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    Holmes, Ian

    TitleComputational Biologist Fac SE
    SchoolLawrence Berkeley National Lab
    DepartmentMolecular Biophys & Integ Bio
    Address1 Cyclotron Road
    Berkeley CA 94720
    Phone510/495-2621
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      Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Researchers can login to make corrections and additions, or contact us for help.
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      1. Holmes I. Solving the master equation for Indels. BMC Bioinformatics. 2017 May 12; 18(1):255. PMID: 28494756.
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      2. Holmes I, Mungall CJ. BioMake: a GNU Make-compatible utility for declarative workflow management. Bioinformatics. 2017 May 09. PMID: 28486579.
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      3. Buels R, Yao E, Diesh CM, Hayes RD, Munoz-Torres M, Helt G, Goodstein DM, Elsik CG, Lewis SE, Stein L, Holmes I. JBrowse: a dynamic web platform for genome visualization and analysis. Genome Biol. 2016; 17(1):66. PMID: 27072794.
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      4. Santiago-Ortiz J, Ojala DS, Westesson O, Weinstein JR, Wong SY, Steinsapir A, Kumar S, Holmes I, Schaffer DV. AAV ancestral reconstruction library enables selection of broadly infectious viral variants. Gene Ther. 2015 Dec; 22(12):934-46. PMID: 26186661.
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      5. Lee E, Helt GA, Reese JT, Munoz-Torres MC, Childers CP, Buels RM, Stein L, Holmes I, Elsik CG, Lewis SE. Web Apollo: a web-based genomic annotation editing platform. Genome Biol. 2013; 14(8):R93. PMID: 24000942.
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      6. Westesson O, Holmes I. Developing and applying heterogeneous phylogenetic models with XRate. PLoS One. 2012; 7(6):e36898. PMID: 22693624.
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      7. Westesson O, Lunter G, Paten B, Holmes I. Accurate reconstruction of insertion-deletion histories by statistical phylogenetics. PLoS One. 2012; 7(4):e34572. PMID: 22536326.
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      8. Westesson O, Skinner M, Holmes I. Visualizing next-generation sequencing data with JBrowse. Brief Bioinform. 2013 Mar; 14(2):172-7. PMID: 22411711.
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      9. Holmes I, Harris K, Quince C. Dirichlet multinomial mixtures: generative models for microbial metagenomics. PLoS One. 2012; 7(2):e30126. PMID: 22319561.
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      10. Westesson O, Barquist L, Holmes I. HandAlign: Bayesian multiple sequence alignment, phylogeny and ancestral reconstruction. Bioinformatics. 2012 Apr 15; 28(8):1170-1. PMID: 22285828.
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      11. Mørk S, Holmes I. Evaluating bacterial gene-finding HMM structures as probabilistic logic programs. Bioinformatics. 2012 Mar 1; 28(5):636-42. PMID: 22215819.
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      12. Bateman A, Agrawal S, Birney E, Bruford EA, Bujnicki JM, Cochrane G, Cole JR, Dinger ME, Enright AJ, Gardner PP, Gautheret D, Griffiths-Jones S, Harrow J, Herrero J, Holmes I, Huang HD, Kelly KA, Kersey P, Kozomara A, Lowe TM, Marz M, Moxon S, Pruitt KD, Samuelsson T, Stadler PF, Vilella AJ, Vogel JH, Williams KP, Wright MW, Zwieb C. RNAcentral: A vision for an international database of RNA sequences. RNA. 2011 Nov; 17(11):1941-6. PMID: 21940779.
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      13. Skinner ME, Holmes I. Setting up the JBrowse genome browser. Curr Protoc Bioinformatics. 2010 Dec; Chapter 9:Unit 9.13. PMID: 21154710.
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      14. Bradley RK, Holmes I. Evolutionary triplet models of structured RNA. PLoS Comput Biol. 2009 Aug; 5(8):e1000483. PMID: 19714212.
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      15. Bradley RK, Uzilov AV, Skinner ME, Bendaña YR, Barquist L, Holmes I. Evolutionary modeling and prediction of non-coding RNAs in Drosophila. PLoS One. 2009; 4(8):e6478. PMID: 19668382.
