• Event
  • Science

Genome 10K and Genome Science Conference

Start date:

Tuesday 29 August

End date:

Friday 1 September 2017


Norwich Research Park


Federica Di Palma, Amanda Chong, Wilfried Haerty, Emily Angiolini, Dawn Turnbull

Registration deadline:

Early Bird Registration deadline 31 May 2017. Registration closes 31 July 2017.


Standard Early Bird £250; Standard Late £330; Student Early Bird £150; Student Late £200; Day Delegate Early Bird £70 (per day); Day Delegate Late £100 (per day)

Genome 10K Logo
Genome Science logo

We are delighted to host both the Genome 10K 2017 conference and the Genome Science 2017 conference in parallel here in Norwich.

About the event.

For the first time, Norwich, UK will host two distinguished conferences - Genome 10K 2017; the biannual conference exploring critical topics essential for understanding how complex animal life evolved through changes in DNA and how we can use this to help save dying species; and Genome Science 2017 - an annual meeting exploring advances in genomics technology and computational methodologies as well as innovation in its application.

The growing Genome 10K Community of Scientists (G10KCOS), made up of leading scientists representing major zoos, museums, research centers, and universities around the world, is dedicated to coordinating efforts in a major tissue specimen collection that will lay the groundwork for a large-scale sequencing and analysis project.

The mission of the Genome 10K COS is to assemble a genomic zoo of some 10,000 vertebrate species to help to understand how complex animal life evolved through changes in DNA and use this knowledge to become better stewards of the planet.

The Genome 10K Project was founded by David Haussler, Oliver Ryder, and Stephen O'Brien, who launched the project in April 2009 at a three-day meeting at the University of California, Santa Cruz.

The Genome Science meeting started out life in 2011 as the UK Next Generation Sequencing meeting, hosted by the DeepSeq facility at the University of Nottingham. Since then it has evolved and grown to be a successful event attracting in the region of 250 delegates each year. This meeting represents a fantastic opportunity for both academia and industry to engage, sharing advances, innovations and challenges in working with -omics data.

In addition to a programme packed full of interesting sessions, we have some fantastic invited speakers who will epitomise the prestige and strength of these conferences. There will also be plenty of networking opportunities, such as the social mixer and conference dinner, as well as the poster sessions. We believe training is crucial to the success of all research projects, including the G10K project and its long-term attainment of objectives. Alongside training for early career researchers we will also include parallel Special Interest Group sessions, which will monitor progress in the sector and set new milestones of the G10K project.


Programme Key

Open/closeG10KGenome ScienceShared SessionsTrainingBreaks

Day 1 Tuesday 29 August

9:30 - 12:30 Science Communication Workshop
Watson & Crick

Welcome: Federica Di Palma (Earlham Institute), Tom McCabe (Norfolk County Council), Sally Ann Forsyth (Norwich Research Park)
Main Auditorium

Plenary 1

Main Auditorium



Adam Phillipy
Towards the gapless assembly of complete vertebrate genomes

Kathy Belov
Saving the Tasmanian devil from extinction
15:00 - 15:30Coffee Break

Session 1a

Main Auditorium
Vertebrate Genomics
Chair: Federica Di Palma

Session 1b

Watson & Crick
Plant Genomics
Chair: Laura-Jayne Gardiner

Session 1c

Franklin & Wilkins
Microbial Genomics
Chair: Kate Baker

15:30 Alex Cagan
Comparative genomics of animal domestication
Ksenia Krasileva
Evolution of plant immune receptors
John Lees
Scalable pan-genome-wide association studies in bacteria
16:00 Gaik Tamazian
(01) Comparative whole-genome study of eleven Felidae species from six lineages
Andrea Harper
Using Associative Transcriptomics to predict tolerance to ash dieback disease in European ash trees
Gemma Langridge
Contaminant or infective agent? Re-classifying the staphylococci for modern medicine
16:15 Rebecca Jennings
(02) A Cross-Species Bioinformatics and FISH approach to physical mapping of Mammalian Genomes
16:30 Will Nash
(03) Expansion of gene families and signatures of selection in the Australian marsupials
Steve Kelly
(O5) The evolution of photosynthetic efficiency
Susanna Salter
(O7) A novel species of human nasopharyngeal bacteria, distantly related to the avian pathogen Ornithobacterium rhinotracheale
16:45 Neil Gemmell
(04) The tuatara genome project— Unlocking the genome of a living fossil
Bernardo Clavijo
(O6) Designing multi-genome graphs for crop genomics and genetics: a wheat-centric view
Mark McMullan
(O8) The population genetics of the ash dieback invasion of Europe highlights huge adaptive potential of the causal fungus, Hymenoscyphus fraxineus
17:00 TBC
18:00 Social Mixer
Earlham Institute
Introduction: Sally Ann Forsyth

Day 2 Wednesday 30 August

Session 2a

Main Auditorium
Evolutionary Genomics
Chair: Beth Shapiro

Session 2b

Watson & Crick
Clinical and Translational Genomics
Chair: Jonathan Coxhead

Session 2c

Franklin & Wilkins
Agricultural Genomics
Chair: Mick Watson

9:00 Emma Teeling
Growing old yet staying young: A genomic perspective on bats’ extraordinary longevity
Joris Veltmann
De novo mutations in genetic disease
Alan Archibald
Precision engineering for PRRSV resistance in pigs
9:30 Joel Armstrong
(O9) A reference-free whole-genome alignment of hundreds of mammalian genomes
Matthew Hurles
Deciphering Developmental Disorders
Nicola Patron
Engineering Plant Genomes for Farming and Pharming
9:45 Elinor Karlsson
(O10) The 200 Mammals Genome Project: Understanding Evolutionary Conservation at Single Base Resolution
10:00 Daniel Macqueen
(O11) Whole genome duplication and the evolution of salmonid fish: the state-of the art
Vladimir Teif
(O13) Nucleosome positioning as a cell memory in cancer transitions
Katrina Morris
(O15) Downregulation of immune genes in quail in response to H5N1 infection
10:15 Yannick Wurm
(O12) The evolution of social chromosomes in fire ants
Weronika Gutowska-Ding
(O14) Good or bad sequencing data? Setting a benchmark for the quality of diagnostic NGS in the lab
Gil Ronen
(O16) Pan-genome assembly of population haplotypes provides a comprehensive solution to common obstacles in modern breeding
10:30 - 11:00Coffee Break

Session 3a

Main Auditorium
Conservation Genomics
Chair: Emma Teeling

Session 3b

Watson & Crick
Developmental Biology
Chair: Aziz Aboobakar

Session 3c

Franklin & Wilkins
Microbial Communities
Chair: Nick Loman

11:00 Beth Shapiro
The genomic consequences of inbreeding in mountain lions, Puma concolor
Kristin Tessmar
Genomic and transcriptomic approaches for the study of daily, monthly and seasonal timing
Mads Albertsen
Towards a fully populated tree of life
11:30 Matthew D. Clark
(O17) Conservation genomics of the pink pigeon
Andrea Munsterberg
Cellular dynamics and lineage specification in developing somites
Lindsay Hall
Early life microbial communities
11:45 Taras K. Oleksyk
(O18) Novel genome assembly approach contributes to natural history and conservation of the Hispaniolan solenodon, Solenodon paradoxus
12:00 Katrina Morris
(O19) Characterisation of koala lactation genes using a combined transcriptomic, proteomic and genomic approach
Carlos R. Infante
(O21) Enhancers and the convergent evolution of limb reduction in squamates
Christopher Quince
(O23) DESMAN: a new tool for De novo Extraction of Strains from MetAgeNomes
12:15 Antonia Ford
(O20) Genomic approaches to identification and preservation of wild tilapia species and unique genetic resources
Dominik Handler
(O22) Using long reads to understand small RNAs
Sam Nicholls
(O24) Hansel and Gretel: A fairy tale of recovering haplotypes from metagenomes with a happy ending
12:30 - 13:30Posters - Odd Numbers

Session 4a

Main Auditorium
Sequencing Technology and Developments
Chair: Mike Quail

Session 4b

Watson & Crick
Meet the Editors

G10KGS Careers Workshop: Effective CVs for academic and industry research

Dr Rebecca Wyand, Dr Rosemary Bass

13:30 - 14:30 Core Workshop

14:45 - 17:00 1 to 1 Consultations

Slots are as follows:

14:45 - 15:00

15:00 - 15:15

15:15 - 15:30


15:45 - 16:00

16:00 - 16:15

16:15 - 16:30

16:30 - 16:45

16:45 - 17:00

You can sign up for an individual consultation at the Conference Reception.

