The Next Generation of Genomics Symposium - May 31 and June 1 We are proud to host the Next Generation of Genomics Symposium so that the young researchers in the field of genomics can present their amazing research. Register for a presentation If you are an MSc, PhD student, or postdoc and would like to present your scientific research to the others, please fill out the form by May 6. The Next Generation of Genomics registration We are particularly pleased that Dr. Amanda Warr from the Roslin Institute, Dr. Alex Twyford from the Institute of Evolutionary Biology, Dr. Joshua Quick from the University of Birmingham and Dr. Benjamin Werner from the CRUK Barts Centre will be keynote speakers. This will be an online event that will be open to a wider audience. Join us and stay in touch with the Genomics at Edinburgh community. The event will take place on Tuesday, May 31 between 1:00pm and 4:00pm and on Wednesday, June 1 from 9:30am to 12:30pm. Speakers: Dr. Amanda Warr - BBSRC Discovery Fellow at The Roslin Institute, Long reads and small genomes: No assembly required? Amanda began working with Nanopore sequencing during her PhD and now spends a similar amount of time in the lab using the MinION and PromethION sequencing platforms. Amanda has also founded the Scottish Nanopore User Group ION _BRU, which provides networking and educational opportunities for other Nanopore users in Scotland. Projects and collaborations she has been involved in include work on antimicrobial resistance, viral epidemiology, diagnostics and genome assembly in mammals, birds, viruses and microbiomes of various species. Her recent projects have focused on sequencing the microbiome, sequencing cell lines of Marek's Disease Virus, and tracking the spread of African Swine Fever Virus and Porcine Reproductive and Respiratory Syndrome Virus in the Philippines, all using long read sequencing. This year, Amanda will begin a Discovery Fellowship focused on the relationship between the gut microbiome and the innate immune response to gut viruses in swine. Dr Alex Twyford - Lecturer in Botany at the University of Edinburgh and a Research Associate at the Royal Botanic Garden Edinburgh, Genomic fruits from the green tree of life Alex is an evolutionary biologist interested in speciation and adaptation in flowering plants. He received his PhD in 2012 from the Royal Botanic Garden Edinburgh & University of Edinburgh in collaboration with Catherine Kidner and Richard Ennos. He then moved to Syracuse, Upstate New York to conduct postdoctoral research with Jannice Friedman. In August 2014, he returned to the University of Edinburgh as a NERC Independent Research Fellow. His research interests include the evolution of postglacial diversity in Euphrasia, the maintenance of chromosome inversions in Mimulus, and the origins of diversity in tropical begonias. Dr Joshua Quick - UKRI Future Leaders Fellow at the University of Birmingham, Single-cell sequencing techniques for metagenomics and antibiotic resisitance prediction Joshua is developing novel methods for rapid prediction of antimicrobial resistance (AMR). He is a molecular biologist who specialises in next-generation sequencing and has worked on both bacterial genomics and viral surveillance of disease outbreaks. He travelled to Guinea in West Africa and set up the first mobile laboratory to conduct viral surveillance during the West African Ebola virus epidemic. He also developed an amplicon-based sequencing method that has been used for Zika, yellow fever, dengue, chikungunya, Ebola virus, and SARS-CoV-2. He is currently focusing on single-cell bacterial technology as an approach to combat the growing threat of resistance by rapidly identifying resistance genes in clinical samples. Dr Benjamin Werner - UKRI Future Leaders Fellow at the CRUK Barts Centre, Title TBC Benjamin's group combines mathematics, computer simulations and genomic information to study evolutionary processes. They aim to understand how a tumour's evolutionary history is reflected in its genome, how evolution can be quantified in individual tumours, and how this information predicts future evolution. They are also interested in non-somatic evolutionary processes, particularly