Damian Counsell

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==News==
==News==
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==Who I am==
==Who I am==
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http://bioinformatics.org/~counsell/images/DamianCounsell29Nov02.jpg
http://bioinformatics.org/~counsell/images/DamianCounsell29Nov02.jpg
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===Introduction===
===Introduction===
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Hello. My name is Damian Counsell. Until August 2005 I was a [http://bioinformatics.org/faq/#definitions Bioinformatics] Specialist in the United Kingdom [http://www.mrc.ac.uk/ Medical Research Council]'s [http://www.rfcgr.mrc.ac.uk/ Rosalind Franklin Centre for Genomics Research]. I am still a director of Bioinformatics.Org, on the Advisory Panel of [http://www.touchbriefings.com/cdps/cditem.cfm?NID=1619 &lt;cite&gt;Future Drug Discovery&lt;/cite&gt;], but I am not a scientist.
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Hello. My name is Damian Counsell. Until August 2005 I was a [http://bioinformatics.org/faq/#definitions Bioinformatics] Specialist in the United Kingdom [http://www.mrc.ac.uk/ Medical Research Council]'s [http://www.rfcgr.mrc.ac.uk/ Rosalind Franklin Centre for Genomics Research]. I am still a director of Bioinformatics.Org, on the Advisory Panel of [http://www.touchbriefings.com/cdps/cditem.cfm?NID=1619 <cite>Future Drug Discovery</cite>], but I am not a scientist.
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I no longer do experiments or contribute to peer-reviewed papers and I do not call myself an &quot;expert&quot;. 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.
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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===
===Contact details===
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Bioinformatics offers [http://bioinformatics.org/~counsell/papers/Counsell03_education.pdf challenges and opportunities in pedagogy].
Bioinformatics offers [http://bioinformatics.org/~counsell/papers/Counsell03_education.pdf challenges and opportunities in pedagogy].
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===[http://www.emboss.org/ &lt;span class=&quot;EMBOSS&quot;&gt;EMBOSS&lt;/span&gt;]===
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===[http://www.emboss.org/ <span class="EMBOSS">EMBOSS</span>]===
I have been involved with this wonderful suite of free (as in speech and free as in beer) software.
I have been involved with this wonderful suite of free (as in speech and free as in beer) software.
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1995--1996: [http://www.bg.ic.ac.uk/MSc/ MSc. Physical Science and Engineering in Medicine], [http://www.imperial.ac.uk/ Imperial College], London
1995--1996: [http://www.bg.ic.ac.uk/MSc/ MSc. Physical Science and Engineering in Medicine], [http://www.imperial.ac.uk/ Imperial College], London
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dissertation: &quot;&lt;cite&gt;An Investigation into Scale-space Texture Measures&lt;/cite&gt;&quot; &lt;br /&gt; ---extension of 2D image analysis texture measures into 3D for the segmentation of MR brain images in schizophrenics and others
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dissertation: "<cite>An Investigation into Scale-space Texture Measures</cite>" <br /> ---extension of 2D image analysis texture measures into 3D for the segmentation of MR brain images in schizophrenics and others
1986--1990: [http://www.admissions.ox.ac.uk/courses/physi.shtml B.A. Physiological Sciences], [http://web.balliol.ox.ac.uk/ Balliol College], [http://www.ox.ac.uk/ University of Oxford]
1986--1990: [http://www.admissions.ox.ac.uk/courses/physi.shtml B.A. Physiological Sciences], [http://web.balliol.ox.ac.uk/ Balliol College], [http://www.ox.ac.uk/ University of Oxford]
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dissertation: &quot;[http://bioinformatics.org/~counsell/papers/Poole91.pdf &lt;cite&gt;The Effect of Inorganic Phosphate on ''Rhodobacter Sphaeroides''' Motility&lt;/cite&gt;]&quot; &lt;br /&gt; ---digital imaging computer tracking of cell motion in different media