13:30 Aaron McKenna
Information and storage recovery using the diversity of second-generation sequencing technologies
Laurie Goodman and Scott Edmunds

Genome Biology
Andrew Cosgrove


14:00 Deanna Church
(O25) Linked-Reads enable efficient de novo, diploid assembly
14:15 Rebecca O'Connor
(O26) Novel approach to chromosome-level mapping of avian genomes doubles the number of assemblies
14:30 Iliana Bista
(O27) Scaling up the generation of reference quality genomes across a range of vertebrate diversity
14:45 Ian Fiddes
(O28) Comparative Annotation Toolkit (CAT) - simultaneous annotation of related genomes using a high quality reference
15:00 Lesley Shirley
(O29) High Throughput Genomics Enabled by NEBNext Ultra II FS
15:15 - 15:45 Coffee Break

Session 5a

Main Auditorium
Genome Informatics
Chair: Rob Davey

Session 5b

Watson & Crick
Meet the Editors (cont.)

15:45 Doreen Ware
16:15 Colin Dewey
(O30) Genome-wide characterization of RNA processing event dependencies
16:30 Daniel Mapleson
(O31) Sequence alignment using optical correlation
16:45 John Davey
(O32) Chromosome assemblies with Oxford Nanopore sequencing
17:00 William Chow
(O33) gEVAL, a web-based browser to help you evaluate and assess the state of your assembly
17:15 Jonas Korlach
(O34) Full-length Transcript (Iso-Seq) Profiling for Improved Genome Annotations
18:00 Conference Dinner
The Halls

Day 3 Thursday 31 August

Session 6a

Main Auditorium
Population Genomics
Chair: Wilfried Haerty

Session 6b

Watson & Crick
Sponsors Showcase
Chair: Darren Heavens

9:00 Richard Durbin
Whole genome sequence studies of the Lake Malawi cichlid adaptive radiation
Sarah Cossey (EI) and Spencer Lamb (Verne Global)
Why Icelandic HPC is Bioinformatics’ best friend
9:15 Adam Peltan (NEB)
NEBNext®: Optimised Workflows for NGS Library Preparation
9:30 Gemma Murray
(O35) Natural selection shaped the rise and fall of passenger pigeon genomic diversity
Gaurav Kaul (Intel)
AI + Precision Medicine + Moore’s Law = The 21st Century virtuous cycle
9:45 Kai Zeng
(O36) Determinants of the efficacy of natural selection on coding and noncoding variability in two passerine species
Klaus Hentrich (TTPLabtech)
Automated low-volume liquid handling for cost-effective NGS library preparation and single cell genomics
10:00 Alicia C. Bertolotti
(O37) Copy number variation in the Atlantic salmon (Salmo salar) genome
Deanna Church (10x Genomics)
The Chromium System for Enabling High Resolution Biology
10:15 Maribet Gamboa
(O38) Genome-wide signatures of local adaptation in SNP loci and proteins of stonefly populations along a latitudinal gradient in Japan
Kay Körner (Eppendorf)
Yield, Specificity and Inhibition of PCR: how to get better results!
10:30 - 11:00Coffee Break

Session 7a

Main Auditorium
Chair: Iain Macaulay

Session 7b

Watson & Crick
Sponsors Showcase
Chair: Chris Watkins

11:00 Muzlifah Haniffa
Deconstructing the immune system using single cell technologies
Mark Mooney (DNAnexus)
Creating Community in the Cloud
11:15 Thomas Keane (EMBL-EBI rep BioNano)
Acomys genome project: A comparative genomic framework for evolutionary and biomedical studies
11:30 Tamir Chandra
Understanding cellular heterogeneity in cellular senescence and ageing through single cell transcriptomics
Brad Hehli (Perkin Elmer)
A Comparison of 16S Amplicons in Microbial Community Standards & Environmental Samples
11:45 Michelle Vierra (PacBio)
PacBio SMRT Sequencing on the Sequel System: higher throughput, lower cost, better science
12:00 Stephen Sansom
Transcript structures in the thymus: improvised or rehearsed?
Cindy Lawley (Illumina)
Sequencing and Array-based methods for resolving genomic inquiry
12:30 - 13:30Posters - Even Numbers

Plenary 2

Main Auditorium
Chair: TBC

13:30 Peter Holland
Homeobox genes and animal evolution: from duplication to divergence
14:15 Hilary Burton
Genomics in healthcare: the challenges of complexity
15:00Close of Conference
15:00 - 15:30Coffee Break
15:30 - 17:00

Working Group 1

Introductions, mission and refining selection of ordinal level species

Chair: Erich Jarvis


Introductions, mission, and species selection rationale
Erich Jarvis, Rockefeller University, NY, USA; Steve O’Brien, St. Petersburg State University, Russia


Tissue and permit requirements for near chromosomal level assemblies
Olivier Fredrigo, Rockefeller University, NY, USA


Breakout groups for refining draft ordinal species list
(Integration with B10K, Bat1K and 200 mammal projects)

Mammal leads: Oliver Ryder, Warren Johnson, Emma Teeling, Federica Di-Palma, Elinor Karlsson, Harris Lewin (Harris in absentia)

Bird leads: Erich Jarvis, Guojie Zhang (in absentia), Tom Gilbert (in absentia)

Fish leads: Byrappa Venkatesh, Richard Durbin

Amphibian leads: Andrew Crawford (Skype in and represented by Kathryn Elmer)

Reptile leads: Robert Murphy


Group discussion to finalize ordinal species list

Career Development
Darwin Training Room, EI

Laurie Goodman (GigaScience)
Andrew Cosgrove (Genome Biology)

Day 4 Friday 1 September


Working Group 2

Settling on assembly approach for ordinal level species
Chair: Adam Phillippy


Proposed approach going forward for near gapless, chromosomal level, and phased assemblies
Adam Phillippy, NIH, Bethesda MD, USA


Proposed alternatives for long-range scaffolding
Richard Durbin, Sanger Institute and Cambridge University, UK


Proposed path towards near perfect G10K assemblies
Gene Myers, Max Planck Institute, Dresden, Germany


200 mammal family project: Short read alternatives and G10K criteria
Elinor Karlsson, Broad MIT, USA; Federica Di-Palma, Earlham, UK

Group discussion to finalize assembly approach for ordinal project


De novo assembly
25 places
Darwin Training Room, EI


Differential Expression Analysis and Visualisation using Galaxy
25 places
Chris Lamb Training Suite

10:30 - 10:45Coffee Break
10:45 - 12:30

Working Group 3

Settling on annotation approach for ordinal level species
Chair: Paul Flicek


Proposed Ensembl annotation pipeline and requirements for VGP reference chromosomal level, diploid genomes
Fergal Martin and Paul Flicek, EMBL-EBI, Hinxton, UK


Proposed NCBI annotation pipeline and requirements for VGP reference chromosomal level, diploid genomes
Francoise Thibaud-Nissen and Kim Pruit, NCBI, Washington DC, USA


Proposed UCSC alignment and annotation approach for ordinal level diploid genomes: lessons from the 200 mammals project
Ian Fiddes, Joel Armstrong, and Benedict Paten, UCSC, Santa Cruz, USA

Group discussion to finalize requirements and paths for annotations

12:30 Lunch
12:30 - 14:00

Working Group 4

Deciding on projects to be conducted with ordinal level species
Chair: Erich Jarvis


Get food and settle at tables


Suggested major VGP projects, publications, and proposed mechanism of credit with ordinal level genomes
Erich Jarvis, Rockefeller University, NY, USA


Species and trait database for ordinal level and beyond
Klaus-Peter Koepfli, Smithsonian Conservation Unit, D.C. USA


Group discussion to generate list of proposed projects

14:00 - 14:30Coffee Break
14:30 - 15:30

Working Group 5

Raising remaining funds for ordinal level species
Chair: Beth Shapiro


Crowd funding among scientists, outreach, and donation website for genomes
Sadye Paez, Rockefeller University, NY, USA


Proposed plans for foundation and other funding
Beth Shapiro, UCSC, Santa Cruz, USA


Group discussion on plans for raising funds

15:30 - 15:45
Coffee Break
15:45 - 17:00

Working Group 6

Settling on person roles, finalizing species list, and plans for coming year
Chair: Erich Jarvis


Summary of workshop outcomes
Erich Jarvis, Rockefeller University, NY, USA


Finalizing agreements to species list, genome assembly, annotations, projects, funding, timeline, and person roles

Close of G10K-VGP workshop

17:00 - 18:00

Closed-door G10K council business meeting

121 Partnering- networking opportunities.

Norwich Research Park logo

Norwich Research Park is delighted to be a sponsor for the Genome 10K conference and Genome Science conference 2017.

