Andreas Heger

Summary

Affiliation: University of Oxford
Country: UK

Publications

  1. ncbi request reprint Accurate estimation of gene evolutionary rates using XRATE, with an application to transmembrane proteins
    Andreas Heger
    Department of Physiology, Anatomy and Genetics, MRC Functional Genomics Unit, University of Oxford, Oxford, UK
    Mol Biol Evol 26:1715-21. 2009
  2. pmc GAT: a simulation framework for testing the association of genomic intervals
    Andreas Heger
    MRC CGAT Programme and Functional Genomics Unit, MRC Functional Genomics Unit, Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, UK
    Bioinformatics 29:2046-8. 2013
  3. pmc Molecular evolution of genes in avian genomes
    Kiwoong Nam
    Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, Norbyvagen 18D, Uppsala, S 752 36, Sweden
    Genome Biol 11:R68. 2010
  4. pmc Transcriptomic analysis supports similar functional roles for the two thymuses of the tammar wallaby
    Emily S W Wong
    Faculty of Veterinary Sciences, University of Sydney, Sydney, NSW 2006, Australia
    BMC Genomics 12:420. 2011
  5. pmc Rapid bursts of androgen-binding protein (Abp) gene duplication occurred independently in diverse mammals
    Christina M Laukaitis
    Department of Medical Genetics, University of Washington, Seattle, USA and Division of Human Biology, Fred Hutchinson CancerResearch Center, Seattle, USA
    BMC Evol Biol 8:46. 2008
  6. pmc Variable strength of translational selection among 12 Drosophila species
    Andreas Heger
    MRC Functional Genetics Unit, Department of Physiology, Anatomy, and Genetics, University of Oxford, Oxford OX1 3QX, United Kingdom
    Genetics 177:1337-48. 2007
  7. pmc Evolutionary rate analyses of orthologs and paralogs from 12 Drosophila genomes
    Andreas Heger
    Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford OX1 3QX, United Kingdom
    Genome Res 17:1837-49. 2007
  8. pmc Uncertainty in homology inferences: assessing and improving genomic sequence alignment
    Gerton Lunter
    MRC Functional Genetics Unit, Department of Physiology, Anatomy, and Genetics, University of Oxford, Oxford OX1 3QX, United Kingdom
    Genome Res 18:298-309. 2008
  9. pmc CGAT: computational genomics analysis toolkit
    David Sims
    CGAT, MRC Functional Genomics Unit, Department of Physiology, Anatomy and Genetics, Parks Road, Oxford OX1 3PT, UK
    Bioinformatics 30:1290-1. 2014
  10. pmc OPTIC: orthologous and paralogous transcripts in clades
    Andreas Heger
    Department of Physiology, Anatomy and Genetics, MRC Functional Genetics Unit, University of Oxford, Le Gros Clark Building, Oxford OX1 3QX, UK
    Nucleic Acids Res 36:D267-70. 2008

