Jonathan Schug

Summary

Affiliation: University of Pennsylvania
Country: USA

Publications

  1. pmc Predicting gene ontology functions from ProDom and CDD protein domains
    Jonathan Schug
    Center for Bioinformatics, Computational Biology and Informatics Laboratory, University of Pennsylvania, Philadelphia, PA 19104, USA
    Genome Res 12:648-55. 2002
  2. pmc Promoter features related to tissue specificity as measured by Shannon entropy
    Jonathan Schug
    Center for Bioinformatics, University of Pennsylvania, Philadelphia, PA 19104, USA
    Genome Biol 6:R33. 2005
  3. ncbi request reprint The Plasmodium genome database
    Jessica 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
  4. pmc Epigenomic plasticity enables human pancreatic α to β cell reprogramming
    Nuria C Bramswig
    Department of Genetics and Institute for Diabetes, Obesity and Metabolism, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
    J Clin Invest 123:1275-84. 2013
  5. pmc Tissue-specific regulation of mouse microRNA genes in endoderm-derived tissues
    Yan Gao
    Department of Medicine, University of Pennsylvania School of Medicine, Philadelphia, PA 19104 6145, USA
    Nucleic Acids Res 39:454-63. 2011
  6. pmc Re-expression of GATA2 cooperates with peroxisome proliferator-activated receptor-gamma depletion to revert the adipocyte phenotype
    Michael Schupp
    Division of Endocrinology, Diabetes, and Metabolism, Department of Medicine, Univ of Pennsylvania School of Medicine, 700 CRB, 415 Curie Blvd, Philadelphia, PA 19104 6149, USA
    J Biol Chem 284:9458-64. 2009
  7. pmc Foxa2 and H2A.Z mediate nucleosome depletion during embryonic stem cell differentiation
    Zhaoyu Li
    Department of Genetics and Institute of Diabetes, Obesity and Metabolism, School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
    Cell 151:1608-16. 2012
  8. pmc Research resource: the pdx1 cistrome of pancreatic islets
    Cynthia Khoo
    Institute for Diabetes, Obesity, and Metabolism, University of Pennsylvania School of Medicine, Philadelphia, PA 19104, USA
    Mol Endocrinol 26:521-33. 2012
  9. pmc Extracting transcription factor targets from ChIP-Seq data
    Geetu Tuteja
    Department of Genetics and Institute of Diabetes, Obesity and Metabolism, University of Pennsylvania School of Medicine, Philadelphia, PA 19104, USA
    Nucleic Acids Res 37:e113. 2009
  10. pmc Foxa1 and Foxa2 maintain the metabolic and secretory features of the mature beta-cell
    Nan Gao
    Department of Genetics, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania 19104 6145, USA
    Mol Endocrinol 24:1594-604. 2010

