User:DerekGatherer

Senior Computer Officer, MRC Virology Unit

Research Interests
Interests

Currently active projects:
 * Next Generation Sequencing assembly of herpesvirus genomes
 * Evolutionary origins of influenza viruses
 * Trying to think a bit more about how to do systems biology in viruses

Somewhat dormant projects: (potentially looking for an undergrad project student to help out) Recently completed (usually published) projects with no plans for imminent resuscitation:
 * Rate of evolution in herpesviruses
 * Phylogenetic analysis of G protein-coupled receptors (GPCRs) in viral genomes.
 * Positive/diversifying selection in viral genomes (influenza, Epstein-Barr virus and others).
 * The G+C frontier of the rat cytomegalovirus (RCMV) and other viral genomes.
 * Rapid serotyping of influenza haemagglutinin DNA/protein sequences.
 * Phylogenetic analysis of interleukin-10 homologues in viral genomes.
 * Genome signatures as a classificatory tool in viruses.
 * Word-like strings ("vocabulary analysis") in proteins and its structural significance.
 * Periodicity in proteins and its structural significance.
 * The systems biology of Walter Elsasser (1904-1991).

Education and CV

 * Certificate in Quantitative Methods, Heriot-Watt University, 2002
 * Cert.Ed., Liverpool John Moores University, 1997 (University Teaching Certificate)
 * Ph.D, University of London, 1991 (Molecular Developmental Biology)
 * B.Sc, University of Glasgow, 1986 (Genetics)
 * MRC Virology Unit, Glasgow, since 2003
 * Pharma-biotech industry, Glasgow/Florida/Cambridge, 1999-2003
 * Lecturer in Molecular Genetics, Liverpool John Moores University, 1996-1999
 * Post-docs, Quito/Warwick/Cambridge, 1991-1996
 * Ph.D. student, then research assistant, London/Glasgow, 1986-1990
 * Undergrad, Glasgow, 1982-1986

Publications
See also: Official MRC pages (old)

Selected publications:


 * 72. Gatherer D (2010) The Little Ice Age and the emergence of influenza A. Med Hypotheses 2010 Apr 15. [Epub ahead of print]


 * 71. Dhillon S, Witteveldt J, Gatherer D, Owsianka AM, Zeisel MB, Zahid MN, Rychlowska M, Foung SK, Baumert TF, Angus AG, Patel AH.Mutations within a conserved region of the hepatitis C virus E2 glycoprotein that influence virus-receptor interactions and sensitivity to neutralizing antibodies. J Virol. 2010 Mar 17. [Epub ahead of print]


 * 70. Gatherer D. (2010) So what do we really mean when we say that systems biology is holistic? BMC Syst Biol. 42 22.


 * 69. Gatherer D (2010) Passage in egg culture is a major cause of apparent positive selection in influenza B haemagglutinin. Journal of Medical Virology  82 123-127.


 * 68. Gatherer D (2009) On the origin of influenza A hemagglutinin.  Indian Journal of Microbiology 49 352-357.


 * 67. Gatherer D (2009) Peptide vocabulary analysis reveals ultra-conservation and homonymity in protein sequences. Bioinformatics & Biology Insights 1 101-126.


 * 66. Ehlers B, Spieß K, Leendertz F, Peeters M, Boesch C, Gatherer D, McGeoch DJ (2009) Lymphocryptovirus phylogeny and the origins of Epstein-Barr virus. J Gen Virol. 91 630-642.


 * 65. Gatherer D (2009) The 2009 H1N1 influenza outbreak in its historical context. Journal of Clinical Virology 45 174-178.


 * 64. Cunningham C, Gatherer D, Hilfrich B, Baluchova K, Dargan DJ, Thomson M, Griffiths PD, Wilkinson GW, Schulz TF, Davison AJ (2009) Sequences of complete human cytomegalovirus genomes from infected cell cultures and clinical specimens. J Gen Virol.</I> 91 605-615.


 * 63. Alcendor DJ, Zong J, Dolan A, Gatherer D, Davison AJ, Hayward GS (2009) Patterns of divergence in the vCXCL and vGPCR gene clusters in primate cytomegalovirus genomes. Virology</I> 395 21-32.


 * 62. Bradley AJ, Lurain NS, Ghazal P, Trivedi U, Cunningham C, Baluchova K, Gatherer D, Wilkinson GWG, Dargan DJ & Davison AJ (2009) High-throughput sequence analysis of variants of human cytomegalovirus strains Towne and AD169. Journal of General Virology</I>  90 2375-2380.


