Michael, ...
The Minimum Information for Biological and Biomedical Investigations (MIBBI) project provides a resource for those exploring the range of extant minimum information checklists and fosters coordinated...
Yan, Bin, Chen, Guang, Saigal, Kunal, Yang, Xinping, Jensen, Shane T, Van Waes, Carter, ...
Abstract Background Aberrant activation of the nuclear factor kappaB (NF- κ B) pathway has been previously implicated as a crucial signal promoting tumorigenesis. However, how NF- κ B acts as a key...
ToxoDB: an integrated Toxoplasma gondii database resource (2008)
Gajria, Bindu, Bahl, Amit, Brestelli, John, Dommer, Jennifer, Fischer, Steve, Gao, Xin, ...
ToxoDB (http://ToxoDB.org) is a genome and functional genomic database for the protozoan parasite Toxoplasma gondii. It incorporates the sequence and annotation of the T. gondii ME49 strain, as well...
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...
Mitchell Guttman, Carolyn Mies, Katarzyna Dudycz-Sulicz, Sharon J. Diskin, Don A. Baldwin, Christian J. Stoeckert Jr., ...
Genomic aberrations recurrent in a particular cancer type can be important prognostic markers for tumor progression. Typically in early tumorigenesis, cells incur a breakdown of the DNA replication...
Gupta, Rana K., Gao, Nan, Gorski, Regina K., White, Peter, Hardy, Olga T., Rafiq, Kiran, ...
The failure to expand functional pancreatic β-cell mass in response to increased metabolic demand is a hallmark of type 2 diabetes. Lineage tracing studies indicate that replication of existing...
Clustering of genes into regulons using integrated modeling-COGRIM (2007)
Chen, Guang, Jensen, Shane T, Stoeckert, Christian J
Abstract We present a Bayesian hierarchical model and Gibbs Sampling implementation that integrates gene expression, ChIP binding, and transcription factor motif data in a principled and robust...
ApiDB: integrated resources for the apicomplexan bioinformatics resource center (2007)
Cristina Aurrecoechea, Mark Heiges, Haiming Wang, Zhiming Wang, Steve Fischer, John Miller, ...
resource center
ApiDB: integrated resources for the apicomplexan bioinformatics resource center (2007)
Aurrecoechea, Cristina, Heiges, Mark, Wang, Haiming, Wang, Zhiming, Fischer, Steve, Rhodes, Philippa, ...
ApiDB (http://ApiDB.org) represents a unified entry point for the NIH-funded Apicomplexan Bioinformatics Resource Center (BRC) that integrates numerous database resources and multiple data types. 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...
A simple spreadsheet-based, MIAME-supportive format for microarray data: MAGE-TAB (2006)
Rayner, Tim F, Rocca-Serra, Philippe, Spellman, Paul T, Causton, Helen C, Farne, Anna, Holloway, Ele, ...
Abstract Background Sharing of microarray data within the research community has been greatly facilitated by the development of the disclosure and communication standards MIAME and MAGE-ML by the...
Bayesian variable selection and data integration for biological regulatory networks (2006)
Jensen, Shane T., Chen, Guang, Stoeckert, Christian J.
A substantial focus of research in molecular biology are gene regulatory networks: the set of transcription factors and target genes which control the involvement of different biological processes in...
OrthoMCL-DB: querying a comprehensive multi-species collection of ortholog groups (2006)
Mackey, Aaron J, Stoeckert, Christian J, Roos, David S
The OrthoMCL database (http://orthomcl.cbil.upenn.edu) houses ortholog group predictions for 55 species, including 16 bacterial and 4 archaeal genomes representing phylogenetically diverse lineages,...
The SOFG Anatomy Entry List (SAEL): An Annotation Tool for Functional Genomics Data (2006)
Helen Parkinson, Stuart Aitken, Richard A. Baldock, Albert Burger, Terry F. Hayamizu, ...
A great deal of data in functional genomics studies needs to be annotated with low-resolution anatomical terms. For example, gene expression assays based on manually dissected samples (microarray,...
