Our contributing writers to the Wellcome Sanger Institute Blog.
Ludmil was a PhD student in the Cancer Genome Project where he worked under the supervision of Mike Stratton on identifying and understanding the mutational processes that cause cancer.
Browen Aken was the Wellcome Sanger Institute Ensembl Genebuild Team Project Leader. At the time of her blog post, she had eight years’ experience in automatic gene annotation. Ensembl annotates protein-coding and non-protein coding genes on vertebrate genomes. Gene annotation comes with a number of challenges and each annotation project is different because the data that the team works with is different. Some of the annotation challenges are:
- When genome assemblies are very fragmented, full length protein-coding genes cannot fit onto short pieces of DNA
- A reference genome assembly is usually a single path through the genome, often made from the DNA of one individual. However, the protein sequences that we map to this reference genome come from different individuals from the same species and sometimes also from different species. We need to carefully filter our alignments to make sure that we’ve placed them correctly, even when they don’t match the genome 100 per cent.
- With next-generation transcriptome sequencing, it is a challenge to piece together the full length of a transcript when each read is only about 100 bases long
- Storage space can also be a limitation when data sets are very large
Roberto is a Staff Scientist in Dominic Kwiatkowski’s group and is involved in the analysis of natural genetic variation in the Plasmodium parasites that cause malaria. His primary focus is at the intersection of theoretical and empirical approaches aimed at characterising and understanding the evolution of the malaria parasite and its clinical consequences such as the emergence of drug resistance. Based in the Wellcome Sanger Institute’s Malaria Programme, Roberto works closely with the colleagues at the Wellcome Trust Centre for Human Genetics at University of Oxford and supports several global collaborations including the MalariaGEN P. falciparum Community Project and Pf3k.
Blessing was a PhD student in the Bacterial Pathogenesis team at the Wellcome Sanger Institute. She studied the intestinal microbiota in healthy individuals and patients with severe Clostridium difficile infection treated with faecal transplants. She is interested in developing a bacteriotheraphy for the treatment of recurrent C. difficile infections in humans.
Eva was a PhD student in the NIH-Oxford-Cambridge Scholars Program. She worked with Paul Kellam in the Virus Genomics group and with Richard Koup and Daniel Douek at the Vaccine Research Center, National Institute of Allergy and Infectious Disease, studying immune repertoires in SIV infection.
Qasim joined the Human Evolution Team at the Sanger Institute in 2008 and is both part of the Analysis Group of The 1000 Genomes Project and responsible for the Human Evolution Team’s wet lab. His research focuses on the analyses of DNA variation in humans and primates in order to understand molecular evolutionary processes. He also carries out targeted re-sequencing of several human Y chromosomes from different parts of the world in order to refine the Y phylogeny. Using this approach he has helped to have identified a common set of primers which are available for investigators who are interested in particular Y-chromosomal lineages.
Kate was a Postdoctoral Development Fellow in the Pathogen Genomics group at the Wellcome Sanger Institute, working on the molecular epidemiology of enteric pathogens.
Colin is an engineer at the Wellcome Sanger Institute.
Lars was a PhD student at the Wellcome Sanger Institute and EMBL-EBI with Alex Bateman. He worked on a variety of projects in bacterial genomics including transposon-insertion sequencing and analysis of non-coding RNA.
Josefin Bartholdson was a Postdoctoral Fellow in Gavin Wright’s Cell surface signalling research team. She did a PhD at the University of Edinburgh where she studied virulence factors of the Cystic Fibrosis pathogen Burkholderia cenocepacia. She joined the Wellcome Sanger Institute in 2009 to work on malaria host-pathogen interactions.
Enrica is a postdoctoral fellow at the Wellcome Sanger Institute. In 2011 she joined Dr Gavin Wright’s group to study the molecular basis of mammalian sperm-egg recognition.
Ewan is one of the founders of the Ensembl genome browser. Together with Dr Rolf Apweiler, he has strategic responsibility and oversight for bioinformatics services at EMBL-EBI.
Vesna Boraska is Assistant Professor of Medical Biology at the University of Split School of Medicine, Split, Croatia. She is also a visiting scientist in Ele Zeggini’s Applied Statistical Genetics group at the Wellcome Sanger Institute. Vesna’s scientific interests reside in the area of genetic analyses of complex traits and diseases. Her recent work includes genome-wide association studies of brachial circumference, eating disorder-related phenotypes and genetic variants differences between males and females. She is currently primary analyst for the Wellcome Trust Case Control Consortium 3 analysis of anorexia nervosa.
