Curriculum Vitae - Bioinformatics

Dr. Jeremy D. Parsons

Personal Details

Name: Jeremy David Parsons
Phone: +61 413 828 166
+44 7913 024857
Personal email: jp[a t]jeremyparsons .com
Consulting website: http://www.littlest.co.uk/
Marital Status: Single
Nationality: British
Work Address: "Admont",
Gravel Path,
Berkhamsted,
Herts.
HP4 2PQ
England

Academic Qualifications

Technical Skills

Career

2015 - 2016 Garvan Institute of Medical Research, Immunology Dept., Australia
  • Differential Expression Analyses in mice. RNAseq pipelines.
  • Endogenonous Retrovirus (ERV) expression
  • Transcriptional control of Immune Response (IR) genes by ERV TFBS motifs.
  • R presentation graphics and signal compression for heatmaps.
2011 - 2014 University of Queensland Bioinformatics with QFAB and Phil Hugenholtz, Brisbane, Australia
  • Metagenomic analyses of mouse and sheep digestion
  • Bacterial genome assembly including difficult 16S repeat regions
  • Initial Macadamia and Koala genome assemblies and analyses.
  • Transcriptomics and Differential Expression analyses in Sugar Cane and bacteria
  • Web databases, Bioinformatics support and analysis, pipeline scripting and Java Programming
  • BRAEMBL project and many others
2010 - 2011 Bioinformatics research & genome comparisons: Byrappa Venkatesh, Singapore
  • DNA Assembly and analysis, pipeline scripting and Java Programming
  • Studying Vertebrate evolution using Elephant Shark as a reference genome
  • NGS Roche 454 Linker and adapter removal via sensitive parallel alignments
2008 - 2009 Cheminformatics at European Patent Office (EPO Den Haag) with Stephane Nauche
  • Java Programming and Natural Language Parsing
    • Discovering new chemicals in EPO patent images and text
    • Parsing scientific literature using OSCAR 3
    • XML handlling, databases and Java servlets
2007 ACI Worldwide
  • Java Programming
    • Introduction to electronic payments
    • User interface design in Java
2006 - 2007 Reuters
  • JRisk Programmer
    • Financial software training
    • Java J2EE bugfixing
2006 - Contract Building Research Establishment
  • Analyst and Programmer
    • Image processing applications for visual analysis of timber
    • Multi-threaded Java analysis pipeline and GUI
2003 - 2005 Paradigm Therapeutics
  • Senior Bioinformatician (analyst/programmer) with a special focus on phenotype database development.
    • - Flexible data collection, querying and MIS report generation
    • - PostgreSQL DB with Java Beans, JSP, JSTL, and servlets
  • Systems support including networking and centralized Linux servers for Macs and Linux desktops
2002 - 2003 Bioinformatics consulting at littlest.co.uk
  • General bioinformatics support
  • Development of parallel text indexing and publishing tools - Java, AWT, Swing, Regular Expressions, PVM, C
2001 - 2002 Bioinformatics at Lion Bioscience Ltd, Cambridge, UK. with Thure Etzhold
  • Analyst and programmer for client/server systems including a graphical SRS PRISMA viewer - Java, Swing (large canvas component), XML specifications, Icarus
  • Bioinformatics support and documentation
1999 - 2000 Bioinformatics at Cereon Genomics, Boston, MA, USA. with Stan Letovsky & David Bush
  • Positional cloning and analysis of plant disease resistance genes - Databases, Perl, UNIX scripting, regular expressions
  • Analysis database support, user training - Java, servlets
1997- 1999 Post-doctoral research at European Bioinformatics Institute with Tom Flores, Geoff Barton and Patricia Rodriguez-Tomé
  • Sequence chromatogram (DNA trace file) browsing client/server systems
    • - Analyst and programmer: Java parsing, communication and graphics on scrolling canvas
  • Linking Biological Databases using CORBA leading a five nation European consortium.
  • Architect and programmer for a parallel distributed incremental DNA sequence alignment system that worked across 2-40 processors - 'C' and PVM
  • Java client applications combining multiple data sources into graphical data summaries
  • C++ server and CORBA wrapper for EST alignments and CORBA supercluster application
1996-1997 Bioinformatics research and support for Zeneca Pharmaceuticals with Rakesh Anand and David Pioli
  • Positional cloning support for arthritis research
  • Bioinformatics programming including an email and web-based sequence alert system - Perl
  • System support - Solaris and Linux
  • Graphical client interfaces and general bioinformatics - Java
1993 - 1995 Post-doctoral research at Bob Waterston's Genome Sequencing Center, Washington University St. Louis. with LaDeana Hillier
  • Development of sequence analysis and visualisation tools including ESTCluster and Miropeats(PrintRepeats)
    • - C, Perl and PostScript programming
  • Managing and training new programmers for a joint project with David States' group at IBC
  • System administration - Solaris and MacOS
  • Studies of variables in DNA sequence production efficiency - Postgres DBMS and SQL querying
  • Image analysis of sequence gels and lane tracking algorithms, EST clustering, DNA sequence asssembly - 'C', and X11 graphics
1989-1993 Ph.D. in University of Cambridge Dept. of Medicine, lead by Sydney Brenner (Nobel Laureate)
  • Ph.D. Thesis title is "Computer Analysis of Molecular Sequences" supervised by Martin Bishop
  • Clustering partially sequenced cDNA sequences (ESTs) - 'C'
  • Visualisation of dipeptide frequencies. - UNIX shell and PostScript
1989 University of Cambridge Computing Service Research Associate: Colleges Project Officer.
1987-88 University of Kent at Canterbury - Two years of computer science including a parallel processing research project in communications entitled "Implementing the X-25 Data Link Protocol in Occam 2"
1984-1987 University of Sheffield studying microbiology, chemistry and basic computing
1984 Self-employed: writing graphical computer games in 6809 assembly language: one sold over 4000 copies.

