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John Hancock

Visiting Scientist - MRC Mammalian Genetics Unit

Position - Company  
PI and work package leader - ENFIN

ENFIN was an EC-funded Network of Excellence aimed at developing systems biology approaches in Europe.

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Nov 2005 - Apr 2011
Head of Bioinformatics - MRC Mammalian Genetics Unit

My group explored the relationship between genotype and phenotype in mouse models. We developed the EuroPhenome database of raw phenotyping data from the EUMODIC project and the accompanying EMPReSS database of SOPs and we contributed to the development of the ontological description of mouse phenotypes, particularly through implementing the E+Q approach to phenotype description. We also had interests in systems biology (modelling processes taking place in pancreatic beta cells) and genome evolution (especially amino acid repeats in proteins and gene factories - regions of accentuated gene duplication).

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Jun 2002 - Mar 2011
Co-coordinator - CASIMIR

Coordinated jointly with Paul Schofield in Cambridge, CASIMIR (Coordination and Sustainability of International Mouse Informatics Resources) was an FP6 Coordination Action which held a number of international meetings to develop principles and policies for the mouse informatics commuity.

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Feb 2007 - Jul 2010
Work package leader - Infrafrontier

Infrafrontier is laying the basis for a network of mouse clinics across Europe. I led the bioinformatics work package, which prepared reports on the IT requirements for new mouse clinics, for the first two years of the project.

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Mar 2008 - Mar 2010
Work package leader - EUMODIC

EUMODIC built on EUMORPHIA to pilot the systematic phenotyping of mouse lines, primarily from the International Knockout Mouse Project. As part of this my group constructed the EuroPhenome database (http://www.europhenome.org).

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Feb 2007 - Mar 2010
Coordinator - Interphenome

Interphenome is an international discussion forum for the global mouse informatics community with special emphasis on phenotype data standards and availability. http://www.interphenome.org

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Feb 2006 - Nov 2009
Work package leader - EUMORPHIA

EUMORPHIA developed standardised phenotyping procedures for laboratory mouse lines. My role as head of the Bioinformatics work package was to manage the development of infrastructure for the project. As part of this we developed a database of phenotyping protocols, EMPReSS. We also developed the use of the E+Q ontology formalism for the description of mouse phenotypes.

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Oct 2002 - Mar 2006
Reader in Computational Biology - Royal Holloway University of London

Projects included the role of DNA repeats in genome evolution and a database of validated plant promoters. Taught a 3rd year course in Bioinformatics for computer science students.

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2000 - 2002
Head of Comparative Sequence Analysis Group - MRC Clinical Sciences Centre

Focussing on the evolution of amino acid repeats, especially polyglutamine repeats in disease genes, and microsatellites.

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1994 - 2000
Research Fellow - Australian National University

Main focus was on the role of cryptic DNA repeats in genome and rRNA evolution

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1991 - 1994
Postdoc - University of Cambridge

Evolution of rDNA and rRNAs; identified complementary slippage as a mechanism for the incorporation of simple repeats into rRNA variable regions

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1985 - 1991
Postdoc - Imperial College London

Work on microtubule-associated protein - DNA interaction

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1982 - 1985
Postdoc - Max Planck Institute for Molecular Genetics

Structure of 5S rRNA and its interaction with binding proteins

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1978 - 1982
Visiting Scientist - University of Cambridge

I will be visiting Paul Schofield and colleagues in the Dept of Physiology, Development and Neuroscience on a regular basis.

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Sep 2011 - Present
Guest Associate Editor - Frontiers Research Foundation

I'm editing a Special Topic on Biological Ontologies for Frontiers in Bioinformatics and Computational Biology. See http://www.frontiersin.org/bioinformatics_and_computational_biology/specialtopics

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May 2011 - Present
Visiting Scientist - MRC Mammalian Genetics Unit

I am continuing my interest in phenotype informatics, including ontology development and use, and in repeat evolution.

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Apr 2011 - Present
Visiting Scientist - MRC Mammalian Genetics Unit

I recently took early retirement as head of the Bioinformatics Group at MRC Harwell, which specialises in mouse genetics. My specialist areas are phenotype data analysis and ontologies, sequence analysis with an emphasis on evolutionary analysis, repetitive sequences in proteins and genomes.

