Boris Lenhard

Summary

Affiliation: Center for Genomics and Bioinformatics
Country: Sweden

Publications

  1. ncbi request reprint TFBS: Computational framework for transcription factor binding site analysis
    Boris Lenhard
    Bioinformatics Unit, Center for Genomics and Bioinformatics, Karolinska Institutet, Stockholm, Sweden
    Bioinformatics 18:1135-6. 2002
  2. pmc In silico detection of sequence variations modifying transcriptional regulation
    Malin C Andersen
    Department of Gene Technology, School of Biotechnology, AlbaNova University Center, Royal Institute of Technology KTH, Stockholm, Sweden
    PLoS Comput Biol 4:e5. 2008
  3. pmc Exploring hepatic hormone actions using a compilation of gene expression profiles
    Nina Ståhlberg
    Department of Molecular Medicine, Karolinska Institute, 17176 Stockholm, Sweden
    BMC Physiol 5:8. 2005
  4. pmc Identification of functional SNPs in the 5-prime flanking sequences of human genes
    Salim Mottagui-Tabar
    Center for Genomics and Bioinformatics, Karolinska Institutet, SE 17177 Stockholm, Sweden
    BMC Genomics 6:18. 2005
  5. pmc ConSite: web-based prediction of regulatory elements using cross-species comparison
    Albin Sandelin
    Center for Genomics and Bioinformatics, Karolinska Institutet, Berzelius vag 35, S 17177 Stockholm, Sweden
    Nucleic Acids Res 32:W249-52. 2004
  6. pmc JASPAR: an open-access database for eukaryotic transcription factor binding profiles
    Albin Sandelin
    Center for Genomics and Bioinformatics, Karolinska Institutet, Berzelius vag 35, S 17177 Stockholm, Sweden
    Nucleic Acids Res 32:D91-4. 2004
  7. pmc Arrays of ultraconserved non-coding regions span the loci of key developmental genes in vertebrate genomes
    Albin Sandelin
    Center for Genomics and Bioinformatics, Karolinska Institutet, Stockholm, Sweden
    BMC Genomics 5:99. 2004
  8. ncbi request reprint Integrated analysis of yeast regulatory sequences for biologically linked clusters of genes
    Albin Sandelin
    Center for Genomics and Bioinformatics, Karolinska Institutet, Stockholm, Sweden
    Funct Integr Genomics 3:125-34. 2003
  9. pmc Regulog analysis: detection of conserved regulatory networks across bacteria: application to Staphylococcus aureus
    Wynand B L Alkema
    Center for Genomics and Bioinformatics, Karolinska Institutet, Stockholm, Sweden
    Genome Res 14:1362-73. 2004
  10. pmc Gene characterization index: assessing the depth of gene annotation
    Danielle Kemmer
    Center for Genomics and Bioinformatics, Karolinska Institute, Stockholm, Sweden
    PLoS ONE 3:e1440. 2008