 * 61. Leendertz FH, Deckers M, Schempp W, Lankester F, Boesch C, Hohmann G, Mugisha L, Dolan A, Gatherer D, McGeoch DJ & Ehlers B (2009) Novel cytomegaloviruses in free-ranging and captive great apes: phylogenetic evidence for bidirectional horizontal transmission. Journal of Virology</I>  90 2386-2394.


 * 60. Gatherer D (2008) Evolution of the G+C content frontier in the rat cytomegalovirus genome. Virology: Research and Treatment</I> 1 75-86.


 * 59. Bhella D, Gatherer D, Chaudhry Y, Pink R & Goodfellow IG (2008) Structural insights into calicivirus attachment and uncoating. Journal of Virology</I> 82 8051-8058.


 * 58. Jayawardane G, Russell GC, Thomson J, Deane D, Cox H, Gatherer D, Ackermann M, Haig DM & Stewart JP (2008) A captured viral interleukin-10 gene with cellular exon structure. Journal of General Virology</I> 89 2447-2455.


 * 57. Gatherer D (2008) Finite universe of discourse. The systems biology of Walter Elsasser (1904-1991) The Open Biology Journal</I> 1 9-20.


 * 56. Bradley AJ, Kovács IJ, Gatherer D, Dargan DJ, Alkharsah KR, Chan PK, Carman WF, Dedicoat M, Emery VC, Geddes CC, Gerna G, Ismaeil BB, Kaye S, McGregor A, Moss PA, Pusztai R, Rawlinson WD, Schulz TF & Davison AJ (2008) Genotypic analysis of two hypervariable human cytomegalovirus genes Journal of Medical Virology</I> 80 1615-1623.


 * 55. McGeoch DJ, Davison AJ, Dolan A, Gatherer D and Sevilla-Reyes E (2008) Molecular evolution of the Herpesvirales. In: Domingo E, Parrish CR & Holland JJ (eds) Origin and Evolution of Viruses.</i> 2nd ed. pp. 447-475 Oxford: Elsevier


 * 54. Gatherer D (2007) TreeAdder: a tool to assist the optimal positioning of a new leaf into an existing phylogenetic tree. The Open Bioinformatics Journal</i>  1 1-2.


 * 53. Gatherer D (2007) Genome signatures, self-organizing maps and higher order phylogenies: a parametric analysis. Evolutionary Bioinformatics</I>  3 211-236.


 * 52. Gatherer D (2007) Voting in Eurovision: shared tastes or cultural epidemic? Empirical Text & Culture Research</I> 3 72-83.


 * 51. Beyler R & Gatherer D (2007) Walter Elsasser (biography). In: Dictionary of Scientific Biography</I>, new ed. New York: Charles Scribner's Sons Inc.


 * 50. Gatherer D (2007) Less is more: the battle of Moore's Law against Bremermann's Limit on the field of systems biology.  BMC Systems Biology</I>  1 supp.1 53.


 * 49. McGeoch DJ & Gatherer D (2007) Lineage structures in the genome sequences of three Epstein-Barr virus strains. Virology 359 1-5 [Abstract]


 * 48. Dolan A, Addison C, Gatherer D, Davison AJ & McGeoch DJ (2006) The genome of Epstein-Barr virus type 2 strain AG876. Virology 350 164-170 [Abstract] [cited 7 times]


 * 47. Gatherer D (2006) Comparison of Eurovision Song Contest simulation with actual results reveals shifting patterns of collusive voting alliances. Journal of Artificial Societies and Social Simulation 2 [cited 3 times]


 * 46. Gatherer D (2006) Cultural evolution: the biological perspective. Parallax 12 57-68. [Link]


 * 45. Gatherer D (2005) Finding a niche for memetics in the 21st century. Journal of Memetics - Evolutionary Models of Information Transmission, 9


 * 44. McGeoch DJ, Gatherer D & Dolan A (2005) On phylogenetic relationships among major lineages of the Gammaherpesvirinae. Journal of General Virology 86 307-316. [cited 16 times]


 * 43. Gatherer D & McEwan NR (2005) Phylogenetic differences in content and intensity of periodic proteins. J. Mol. Evol. 60 447-461. [Abstract] [cited once]


 * 42. McGeoch DJ & Gatherer D (2005) Integrating reptilian herpesviruses into the family Herpesviridae. Journal of Virology 79 725-731. [cited 8 times]


 * 41. Gatherer D (2004) The inherent instability of memetic systems: use of a genetic algorithm to solve a parameter optimisation problem in a memetic simulation Journal of Memetics - Evolutionary Models of Information Transmission, 9.