Detail Information

Publications27

  1. ncbi request reprint Accurate estimation of gene evolutionary rates using XRATE, with an application to transmembrane proteins
    Andreas Heger
    Department of Physiology, Anatomy and Genetics, MRC Functional Genomics Unit, University of Oxford, Oxford, UK
    Mol Biol Evol 26:1715-21. 2009
    ..Less stringent purifying selection is thus a general property of the extracellular milieu, rather than being specific to only soluble and secreted proteins...
  2. pmc GAT: a simulation framework for testing the association of genomic intervals
    Andreas Heger
    MRC CGAT Programme and Functional Genomics Unit, MRC Functional Genomics Unit, Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, UK
    Bioinformatics 29:2046-8. 2013
    ..This question arises, for example, when interpreting ChIP-Seq or RNA-Seq data in functional terms. Because genome organization is complex, answering this question is non-trivial...
  3. pmc Molecular evolution of genes in avian genomes
    Kiwoong Nam
    Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, Norbyvagen 18D, Uppsala, S 752 36, Sweden
    Genome Biol 11:R68. 2010
    ....
  4. pmc Transcriptomic analysis supports similar functional roles for the two thymuses of the tammar wallaby
    Emily S W Wong
    Faculty of Veterinary Sciences, University of Sydney, Sydney, NSW 2006, Australia
    BMC Genomics 12:420. 2011
    ..Here, we used pyrosequencing to compare the transcriptomes of a cervical and thoracic thymus from a single 178 day old tammar wallaby...
  5. pmc Rapid bursts of androgen-binding protein (Abp) gene duplication occurred independently in diverse mammals
    Christina M Laukaitis
    Department of Medical Genetics, University of Washington, Seattle, USA and Division of Human Biology, Fred Hutchinson CancerResearch Center, Seattle, USA
    BMC Evol Biol 8:46. 2008
    ..Questions arise from imperfections in the initial mouse genome assembly and a dearth of information about the gene family structure in other rodents and mammals...
  6. pmc Variable strength of translational selection among 12 Drosophila species
    Andreas Heger
    MRC Functional Genetics Unit, Department of Physiology, Anatomy, and Genetics, University of Oxford, Oxford OX1 3QX, United Kingdom
    Genetics 177:1337-48. 2007
    ..The strength of translational selection was predicted to have varied between species largely according to their phylogeny, with the D. melanogaster group species exhibiting the strongest degree of selection...
  7. pmc Evolutionary rate analyses of orthologs and paralogs from 12 Drosophila genomes
    Andreas Heger
    Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford OX1 3QX, United Kingdom
    Genome Res 17:1837-49. 2007
    ..Duplications were significantly more frequent among trypsin-like proteases and DM8 putative lipid-binding domain proteins...
  8. pmc Uncertainty in homology inferences: assessing and improving genomic sequence alignment
    Gerton Lunter
    MRC Functional Genetics Unit, Department of Physiology, Anatomy, and Genetics, University of Oxford, Oxford OX1 3QX, United Kingdom
    Genome Res 18:298-309. 2008
    ..Alignment errors are inevitable, and should be considered when drawing conclusions from alignments. Software and alignments to assist researchers in doing this are provided at http://genserv.anat.ox.ac.uk/grape/...
  9. pmc CGAT: computational genomics analysis toolkit
    David Sims
    CGAT, MRC Functional Genomics Unit, Department of Physiology, Anatomy and Genetics, Parks Road, Oxford OX1 3PT, UK
    Bioinformatics 30:1290-1. 2014
    ..The tools can both be run from the Unix command line and installed into visual workflow builders, such as Galaxy...
  10. pmc OPTIC: orthologous and paralogous transcripts in clades
    Andreas Heger
    Department of Physiology, Anatomy and Genetics, MRC Functional Genetics Unit, University of Oxford, Le Gros Clark Building, Oxford OX1 3QX, UK
    Nucleic Acids Res 36:D267-70. 2008
    ..Gene predictions, multiple alignments and phylogenetic trees are freely available to browse and download from http://genserv.anat.ox.ac.uk/clades. Further genomes and clades will be added in the future...
  11. pmc Pfam: the protein families database
    Robert D Finn
    HHMI Janelia Farm Research Campus, 19700 Helix Drive, Ashburn, VA 20147 USA, European Molecular Biology Laboratory, European Bioinformatics Institute EMBL EBI, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK, MRC Functional Genomics Unit, Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, OX1 3QX, UK, Institute of Biotechnology and Department of Biological and Environmental Sciences, University of Helsinki, PO Box 56 Viikinkaari 5, 00014 Helsinki, Finland and Stockholm Bioinformatics Center, Swedish eScience Research Center, Department of Biochemistry and Biophysics, Science for Life Laboratory, Stockholm University, PO Box 1031, SE 17121 Solna, Sweden
    Nucleic Acids Res 42:D222-30. 2014
    ..Notably, we now provide family alignments based on four different representative proteome sequence data sets and a new interactive DNA search interface. We also discuss the mapping between Pfam and known 3D structures. ..
  12. doi request reprint Sequencing depth and coverage: key considerations in genomic analyses
    David Sims
    Computational Genomics Analysis and Training Programme, Medical Research Council Functional Genomics Unit, Department of Physiology, Anatomy and Genetics, Le Gros Clark Building, University of Oxford, Parks Road, Oxford OX1 3PT, UK
    Nat Rev Genet 15:121-32. 2014
    ....
  13. pmc PairsDB atlas of protein sequence space
    Andreas Heger
    MRC Functional Genetics Unit, University of Oxford, UK
    Nucleic Acids Res 36:D276-80. 2008
    ..Moreover, query-anchored stacked sequence alignments, profiles and consensus sequences are useful in studies of sequence conservation patterns for clues about possible functional sites...