The MGED Ontology: A Framework for Describing Functional Genomics Experiments (2006)
Christian J. Stoeckert, Helen Parkinson
The Microarray Gene Expression Data (MGED) society was formed with an initial focus on experiments involving microarray technology. Despite the diversity of applications, there are common concepts...
The MGED Ontology: a resource for semantics-based description of microarray experiments (2006)
Patricia L. Whetzel, Helen Parkinson, Helen C. Causton, Liju Fan, Fostel Gilberto, Fragoso Laurence Game, ...
* Corresponding authors
Olga T. Hardy, Hans E. Hohmeier, Thomas C. Becker, Elisabetta M, Nicolai M. Doliba, Rana K. Gupta, ...
Recent advances in functional genomics afford the opportunity to interrogate the expression profiles of thousands of genes simultaneously and examine the function of these genes in a high-throughput...
* Corresponding authors (2006)
Tim F Rayner, Paul T Spellman, Helen C Causton, Anna Farne, Ele Holloway, Rafael A Irizarry, ...
A simple spreadsheet-based, MIAME-supportive format for
Date, Shailesh V., Stoeckert, Christian J.
Many thousands of proteins encoded by the genome of Plasmodium falciparum, the causal organism of the deadliest form of human malaria, are of unknown function. It is of utmost importance that these...
Diskin, Sharon J., Eck, Thomas, Greshock, Joel, Mosse, Yael P., Naylor, Tara, Stoeckert, Christian J., ...
Regions of gain and loss of genomic DNA occur in many cancers and can drive the genesis and progression of disease. These copy number aberrations (CNAs) can be detected at high resolution by using...
The MGED Ontology: a resource for semantics-based description of microarray experiments (2006)
Whetzel, Patricia L., Parkinson, Helen, Causton, Helen C., Fan, Liju, Fostel, Jennifer, Fragoso, Gilberto, ...
Motivation: The generation of large amounts of microarray data and the need to share these data bring challenges for both data management and annotation and highlights the need for standards. MIAME...
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...
Date, Shailesh V., Stoeckert, Christian J.
Many thousands of proteins encoded by the genome of Plasmodium falciparum, the causal organism of the deadliest form of human malaria, are of unknown function. It is of utmost importance that these...
Diskin, Sharon J., Eck, Thomas, Greshock, Joel, Mosse, Yael P., Naylor, Tara, Stoeckert, Christian J., ...
Regions of gain and loss of genomic DNA occur in many cancers and can drive the genesis and progression of disease. These copy number aberrations (CNAs) can be detected at high resolution by using...
OrthoMCL-DB: querying a comprehensive multi-species collection of ortholog groups (2006)
Chen, Feng, Mackey, Aaron J., Stoeckert, Christian J., Roos, David S.
The OrthoMCL database (http://orthomcl.cbil.upenn.edu) houses ortholog group predictions for 55 species, including 16 bacterial and 4 archaeal genomes representing phylogenetically diverse lineages,...
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...
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...
Defining the mammalian CArGome (2005)
Sun, Qiang, Chen, Guang, Streb, Jeffrey W., Long, Xiaochun, Yang, Yumei, Stoeckert, Christian J., ...
Serum response factor (SRF) binds a 1216-fold degenerate cis element known as the CArG box. CArG boxes are found primarily in muscle- and growth-factor-associated genes although the full spectrum of...
Grant, Gregory R., Liu, Junmin, Stoeckert, Christian J.
Summary: Searching for differentially expressed genes is one of the most common applications for microarrays, yet statistically there are difficult hurdles to achieving adequate rigor and...
Grant, Gregory R., Liu, Junmin, Stoeckert, Christian J.
Searching for differentially expressed genes is one of the most common applications for microarrays, yet statistically there are difficult hurdles to achieving adequate rigor and practicality. False...