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dissertation: "[http://bioinformatics.org/~counsell/papers/Poole91.pdf <cite>The Effect of Inorganic Phosphate on ''Rhodobacter Sphaeroides''' Motility</cite>]" <br /> ---digital imaging computer tracking of cell motion in different media
===Work===
===Work===
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===Research===
===Research===
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[http://bioinformatics.org/~counsell/papers/Booms_et_al_2006_EBP_MMP1.pdf &lt;cite&gt;A Fibrillin-1-Fragment Containing the Elastin-Binding-Protein GxxPG Consensus Sequence Upregulates Matrix Metalloproteinase-1: Biochemical and Computational Analysis&lt;/cite&gt;]&lt;br /&gt;''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''&lt;br /&gt;[http://www.elsevier.com/wps/find/journaldescription.cws_home/622889/description#description &lt;cite&gt;Journal of Molecular and Cellular Cardiology&lt;/cite&gt;] (2006), &lt;span class=&quot;JournalVolume&quot;&gt;40&lt;/span&gt;, ''pp''234--246
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[http://bioinformatics.org/~counsell/papers/Booms_et_al_2006_EBP_MMP1.pdf <cite>A Fibrillin-1-Fragment Containing the Elastin-Binding-Protein GxxPG Consensus Sequence Upregulates Matrix Metalloproteinase-1: Biochemical and Computational Analysis</cite>]<br />''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''<br />[http://www.elsevier.com/wps/find/journaldescription.cws_home/622889/description#description <cite>Journal of Molecular and Cellular Cardiology</cite>] (2006), <span class="JournalVolume">40</span>, ''pp''234--246
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&lt;cite&gt;[http://www.sciencedirect.com/science?_ob=ArticleURL&amp;_udi=B6WG1-49HMSVT-1&amp;_user=776054&amp;_coverDate=09%2F24%2F2003&amp;_alid=119697068&amp;_rdoc=1&amp;_fmt=summary&amp;_orig=search&amp;_qd=1&amp;_cdi=6809&amp;_sort=d&amp;_docanchor=&amp;view=c&amp;_acct=C000042238&amp;_version=1&amp;_urlVersion=0&amp;_userid=776054&amp;md5=874828e49c00691013ae52200e9af3ef 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]&lt;/cite&gt;&lt;br /&gt; Jennifer I. Semple, Benjamin Lehner, Stephanie Brown, Damian Counsell, R. Duncan Campbell, Christopher M. Sanderson &lt;br /&gt;[http://www.academicpress.com/genomics &lt;cite&gt;Genomics&lt;/cite&gt;] (2004), &lt;span class=&quot;JournalVolume&quot;&gt;83&lt;/span&gt;, ''pp''153--167
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<cite>[http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6WG1-49HMSVT-1&_user=776054&_coverDate=09%2F24%2F2003&_alid=119697068&_rdoc=1&_fmt=summary&_orig=search&_qd=1&_cdi=6809&_sort=d&_docanchor=&view=c&_acct=C000042238&_version=1&_urlVersion=0&_userid=776054&md5=874828e49c00691013ae52200e9af3ef 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]</cite><br /> Jennifer I. Semple, Benjamin Lehner, Stephanie Brown, Damian Counsell, R. Duncan Campbell, Christopher M. Sanderson <br />[http://www.academicpress.com/genomics <cite>Genomics</cite>] (2004), <span class="JournalVolume">83</span>, ''pp''153--167
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&lt;cite&gt;[http://circ.ahajournals.org/cgi/content/abstract/01.CIR.0000056522.82563.5F  Mutations in the Human Muscle LIM Protein Gene in Families With Hypertrophic Cardiomyopathy]&lt;/cite&gt;&lt;br /&gt; 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&lt;br /&gt;[http://circ.ahajournals.org/ &lt;cite&gt;Circulation&lt;/cite&gt;] (2003), &lt;span class=&quot;JournalVolume&quot;&gt;107&lt;/span&gt;, ''pp''1390--1395
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<cite>[http://circ.ahajournals.org/cgi/content/abstract/01.CIR.0000056522.82563.5F  Mutations in the Human Muscle LIM Protein Gene in Families With Hypertrophic Cardiomyopathy]</cite><br /> 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<br />[http://circ.ahajournals.org/ <cite>Circulation</cite>] (2003), <span class="JournalVolume">107</span>, ''pp''1390--1395
