Former Group Members

David Martin   - Was the Post Genomics and Molecular Interactions Centre Bioinformatics Scientific Officer. David graduated with a degree in Chemistry from Kings College London in 1991. He completed a PhD in protein structure/function at the MRC Clinical Sciences Centre, Hammersmith  in Ted Tuddenham's group before taking up an EMBO postdoctoral fellowship in Oslo. An EU TMR fellowship as part of the GeneQuiz project allowed David to develop his bioinformatics skills and he took the position as Head of the Norwegian EMBNet node  at the University of Oslo in August 1999. Following his move to Dundee in March 2001 David had a broad responsibility to develop bioinformatics support, training and services for the emerging data intensive science that is going on in the School of Life Sciences.  David's scientific interests include genome annotation and data management. He has developed the GOtcha Tool which annotates sequences with GO term.  He also  collects genomes to annotate, preferably ones from nasty organisms such as Malaria and Sleeping Sickness. His interest is in improving the annotations, working out how to tell the annotations have improved (not as easy as you might think) and looking at these anntoations in a systems biology context.

His external interests seem to involve rebuilding cars, houses and boats when he isn't out in the mountains or enjoying family life.  He also plays the clarinet and saxophone but not as well as you'd want to be listening to.

Google Scholar Citations.

David Moved to Dundee in 2001.

In July 2013 David took up a new position as a Senior Lecturer in the School of Learning and Teaching, College of Life Sciences.  In this new job he is making great strides to get programming, data analysis and bioinformatics integrated into the undergraduate courses at Dundee!

Tara Eckenrode: Tara joined us as a Ph.D. student and  worked on the analysis and prediction of protein-protein interactions.

Tara joined the group on 1st November 2010 and successfully defended her Ph.D. in record time on 8th Feb 2013!  Her examiners were David Westhead from Leeds and David Norman (Dundee).  Tara has now returned to the USA to pursue a new career outside science.

Manikhandan Mudaliar (“Mani”):  joined us to work as part of the Data Analysis Group.   Prior to joining the group he worked at  the Translational Medicine Research Collaboration (TMRC), Dundee as a bioinformatics analyst where he was involved in a canine lymphoma  translational project, colorectal cancer biomarker discovery and COPD  biomarker discovery projects.  Although now working in bioinformatics research, he was originally trained as a veterinarian and  obtained a professional veterinary degree (BVSc & AH), from Nagpur Veterinary  College, India. Mani then worked as a Veterinary Officer for the Government of Tamil Nadu for 9  years. His immense desire to keep abreast in the cutting edge of drug  discovery brought him to the UK to do an MSc in Bioinformatics at Cranfield University before moving to his job at the TMRC.

Mani joined the group on 1st April 2011.

Mani moved on to a 3-year appointment at the University of Glasgow on 9th July 2012.

Peter Troshin:  Peter was supported by a number of grants including the BBSRC Structural Proteomics Inititiative to develop computational systems based on webservices and other technologies.   He is the author of the novel JABAWS portable web-services environment.

Peter joined the group on 1st July 2009.

Peter moved to become an independent software consultant on 1st January 2012.

Michelle Scott - Caledonian Research Fellow and formerly Canadian Institutes of Health Research (CIHR) funded fellow.

After a bachelor degree in biochemistry at the Universite de Montreal and a Masters in biochemistry and molecular biology under the supervision of Karl Riabowol at the University of Calgary near the beautiful Canadian Rockies, Michelle decided that she missed math and physics.  As a consequence, she undertook a degree in computer engineering at McGill University in Montreal.  After two years, she switched to a PhD in bioinformatics/biochemistry at McGill under the co-supervision of Mike Hallett and David Thomas, studying protein subcellular localization.  She moved to Dundee in the fall of 2005 to work as a CIHR post-doctoral fellow.  Michelle is interested in protein-protein interaction networks with a particular focus on the nucleolus.

Starting date: 1st December 2005.

Michelle moved on at the end of July 2011  to start her own research group at the Universite de Sherbrooke Canada..

 Tom Walsh - did his first degree in Biochemistry at Trinity College Dublin and then moved to University College Dublin for a PhD on modelling cytokine receptor complexes. He moved to Dundee in July 2002 to work on the EC funded project TEMBLOR.

TEMBLOR was funded by European Community Contract No. QLRI-CT-2001-00015 for "TEMBLOR"  under the specific RTD programme "Quality  of Life and Management of Living Resources" Tom maintains the group's MSD  installation and his other interests include writing a Perl library for interfacing with the SCOP database hierarchy running STAMP searches in parallel on the group's computing cluster and building a database of pairwise structure comparisons of SCOP domains.

From 1st July 2005 Tom  transferred to a SHEFC funded position as part of the Scottish Bioinformatics Research Network (SBRN) and continued in this role on other funding until 2011.