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      16. Skinner ME, Uzilov AV, Stein LD, Mungall CJ, Holmes I. JBrowse: a next-generation genome browser. Genome Res. 2009 Sep; 19(9):1630-8. PMID: 19570905.
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      17. Bradley RK, Roberts A, Smoot M, Juvekar S, Do J, Dewey C, Holmes I, Pachter L. Fast statistical alignment. PLoS Comput Biol. 2009 May; 5(5):e1000392. PMID: 19478997.
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      18. Westesson O, Holmes I. Accurate detection of recombinant breakpoints in whole-genome alignments. PLoS Comput Biol. 2009 Mar; 5(3):e1000318. PMID: 19300487.
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      19. Paten B, Herrero J, Fitzgerald S, Beal K, Flicek P, Holmes I, Birney E. Genome-wide nucleotide-level mammalian ancestor reconstruction. Genome Res. 2008 Nov; 18(11):1829-43. PMID: 18849525.
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      20. Varadarajan A, Bradley RK, Holmes I. Tools for simulating evolution of aligned genomic regions with integrated parameter estimation. Genome Biol. 2008; 9(10):R147. PMID: 18840304.
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      21. Bradley RK, Pachter L, Holmes I. Specific alignment of structured RNA: stochastic grammars and sequence annealing. Bioinformatics. 2008 Dec 1; 24(23):2677-83. PMID: 18796475.
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      22. Barquist L, Holmes I. xREI: a phylo-grammar visualization webserver. Nucleic Acids Res. 2008 Jul 1; 36(Web Server issue):W65-9. PMID: 18522975.
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      23. Bendaña YR, Holmes I. Colorstock, SScolor, Ratón: RNA alignment visualization tools. Bioinformatics. 2008 Feb 15; 24(4):579-80. PMID: 18218657.
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      24. Evolution of genes and genomes on the Drosophila phylogeny. Nature. 2007 Nov 8; 450(7167):203-18. PMID: 17994087.
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      25. Holmes I. Phylocomposer and phylodirector: analysis and visualization of transducer indel models. Bioinformatics. 2007 Dec 1; 23(23):3263-4. PMID: 17804439.
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      26. Bradley RK, Holmes I. Transducers: an emerging probabilistic framework for modeling indels on trees. Bioinformatics. 2007 Dec 1; 23(23):3258-62. PMID: 17804440.
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      27. Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature. 2007 Jun 14; 447(7146):799-816. PMID: 17571346.
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      28. Margulies EH, Cooper GM, Asimenos G, Thomas DJ, Dewey CN, Siepel A, Birney E, Keefe D, Schwartz AS, Hou M, Taylor J, Nikolaev S, Montoya-Burgos JI, Löytynoja A, Whelan S, Pardi F, Massingham T, Brown JB, Bickel P, Holmes I, Mullikin JC, Ureta-Vidal A, Paten B, Stone EA, Rosenbloom KR, Kent WJ, Bouffard GG, Guan X, Hansen NF, Idol JR, Maduro VV, Maskeri B, McDowell JC, Park M, Thomas PJ, Young AC, Blakesley RW, Muzny DM, Sodergren E, Wheeler DA, Worley KC, Jiang H, Weinstock GM, Gibbs RA, Graves T, Fulton R, Mardis ER, Wilson RK, Clamp M, Cuff J, Gnerre S, Jaffe DB, Chang JL, Lindblad-Toh K, Lander ES, Hinrichs A, Trumbower H, Clawson H, Zweig A, Kuhn RM, Barber G, Harte R, Karolchik D, Field MA, Moore RA, Matthewson CA, Schein JE, Marra MA, Antonarakis SE, Batzoglou S, Goldman N, Hardison R, Haussler D, Miller W, Pachter L, Green ED, Sidow A. Analyses of deep mammalian sequence alignments and constraint predictions for 1% of the human genome. Genome Res. 2007 Jun; 17(6):760-74. PMID: 17567995.