Collaborators

Detail Information

Publications41

  1. pmc Predicting gene ontology functions from ProDom and CDD protein domains
    Jonathan 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...
  2. pmc Promoter features related to tissue specificity as measured by Shannon entropy
    Jonathan 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...
  3. ncbi request reprint The Plasmodium genome database
    Jessica 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
  4. pmc Epigenomic plasticity enables human pancreatic α to β cell reprogramming
    Nuria C Bramswig
    Department of Genetics and Institute for Diabetes, Obesity and Metabolism, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
    J Clin Invest 123:1275-84. 2013
    ..Thus, mammalian pancreatic islet cells display cell-type-specific epigenomic plasticity, suggesting that epigenomic manipulation could provide a path to cell reprogramming and novel cell replacement-based therapies for diabetes...
  5. pmc Tissue-specific regulation of mouse microRNA genes in endoderm-derived tissues
    Yan Gao
    Department of Medicine, University of Pennsylvania School of Medicine, Philadelphia, PA 19104 6145, USA
    Nucleic Acids Res 39:454-63. 2011
    ..We determined that the same transcriptional regulatory mechanisms govern tissue-specific gene expression of both mRNA and microRNA encoding genes in mammals...
  6. pmc Re-expression of GATA2 cooperates with peroxisome proliferator-activated receptor-gamma depletion to revert the adipocyte phenotype
    Michael Schupp
    Division of Endocrinology, Diabetes, and Metabolism, Department of Medicine, Univ of Pennsylvania School of Medicine, 700 CRB, 415 Curie Blvd, Philadelphia, PA 19104 6149, USA
    J Biol Chem 284:9458-64. 2009
    ..These results suggest that PPARgamma-independent down-regulation of GATA2 prevents reversion of mature adipocytes after PPARgamma depletion...
  7. pmc Foxa2 and H2A.Z mediate nucleosome depletion during embryonic stem cell differentiation
    Zhaoyu Li
    Department of Genetics and Institute of Diabetes, Obesity and Metabolism, School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
    Cell 151:1608-16. 2012
    ..Thus, both epigenetic and genetic regulators cooperate to control nucleosome dynamics during ES cell fate decisions...
  8. pmc Research resource: the pdx1 cistrome of pancreatic islets
    Cynthia Khoo
    Institute for Diabetes, Obesity, and Metabolism, University of Pennsylvania School of Medicine, Philadelphia, PA 19104, USA
    Mol Endocrinol 26:521-33. 2012
    ....
  9. pmc Extracting transcription factor targets from ChIP-Seq data
    Geetu Tuteja
    Department of Genetics and Institute of Diabetes, Obesity and Metabolism, University of Pennsylvania School of Medicine, Philadelphia, PA 19104, USA
    Nucleic Acids Res 37:e113. 2009
    ..We also use GLITR to address the issue of sequencing depth, and show that sequencing biological replicates identifies far more binding regions than re-sequencing the same sample...
  10. pmc Foxa1 and Foxa2 maintain the metabolic and secretory features of the mature beta-cell
    Nan Gao
    Department of Genetics, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania 19104 6145, USA
    Mol Endocrinol 24:1594-604. 2010
    ..These data demonstrate that Foxa1 and Foxa2 play crucial roles in the development and maintenance of beta-cell-specific secretory and metabolic pathways...
  11. pmc 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...
  12. pmc Propagation of adipogenic signals through an epigenomic transition state
    David 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...
  13. pmc The transcriptional response of the islet to pregnancy in mice
    Sebastian Rieck
    Department of Genetics and Institute for Diabetes, Obesity and Metabolism, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania 19104 6145, USA
    Mol Endocrinol 23:1702-12. 2009
    ....
  14. pmc EPConDB: a web resource for gene expression related to pancreatic development, beta-cell function and diabetes
    Joan 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...
  15. pmc Dnmt1 is essential to maintain progenitors in the perinatal intestinal epithelium
    Ellen N Elliott
    Department of Genetics and Institute for Diabetes, Obesity and Metabolism, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
    Development 142:2163-72. 2015
    ..These results demonstrate an essential role for Dnmt1 in maintaining genomic stability during intestinal development and the establishment of intestinal crypts. ..
  16. pmc Epigenetic regulation of the DLK1-MEG3 microRNA cluster in human type 2 diabetic islets
    Vasumathi Kameswaran
    Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA Institute for Diabetes, Obesity, and Metabolism, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
    Cell Metab 19:135-45. 2014
    ..Our results support a role for microRNAs and their epigenetic control by DNA methylation in the pathogenesis of T2DM...
  17. pmc Foxa2-dependent hepatic gene regulatory networks depend on physiological state