ApiEST-DB: analyzing clustered EST data of the apicomplexan parasites (2004)
Li Li, Jonathan Crabtree, Steve Fischer, Deborah Pinney, Christian J. Stoeckert, L. David Sibley, ...
ApiEST-DB
An object model and database for functional genomics (2004)
Jones, Andrew, Hunt, Ela, Wastling, Jonathan M., Pizarro, Angel, Stoeckert, Christian J.
Motivation: Large-scale functional genomics analysis is now feasible and presents significant challenges in data analysis, storage and querying. Data standards are required to enable the development...
An object model and database for functional genomics (2004)
Jones, Andrew, Hunt, Ela, Wastling, Jonathan, Pizarro, Angel, Stoeckert, Christian J.
Motivation: Large scale functional genomics analysis is now feasible, and presents significant challenges in data analysis, storage and querying. Data standards are required to enable the development...
An object model and database for functional genomics (2004)
Jones, Andrew, Hunt, Ela, Wastling, Jonathan, Pizarro, Angel, Stoeckert, Christian J.
Motivation: Large scale functional genomics analysis is now feasible, and presents significant challenges in data analysis, storage and querying. Data standards are required to enable the development...
ApiEST-DB: analyzing clustered EST data of the apicomplexan parasites (2004)
Li, Li, Crabtree, Jonathan, Fischer, Steve, Pinney, Deborah, Stoeckert, Christian J., Sibley, L. David, ...
ApiEST‐DB (http://www.cbil.upenn.edu/paradbs‐servlet/) provides integrated access to publicly available EST data from protozoan parasites in the phylum Apicomplexa. The database currently...
An object model and database for functional genomics (2004)
Jones, Andrew, Hunt, Ela, Wastling, Jonathan, Pizarro, Angel, Stoeckert, Christian J.
Motivation: Large scale functional genomics analysis is now feasible, and presents significant challenges in data analysis, storage and querying. Data standards are required to enable the development...
An object model and database for functional genomics (2004)
Jones, Andrew, Hunt, Ela, Wastling, Jonathan, Pizarro, Angel, Stoeckert, Christian J.
Motivation: Large scale functional genomics analysis is now feasible, and presents significant challenges in data analysis, storage and querying. Data standards are required to enable the development...
Zhu, Yunxia, King, Benjamin L, Parvizi, Babak, Brunk, Brian P, Stoeckert, Christian J, Quackenbush, John, ...
Abstract Databases of experimentally generated and computationally derived transcript sequences are valuable resources for genome analysis and annotation. The utility of such databases is enhanced...
OrthoMCL: Identification of Ortholog Groups for Eukaryotic Genomes (2003)
Li, Li, Stoeckert, Christian J., Roos, David S.
The identification of orthologous groups is useful for genome annotation, studies on gene/protein evolution, comparative genomics, and the identification of taxonomically restricted sequences....
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...
Li, Li, Brunk, Brian P., Kissinger, Jessica C., Pape, Deana, Tang, Keliang, Cole, Robert H., ...
Large-scale EST sequencing projects for several important parasites within the phylum Apicomplexa were undertaken for the purpose of gene discovery. Included were several parasites of medical...
Design and implementation of microarray gene expression markup language (MAGE-ML) (2002)
Spellman, Paul T, Miller, Michael, Stewart, Jason, Troup, Charles, Sarkans, Ugis, Chervitz, Steve, ...
Abstract Background Meaningful exchange of microarray data is currently difficult because it is rare that published data provide sufficient information depth or are even in the same format from one...
© 2002 Spellman et al., licensee BioMed Central Ltd (2002)
Paul T Spellman, Michael Miller, Jason Stewart, Charles Troup, Steve Chervitz, Derek Bernhart, ...
The electronic version of this article is the complete one and can be found online at
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...
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"...
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., ...
Manduchi, Elisabetta, Grant, Gregory R., McKenzie, Steven E., Overton, G. Christian, Surrey, Saul, Stoeckert, Christian J.
Motivation: A protocol is described to attach expression patterns to genes represented in a collection of hybridization array experiments. Discrete values are used to provide an easily interpretable...
