Genomes and Genes
Christian J Stoeckert
Affiliation: University of Pennsylvania
- Microarray databases: standards and ontologiesChristian J Stoeckert
Center for Bioinformatics and Department of Genetics, University of Pennsylvania, 423 Guardian Drive, Philadelphia, Pennsylvania 19104 6021, USA
Nat Genet 32:469-73. 2002..The adoption of common standards and ontologies for the management and sharing of microarray data is essential and will provide immediate benefit to the research community...
- EPConDB: a web resource for gene expression related to pancreatic development, beta-cell function and diabetesJoan M Mazzarelli
Department of Genetics, School of Medicine, Center for Bioinformatics, University of Pennsylvania, Philadelphia, PA 19104, USA
Nucleic Acids Res 35:D751-5. 2007..EPConDB provides database queries and tools to examine the relationship between a gene, its transcriptional regulation, protein function and expression in pancreatic tissues...
- ToxoDB: an integrated Toxoplasma gondii database resourceBindu Gajria
Department of Biology, Department of Genetics, Center for Bioinformatics, University of Pennsylvania, Philadelphia, PA, USA
Nucleic Acids Res 36:D553-6. 2008..ToxoDB has matured significantly since its initial release. Here we outline the numerous updates with respect to the data and increased functionality available on the website...
- Coexisting proinflammatory and antioxidative endothelial transcription profiles in a disturbed flow region of the adult porcine aortaAnthony G Passerini
Institute for Medicine and Engineering, Department of Bioengineering, University of Pennsylvania, Philadelphia, PA 19104, USA
Proc Natl Acad Sci U S A 101:2482-7. 2004..The introduction of additional risk factors may shift this balance to favor lesion development...
- PlasmoDB: the Plasmodium genome resource. A database integrating experimental and computational dataAmit Bahl
Department of Biology, University of Pennsylvania, Philadelphia, PA 19104, USA
Nucleic Acids Res 31:212-5. 2003..The software used to develop PlasmoDB has been used to create a second Apicomplexan parasite genome database, ToxoDB (http://ToxoDB.org)...
- Prelesional arterial endothelial phenotypes in hypercholesterolemia: universal ABCA1 upregulation contrasts with region-specific gene expression in vivoMete Civelek
Institute for Medicine and Engineering, University of Pennsylvania, Philadelphia, PA 19104, USA
Am J Physiol Heart Circ Physiol 298:H163-70. 2010..Both region-specific and ubiquitous (ABCA1) phenotype changes were identified as early prelesional responses of the endothelium to hypercholesterolemia...
- Using OrthoMCL to assign proteins to OrthoMCL-DB groups or to cluster proteomes into new ortholog groupsSteve Fischer
Center for Bioinformatics, University of Pennsylvania, Philadelphia, Pennsylvania, USA
Curr Protoc Bioinformatics . 2011..This method maps the uploaded proteins to existing groups in OrthoMCL-DB. Alternatively, if you have proteins from a set of genomes that need to be grouped, you can download, install, and run the stand-alone OrthoMCL software...
- Expansion of adult beta-cell mass in response to increased metabolic demand is dependent on HNF-4alphaRana K Gupta
Department of Genetics and Institute for Diabetes, Obesity, and Metabolism, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania 19104, USA
Genes Dev 21:756-69. 2007..Together, these results indicate that HNF-4alpha is essential for the physiological expansion of adult beta-cell mass in response to increased metabolic demand...
- ApiEST-DB: analyzing clustered EST data of the apicomplexan parasitesLi Li
Department of Biology, Center for Bioinformatics, University of Pennsylvania, Philadelphia, PA 19104, USA
Nucleic Acids Res 32:D326-8. 2004....
- Coronary artery endothelial transcriptome in vivo: identification of endoplasmic reticulum stress and enhanced reactive oxygen species by gene connectivity network analysisMete Civelek
Department of Bioengineering, Institute for Medicine and Engineering, University of Pennsylvania, Philadelphia, PA 19104, USA
Circ Cardiovasc Genet 4:243-52. 2011..Endothelial function is central to the localization of atherosclerosis. The in vivo endothelial phenotypic footprints of arterial bed identity and site-specific atherosusceptibility are addressed...
- Comparative analysis of RNA-Seq alignment algorithms and the RNA-Seq unified mapper (RUM)Gregory R Grant
Penn Center for Bioinformatics, University of Pennsylvania School of Medicine, Philadelphia, PA 19104, USA
Bioinformatics 27:2518-28. 2011..The exercise to rigorously compare all viable published RNA-Seq algorithms has not been performed previously...