We are hosting a 121 partnering platform which will allow you to pre-book meetings with other delegates and enhance your networking opportunities while you are at the conference.

Our 121 partnering site will go live on 9th August. To register and to schedule 121 meetings visit http://genome10k.meeting-mojo.com

Reception at Norwich Castle.

Delegates are invited to attend an evening reception at Norwich Castle on Thursday 31 August. You will be treated to a VIP tour of the new Nelson exhibition and there will be plenty of free time to explore the other areas of the museum, including an art gallery, Egyptian exhibit and Saxon jewellery collection. The evening will finish with a buffet and drinks.

Register for the reception.

The agenda for the evening is as follows:

  • 5pm – Coach collects delegates from Norwich Research park and transfer to Norwich Castle
  • 5:20pm – Arrive at Norwich Castle for drinks and welcome from Norfolk County Council Chairman Cllr John Ward
  • 5:45pm – Move to the TCA area for a talk on the exhibits, including the highlights of the Nelson Exhibition: major exhibition focusing on Admiral Lord Nelson, incorporating significant objects connected to the man himself, and examining the extraordinary way in which his achievements have continued to exert a powerful fascination in the two hundred years since his death. Includes objects from Norwich Castle’s own collections along with major loans from the National Maritime Museum, Greenwich, including the Jacket and Sword Nelson wore at the Battle of the Nile. The exhibition is only running for two months and for some of the items displayed this will be the last time the public will be able to view.
  • 6:15pm – Free roaming of Norwich Castle, incl Nelson exhibition.
  • 7pm – Buffet and drinks in the Castle Keep
  • 8pm – Close. Coach transfers. Destination(s)

Norwich Castle Keep by Nick Garrod, CC BY-NC-ND 2.0.

Norwich Castle

Plenary speakers.

Invited speakers.


Talk details.


To understand the evolution of animals, we must understand genomes and development. One of the most important discoveries in 20th century biology was the finding that widely different animal species use similar genes, such as homeobox genes, to build their embryos. But if the genes are conserved, why do animal species look so different? Does evolution subtly change the regulation of key genes, or change the number of genes, or change their protein coding sequences? Examples of all three routes have been revealed through comparative genomics, including some surprising examples of how evolution changed the number and function of homeobox genes in mammalian evolution.

About Professor Peter Holland

Peter Holland is the Linacre Professor of Zoology at the University of Oxford, UK. After a degree in Zoology from Oxford and a PhD in Genetics from London, he has held academic posts at the Universities of Reading and Oxford. His research into animal genomes and evolution, spanning marine invertebrates, fish, insects and mammals, has been recognized by award of the Kowalevsy Medal, De Snoo Medal, Linnean Medal, Frink Medal and Genetics Society Medal. He was elected to Fellowship of the Royal Society in 2003.


Kathy’s research team have demonstrated that Tasmanian devils have extremely low levels of genetic diversity at the Major Histocompatibility Complex (MHC) providing an opportunity for Tasmanian Devil Facial Tumour Disease (DFTD), a rare contagious cancer, to spread through devil populations without encountering histocompatibility barriers. They continue this research by studying the relationship between MHC type and disease susceptibility in devil populations, as well as the impact of the emergence and evolution of DFTD strains using genomics technologies.

About Professor Kathy Belov

Professor Kathy Belov is based in the Faculty of Veterinary Science at the University of Sydney. Kathy’s research expertise covers comparative genomics and immunogenetics of Australian wildlife. As well as core research into the Tasmanian Devil Facial Tumour Disease and the genetic management of the Tasmanian devil insurance programme, Kathy’s research team have participated in the opossum, platypus and wallaby genome projects where they have gained insights into genes involved in immunity and defense.They are now working on the koala and echidna genomes. Kathy has received two Eureka awards, the Crozier medal and the Fenner medal for her research.


A complete and accurate genome sequence forms the basis of all downstream genomic analyses. However, even the human reference genome remains imperfect, which affects the quality of experiments and can mask true genomic variations. For most other species, quality reference genomes do not exist. Long-read sequencing technologies from Pacific Biosciences and Oxford Nanopore have begun to correct this deficiency and have enabled the automated reconstruction of reference-quality genomes at relatively low cost. Further combination of these technologies with complementary scaffolding and phasing approaches such as chromatin conformation capture (Hi-C) may soon enable the complete reconstruction vertebrate haplotypes. I will review recent application of these approaches, and present a strategy for the automated assembly of hundreds of high-quality vertebrate reference genomes for the Genome10K project.

About Dr Adam Phillippy

Dr. Phillippy is head of the Genome Informatics Section and a tenure-track investigator in the Computational and Statistical Genomics Branch at the National Human Genome Research Institute. In 2000, Dr. Phillippy began working as a bioinformatics research assistant for Dr. Arthur Delcher at Loyola University Maryland, and received his B.S. in computer science in 2002. Following this, he worked for four years at The Institute for Genomic Research (TIGR) under the supervision of Dr. Mihai Pop, where he developed several foundational tools for genome assembly and alignment. Dr. Phillippy was also an integral contributor to TIGR's investigation of the 2001 anthrax attacks, having developed methods that were key to tracing the source of the outbreak. In 2006, he began his graduate work under the advising of Dr. Steven Salzberg at the University of Maryland, researching new methods for pathogen detection using PCR, microarrays and DNA sequencing.

Dr. Phillippy received his Ph.D. in computer science in 2010, and immediately joined the National Biodefense Analysis and Countermeasures Center (NBACC) as a principal investigator, where he established and led the National Bioforensic Analysis Center's first bioinformatics group. During this time, he pioneered the use of single-molecule sequencing for the reconstruction of complete genomes, and helped the NBACC become the first laboratory in the United States to achieve ISO 17025 accreditation for whole-genome sequencing.

In 2015, Dr. Phillippy joined the National Human Genome Research Institute and founded the Genome Informatics Section, where his current research group resides.


Genomic technologies have greatly enhanced our understanding of health and disease. Sequencing has become cheaper and quicker, whilst our increasing ability to interpret the data using huge computer power and very big databases, means that genomic testing can now influence clinical decisions in many areas of medicine. Whilst new possibilities continue to escalate, moving from scientific research to tried, tested and routine healthcare is not straightforward.

In this presentation I will outline some of the many dimensions of genomics in healthcare including disease prevention, making a precise diagnosis in rare and more common diseases, choosing drug treatments and assessing reproductive risk. I will explore some of the challenges facing health systems, which arise in part from the complexity of genomic information and the fast-moving nature of the technologies, but also include organisational and professional challenges: for example, the regulatory and practical difficulties of sharing personal data in health systems, or the educational programmes required to ensure that all healthcare professionals can use genetic testing appropriately and safely in their practice.

As health systems face the demands of an ageing population, a constant stream of emerging technologies and raised public expectations, I will suggest that using genomics effectively can be part of the solution. Together with other biomedical and even digital technologies, it can enable a move towards more personalised healthcare and a shift from end-stage ‘rescue’ to prevention and earlier diagnosis.

About Hilary Burton

Dr Hilary Burton is the Director and one of the founder members of the PHG Foundation and a Fellow of Hughes Hall, Cambridge. The PHG Foundation is a not for profit organisation with a special focus on how genomic and other technologies can provide more effective personalised healthcare and improve population health http://www.phgfoundation.org/. Qualified in medicine at Oxford University, Hilary subsequently trained in public health in the Eastern Region and worked as a consultant in Cambridge.