EpoDB: a database of genes expressed during vertebrate erythropoiesis (1998)
Fidel Salas, Juergen Haas, Brian Brunk, Christian J. Stoeckert, G. Christian Overton
EpoDB is a database designed for the study of gene regulation during differentiation and development of vertebrate red blood cells. In building EpoDB, we have taken the in advance approach to the...
EpoDB: a database of genes expressed during vertebrate erythropoiesis (1998)
Fidel Salas, Juergen Haas, Brian Brunk, Christian J. Stoeckert, G. Christian Overton
EpoDB is a database designed for the study of gene regulation during differentiation and development of vertebrate red blood cells. In building EpoDB, we have taken the in advance approach to 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 annotation...
Design and implementation of microarray gene expression markup language (MAGE-ML)
Spellman, Paul T, Miller, Michael, Stewart, Jason, Troup, Charles, Sarkans, Ugis, Chervitz, Steve, ...
Meaningful exchange of microarray data is currently difficult because it is rare that published data provide sufficient information depth or are even in the same format from one publication to...
A molecular profile of a hematopoietic stem cell niche
Hackney, Jason A., Charbord, Pierre, Brunk, Brian P., Stoeckert, Christian J., Lemischka, Ihor R., Moore, Kateri A.
The hematopoietic microenvironment provides a complex molecular milieu that regulates the self-renewal and differentiation activities of stem cells. We have characterized a stem cell supportive...
Zhu, Yunxia, King, Benjamin L, Parvizi, Babak, Brunk, Brian P, Stoeckert, Christian J, Quackenbush, John, ...
The analysis and results are presented of a semi-automated process of connecting transcript assemblies with highly curated biological information for mouse genes that is available through the Mouse...
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...
ApiEST-DB: analyzing clustered EST data of the apicomplexan parasites
Li, Li, Crabtree, Jonathan, Fischer, Steve, Pinney, Deborah, Stoeckert, Christian J., Sibley, L. David, ...
ApiEST-DB (http://www.cbil.upenn.edu/paradbs-servlet/) provides integrated access to publicly available EST data from protozoan parasites in the phylum Apicomplexa. The database currently...
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...
Passerini, Anthony G., Polacek, Denise C., Shi, Congzhu, Francesco, Nadeene M., Manduchi, Elisabetta, Grant, Gregory R., ...
In the arterial circulation, regions of disturbed flow (DF), which are characterized by flow separation and transient vortices, are susceptible to atherogenesis, whereas regions of undisturbed...
OrthoMCL: Identification of Ortholog Groups for Eukaryotic Genomes
Li, Li, Stoeckert, Christian J., Roos, David S.
The identification of orthologous groups is useful for genome annotation, studies on gene/protein evolution, comparative genomics, and the identification of taxonomically restricted sequences....
Li, Li, Brunk, Brian P., Kissinger, Jessica C., Pape, Deana, Tang, Keliang, Cole, Robert H., ...
Large-scale EST sequencing projects for several important parasites within the phylum Apicomplexa were undertaken for the purpose of gene discovery. Included were several parasites of medical...
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...
OrthoMCL-DB: querying a comprehensive multi-species collection of ortholog groups
Chen, Feng, Mackey, Aaron J., Stoeckert, Christian J., Roos, David S.
The OrthoMCL database () houses ortholog group predictions for 55 species, including 16 bacterial and 4 archaeal genomes representing phylogenetically diverse lineages, and most currently available...
Defining the mammalian CArGome
Sun, Qiang, Chen, Guang, Streb, Jeffrey W., Long, Xiaochun, Yang, Yumei, Stoeckert, Christian J., ...
Serum response factor (SRF) binds a 1,216-fold degenerate cis element known as the CArG box. CArG boxes are found primarily in muscle and growth factor-associated genes though the full spectrum of...
Date, Shailesh V., Stoeckert, Christian J.