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Jun 2002 - Present
Degree - University  
PhD, Genetics - University of Edinburgh

"Studies on the mechanism of chromosome banding" supervised by Adrian Sumner

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1975 - 1980
BSc (Hons), Cell & Molecular Biology - King's College London 1972 - 1975
Publication Info
Integration of global resources for human genetic variation and disease. Schofield PN, Hancock JM Hum Mutat. 33(5):813-6. doi: 10.1002/humu.22079. April 6, 2012. View on PubMed.
Embryonic over-expression of RAGE by alveolar epithelium induces an imbalance between proliferation and apoptosis. Stogsdill JA, Stogsdill MP, Porter JL, Hancock JM, Robinson AB, Reynolds PR Am J Respir Cell Mol Biol. :. doi: 10.1165/rcmb.2011-0385OC. February 16, 2012. View on PubMed.
Anatomy ontologies and potential users: bridging the gap. Travillian RS, Adamusiak T, Burdett T, Gruenberger M, Hancock J, Mallon AM, Malone J, Schofield P, Parkinson H J Biomed Semantics. 2 Suppl 4:S3. doi: 10.1186/2041-1480-2-S4-S3. August 9, 2011. View on PubMed.
Protein coalitions in a core mammalian biochemical network linked by rapidly evolving proteins. Ainali C, Simon M, Freilich S, Espinosa O, Hazelwood L, Tsoka S, Ouzounis CA, Hancock JM BMC Evol Biol. 11:142. doi: 10.1186/1471-2148-11-142. May 25, 2011. View on PubMed.
A gene-phenotype network for the laboratory mouse and its implications for systematic phenotyping. Espinosa O, Hancock JM PLoS One. 6(5):e19693. doi: 10.1371/journal.pone.0019693. May 19, 2011. View on PubMed.
Towards BioDBcore: a community-defined information specification for biological databases. Gaudet P, Bairoch A, Field D, Sansone SA, Taylor C, Attwood TK, Bateman A and 32 others Database (Oxford). 2011:baq027. doi: 10.1093/database/baq027. January 4, 2011. View on PubMed.
Towards BioDBcore: a community-defined information specification for biological databases. Gaudet P, Bairoch A, Field D, Sansone SA, Taylor C, Attwood TK, Bateman A and 32 others Nucleic Acids Res. 39(Database issue):D7-10. doi: 10.1093/nar/gkq1173. November 18, 2010. View on PubMed.
Research funding. Sustaining the data and bioresource commons. Schofield PN, Eppig J, Huala E, de Angelis MH, Harvey M, Davidson D, Weaver T and 7 others Science. 330(6004):592-3. doi: 10.1126/science.1191506. October 29, 2010. View on PubMed.
Finding and sharing: new approaches to registries of databases and services for the biomedical sciences. Smedley D, Schofield P, Chen CK, Aidinis V, Ainali C, Bard J, Balling R and 23 others Database (Oxford). 2010:baq014. doi: 10.1093/database/baq014. July 6, 2010. View on PubMed.
Mouse Resource Browser--a database of mouse databases. Zouberakis M, Chandras C, Swertz M, Smedley D, Gruenberger M, Bard J, Schughart K and 5 others Database (Oxford). 2010:baq010. doi: 10.1093/database/baq010. July 6, 2010. View on PubMed.
Phenotype ontologies for mouse and man: bridging the semantic gap. Schofield PN, Gkoutos GV, Gruenberger M, Sundberg JP, Hancock JM Dis Model Mech. 3(5-6):281-9. doi: 10.1242/dmm.002790. June 2010. View on PubMed.
XGAP: a uniform and extensible data model and software platform for genotype and phenotype experiments. Swertz MA, Velde KJ, Tesson BM, Scheltema RA, Arends D, Vera G, Alberts R and 13 others Genome Biol. 11(3):R27. doi: 10.1186/gb-2010-11-3-r27. March 9, 2010. View on PubMed.
EuroPhenome: a repository for high-throughput mouse phenotyping data. Morgan H, Beck T, Blake A, Gates H, Adams N, Debouzy G, Leblanc S and 13 others Nucleic Acids Res. 38(Database issue):D577-85. doi: 10.1093/nar/gkp1007. November 23, 2009. View on PubMed.