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&lt;cite&gt;[http://bioinformatics.org/~counsell/papers/Pappenberger03.pdf Crystal structure of the CCT \u03b3 apical domain: implications for substrate binding to the eukaryotic cytosolic chaperonin]&lt;/cite&gt;&lt;br /&gt; Günter Pappenberger, Julie A. Wilsher, S. Mark Roe, Damian J. Counsell, Keith R. Willison, Laurence H. Pearl&lt;br /&gt;[http://www.elsevier.com/locate/issn/0022-2836/ &lt;cite&gt;Journal of Molecular Biology&lt;/cite&gt;] (2002), &lt;span class=&quot;JournalVolume&quot;&gt;318&lt;/span&gt;, ''pp''1367-79
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<cite>[http://bioinformatics.org/~counsell/papers/Pappenberger03.pdf Crystal structure of the CCT \u03b3 apical domain: implications for substrate binding to the eukaryotic cytosolic chaperonin]</cite><br /> Günter Pappenberger, Julie A. Wilsher, S. Mark Roe, Damian J. Counsell, Keith R. Willison, Laurence H. Pearl<br />[http://www.elsevier.com/locate/issn/0022-2836/ <cite>Journal of Molecular Biology</cite>] (2002), <span class="JournalVolume">318</span>, ''pp''1367-79
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&lt;cite&gt;HLA-B27 Subtyping by single-strand conformation polymorphisms (SSCP) in Caucasoids, Negroids and Inuits from Greenland&lt;/cite&gt;&lt;br /&gt; Cornelis F, Pile K, Hill A, Liote F, Rowland-Jones S, Counsell D, Toubert A, Lathrop M, McMichael A, Bardin T, Bell J&lt;br /&gt;[http://www3.interscience.wiley.com/cgi-bin/jhome/76509746 &lt;cite&gt; Arthritis and Rheumatism&lt;/cite&gt;] (1992), &lt;span class=&quot;JournalVolume&quot;&gt;35, supplement&lt;/span&gt;, ''pp''S182--S182
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<cite>HLA-B27 Subtyping by single-strand conformation polymorphisms (SSCP) in Caucasoids, Negroids and Inuits from Greenland</cite><br /> Cornelis F, Pile K, Hill A, Liote F, Rowland-Jones S, Counsell D, Toubert A, Lathrop M, McMichael A, Bardin T, Bell J<br />[http://www3.interscience.wiley.com/cgi-bin/jhome/76509746 <cite> Arthritis and Rheumatism</cite>] (1992), <span class="JournalVolume">35, supplement</span>, ''pp''S182--S182
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&lt;cite&gt;[http://bioinformatics.org/~counsell/papers/Poole91.pdf The Effect of phosphate on the motility of ''Rhodobacter sphaeroides'']&lt;/cite&gt;&lt;br /&gt; P. S. Poole, S. Brown, D. Counsell and J. P. Armitage&lt;br /&gt;[http://www.sciencedirect.com/science/journal/03781097 &lt;cite&gt;FEMS Microbiology Letters&lt;/cite&gt;] (1991), &lt;span class=&quot;JournalVolume&quot;&gt;79&lt;/span&gt;, ''pp''1--4
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<cite>[http://bioinformatics.org/~counsell/papers/Poole91.pdf The Effect of phosphate on the motility of ''Rhodobacter sphaeroides'']</cite><br /> P. S. Poole, S. Brown, D. Counsell and J. P. Armitage<br />[http://www.sciencedirect.com/science/journal/03781097 <cite>FEMS Microbiology Letters</cite>] (1991), <span class="JournalVolume">79</span>, ''pp''1--4
===Reviews===
===Reviews===
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&lt;cite&gt;[http://bioinformatics.org/~counsell/papers/Counsell04_Cambridge_meeting.pdf Meeting Review: Workshop---Predicting the Structure of Biological Molecules]&lt;/cite&gt;&lt;br /&gt; Damian Counsell &lt;br /&gt;[http://www.wiley.co.uk/wileychi/genomics/cfg.html &lt;cite&gt;Comparative and Functional Genomics&lt;/cite&gt;] (2004), &lt;span class=&quot;JournalVolume&quot;&gt;5&lt;/span&gt;, issue: 6/7, ''pp''480--490
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<cite>[http://bioinformatics.org/~counsell/papers/Counsell04_Cambridge_meeting.pdf Meeting Review: Workshop---Predicting the Structure of Biological Molecules]</cite><br /> Damian Counsell <br />[http://www.wiley.co.uk/wileychi/genomics/cfg.html <cite>Comparative and Functional Genomics</cite>] (2004), <span class="JournalVolume">5</span>, issue: 6/7, ''pp''480--490