Since 1997 at the PHG Foundation Hilary has focused on the genomics context for population health, and, in particular, has led national work on the implementation of new technologies in mainstream UK health services. As a member of the Joint Committee on Medical Genetics, she was the main author of a report looking at the service implications of introducing genomics across a wide range of clinical specialties. In pursuing this further she is currently chairman of a national RCP Steering Group, which aims to promote increased awareness and competence in genomics amongst UK physicians http://www.phgfoundation.org/project/mainstream_medicine/.

Hilary has also written about the importance of genomic technologies in enabling personalised healthcare and prevention. In 2011/2 she sat on the UK Government Human Genomics Strategy Group and is currently a member of the UK Genetic Testing Network Clinical and Scientific Advisory Group and the Joint Committee on Genomic Medicine of the Medical Royal Colleges.


Genome-wide association studies (GWAS) have long been a staple of human genetics. In the simplest case a population-matched cohort of unrelated individuals with and without a disease or trait is genotyped, and then every marker (SNP) is tested for association with the phenotype. The ease of design has allowed very large cohorts to be recruited to these studies, yielding excellent power for linking genotype to phenotype. With the recent availability of populations hundreds or thousands of sequenced bacterial isolates interest has developed in applying the same technique to relevant pathogen phenotypes such as drug resistance and invasive potential. However, the highly variable pan-genome and potentially confounding strong population structure of bacteria make GWAS difficult to apply in the same way. In this talk I will describe Sequence Element Enrichment analysis (SEER), a method we have published which overcomes these issues by using k-mers as a generalised sequence variant along with appropriate population structure corrections. SEER is freely available and scales to thousands of genomes, and has been used to discover variants affecting invasive potential of S. pyogenes and region specific patterns of B. pseudomallei. Finally, I will describe recent work which pushes the limits of GWAS, testing the contribution of rare and structural variants to bacterial phenotypes.

About John Lees

John Lees is a PhD student, primarily studying the integration of sequencing data from both host and pathogen in cases of bacterial meningitis. He is also interested in phylogenetics and methods for genotype-phenotype association in bacteria.


How is it possible that severe early-onset disorders are mostly genetic in origin, even though the disorders are not inherited because of their effect on fitness? Genomic studies in patient-parent trios have recently indicated that most of these disorders are caused by de novo germline mutations, arising mostly in the paternal lineage.

In this presentation I will discuss our research on the causes and consequences of de novo mutations using novel genomic approaches. I will illustrate all of this using severe intellectual disability as a model, for which we are making rapid progress and now have the opportunity to provide medically relevant information to the majority of patients and families involved.


Synthetic biology applies engineering principles to biology for the construction of novel biological systems designed for useful purposes. It advocated for standards and foundational technologies to facilitate biological engineering. Defining standards for plants has enabled us to automate parallel DNA assembly at nanoscales, removing research bottlenecks and providing the international plant community access to reusable, interoperable, characterized, standard DNA parts. We are applying these principles to programmable genome engineering tools for multiplexed targeted mutagenesis and for the development of tunable, orthologous regulatory elements, synthetic transcription factors and genetic logic gates.

About Nicola Patron

Nicola is a molecular and synthetic biologist interested in the natural and engineered transfer of genetic material between genomes of different species. Her lab is focused on engineering photosynthetic organisms for industrial biotechnology and crops that are healthier to consume and less environmentally damaging to cultivate.


The adaptive radiations of haplochromine cichlid fish in the East African great lakes provide paradigmatic systems to study the dynamics of species formation, and of natural and sexual selection. The most extensive radiation is in Lake Malawi, where in the last million years or so one or a few ancestral populations have given rise to a flock of more than 500 species, filling almost all piscine ecological niches in the lake.

Over the past few years we have collected with collaborators over 2500 samples and sequenced the whole genomes of over 300 fish from over 100 species of Lake Malawi cichlids. All species are genetically close, with pairwise divergence typically between 0.1 and 0.25%, compared to heterozygosity between 0.05 and 0.15%. In addition to extensive incomplete lineage sorting, we see strong signals of gene flow between clades at different levels in the radiation, based on PCA, F statistics and related methods. There appear to be several long chromosomal regions exhibiting unusual phylogeny, perhaps indicative of a role for large inversions in species separation.

At a finer scale, although for close species pairs Fst can be under 20%, we also see local spikes or “islands” of high differentiation that are statistically significant under simple models of population separation, suggestive of loci under selection. Finally, at a functional level, we see higher non-synonymous to synonymous differences between species in genes involved in retinal processing, the innate immune system, oxygen transport, and a number of other pathways.

About Richard Durbin

Richard Durbin is a Senior Group Leader at the Wellcome Trust Sanger Institute, where he has been since its founding in 1992. He has been involved in a succession of large scale genome sequencing projects, including co-leading the 1000 Genomes Project. His current research is focused on studying genome variation and genome evolution, and methods for processing population scale whole genome sequencing data. He has also made many contributions to biological sequence analysis, including developing methods for sequence alignment using Hidden Markov models and suffix array methods, and developing genomic databases including Pfam, Ensembl, and TreeFam. Richard is an Honorary Professor in Computational Genomics at Cambridge University, a Member of EMBO and a Fellow of the Royal Society.


Beth Shapiro*, Nedda Saremi, Megan Supple, Gemma Murray, Richard E. Green, Eduardo Eisirik and the puma genome sequencing consortium

Human land-use changes, including deforestation and establishment of roads and highways, can obstruct natural dispersal and migration corridors, leading to population isolation and inbreeding. Among the most affected species in North America by human land-use changes is the mountain lion, Puma concolor. Once distributed across North America, mountain lions are today found only in southern Florida and the western part of the continent.

To explore the genomic consequences of increasing isolation between mountain lion populations, we sequenced and assembled a chromosome-scale de novo genome from a mountain lion from the Santa Cruz mountains, 36M, and generate high coverage resequencing data from mountain lions from populations across North America and Brazil. Using these data, we investigated the relative timing of onset and duration of inbreeding within potentially distinct mountain lion populations. North American mountain lions contain significantly less genomic diversity than Brazilian mountain lions, but show varying levels of inbreeding that does not correspond directly to present-day barriers between them. Finally, we explore the selective consequences of inbreeding on North American mountain lions, and identify genomic changes that may have evolved as a consequence of increased interaction with humans.

About Beth Shapiro

My research aims to better understand how populations and species change through time, in particular in in response to environmental and other changes to their habitat. To address this, my group uses the latest experimental and computational approaches to analyze genetic information isolated from fossil and archived remains. I am particularly interested in learning what drives two particularly important evolutionary processes: speciation and extinction.


The domestication of animal species was essential for the emergence of complex human societies. Despite its importance there is much about the domestication process that we still do not know. Domesticated species tend to share a suite of phenotypic traits referred to as the ‘domestication syndrome’. However, whether these phenotypic similarities are the result of convergence at the genetic level remains unclear. We generated whole-genome sequences from experimentally domesticated Norway rats and American mink, and identified genes and putatively functional variants that may underlie the phenotypic differences seen in the domesticated animals.

When we combine these data with whole-genome sequences from multiple pairs of domestic animals and their wild sister species we find biological pathways that appear to be recurrently affected by the domestication process across all domesticated animal species. One of these is the ErbB signalling pathway, involved in the development of the reproductive system and neural crest migration.

About Alex Cagan

Alex Cagan investigates evolutionary processes in somatic tissue. His research focuses on characterising mutation and selection in healthy tissues and how this relates to cancer and ageing.

Evolution is often considered to be an almost imperceptibly slow process. However, the cells that compose our own bodies are constantly acquiring mutations. Some of these mutations may influence cellular phenotypes, such as growth, resulting in clonal expansions. Over time the body may become a patchwork of clones. These processes may have profound implications for cancer progression and ageing. Due to technical limitations this evolutionary landscape has remained almost totally unexplored. I work with laser capture microdissection and genome sequencing to describe and understand processes of somatic evolution. I seek to adapt methods from comparative evolutionary genomics to gain new insights into evolution within the body.