Publications: Scopus: 7402708504 , ORCID: 0000-0003-1716-731X

2016 Paungfoo-Lonhienne, Chanyarat; Lonhienne, Thierry G. A.; Yeoh, Yun Kit; Donose, Bogdan C.; Webb, Richard I.; Parsons, Jeremy; Liao, Webber; Sagulenko, Evgeny; Lakshmanan, Prakash; Hugenholtz, Philip; Schmidt, Susanne; Ragan, Mark A.;, Crosstalk between sugarcane and a plant-growth promoting Burkholderia species, Nature Scientific Reports 6:37389 DOI: 10.1038/srep37389
2016 Kate L. Ormerod, Jeremy D. Parsons, Philip Hugenholtz et al., Genomic characterization of the uncultured Bacteroidales family S24-7 inhabiting the guts of homeothermic animals Microbiome 4:36 DOI: 10.1186/s40168-016-0181-2
2013 Mohammad Tawhidul Islam, Jeremy Parsons et al., Unlocking the Puzzling Biology of the Black Périgord Truffle Tuber melanosporum, J. Proteome Res.,12, pp 5349-5356., DOI: 10.1021/pr400650c
2000 Parsons, J.D. and Rodriguez-Tomé P., JESAM: CORBA software components to create and publish EST alignments and clusters, Bioinformatics, 16, 313-325.
1999 Parsons, Jeremy D., Buehler, Eugen, and Hillier, LaDeana, DNA Sequence Chromatogram Browsing Using JAVA and CORBA., Genome Res., 9, 277-281.
1996 Hillier, L, Parsons, J.D., et al., Generation and Analysis of 280,000 Human Expressed Sequence Tags, Genome Research, 6, 807-828.
1996 Cooper, Matthew L., Maffitt, David R., Parsons, Jeremy.D., Hillier, LaDeana, and States, David J., Lane Tracking Software for Four-color Fluorescence-based Electorphoretic Gel Images, Genome Res, 6, 1110-1117.
1995 Berks, M., and the C. elegans Genome Mapping and Sequencing Consortium, The C. elegans Genome Sequencing Project, Genome Res., 5,99-104.
1995 Parsons, J.D., Miropeats: Graphical DNA Sequence Comparisons, Comput. Applic. Biosci., 11, 615-619.
1995 Parsons, J.D., Improved Tools for DNA Comparison and Clustering, Comput. Applic. Biosci., 11, 603-613
1994 Johnston,M., Parsons,J., et al., Complete Nucleotide Sequence of Saccharomyces Cerevisiae Chromosome VIII. Science, 265, 2077-2082
1992 Duff, K., Parsons J., and Hodgeman, T.C., Secondary structure analysis identifies a putative mouse protein demonstrating similarity to the repeat units found in CDC4, the G protein B subunits and related proteins., J. DNA Seq. and Map., 3, 213-220.
1992 Parsons, J.D., Brenner, S. and Bishop, M.J., (1992), Clustering cDNA Sequences, Comput. Applic. Biosci., 8, 461-466
1991 Poster at Cold Spring Harbor - Clustering DNA Sequences

Other Qualifications

Interests and Activities