Detail Information

Publications35

  1. ncbi request reprint TFBS: Computational framework for transcription factor binding site analysis
    Boris Lenhard
    Bioinformatics Unit, Center for Genomics and Bioinformatics, Karolinska Institutet, Stockholm, Sweden
    Bioinformatics 18:1135-6. 2002
    ..It implements objects representing specificity profile matrices, binding sites and sets thereof, pattern generators, and pattern database interfaces. The modules are interoperable with the BioPerl open source system...
  2. pmc In silico detection of sequence variations modifying transcriptional regulation
    Malin C Andersen
    Department of Gene Technology, School of Biotechnology, AlbaNova University Center, Royal Institute of Technology KTH, Stockholm, Sweden
    PLoS Comput Biol 4:e5. 2008
    ..The RAVEN system is available at http://www.cisreg.ca for all researchers interested in the detection and characterization of regulatory sequence variation...
  3. pmc Exploring hepatic hormone actions using a compilation of gene expression profiles
    Nina Ståhlberg
    Department of Molecular Medicine, Karolinska Institute, 17176 Stockholm, Sweden
    BMC Physiol 5:8. 2005
    ....
  4. pmc Identification of functional SNPs in the 5-prime flanking sequences of human genes
    Salim Mottagui-Tabar
    Center for Genomics and Bioinformatics, Karolinska Institutet, SE 17177 Stockholm, Sweden
    BMC Genomics 6:18. 2005
    ..Robust methods for the identification of functional SNPs are therefore crucial. We report one such experimental approach...
  5. pmc ConSite: web-based prediction of regulatory elements using cross-species comparison
    Albin Sandelin
    Center for Genomics and Bioinformatics, Karolinska Institutet, Berzelius vag 35, S 17177 Stockholm, Sweden
    Nucleic Acids Res 32:W249-52. 2004
    ..Programming modules and biological databases that form the foundation of the ConSite service are freely available to the research community. ConSite is available at http:/www.phylofoot.org/consite...
  6. pmc JASPAR: an open-access database for eukaryotic transcription factor binding profiles
    Albin Sandelin
    Center for Genomics and Bioinformatics, Karolinska Institutet, Berzelius vag 35, S 17177 Stockholm, Sweden
    Nucleic Acids Res 32:D91-4. 2004
    ..JASPAR is available at http://jaspar. cgb.ki.se...
  7. pmc Arrays of ultraconserved non-coding regions span the loci of key developmental genes in vertebrate genomes
    Albin Sandelin
    Center for Genomics and Bioinformatics, Karolinska Institutet, Stockholm, Sweden
    BMC Genomics 5:99. 2004
    ..Here, we focus on UCRs that cluster around genes involved in early vertebrate development; genes conserved over 450 million years of vertebrate evolution...
  8. ncbi request reprint Integrated analysis of yeast regulatory sequences for biologically linked clusters of genes
    Albin Sandelin
    Center for Genomics and Bioinformatics, Karolinska Institutet, Stockholm, Sweden
    Funct Integr Genomics 3:125-34. 2003
    ..YRSA is available at http://yrsa.cgb.ki.se. [YRSA: ancient Scandinavian name meaning old she-bear (Latin Ursus arctos = brown bear/grizzly).]..
  9. pmc Regulog analysis: detection of conserved regulatory networks across bacteria: application to Staphylococcus aureus
    Wynand B L Alkema
    Center for Genomics and Bioinformatics, Karolinska Institutet, Stockholm, Sweden
    Genome Res 14:1362-73. 2004
    ..A total of 125 regulogs were found in this organism, including both well-defined functional groups and a subset with unknown functions...
  10. pmc Gene characterization index: assessing the depth of gene annotation
    Danielle Kemmer
    Center for Genomics and Bioinformatics, Karolinska Institute, Stockholm, Sweden
    PLoS ONE 3:e1440. 2008
    ....
  11. ncbi request reprint A cladistic model of ACE sequence variation with implications for myocardial infarction, Alzheimer disease and obesity
    Hagit Katzov
    Center for Genomics and Bioinformatics, Karolinska Institute, Berzelius väg 35 171 77, Stockholm, Sweden
    Hum Mol Genet 13:2647-57. 2004
    ....
  12. pmc GeneLynx mouse: integrated portal to the mouse genome
    Boris Lenhard
    Center for Genomics and Bioinformatics, Karolinska Institutet, 17177 Stockholm, Sweden
    Genome Res 13:1501-4. 2003
    ..As a result of the integration of the human and mouse systems, GeneLynx now serves as a powerful comparative genomics data mining resource. GeneLynx Mouse can be freely accessed at http://mouse.genelynx.org...
  13. pmc Identification of conserved regulatory elements by comparative genome analysis
    Boris Lenhard
    Center for Genomics and Bioinformatics, Karolinska Institutet, 171 77 Stockholm, Sweden
    J Biol 2:13. 2003