  14. pmc Accelerated evolution of PAK3- and PIM1-like kinase gene families in the zebra finch, Taeniopygia guttata
    Lesheng Kong
    Medical Research Council Functional Genomics Unit, Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, United Kingdom
    Mol Biol Evol 27:1923-34. 2010
    ..Nevertheless, our results show how ancient and conserved intracellular signaling molecules can be co-opted, following duplication, thereby resulting in lineage-specific functions, presumably affecting the zebra finch testis and brain...
  15. pmc An analysis of the gene complement of a marsupial, Monodelphis domestica: evolution of lineage-specific genes and giant chromosomes
    Leo Goodstadt
    MRC Functional Genetics Unit, University of Oxford, Department of Physiology, Oxford, UK
    Genome Res 17:969-81. 2007
    ..In particular, we propose that the higher G+C content of the Monodelphis X chromosome is a direct consequence of its small size relative to the giant autosomes...
  16. pmc A ChIP-seq defined genome-wide map of vitamin D receptor binding: associations with disease and evolution
    Sreeram V Ramagopalan
    Wellcome Trust Centre for Human Genetics, University of Oxford, Headington, Oxford OX3 7BN, United Kingdom
    Genome Res 20:1352-60. 2010
    ..ChIP-seq determination of transcription factor binding, in combination with GWA data, provides a powerful approach to further understanding the molecular bases of complex diseases...
  17. pmc Insights into the evolution of Darwin's finches from comparative analysis of the Geospiza magnirostris genome sequence
    Chris M Rands
    Department of Physiology, Anatomy, and Genetics, MRC Functional Genomics Unit, University of Oxford, Oxford, OX1 3PT, UK
    BMC Genomics 14:95. 2013
    ..Here we report evolutionary analyses of genome of the large ground finch, Geospiza magnirostris...
  18. pmc Epigenetic conservation at gene regulatory elements revealed by non-methylated DNA profiling in seven vertebrates
    Hannah K Long
    Department of Biochemistry, University of Oxford, Oxford, United Kingdom Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, United Kingdom
    elife 2:e00348. 2013
    ..Together these findings demonstrate an ancient logic for NMI usage at gene promoters and reveal an unprecedented level of epigenetic conservation across vertebrate evolution. http://dx.doi.org/10.7554/eLife.00348.001...
  19. ncbi request reprint Sensitive pattern discovery with 'fuzzy' alignments of distantly related proteins
    Andreas Heger
    Institute of Biotechnology, P O Box 56, 00014 University of Helsinki Finland
    Bioinformatics 19:i130-7. 2003
    ..The targeted patterns-as gleaned from structure comparisons-are too sparse for statistically significant signals of sequence similarity and accurate multiple sequence alignment...
  20. ncbi request reprint Genome sequence, comparative analysis and haplotype structure of the domestic dog
    Kerstin Lindblad-Toh
    Broad Institute of Harvard and MIT, 320 Charles Street, Cambridge, Massachusetts 02141, USA
    Nature 438:803-19. 2005
    ..The current SNP map now makes it possible for genome-wide association studies to identify genes responsible for diseases and traits, with important consequences for human and companion animal health...
  21. ncbi request reprint Evolution of genes and genomes on the Drosophila phylogeny
    Andrew G Clark
    Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14853, USA
    Nature 450:203-18. 2007
    ..These may prove to underlie differences in the ecology and behaviour of these diverse species...
  22. ncbi request reprint Genome of the marsupial Monodelphis domestica reveals innovation in non-coding sequences
    Tarjei S Mikkelsen
    Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, Massachusetts 02142, USA
    Nature 447:167-77. 2007
    ..A substantial proportion of these eutherian-specific CNEs arose from sequence inserted by transposable elements, pointing to transposons as a major creative force in the evolution of mammalian gene regulation...
  23. pmc Genome analysis of the platypus reveals unique signatures of evolution
    Wesley C Warren
    Genome Sequencing Center, Washington University School of Medicine, Campus Box 8501, 4444 Forest Park Avenue, St Louis, Missouri 63108, USA
    Nature 453:175-83. 2008
    ..Sequencing of this genome now provides a valuable resource for deep mammalian comparative analyses, as well as for monotreme biology and conservation...
  24. ncbi request reprint The global trace graph, a novel paradigm for searching protein sequence databases
    Andreas Heger
    Institute of Biotechnology, P O Box 56 Viikinkaari 5, FI 00014 University of Helsinki, Finland
    Bioinformatics 23:2361-7. 2007
    ..The evolutionary signal can be difficult to detect because functional sites may consist of non-contiguous residues while segments in-between may be mutated without affecting fold or function...
  25. ncbi request reprint Accurate detection of very sparse sequence motifs
    Andreas Heger
    Institute of Biotechnology, University of Helsinki, Finland
    J Comput Biol 11:843-57. 2004
    ....
  26. pmc ADDA: a domain database with global coverage of the protein universe
    Andreas Heger
    Institute of Biotechnology, University of Helsinki, 00014 Helsinki, Finland
    Nucleic Acids Res 33:D188-91. 2005
    ..The data are freely available for downloading and querying via a web interface (http://ekhidna.biocenter.helsinki.fi:9801/sqgraph/pairsdb)...
  27. ncbi request reprint Exhaustive enumeration of protein domain families
    Andreas Heger
    EMBL EBI, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
    J Mol Biol 328:749-67. 2003
    ..The data are publicly available at ftp://ftp.ebi.ac.uk/pub/contrib/heger/adda...