Many thousands of proteins encoded by the genome of Plasmodium falciparum, the causal organism of the deadliest form of human malaria, are of unknown function. It is of utmost importance that these...
A simple spreadsheet-based, MIAME-supportive format for microarray data: MAGE-TAB
Rayner, Tim F, Rocca-Serra, Philippe, Spellman, Paul T, Causton, Helen C, Farne, Anna, Holloway, Ele, ...
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...
Design and implementation of microarray gene expression markup language (MAGE-ML)
Spellman, Paul T, Miller, Michael, Stewart, Jason, Troup, Charles, Sarkans, Ugis, Chervitz, Steve, ...
Meaningful exchange of microarray data is currently difficult because it is rare that published data provide sufficient information depth or are even in the same format from one publication to...
A molecular profile of a hematopoietic stem cell niche
Hackney, Jason A., Charbord, Pierre, Brunk, Brian P., Stoeckert, Christian J., Lemischka, Ihor R., Moore, Kateri A.
The hematopoietic microenvironment provides a complex molecular milieu that regulates the self-renewal and differentiation activities of stem cells. We have characterized a stem cell supportive...
Zhu, Yunxia, King, Benjamin L, Parvizi, Babak, Brunk, Brian P, Stoeckert, Christian J, Quackenbush, John, ...
The analysis and results are presented of a semi-automated process of connecting transcript assemblies with highly curated biological information for mouse genes that is available through the Mouse...
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...
ApiEST-DB: analyzing clustered EST data of the apicomplexan parasites
Li, Li, Crabtree, Jonathan, Fischer, Steve, Pinney, Deborah, Stoeckert, Christian J., Sibley, L. David, ...
ApiEST-DB (http://www.cbil.upenn.edu/paradbs-servlet/) provides integrated access to publicly available EST data from protozoan parasites in the phylum Apicomplexa. The database currently...
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...
Passerini, Anthony G., Polacek, Denise C., Shi, Congzhu, Francesco, Nadeene M., Manduchi, Elisabetta, Grant, Gregory R., ...
In the arterial circulation, regions of disturbed flow (DF), which are characterized by flow separation and transient vortices, are susceptible to atherogenesis, whereas regions of undisturbed...
OrthoMCL: Identification of Ortholog Groups for Eukaryotic Genomes
Li, Li, Stoeckert, Christian J., Roos, David S.
The identification of orthologous groups is useful for genome annotation, studies on gene/protein evolution, comparative genomics, and the identification of taxonomically restricted sequences....
Li, Li, Brunk, Brian P., Kissinger, Jessica C., Pape, Deana, Tang, Keliang, Cole, Robert H., ...
Large-scale EST sequencing projects for several important parasites within the phylum Apicomplexa were undertaken for the purpose of gene discovery. Included were several parasites of medical...
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...
OrthoMCL-DB: querying a comprehensive multi-species collection of ortholog groups
Chen, Feng, Mackey, Aaron J., Stoeckert, Christian J., Roos, David S.
The OrthoMCL database () houses ortholog group predictions for 55 species, including 16 bacterial and 4 archaeal genomes representing phylogenetically diverse lineages, and most currently available...
Defining the mammalian CArGome
Sun, Qiang, Chen, Guang, Streb, Jeffrey W., Long, Xiaochun, Yang, Yumei, Stoeckert, Christian J., ...
Serum response factor (SRF) binds a 1,216-fold degenerate cis element known as the CArG box. CArG boxes are found primarily in muscle and growth factor-associated genes though the full spectrum of...
Date, Shailesh V., Stoeckert, Christian J.
Many thousands of proteins encoded by the genome of Plasmodium falciparum, the causal organism of the deadliest form of human malaria, are of unknown function. It is of utmost importance that these...
A simple spreadsheet-based, MIAME-supportive format for microarray data: MAGE-TAB
Rayner, Tim F, Rocca-Serra, Philippe, Spellman, Paul T, Causton, Helen C, Farne, Anna, Holloway, Ele, ...