    Irina M Bochkis
    Department of Genetics and Institute for Diabetes, Obesity and Metabolism, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania, USA
    Physiol Genomics 38:186-95. 2009
    ..We show that Foxa2 interacts with different transcription factors to achieve gene expression responses appropriate for each physiologic state...
  18. pmc The nucleosome map of the mammalian liver
    Zhaoyu Li
    Department of Genetics, School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA Institute of Diabetes, Obesity and Metabolism, School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
    Nat Struct Mol Biol 18:742-6. 2011
    ....
  19. pmc Foxl1-Cre-marked adult hepatic progenitors have clonogenic and bilineage differentiation potential
    Soona Shin
    Department of Genetics, University of Pennsylvania School of Medicine, Philadelphia, USA
    Genes Dev 25:1185-92. 2011
    ..Thus, the Foxl1-Cre; RosaYFP model allows for easy isolation of adult hepatic progenitor cells that can be expanded and differentiated in culture...
  20. pmc DNA methylation is required for the control of stem cell differentiation in the small intestine
    Karyn L Sheaffer
    Department of Genetics, Institute for Diabetes, Obesity, and Metabolism, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
    Genes Dev 28:652-64. 2014
    ..We establish that the loss of DNA methylation at intestinal stem cell gene enhancers causes inappropriate gene expression and delayed differentiation. ..
  21. pmc Dynamic recruitment of microRNAs to their mRNA targets in the regenerating liver
    Jonathan Schug
    Department of Genetics and Institute for Diabetes, Obesity and Metabolism, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
    BMC Genomics 14:264. 2013
    ..Validation of physiologic miRNA targets has been met with significant challenges. We employed HITS-CLIP to identify which miRNAs participate in liver regeneration, and to identify their target mRNAs...
  22. pmc Foxa1 and Foxa2 are essential for sexual dimorphism in liver cancer
    Zhaoyu Li
    Department of Genetics and Institute for Diabetes, Obesity, and Metabolism, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
    Cell 148:72-83. 2012
    ..Thus, Foxa factors and their targets are central for the sexual dimorphism of HCC...
  23. pmc Genome-wide analysis of histone modifications in human pancreatic islets
    Reena Bhandare
    Department of Genetics, University of Pennsylvania School of Medicine, Philadelphia, PA 19104, USA
    Genome Res 20:428-33. 2010
    ..Our global map of histone marks will serve as an important resource for understanding the epigenetic basis of type 2 diabetes...
  24. pmc PPARgamma and C/EBP factors orchestrate adipocyte biology via adjacent binding on a genome-wide scale
    Martina 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...
  25. pmc CREB-mediated alterations in the amygdala transcriptome: coordinated regulation of immune response genes following cocaine
    Laurel E Ecke
    Department of Pharmacology, University of Pennsylvania School of Medicine, Philadelphia, PA, USA
    Int J Neuropsychopharmacol 14:1111-26. 2011
    ....
  26. doi request reprint Using TESS to predict transcription factor binding sites in DNA sequence
    Jonathan Schug
    University of Pennsylvania, Philadelphia, Pennsylvania, USA
    Curr Protoc Bioinformatics . 2008
    ..Because of this, binding sites for a factor can typically be found at random every few hundred to a thousand base pairs. TESS has features to help sort through and evaluate the significance of predicted sites...
  27. pmc Single-Cell Mass Cytometry Analysis of the Human Endocrine Pancreas
    YUE J WANG
    Department of Genetics and Institute for Diabetes, Obesity, and Metabolism, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
    Cell Metab 24:616-626. 2016
    ..High-dimensional analysis of our marker protein expression revealed three major clusters of beta cells within individuals. Proliferating beta cells are confined to two of the clusters...
  28. pmc Genome-wide mapping of histone H4 serine-1 phosphorylation during sporulation in Saccharomyces cerevisiae
    Jerome Govin
    Department of Cell and Developmental Biology, University of Pennsylvania, Philadelphia, PA 19104, USA
    Nucleic Acids Res 38:4599-606. 2010
    ..These studies indicate distinctive features of a histone H4 modification marking system during sporulation compared with DSB repair...
  29. pmc MicroRNAs control intestinal epithelial differentiation, architecture, and barrier function
    Lindsay B McKenna
    Department of Genetics, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania 19103, USA
    Gastroenterology 139:1654-64, 1664.e1. 2010
    ..We aimed to quantify the complete miRNA expression profile of the mammalian intestinal mucosa and to determine the contribution of miRNAs to intestinal homeostasis using genetic means...
  30. pmc Aging-Dependent Demethylation of Regulatory Elements Correlates with Chromatin State and Improved β Cell Function
