Damian Counsell

From Bioinformatics.Org Wiki

Contents 1 News 2 Who I am 2.1 Introduction 2.2 Contact details 2.2.1 Email address 2.2.2 Secure email 2.2.3 Universal Resource Locator 3 Interests 3.1 Protein bioinformatics 3.2 Bioinformatics education 3.3 EMBOSS 4 CV/Résumé 4.1 Study 4.2 Work 5 Publications 5.1 Research 5.2 Reviews 5.3 Posters and presentations 5.4 Electronic 5.5 Popular Science 6 Useful stuff for anyone 6.1 Bioinformatics FAQ 6.2 Writing up 6.3 My Personal Web pages

News

The Rosalind Franklin Centre, formerly the Human Genome Mapping Project Resource Centre, has closed down. This page really is academic.

I am now a consultant. You can reach me via my personal email contact page

Who I am

Introduction

Hello. My name is Damian Counsell. Until August 2005 I was a Bioinformatics Specialist in the United Kingdom Medical Research Council's Rosalind Franklin Centre for Genomics Research. I am still a director of Bioinformatics.Org, on the Advisory Panel of Future Drug Discovery, but I am not a scientist.

I no longer do experiments or contribute to peer-reviewed papers 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

http://bioinformatics.org/~counsell/images/email.jpg

Secure email

my new signed PGP public key will appear here

Universal Resource Locator

http://bioinformatics.org/~counsell/

Interests

Protein bioinformatics

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

• investigating function by sequence comparison within and between families of proteins,
• sequence-structure alignment for comparative modelling of proteins, and
• the meaning of homology between proteins and protein folds.

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, Rosalind Franklin Centre for Genomic Research, Cambridge

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

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

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

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

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

Publications

Research

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 \u03b3 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

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

[talks/Tucson.pdf 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"?

My Personal Web pages

My personal pages are at counsell.com.