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&lt;cite&gt;[http://bioinformatics.org/~counsell/papers/Counsell03_education.pdf A Review of Bioinformatics education in the UK]&lt;/cite&gt;&lt;br /&gt; Damian Counsell &lt;br /&gt;[http://www.henrystewart.com/journals/bib/ &lt;cite&gt;Briefings in Bioinformatics&lt;/cite&gt;] (2003), &lt;span class=&quot;JournalVolume&quot;&gt;4&lt;/span&gt;, ''pp''7--21
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<cite>[http://bioinformatics.org/~counsell/papers/Counsell03_education.pdf A Review of Bioinformatics education in the UK]</cite><br /> Damian Counsell <br />[http://www.henrystewart.com/journals/bib/ <cite>Briefings in Bioinformatics</cite>] (2003), <span class="JournalVolume">4</span>, ''pp''7--21
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&lt;cite&gt;[http://bioinformatics.org/~counsell/papers/Counsell02_OReillyBioinformaticsMeeting.pdf Meeting Review: 2002 O'Reilly Bioinformatics Technology Conference]&lt;/cite&gt;&lt;br /&gt; Damian Counsell &lt;br /&gt;[http://www.wiley.co.uk/wileychi/genomics/cfg.html &lt;cite&gt;Comparative and Functional Genomics&lt;/cite&gt;] (2002), &lt;span class=&quot;JournalVolume&quot;&gt;3&lt;/span&gt;, ''pp''264--269
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<cite>[http://bioinformatics.org/~counsell/papers/Counsell02_OReillyBioinformaticsMeeting.pdf Meeting Review: 2002 O'Reilly Bioinformatics Technology Conference]</cite><br /> Damian Counsell <br />[http://www.wiley.co.uk/wileychi/genomics/cfg.html <cite>Comparative and Functional Genomics</cite>] (2002), <span class="JournalVolume">3</span>, ''pp''264--269
===Posters and presentations===
===Posters and presentations===
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&lt;cite&gt;[talks/Tucson.pdf How can we build a bioinformatics programme that works?]&lt;/cite&gt;&lt;br /&gt; Damian Counsell &lt;br /&gt;[http://conferences.oreillynet.com/pub/w/17/presentations.html  &lt;cite&gt;The O'Reilly Bioinformatics Technology Conference&lt;/cite&gt;]&lt;nowiki&gt;; Tucson, AZ, USA; 28--31 January 2002 &lt;/nowiki&gt;
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<cite>[talks/Tucson.pdf How can we build a bioinformatics programme that works?]</cite><br /> Damian Counsell <br />[http://conferences.oreillynet.com/pub/w/17/presentations.html  <cite>The O'Reilly Bioinformatics Technology Conference</cite>]<nowiki>; Tucson, AZ, USA; 28--31 January 2002 </nowiki>
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&lt;cite&gt;Evolution of a protein folding machine, a bioinformatic view of CCT&lt;/cite&gt;&lt;br /&gt; Damian Counsell &lt;br /&gt;[http://www.weizmann.ac.il/sb/index.html Structural Biology Department], [http://www.weizmann.ac.il/ Weizmann Institute]&lt;nowiki&gt;; Rehovot, Israel; September 2001 &lt;/nowiki&gt;&lt;br /&gt;[http://www.med.ic.ac.uk/divisions/52/neuro/home.asp Neurogenetics Department], [http://www.imperial.ac.uk/medicine/ Imperial College School of Medicine]&lt;nowiki&gt;; St Mary's Campus, London, UK; November 2000 &lt;/nowiki&gt;
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<cite>Evolution of a protein folding machine, a bioinformatic view of CCT</cite><br /> Damian Counsell <br />[http://www.weizmann.ac.il/sb/index.html Structural Biology Department], [http://www.weizmann.ac.il/ Weizmann Institute]<nowiki>; Rehovot, Israel; September 2001 </nowiki><br />[http://www.med.ic.ac.uk/divisions/52/neuro/home.asp Neurogenetics Department], [http://www.imperial.ac.uk/medicine/ Imperial College School of Medicine]<nowiki>; St Mary's Campus, London, UK; November 2000 </nowiki>
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&lt;cite&gt;CCT: A tar-pit, a folding machine and a biology lesson&lt;/cite&gt;&lt;br /&gt; Damian Counsell &lt;br /&gt;[http://www.neci.nec.com/ NEC Research Institute]&lt;nowiki&gt;; Princeton, NJ, USA; September 1999 &lt;/nowiki&gt;
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<cite>CCT: A tar-pit, a folding machine and a biology lesson</cite><br /> Damian Counsell <br />[http://www.neci.nec.com/ NEC Research Institute]<nowiki>; Princeton, NJ, USA; September 1999 </nowiki>