- Assessing the significance of conserved genomic aberrations using high resolution genomic microarraysMitchell Guttman
Penn Center for Bioinformatics, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
PLoS Genet 3:e143. 2007..The algorithm has been fully implemented and tested and is freely available as a Java application at http://www.cbil.upenn.edu/MSA...
- Discovery approaches to UPR in athero-susceptible endothelium in vivoMete Civelek
Institute for Medicine and Engineering, University of Pennsylvania, Philadelphia, Pennsylvania, USA
Methods Enzymol 489:109-26. 2011..Here, we outline global genomic profiling, pathway analyses, and gene connectivity approaches to the identification of UPR and associated pathways as discrete markers of athero-susceptibility in arterial endothelium...
- The Plasmodium genome databaseJessica C Kissinger
Department of Biology and Genetics, Center for Bioinformatics and Genomics Institute, University of Pennsylvania, Philadelphia, 19104 6018, USA
Nature 419:490-2. 2002
- Novel genes identified by manual annotation and microarray expression analysis in the pancreasJoan M Mazzarelli
Center for Bioinformatics, School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
Genomics 88:752-61. 2006..Interestingly, when we investigated the novel transcripts for their overlap with noncoding microRNAs, we found that 1 of the novel transcripts overlapped a known microRNA gene...
- The MGED Ontology: a resource for semantics-based description of microarray experimentsPatricia L Whetzel
Center for Bioinformatics and Department of Genetics, University of Pennsylvania School of Medicine, USA
Bioinformatics 22:866-73. 2006....
- PlasmoDB v5: new looks, new genomesChristian J Stoeckert
Department of Genetics, 1415 Blockley Hall, Center for Bioinformatics, 423 Guardian Drive, University of Pennsylvania, Philadelphia, PA 19104, USA
Trends Parasitol 22:543-6. 2006..This new release includes additional Plasmodium genomes and a newly designed website. The new site reflects the status of PlasmoDB as a member of a linked family of Apicomplexan databases...
- Regional determinants of arterial endothelial phenotype dominate the impact of gender or short-term exposure to a high-fat dietAnthony G Passerini
Institute for Medicine and Engineering, University of Pennsylvania, Philadelphia, PA, USA
Biochem Biophys Res Commun 332:142-8. 2005..The results implicate regional hemodynamics as a predominant epigenetic determinant of endothelial phenotypic heterogeneity underlying atherosusceptibility in vivo...
- Conservation and divergence of known apicomplexan transcriptional regulonsKobby Essien
Department of Bioengineering, University of Pennsylvania, 240 SkirkanichHall, Philadelphia, Pennsylvania 19104, USA
BMC Genomics 11:147. 2010..Even less is known about how regulon systems, consisting of transcription factors and target genes together with their associated biological process, evolve in these diverse parasites...
- Computational analysis of constraints on noncoding regions, coding regions and gene expression in relation to Plasmodium phenotypic diversityKobby Essien
Department of Bioengineering, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
PLoS ONE 3:e3122. 2008..The genetic bases of phenotypic differences between parasites can be understood, in part, by investigating constraints on gene expression and genic sequences, both coding and regulatory...
- The Strategies WDK: a graphical search interface and web development kit for functional genomics databasesSteve Fischer
Center for Bioinformatics, University of Pennsylvania, Philadelphia, PA, USA
Database (Oxford) 2011:bar027. 2011..The Strategies WDK uses a configurable MVC architecture that is compatible with most genomics and biological warehouse databases, and is available for download at code.google.com/p/strategies-wdk. Database URL: www.eupathdb.org...
- OrthoMCL: identification of ortholog groups for eukaryotic genomesLi Li
Department of Biology and Genetics, Center for Bioinformatics, and Genomics Institute, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
Genome Res 13:2178-89. 2003..cbil.upenn.edu/gene-family). Analysis of clusters incorporating P. falciparum genes identifies numerous enzymes that were incompletely annotated in first-pass annotation of the parasite genome...
- Chronic endoplasmic reticulum stress activates unfolded protein response in arterial endothelium in regions of susceptibility to atherosclerosisMete Civelek
Institute for Medicine and Engineering, University of Pennsylvania, 1010 Vagelos Laboratories, 3340 Smith Walk, Philadelphia, PA 19104, USA
Circ Res 105:453-61. 2009....
- Propagation of adipogenic signals through an epigenomic transition stateDavid J Steger
Division of Endocrinology, Diabetes, and Metabolism, Department of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
Genes Dev 24:1035-44. 2010..Thus, the conversion of preadipocyte to adipocyte involves the formation of an epigenomic transition state that is not observed in cells at the beginning or end of the differentiation process...