    ..Mutations are more likely to be disruptive if they appear in functional sites, resulting in a measurable difference in evolution rates between functional and non-functional genomic segments...
  14. pmc JASPAR, the open access database of transcription factor-binding profiles: new content and tools in the 2008 update
    Jan Christian Bryne
    Computational Biology Unit, Bergen Center for Computational Science, University of Bergen, Thormøhlensgate 55, N 5008 Bergen, Norway
    Nucleic Acids Res 36:D102-6. 2008
    ..JASPAR is available at http://jaspar.genereg.net...
  15. ncbi request reprint The random versus fragile breakage models of chromosome evolution: a matter of resolution
    Thomas S Becker
    Sars Centre, University of Bergen, Bergen, Norway
    Mol Genet Genomics 278:487-91. 2007
    ..These findings cannot be accommodated by the random breakage model and suggest that this view of genome and chromosomal evolution requires substantial reassessment...
  16. ncbi request reprint Mammalian RNA polymerase II core promoters: insights from genome-wide studies
    Albin Sandelin
    Genome Exploration Research Group Genome Network Project Core Group, RIKEN Genomic Sciences Center GSC, RIKEN Yokohama Institute, 1 7 22, Suehiro cho, Tsurumi ku, Yokohama, Kanagawa, 230 0045, Japan
    Nat Rev Genet 8:424-36. 2007
    ..A comprehensive survey of mammalian promoters is a major step towards describing and understanding transcriptional control networks...
  17. pmc Genomic regulatory blocks encompass multiple neighboring genes and maintain conserved synteny in vertebrates
    Hiroshi Kikuta
    Sars Centre for Marine Molecular Biology, University of Bergen, 5008 Bergen, Norway
    Genome Res 17:545-55. 2007
    ..These findings explain the absence of evolutionary breakpoints from large vertebrate chromosomal segments and will aid in the recognition of position effect mutations within human GRBs...
  18. ncbi request reprint A global genomic transcriptional code associated with CNS-expressed genes
    Peter J Bailey
    Department of Cell and Molecular Biology, Medical Nobel Institute, Karolinska Institute, S 171, 77 Stockholm, Sweden
    Exp Cell Res 312:3108-19. 2006
    ....
  19. pmc Complex Loci in human and mouse genomes
    Pär G Engström
    Computational Biology Unit, Bergen Center for Computational Science, University of Bergen, Bergen, Norway
    PLoS Genet 2:e47. 2006
    ..Complex loci are ubiquitous, host numerous nonconserved gene structures and lineage-specific exonification events, and may have a cis-regulatory impact on the member genes...
  20. pmc Ancora: a web resource for exploring highly conserved noncoding elements and their association with developmental regulatory genes
    Pär G Engström
    Computational Biology Unit, Bergen Center for Computational Science, University of Bergen, Thormøhlensgate, N 5008 Bergen, Norway
    Genome Biol 9:R34. 2008
    ..Ancora includes a genome browser that shows HCNE locations and features novel HCNE density plots as a powerful tool to discover developmental regulatory genes and distinguish their regulatory elements and domains...
  21. ncbi request reprint Genome-wide analysis of mammalian promoter architecture and evolution
    Piero Carninci
    Genome Exploration Research Group, RIKEN Genomic Sciences Center, RIKEN Yokohama Institute, 1 7 22 Suehiro cho, Tsurumi ku, Yokohama, Kanagawa, 230 0045, Japan
    Nat Genet 38:626-35. 2006
    ..These data permit genome-scale identification of tissue-specific promoters and analysis of the cis-acting elements associated with them...
  22. pmc Integrative annotation of 21,037 human genes validated by full-length cDNA clones
    Tadashi Imanishi
    Integrated Database Group, Biological Information Research Center, National Institute of Advanced Industrial Science and Technology, Tokyo, Japan
    PLoS Biol 2:e162. 2004
    ..The H-InvDB platform represents a substantial contribution to resources needed for the exploration of human biology and pathology...
  23. ncbi request reprint New technologies, new findings, and new concepts in the study of vertebrate cis-regulatory sequences
    Jose Luis Gomez-Skarmeta
    Centro Andaluz de Biologia del Desarrollo, Universidad Pablo Olavide, Seville, Spain
    Dev Dyn 235:870-85. 2006
    ....
  24. pmc A new generation of JASPAR, the open-access repository for transcription factor binding site profiles
    Dominique Vlieghe
    Department for Molecular Biomedical Research DMBR, VIB Ghent University, Technologiepark 927 B 9052, Ghent Zwijnaarde, Belgium
    Nucleic Acids Res 34:D95-7. 2006
    ..JASPAR phyloFACTS serves as a non-redundant extension to JASPAR CORE, enhancing the overall breadth of JASPAR for promoter sequence analysis. The new release of JASPAR is available at http://jaspar.genereg.net...