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      29. Klosterman PS, Uzilov AV, Bendaña YR, Bradley RK, Chao S, Kosiol C, Goldman N, Holmes I. XRate: a fast prototyping, training and annotation tool for phylo-grammars. BMC Bioinformatics. 2006; 7:428. PMID: 17018148.
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      30. Graham KL, Fleming FE, Halasz P, Hewish MJ, Nagesha HS, Holmes I, Takada Y, Coulson BS. Rotaviruses interact with alpha4beta7 and alpha4beta1 integrins by binding the same integrin domains as natural ligands. J Gen Virol. 2005 Dec; 86(Pt 12):3397-408. PMID: 16298987.
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      31. Kalawsky RS, Nee SP, Holmes I, Coveney PV. A grid-enabled lightweight computational steering client: a .NET PDA implementation. Philos Trans A Math Phys Eng Sci. 2005 Aug 15; 363(1833):1885-94. PMID: 16099755.
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      32. Holmes I. Accelerated probabilistic inference of RNA structure evolution. BMC Bioinformatics. 2005; 6:73. PMID: 15790387.
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      33. Holmes I. Using evolutionary Expectation Maximization to estimate indel rates. Bioinformatics. 2005 May 15; 21(10):2294-300. PMID: 15731213.
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      34. Holmes I. A probabilistic model for the evolution of RNA structure. BMC Bioinformatics. 2004 Oct 26; 5:166. PMID: 15507142.
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      35. Cui X, Nagesha HS, Holmes I. Mapping of conformational epitopes on capsid protein VP2 of infectious bursal disease virus by fd-tet phage display. J Virol Methods. 2003 Dec; 114(1):109-12. PMID: 14599686.
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      36. Cui X, Nagesha HS, Holmes I. Identification of crucial residues of conformational epitopes on VP2 protein of infectious bursal disease virus by phage display. J Virol Methods. 2003 Apr; 109(1):75-83. PMID: 12668271.
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      37. Holmes I. Using guide trees to construct multiple-sequence evolutionary HMMs. Bioinformatics. 2003; 19 Suppl 1:i147-57. PMID: 12855451.
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      38. Holmes I. Transcendent elements: whole-genome transposon screens and open evolutionary questions. Genome Res. 2002 Aug; 12(8):1152-5. PMID: 12176921.
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      39. Holmes I, Rubin GM. An expectation maximization algorithm for training hidden substitution models. J Mol Biol. 2002 Apr 12; 317(5):753-64. PMID: 11955022.
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      40. Jolly CL, Huang JA, Holmes I. Selection of rotavirus VP4 cell receptor binding domains for MA104 cells using a phage display library. J Virol Methods. 2001 Oct; 98(1):41-51. PMID: 11543883.
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      41. Holmes I, Bruno WJ. Evolutionary HMMs: a Bayesian approach to multiple alignment. Bioinformatics. 2001 Sep; 17(9):803-20. PMID: 11590097.
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      42. Jolly CL, Beisner BM, Ozser E, Holmes I. Non-lytic extraction and characterisation of receptors for multiple strains of rotavirus. Arch Virol. 2001 Jul; 146(7):1307-23. PMID: 11556708.
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      43. Jolly CL, Beisner BM, Holmes I. Rotavirus infection of MA104 cells is inhibited by Ricinus lectin and separately expressed single binding domains. Virology. 2000 Sep 15; 275(1):89-97. PMID: 11017790.
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      44. Huang JA, Wang L, Firth S, Phelps A, Reeves P, Holmes I. Rotavirus VP7 epitope mapping using fragments of VP7 displayed on phages. Vaccine. 2000 Apr 28; 18(21):2257-65. PMID: 10717346.
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      45. Wang L, Huang JA, Nagesha HS, Smith SC, Phelps A, Holmes I, Martyn JC, Coloe PJ, Reeves PR. Bacterial expression of the major antigenic regions of porcine rotavirus VP7 induces a neutralizing immune response in mice. Vaccine. 1999 Jun 4; 17(20-21):2636-45. PMID: 10418913.
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      46. Beisner B, Kool D, Marich A, Holmes I. Characterisation of G serotype dependent non-antibody inhibitors of rotavirus in normal mouse serum. Arch Virol. 1998; 143(7):1277-94. PMID: 9722874.