Models for financial sustainability of biological databases and resources. Chandras C, Weaver T, Zouberakis M, Smedley D, Schughart K, Rosenthal N, Hancock JM, Kollias G, Schofield PN, Aidinis V Database (Oxford). 2009:bap017. doi: 10.1093/database/bap017. October 23, 2009. View on PubMed.
MouseBook: an integrated portal of mouse resources. Blake A, Pickford K, Greenaway S, Thomas S, Pickard A, Williamson CM, Adams NC and 8 others Nucleic Acids Res. 38(Database issue):D593-9. doi: 10.1093/nar/gkp867. October 23, 2009. View on PubMed.
Post-publication sharing of data and tools. Schofield PN, Bubela T, Weaver T, Portilla L, Brown SD, Hancock JM, Einhorn D and 4 others Nature. 461(7261):171-3. doi: 10.1038/461171a. September 10, 2009. View on PubMed.
Mouse, man, and meaning: bridging the semantics of mouse phenotype and human disease. Hancock JM, Mallon AM, Beck T, Gkoutos GV, Mungall C, Schofield PN Mamm Genome. 20(8):457-61. doi: 10.1007/s00335-009-9208-3. August 2, 2009. View on PubMed.
Practical application of ontologies to annotate and analyse large scale raw mouse phenotype data. Beck T, Morgan H, Blake A, Wells S, Hancock JM, Mallon AM BMC Bioinformatics. 10 Suppl 5:S2. doi: 10.1186/1471-2105-10-S5-S2. May 6, 2009. View on PubMed.
Planning the human variome project: the Spain report. Kaput J, Cotton RG, Hardman L, Watson M, Al Aqeel AI, Al-Aama JY, Al-Mulla F and 96 others Hum Mutat. 30(4):496-510. doi: 10.1002/humu.20972. April 2009. View on PubMed.
Phylogenetic inference under recombination using Bayesian stochastic topology selection. Webb A, Hancock JM, Holmes CC Bioinformatics. 25(2):197-203. doi: 10.1093/bioinformatics/btn607. January 15, 2009. View on PubMed.
The functional annotation of mammalian genomes: the challenge of phenotyping. Brown SD, Wurst W, Kühn R, Hancock JM Annu Rev Genet. 43:305-33. doi: 10.1146/annurev-genet-102108-134143. 2009. View on PubMed.
Tandem and cryptic amino acid repeats accumulate in disordered regions of proteins. Simon M, Hancock JM Genome Biol. 10(6):R59. doi: 10.1186/gb-2009-10-6-r59. 2009. View on PubMed.
Solutions for data integration in functional genomics: a critical assessment and case study. Smedley D, Swertz MA, Wolstencroft K, Proctor G, Zouberakis M, Bard J, Hancock JM, Schofield P Brief Bioinform. 9(6):532-44. doi: 10.1093/bib/bbn040. November 2008. View on PubMed.
Promoting coherent minimum reporting guidelines for biological and biomedical investigations: the MIBBI project. Taylor CF, Field D, Sansone SA, Aerts J, Apweiler R, Ashburner M, Ball CA and 50 others Nat Biotechnol. 26(8):889-96. doi: 10.1038/nbt.1411. August 2008. View on PubMed.
Phenobabelomics--mouse phenotype data resources. Hancock JM, Mallon AM Brief Funct Genomic Proteomic. 6(4):292-301. doi: 10.1093/bfgp/elm033. January 11, 2008. View on PubMed.
EuroPhenome and EMPReSS: online mouse phenotyping resource. Mallon AM, Blake A, Hancock JM Nucleic Acids Res. 36(Database issue):D715-8. doi: 10.1093/nar/gkm728. September 28, 2007. View on PubMed.
Phenostat: visualization and statistical tool for analysis of phenotyping data. Reuveni E, Carola V, Banchaabouchi MA, Rosenthal N, Hancock JM, Gross C Mamm Genome. 18(9):677-81. doi: 10.1007/s00335-007-9042-4. August 3, 2007. View on PubMed.
A kinetic core model of the glucose-stimulated insulin secretion network of pancreatic beta cells. Jiang N, Cox RD, Hancock JM Mamm Genome. 18(6-7):508-20. doi: 10.1007/s00335-007-9011-y. May 21, 2007. View on PubMed.