Tom claims to be able to program in Fortran and play the accordion but the group has so far been spared these dubious accomplishments.  In his spare time he enjoys collecting useless trivia.

On 1st August 2011 after 9 years in the group, Tom left to take up a job within the College of Life Sciences HPC team. Tom will still be supporting our systems but will have other new responsibilities in his new position.

Dan Bolser: Post Doc with David Martin working on BBSRC funded  Potato genome sequencing project in collaboration with the Scottish Crop Research Institute.

Dan joined David’s  group on 21st July 2008 and after getting his work published in Nature, moved on to new challenges in July 2011 and then took up a job at the European Bioinformatics Institute.

Mark McDowall: BBSRC Funded
Ph.D. Student.

Mark did his undergraduate degree at the University of Durham in Molecular Biology and Biochemistry.   Realising that he enjoyed computers more than pipettes and  gels, he went to the University of York to do an MRes in Bioinformatics.       After taking a year out working in the IT department at the City of York  Council he jumped ship and ventured north to start a Ph.D. on the prediction of protein-protein interactions.

When he is not programming or reading papers he enjoys photography, walking,  cycling and badminton, plus when he gets the chance,  jive and ballroom dancing.

Mark joined the group on 10th September 2007, then moved on to the European Bioinformatics Instititute in October 2010 to work as part of the Ensembl team.  He submitted his Thesis on 5th April 2011 and successfully defended it on 23rd May 2011.  His examiners were Christine Orengo and Ruth Brenk.

Christelle Robert - Scottish Crop Research Institute (SCRI) student based at SCRI with primary supervision by Frank Wright and Leighton Pritchard at the SCRI but co-supervised by Geoff.

Christelle successfully defended her Ph.D. thesis on 15th Jan 2010.  Her examiners were Prof. David Westhead of Leeds University and Prof. Tracy Palmer.

Christelle is now working at the Roslin Institute.

Ian OvertonBBSRC Funded  to work on the project “Structural Proteomics of Rational Targets” SPoRT as part of the Scottish Structural Proteomics Facility (SSPF)." Prior to joining Geoff's group he was in Manchester (then UMIST) doing doctoral research with Simon Hubbard, which focused on the Chicken Proteome, Transcriptome & Genome. Before his
Ph.D., he worked as a Bioinformatics Officer with Provalis plc. and spent over
six months travelling South East Asia and Australasia, largely on his own. He read Biochemistry at Oxford University, obtaining an undergraduate Masters degree. He has also worked with Astra-Zeneca at the bench.   He is interested in the relationships between protein structure/sequence and function, molecular dissection of biochemical mechanisms, and the development of rational therapeutic strategies. 

Starting Date:  1st December  2004.

In 2009 Ian  won a prestigious Royal Society of Edinburgh Research Fellowship to develop his own research group at the MRC Human Genetics Unit, Edinburgh.  Ian started his Fellowship in October 2009.

Cathy Stephenson Scottish Funding Council (SFC) Funded SBRN Adminstrator.

Cathy was the Administrator for the SBRN grant from 15th October 2005 four four years.  Cathy also looked after the group’s secretarial needs as well as developing new grant application procedures for the College of Life Sciences.   Quite apart from her big impact on the research and smooth running of the group, Cathy did great things for our social calendar and made sure we all celebrated birthdays!!

Jonathan Manning - Jon started in the group in October 2004 after a Master of Research in Bioinformatics at the University of Leeds. This followed a Bachelors degree in Biochemistry (also at Leeds), which included an industrial year in sunny Florida studying the genetics of Parkinsonism, and a computer-based dissertation project examining the role of water in protein-protein interfaces. He rapidly discovered that in contrast to lab work, with computers, any problems could for the most part reliably be traced to himself, rather than dodgy enzymes or broken pipettes.  Jon decided the laboratory was an environment best left to those with more patience, and his lab coat has been consigned to the bottom drawer ever since.

When not looking goofy in photographs, Jon likes to spend time attempting to deprogram his namby-pamby southern ways by walking up and down steep bits of the Scottish landscape at weekends with the university rucksack club. He invariably regrets the decision to do so come Sunday evening, but somehow forgets it when, after a few beers, the signup sheet is proffered. Other interests include beer, wine, cooking, swimming, cycling, and too much TV.

While not entirely sure what his 'life after PhD' will be, Jon's grateful to Geoff and the BBSRC for allowing him to do interesting biological research in combination with messing around on the computer. 

Jon submitted his Thesis in January 2008 and passed his viva on 2nd May 2008.  His examiners were Prof David Jones from UCL and Dr Ruth Brenk.  He started work at Edinburgh University in early Feb. 2008.