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      47. Wang L, Huang JA, Phelps A, Firth S, Holmes I, Reeves PR. Periplasmic expression of part of the major rotavirus capsid protein VP7 containing all the three antigenic regions in Escherichia coli. Gene. 1996 Oct 24; 177(1-2):155-62. PMID: 8921861.
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      48. Holmes I. Development of rotavirus molecular epidemiology: electropherotyping. Arch Virol Suppl. 1996; 12:87-91. PMID: 9015105.
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      49. Lazdins I, Coulson BS, Kirkwood C, Dyall-Smith M, Masendycz PJ, Sonza S, Holmes I. Rotavirus antigenicity is affected by the genetic context and glycosylation of VP7. Virology. 1995 May 10; 209(1):80-9. PMID: 7747487.
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      50. Theophilos MB, Huang JA, Holmes I. Avian reovirus sigma C protein contains a putative fusion sequence and induces fusion when expressed in mammalian cells. Virology. 1995 Apr 20; 208(2):678-84. PMID: 7747439.
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      51. Huang JA, Nagesha HS, Holmes I. Comparative sequence analysis of VP4s from five Australian porcine rotaviruses: implication of an apparent new P type. Virology. 1993 Sep; 196(1):319-27. PMID: 8395121.
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      52. Kool DA, Holmes I. The avian rotavirus Ty-1 Vp7 nucleotide and deduced amino acid sequences differ significantly from those of Ch-2 rotavirus. Arch Virol. 1993; 129(1-4):227-34. PMID: 8385915.
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      53. Kool DA, Matsui SM, Greenberg HB, Holmes I. Isolation and characterization of a novel reassortant between avian Ty-1 and simian RRV rotaviruses. J Virol. 1992 Nov; 66(11):6836-9. PMID: 1328691.
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      54. Nagesha HS, Huang J, Holmes I. A variant serotype G3 rotavirus isolated from an unusually severe outbreak of diarrhoea in piglets. J Med Virol. 1992 Oct; 38(2):79-85. PMID: 1334131.
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      55. Huang JA, Nagesha HS, Snodgrass DR, Holmes I. Molecular and serological analyses of two bovine rotaviruses (B-11 and B-60) causing calf scours in Australia. J Clin Microbiol. 1992 Jan; 30(1):85-92. PMID: 1310336.
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      56. Nagesha HS, Holmes I. Direct serotyping of porcine rotaviruses using VP7-specific monoclonal antibodies by an enzyme immunoassay. J Med Virol. 1991 Nov; 35(3):206-11. PMID: 1666648.
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      57. Nagesha HS, Holmes I. VP4 relationships between porcine and other rotavirus serotypes. Arch Virol. 1991; 116(1-4):107-18. PMID: 1705788.
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      58. Reeves PR, Johnson MA, Holmes I, Dyall-Smith ML. Expression of rotavirus VP7 antigens in fusions with bacterial proteins. Res Microbiol. 1990 Sep-Oct; 141(7-8):1019-25. PMID: 1966251.
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      59. Sethabutr O, Unicomb LE, Holmes I, Taylor DN, Bishop RF, Echeverria P. Serotyping of human group A rotavirus with oligonucleotide probes. J Infect Dis. 1990 Aug; 162(2):368-72. PMID: 2165109.
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      60. Nagesha HS, Huang J, Hum CP, Holmes I. A porcine rotavirus strain with dual VP7 serotype specificity. Virology. 1990 Mar; 175(1):319-22. PMID: 2155514.
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      61. Nagesha HS, Brown LE, Holmes I. Neutralizing monoclonal antibodies against three serotypes of porcine rotavirus. J Virol. 1989 Aug; 63(8):3545-9. PMID: 2545925.
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      62. Nuttall SD, Hum CP, Holmes I, Dyall-Smith ML. Sequences of VP9 genes from short and supershort rotavirus strains. Virology. 1989 Aug; 171(2):453-7. PMID: 2548328.
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      63. Hum CP, Dyall-Smith ML, Holmes I. The VP7 gene of a new G serotype of human rotavirus (B37) is similar to G3 proteins in the antigenic c region. Virology. 1989 May; 170(1):55-61. PMID: 2541556.