 * 40. Gatherer D (2004) Birth of a meme: the origin and evolution of collusive voting patterns in the Eurovision Song Contest.  Journal of Memetics - Evolutionary Models of Information Transmission, 8. [cited 4 times]


 * 39. Dolan A, Cunningham C, Hector RD, Hassan-Walker AF, Lee L, Addison C, Dargan DJ, McGeoch DJ, Gatherer D, Emery VC, Griffiths PD, Sinzger C, McSharry BP, Wilkinson GWG &amp; Davison AJ (2004) Genetic content of wild-type human cytomegalovirus. Journal of General Virology 85 1301-1312. [cited 75 times]


 * 38. Illand M, Adams F, Gatherer D, Henry B & Grassie M (2003) Cloning and characterisation of GPR26, a CNS-restricted orphan GPCR. British Neuroscience Association Abstracts. 12.14 


 * 37. Gatherer D & McEwan NR (2003) Analysis of sequence periodicity in E.coli proteins: empirical investigation of the ‘duplication and divergence’ theory of protein evolution. J. Mol. Evol. 57 149-158. [Abstract][cited 5 times]


 * 36. Gatherer D (2002) Identifying cases of social contagion using memetic isolation: comparison of the dynamics of a multisociety simulation with an ethnographic data set.  Journal of Artificial Societies and Social Simulation 5, no. 4 [cited 6 times]


 * 35. Gatherer D (2002) Update to: Adaptation of standard spreadsheet software for the analysis of DNA sequences. In: Brown SB (ed.) BioComputing: Computer Tools for Biologists. Eaton Publishing, Westborough MA.


 * 34. Garmendia-Doval B & Gatherer D (2002) Meeting Report: Engineering and Physical Sciences Research Council Network on Evolvability in Biology and Software Systems Symposium on Software Evolution and Evolutionary Computation, University of Hertfordshire, UK 7th - 8th February 2002. Journal of Memetics - Evolutionary Models of Information Transmission, 6.


 * 33. Gatherer D (2002) The spread of irrational behaviours by contagion: an agent micro-simulation.  Journal of Memetics - Evolutionary Models of Information Transmission, 6. [cited 4 times]


 * 32. Grassie MA, Gatherer D & Semple CAM (2001) G-protein coupled receptor ORG3 and its use in drug screening, diagnosis and treatment of mental disorders. PCT Int. Appl. 31 pp. CODEN: PIXXD2 WO0190189 A2 20011129 CAN 136:15956 AN 2001:868528 CAPLUS.


 * 31. Gatherer D (2001) Modelling the effects of memetic taboos on genetic homosexuality. Journal of Memetics - Evolutionary Models of Information Transmission, 4. [cited 3 times]


 * 30. McEwan NR, Gatherer D, Eschenauer SCP, Wallace RJ & Newbold CJ (2000). Codon utilisation in actin sequences from the rumen protozoan Entodinium caudatum. 3rd Joint Symposium of Japan & Korea on Rumen Metabolism & Physiology (Abstract). Proceedings of the Japanese Society for Rumen Metabolism and Physiology 11, 75


 * 29. McEwan NR, Gatherer D, Eschenlauer SCP, McIntosh FM, Calza RE, Wallace RJ & Newbold CJ (2000) An unusual codon usage pattern in the ciliate family Ophryoscolecidae and its implications for determining the source of cloned DNA. Anaerobe 6, 21-28. [cited 3 times]


 * 28. McEwan NR & Gatherer D (1999) Codon indices as a predictor of gene functionality in a Frankia operon. Canadian Journal of Botany 77, 1287-1292. [cited 6 times]


 * 27. Gatherer D (1999) The memetics of design. In: Bentley P (ed.) Evolutionary Design by Computers. pp.91-103. Morgan Kauffman Publishers, San Francisco. [cited 5 times]


 * 26. Gatherer D (1999) A plea for methodological Darwinism - a commentary on Rose's paper: Controversies in meme theory Journal of Memetics - Evolutionary Models of Information Transmission, 3.