Mouse Phenotype Database Integration Consortium: integration [corrected] of mouse phenome data resources. Hancock JM, Adams NC, Aidinis V, Blake A, Bogue M, Brown SD, Chesler EJ and 31 others Mamm Genome. 18(3):157-63. doi: 10.1007/s00335-007-9004-x. April 10, 2007. View on PubMed.
Understanding mammalian genetic systems: the challenge of phenotyping in the mouse. Brown SD, Hancock JM, Gates H PLoS Genet. 2(8):e118. doi: 10.1371/journal.pgen.0020118. August 25, 2006. View on PubMed.
The mouse genome. Brown SD, Hancock JM Genome Dyn. 2:33-45. doi: 10.1159/000095091. 2006. View on PubMed.
Gene factories, microfunctionalization and the evolution of gene families. Hancock JM Trends Genet. 21(11):591-5. doi: 10.1016/j.tig.2005.08.008. September 8, 2005. View on PubMed.
EMPReSS: European mouse phenotyping resource for standardized screens. Green EC, Gkoutos GV, Lad HV, Blake A, Weekes J, Hancock JM Bioinformatics. 21(12):2930-1. doi: 10.1093/bioinformatics/bti441. June 15, 2005. View on PubMed.
CRAVE: a database, middleware and visualization system for phenotype ontologies. Gkoutos GV, Green EC, Greenaway S, Blake A, Mallon AM, Hancock JM Bioinformatics. 21(7):1257-62. doi: 10.1093/bioinformatics/bti147. April 1, 2005. View on PubMed.
Simple sequence repeats in proteins and their significance for network evolution. Hancock JM, Simon M Gene. 345(1):113-8. doi: 10.1016/j.gene.2004.11.023. January 17, 2005. View on PubMed.
Using ontologies to describe mouse phenotypes. Gkoutos GV, Green EC, Mallon AM, Hancock JM, Davidson D Genome Biol. 6(1):R8. doi: 10.1186/gb-2004-6-1-r8. December 20, 2004. View on PubMed.
A bigger mouse? The rat genome unveiled. Hancock JM Bioessays. 26(10):1039-42. doi: 10.1002/bies.20121. October 2004. View on PubMed.
Organization and evolution of a gene-rich region of the mouse genome: a 12.7-Mb region deleted in the Del(13)Svea36H mouse. Mallon AM, Wilming L, Weekes J, Gilbert JG, Ashurst J, Peyrefitte S, Matthews L and 12 others Genome Res. 14(10A):1888-901. doi: 10.1101/gr.2478604. September 13, 2004. View on PubMed.
Ontologies for the description of mouse phenotypes. Gkoutos GV, Green EC, Mallon AM, Blake A, Greenaway S, Hancock JM, Davidson D Comp Funct Genomics. 5(6-7):545-51. doi: 10.1002/cfg.430. 2004. View on PubMed.
Building mouse phenotype ontologies. Gkoutos GV, Green EC, Mallon AM, Hancock JM, Davidson D Pac Symp Biocomput. :178-89. 2004. View on PubMed.
A phylogenetic approach to assessing the significance of missense mutations in disease genes. Santibáñez Koref MF, Gangeswaran R, Santibáñez Koref IP, Shanahan N, Hancock JM Hum Mutat. 22(1):51-8. doi: 10.1002/humu.10235. July 2003. View on PubMed.
PlantProm: a database of plant promoter sequences. Shahmuradov IA, Gammerman AJ, Hancock JM, Bramley PM, Solovyev VV Nucleic Acids Res. 31(1):114-7. January 1, 2003. View on PubMed.
Genome size and the accumulation of simple sequence repeats: implications of new data from genome sequencing projects. Hancock JM Genetica. 115(1):93-103. May 2002. View on PubMed.
Detecting cryptically simple protein sequences using the SIMPLE algorithm. Albà MM, Laskowski RA, Hancock JM Bioinformatics. 18(5):672-8. May 2002. View on PubMed.
Rapid restructuring of bicoid-dependent hunchback promoters within and between Dipteran species: implications for molecular coevolution. McGregor AP, Shaw PJ, Hancock JM, Bopp D, Hediger M, Wratten NS, Dover GA Evol Dev. 3(6):397-407. December 2001. View on PubMed.
A relationship between lengths of microsatellites and nearby substitution rates in mammalian genomes. Santibáñez-Koref MF, Gangeswaran R, Hancock JM Mol Biol Evol. 18(11):2119-23. doi: 10.1093/oxfordjournals.molbev.a003753. November 2001. View on PubMed.