co-evolutionary processes of interacting species and the resulting stochastic dynamics. His lab has been involved in coevolutionary experiments in predator-prey systems. This involves understanding how diversity arises and is maintained and how to interpret complicated population genetic data in the context of coevolutionary processes. Presentations from early career researchers The Next generation of Genomics Symposium agenda Tuesday, May 31, 2022 13.00 – 13.10 Welcome and Introduction Mick Watson, Director Genomics at Edinburgh 13.10 - 13.40 Genomic fruits from the green tree of life Alex Twyford, The institute of Evolutionary Biology 13.40 – 13.45 Revealing functional and genomic differences between two species of the megadiverse genus Begonia Katie Emelianova, The Royal Botanic Garden Edinburgh 13.45 – 13.50 Sequencing and assembling a monster plant genome Lucia Campos-Dominguez, Institute of Evolutionary Biology 13.50 – 13.55 De novo genome sequencing and assembly of an industrially-relevant microalga Martina Dajak, Institute of Quantitative Biology, Biochemistry and Biotechnology 13.55 – 14.00 Genomic and phenotypic characterization of finger millet Jon Bancic, The Roslin Institute 14.00 -14.05 Genomic prediction into future crop growing environments Daniel Tolhurst, The Roslin Institute 14.05 – 14.10 Biofoundry DNA assembly validation using long reads Peter Vegh, Edinburgh Genome Foundry 14.10 – 14.25 Break 14.25 -14.55 The evolutionary dynamics of chromosomal and extra-chromosomal DNA in human cancers Benjamin Werner, CRUK Barts Centre 14.55 – 15.05 Imputed transcriptome risk scores reveal gene expression-based resemblance among human couples for height Vasilios Raptis, Institute of Genetics and Cancer 15.05 – 15.10 Marked regional glial heterogeneity in the human white matter of the central nervous system Luise Seeker, Centre for Regenerative Medicine 15.10 – 15.15 Analysis of genomic, mitochondrial and bacterial DNA using shotgun metagenomics sequencing of circulating blood cell-free DNA in Inflammatory Bowel Disease (IBD) Shaun Chuah, Centre for Inflammation Research 15.15 – 15.20 Elucidating long range connectivity of the entorhinal cortex through Multiplexed Analysis of Projections by Sequencing Sara Gómez Arnaiz, Centre for Discovery Brain Sciences 15.20 -15.30 Fast and Efficient Genotype Compression for Genome-Wide Association Studies Mulya Agung, MRC University Unit for Human Genetics 15.30 – 15.35 Towards ultra-rapid microbial cf-DNA Nanopore Sequencing for detection of sepsis-causing pathogens Ana Martinez-Lopez, Heriot Watt University - UoE Infection Medicine 15.35 – 15.45 Single-cell transcriptomics defines pathogenic macrophages in murine liver fibrosis Eleni Papachristoforou, Centre of Inflammation Research 15.45 – 15.50 Harnessing genome characterisation to uncover disease mechanisms Silvia Shen, Institute of Evolutionary Biology, Institute for Cancer and Genetics 15.50– 15.55 A Nextflow pipeline for reproducible transcriptome-driven codon usage analysis Anima Sutradhar, IQB3 - Centre for Systems and Synthetic Biology 15.55 – 16.00 Closing remarks Mick Watson, Director Genomics at Edinburgh Wednesday, June 1, 2022 09.30 – 09.35 Welcome Mick Watson, Director Genomics at Edinburgh 09.35 – 10:05 Single-cell sequencing techniques for metagenomics and antibiotic resistance prediction Joshua Quick, University of Birmingham 10.05 – 10.10 Identifying germline progenitors through single cell multiomics Sara Gonzalez Brito, Centre for Regenerative Medicine 10.10 – 10.15 OTX2 modulates chromatin accessibility at somatic enhancers Elisa Barbieri, Institute for Stem Cell Research 10.15 – 10.20 Associations of major psychiatric disorders and cross-disorder polygenic risk scores with inflammatory blood markers Amelia Edmondson-Stait, Psychiatry Department 10.20 – 10.25 Comparative population genomics of red squirrels in Scotland: understanding diversity in a key stronghold Melissa Marr, The Royal (Dick) School of Veterinary Studies 10.25 – 10.35 Genomic consequences of conservation management strategies in scimitar-horned oryx Emily Humble, The Royal (Dick) School of Veterinary Studies 10.35 – 10.40 Environmental genomics as a new tool