ApiDB: integrated resources for the apicomplexan bioinformatics resource center
Aurrecoechea, Cristina, Heiges, Mark, Wang, Haiming, Wang, Zhiming, Fischer, Steve, Rhodes, Philippa, ...
ApiDB () represents a unified entry point for the NIH-funded Apicomplexan Bioinformatics Resource Center (BRC) that integrates numerous database resources and multiple data types. The phylum...
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...
Diskin, Sharon J., Eck, Thomas, Greshock, Joel, Mosse, Yael P., Naylor, Tara, Stoeckert, Christian J., ...
Regions of gain and loss of genomic DNA occur in many cancers and can drive the genesis and progression of disease. These copy number aberrations (CNAs) can be detected at high resolution by using...
Clustering of genes into regulons using integrated modeling-COGRIM
Chen, Guang, Jensen, Shane T, Stoeckert, Christian J
COGRIM, an implementation that integrates gene expression, ChIP binding and transcription factor motif data, is described and applied to both unicellular and mammalian organisms.
Guttman, Mitchell, Mies, Carolyn, Dudycz-Sulicz, Katarzyna, Diskin, Sharon J, Baldwin, Don A, Stoeckert, Christian J, ...
Genomic aberrations recurrent in a particular cancer type can be important prognostic markers for tumor progression. Typically in early tumorigenesis, cells incur a breakdown of the DNA replication...
Expansion of adult β-cell mass in response to increased metabolic demand is dependent on HNF-4α
Gupta, Rana K., Gao, Nan, Gorski, Regina K., White, Peter, Hardy, Olga T., Rafiq, Kiran, ...
The failure to expand functional pancreatic β-cell mass in response to increased metabolic demand is a hallmark of type 2 diabetes. Lineage tracing studies indicate that replication of existing...
ToxoDB: an integrated Toxoplasma gondii database resource
Gajria, Bindu, Bahl, Amit, Brestelli, John, Dommer, Jennifer, Fischer, Steve, Gao, Xin, ...
ToxoDB (http://ToxoDB.org) is a genome and functional genomic database for the protozoan parasite Toxoplasma gondii. It incorporates the sequence and annotation of the T. gondii ME49 strain, as well...
Yan, Bin, Chen, Guang, Saigal, Kunal, Yang, Xinping, Jensen, Shane T, Van Waes, Carter, ...
Detailed analysis of NFκB regulons in 1,265 genes differentially expressed in head and neck cancer cell lines differing in p53 status revealed a cross talk between NFkB and specific signaling...
The MGED Ontology: A Framework for Describing Functional Genomics Experiments
Stoeckert, Christian J., Parkinson, Helen
The Microarray Gene Expression Data (MGED) society was formed with an initial focus on experiments involving microarray technology. Despite the diversity of applications, there are common concepts...
The SOFG Anatomy Entry List (SAEL): An Annotation Tool for Functional Genomics Data
Parkinson, Helen, Aitken, Stuart, Baldock, Richard A., Bard, Jonathan B. L., Burger, Albert, Hayamizu, Terry F., ...
A great deal of data in functional genomics studies needs to be annotated with low-resolution anatomical terms. For example, gene expression assays based on manually dissected samples (microarray,...
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...
Aurrecoechea, Cristina, Brestelli, John, Brunk, Brian P., Carlton, Jane M., Dommer, Jennifer, Fischer, Steve, ...
GiardiaDB (http://GiardiaDB.org) and TrichDB (http://TrichDB.org) house the genome databases for Giardia lamblia and Trichomonas vaginalis, respectively, and represent the latest additions to the...
PlasmoDB: a functional genomic database for malaria parasites
Aurrecoechea, Cristina, Brestelli, John, Brunk, Brian P., Dommer, Jennifer, Fischer, Steve, Gajria, Bindu, ...
PlasmoDB (http://PlasmoDB.org) is a functional genomic database for Plasmodium spp. that provides a resource for data analysis and visualization in a gene-by-gene or genome-wide scale. PlasmoDB...