Greg Machray - A native Dundonian and only Scotsman in the group, Greg joined the group after completing his first degree in Biochemistry at the University Of Dundee in summer 2003. He started his BBSRC funded Ph.D. project in October 2003 and is  jointly supervised by Mike Ferguson.  Although his project is generally computer-based, both supervisors are threatening to force wet lab work on him before three years is up.  Contrary to popular belief, Greg has left the confines of the city of Dundee several times - although it's so nice here he doesn't really see the point.  His activities between work and above boundaries are varied, in particular he enjoys beating the unmentionables out of all comers thrice weekly at the University Ju Jitsu club and at the Scottish Ju Jitsu Association headquarters.  Such training sessions are inevitably followed by a drink or two "to aid the healing process" and "to promote recovery". 

Greg left during 2007 to take up a programming job in London.

Johan van Niekerk BBSRC Funded to work on the project “Structural Proteomics of Rational Targets” SPoRT as part of the Scottish Structural Proteomics Facility (SSPF).  Jo completed a BSc in Genetics with Biochemistry and Zoology subjects at The University of Pretoria (South Africa) in 1998, after which he started studying Computer Science. He started working it the IT industry in 2000, working on many different kinds of projects, most having two things in common: They seemed to require some sort of database design work, and they were completely unrelated to Biology.

Out of his interest in biology, he started doing a distance learning MSc in Bioinformatics through Manchester University in 2002. He moved to Scotland in 2004, hoping to be a little closer to the action in Bioinformatics research.

He joined Geoff’s group in November 2004, and is happy to be working in a place where his colleagues know the real link between Entrez, Tea-coffee and Java.  Jo is the LIMS manager for the SSPF (Scottish Structural Proteomics Facility).
 

Starting Date:  8th November 2004.

In August 2007 Jo moved on to a job with Ingres at Melbourne Australia.

Emily Jefferson: PostDoc on the ENFIN EU Network of Excellence project. 
After completing her first degree in biochemistry at the University of StAndrews, Emily joined the group in October 2003 on a BBSRC funded studentship working on the analysis and prediction of protein-protein interactions.  Having completed her thesis, (examiners Prof. Janet Thornton, EBI and Prof. Daan van Aalten) she joined the ENFIN project on 1st November 2006.
 

In June 2007 Emily moved out of science to a job with a financial services company in Oxfordshire.

From October 2010 Emily took time out to cycle around the world and raise money for Oxfam!

In October 2012 Emily returned to Dundee as the eHealth Development Programme Manager in the Health Informatics Centre at Dundee.

Andrew Waterhouse - BBSRC Funded research assistant working on development of the JalView alignment viewer/editor as part of the Visualisation and Analysis of Biological Sequences Alignments and Structures project.  With a degree in Natural Sciences from Cambridge and an MSc in Information Technology from Heriot-Watt University Andrew worked for the Mouse Atlas project at the Human Genetics Unit in Edinburgh as a Java Developer before moving further north.  Andrew joined the Barton group from a Dundee based mobile phone software company and is hoping to bring DNA/Protein sequence analysis tools to the mobile phone market.

Andrew spends his spare time mountain biking the local and not so local hills or playing football for the aptly named Cannonfodder FC. Initially the move to Dundee promised to bring him closer to the snowfields of Glenshee and Aviemore, but after realising the Scottish snow season invariably lasts for 2 days in February is happy to go bagging the Monroes by foot alone.

Starting Date:  13th September 2004.

25th May 2007: Andrew has now moved on to a position at the Riken Institute, Yokohama, Japan.  In 2011, Andrew moved back to Europe to a position in Switzerland with Torsten Schwede.

Diego Miranda-Saavedra - is a Wellcome Trust 4-Year programme Ph.D. student.  He joined the Group from September 2003 to complete a Ph.D. over the next three years.

Diego successfully defended his Ph.D. thesis on protein kinase annotation and kinome comparison on 3rd May 2007 and is now a post-doc in Bertie Gottgens’ group in the Department of Haematology, Cambridge Institute for Medical Research, University of Cambridge.

In October 2009 Diego moved on to a Group Leader position at the Immunology Frontier Research Institute, Osaka University, Japan.

In October 2013 Diego returned to the UK to take up a position as Reader at the University of Newcastle.

Philip Quinlan   - is a programmer who worked with David Martin on the TACTICS project at in the medical school.  He is now based 100% there.






 

Jonathan Barber   - joined the group in October 2001 as a BBSRC funded Ph.D. student, after graduating  from Imperial  College  with a degree in Biotechnology, during which he  spent a year working at (the then) GlaxoWellcome looking at medium-throughput  screening.   Disliking the fact that biology practicals never ever work due to the  biology involved, he  decided to weather the nondeterminism of computers  instead, where some other poor sod has done all the donkey work, and you get to  sit down more.