to trace the origin of falsified antimicrobials Carla Perez Mon, The Royal (Dick) School of Veterinary Studies 10.40 – 10.50 Population genetics of an elusive marine predator, the Atlantic white-sided dolphin (Lagenorhynchus acutus), across the eastern North Atlantic Marc-Alexander Gose, The Royal (Dick) School of Veterinary Studies 10.50 – 10.55 Genome structural variation landscape in Nile Tilapia Zexin Jiao, The Roslin Institute 10.55 – 11.10 Break 11.10 – 11.40 Long reads and small genomes: No assembly required? Amanda Warr, The Roslin Institute 11.40 – 11.50 DoGsTAils: Developing nanopore-based diagnostic approaches for the effective antimicrobial stewardship of canine infections Natalie Ring, The Roslin Institute 11.50 – 11.55 Third-generation sequencing to create a complete genome of Trypanosoma brucei Xin Lan, Zhejiang University-University of Edinburgh Institute (ZJE) 11.55 – 12.00 Characterising a neo-sex chromosome in a fly with single-sex broods Robert Baird, Institute of Evolutionary Biology 12.00 – 12.05 Understanding the resilience of wild birds to climate change Zhou Wu, The Roslin institute 12.05 – 12.10 Investigating the genetic architecture of complex traits in Soay sheep Caelinn James, Institute of Evolutionary Biology 12.10 – 12.15 Building genomic resources for dairy development in Rwanda Oluyinka Opoola, Centre for Tropical Livestock Genetics and Health (CTLGH) 12.15 – 12.20 Exploring the microbiota of livestock using metagenomics Laura Glendinning, The Roslin Institute 12.20 – 12.25 Investigating the impact of database choice on the accuracy of metagenomic read classification for the rumen microbiome Rebecca Smith, The Roslin Institute 12.25 – 12.30 Closing remarks Mick Watson, Director Genomics at Edinburgh May 31 2022 14.00 - Jun 01 2022 13.30 The Next Generation of Genomics Symposium - May 31 and June 1 We are pleased to announce that we will be holding our first event for young genome researchers on May 31 and June 1, 2022. Register here
The Next Generation of Genomics Symposium - May 31 and June 1 We are proud to host the Next Generation of Genomics Symposium so that the young researchers in the field of genomics can present their amazing research. Register for a presentation If you are an MSc, PhD student, or postdoc and would like to present your scientific research to the others, please fill out the form by May 6. The Next Generation of Genomics registration We are particularly pleased that Dr. Amanda Warr from the Roslin Institute, Dr. Alex Twyford from the Institute of Evolutionary Biology, Dr. Joshua Quick from the University of Birmingham and Dr. Benjamin Werner from the CRUK Barts Centre will be keynote speakers. This will be an online event that will be open to a wider audience. Join us and stay in touch with the Genomics at Edinburgh community. The event will take place on Tuesday, May 31 between 1:00pm and 4:00pm and on Wednesday, June 1 from 9:30am to 12:30pm. Speakers: Dr. Amanda Warr - BBSRC Discovery Fellow at The Roslin Institute, Long reads and small genomes: No assembly required? Amanda began working with Nanopore sequencing during her PhD and now spends a similar amount of time in the lab using the MinION and PromethION sequencing platforms. Amanda has also founded the Scottish Nanopore User Group ION _BRU, which provides networking and educational opportunities for other Nanopore users in Scotland. Projects and collaborations she has been involved in include work on antimicrobial resistance, viral epidemiology, diagnostics and genome assembly in mammals, birds, viruses and microbiomes of various species. Her recent projects have focused on sequencing the microbiome, sequencing cell lines of Marek's Disease Virus, and tracking the spread of African Swine Fever Virus and Porcine Reproductive and Respiratory Syndrome Virus in the Philippines, all using long read sequencing. This year, Amanda will begin a Discovery Fellowship focused on the relationship between the gut microbiome and the innate immune response to gut viruses in swine. Dr Alex Twyford - Lecturer in Botany at the University of Edinburgh and a Research Associate at the Royal Botanic Garden Edinburgh, Genomic fruits from the green tree of