Damian Counsell

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News

Although I work as an external consultant to a biotech-pharma company that is physically based on academic premises, I no longer work in academic science. I am no longer an employee of the Medical Research Council or a university. This page is just a convenient resource I can point academic queries at.

If you would like me to help you with something in person, you can reach me via my business contact page and I will give you a quote.

Who I am

Damian Counsell

Introduction

Hello. My name is Damian Counsell.

In 2008, I co-authored this European Commission report on sharing scientific data, I am still a director of Bioinformatics.Org, and, apparently, on the Advisory Panel of Future Drug Discovery---from time to time, I also give talks to people from drug companies.

Until August 2005, I was a Bioinformatics Specialist in the United Kingdom Medical Research Council's Human Genome Mapping Project Resource Centre.

I do not do laboratory experiments and I do not call myself an "expert". I do not append or prepend any titles to my name. If anyone else tries this kind of thing on when citing or quoting me, they are doing so without my blessing.

Contact details

phone/voicemail: +44 (0)7967 026293

Email address

my firstname [at] my surname [dot] com

Universal Resource Locator

http://bioinformatics.org/~counsell/

Contents

Interests

Protein bioinformatics

I was interested in some simple, but, I believed, important problems in protein bioinformatics:


Bioinformatics education

Bioinformatics offers challenges and opportunities in pedagogy.

EMBOSS

I have been involved with this wonderful suite of free (as in speech and free as in beer) software.

CV/Résumé

Study

1995--1996: MSc. Physical Science and Engineering in Medicine, Imperial College, London

dissertation: "An Investigation into Scale-space Texture Measures"
---extension of 2D image analysis texture measures into 3D for the segmentation of MR brain images in schizophrenics and others

1986--1990: B.A. Physiological Sciences, Balliol College, University of Oxford

dissertation: "The Effect of Inorganic Phosphate on Rhodobacter Sphaeroides' Motility"
---digital imaging computer tracking of cell motion in different media

Work

2001--2005: Bioinformatics Specialist, The Human Genome Mapping Project Resource Centre [latterly: The Rosalind Franklin Centre for Genomic Research], Cambridge, UK

1997--2001: Bioinformatics Computing Officer, Institute of Cancer Research, London, UK

1996--1997: Biological Content Developer, Electronic Press (BioMedNet), London, UK

1992--1995: Research Assistant: Cell Biology, Sir William Dunn School of Pathology, University of Oxford, UK

1991--1992: Research Assistant: Immunology, Nuffield Department of Medicine, Institute of Molecular Medicine, University of Oxford, UK

1990--1991: Technician, Nuffield Department of Medicine, Institute of Molecular Medicine, University of Oxford, UK

Publications

Research

Towards a European e-Infrastructure for e-Science Digital Repositories
Alison Macdonald, Philip Lord, Damian Counsell, Melanie Dulong du Rosnay, Isabel Galina, Neil Beagrie, Daphne Charles, Robert Beagrie, Pawel Plaszcak, Pawel Jarosz, Paul Pillar, Richard Sinnott, Hanne Mostecky
European Commission Information Society and Media (2008)

A Fibrillin-1-Fragment Containing the Elastin-Binding-Protein GxxPG Consensus Sequence Upregulates Matrix Metalloproteinase-1: Biochemical and Computational Analysis
Patrick Booms, Andreas Ney, Frank Barthel, Gautier Moroy, Damian Counsell, Christoph Gille, Gao Guo, Reinhard Pregla, Stefan Mundlos, Alain J. P. Alix, Peter N. Robinson
Journal of Molecular and Cellular Cardiology (2006), 40, pp234--246

Use of a stringent high-throughput yeast two-hybrid strategy to study human protein-protein interactions: analyses of all intracellular proteins encoded within the human MHC class III region
Jennifer I. Semple, Benjamin Lehner, Stephanie Brown, Damian Counsell, R. Duncan Campbell, Christopher M. Sanderson
Genomics (2004), 83, pp153--167

Mutations in the Human Muscle LIM Protein Gene in Families With Hypertrophic Cardiomyopathy
Christian Geier, Andreas Perrot, Cemil Özcelik, Priska Binner, Damian Counsell, Katrin Hoffmann, Bernhard Pilz, Yvonne Martiniak, Katja Gehmlich, Peter F.M. van der Ven, Dieter O. Fürst, Arnold Vornwald, Eberhard von Hodenberg, Peter Nürnberg, Thomas Scheffold, Rainer Dietz, and Karl Josef Osterziel
Circulation (2003), 107, pp1390--1395

Crystal structure of the CCT γ apical domain: implications for substrate binding to the eukaryotic cytosolic chaperonin
Günter Pappenberger, Julie A. Wilsher, S. Mark Roe, Damian J. Counsell, Keith R. Willison, Laurence H. Pearl
Journal of Molecular Biology (2002), 318, pp1367-79