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&lt;cite&gt;Prediction of CCT substrate binding sites by bioinformatic methods&lt;/cite&gt;&lt;br /&gt; Damian Counsell, [http://www.icr.ac.uk/cmb/teams/folding/contacts/contacts.html  Keith Willison]&lt;br /&gt;[http://www.ocms.ox.ac.uk/ocms/EMBOworkshop.html &lt;cite&gt;EMBO Workshop on Protein Folding and Misfolding inside and outside the Cell&lt;/cite&gt;]&lt;nowiki&gt;; &lt;/nowiki&gt;[http://www.stcatz.ox.ac.uk/ St Catherine's College], [http://www.ox.ac.uk/ University of Oxford], UK; 25--28 March 1998
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<cite>Prediction of CCT substrate binding sites by bioinformatic methods</cite><br /> Damian Counsell, [http://www.icr.ac.uk/cmb/teams/folding/contacts/contacts.html  Keith Willison]<br />[http://www.ocms.ox.ac.uk/ocms/EMBOworkshop.html <cite>EMBO Workshop on Protein Folding and Misfolding inside and outside the Cell</cite>]<nowiki>; </nowiki>[http://www.stcatz.ox.ac.uk/ St Catherine's College], [http://www.ox.ac.uk/ University of Oxford], UK; 25--28 March 1998
===Electronic===
===Electronic===
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[http://bioinformatics.org/faq/ &lt;cite&gt;The Bioinformatics FAQ&lt;/cite&gt;]&lt;br /&gt;[http://bioinformatics.org/ Bioinformatics.Org]&lt;nowiki&gt;; 1999-- &lt;/nowiki&gt;&lt;br /&gt;[http://www.rfcgr.mrc.ac.uk/CCP11/index.jsp The Bioinformatics Resource]&lt;nowiki&gt;; 2001-- &lt;/nowiki&gt;
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[http://bioinformatics.org/faq/ <cite>The Bioinformatics FAQ</cite>]<br />[http://bioinformatics.org/ Bioinformatics.Org]<nowiki>; 1999-- </nowiki><br />[http://www.rfcgr.mrc.ac.uk/CCP11/index.jsp The Bioinformatics Resource]<nowiki>; 2001-- </nowiki>
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&lt;cite&gt;[http://www.counsell.com/wordforthewise/ Word for the Wise]&lt;nowiki&gt;: A Guide to preparing Scientific documents with &lt;/nowiki&gt;[http://www.microsoft.com/office/word/ Microsoft Word]&lt;/cite&gt;&lt;br /&gt;MRC-HGMP; 2001-- &lt;br /&gt;[http://www.icr.ac.uk/ Institute of Cancer Research]&lt;nowiki&gt;; 1998-- &lt;/nowiki&gt;
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<cite>[http://www.counsell.com/wordforthewise/ Word for the Wise]<nowiki>: A Guide to preparing Scientific documents with </nowiki>[http://www.microsoft.com/office/word/ Microsoft Word]</cite><br />MRC-HGMP; 2001-- <br />[http://www.icr.ac.uk/ Institute of Cancer Research]<nowiki>; 1998-- </nowiki>
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&lt;cite&gt;Bioinformatics&lt;/cite&gt;&lt;br /&gt;Perspectives in Oncology: Cancer Sciences Website &lt;br /&gt;[http://www.icr.ac.uk/ Institute of Cancer Research]&lt;nowiki&gt;; 2001-- &lt;/nowiki&gt;
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<cite>Bioinformatics</cite><br />Perspectives in Oncology: Cancer Sciences Website <br />[http://www.icr.ac.uk/ Institute of Cancer Research]<nowiki>; 2001-- </nowiki>
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&lt;cite&gt;[http://users.path.ox.ac.uk/~pcook/stattrav.htm Stationary Traveller]&lt;/cite&gt;&lt;br /&gt;[http://www.path.ox.ac.uk/ Sir William Dunn School of Pathology Website]&lt;br /&gt;[http://www.ox.ac.uk/ University of Oxford]&lt;nowiki&gt;; 1994 &lt;/nowiki&gt;
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<cite>[http://users.path.ox.ac.uk/~pcook/stattrav.htm Stationary Traveller]</cite><br />[http://www.path.ox.ac.uk/ Sir William Dunn School of Pathology Website]<br />[http://www.ox.ac.uk/ University of Oxford]<nowiki>; 1994 </nowiki>
===Popular Science===
===Popular Science===
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&lt;cite&gt;[http://bioinformatics.org/~counsell/papers/Counsell04_HackingTheCodeOfLife.pdf Hacking the Code of Life]&lt;/cite&gt;&lt;br /&gt; Damian Counsell &lt;br /&gt;[http://www.linuxuser.co.uk/ &lt;cite&gt;Linux User&lt;/cite&gt;] (December 2004), &lt;span class=&quot;JournalVolume&quot;&gt;42&lt;/span&gt;, ''pp''22--31 [NOTE: THIS ARTICLE WENT TO PRESS BEFORE I HAD REVISED IT---IT CONTAINS ERRORS. I DID NOT APPROVE THE TITLE OR THE SUMMARY.]