Mathieu studied Agronomy at the National Higher Agronomic School (France) and at McGill University (Canada). He completed his PhD in 2007 at the Pasteur Institute (France) studying the evolution of Group B Streptococcus, the leading cause of neonatal infections. In 2009, Mathieu undertook a postdoctoral position with Oliver Billker at the Wellcome Sanger Institute (United Kingdom). His work aims at identifying the molecular links between essential signalling molecules which allow malaria parasites to successfully progress through their life cycle. Specifically, he is interested in characterizing the cGMP- and calcium-dependent signalling pathways. This involves the combination of Plasmodium-specific genetic approaches, chemical biology, and quantitative molecular phenotyping.
Andrew Brown is a Postdoctoral Fellow in the Genome Informatics group at the Wellcome Sanger Institute where he works on the EuroBATS project. Andrew received his PhD from Imperial College London in 2008, studying genetic control of gene expression in inbred rats. After his PhD he moved to Oslo, where he worked on the genetics behind brain function and mental illness, looking for genetic reasons for different brain reactions to looking at images of faces. As part of the EuroBATS project at the Sanger Institute, Andrew’s work looks to construct a more complete picture of the ageing process by integrating what we see occurring in the cell with all of the other information that has been collected about a much studied group of people.
Josie Bryant is currently a PhD student in the Pathogen Genomics group led by Julian Parkhill at the Wellcome Sanger Institute. Her work focuses on using whole genome sequencing to understand the evolution and transmission of pathogenic Mycobacteria.
Marija did her PhD at the Sanger Institute with Dr Alex Bateman and she now works as a postdoctoral researcher in Madan Babu’s group at the MRC Laboratory of Molecular Biology in Cambridge. Marija’s work is centred on studying different processes that generate protein diversity and a likely impact of the introduced changes in protein sequences. This includes larger changes that emerged during protein evolution, protein variation among individuals of the same species, or differences in protein products of the same gene when it is expressed in different tissue types.
Leyla is science manager in Julian Rayner’s malaria team. Leyla was born in Bogota, Colombia, where she completed her first degree. She completed her PhD at the Universidad Complutense in Spain and then moved to the UK as a Postdoctoral Fellow at the University of London, where she investigated on the mechanisms of resistance to artemisinins in P. falciparum. She joined the Wellcome Sanger Institute in 2009.
Amy is currently undertaking her postdoctoral research in the Pathogen Genomics team under Julian Parkhill. She looks for non-obvious and new antibiotic resistance genes in pathogenic bacteria from hospitals by combining high-throughput next-generation sequencing techniques with large-scale transposon mutagenesis via the Transposon Directed Insertion Sequencing method.
Susana Campino is a staff scientist in Dominic Kwiatkowski’s Malaria Genetics Group. Susana’s main interest since her PhD is on malaria genetics in the host and parasite, with a particular focus on which genetic polymorphisms, in both genomes, may modify response to infection and disease progression.
Stefania is a postdoctoral research associate at the Wellcome Sanger Institute. She works in Toni Vidal-Puig’s group, which investigates molecular mechanisms that control energy expenditure and brown fat activation.
Keren used exome sequencing to identify genes that cause developmental disease, and zebrafish embryos to model those genes. Phenotypes she has studied include microcephalic osteodysplastic primordial dwarfism, congenital muscular dystrophy, prenatal structural abnormalities and intellectual disability. She is also interested in scientific publishing, and is an editor for the Cambridge Student Journal of Genetics, and for BlueSci magazine.
Tamir is a Postdoctoral Fellow at the Wellcome Sanger Institute. He works with Wolf Reik at the Babraham and Sanger Institutes on the nuclear biology of cellular ageing, with implications for cancer and ageing. Tamir has a long standing interest in senescence biology and did his PhD at the Cancer Research UK Institute in Cambridge with Masashi Narita on chromatin dynamics in senescent cells.
Lia is a PhD student in the Parasite Genomics team studying gene expression in malaria parasites. Her main interest to use improved RNA-seq methods to study how genes are expressed in the malaria lifecycle.
Mary was a member of the Media, PR and Communications team at the Sanger Institute.
