The Centre for Genome-Enabled Biology and Medicine (CGEBM) brings together researchers who use genomics approaches from across the University of Aberdeen and beyond.
The CGEBM management group comprise:
Dr. Elaina Collie-Duguid
Elaina Collie-Duguid manages the CGEBM.
Dr. Collie-Duguid established the Aberdeen microarray facility and has been running genomics core facilities since 2001, delivering a successful service to researchers.
Further, Dr. Collie-Duguid has research interests in the molecular and cellular mechanisms controlling tumorigenesis, survival of cancer patients and chemoresistance in solid tumours, with a particular focus on breast cancer. Biomarker discovery for prediction of clinical outcomes, including response to therapy; and novel drug target identification and drug development are key elements of her translational research programme.
Further, Dr. Collie-Duguid has research interests in the molecular and cellular mechanisms controlling tumorigenesis, survival of cancer patients and chemoresistance in solid tumours, with a particular focus on breast, colorectal (bowel) and lung cancers. Biomarker discovery for prediction of clinical outcomes, including response to therapy; and novel drug target identification and drug development are key elements of her translational research programme.
Prof. Zosia Miedzybrodzka and Prof. James Prosser OBE
Jim Prosser is Professor of Environmental Microbiology in the School of Biological Sciences. His research aims to increase our understanding of the diversity and ecosystem function of microorganisms in natural environments and he has particular interests in the ecology of soil ammonia oxidising bacteria and archaea. Prof Prosser was awarded an OBE in 2012 for services to environmental science and is a Fellow of the Royal Society, a Fellow of the Royal Society of Edinburgh, a Fellow of the Society of Biology and a Fellow of the American Academy of Microbiology.
Prof. Miedzybrodzka is a professor in Medical Genetics and an honorary consultant clinical geneticist and leads NHS Genetics laboratory and clinical services for the North of Scotland. Her research uses the laboratory and clinical skills of the genetics team to research in the field of genetic medicine. The complete integration of the medical genetics research group with the NHS diagnostic labs and clinics creates a superb environment for fostering research that offers collaborators the state of the art equipment, scientific and clinical expertise within the genetics team, and the long established genetics DNA collections. She leads work on the aetiology of the common foot malformation congenital talipes equinovarus, the role of the transcription regulator gene EIF4E in autism, translational projects in molecular pathology of gastro-oesophageal cancer, investigation of the potential of Scottish neonatal bloodspots and improving clinical care for patients with, and at risk of Huntington's disease. As a grantholder in the MRC funded Genepool collaboration, Zosia established the NGS bioinformatics service in Aberdeen, and brings this facility with the equipment and clinical resources of the North of Scotland NHS to CGEBM.
Dr. Sophie Shaw
Dr Shaw joined CGEBM as a bioinformatician in May 2015 from the University of Exeter where she completed her PhD in Biological Sciences investigating the phenotypic impact of allele specific expression. Following her PhD, Dr Shaw undertook a post-doctoral position researching transcriptional responses during environmental inter-species interactions. She brings a background in ecological and environmental genomics (eDNA), with core expertise in RNA-seq and functional annotation, and whole genome sequencing and assembly, along with skills in fungal and plant molecular biology.
Dr Shaw has experience in the delivery of bioinformatics training modules in varied genomics analyses, including UNIX, short read genomics, assembly methods, RAD sequencing, transcriptomics, and shotgun whole genome and amplicon based metagenomics. Dr Shaw brings these skills to the training portfolio currently being delivered to the University of Aberdeen research community by CGEBM.
Dr. Antonio Ribeiro
Antonio Ribeiro joined CGEBM as a bioinformatician in August 2015. Antonio brings expertise in DNA sequence alignment and SNP calling obtained during his PhD within the Bioinformatics group at The James Hutton Institute (JHI), Dundee. He has 7 years of experience in processing and analysis of NGS data using third-party open source tools and custom scripts, developed or optimised by him, primarily using Bash scripting, Java and Perl. Antonio has an MSc in Computational and Systems Biology and specialisations in Computer Networks and Information Systems Development.