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<cite>[http://bioinformatics.org/~counsell/papers/Counsell04_HackingTheCodeOfLife.pdf Hacking the Code of Life]</cite><br /> Damian Counsell <br />[http://www.linuxuser.co.uk/ <cite>Linux User</cite>] (December 2004), <span class="JournalVolume">42</span>, ''pp''22--31 [NOTE: THIS ARTICLE WENT TO PRESS BEFORE I HAD REVISED IT---IT CONTAINS ERRORS. I DID NOT APPROVE THE TITLE OR THE SUMMARY.]
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&lt;cite&gt;[http://bioinformatics.org/~counsell/papers/Counsell01_HackingTheGenome.pdf Hacking the Genome]&lt;/cite&gt;&lt;br /&gt; Damian Counsell &lt;br /&gt;[http://www.linuxuser.co.uk/ &lt;cite&gt;Linux User&lt;/cite&gt;] (June 2001), &lt;span class=&quot;JournalVolume&quot;&gt;11&lt;/span&gt;, ''pp''26--29
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<cite>[http://bioinformatics.org/~counsell/papers/Counsell01_HackingTheGenome.pdf Hacking the Genome]</cite><br /> Damian Counsell <br />[http://www.linuxuser.co.uk/ <cite>Linux User</cite>] (June 2001), <span class="JournalVolume">11</span>, ''pp''26--29
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[http://bioinformatics.org/~counsell/papers/Counsell00_OpenSourceGenome.pdf &lt;cite&gt;Open Source and the Human Genome Project&lt;/cite&gt;]&lt;br /&gt; Damian Counsell &lt;br /&gt;[http://www.becta.org.uk/ Becta] Technology R&amp;E Seminar: [http://www.becta.org.uk/corporate/corporate.cfm?section=7_1&amp;id=2609  &lt;cite&gt;Open Source software and its potential impact on education&lt;/cite&gt;]&lt;nowiki&gt;; &lt;/nowiki&gt;[http://www.cutp.co.uk/techcen.htm Techno Centre, Coventry University Technology Park], Warwickshire, UK; 25 July 2000
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[http://bioinformatics.org/~counsell/papers/Counsell00_OpenSourceGenome.pdf <cite>Open Source and the Human Genome Project</cite>]<br /> Damian Counsell <br />[http://www.becta.org.uk/ Becta] Technology R&E Seminar: [http://www.becta.org.uk/corporate/corporate.cfm?section=7_1&id=2609  <cite>Open Source software and its potential impact on education</cite>]<nowiki>; </nowiki>[http://www.cutp.co.uk/techcen.htm Techno Centre, Coventry University Technology Park], Warwickshire, UK; 25 July 2000
==Useful stuff for anyone==
==Useful stuff for anyone==
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===[http://www.counsell.com/wordforthewise/ Writing up]===
===[http://www.counsell.com/wordforthewise/ Writing up]===
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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 [http://www.counsell.com/wordforthewise/ download] a copy of &quot;Word for the Wise&quot;?
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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 [http://www.counsell.com/wordforthewise/ download] a copy of "Word for the Wise"?
===[http://www.counsell.com/ My Personal Web pages]===
===[http://www.counsell.com/ My Personal Web pages]===
My personal pages are at [http://www.counsell.com/ counsell.com].
My personal pages are at [http://www.counsell.com/ counsell.com].

Latest revision as of 03:01, 24 November 2010

Contents

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:

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.

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