- Clustering of genes into regulons using integrated modeling-COGRIMGuang Chen
Department of Bioengineering, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
Genome Biol 8:R4. 2007..In these applications, we demonstrate the ability to predict gene-transcription factor interactions with reduced numbers of false-positive findings and to make predictions beyond what is obtained when single types of data are considered...
- Development of FuGO: an ontology for functional genomics investigationsPatricia L Whetzel
Center for Bioinformatics and Department of Genetics, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania 19104, USA
OMICS 10:199-204. 2006....
- Transcriptional program of the endocrine pancreas in mice and humansKlaus H Kaestner
Department of Genetics, University of Pennsylvania, Philadelphia 19104, USA
Diabetes 52:1604-10. 2003..We show that this PancChip is highly enriched for genes expressed in the endocrine pancreas. The mouse and human clone sets and corresponding arrays will be important resources for diabetes research...
- Gene discovery in the apicomplexa as revealed by EST sequencing and assembly of a comparative gene databaseLi Li
Department of Biology, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
Genome Res 13:443-54. 2003..These genes likely mediate the novel biological features of members of the Apicomplexa and hence offer great potential for biological investigation and as possible therapeutic targets...
- Fidelity and enhanced sensitivity of differential transcription profiles following linear amplification of nanogram amounts of endothelial mRNADenise C Polacek
Institute for Medicine and Engineering, University of Pennsylvania, Philadelphia 19104, USA
Physiol Genomics 13:147-56. 2003....
- PPARgamma and C/EBP factors orchestrate adipocyte biology via adjacent binding on a genome-wide scaleMartina I Lefterova
Institute for Diabetes, Obesity, and Metabolism, and Division of Endocrinology, Diabetes, and Metabolism, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania 19104, USA
Genes Dev 22:2941-52. 2008..Thus, PPARgamma and C/EBP factors cooperatively orchestrate adipocyte biology by adjacent binding on an unanticipated scale...
- OrthoMCL-DB: querying a comprehensive multi-species collection of ortholog groupsFeng Chen
Department of Chemistry, Center for Bioinformatics, Penn Genomics Institute, University of Pennsylvania, Philadelphia, PA 19104 6018, USA
Nucleic Acids Res 34:D363-8. 2006..OrthoMCL-DB provides a centralized warehouse for orthology prediction among multiple species, and will be updated and expanded as additional genome sequence data become available...
- Analysis and management of microarray gene expression dataGregory R Grant
University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania, USA
Curr Protoc Mol Biol . 2007....
- Functional genomics databases on the webChristian J Stoeckert
Center for Bioinformatics and Department of Genetics, University of Pennsylvania, Philadelphia, PA 19104, USA
Cell Microbiol 7:1053-9. 2005..Functional genomic databases are not yet very common; however, there are a few focused on microbial genomes and a couple integrative systems are available for setting up functional genomics databases...
- EuPathDB: the eukaryotic pathogen databaseCristina Aurrecoechea
Center for Tropical and Emerging Global Diseases, University of Georgia, Athens, GA 30602, USA
Nucleic Acids Res 41:D684-91. 2013..The manuscript herein describes updates to EuPathDB since the previous report published in NAR in 2010...
- Computational modeling of the Plasmodium falciparum interactome reveals protein function on a genome-wide scaleShailesh V Date
Center for Bioinformatics, Department of Genetics, School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
Genome Res 16:542-9. 2006..falciparum; for instance, a deficit of nearly 26% in terms of predicted interactions is observed against P. yoelii, because of missing ortholog partners in pairs of functionally linked proteins...
- Using ontologies to annotate microarray experimentsPatricia L Whetzel
Department of Genetics, Center for Bioinformatics, University of Pennsylvania School of Medicine, Philadelphia, PA, USA
Methods Enzymol 411:325-39. 2006..The MO is freely available and has been incorporated into the annotation systems of several public microarray database systems...
- AnnotCompute: annotation-based exploration and meta-analysis of genomics experimentsJie Zheng
Department of Genetics, Center for Bioinformatics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
Database (Oxford) 2011:bar045. 2011..Nonetheless, tools such as AnnotCompute may provide an incentive for richer annotations of experiments. Database URL: http://www.cbil.upenn.edu/annotCompute/..
- Functional genomics of the beta-cell: short-chain 3-hydroxyacyl-coenzyme A dehydrogenase regulates insulin secretion independent of K+ currentsOlga T Hardy
Department of Genetics, University of Pennsylvania School of Medicine, 415 Curie Boulevard, 560 Clinical Research Building, Philadelphia, Pennsylvania 19104, USA
Mol Endocrinol 21:765-73. 2007..Our results suggest a molecular explanation for the hyperinsulinemia hypoglycemic seen in patients with SCHAD deficiency...
