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Bioinformatics Minisymposium at the University of Dundee

Geoff Barton

Friday, 5 September 2014 from 09:00 to 15:30 (BST)

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Bioinformatics Mini-Symposium at the University of Dundee


Friday 5th September 2014, D’Arcy Thompson Lecture Theatre, Tower Building


This meeting should appeal to anyone who is analysing biological data, particularly from high-throughput methods such as DNA sequencing or developing methods to extract knowledge from large data collections. The meeting presents a rare opportunity to hear international speakers who have all made important contributions to the field of bioinformatics.


Come and hear Dr Toby Gibson from the European Molecular Biology Laboratory (EMBL) Heidelberg, is co-author of the clustalW multiple alignment program and one of the most highly cited scientists in any field. He is an expert on biological sequence and pathway analysis. Dr Mike Gribskov of Purdue University, USA, is famous for his development of early “profile” sequence database search methods. He is a former president of the International Society of Computational Biology (ISCB) and remains an authority on the application of computational methods in biology.


As well as these international speakers, we will have talks from speakers closer to home. Dr Daniel Rigden is senior lecturer in post-genomics bioinformatics at the University of Liverpool. His interests focus on protein sequence/structure analysis and the study of evolution. Dr Jim Procter from the University of Dundee is the main developer and co-ordinator of the popular Jalview multiple sequence alignment workbench and will be giving an update on the new developments to that tool while Prof. Geoff Barton, also from Dundee will describe some his group’s other work in bioinformatics technique development and applications to high-throughput sequencing. He will also introduce the new Centre for Translational and Interdisciplinary Research at Dundee. Dr David Martin of the College of Life Sciences, School of Learning and Teaching, Dundee, will talk about his experiences of developing methods to educate biologists in computational techniques. Last but not least, we are delighted that Prof. Richard Baldock of the MRC-Human Genetics Unit will be able to speak about his experiences in large scale image analysis on the mouse atlas.


There will be ample time over a buffet lunch and coffee/tea breaks to meet the speakers. Although unable to speak this year, we will also be joined by Dr Michele Clamp who during her time at the Wellcome Trust Sanger Institute was the chief architect of the Ensembl genome analysis pipeline and has worked since at the Broad Institute at MIT/Harvard and Bioteam, Boston, USA and is now leading a team of bioinformaticians at Harvard. Michele is an authority on large-scale genome analysis.


The registration fee covers the cost of lunch and all refreshments.


Confirmed Speakers:


           Prof Michael Gribskov, Purdue University, USA

           Dr Toby Gibson, European Molecular Biology Laboratory, Heidelberg, Germany

           Dr Jim Procter, University of Dundee

           Dr Daniel
Rigden, University of Liverpool

           Dr David Martin, University of Dundee

           Dr Andrei Pisliakov, University of Dundee

           Prof Richard Baldock, MRC Human Genetics Unit, Edinburgh

           Prof Geoff Barton, University of Dundee


Provisional programme and biographies (22 July Version)


Friday 5th Sept 2014- Bioinformatics mini-Symposium at the University of Dundee






Geoff Barton




Daniel Rigden



Jim Procter






Toby Gibson



Richard Baldock






David Martin



Andrei Pisliakov





Mike Gribskov









Speakers:        Geoff Barton                          

                        Jim Procter

                        Daniel Rigden

                        Michael Gribskov

                        Richard Baldock

                        Toby Gibson

                        Andrei Pisliakov

                        David Martin














Prof. Richard Baldock

Biomedical Systems Analysis

Head of Biomedical Systems Analysis
Medical Research Council

Human Genetics Unit, Edinburgh.




Research Areas

My background is in theoretical physics and my research in the Human Genetics Unit is directed to understanding the genetic control of development. In collaboration with Dr Duncan Davidson I have developed the atlas-based concept for spatio-temporal databases in biomedicine and in particular the Edinburgh Mouse Atlas and associated databases (www.e-mouseatlas.org). In this context my research interests span image processing for 3D model reconstruction, spatio-temporal data-mapping, in situ gene-expression pattern analysis, bioinformatics, atlas-based biomedical databases, high throughput data capture and analysis, data/database interoperability and e-science.


The Mouse Atlas programme has a pivotal role in the delivery of embryo gene-expression resources internationally with direct involvement in special systems databases (www.gudmap.org, www.euregene.org), high throughput data capture (www.eurexpress.org), human embryo (www.ncl.ac.uk/ihg/EADHB, www.dgemap.org) and most recently a chick embryo atlas.



Dr Daniel Rigden

Reader in post-genomic bioinformatics

University of Liverpool


Daniel Rigden is Senior Lecturer in post-Genomic Bioinformatics at the University of Liverpool.  His work in the field dates back to PhD student days in Edinburgh.  After a few years in crystallography at Edinburgh and Leeds he returned to bioinformatics during 5 years spent working in Brazil.  These days he has broad interests in protein sequence and structure bioinformatics exploring the evolution of protein function.  A particular interest is ab initio protein structure
modelling for which he has found novel applications.