When not shackled to his desk, Jon juggles, reads and drinks. Sometimes all  at the same time, with predictably soggy results. Also, he's a fan of the  cinema, especially the DCA, which is  groovy. At least one evening a week he runs around chasing after a football  trying his best to kick the damn thing. Not to be outdone by the other musical  virtuosos in the group, he's currently looking for someone in the area to teach  him how to play the flute so he can inflict his ability on other people unlucky  enough to stray within range.

Dundee's fab, honest, come and join us. Although whether you trust a man who  uses the words "fab" and "groovy" is another matter.

Jon defended his Thesis in August 2005 and is now following a career in Unix systems adminstration in the College of Life Sciences.

During 2009 Jon moved to Portugal where he is continuing his career in systems administration.

Sorry, no photo!

Sebastian Becker - was a summer student for July-Sept  2005.  He worked with Jim Procter on developing code to generate Jalview XML files.

Bettina Leonhardt  - was a summer student for the months of August and September 2004.  Bettina was from the University of Saarbruecken, Germany  and wrote a perl library and  web interface to alscript

Andy Sanwell   - Was a visitor to the group and applied his training in computer science to a number of problems.  In particular he polished the latest version of the STAMP package for protein structure comparison and alignment, and set up STAMP to scan the PDB on our Linux cluster.

Andy is currently spending more time on his other homebuilding projects at Perth.

Patrick Audley - Joined the Group on 1st May 2002 as Unix systems administrator and general computing Guru.  Although based in the Group, Patrick had wide responsibility for high performance computing and networking in the Wellcome Trust Biocentre.   While he didn’t always sit on the desk, he found it helps, sometimes...  Patrick has his own extensive web site.

After two years transforming the computing systems in the Faculty of Life Sciences, Patrick has now returned to Canada.

Andreas Schlicker - Was a  summer student from the University of Saarbruecken, Germany who worked in the group during August and September 2003.

Susanne Eyrisch - Was a summer student from the University of Saarbruecken, Germany who worked in the group during August and September 2003.  With Andreas, she developed a web interface to the STAMP structural comparison program.

Caleb Webber graduated from the University of Warwick in October 1995 with a degree in Biological Sciences with Molecular Genetics. After a little rest from academia, he started work in the wEST radiation hybrid mapping group, Wellcome Trust Centre For Human Genetics, handling and developing their automated lab systems and bioinformatics. A chance introduction at this seemingly innocent venue led him to sign  away the next three years working for a PhD under Geoff's guidance! Arriving at the EBI in December 1998, Caleb is currently examining the usefulness of primary structure comparison tools and hopes very much to head off into the trendy world of comparitive genome research.

Caleb spends all his free time singing and playing in a band called "Halo", described as "local  dance/rock crossover types mixing grungey guitars with house  beats and trip-hop atmospherics" by the music press.  You can find out for yourself at www.bosstunes.com.

After successfully defending his Thesis on 1st April 2003 (examiners David Jones, UCL and Ewan Birney (EBI), Caleb now works in the Ponting Group at the University of Oxford.  He recently became a group leader there with research in Neurological Disease Genomics.

Goulven Kerbellec - Is a computer science summer student from Nantes, France.  He spent three months from 1 June 2002 in the group developing web interfaces to software.  While with us Goulven developed an interface to our database searching program SCANPS.

Steve Searle :-)  

Steve joined the group at EBI  in February 1999 from the University of Bath.

In June 2001 Steve moved to a job working on the Ensembl project at the Sanger Institute.  Steve now heads the Sanger software development team for the  Ensembl project!

Uwe Dengler :-)  

Uwe joined the group at EBI in March 1999.  He worked mainly on the 3Dee domains database and moved on to a job with Novartis in Switzerland in Dec 2000.

James Cuff completed his BSc at Manchester University in June '96, during which a on year placement  was spent at the Company Research Laboratory, BNFL.  Previous research has included work with novel zeolite compounds, pthalocyanines and a final year honours project in protein structure prediction.  James joined the group in Oct. '96 on a joint venture between the MRC, and the OCMS.  He is currenly attempting to survive his PhD in protein structure prediction.  

James has no leisure time as Geoff is always giving him jobs to do :-)  

James successfully defended his  Thesis in March 2000.

After a period working for Inpharmatica, James has now returned to Hinxton and is a Group Leader at the Sanger Institute.

James has now moved on again to the Broad Institute in Boston, USA.

In 2006 James moved again to Harvard University as Head of the Faculty of Arts and Science Research Computing.

Nirmala :-)  was a sabbatical visitor for 1999  from the company Novartis in the USA.  She worked on combining the MAP fold recognition method with NMR data.  Nirmala returned to the US in January 2000.

Sorry, no photo!

Scary low-res pictures of Richard, Rob, Craig and Andras were taken with the built-in camera on a Silicon Graphics’ Indy computer.  At the time (1993) having a camera on a computer was a real novelty!  We all thought it was just a pointless sales gimmick since all we wanted a computer for was to crunch numbers!