HLA-B27 Subtyping by single-strand conformation polymorphisms (SSCP) in Caucasoids, Negroids and Inuits from Greenland
Cornelis F, Pile K, Hill A, Liote F, Rowland-Jones S, Counsell D, Toubert A, Lathrop M, McMichael A, Bardin T, Bell J
Arthritis and Rheumatism (1992), 35, supplement, ppS182--S182

The Effect of phosphate on the motility of Rhodobacter sphaeroides
P. S. Poole, S. Brown, D. Counsell and J. P. Armitage
FEMS Microbiology Letters (1991), 79, pp1--4

Reviews

Book Review: Bioinformatics and Molecular Evolution
Damian Counsell
Comparative and Functional Genomics (2005), 6, issue: 5/6, pp317--319

Meeting Review: Workshop---Predicting the Structure of Biological Molecules
Damian Counsell
Comparative and Functional Genomics (2004), 5, issue: 6/7, pp480--490

A Review of Bioinformatics education in the UK
Damian Counsell
Briefings in Bioinformatics (2003), 4, pp7--21

Meeting Review: 2002 O'Reilly Bioinformatics Technology Conference
Damian Counsell
Comparative and Functional Genomics (2002), 3, pp264--269

Posters and presentations

Digital archiving: pharma as a model for good practice
Damian Counsell and Philip Lord
The Records Management Society, Town Hall, Wigan, UK; 3 April 2008

The GAMP electronic data archiving guidelines---an update and practical implementations
Damian Counsell and Philip Lord
Data Management for the Pharmaceutical Industry, Informa Life Sciences, London, UK; 9--10 July 2008

How can we build a bioinformatics programme that works?
Damian Counsell
The O'Reilly Bioinformatics Technology Conference; Tucson, AZ, USA; 28--31 January 2002

Evolution of a protein folding machine, a bioinformatic view of CCT
Damian Counsell
Structural Biology Department, Weizmann Institute; Rehovot, Israel; September 2001
Neurogenetics Department, Imperial College School of Medicine; St Mary's Campus, London, UK; November 2000

CCT: A tar-pit, a folding machine and a biology lesson
Damian Counsell
NEC Research Institute; Princeton, NJ, USA; September 1999

Prediction of CCT substrate binding sites by bioinformatic methods
Damian Counsell, Keith Willison
EMBO Workshop on Protein Folding and Misfolding inside and outside the Cell; St Catherine's College, University of Oxford, UK; 25--28 March 1998

Electronic

The Bioinformatics FAQ
Bioinformatics.Org; 1999--
The Bioinformatics Resource; 2001--

Word for the Wise: A Guide to preparing Scientific documents with Microsoft Word
MRC-HGMP; 2001--
Institute of Cancer Research; 1998--

Bioinformatics
Perspectives in Oncology: Cancer Sciences Website
Institute of Cancer Research; 2001--

Stationary Traveller
Sir William Dunn School of Pathology Website
University of Oxford; 1994

Popular Science

Hacking the Code of Life
Damian Counsell
Linux User (December 2004), 42, pp22--31 [NOTE: THIS ARTICLE WENT TO PRESS BEFORE I HAD REVISED IT---IT CONTAINS ERRORS. I DID NOT APPROVE THE TITLE OR THE SUMMARY.]

Hacking the Genome
Damian Counsell
Linux User (June 2001), 11, pp26--29

Open Source and the Human Genome Project
Damian Counsell
Becta Technology R&E Seminar: Open Source software and its potential impact on education; Techno Centre, Coventry University Technology Park, Warwickshire, UK; 25 July 2000

Useful stuff for anyone

Bioinformatics FAQ

I write and curate the Bioinformatics FAQ at Bioinformatics.Org.

Writing up

If you are a student or pupil who has to prepare a thesis or scientific project, and have to use Microsoft Word to do it, why not download a copy of "Word for the Wise"?

Useful stuff for my students

I have removed all of the notes and presentations that were previously in this section because they are now out of date.

EMBnet

Protein Structure Bioinformatics, EMBnet, Metapontum Agrobios Consortium, Italy

Institute of Cancer Research

PhD module Perspectives in Oncology: Bioinformatics, Institute of Cancer Research, London, UK

Imperial College

Bioinformatics for MRes. Biomolecular Sciences, Imperial College, London, UK

Sequence Analysis MSc. Computational Genetics and Bioinformatics, Imperial College, London, UK

RFCGR

Protein Structure Prediction, Genetics, Cambridge, UK

Useless stuff for everyone

My Personal Web pages

My personal pages are at damiancounsell.com.

Copyright

All text © Damian Counsell, 2001--2009