    Dana Avrahami
    Department of Genetics and Institute for Diabetes, Obesity, and Metabolism, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA Endocrinology and Metabolism Service, Hadassah Hebrew University Medical Center, Jerusalem 91120, Israel
    Cell Metab 22:619-32. 2015
    ..Strikingly, we find β cell function improved in aged mice, as predicted by the changes in methylome and transcriptome. Thus, aging of terminally differentiated cells in mammals is not always coupled to functional decline...
  31. pmc Islet-1 Is essential for pancreatic β-cell function
    Benjamin N Ediger
    Department of Pathology and Laboratory Medicine, Children s Hospital of Philadelphia, Philadelphia, PA Department of Medicine and Institute for Diabetes, Obesity, and Metabolism, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
    Diabetes 63:4206-17. 2014
    ..Thus Isl-1 is essential for postnatal β-cell function, directly regulates Pdx1 and Slc2a2, and has a mature β-cell cistrome distinct from that of pancreatic endocrine progenitors...
  32. pmc Inherited mutations in the helicase RTEL1 cause telomere dysfunction and Hoyeraal-Hreidarsson syndrome
    Zhong Deng
    Program in Gene Expression and Regulation, The Wistar Institute, Philadelphia, PA 19104, USA
    Proc Natl Acad Sci U S A 110:E3408-16. 2013
    ..Finally, we show that human RTEL1 interacts with the shelterin protein TRF1, providing a potential recruitment mechanism of RTEL1 to telomeres. ..
  33. pmc Histone deacetylase 3 is an epigenomic brake in macrophage alternative activation
    Shannon E Mullican
    Division of Endocrinology, Diabetes, and Metabolism, Department of Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
    Genes Dev 25:2480-8. 2011
    ..Thus, HDAC3 functions in alternative activation as a brake whose release could be of benefit in the treatment of multiple inflammatory diseases...
  34. doi request reprint ChIP-Seq: Library Preparation and Sequencing
    Karyn L Sheaffer
    Department of Genetics, and Institute for Diabetes, Obesity and Metabolism, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
    Methods Mol Biol 1402:101-17. 2016
    ..Here we describe methods to isolate chromatin from tissues, immunoprecipitate DNA bound to a protein of interest, and perform next-generation sequencing to identify a genome-wide DNA-binding pattern...
  35. pmc Genome-wide analyses of ChIP-Seq derived FOXA2 DNA occupancy in liver points to genetic networks underpinning multiple complex traits
    Matthew E Johnson
    Division of Human Genetics M E J, S F A G and Department of Pathology and Laboratory Medicine A D W, The Children s Hospital of Philadelphia, and Department of Genetics and Institute of Diabetes, Obesity, and Metabolism J S, K H K, S F A G, and Department of Pediatrics S F A G, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104
    J Clin Endocrinol Metab 99:E1580-5. 2014
    ..Our hypothesis was that this DNA-binding protein regulates the expression of a set of molecular pathways critical to endocrine traits...
  36. pmc PlasmoDB: the Plasmodium genome resource. A database integrating experimental and computational data
    Amit 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)...
  37. pmc 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...
  38. pmc Glucocorticoid receptor-dependent gene regulatory networks
    Phillip Phuc Le
    Department of Genetics, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania, USA
    PLoS Genet 1:e16. 2005
    ..Together, our results further our understanding of the GR and its targets, and provide the basis for more targeted glucocorticoid therapies...
  39. pmc Orthogonal analysis of C/EBPbeta targets in vivo during liver proliferation
    Joshua R Friedman
    Department of Genetics, Bioinformatics Core, University of Pennsylvania School of Medicine, Philadelphia, PA 19104, USA
    Proc Natl Acad Sci U S A 101:12986-91. 2004
    ..This approach is generally applicable to the discovery of direct, biologically relevant targets of mammalian transcription factors...
  40. ncbi request reprint Drug-induced alterations in gene expression of the asexual blood forms of Plasmodium falciparum
    Anusha Munasinghe Gunasekera
    Department of Immunology and Infectious Diseases, Harvard School of Public Health, Boston MA 02115, USA
    Mol Microbiol 50:1229-39. 2003
    ..Several others, however, were derived from unexpected categories, including a large number of unknown open reading frames (ORFs), whose induction after drug exposure may provide first hints to their possible function...
  41. ncbi request reprint Widespread distribution of antisense transcripts in the Plasmodium falciparum genome
    Anusha Munasinghe Gunasekera
    Department of Immunology and Infectious Diseases, Harvard School of Public Health, Harvard University, 665 Huntington Avenue, Boston, MA 02115, USA
    Mol Biochem Parasitol 136:35-42. 2004
    ..Taken together, this data may provide first hints as to the possible function of antisense transcription in this system...