Stefan Enroth

Summary

Publications

  1. pmc Cancer associated epigenetic transitions identified by genome-wide histone methylation binding profiles in human colorectal cancer samples and paired normal mucosa
    Stefan Enroth
    The Linnaeus Centre for Bioinformatics, Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, Sweden
    BMC Cancer 11:450. 2011
  2. pmc Whole-genome maps of USF1 and USF2 binding and histone H3 acetylation reveal new aspects of promoter structure and candidate genes for common human disorders
    Alvaro Rada-Iglesias
    Department of Genetics and Pathology, Rudbeck Laboratory, Uppsala University, SE 75185 Uppsala, Sweden
    Genome Res 18:380-92. 2008
  3. pmc Integrative epigenomic and genomic analysis of malignant pheochromocytoma
    Johanna Sandgren
    Department of Surgical Sciences, Uppsala University, Uppsala University Hospital, SE 75185 Uppsala, Sweden
    Exp Mol Med 42:484-502. 2010
  4. ncbi request reprint Histone H3 lysine 27 trimethylation in adult differentiated colon associated to cancer DNA hypermethylation
    Alvaro Rada-Iglesias
    Department of Genetics and Pathology, Rudbeck Laboratory, Uppsala University, Uppsala, Sweden
    Epigenetics 4:107-13. 2009
  5. doi request reprint Novel genes in cell cycle control and lipid metabolism with dynamically regulated binding sites for sterol regulatory element-binding protein 1 and RNA polymerase II in HepG2 cells detected by chromatin immunoprecipitation with microarray detection
    Mehdi Motallebipour
    Department of Genetics and Pathology, Rudbeck Laboratory, Uppsala University, Uppsala, Sweden
    FEBS J 276:1878-90. 2009
  6. doi request reprint Long noncoding RNA-mediated maintenance of DNA methylation and transcriptional gene silencing
    Faizaan Mohammad
    Science for Life Laboratory, Department of Immunology, Genetics and Pathology, Dag Hammarskjölds väg 20, Uppsala University, Uppsala, Sweden
    Development 139:2792-803. 2012
  7. pmc Nucleosomes are well positioned in exons and carry characteristic histone modifications
    Robin Andersson
    The Linnaeus Centre for Bioinformatics, Uppsala University, Sweden
    Genome Res 19:1732-41. 2009
  8. doi request reprint Kcnq1ot1 antisense noncoding RNA mediates lineage-specific transcriptional silencing through chromatin-level regulation
    Radha Raman Pandey
    Department of Genetics and Pathology, Dag Hammarskjölds väg 20, Rudbeck Laboratory, Uppsala University, 751 85 Uppsala, Sweden
    Mol Cell 32:232-46. 2008
  9. ncbi request reprint The LCB Data Warehouse
    Adam Ameur
    The Linnaeus Centre for Bioinformatics, Uppsala University, Sweden
    Bioinformatics 22:1024-6. 2006
  10. pmc Combinations of histone modifications mark exon inclusion levels
    Stefan Enroth
    The Linnaeus Centre for Bioinformatics, Department of Cell and Molecular Biology, Science for Life Laboratory, Biomedical Center, Uppsala University, Uppsala, Sweden
    PLoS ONE 7:e29911. 2012

