Prof Julian Gough - Principal Investigator
I did my undergraduate degree in Physics and Mathematics (joint hon.s) then moved on to a PhD in theoretical and computational molecular biology gaining a foundation in protein structure. Combining protein structure with sequences coming out of genome projects I worked on protein domain analysis and evolution. I continue to work by applying bioinformatics tools to answer biological questions, sometimes developing new methods to achieve this goal, with awareness of evolution always a theme. My interests have now expanded from protein domains in cellular organisms in several dimensions, but based on the same principles to include: transcription, regulation and cell fate; non-coding sequence; intrinsically disordered proteins; function and phenotype prediction; viral evolution; mutation analysis; drug repurposing; continuous monitoring devices; directed evolution.
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Dr Hai Fang - Post Doctoral Researcher
I have a great interest in genome-scale data mining: I developed the database of domain-centric ontologies to aid in functional genomics and phenotype prediction; applied network techniques to identify the possible connections among drugs, diseases and phenotypes; used the tree of life to study network evolution. I have also published several papers about transcriptome data mining which is unique in topology-preserving selection and clustering.
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Matt Oates - Post Doctoral Researcher
My PhD focusses on finding remote homology within cell signalling pathways across the Eukaryotic tree of life. Specifically investigating how function of signalling pathways may be preserved through disordered protein interactions and PPI network rewiring, facilitating modular domain rearrangement and repurposing.
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Dr Dimitrios V. Vavoulis - Post Doctoral Researcher
I am a trained biologist-turned-computational-scientist. I hold a BSc in Biology, an MSc with Distinction in Environmental Biology, an MSc with Distinction in Evolutionary and Adaptive Systems and a PhD in Neuroscience. After I finished my PhD, I worked for 4 years as a postdoc in the Computational Biology and Bioimaging Group at the University of Warwick and then I moved to the Computational Genomics Group at the University of Bristol. Before I joined Julian Gough's group, my work focused on developing data-driven, biologically plausible computational models of neurons and neural networks. At my present post, I develop statistical methods for clustering high-dimensional, high-volume gene expression data. The driving force underlying my work has always been a keen interest in applying computational methodologies for modelling and data analysis in the Life Sciences.
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Jon Stahlhacke - Research Assistant
Assisting on the development of core resources such as SUPERFAMILY, dcGO and D2P2.
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Ben Smithers - PhD Candidate
Having recently started my PhD, I am new to the field of Computational Genomics. My interested in driven by the 'Big Data' problems in Biology, notably in the analysis of Next Generation Sequences using distributed and high-performance computing. Currently, my focus is on performing protein homology in the context of ever-increasing genomic data.
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Jan Zaucha - PhD Candidate
A recent PhD student.
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Natalie Thurlby - PhD Candidate
A recent PhD student.
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Group Alumni:


Chris Musselle - Alumnus
I completed my PhD in Computer Science at the University of Bristol in 2012 looking at the online monitoring and analysis of multiple data streams. The work successfully implemented a change point detection algorithm using iterative dimensionality reduction techniques. My current research project is in the field of Population Genetics, looking at how next generation sequencing technologies can be harnessed to analyse genetic variability at the population level. I am currently developing a series of computational tools to aid in the pipeline of data analysis and manipulation from the raw sequence reads to variant discovery.
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Adam Sardar - Alumnus
I study protein-domain evolution. The core focus of my PhD is on the consistency of the concept of a tree of life with the evolutionary history of sequenced cellular genomes. I am also interestd in the transcribed proteome and in the genetic causes of yeast multicellularity. My passion for computational biology is the problem solving aspect; there are so many questions that we have are just starting to be able to answer thanks to the explosion of sequence data and the development of intelligent algorithms with which to study it.
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Dr Hashem Shihab - Alumnus
Hashem completed his PhD using hidden Markov models to predict the functional consequences of genetic variation (single base-pair mutations as well as gross insertions and deletions) and investigate the molecular mechanisms of human disease/cancer. Hashem developed the Functional Analysis through Hidden Markov Models (FATHMM) software and now works as a Research Associate within the MRC Integrative Epidemiology Unit at the University of Bristol.
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Dr Owen Rackham - Alumnus
In 2013 Owen graduated with a PhD in Complexity Sciences looking at understanding the complexity of the cell at various levels. His work looked at synaptic plasticity in the brain, protein evolution and finally cell reprogramming. His main interests include the application of mathematics and complex systems thinking to molecular biology and bioinformatics. In particular he focused on the application of machine learning and graph theory in the field of regenerative medicine through next generation sequence analysis. The current era of biology is having to deal with vast quantities of data and Owen felt that it's the role of the computer scientist and bioinformatician to work in unison with biologists to get the most out of this data in an efficient and meaningful way. Owen left the group in September 2013 after a year's postdoctoral position, to work at the MRC Clinical Sciences Centre: Integrative Biology department.
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Dr Ralph Pethica - Alumnus
Ralph did his PhD in the group using computational methods to investigate the ways in which new families of protein domains evolve. Ralph also developed TreeVector - Integrated Phylogenetic Trees Using SVG. Ralph completed in 2011 and after graduating Ralph moved to Google and worked as a product manager.
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Dr David Morais - Alumnus
David joined the group in 2010 to work on the SUPERFAMILY resource. He made significant contributions to the underlying infrastructure, migrating many services to the cloud, whilst also working on a forthcoming homology benchmark paper. He left in 2011 to move to Montreal with his wife and daughter (pictured) and now works at Reseau Quebecois de Calcul de Haute Performance (Quebec Network of High Performance Computing).
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Dr Martin Madera - Alumnus
Martin first started work in bioinformatics working as a summer student at the MRC Laboratory of Molecular biology in Cambridge doing the work with Julian on comparing hidden Markov model methods that was later published during his PhD which he went on to do in the same lab. After graduating Martin did a post-doc at UCSC with Kevin Karplus before joining the group here in Bristol where he published PRC the profile comparer for hidden Markov models.
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