- PlasmoDB: the Plasmodium genome resource. An integrated database providing tools for accessing, analyzing and mapping expression and sequence data (both finished and unfinished)Amit Bahl
Department of Biology, University of Pennsylvania, 415 South University Avenue, Philadelphia, PA 19104 6018, USA
Nucleic Acids Res 30:87-90. 2002..g. by malaria researchers working in the field). The goal of PlasmoDB is to enhance utilization of the vast quantities of data emerging from genome-scale projects by the global malaria research community...
- Ontodog: a web-based ontology community view generation toolJie Zheng
Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104 and Unit for Laboratory Animal Medicine, Department of Microbiology and Immunology, Center for Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA
Bioinformatics 30:1340-2. 2014..We demonstrate the application of Ontodog for the generation of community views using the Ontology for Biomedical Investigations as the source ontology...
- Stat and interferon genes identified by network analysis differentially regulate primitive and definitive erythropoiesisEmily Greenfest-Allen
Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA stoec
BMC Syst Biol 7:38. 2013..Inferred networks are strongly connected and do not fit a scale-free model, making it difficult to identify essential regulators using the hub-essentiality standard...
- A practical false discovery rate approach to identifying patterns of differential expression in microarray dataGregory R Grant
Center for Bioinformatics, University of Pennsylvania, 1429 Blockley Hall, 423 Guardian Drive, Philadelphia, PA 19104 6021, USA
Bioinformatics 21:2684-90. 2005..For example, the log transform can both help and hurt at the same time, depending on the gene. We examine issues surrounding the SAM 'fudge factor' parameter, and how to handle these issues by optimizing with respect to power...
- Neuron-specific mRNA complexity responses during hippocampal apoptosis after traumatic brain injuryPaolo G Marciano
Departments of Neuroscience, Center for Bioinformatics, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
J Neurosci 24:2866-76. 2004....
- Promoter features related to tissue specificity as measured by Shannon entropyJonathan Schug
Center for Bioinformatics, University of Pennsylvania, Philadelphia, PA 19104, USA
Genome Biol 6:R33. 2005..A genome-wide analysis of promoters in the context of gene-expression patterns in tissue surveys provides a means of identifying the general principles for these mechanisms...
- Common objects: think global, act localChristian J Stoeckert
Department of Genetics and Center for Bioinformatics, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
OMICS 7:103-4. 2003
- Comparison of different labeling methods for two-channel high-density microarray experimentsElisabetta Manduchi
Center for Bioinformatics, Univ of Pennsylvania, Philadelphia, Pennsylvania 19104 6021, USA
Physiol Genomics 10:169-79. 2002..These findings are helping to guide our decisions on what labeling method to use for subsequent studies, based on the purpose of a specific study and its limitations in terms of available material...
- Functional genomics of the endocrine pancreas: the pancreas clone set and PancChip, new resources for diabetes researchL Marie Scearce
Department of Genetics, University of Pennsylvania, 415 Curie Boulevard, Philadephia, PA 19104, USA
Diabetes 51:1997-2004. 2002..5 through adulthood in mice. The clone set and corresponding array are useful resources for diabetes research...
- Predicting gene ontology functions from ProDom and CDD protein domainsJonathan Schug
Center for Bioinformatics, Computational Biology and Informatics Laboratory, University of Pennsylvania, Philadelphia, PA 19104, USA
Genome Res 12:648-55. 2002..The domain-function associations and function assignments are available from our website http://www.cbil.upenn.edu/GO...
- Integrating computationally assembled mouse transcript sequences with the Mouse Genome Informatics (MGI) databaseYunxia Zhu
Mouse Genome Informatics, The Jackson Laboratory, Bar Harbor, ME 04609, USA
Genome Biol 4:R16. 2003..We present the analysis and results of a semi-automated process of connecting transcript assemblies with highly curated biological information for mouse genes that is available through the Mouse Genome Informatics (MGI) database...
- Standards for microarray dataCatherine A Ball
Science 298:539. 2002
- A molecular profile of a hematopoietic stem cell nicheJason A Hackney
Department of Molecular Biology, Princeton University, Princeton, NJ 08544 Laboratoire d Hematopoièse, Faculte de Medecine, Universite de Tours, 37041 Tours Cedex 1, France
Proc Natl Acad Sci U S A 99:13061-6. 2002..The data have been assembled into a biological process oriented database, and represent a molecular profile of a candidate stem cell niche...