Penny is a computational biologist working with the Pfam database under Alex Bateman. With Alex’s promotion to Head of Protein Clusters at the EBI, this is where the database, formerly at the Sanger Institute, is now housed. Annotating the database involves identifying new families of protein-domains and trying to determine their structural and functional significance.
Susie Cooke is a former post-doc with the Cancer Genome Project. Her main research interest is characterising large-scale structural alterations of the cancer genome.
Vincenza is a research scientist at the National Research Council in Italy and a visiting scientist in the Human Evolution team at the Sanger Institute. She works on several projects to understand the processes that lead to the current levels and distribution of genomic variation in humans.
Cecile is a senior staff scientist at the Wellcome Sanger Institute, where she works in the Cell Surface Signalling Laboratory.
Tim is Head of Scientific Computing, responsible for the thousands of servers, multi-petabytes of storage, databases and web services used by Institute scientists in their research. Initially a cell biologist with interest in cell cycle checkpoints, he has since his PhD been involved in bioinformatics programming and IT service provision, at the University of Cambridge, then Incyte Genomics, and for the last 11 years at the Sanger Institute.
Laura was a PhD student in the Microbial Pathogenesis team at the Wellcome Sanger Institute. Her main focus was to understand the molecular basis of C. difficile infection. She used high-throughput transcriptome sequencing and proteomics to determine the C. difficile sporulation programme at the whole-genome level, with the aim of linking this back to its role in the disease and transmission of the pathogen.
Janina is a Postdoctoral Fellow in the Pathogen Genomics group at the Wellcome Sanger Institute.
Philip is a bioinformatician at National Genomics Infrastructure at the Science for Life Laboratory in Stockholm, Sweden. Previously he worked with Wolf Reik at the Babraham Institute in Cambridge. His core interests are in the field of epigenetics, with particular emphasis on bisulfite sequencing, HiC data analysis and systems approaches to data analysis. You can find out more at his site: http://phil.ewels.co.uk/
Maria gained her Doctorate by immobilising pectic enzymes for juice clarification in her native Spain. She has worked at the Wellcome Sanger Institute since 1999 and enjoys looking into bacterial (mostly Salmonella) accessory and unique genomic regions. She is a Senior Research Assistant.
Daniel is a Group leader in Computational Genomics at the Wellcome Sanger Institute. His group works on understanding how mutations affect the regulation of gene expression.
Astrid Gall was a Staff Scientist in the Virus Genomics group at the Wellcome Sanger Institute. She led the group’s research on HIV-1 and managed large-scale sequencing efforts based on her universal method for deep sequencing of HIV-1 genomes across the global diversity. Her research focused on (i) evolutionary dynamics of HIV-1 within the host, (ii) interaction of the virus with the adaptive immune system and (iii) influence of viral and host factors on progression to AIDS. Astrid has a wider interest in diversity, evolution and host-virus interaction of medically important, highly variable RNA viruses, concerning animal, human and zoonotic viruses.
Moritz is a Postdoctoral Fellow in the Cancer Genome Project. With Peter Campbell he works on bioinformatics algorithms for analysing and understanding sequencing data from cancer patients.
Fran Glover worked at the Sanger Institute for one week’s work experience with the media and PR team. Fran was 16 at the time she wrote her post and she was attending Stamford High School in Lincolnshire. She had just finished her GCSEs and was expecting to study French, Spanish, Psychology and Biology for her A levels in the next year.
Isabel was a Visiting Scientist at the Sanger Institute with the ERA-EDTA postdoctoral fellowship program. She works under the supervision of Vijay Yadav, studying the mechanisms that underlie bone loss in ageing.
Nicola is a Principal Animal Technician and Named Animal Care and Welfare Officer of the Aquatics area in the Research Support Facility. Nicola works a part of a team of technicians whose interests centre on the dietary and environmental aspects affecting the wellbeing of the aquatic species they manage and care for. Nicola and the team supported the research of the Zebrafish Mutation Project of the Wellcome Sanger Institute.
Deepti is a post-doctoral researcher working with Manj Sandhu at the Sanger Institute. Her research primarily focuses on the study of genetic diversity in Africa, and how this affects disease susceptibility.
Tom is a member of the Parasite genomics group at the Wellcome Sanger Institute.