  25. ncbi request reprint Variants of CYP46A1 may interact with age and APOE to influence CSF Abeta42 levels in Alzheimer's disease
    Annica Johansson
    Department of Clinical Neuroscience, Sahlgrenska University Hospital, Goteborg University, Goteborg, Sweden
    Hum Genet 114:581-7. 2004
    ..Our results provide an important independent replication of previous findings, supporting the existence of CYP46A1 sequence variants that contribute to variability in beta-amyloid metabolism...
  26. pmc The H-Invitational Database (H-InvDB), a comprehensive annotation resource for human genes and transcripts
    Chisato Yamasaki
    Japan Biological Information Research Center, Japan Biological Informatics Consortium, Japan
    Nucleic Acids Res 36:D793-9. 2008
    ....
  27. pmc Retroviral enhancer detection insertions in zebrafish combined with comparative genomics reveal genomic regulatory blocks - a fundamental feature of vertebrate genomes
    Hiroshi Kikuta
    Sars Centre for Marine Molecular Biology, University of Bergen, Thormoehlensgate, 5008 Bergen, Norway
    Genome Biol 8:S4. 2007
    ..We discuss these findings in light of evolution of vertebrate chromosomal architecture and the identification of human disease mutations...
  28. pmc RNAdb--a comprehensive mammalian noncoding RNA database
    Ken C Pang
    ARC Special Research Centre for Functional and Applied Genomics, Institute for Molecular Bioscience, University of Queensland, Brisbane, Queensland 4072, Australia
    Nucleic Acids Res 33:D125-30. 2005
    ..The database will be useful as a foundation for the emerging field of RNomics and the characterization of the roles of ncRNAs in mammalian gene expression and regulation...
  29. pmc Genomic regulatory blocks underlie extensive microsynteny conservation in insects
    Pär G Engström
    Computational Biology Unit, Bergen Center for Computational Science, University of Bergen, Bergen 5008, Norway
    Genome Res 17:1898-908. 2007
    ..The structural and functional equivalence between insect and vertebrate GRBs marks them as an ancient feature of metazoan genomes and as a key to future studies of development and gene regulation...
  30. pmc Mammalian microRNA prediction through a support vector machine model of sequence and structure
    Ying Sheng
    Computational Biology Unit, Bergen Center for Computational Science, University of Bergen, Bergen, Norway
    PLoS ONE 2:e946. 2007
    ..The possibility that there are more of them expressed at lower levels or in more specialized expression contexts calls for the exploitation of genome sequence information to accelerate their discovery...
  31. pmc Alternative promoter usage of the membrane glycoprotein CD36
    Malin Andersen
    Department of Biotechnology, AlbaNova University Center, Royal Institute of Technology KTH, 106 91 Stockholm, Sweden
    BMC Mol Biol 7:8. 2006
    ..We have investigated the expression patterns of five alternative first exons of the CD36 gene in several human tissues and cell types, to better understand the molecular details behind its regulation...
  32. pmc RNAdb 2.0--an expanded database of mammalian non-coding RNAs
    Ken C Pang
    ARC Special Research Centre for Functional and Applied Genomics, Institute for Molecular Bioscience, University of Queensland, Brisbane, Queensland 4072, Australia
    Nucleic Acids Res 35:D178-82. 2007
    ..To access RNAdb, visit http://research.imb.uq.edu.au/RNAdb...
  33. ncbi request reprint In vivo transcript profiling and phylogenetic analysis identifies suppressor of cytokine signaling 2 as a direct signal transducer and activator of transcription 5b target in liver
    Oscar M Vidal
    Department of Molecular Medicine and Surgery, Karolinska Institutet 17176 Stockholm, Sweden
    Mol Endocrinol 21:293-311. 2007
    ..In summary, we demonstrate the power of combining transcript profiling with phylogenetic sequence analysis to define novel regulatory paradigms...
  34. pmc Transcriptional and structural impact of TATA-initiation site spacing in mammalian core promoters
    Jasmina Ponjavic
    Genome Exploration Research Group Genome Network Project Core Group, RIKEN Genomic Sciences Center, RIKEN Yokohama Institute, Yokohama, Kanagawa, 230 0045, Japan
    Genome Biol 7:R78. 2006
    ..The lack of precise transcription start site (TSS) locations linked with expression information has impeded genome-wide characterization of the interaction between TATA and the pre-initiation complex...
  35. pmc Transcript annotation in FANTOM3: mouse gene catalog based on physical cDNAs
    Norihiro Maeda
    Genome Science Laboratory, Discovery Research Institute, RIKEN Wako Institute, Wako, Japan
    PLoS Genet 2:e62. 2006
    ....