- Design and implementation of microarray gene expression markup language (MAGE-ML)Paul T Spellman
Department of Cell and Molecular Biology, University of California at Berkeley, Berkeley, CA 94720 3206, USA
Genome Biol 3:RESEARCH0046. 2002..Only when data can be easily exchanged will the entire biological community be able to derive the full benefit from such microarray studies...
- ApiDB: integrated resources for the apicomplexan bioinformatics resource centerCristina Aurrecoechea
Center for Tropical and Emerging Global Diseases, Athens, GA, USA
Nucleic Acids Res 35:D427-30. 2007..Through the ApiDB site, users may pose queries and search all available apicomplexan data and tools, or they may visit individual component organism databases...
- The underlying principles of scientific publicationCatherine A Ball
Bioinformatics 18:1409. 2002
- An object model and database for functional genomicsAndrew Jones
Department of Computing Science, University of Glasgow, Glasgow, UK
Bioinformatics 20:1583-90. 2004..We believe that all types of functional genomics experiments should be annotated in a consistent manner, and we hope to open up new ways of comparing multiple datasets used in functional genomics...
- A simple spreadsheet-based, MIAME-supportive format for microarray data: MAGE-TABTim F Rayner
European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
BMC Bioinformatics 7:489. 2006..However, the complexity of the MAGE-ML format has made its use impractical for laboratories lacking dedicated bioinformatics support...
- STAC: A method for testing the significance of DNA copy number aberrations across multiple array-CGH experimentsSharon J Diskin
Division of Oncology, Children s Hospital of Philadelphia, Pennsylvania 19104, USA
Genome Res 16:1149-58. 2006..We conclude that STAC is a powerful tool for identifying nonrandom genomic amplifications and deletions across multiple experiments. A Java version of STAC is freely available for download at http://cbil.upenn.edu/STAC...
- The Functional Genomics Experiment model (FuGE): an extensible framework for standards in functional genomicsAndrew R Jones
School of Computer Science, University of Manchester, Oxford Road, Manchester, M13 9PL, UK
Nat Biotechnol 25:1127-33. 2007..Such advances are important for transparent data management and mining in functional genomics and systems biology...
- Defining the mammalian CArGomeQiang Sun
Cardiovascular Research Institute, University of Rochester School of Medicine, Rochester, NY 14642, USA
Genome Res 16:197-207. 2006..We suggest one function of SRF is that of an ancient master regulator of the actin cytoskeleton...
- Plasmodium research in the postgenomic eraManoj Duraisingh
Department of Immunology and Infectious Diseases, Harvard School of Public Health Building I, Room 715, 665 Huntington Avenue, Boston, MA 02115, USA
Trends Parasitol 22:1-4. 2006....
- Systems biology-defined NF-kappaB regulons, interacting signal pathways and networks are implicated in the malignant phenotype of head and neck cancer cell lines differing in p53 statusBin Yan
Head and Neck Surgery Branch, NIDCD, National Institutes of Health, Bethesda, MD 20892, USA
Genome Biol 9:R53. 2008..However, how NF-kappaB acts as a key regulatory node to modulate global gene expression, and contributes to the malignant heterogeneity of head and neck cancer, is not well understood...
- Comparative genomics of the neglected human malaria parasite Plasmodium vivaxJane M Carlton
The Institute for Genomic Research J Craig Venter Institute, 9704 Medical Research Drive, Rockville, Maryland 20850, USA
Nature 455:757-63. 2008..Completion of the P. vivax genome provides the scientific community with a valuable resource that can be used to advance investigation into this neglected species...
- Minimum information specification for in situ hybridization and immunohistochemistry experiments (MISFISHIE)Eric W Deutsch
Institute for Systems Biology, 1441 N 34th Street, Seattle, Washington 98103, USA
Nat Biotechnol 26:305-12. 2008..This specification has benefited the consortium within which it was developed and is expected to benefit the wider research community. We welcome feedback from the scientific community to help improve our proposal...
- Development of the Minimum Information Specification for In Situ Hybridization and Immunohistochemistry Experiments (MISFISHIE)Eric W Deutsch
Institute for Systems Biology, Seattle, Washington 98103, USA
OMICS 10:205-8. 2006..The full specification will soon be published as a version 1.0 proposal to the community, upon which a more full discussion must take place so that the final specification may be achieved with the involvement of the whole community...
- Promoting coherent minimum reporting guidelines for biological and biomedical investigations: the MIBBI projectChris F Taylor
European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
Nat Biotechnol 26:889-96. 2008
- Annotation-based meta-analysis of microarray experimentsChristian Stoeckert; Fiscal Year: 2008..This can further facilitate integration of data of different types to address a scientific question of interest. These benefits may encourage better annotation of experiments and use of standards. ..