Associative Transcriptomics (AT) is a potent method, first developed in the crop plant Brassica napus, enabling rapid identification of gene sequence and expression markers associated with trait variation in diversity panels. It can be effective even when advanced genomic resources are unavailable, making it a valuable tool for studying traits in non-model species. Most recently, we applied AT to the problem of ash dieback disease, a fungal disease affecting ash trees which was first discovered in the UK in 2012.

Using a Danish ash diversity panel varying for susceptibility to the disease, we discovered expression-based markers that could be used to identify trees with high levels of tolerance to the disease. In addition, information about the genes in which the markers are located, is revealing clues to the mechanisms underlying the ability of some trees to tolerate the disease.

About Andrea Harper

Dr Harper's lab is focused on utilising next-generation sequencing data for the development of statistical genetic and systems biology methods, such as associative transcriptomics, to identify the underlying genetic control of important traits in plants.


Second-generation sequencing has been traditionally seen in terms of a key trade-off: a huge increase in information recovery at the cost of information fragmentation. Here we show that such weaknesses can be overcome by leveraging a series of inventive techniques developed by the field at large. First, we demonstrate that second-generation sequencing can be used to recover chromosomal level contiguity in the de novo genome assembly of a previously unsequenced Muridae species. In addition, we demonstrate it's utility in recovering the 'orthogonal genome': human engineered information storage within the genomes of single living cells, and its application to tracing whole-organism lineage.


Life is controlled by multiple rhythms. While the interaction of the circadian clock with environmental stimuli is well documented, its relationship to endogenous oscillators with other periods, as well as natural timing variation between individuals of the same species is little understood.

The marine bristle worm Platynereis dumerilii harbors a light-entrained circadian, as well as a monthly (circalunar) clock. Our first studies suggest that the circalunar clock persists even when circadian clock function is disrupted as evidenced by the complete absence of molecular and behavioral circadian oscillatory patterns. However, the circalunar clock impacts on the circadian clock on two levels:

a) It regulates the level of a subset of core circadian clock genes.

b) In addition to its molecular input, we furthermore find that the circalunar clock changes the period and power of circadian behavior, although the period length of the daily transcriptional oscillations remains unaltered.

In order to study the molecular and cellular nature of its circalunar clock, as well as its interaction with the circadian clock, we have established transient and stable transgenesis, inducible specific cell ablations, chemical inhibitors, as well as TALEN-mediated genome engineering. We have been investigating the extent of transcript changes in the brain caused by the circalunar clock and compare these changes to other major conditions (sex determination, maturation) occurring during the life of the worm, as well as to the known extent of transcript changes caused by the circadian clock.

The marine midge Clunio marinus possesses a circadian clock, and in addition acquired a circalunar clock during the past 20.000 years. Strains of different geographic origins exhibit differences in their circalunar and circadian timing (“chronotypes”), which are genetically encoded and map to 3 quantitative trait loci (QTLs). We sequenced and assembled the 90Mbp genome of the midge and mapped the QTLs to the molecular map. Based on subsequent single nucleotide polymorphism (SNP) analyses differentially fixed in different timing strains, and molecular studies, we suggest that circadian chronotypes in Clunio are caused by activity variants in the enzyme CaMKII.

Given its evolutionary conservation and prominent role in the mammalian brain, it is tempting to speculate, that CaMKII could play a similar role in mammals, and could thus provide a molecular link between extreme chronotypes and frequently co-occurring neuropsychological diseases.

About Kristin Tessmar-Raible

The main interest of my lab is to investigate how solar and lunar light are sensed by the nervous system and how this light information impacts on the animals' information processing and endogenous clocks.

In particular, we aim to decipher the neuron types and molecules underlying fundamental, yet unexplored monthly oscillators (so-called circalunar clocks), using the bristle worm Platynereis dumerilii and the midge Clunio marinus.


Understanding evolution of plant immunity is necessary to inform rational approaches for genetic control of plant diseases. The plant immune system is innate, encoded in the germline, yet plants are capable of recognizing diverse rapidly evolving pathogens. Availability of plant genomes plant species allowed us to elucidate evolutionary history of plant immune receptors of Nucleotide-Binding Leucine Rich Repeat class (NLRs) that provide genetic diversity to recognize pathogens and induce signaling cascade. We identified the ‘core’ and highly variable sub-clades of NLRs from across 60 plant species, including previously understudied monocots and uncovered sub-family clade expansions. A recent paradigm in NLR-based recognition of pathogens involves NLRs with exogenous gene fusions, called integrated domains (NLR-IDs) that can serve as baits for pathogen-derived effectors. We have shown that NLR-IDs are prevalent across flowering plants and identified their ID repertoires. We uncovered a clade of NLRs that is undergoing repeated independent integration events that produces diverse NLR fusions to other genes. This NLR clade is ancestral in grasses with members often found on syntenic chromosomes while integrated domains are exchanged from different genomic locations. Sequence analyses revealed that DNA transposition or ectopic recombination are most likely mechanisms of NLR-ID formation. The identification of a subclass of NLRs that is naturally adapted to new domain integration can inform biotechnological approaches for generating synthetic receptors with novel pathogen ‘traps’.

About Ksenia Krasileva

Ksenia is a Group Leader at the Earlham Institute and The Sainsbury Laboratory. Dr. Krasileva has expertise in bioinformatics and genomics, plant biology and plant-microbe interactions. She holds both Bachelors of Science and PhD degrees from University of California, Berkeley where she studied plant innate immunity in Arabidopsis and got her training in Genomic and Computational Biology. For the past four years she has focused on wheat, first as a post-doctoral fellow with Jorge Dubcovsky (University of California Davis and Howard Hughes Medical Institute) where Dr. Krasileva was awarded a prestigious USDA NIFA Fellowship “Developing Functional Genomics for Wheat” and now with her own team at EI/TSL.

Dr. Krasileva is a co-developer of wheat exome capture and one of the leads on generating wheat reverse genetic resource "in silico TILLING". She maintains her research interests in the biology of wheat genome, evolution of plant innate immunity and functional analyses of plant immune receptors. Her group rapidly adopts new technologies and successfully combines fundamental and translational research to better understand plants and to generate crops with durable resistance to pathogens.


A complete and accurate genome sequence forms the basis of all downstream genomic analyses. However, even the human reference genome remains imperfect, which affects the quality of experiments and can mask true genomic variations. For most other species, quality reference genomes do not exist. Long-read sequencing technologies from Pacific Biosciences and Oxford Nanopore have begun to correct this deficiency and have enabled the automated reconstruction of reference-quality genomes at relatively low cost. Further combination of these technologies with complementary scaffolding and phasing approaches such as chromatin conformation capture (Hi-C) may soon enable the complete reconstruction vertebrate haplotypes. I will review recent application of these approaches, and present a strategy for the automated assembly of hundreds of high-quality vertebrate reference genomes for the Genome10K project.

About Adam Phillippy

Dr. Phillippy is head of the Genome Informatics Section and a tenure-track investigator in the Computational and Statistical Genomics Branch at the National Human Genome Research Institute. In 2000, Dr. Phillippy began working as a bioinformatics research assistant for Dr. Arthur Delcher at Loyola University Maryland, and received his B.S. in computer science in 2002. Following this, he worked for four years at The Institute for Genomic Research (TIGR) under the supervision of Dr. Mihai Pop, where he developed several foundational tools for genome assembly and alignment. Dr. Phillippy was also an integral contributor to TIGR's investigation of the 2001 anthrax attacks, having developed methods that were key to tracing the source of the outbreak. In 2006, he began his graduate work under the advising of Dr. Steven Salzberg at the University of Maryland, researching new methods for pathogen detection using PCR, microarrays and DNA sequencing.

Dr. Phillippy received his Ph.D. in computer science in 2010, and immediately joined the National Biodefense Analysis and Countermeasures Center (NBACC) as a principal investigator, where he established and led the National Bioforensic Analysis Center's first bioinformatics group. During this time, he pioneered the use of single-molecule sequencing for the reconstruction of complete genomes, and helped the NBACC become the first laboratory in the United States to achieve ISO 17025 accreditation for whole-genome sequencing.

In 2015, Dr. Phillippy joined the National Human Genome Research Institute and founded the Genome Informatics Section, where his current research group resides.


