E. Sonnhammer

Personal Home Page

http://www.sbc.su.se/~erison/

Articles in Scholarly Journals [Incomplete List]

  1. Focusing on RISC assembly in mammalian cells
    Biochemical and Biophysical Research Communications, vol. 368, no. 3, pp. 703–708, 2008
  2. Domain Tree-Based Analysis of Protein Architecture Evolution
    Molecular Biology and Evolution, vol. 25, no. 2, pp. 254–264, 2008
  3. Sub-grouping and sub-functionalization of the RIFIN multi-copy protein family
    BMC Genomics, vol. 9, no. 1, p. 19, 2008
  4. High-Throughput In Vivo Analysis of Gene Expression in Caenorhabditis elegans
    PLoS Biology, vol. 5, no. 9, p. e237, 2007
  5. Automatic extraction of reliable regions from multiple sequence alignments
    BMC Bioinformatics, vol. 8, no. Suppl 5, p. S9, 2007
  6. InParanoid 6: eukaryotic ortholog clusters with inparalogs
    Nucleic Acids Research, vol. 36, no. Database, pp. D263–D266, 2007
  7. Advantages of combined transmembrane topology and signal peptide prediction--the Phobius web server
    Nucleic Acids Research, vol. 35, no. Web Server, pp. W429–W432, 2007
  8. The Pfam protein families database
    Nucleic Acids Research, vol. 36, no. Database, pp. D281–D288, 2007
  9. Membrane topology of the Drosophila OR83b odorant receptor
    FEBS Letters, vol. 581, no. 29, pp. 5601–5604, 2007
  10. PfamAlyzer: domain-centric homology search
    Bioinformatics, vol. 23, no. 24, pp. 3382–3383, 2007
  11. Chromosomal clustering of nuclear genes encoding mitochondrial and chloroplast proteins in Arabidopsis
    Trends in Genetics, vol. 22, no. 11, pp. 589–593, 2006
  12. Overview and comparison of ortholog databases
    Drug Discovery Today: Technologies, vol. 3, no. 2, pp. 137–143, 2006
  13. Pfam: clans, web tools and services
    Nucleic Acids Research, vol. 34, no. 90001, pp. D247–D251, 2006
  14. Kalign, Kalignvu and Mumsa: web servers for multiple sequence alignment
    Nucleic Acids Research, vol. 34, no. Web Server, pp. W596–W599, 2006
  15. Automatic clustering of orthologs and inparalogs shared by multiple proteomes
    Bioinformatics, vol. 22, no. 14, pp. e9–e15, 2006
  16. Prediction of Function Divergence in Protein Families Using the Substitution Rate Variation Parameter Alpha
    Molecular Biology and Evolution, vol. 23, no. 7, pp. 1406–1413, 2006
  17. A general model of G protein-coupled receptor sequences and its application to detect remote homologs
    Protein Science, vol. 15, no. 3, pp. 509–521, 2006
  18. BMC Genomics, vol. 7, no. 1, p. 48, 2006
  19. A novel transmembrane topology of presenilin based on reconciling experimental and computational evidence
    FEBS Journal, vol. 272, no. 11, pp. 2727–2733, 2005
  20. siRNAdb: a database of siRNA sequences
    Nucleic Acids Research, vol. 33, no. 5, pp. 1737–1737, 2005
  21. BMC Bioinformatics, vol. 6, no. 1, p. 108, 2005
  22. BMC Bioinformatics, vol. 6, no. 1, p. 298, 2005
  23. BMC Bioinformatics, vol. 6, no. 1, p. 99, 2005
  24. Automatic assessment of alignment quality
    Nucleic Acids Research, vol. 33, no. 22, pp. 7120–7128, 2005
  25. Large-scale prediction of function shift in protein families with a focus on enzymatic function
    Proteins: Structure, Function, and Bioinformatics, vol. 60, no. 4, pp. 758–768, 2005
  26. Assessment of Protein Distance Measures and Tree-Building Methods for Phylogenetic Tree Reconstruction
    Molecular Biology and Evolution, vol. 22, no. 11, pp. 2257–2264, 2005
  27. An HMM posterior decoder for sequence feature prediction that includes homology information
    Bioinformatics, vol. 21, no. suppl_1, pp. i251–i257, 2005
  28. ChromoWheel: a new spin on eukaryotic chromosome visualization
    Bioinformatics, vol. 20, no. 4, pp. 576–577, 2004
  29. Sfixem--graphical sequence feature display in Java
    Bioinformatics, vol. 20, no. 15, pp. 2488–2490, 2004
  30. Transition Priors for Protein Hidden Markov Models: An Empirical Study towards Maximum Discrimination
    Journal of Computational Biology, vol. 11, no. 1, pp. 181–193, 2004
  31. Exploring the foundation of genomics: a Northern blot reference set for the comparative analysis of transcript profiling technologies
    Comparative and Functional Genomics, vol. 5, no. 8, pp. 584–595, 2004
  32. OrthoDisease: A database of human disease orthologs
    Human Mutation, vol. 24, no. 2, pp. 112–119, 2004
  33. A Combined Transmembrane Topology and Signal Peptide Prediction Method
    Journal of Molecular Biology, vol. 338, no. 5, pp. 1027–1036, 2004
  34. Improving Profile HMM Discrimination by Adapting Transition Probabilities
    Journal of Molecular Biology, vol. 338, no. 4, pp. 847–854, 2004
  35. Conspicuous accumulation of transcription elongation repressor hrp130/CA150 on the intron-rich Balbiani ring 3 gene
    Chromosoma, vol. 113, no. 5, pp. 244–257, 2004