life Alex is an evolutionary biologist interested in speciation and adaptation in flowering plants. He received his PhD in 2012 from the Royal Botanic Garden Edinburgh & University of Edinburgh in collaboration with Catherine Kidner and Richard Ennos. He then moved to Syracuse, Upstate New York to conduct postdoctoral research with Jannice Friedman. In August 2014, he returned to the University of Edinburgh as a NERC Independent Research Fellow. His research interests include the evolution of postglacial diversity in Euphrasia, the maintenance of chromosome inversions in Mimulus, and the origins of diversity in tropical begonias. Dr Joshua Quick - UKRI Future Leaders Fellow at the University of Birmingham, Single-cell sequencing techniques for metagenomics and antibiotic resisitance prediction Joshua is developing novel methods for rapid prediction of antimicrobial resistance (AMR). He is a molecular biologist who specialises in next-generation sequencing and has worked on both bacterial genomics and viral surveillance of disease outbreaks. He travelled to Guinea in West Africa and set up the first mobile laboratory to conduct viral surveillance during the West African Ebola virus epidemic. He also developed an amplicon-based sequencing method that has been used for Zika, yellow fever, dengue, chikungunya, Ebola virus, and SARS-CoV-2. He is currently focusing on single-cell bacterial technology as an approach to combat the growing threat of resistance by rapidly identifying resistance genes in clinical samples. Dr Benjamin Werner - UKRI Future Leaders Fellow at the CRUK Barts Centre, Title TBC Benjamin's group combines mathematics, computer simulations and genomic information to study evolutionary processes. They aim to understand how a tumour's evolutionary history is reflected in its genome, how evolution can be quantified in individual tumours, and how this information predicts future evolution. They are also interested in non-somatic evolutionary processes, particularly co-evolutionary processes of interacting species and the resulting stochastic dynamics. His lab has been involved in coevolutionary experiments in predator-prey systems. This involves understanding how diversity arises and is maintained and how to interpret complicated population genetic data in the context of coevolutionary processes. Presentations from early career researchers The Next generation of Genomics Symposium agenda Tuesday, May 31, 2022 13.00 – 13.10 Welcome and Introduction Mick Watson, Director Genomics at Edinburgh 13.10 - 13.40 Genomic fruits from the green tree of life Alex Twyford, The institute of Evolutionary Biology 13.40 – 13.45 Revealing functional and genomic differences between two species of the megadiverse genus Begonia Katie Emelianova, The Royal Botanic Garden Edinburgh 13.45 – 13.50 Sequencing and assembling a monster plant genome Lucia Campos-Dominguez, Institute of Evolutionary Biology 13.50 – 13.55 De novo genome sequencing and assembly of an industrially-relevant microalga Martina Dajak, Institute of Quantitative Biology, Biochemistry and Biotechnology 13.55 – 14.00 Genomic and phenotypic characterization of finger millet Jon Bancic, The Roslin Institute 14.00 -14.05 Genomic prediction into future crop growing environments Daniel Tolhurst, The Roslin Institute 14.05 – 14.10 Biofoundry DNA assembly validation using long reads Peter Vegh, Edinburgh Genome Foundry 14.10 – 14.25 Break 14.25 -14.55 The evolutionary dynamics of chromosomal and extra-chromosomal DNA in human cancers Benjamin Werner, CRUK Barts Centre 14.55 – 15.05 Imputed transcriptome risk scores reveal gene expression-based resemblance among human couples for height Vasilios Raptis, Institute of Genetics and Cancer 15.05 – 15.10 Marked regional glial heterogeneity in the human white matter of the central nervous system Luise Seeker, Centre for Regenerative Medicine 15.10 – 15.15 Analysis of genomic, mitochondrial and bacterial DNA using shotgun metagenomics sequencing of circulating blood cell-free DNA in Inflammatory Bowel Disease (IBD) Shaun Chuah, Centre for Inflammation Research 15.15 – 15.20 Elucidating long range connectivity of the entorhinal cortex through Multiplexed Analysis