Research Topics
Genomes and GenesSpecies | Andreas HegerSummaryAffiliation: University of Oxford Country: UK Publications
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Detail Information
Publications
Accurate estimation of gene evolutionary rates using XRATE, with an application to transmembrane proteinsAndreas 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...
Molecular evolution of genes in avian genomesKiwoong Nam
Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, Norbyvagen 18D, Uppsala, S 752 36, Sweden
Genome Biol 11:R68. 2010....- Transcriptomic analysis supports similar functional roles for the two thymuses of the tammar wallabyEmily 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... - Rapid bursts of androgen-binding protein (Abp) gene duplication occurred independently in diverse mammalsChristina 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... - Variable strength of translational selection among 12 Drosophila speciesAndreas 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... - Evolutionary rate analyses of orthologs and paralogs from 12 Drosophila genomesAndreas 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... - Uncertainty in homology inferences: assessing and improving genomic sequence alignmentGerton 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/... - PairsDB atlas of protein sequence spaceAndreas 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... - Accelerated evolution of PAK3- and PIM1-like kinase gene families in the zebra finch, Taeniopygia guttataLesheng 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... - A ChIP-seq defined genome-wide map of vitamin D receptor binding: associations with disease and evolutionSreeram 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... - OPTIC: orthologous and paralogous transcripts in cladesAndreas 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... - An analysis of the gene complement of a marsupial, Monodelphis domestica: evolution of lineage-specific genes and giant chromosomesLeo 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... 
Sensitive pattern discovery with 'fuzzy' alignments of distantly related proteinsAndreas Heger
Institute of Biotechnology, P.O. Box 56, 00014 University of Helsinki Finland
Bioinformatics 19:i130-7. 2003..We demonstrate the discovery of biologically meaningful patterns in an extremely diverse superfamily related to urease...- Genome analysis of the platypus reveals unique signatures of evolutionWesley 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... - Genome of the marsupial Monodelphis domestica reveals innovation in non-coding sequencesTarjei 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... - Genome sequence, comparative analysis and haplotype structure of the domestic dogKerstin 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... - Evolution of genes and genomes on the Drosophila phylogenyAndrew 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... - The global trace graph, a novel paradigm for searching protein sequence databasesAndreas 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... - Accurate detection of very sparse sequence motifsAndreas Heger
Institute of Biotechnology, University of Helsinki, Finland
J Comput Biol 11:843-57. 2004.... - ADDA: a domain database with global coverage of the protein universeAndreas 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)... - Exhaustive enumeration of protein domain familiesAndreas 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...