Prof. Michael Gribskov

Dept. of Biological Science

Purdue University, USA


The sequence, structure and evolution of proteins are intimately intertwined. This is especially apparent for large protein families such as the protein kinases. Genomics and other high-throughput techniques have made a wealth of information describing proteins, their expression and their interactions available. We try to use this information to understand the function, regulation, and origin of protein families suchs as protein kinases, protein phosphatases, membrane transporters, and participants in the ubiquitin-mediated protein degradation cascade.

More broadly, we develop computational methods for finding patterns in sequences an structures that allow us to make inferences, of the kinds discussed above, about the relationships between sequence, structure and function. These methods include elements datamining, machine learning, modeling, and simulation in the context of biological data. My group is interested in applications to protein motifs, DNA signals (transcription factor binding sites) and modules, and RNA structures.

These studies drive our development of computational tools to find and define protein and nucleic acid sequence and structural patterns, the development of electronic data laboratories, and the development of approaches to interoperation of electronic tools and resources.

I am on the editorial board of Bioinformatics, the Journal of Computational Biology and Chemistry and the Journal of Molecular Microbiology & Biotechnology. I am also past president of the International Society for Computational Biology.







Prof. Geoff Barton FSB

Professor of Bioinformatics

College of Life Sciences

University of Dundee, UK



Geoff Barton did his first degree in Biochemistry at the University of Manchester. He then performed Ph.D. research supervised by Mike Sternberg in the Department of Crystallography, Birkbeck College, University of London before spending two years as an ICRF Fellow working with Chris Rawlings at the Imperial Cancer Research Fund Labs. in London. In 1989 he was awarded a Royal Society University Research Fellowship to set up his own group in the Lab of Molecular Biophysics, University of Oxford. From April 1995 until October 1997, Geoff was also Head of Genome Informatics at the Wellcome Trust Centre for Human Genetics.  From 1st October 1997-July 2001 Geoff was a Research and Development Team Leader at the EMBL European Bioinformatics Institute.  From 1st January 1998-July 2001 Geoff was also head of the European Macromolecular Structure Database at EBI which is now known as the Protein Data Bank in Europe (PDBe). Geoff has been Professor of Bioinformatics at the College of Life Sciences, University of Dundee since 30th March 2001.  His research has long focused on the analysis and prediction of protein structure from the amino acid sequence. In connection with this, his group have developed a range of computer programs and databases for protein sequence analysis (Jalview – www.jalview.org) protein structure prediction (JPred – www.compbio.dundee.ac.uk/jpred) and the prediction of protein-protein interactions (www.compbio.dundee.ac.uk/pips). Over the last few years he has turned attention to the analysis of novel small RNAs and gene expression by deep sequencing. Geoff has published over 100 refereed papers which have received an average of more than 100 citations/paper. See www.compbio.dundee.ac.uk for more information.





Dr Jim Procter

College of Life Sciences

University of Dundee, UK


Jim Procter is a senior post-doctoral researcher working in the Computational Biology group within the College of Life Sciences at the University of Dundee. He received a B.Sc. (hons.) in Chemistry from the University of York and an M.Sc. in Computer Science from the University of Leeds in the UK, before studying for a Ph.D. at the Research School of Chemistry at the Australian National University. His research is motivated by a long standing interest in the application of technology to enable scientific research and effectively communicate knowledge. He co-founded the VIZBI conference series (www.vizbi.org), which showcases the state of the art for biological data visualisation, and is the coordinator and principal developer of the Jalview (www.jalview.org) open source alignment visualization workbench, with support from the UK’s Biotechnology and Biological Sciences Research Council (www.bbsrc.ac.uk).





Dr. Toby Gibson
European Molecular Biology Laboratory
Heidelberg, Germany




PhD 1984, Cambridge University, UK. Postdoctoral research at the Laboratory of Molecular Biology, Cambridge, UK. Team Leader at EMBL since 1986.






Dr Andrei Pisliakov

Division of Physics and College of Life Sciences

University of Dundee





Dr David Martin

School of Learning and Teaching, College of Life Sciences

University of Dundee





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 terms. 

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 working to get programming, data analysis and bioinformatics integrated into the undergraduate courses at Dundee!


Do you have questions about Bioinformatics Minisymposium at the University of Dundee? Contact Geoff Barton

When & Where

University of Dundee
D'Arcy Thompson Lecture Theatre, Tower Building Nethergate, University of Dundee
DD1 4HN Dundee
United Kingdom

Friday, 5 September 2014 from 09:00 to 15:30 (BST)

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