A role for selection in regulating the evolutionary emergence of disease-causing and other coding CAG repeats in humans and mice. Hancock JM, Worthey EA, Santibáñez-Koref MF Mol Biol Evol. 18(6):1014-23. doi: 10.1093/oxfordjournals.molbev.a003873. June 2001. View on PubMed.
Extreme length and length variation in the first ribosomal internal transcribed spacer of ladybird beetles (Coleoptera: Coccinellidae). von der Schulenburg JH, Hancock JM, Pagnamenta A, Sloggett JJ, Majerus ME, Hurst GD Mol Biol Evol. 18(4):648-60. doi: 10.1093/oxfordjournals.molbev.a003845. April 2001. View on PubMed.
The comparative genomics of polyglutamine repeats: extreme differences in the codon organization of repeat-encoding regions between mammals and Drosophila. Albà MM, Santibáñez-Koref MF, Hancock JM J Mol Evol. 52(3):249-59. March 2001. View on PubMed.
How slippage-derived sequences are incorporated into rRNA variable-region secondary structure: implications for phylogeny reconstruction. Hancock JM, Vogler AP Mol Phylogenet Evol. 14(3):366-74. doi: 10.1006/mpev.1999.0709. March 2000. View on PubMed.
Analysis of the primary sequence and secondary structure of the unusually long SSU rRNA of the soil bug, Armadillidium vulgare. Choe CP, Hancock JM, Hwang UW, Kim W J Mol Evol. 49(6):798-805. December 1999. View on PubMed.
Amino acid reiterations in yeast are overrepresented in particular classes of proteins and show evidence of a slippage-like mutational process. Mar Albà M, Santibáñez-Koref MF, Hancock JM J Mol Evol. 49(6):789-97. December 1999. View on PubMed.
Conservation of polyglutamine tract size between mice and humans depends on codon interruption. Albà MM, Santibáñez-Koref MF, Hancock JM Mol Biol Evol. 16(11):1641-4. doi: 10.1093/oxfordjournals.molbev.a026077. November 1999. View on PubMed.
High sequence turnover in the regulatory regions of the developmental gene hunchback in insects. Hancock JM, Shaw PJ, Bonneton F, Dover GA Mol Biol Evol. 16(2):253-65. doi: 10.1093/oxfordjournals.molbev.a026107. February 1999. View on PubMed.
A common binding site on the microsomal triglyceride transfer protein for apolipoprotein B and protein disulfide isomerase. Bradbury P, Mann CJ, Köchl S, Anderson TA, Chester SA, Hancock JM, Ritchie PJ and 6 others J Biol Chem. 274(5):3159-64. January 29, 1999. View on PubMed.
The structure of vitellogenin provides a molecular model for the assembly and secretion of atherogenic lipoproteins. Mann CJ, Anderson TA, Read J, Chester SA, Harrison GB, Köchl S, Ritchie PJ and 11 others J Mol Biol. 285(1):391-408. doi: 10.1006/jmbi.1998.2298. January 8, 1999. View on PubMed.
Trinucleotide expansion diseases in the context of micro- and minisatellite evolution, Hammersmith Hospital, April 1-3, 1998. Hancock JM, Santibáñez-Koref MF EMBO J. 17(19):5521-4. doi: 10.1093/emboj/17.19.5521. October 1, 1998. View on PubMed.
Modelling the secondary structures of slippage-prone hypervariable RNA regions: the example of the tiger beetle 18S rRNA variable region V4. Hancock JM, Vogler AP Nucleic Acids Res. 26(7):1689-99. April 1, 1998. View on PubMed.
Phylogenetic analysis of slippage-like sequence variation in the V4 rRNA expansion segment in tiger beetles (Cicindelidae). Vogler AP, Welsh A, Hancock JM Mol Biol Evol. 14(1):6-19. doi: 10.1093/oxfordjournals.molbev.a025703. January 1997. View on PubMed.
Simple sequences in a "minimal' genome. Hancock JM Nat Genet. 14(1):14-5. doi: 10.1038/ng0996-14. September 1996. View on PubMed.
Simple sequences and the expanding genome. Hancock JM Bioessays. 18(5):421-5. doi: 10.1002/bies.950180512. May 1996. View on PubMed.