Ellen Smith joined the CGEBM as a bioinformatician in December 2019. She has recently graduated with an MSc in Bioinformatics from the University of Edinburgh and holds an honours degree in Genetics from the University of Glasgow.
Dr. Jin Pu
Dr Jin Pu is a research fellow in CGEBM. She qualified as an MD and a clinical haematologist in Chinese PLA General Hospital and Medical School of Chinese PLA, Beijng, China before she started her PhD at the University of Aberdeen. Following her PhD, she undertook a post-doctoral and independent research fellow position and led projects investigating cell polarity, tissue regeneration, tumorigenesis and metastasis. She has published more than 20 high-impact scientific research articles and was a key contributor to a Nature paper.
In CGEBM, Dr Pu supports a wide range of genomics research projects and delivers next generation sequencing (NGS) services supported by CGEBM, including microbiome analysis, variant detection, RNA-seq, whole exome and whole genome sequencing, metagenomics and ChIP-seq, to our internal and external clients. Dr Jin Pu manages and delivers the Sanger sequencing and genetic analysis facility provided for RESAS research at the Rowett institute.
Dr. Zeynab Heidari
Dr Heidari joined the CGEBM laboratory team in May 2017. She graduated in August 2015 from the University of Aberdeen with a PhD degree in Molecular Biology. She also holds a Bachelor degree in Genetics with honours.
Her PhD work has lead her to focus on particular areas of interest including gene expression, RNA and DNA isolation, promoter analysis, ELISA, primary cell culture, DNA transfection, live cell imaging, and microarray.
Dr. Ewan Campbell
Dr Campbell moved from the School of Biological Sciences to CGEBM in 2018 after working as a senior research fellow for over 5 years at the University. His main expertise lies in the molecular biology of arthropod pests of agricultural and economic importance, most significantly, the major pathogen of Honey bees, Varroa destructor mites. He is interested in both fundamental and translational research and has over 10 years of experience using cutting edge molecular tools to solve real world problems; including the use of NGS, RNAi gene knockdown, complex library preparation and proteomics. Ewan's work has led to patent filed applications with industrial partners and novel molecular toolboxes for gene expression assays and RNAi. He has a keen interest in developing novel molecular techniques and collaborating with researchers across the University to deliver NGS solutions to complex biological questions.
Biostatistics - Dr. Alex Douglas
Alex Douglas works within the School of Biological Sciences, where he does statistics and bioinformatics. Alex provides expert biostatistics support for genomics studies.
His interests include: statistical approaches for QTL mapping in model organisms using GWAS; QTL mapping in non-model organisms using RAD-sequencing and genome linkage mapping; downstream statistical analysis of RNA-seq, ChIP-seq and metabolomic data; integration of 'omics' data using network analysis; statistical modelling of qPCR data and modelling differential gene expression using microarray platforms.
Former CGEBM Team Members
Prof. David Salt - Co-director
Dr. Susan Fairley - Bioinformatician
Dr. Eduardo De Paiva Alves - Bioinformatician
Matthew Gemmell - Bioinformatician
Dr. Marius Wenzel - Bioinformatician
Brennan Martin - Research Technician
Diane Stewart - Research Technician
Dr. Emma Sproston - Research Technician
Dr. Anthony Redmond - PhD Student
"Exploiting Shark Sequence Data to Understand Vertebrate Evolution" with Dr. Helen Dooley
Dr. Nicola Morrice - PhD Student
"Genome-Wide DNA Binding Studies to Interrogate Retinoic Acid Receptor-Signalling in Models of Obesity and Type 2 Diabetes" with Dr. Nimesh Mody
Dr. Eva Weber - PhD Student
"Single-Cell Genomics and Transcriptomics to Determine the Ecosystem Functions of Undiscovered Soil Microbes" with Dr. Cecile Gubry-Rangin
Dr. Davina Derous - PhD Student
"Transcriptomic Analysis of Graded Caloric Restriction in the Mouse" with Dr. Alex Douglas
Stephanie Andraos - MSc Project Student
Victoria Gray - MSc Project Student