 * 25. Gatherer D (1998) Why the `Thought Contagion' metaphor is retarding the progress of memetics Journal of Memetics - Evolutionary Models of Information Transmission, 2. [cited 24 times]


 * 24. McEwan CEA, Gatherer D &amp; McEwan NR (1998) Nitrogen-fixing aerobic bacteria have higher genomic GC content than non-fixing species within the same genus. Hereditas 128, 173-178. [cited 10 times]


 * 23. McEwan NR & Gatherer D (1998) The Mutational-Response Index and codon bias in genes from a Frankia nif operon. Theoretical and Applied Genetics 96, 716-718. [cited 5 times]


 * 22. Gatherer D & Manning FCR (1998) Correlation of examination performance with lecture attendance: a comparative study of first year biological sciences undergraduates. Biochemical Education 26, 121-124. [cited 11 times]


 * 21. McEwan NR & Gatherer D (1998) Adaptation of standard spreadsheet software for the analysis of DNA sequences. BioTechniques 24, 131-138. [Abstract][cited 11 times]


 * 20. Gatherer D & McEwan NR (1998) On units of selection in cultural evolution. Journal of Theoretical Biology 192, 409-413. [cited twice]


 * 19. Gatherer D (1998) Meme pools, World 3 and Averroës's vision of immortality. Zygon: Journal of Religion and Science 33, 203-219. [cited once]


 * 18. Gatherer D (1997) The evolution of music: a comparison of Darwinian and dialectical methods. Journal of Social and Evolutionary Systems 20, 75-92. [cited 3 times]


 * 17. Gatherer D (1997) Feyerabend, Dawkins and the politics of cultural diversity. Anarchist Studies 5, 23-43.


 * 16. Gatherer D & McEwan NR (1997) Small regions of preferential codon usage and their effect on overall codon bias - the case of the plp gene. Biochemistry and Molecular Biology International 43, 107-114. [Abstract][cited 8 times]


 * 15. Gatherer D & McEwan NR (1997) The chorionic gonadotropin gene family: constraint amid diversity. In: Andrews M (ed.) Control of Human Fertility. Liverpool John Moores University Seminar Report, p74.


 * 14. McEwan N & Gatherer D (1997) Codon usage in tomatoes (Solanum lycopersicum) Trends in Analytical Life Sciences 1, 182-187.


 * 13. Gatherer D (1997) Macromemetics: towards a framework for the re-unification of philosophy Journal of Memetics - Evolutionary Models of Information Transsmission 1. [cited 13 times]


 * 12. Gatherer D (1996) A stroll across the epigenetic landscape: bringing Waddington's ideas into molecular biology. Early Pregnancy: Biology and Medicine 2, 241-243. [journal page]


 * 11. Gatherer D & Woodland HR (1996) N-acetyl-cysteine produces late respecification of the axis in Xenopus embryos. Developmental Dynamics 205, 395-409.


 * 10. Richardson JC, Gatherer D & Woodland HR (1995) Developmental effects of over-expression of normal and mutated forms of a Xenopus NF-kB homologue. Mechanisms of Development 52, 165-177. [cited 12 times]


 * 9. Gatherer D (1994) Fruitless search for the perfect frog. Daily Telegraph 3rd March 1994, p16 (the runner-up entry in the 1993 Young Science Writer of the Year Competition).


 * 8. Gatherer D (1993) Gene knockouts and murine development. Development, Growth and Differentiation 35, 365-370. [cited 9 times]


 * 7. Gatherer D (1992) Post-implantation development in the mouse (book review) British Society for Developmental Biology Newsletter 26, 13-14.


 * 6. Gatherer D, del Pino EM (1992) Somitogenesis in the marsupial frog, Gastrotheca Riobambae. International Journal of Developmental Biology 36, 283-291.[Abstract] [cited 7 times]


 * 5. Akhurst RJ, FitzPatrick DR, Gatherer D, Millan FA, Slager H (1992) The role of TGF-ßs in mammalian development and neoplasia. Molecular Reproduction and Development32, 127-135. [Abstract][cited 19 times]


 * 4. Akhurst RJ, FitzPatrick DR, Gatherer D, Lehnert SA, Millan FA (1990)Transforming growth factor ß in mammalian embryogenesis. Progress in Growth Factor Research 2, 153-168.[Abstract][cited 30 times]


 * 3. Gatherer D, ten Dijke P, Baird DT, Akhurst RJ (1990) Expression of TGF-ß isoforms during first trimester human embryogenesis. Development 110, 445-460. [cited 67 times]


 * 2. Akhurst RJ, Lehnert SA, Gatherer D, Duffie E (1990) The role of TGF-ß in mouse development. Annals of the New York Academy of Sciences 593, 259-271. [cited 25 times]


 * 1. Connor JM, Gatherer D, Gray FC, Pirrit LA &amp; Affara NA (1986) Assignment of the gene for dyskeratosis congenita to Xq28. Human Genetics 72, 348-351.[Abstract] [cited 58 times]