Of all mammals, bat possess the most unique and peculiar adaptations that render them as excellent models to investigate the mechanisms of extended longevity and potentially halted senescence. Indeed, they are the longest-lived mammals relative to their body size, with the oldest bat caught being 41 years old, living approx. 9.8 times longer than expected. Bats defy the ‘rate-of-living’ theories that propose a positive correlation between body size and longevity as they use twice the energy as other species of considerable size, but live far longer. The mechanisms that bats use to avoid the negative physiological effects of their heightened metabolism and deal with an increased production of deleterious Reactive Oxygen Species (ROS) is not known, however it is suggested that they either prevent or repair ROS damage.

Bats also appear to have resistance to many viral diseases such as rabies, SARS and Ebola and have been shown to be reservoir species for a huge diversity of newly discovered viruses. This suggests that their innate immunity is different to other mammals, perhaps playing a role in their unexpected longevity. Here the potential genomic basis for their rare immunity and exceptional longevity is explored across multiple bat genomes and divergent ‘ageing’ related markers. A novel blood based population-level transcriptomics approach is developed to explore the molecular changes that occur in an ageing wild population of bats to uncover how bats ‘age’ so slowly compared with other mammals. This can provide a deeper understanding of the causal mechanisms of ageing, potentially uncovering the key molecular pathways that can be eventually modified to halt, alleviate and perhaps even reverse this process in man.

About Emma Teeling

Prof. Emma Teeling established the Laboratory of Molecular Evolution and Mammalian Phylogenetics in 2005 and is the Founding Director of the Centre for Irish Bat Research at University College Dublin (UCD). She has been awarded a prestigious European Research Council Starting grant (2012) and a Science Foundation Ireland, President of Ireland Young Researcher Award (2006). Her integrative research in the fields of zoology, phylogenetics, genomics and conservation biology uncovers the genetic signatures of survival that enables species to adapt to an ever-changing environment. The two mains goals of her research are: (1) study unique model species to enable a better understanding of the structure and function of the human genome to inform medicine and molecular biology; (2) understand and therefore conserve, natural populations and environments to promote ecosystem well-being and functioning. She successfully leads a prolific, internationally renowned research team of typically 10 people and has secured over 4.4M in research funding. She is listed in top 100 female Irish scientists (2014) and gave a TEDx talk (2012) > 340,000 downloads.


Porcine Reproductive and Respiratory Syndrome (PRRS) is arguably the most important infectious disease for the world-wide pig industry. The effects of PRRS include late-term abortions and stillbirths in sows and respiratory disease in piglets. The causative agent of the disease is the positive-strand RNA PRRS virus (PRRSV). PRRSV has a narrow host cell tropism, targeting cells of the monocyte/macrophage lineage. One of the host proteins involved in facilitating viral entry is CD163 which has been described as a fusion receptor for PRRSV. CD163 is expressed at high levels on the surface of macrophages, particularly in the respiratory system. The scavenger receptor cysteine-rich domain 5 (SRCR5) region of CD163 has been shown to interact with virus in vitro.
We used CRISPR/Cas9 gene editing technology to generate pigs with a deletion of the CD163 exon 7 which encodes the SRCR5 domain. Deletion of SRCR5 showed no adverse effects in pigs maintained under standard husbandry conditions with normal growth rates and complete blood counts observed. Pulmonary alveolar macrophages (PAMs) and peripheral blood monocytes (PBMCs) were isolated from the animals and assessed in vitro. Both PAMs and macrophages obtained from PBMCs by CSF1 stimulation (PMMs) show the characteristic differentiation and cell surface marker expression of macrophages of the respective origin.

Expression and correct folding of the SRCR5 deletion CD163 on the surface of macrophages and biological activity of the protein as hemoglobin-haptoglobin scavenger was confirmed. Both PAMs and PMMs were challenged with PRRSV genotype 1, subtypes 1, 2, and 3 and PMMs with PRRSV genotype 2. PAMs and PMMs from pigs homozygous for the CD163 exon 7 deletion showed complete resistance to viral infections assessed by replication. Confocal microscopy revealed the absence of replication structures in the SRCR5 CD163 deletion macrophages, indicating an inhibition of infection prior to gene expression, i.e. at entry/fusion or unpacking stages.

About Alan Archibald

Professor Alan L. Archibald FRSE is Deputy Director and Head of Division of Genetics and Genomics at The Roslin Institute, R(D)SVS, University of Edinburgh. Alan's research focuses on understanding the genetic control of complex traits, including responses to infectious disease, in farmed animals, primarily pigs and cattle.


Muzlifah has used functional genomics, comparative biology and more recently single cell RNA sequencing to study human mononuclear phagocytes. In this seminar, she will discuss the power and utility of single cell RNA sequencing to identify new dendritic cells, monocytes and progenitor cells relevant for immunotherapy.

About Professor Muzlifah Haniffa

Muzlifah Haniffa is a Wellcome Trust Senior Research Fellow and Lister Institute Research Fellow. Her clinical and research interests are in dermatology and immunology. Her research programme is focused on understanding the functional heterogeneity of human mononuclear phagocytes.


In many hospital laboratories, non-aureus staphylococci (NAS) are the most common isolates in blood culture. Although S. aureus is considered a true pathogen, NAS is often categorised as a contaminant. However, NAS are an important cause of healthcare associated infections, particularly associated with indwelling medical devices, such as prosthetic joints. They are also a reservoir of antimicrobial resistance genes, with resistance to methicillin and other frequently used antibiotics on the rise.

To investigate the population structure of NAS, we are establishing a diverse collection, currently just over 400 isolates from clinical samples, healthy volunteers and animals. At the Norfolk and Norwich Hospital, the clinical microbiology laboratory identifies isolates to the nearest species match using the gold standard MALDI-TOF method; we have used both MALDI-TOF and Illumina whole genome sequencing to characterise around 300 isolates from the collection.

The lack of a large shared core in NAS directed us to a different approach, but to gain greater resolution over the single gene approach of 16S, we used the concatenated sequence of 16 ribosomal proteins to cluster the strains, resulting in 17 robust cluster (RC) groups. Overlaying the MALDI-TOF species names upon RC groups made it clear that the MALDI-TOF species designations do not necessarily follow the phylogeny. As a test case within NAS, we show that there is a significant phylogenetic distinction between “S. saprophyticus” strains isolated from urinary tract disease and those not causing disease.

Clustering of ribosomal protein sequences has revealed robust clades within Staphylococcus that provide the opportunity to generate a new, biologically sound definition of NAS.

About Gemma Langridge

Gemma is currently a Research Fellow in Molecular Microbiology at UEA. Following on from her biology undergrad in Oxford, Gemma moved to the Wellcome Trust Sanger Institute for her PhD where she studied bacterial metabolism in Salmonella which infect either humans or animals. She also helped develop TraDIS, a technique that allows all bacterial genes required under a specific condition to be assayed at once. As a post-doc at the Sanger, Gemma followed an interest in bacterial niche adaptation as she continued to work on TraDIS and comparative genomics. She moved to her current position at UEA in early 2016 to look at the population structure of non-aureus staphylococci and their role in hospital-acquired infection.


A key event in a healthy cell turning into a cancer cell is the activation of an oncogene. To prevent transforming to a cancer cell, the cell harbouring the oncogene activates a tumour suppressive programme, pushing itself into an irreversible growth arrest, called oncogene induced senescence (OIS). Everyone carries OIS cells, for example in the benign lesions (such as moles) that never progress to malignant cancer. Most of the time these lesions stably exist over decades, but sometimes individual cells escape and progress to cancer. What enables individual cells to turn malignant and how are they different from the cells around them? Here we present single cell transcriptomes of a time-course of human fibroblasts on their way to senescence after oncogene activation. Applying machine learning to order cells along a senescence trajectory, we find an unexpected bifurcation, leading to two distinct senescence endpoints. Each of these endpoints exclusively expresses sets of canonical senescence genes. Most importantly, one population failed to regulate key genes thought essential for the stability of the senescent state, leading to a scenario where the heterogeneity of the benign state might enable escape to malignancy.