Collaborators

Detail Information

Publications17

  1. pmc Cancer associated epigenetic transitions identified by genome-wide histone methylation binding profiles in human colorectal cancer samples and paired normal mucosa
    Stefan Enroth
    The Linnaeus Centre for Bioinformatics, Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, Sweden
    BMC Cancer 11:450. 2011
    ..In order to evaluate their importance in colorectal cancer (CRC), we generated the first genome-wide histone modification profiles in paired normal colon mucosa and tumor samples...
  2. pmc Whole-genome maps of USF1 and USF2 binding and histone H3 acetylation reveal new aspects of promoter structure and candidate genes for common human disorders
    Alvaro Rada-Iglesias
    Department of Genetics and Pathology, Rudbeck Laboratory, Uppsala University, SE 75185 Uppsala, Sweden
    Genome Res 18:380-92. 2008
    ..This expands our understanding about the transcriptional control of metabolic processes and its alteration in metabolic disorders...
  3. pmc Integrative epigenomic and genomic analysis of malignant pheochromocytoma
    Johanna Sandgren
    Department of Surgical Sciences, Uppsala University, Uppsala University Hospital, SE 75185 Uppsala, Sweden
    Exp Mol Med 42:484-502. 2010
    ..Our approach to associate histone methylations and DNA copy number changes to gene expression revealed apparent impact on global gene transcription, and enabled the identification of candidate tumor genes for further exploration...
  4. ncbi request reprint Histone H3 lysine 27 trimethylation in adult differentiated colon associated to cancer DNA hypermethylation
    Alvaro Rada-Iglesias
    Department of Genetics and Pathology, Rudbeck Laboratory, Uppsala University, Uppsala, Sweden
    Epigenetics 4:107-13. 2009
    ..Therefore, the suggested polycomb pre-marking of genes for cancer DNA hypermethylation is not necessarily limited to ES or early precursor cells but can occur later in differentiated tissues...
  5. doi request reprint Novel genes in cell cycle control and lipid metabolism with dynamically regulated binding sites for sterol regulatory element-binding protein 1 and RNA polymerase II in HepG2 cells detected by chromatin immunoprecipitation with microarray detection
    Mehdi Motallebipour
    Department of Genetics and Pathology, Rudbeck Laboratory, Uppsala University, Uppsala, Sweden
    FEBS J 276:1878-90. 2009
    ..Furthermore, we found evidence of sterol-regulated binding of SREBP-1 and RNA polymerase II to HCFC1 and FLNA. From the results of this work, we infer that SREBP-1 may be involved in processes other than lipid metabolism...
  6. doi request reprint Long noncoding RNA-mediated maintenance of DNA methylation and transcriptional gene silencing
    Faizaan Mohammad
    Science for Life Laboratory, Department of Immunology, Genetics and Pathology, Dag Hammarskjölds väg 20, Uppsala University, Uppsala, Sweden
    Development 139:2792-803. 2012
    ..Taken together, this study illustrates the gene-specific maintenance mechanisms operational at the Kcnq1 locus for tissue-specific transcriptional gene silencing and activation...
  7. pmc Nucleosomes are well positioned in exons and carry characteristic histone modifications
    Robin Andersson
    The Linnaeus Centre for Bioinformatics, Uppsala University, Sweden
    Genome Res 19:1732-41. 2009
    ..Thus, exons are not only characterized by their coding capacity, but also by their nucleosome organization, which seems evolutionarily conserved since it is present in both primates and nematodes...
  8. doi request reprint Kcnq1ot1 antisense noncoding RNA mediates lineage-specific transcriptional silencing through chromatin-level regulation
    Radha Raman Pandey
    Department of Genetics and Pathology, Dag Hammarskjölds väg 20, Rudbeck Laboratory, Uppsala University, 751 85 Uppsala, Sweden
    Mol Cell 32:232-46. 2008
    ....
  9. ncbi request reprint The LCB Data Warehouse
    Adam Ameur
    The Linnaeus Centre for Bioinformatics, Uppsala University, Sweden
    Bioinformatics 22:1024-6. 2006
    ..lcb.uu.se/index.phtml?i_login=test. User accounts are created upon request. Additional facilities including plug-ins, user documentation and a password protected data storage system are available from http://www.lcb.uu.se/lcbdw.php..
  10. pmc Combinations of histone modifications mark exon inclusion levels
    Stefan Enroth
    The Linnaeus Centre for Bioinformatics, Department of Cell and Molecular Biology, Science for Life Laboratory, Biomedical Center, Uppsala University, Uppsala, Sweden
    PLoS ONE 7:e29911. 2012
    ..The resulting model was evaluated with cross validation and had an average accuracy of 72% for 27% of the exons, which demonstrates that epigenetic signals substantially mark alternative splicing...
  11. pmc Peak Finder Metaserver - a novel application for finding peaks in ChIP-seq data
    Marcin Kruczyk
    Department of Cell and Molecular Biology, Uppsala University, Husargatan 3, Uppsala, Sweden
    BMC Bioinformatics 14:280. 2013
    ..We present the first meta-server called Peak Finder MetaServer (PFMS) that collects results from several peak finders and produces consensus peaks. Our application accepts three standard ChIP-seq data formats: BED, BAM, and SAM...
  12. pmc Nucleosome regulatory dynamics in response to TGFβ
    Stefan Enroth
    The Linnaeus Centre for Bioinformatics, Biomedical Center, Uppsala University, SE 75124 Uppsala, Sweden
    Nucleic Acids Res 42:6921-34. 2014
    ..Changes in binding affinity were verified for HNF4α by qPCR. Strikingly many of these loci were associated with expression changes, as measured by RNA sequencing. ..
  13. pmc A strand specific high resolution normalization method for chip-sequencing data employing multiple experimental control measurements
    Stefan Enroth
    The Linnaeus Centre for Bioinformatics, Department of Cell and Molecular Biology, Science for Life Laboratory, Biomedical Center, Uppsala University, Box 598, SE 75124 Uppsala, Sweden
    Algorithms Mol Biol 7:2. 2012
    ..abstract:..
  14. pmc SICTIN: Rapid footprinting of massively parallel sequencing data
    Stefan Enroth
    Department of Cell and Molecular Biology, The Linnaeus Centre for Bioinformatics, Uppsala University, Box 598, SE 75124 Uppsala, Sweden
    BioData Min 3:4. 2010
    ..The construction of these footprints is however a time consuming task...
  15. pmc Identification of genetic variants influencing the human plasma proteome
    Asa Johansson
    Department of Immunology, Genetics, and Pathology, Rudbeck Laboratory, SciLifeLab, Uppsala University, 75185 Uppsala, Sweden
    Proc Natl Acad Sci U S A 110:4673-8. 2013
    ..A better understanding of the genetic impact on the plasma proteome is therefore important for evaluating potential biomarkers and therapeutic agents for common diseases...
  16. pmc Genetic adaptation of fatty-acid metabolism: a human-specific haplotype increasing the biosynthesis of long-chain omega-3 and omega-6 fatty acids
    Adam Ameur
    Department of Immunology, Genetics and Pathology, SciLifeLab Uppsala, Rudbeck Laboratory, Uppsala University, Uppsala, Sweden
    Am J Hum Genet 90:809-20. 2012
    ..In the modern world, this haplotype has been associated with lifestyle-related diseases, such as coronary artery disease...
  17. ncbi request reprint Binding sites for metabolic disease related transcription factors inferred at base pair resolution by chromatin immunoprecipitation and genomic microarrays
    Alvaro Rada-Iglesias
    Department of Genetics and Pathology, Rudbeck Laboratory, Uppsala University, Sweden
    Hum Mol Genet 14:3435-47. 2005
    ..Our data suggests that a similar approach could be used for the in vivo characterization of all predicted/uncharacterized TF and that the analysis could be scaled to the whole genome...