Do light-induced pH changes within the chloroplast drive turnip yellow mosaic virus assembly? Rohozinski J, Hancock JM J Gen Virol. 77 ( Pt 2 ):163-5. doi: 10.1099/0022-1317-77-2-163. February 1996. View on PubMed.
Codon repeats in genes associated with human diseases: fewer repeats in the genes of nonhuman primates and nucleotide substitutions concentrated at the sites of reiteration. Djian P, Hancock JM, Chana HS Proc Natl Acad Sci U S A. 93(1):417-21. January 9, 1996. View on PubMed.
Replication slippage in the evolution of potyviruses. Hancock JM, Chaleeprom W, Chaleeprom W, Dale J, Gibbs A J Gen Virol. 76 ( Pt 12):3229-32. doi: 10.1099/0022-1317-76-12-3229. December 1995. View on PubMed.
The contribution of slippage-like processes to genome evolution. Hancock JM J Mol Evol. 41(6):1038-47. December 1995. View on PubMed.
The contribution of DNA slippage to eukaryotic nuclear 18S rRNA evolution. Hancock JM J Mol Evol. 40(6):629-39. June 1995. View on PubMed.
Polycytosine regions contained in DNA hairpin loops interact via a four-stranded, parallel structure similar to the i-motif. Rohozinski J, Hancock JM, Keniry MA Nucleic Acids Res. 22(22):4653-9. November 11, 1994. View on PubMed.
SIMPLE34: an improved and enhanced implementation for VAX and Sun computers of the SIMPLE algorithm for analysis of clustered repetitive motifs in nucleotide sequences. Hancock JM, Armstrong JS Comput Appl Biosci. 10(1):67-70. February 1994. View on PubMed.
Generation of VNTRs and heteroplasmy by sequence turnover in the mitochondrial control region of two elephant seal species. Hoelzel AR, Hancock JM, Dover GA J Mol Evol. 37(2):190-7. August 1993. View on PubMed.
Evolution of sequence repetition and gene duplications in the TATA-binding protein TBP (TFIID). Hancock JM Nucleic Acids Res. 21(12):2823-30. June 25, 1993. View on PubMed.
Detection and quantification of concerted evolution and molecular drive. Dover GA, Linares AR, Bowen T, Hancock JM Methods Enzymol. 224:525-41. 1993. View on PubMed.
Evolution of the cetacean mitochondrial D-loop region. Hoelzel AR, Hancock JM, Dover GA Mol Biol Evol. 8(4):475-93. doi: 10.1093/oxfordjournals.molbev.a040662. July 1991. View on PubMed.
Secondary structure constraints on the evolution of Drosophila 28 S ribosomal RNA expansion segments. Ruiz Linares A, Hancock JM, Dover GA J Mol Biol. 219(3):381-90. June 5, 1991. View on PubMed.
'Compensatory slippage' in the evolution of ribosomal RNA genes. Hancock JM, Dover GA Nucleic Acids Res. 18(20):5949-54. October 25, 1990. View on PubMed.
Molecular coevolution among cryptically simple expansion segments of eukaryotic 26S/28S rRNAs. Hancock JM, Dover GA Mol Biol Evol. 5(4):377-91. doi: 10.1093/oxfordjournals.molbev.a040505. July 1988. View on PubMed.
Evolution of the secondary structures and compensatory mutations of the ribosomal RNAs of Drosophila melanogaster. Hancock JM, Tautz D, Dover GA Mol Biol Evol. 5(4):393-414. doi: 10.1093/oxfordjournals.molbev.a040501. July 1988. View on PubMed.
Complete sequences of the rRNA genes of Drosophila melanogaster. Tautz D, Hancock JM, Webb DA, Tautz C, Dover GA Mol Biol Evol. 5(4):366-76. doi: 10.1093/oxfordjournals.molbev.a040500. July 1988. View on PubMed.
Specificity and biological significance of microtubule-associated protein-DNA interactions in chick. Hancock JM, Burns RG Biochim Biophys Acta. 927(2):163-9. February 18, 1987. View on PubMed.
The role of proteins in the production of different types of chromosome bands. Hancock JM, Sumner AT Cytobios. 35(137):37-46. 1982. View on PubMed.
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