Children with severe, undiagnosed developmental disorders (DDs), including Intellectual Disabilities as well as multi-system congenital malformations, are enriched for damaging de novo mutations (DNMs) in developmentally important genes. Working with the clinical genetic services of the UK and Ireland we have exome sequenced 13,600 families. We have diagnosed thousands of children, by providing the information back to their clinicians. We’ve determined that 40-45% of these children have causal de novo mutations in protein-coding genes, and we’ve identified over 30 novel disorders so far. We’ve also determined that de novo mutations are also enriched in highly conserved regulatory elements that are active in fetal brain, but that these only account for a small minority of as yet undiagnosed patients.

About Dr Matthew Hurles

Dr. Matt Hurles studied Biochemistry at Oxford University, before gaining a PhD in Genetics from the University of Leicester and establishing the Genomic Mutation and Genetic Disease group at the Wellcome Trust Sanger Institute in 2003. From 2003-2011, Matt led major initiatives to characterise structural variation in the human genome, and integrate this knowledge into disease and population genetic studies. His current research interests are in the genetic causes of severe developmental disorders, pre- and post-natally, many of which are caused by new germline mutations, and the causes of variation in germline mutation rates. Matt has had leadership roles in the 1000 genomes project and the UK10K project, and is the principal investigator of the Deciphering Developmental Disorders and Prenatal Assessment of Genomes and Exomes (PAGE) projects. Matt gave the Genetics Society Balfour Lecture in 2009 and the Royal Society Crick Lecture in 2013. In 2017, Matt became the Head of the Human Genetics programme at the Sanger Institute and was elected as a Fellow of the Academy of Medical Sciences.


A fundamental process during both embryo development and stem cell differentiation is the control of cell lineage determination. In developing skeletal muscle, many of the diffusible signalling molecules, transcription factors and non-coding RNAs that contribute to this process have been identified. This has advanced our understanding of the molecular mechanisms underlying the control of cell fate choice. In vertebrate embryos, skeletal muscle is derived from paired somites. These are transient embryonic segments that also contain progenitors for other cell lineages of the musculoskeletal system, such as chondrocytes and axial tendon progenitors. In addition, some endothelial cells, adipocytes and brown fat cells are somite derived. We are developing approaches to examine the full complexity and molecular profiles of progenitor cells that are present in early and later stage somites. This will allow us to delineate molecularly distinct cell types, to define progenitors and lineage relationships, and to identify crucial pathways, hubs and markers for the lineages of the musculoskeletal system. In parallel, we use imaging approaches to assess cellular behaviours during somite maturation, a highly dynamic process that involves significant morphogenetic changes. A more detailed understanding of the key mechanisms and factors involved will be important for stem cell science, regenerative medicine and tissue engineering.

About Dr Andrea Munsterberg

Dr Andrea Munsterberg studied Biology at the University of Heidelberg, Germany; completed her PhD studies at the National Institute for Medical Research, Mill Hill, London, UK; followed by HFSPO and MDA funded Postdoctoral Research at Harvard Medical School, Boston, USA; set up her research laboratory as a Wellcome Trust Career Development Fellow at the Medical Sciences Institute of the University of Dundee, Scotland and moved to the University of East Anglia, where she has been a Professor of Developmental Biology since 2010.


The gut is home to an astonishingly diverse, dynamic, and populous ecosystem. This complex microbial community, termed the microbiota, is critical for host wellbeing. Disturbances in our microbiota, such as via caesarian sections and antibiotic exposure, can lead to increased susceptibility to pathogens, as well as atopic, and chronic inflammatory diseases. Bifidobacteria constitute a substantial proportion of the gut microbiota, particularly during early life and high-levels are associated with the development of mucosal defence. Currently there are many bifidobacterial species and strains with claimed health promoting or ‘probiotic’ attributes, however the mechanisms through which these strains reside within their host and exert benefits is far from complete. In this talk I will discuss the role of the gut microbiota with the host, focusing on the example of bifidobacteria in host colonisation, epithelial cell cross-talk, and pathogen protection.

About Dr Lindsay Hall

I qualified with a BSc (Hons) in Microbiology from the University of Glasgow in 2003. I then went on to study for a PhD in Microbiology and Immunology at the Wellcome Trust Sanger Institute (University of Cambridge) under the supervision of Prof Gordon Dougan.

My thesis focused on designing and creating mucosal vaccines against Mycobacterium tuberculosis and characterising mucosal immune responses (specifically Natural Killer, [NK] cells) induced after oral and intranasal immunisations. My PhD was part funded through the EU sixth framework programme entitled Mucosal Vaccines Against Poverty Related Diseases (MUVAPRED).

In 2007 I took up a postdoctoral position at the APC Microbiome Institute, University College Cork in Ireland. During my time in Cork, I moved into a new mucosal immunology area focused on intestinal inflammatory disorders. My research utilised experimental Ulcerative colitis and enteric pathogen models to understand the protective role of early mucosal immune responses (including NK cells) during acute intestinal inflammation. In Cork, I also started to work on the bacterial communities that inhabit the gut, termed the microbiota, specifically understanding the role of individual members (i.e. Bifidobacterium) and their products (exopolysaccharide capsules) in modulating the critical commensal-host interaction.

I returned to the UK in 2011 to take up a lecturing and Principle Investigator position within the Norwich Medical School, University of East Anglia. In 2013 I was awarded a Wellcome Trust Investigator Award to study the role of early life gut microbiota in colonisation resistance development and was promoted to senior lecturer in 2014. In 2015 I moved to the Institute of Food Research as the Microbiome Research Leader and my team studies the early life microbiota in health and disease.


Epithelial cells of the thymus are remarkable for their ability to promiscuously express nearly all protein coding genes in order to assess the self-reactivity of developing T-cells. Such T-cells must also be able to tolerate the isoform specific epitopes that they will encounter as they monitor the various tissues of the body. Currently, the extent and fidelity of peripheral isoform representation in thymic epithelial cells is only poorly understood. We therefore used population and single-cell transcriptomics to compare transcript architectures between the thymus and peripheral tissues. These data also provide insights into the process by which the isoform repertoire of thymic epithelial cells is generated.

About Dr Stephen Sansom

Dr Stephen Sansom graduated with a BSc (Hons) in Biochemistry from the University of Dundee in 2001. He then studied Developmental Biology at the University of Cambridge as a member of the Wellcome Trust 4-year PhD programme in Developmental Biology. During PhD and post-doctoral studies with Dr Rick Livesey at the Gurdon Institute Dr Sansom used genomic approaches to generate insights into pattern-specification and cell-fate choices in the mammalian neocortex.

Recognising the potential of computational biology in the era of next-generation-sequencing Dr Sansom joined Professor Chris Ponting's Computational Genomics Analysis and Training (CGAT) program as an MRC Career Development Fellow at the University of Oxford in 2011. It was during this time that he developed a strong interest in immunology through collaborative research with Professor Georg Hollander resulting in publication of the first single-cell genomics analysis of promiscuous gene expression in thymic epithelial cells.

After a brief appointment as a Senior Genomics Fellow in the Ponting group, Dr Sansom joined the Kennedy Institute in 2014 to the lead the Computational Genomics team. Here, in addition to a continuing interest in the mechanisms of central tolerance, he collaborates closely with experimental groups to unlock the potential of genomics and single-cell approaches for understanding inflammatory disorders.


Registration is now closed. For registration enquiries, please contact training@earlham.ac.uk.

Registration includes:

  • Access to all lectures
  • Access to poster sessions
  • Access to a choice of special interest groups, training and CPD sessions
  • Conference Dinner
  • Optional transport to the conference venue from UEA accommodation (15 minutes’ walk)

Please note: Accommodation is not included in the registration fee. Accommodation at Paston House, UEA is optional at registration and will be added to the registration fee if selected.

Registration opens: 1 February 2017

Early Bird registration closes: 31 May 2017

Abstract submission deadline: 31 May 2017

Late registration closes: 31 July 2017

Registration details:

Early Bird Registration (1 Feb 2017 - 31 May 2017)Late Registration (1 May 2017 - 31 Jul 2017)
Standard Registration£250£330
Student Registration£150£200
Day Delegate (per day)£70£100


The deadline for submitting abstracts has now passed. For enquiries related to abstracts, please contact training@earlham.ac.uk.