  36. Improved and automated prediction of effective siRNA
    Biochemical and Biophysical Research Communications, vol. 319, no. 1, pp. 264–274, 2004
  37. Inparanoid: a comprehensive database of eukaryotic orthologs
    Nucleic Acids Research, vol. 33, no. Database issue, pp. D476–D480, 2004
  38. siRNAdb: a database of siRNA sequences
    Nucleic Acids Research, vol. 33, no. Database issue, pp. D131–D134, 2004
  39. FunShift: a database of function shift analysis on protein subfamilies
    Nucleic Acids Research, vol. 33, no. Database issue, pp. D197–D200, 2004
  40. BMC Genomics, vol. 5, no. 1, p. 85, 2004
  41. BMC Bioinformatics, vol. 5, no. 1, p. 135, 2004
  42. Genome Biology, vol. 6, no. 1, p. 301, 2004
  43. Comprehensive Analysis of Orthologous Protein Domains Using the HOPS Database
    Genome Research, vol. 13, no. 10, pp. 2353–2362, 2003
  44. Genomic Gene Clustering Analysis of Pathways in Eukaryotes
    Genome Research, vol. 13, no. 5, pp. 875–882, 2003
  45. The Pfam Protein Families Database
    Nucleic Acids Research, vol. 30, no. 1, pp. 276–280, 2002
  46. Quality assessment of multiple alignment programs
    FEBS Letters, vol. 529, no. 1, pp. 126–130, 2002
  47. Reliability of transmembrane predictions in whole-genome data
    FEBS Letters, vol. 532, no. 3, pp. 415–418, 2002
  48. Orthology, paralogy and proposed classification for paralog subtypes
    Trends in Genetics, vol. 18, no. 12, pp. 619–620, 2002
  49. Automated ortholog inference from phylogenetic trees and calculation of orthology reliability
    Bioinformatics, vol. 18, no. 1, pp. 92–99, 2002
  50. Computational antisense oligo prediction with a neural network model
    Bioinformatics, vol. 18, no. 12, pp. 1567–1575, 2002
  51. OrthoGUI: graphical presentation of Orthostrapper results
    Bioinformatics, vol. 18, no. 9, pp. 1272–1273, 2002
  52. NIFAS: visual analysis of domain evolution in proteins
    Bioinformatics, vol. 17, no. 4, pp. 343–348, 2001
  53. MEDUSA: large scale automatic selection and visual assessment of PCR primer pairs
    Bioinformatics, vol. 17, no. 7, pp. 656–657, 2001
  54. Integrated graphical analysis of protein sequence features predicted from sequence composition
    Proteins: Structure, Function, and Genetics, vol. 45, no. 3, pp. 262–273, 2001
  55. Predicting transmembrane protein topology with a hidden markov model: application to complete genomes
    Journal of Molecular Biology, vol. 305, no. 3, pp. 567–580, 2001
  56. Automatic clustering of orthologs and in-paralogs from pairwise species comparisons
    Journal of Molecular Biology, vol. 314, no. 5, pp. 1041–1052, 2001
  57. FAT: a novel domain in PIK-related kinases
    Trends in Biochemical Sciences, vol. 25, no. 5, pp. 225–227, 2000
  58. The Pfam Protein Families Database
    Nucleic Acids Research, vol. 28, no. 1, pp. 263–266, 2000
  59. Classification of Transmembrane Protein Families in the Caenorhabditis elegans Genome and Identification of Human Orthologs
    Genome Research, vol. 10, no. 11, pp. 1679–1689, 2000
  60. Pfam 3.1: 1313 multiple alignments and profile HMMs match the majority of proteins
    Nucleic Acids Research, vol. 27, no. 1, pp. 260–262, 1999
  61. A comparison of sequence and structure protein domain families as a basis for structural genomics
    Bioinformatics, vol. 15, no. 6, pp. 480–500, 1999
  62. Dynamic contact maps of protein structures
    Journal of Molecular Graphics and Modelling, vol. 16, no. 1, pp. 1–5, 1998
  63. Pfam: multiple sequence alignments and HMM-profiles of protein domains
    Nucleic Acids Research, vol. 26, no. 1, pp. 320–322, 1998
  64. Pfam: A comprehensive database of protein domain families based on seed alignments
    Proteins: Structure, Function, and Genetics, vol. 28, no. 3, pp. 405–420, 1997
  65. Sequence of the human immunoglobulin diversity (D) segment locus: a systematic analysis provides no evidence for the use of DIR segments, inverted D segments, “minor” D segments or D-D recombination
    Journal of Molecular Biology, vol. 270, no. 4, pp. 587–597, 1997
  66. Analysis of Protein Domain Families inCaenorhabditis elegans
    Genomics, vol. 46, no. 2, pp. 200–216, 1997
  67. The Imprint of Somatic Hypermutation on the Repertoire of Human Germline V Genes
    Journal of Molecular Biology, vol. 256, no. 5, pp. 813–817, 1996
  68. The C. elegans expression pattern database: a beginning
    Trends in Genetics, vol. 12, no. 9, pp. 370–371, 1996
  69. Volume changes in protein evolution
    Journal of Molecular Biology, vol. 236, no. 4, pp. 1067–1078, 1994
  70. A Workbench for large-scale sequence homology analysis
    Bioinformatics, vol. 10, no. 3, pp. 301–307, 1994
  71. What's in a genome?
    Nature, vol. 358, no. 6384, Article ID 358287a0, 1 pages, 1992