of Projections by Sequencing Sara Gómez Arnaiz, Centre for Discovery Brain Sciences 15.20 -15.30 Fast and Efficient Genotype Compression for Genome-Wide Association Studies Mulya Agung, MRC University Unit for Human Genetics 15.30 – 15.35 Towards ultra-rapid microbial cf-DNA Nanopore Sequencing for detection of sepsis-causing pathogens Ana Martinez-Lopez, Heriot Watt University - UoE Infection Medicine 15.35 – 15.45 Single-cell transcriptomics defines pathogenic macrophages in murine liver fibrosis Eleni Papachristoforou, Centre of Inflammation Research 15.45 – 15.50 Harnessing genome characterisation to uncover disease mechanisms Silvia Shen, Institute of Evolutionary Biology, Institute for Cancer and Genetics 15.50– 15.55 A Nextflow pipeline for reproducible transcriptome-driven codon usage analysis Anima Sutradhar, IQB3 - Centre for Systems and Synthetic Biology 15.55 – 16.00 Closing remarks Mick Watson, Director Genomics at Edinburgh Wednesday, June 1, 2022 09.30 – 09.35 Welcome Mick Watson, Director Genomics at Edinburgh 09.35 – 10:05 Single-cell sequencing techniques for metagenomics and antibiotic resistance prediction Joshua Quick, University of Birmingham 10.05 – 10.10 Identifying germline progenitors through single cell multiomics Sara Gonzalez Brito, Centre for Regenerative Medicine 10.10 – 10.15 OTX2 modulates chromatin accessibility at somatic enhancers Elisa Barbieri, Institute for Stem Cell Research 10.15 – 10.20 Associations of major psychiatric disorders and cross-disorder polygenic risk scores with inflammatory blood markers Amelia Edmondson-Stait, Psychiatry Department 10.20 – 10.25 Comparative population genomics of red squirrels in Scotland: understanding diversity in a key stronghold Melissa Marr, The Royal (Dick) School of Veterinary Studies 10.25 – 10.35 Genomic consequences of conservation management strategies in scimitar-horned oryx Emily Humble, The Royal (Dick) School of Veterinary Studies 10.35 – 10.40 Environmental genomics as a new tool to trace the origin of falsified antimicrobials Carla Perez Mon, The Royal (Dick) School of Veterinary Studies 10.40 – 10.50 Population genetics of an elusive marine predator, the Atlantic white-sided dolphin (Lagenorhynchus acutus), across the eastern North Atlantic Marc-Alexander Gose, The Royal (Dick) School of Veterinary Studies 10.50 – 10.55 Genome structural variation landscape in Nile Tilapia Zexin Jiao, The Roslin Institute 10.55 – 11.10 Break 11.10 – 11.40 Long reads and small genomes: No assembly required? Amanda Warr, The Roslin Institute 11.40 – 11.50 DoGsTAils: Developing nanopore-based diagnostic approaches for the effective antimicrobial stewardship of canine infections Natalie Ring, The Roslin Institute 11.50 – 11.55 Third-generation sequencing to create a complete genome of Trypanosoma brucei Xin Lan, Zhejiang University-University of Edinburgh Institute (ZJE) 11.55 – 12.00 Characterising a neo-sex chromosome in a fly with single-sex broods Robert Baird, Institute of Evolutionary Biology 12.00 – 12.05 Understanding the resilience of wild birds to climate change Zhou Wu, The Roslin institute 12.05 – 12.10 Investigating the genetic architecture of complex traits in Soay sheep Caelinn James, Institute of Evolutionary Biology 12.10 – 12.15 Building genomic resources for dairy development in Rwanda Oluyinka Opoola, Centre for Tropical Livestock Genetics and Health (CTLGH) 12.15 – 12.20 Exploring the microbiota of livestock using metagenomics Laura Glendinning, The Roslin Institute 12.20 – 12.25 Investigating the impact of database choice on the accuracy of metagenomic read classification for the rumen microbiome Rebecca Smith, The Roslin Institute 12.25 – 12.30 Closing remarks Mick Watson, Director Genomics at Edinburgh May 31 2022 14.00 - Jun 01 2022 13.30 The Next Generation of Genomics Symposium - May 31 and June 1 We are pleased to announce that we will be holding our first event for young genome researchers on May 31 and June 1, 2022. Register here
May 31 2022 14.00 - Jun 01 2022 13.30 The Next Generation of Genomics Symposium - May 31 and June 1 We are pleased to announce that we will be holding our first event for young genome researchers on May 31 and June 1, 2022.