Abstract submission:

1 February - 31 May 2017

You may submit an abstract during early bird registration only. You will be permitted to submit your abstract for consideration for:

  • Oral presentation
  • Poster presentation
  • Oral and poster presentation

During submission, you will be required to identify the most appropriate theme aligned to the session topics. The chair persons for that session will form the reviewers panel for your abstract.

Why submit?

  • Peer review of your work
  • A track record of your successes for your CV
  • Opens opportunities for networking
  • Can support manuscript preparation

Eligible abstracts will be subject to selection to receive travel bursaries to allow individuals to attend the conference (details to follow).


Hosted at the Earlham Institute (EI), a cutting edge, contemporary research institute and registered charity, working in an area of rapid technological development and innovation. Established in 2009, EI is strategically funded by the BBSRC to lead the development of a skill base in bioinformatics and a genomics technology platform for UK bioscience.

The Institute is located on the Norwich Research Park, together with its partners: the John Innes Centre, the Institute of Food Research, The Sainsbury Laboratory, the University of East Anglia and the Norfolk and Norwich University Hospital. The Research Park has an excellent reputation for research in plant and microbial sciences, interdisciplinary environmental science and food, diet and health, to which EI contribute strengths in genomics and bioinformatics.

Close links exist between the NRP partners and new opportunities for collaboration in exciting new initiatives are under development. The NRP recently received £26M of government investment to facilitate innovation and further develop infrastructure to attract science and technology companies to the Park to enhance the vibrant environment and realise economic impact from research investment.

The John Innes Conference Centre.

Earlham Institute at night.

Photo: Anthony Cullen.

Earlham Institute atrium.

Photo: Anthony Cullen.

Things to do in Norfolk.

Welcome to Norfolk!

Check out things to do in Norfolk including Family Attractions, History & Heritage, Cycling, Walking, Golf, Birdwatching, Churches & Cathedrals, Where to see the Seals, Steam Railways and much more

What’s on throughout

Cromer Pier Summer Show – the world’s only end-of-pier theatre variety show.

Summer Spectacular Circus & Water Show 2017 at The Hippodrome Circus - The mind-blowing Finale Water Spectacular is one of only three in the world and the only place in Europe that stages such a show with Swimmers, Aerialists and special effects when the ring turns into a giant pool - an unforgettable experience.

Field to Fork Trailer Tour at Holkham - Farming without having to put your wellies on! Families, hop aboard a fascinating tractor trailer tour after a visit to the Field to Fork Experience to see exactly where your food comes from and see one of the finest ‘Downton Abbey’s in all of Britain.

Titanic: Honour & Glory at Time & Tide Museum Great Yarmouth - With this exciting exhibition we explore this famous ship, her sister ships and their owners, the White Star Line, as well as revealing the local links of some of its passengers, all in the environment of a former fish smoking factory.

Until August 31

Banham Zoo’s World Tour! - Grab your passports and fly around the world in just a day! With animals from 6 continents to spot – you’re in for a wild trip!

Saturday August 26

Historic King’s Lynn Walk at Saturday Market Place – walk around the medieval town that used to be in the Hanseatic League and has a huge range of graded buildings.

St Benet's Abbey Boat Trip and Tour at Fairhaven Woodland and Water Garden - Boat trip from Fairhaven Garden to St Benet's Abbey with a 45 minute guided tour of the abbey.

Wherry on view at How Hill National Nature reserve - Look around a beautiful pleasure wherry Hathor and discover her Norfolk and Egyptian heritage. Talk to our volunteers about sailing and preserving these historic vessels.

Breckland Landscape & Heritage Tours at Elveden Estate - Your tour will explore the ruined castles, churches, warren lodges and ancient heaths that make this region of Norfolk and Suffolk unique.

Follow this link to see all events.

Sunday August 27

Family Fun Day at Great Yarmouth Racecourse – enjoy a day at the races!

Open Garden at Hindringham Hall Gardens & Tea Room - Visitors are provided with a map and self guide themselves around the gardens, one of the best in Norfolk.

Learn to Sail at Whitlingham Broad Adventure - An opportunity to get afloat and try sailing a Wayfarer with an instructor on board providing tuition. Ideal for those that prefer to sail with others in a larger dinghy.

Historic re-enactment at Castle Rising Castle - Historical Re-enactment by Buckingham’s Retinue.

Farmers’ market at Sandringham – lots of local produce at the home of the Royal family.

Wherry on view at How Hill National Nature reserve - Look around a beautiful pleasure wherry Hathor and discover her Norfolk and Egyptian heritage. Talk to our volunteers about sailing and preserving these historic vessels.

Breckland Landscape & Heritage Tours at Elveden Estate - Your tour will explore the ruined castles, churches, warren lodges and ancient heaths that make this region of Norfolk and Suffolk unique.

Follow this link to see all events.


Accommodation is reserved at Paston House, University of East Anglia (UEA), a short 15-20 minute walk from the conference venue. The cost of this is £34.00 per night, including breakfast. This is en-suite student accommodation on the UEA campus with access to shops as well as buses to Norwich city centre.

Earlham Institute has also negotiated rates at the following hotels and facilities. When booking a room, please mention that you are attending the ‘Genome 10K Conference’ to ensure that you receive our negotiated rates:

Park Farm Hotel, Hethersett is 4 miles from Earlham Institute to the south of Norwich. This hotel has leisure facilities including a pool and the preferential rate is £90 per night bed and breakfast. A taxi would be required and costs approx. £12, but could be shared at this price.

Maid’s Head Hotel, Norwich is 4.6 miles from Earlham Institute in the centre of Norwich, next to the Cathedral. Here we also attract a beneficial rate of £90 per night bed and breakfast. A taxi, if pre-ordered, would cost around £10.

Transport is arranged to take you from the conference to the conference dinner venue on Wednesday evening at 18:00 for pre-dinner reception at 19:00

Limited transport operating on a first-come, first-served basis is available from the accommodation at UEA to the conference venue.

Conference Dinner:


The conference dinner will be held on 30 August 2017 at 19.30pm in St. Andrew's Hall which is the centrepiece of The Halls and is the name by which many people refer to the whole complex of buildings.

It has a fine, high-beamed ceiling, beautiful stained glass windows, limestone columns and a large polished maple floor. It was originally the nave of the friary and was completed in 1449. The size and beauty of its proportions are impressive without elaborate decoration in keeping with the friars' rule of simplicity.

The stained glass, stone carving and deeply-coloured portraits add richness to the simple backdrop of the building, adding a contemporary feel to this incredibly historical building of civic tradition - the best of both worlds.

Coaches will take you from the conference venue at 18:00 to St Andrews Hall for the conference dinner which is in the very heart of the City of Norwich.

The Norwich Arcade, in the heart of the city centre.

Norwich Arcade

About Norwich.

Norwich as a city has a lot to offer with high street shops, two shopping centres, restaurants, bars, pubs, cinemas, a bowling alley, theatres and much more. The city is also known for Norwich Cathedral (Church of England) and the Cathedral of St John the Baptist (Catholic Church) as well as Norwich Castle which is now an art gallery and museum.

You can find more information about Norwich here.

Just a short journey out of the City and you can also enjoy the Norfolk coast which spans 93 miles with a variety of beaches and coastal landscapes.

You can find more information about what Norfolk has to offer here.




Other supporters.

Conference dinner.

Evening reception.

Poster prizes.

This year the Microbiology Society is pleased to be sponsoring two awards (cash prizes and society memberships) for the best and runner-up Microbial Genomics posters. The Microbiology Society is a membership organisation for scientists who work in all areas of microbiology. See more on the benefits of membership here https://www.microbiologysociety.org/ or follow us on twitter @MicrobioSoc

De novo Assembly Training Workshop.

The venue.

Hosted by Earlham Institute on the Norwich Research Park, UK, enjoy world-class facilities at both EI and the John Innes Conference Centre. We also welcome you to Norwich, a city steeped in history and culture set in the middle of East Anglia.

Address and map.

John Innes Conference Centre
Norwich Research Park

Have any questions?

We'll be happy to support you however you need, just get in touch with our organising team.

EI Genome10K Team, training@earlham.ac.uk

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