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      64. Huang J, Nagesha HS, Dyall-Smith ML, Holmes I. Comparative sequence analysis of VP7 genes from five Australian porcine rotaviruses. Arch Virol. 1989; 109(3-4):173-83. PMID: 2558633.
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      65. Kantharidis P, Dyall-Smith ML, Tregear GW, Holmes I. Nucleotide sequence of UK bovine rotavirus segment 4: possible host restriction of VP3 genes. Virology. 1988 Oct; 166(2):308-15. PMID: 2845645.
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      66. Shaw RD, Mackow ER, Dyall-Smith ML, Lazdins I, Holmes I, Greenberg HB. Serotypic analysis of VP3 and VP7 neutralization escape mutants of rhesus rotavirus. J Virol. 1988 Sep; 62(9):3509-12. PMID: 2457117.
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      67. Nagesha HS, Holmes I. New porcine rotavirus serotype antigenically related to human rotavirus serotype 3. J Clin Microbiol. 1988 Feb; 26(2):171-4. PMID: 2830302.
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      68. Nagesha HS, Hum CP, Bridger JC, Holmes I. Atypical rotaviruses in Australian pigs. Arch Virol. 1988; 102(1-2):91-8. PMID: 2848477.
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      69. Kantharidis P, Dyall-Smith ML, Holmes I. Marked sequence variation between segment 4 genes of human RV-5 and simian SA 11 rotaviruses. Arch Virol. 1987; 93(1-2):111-21. PMID: 3028337.
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      70. Caust J, Dyall-Smith ML, Lazdins I, Holmes I. Glycosylation, an important modifier of rotavirus antigenicity. Arch Virol. 1987; 96(3-4):123-34. PMID: 2444193.
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      71. Dyall-Smith ML, Lazdins I, Tregear GW, Holmes I. Location of the major antigenic sites involved in rotavirus serotype-specific neutralization. Proc Natl Acad Sci U S A. 1986 May; 83(10):3465-8. PMID: 2422651.
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      72. Richardson SC, Mercer LE, Sonza S, Holmes I. Intracellular localization of rotaviral proteins. Arch Virol. 1986; 88(3-4):251-64. PMID: 3010907.
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      73. Lazdins I, Sonza S, Dyall-Smith ML, Coulson BS, Holmes I. Demonstration of an immunodominant neutralization site by analysis of antigenic variants of SA11 rotavirus. J Virol. 1985 Oct; 56(1):317-9. PMID: 2993661.
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      74. Coulson BS, Holmes I. An improved enzyme-linked immunosorbent assay for the detection of rotavirus in faeces of neonates. J Virol Methods. 1984 May; 8(3):165-79. PMID: 6086688.
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      75. Sonza S, Breschkin AM, Holmes I. The major surface glycoprotein of simian rotavirus (SA11) contains distinct epitopes. Virology. 1984 Apr 30; 134(2):318-27. PMID: 6085822.
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      76. Sonza S, Breschkin AM, Holmes I. Derivation of neutralizing monoclonal antibodies against rotavirus. J Virol. 1983 Mar; 45(3):1143-6. PMID: 6300449.
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      77. Bastardo JW, McKimm-Breschkin JL, Sonza S, Mercer LD, Holmes I. Preparation and characterization of antisera to electrophoretically purified SA11 virus polypeptides. Infect Immun. 1981 Dec; 34(3):641-7. PMID: 6174448.
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      78. Lazdins I, Holmes I. Protein synthesis in Bunyamwera virus-infected cells. J Gen Virol. 1979 Jul; 44(1):123-33. PMID: 115963.
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      79. Holmes I, Wark MC, Jack I, Grutzner J. Identification of two possible types of virus particle in rubella-infected cells. J Gen Virol. 1968 Jan; 2(1):37-42. PMID: 5645584.
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      80. Hoogenraad NJ, Hirk FJ, Holmes I, Millis NF. Bacteriophages in rumen contents of sheep. J Gen Virol. 1967 Oct; 1(4):575-6. PMID: 6081706.
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