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Group Members

 

Leader(s)

Dr Alessandro Pandini Dr Alessandro Pandini
Senior Lecturer in Computer Science
My research activity focuses on the development and application of computational methods to study protein dynamics and its role in protein-ligand binding, protein-protein interactions, and protein design. I obtained my PhD in Computational Chemistry at the University of Milan-Bicocca under the supervision of Prof. Laura Bonati. As part of her research group I contributed to the unveil the molecular mechanism of toxic response mediated by binding of dioxins to the Aryl hydrocarbon Receptor. In 2008 I was awarded a Marie Curie Inter European Fellowship to work at the MRC National Institute for Medical Research (NIMR) under the supervision of Dr. Willie R. Taylor and Dr. Jens Kleinjung. From 2011 to 2014 he was a BBSRC-funded postdoctoral research assistant in the group of Prof. Franca Fraternali at King’s College London working on methods to investigate allosteric regulation, and to analyse protein-protein interaction interfaces and networks. During my career I developed and applied novel approaches combining structural bioinformatics and molecular simulation to address challenging biological questions, especially in relation to protein function, allosteric regulation and drug design. I introduced novel points of view in the definition of the limits and potential of molecular docking on theoretical models and in the use of molecular dynamics for drug design and medicinal chemistry. In particular, I developed an innovative computational method to detect local functional motions and to describe allosteric transmission in protein structures. Most recently, in collaboration with Dr. Arianna Fornili (QMUL), I contributed to the development of a novel strategy for biasing the sampling of local states to drive the global conformational transitions in proteins. In collaboration with Dr. Shahid Khan (LBNL – Berkeley Lab) and Dr. Willie Taylor, I have contributed to explain the relationships between residue coevolution and molecular dynamics in two bacterial ring assemblies.

Full members

Professor David Gilbert Professor David Gilbert
Emeritus Honorary Professor
Professor David Gilbert is Leverhulme Emeritus Fellow, Emeritus Professor of Computing and member of the Computational Biology group in the Department of Computer Science. Previously he was Head of School of Information Systems, Computing and Mathematics, and first Dean of the College of Engineering, Design and Physical Sciences, leading its establishment in 2014-15. In his previous post he was Professor of Bioinformatics at the University of Glasgow where he set up and was Director of the Bioinformatics Research Centre. He holds a BSc in experimental Pyschology and a Masters in Education from the University of Bristol, and a Masters and PhD in Computing from Imperial College, London where his research was into modelling concurrent systems using computational logic. David was an EPSRC Research Fellow at the European Bioinformatics Institute, and a Leverhulme Research Fellow in the Department of Biochemistry and Molecular Biology, University College London when designed and developed the TOPS protein topology computational system. I no longer teach, but previously I was Module leader for Level 1 CS1005 Logic & Computation (BSc Computer Science; BSc Business Computing). Tutor for Level 1 group projects. Supervisor for Final Year BSc Computer Science projects. Supervisor for projects in MSc Data Science & Analytics. Giving guest lectures on Intracellular Signalling and Cancer (BB5514) - biosciences
Dr Lorraine Ayad Dr Lorraine Ayad
Lecturer - Computer Science
Lorraine Ayad is currently a Lecturer in the Department of Computer Science, starting in August 2020. She completed her PhD at King's College London in 2019 with a thesis titled Efficient sequence comparison via combining alignment and alignment-free techniques. Lorraine Ayad's current work lies in the creation of algorithms for Computational Molecular Biology. Specifically, this involves identifying and creating algorithms which can aid biological research and also find ways to improve existing algorithms through the reduction of time or space. Bioinformatics tools implemented by Lorraine Ayad: IsoXpressor - a tool to assess transcriptional activity within isochores. CNEFinder - a tool for the identification of conserved non-coding elements in genomes. SMART - a tool to identify supermaximal approximate repeats in a sequence. MARS - a heuristic tool for multiple circular sequence alignment given a set of circular (DNA or Protein) sequences. hCED - a heuristic tool for cyclic edit distance computation given a pair of circular sequences. 2021 - 2022 CS1701 - Group Project (Level 4) CS1702 - Introductory Programming (Level 4) CS1005 - Logic and Computation (Level 4) Membership I am an Associate Fellow of the Higher Education Academy.
Dr Sarath Dantu Dr Sarath Dantu
Lecturer - Computer Science
Associate Lecturer in Department of Computer Science
Miss Yasoda Jayaweera Miss Yasoda Jayaweera
Associate Lecturer (Education) Computer Science
Miss Leila Ghanbar Miss Leila Ghanbar
PhD Student
I am a PhD student working on modelling biological systems in the computer. The focus of my study is to construct a multi-level library of models which could be used individually or as a combination to describe a biological behaviour. I provide protocols to use these models, as well as the library. To build these models, I use Petri nets in the platform of Snoopy. I sue Spike to simulate my models from candl and andl files and use R and Python to analyse the data taken from the models. the focus of my models is mostly on communication and movement as well as division and death of the system. I have built models of quorum sensing and biofilm formation in detail and abstract and have applied the models to design the chemotaxis of Dictyostelium towards cAMPs. Building a library of models in different levels and in different complexity in order to describe and predict the behaviour of biological systems.