Chris Illingworth was a Postdoctoral Fellow in the Population Genomics of Molecular Phenotypes group of Ville Mustonen at the Wellcome Sanger Institute. He was interested in the development of mathematical methods for studying evolutionary processes using cutting edge genomic data.
Stavroula was a Postdoctoral Fellow in the team led by Panos Deloukas, Genetics of Complex Traits in Humans at the Wellcome Sanger Institute. She was involved in the investigation of the associations of genetic variants with complex traits in the context of large-scale GWAS meta-analysis, as well as their interactions with environmental and life-style factors.
Sam is currently a chief research scientist at KEMRI and a Sanger International Fellow working on molecular epidemiology of enteric diseases and antimicrobial resistance in Kenya and the region.
Thomas Keane managed the Vertebrate Resequencing Informatics team at the Wellcome Sanger Institute. His team worked on data processing and sequence variation analysis for large-scale sequencing projects such as the Mouse Genomes Project, 1000 genomes project, and the UK10K project. His particular research interests are in computational methods for detecting sequence variation such as transposable elements and using the variants to dissect the link between genotype and phenotype.
Rob works in the Microbial Pathogenesis team at the Institute, with Professor Gordon Dougan. Rob has a particular interest in the evolution of enteric pathogens in order to predict the emergence of new diseases and as a tool to understand the mechanisms by which current pathogens cause disease. He uses this approach to identify new targets for intervention strategies for global health, diagnostics, and the development of novel vaccines.
Katja Kivinen joined MalariaGEN consortium and Sanger Institute Malaria Programme in 2007. She is involved in all stages of human malaria projects, from strategic planning to data analysis, but her main focus is on managing the progress of human DNA samples through genomic pipelines and acting as an interface between pipeline and faculty teams at Sanger Institute and the MalariaGEN coordination centre in Oxford. Katja is interested in understanding how genetic variation affects an individual’s risk of disease.”
Elizabeth is a post doctoral fellow at the Wellcome Sanger Institute, who is working in the group of Gordan Dougan.
Morag was a postdoc in Karen Steel’s team, studying the genetics of deafness. She worked on the identification and characterisation of novel deafness genes, and was particularly interested in unravelling the complex network of genes regulated by the microRNA miR96, which causes hearing loss when mutated. Karen’s team is now at King’s College, London.
Jimmy Liu was a PhD student in the Statistical Genetics team at the Wellcome Sanger Institute. His research is on the genetics of autoimmune diseases, with a focus on immune-related liver and inflammatory bowel diseases. Using a combination of dense genotyping and whole-genome sequencing approaches, it is hoped that the identification of genetic variants that underlie disease susceptibility along with their biological functions will allow us to develop more complete models of how genetic variation contribute to disease aetiology.
Darren joined the Wellcome Sanger Institute faculty in 2010 in the Mouse and zebrafish programme. His team – Genetics of Instinctive Behaviour – combined comparative genomics, reverse genetics, behavioural testing, and neural activation studies to identify and investigate genes involved in the signalling, sensing and processing of olfactory cues that regulate behaviour. They aimed to understand the genes that instruct animals to detect and respond to social signals with highly stereotyped behaviour.
Jane was a Senior Computer Biologist in the human and vertebrate annotation (Havana) team at the Wellcome Sanger Institute. Her work involved manually annotating primarily the human, mouse and zebrafish genomes. More recently she has been involved in community annotation of the pig genome and currently the rat genome. As well as managing a team of manual annotators, Jane is the lead instructor of Open Door Workshops. In conjunction with Wellcome Trust Advanced Courses she presents human, mouse and zebrafish genome workshops around the world.
Iain is a Postdoctoral Fellow in Professor Chris Ponting’s and Professor Thierry Voet’s groups in the Single Cell Genomics Centre at the Wellcome Sanger Institute.
Matthew works in the Sequencing R&D team at the Sanger Institute where he helps to develop Next-Generation Sequencing protocols and transitions them to an operational setting.
Daniel is a Senior Scientist, and Head of the Molecular Biology and Bioinformatics Unit at the International Centre of Insect Physiology and Ecology (icipe), where he leads a group investigating disease vectors, pathogens, and their interactions. His research uses bioinformatics and molecular approaches. His group contributed the discovery of sensory genes involved in olfaction, genes that enable tsetse to respond to stimuli (e.g. for finding hosts, mating pairs, places to lay their larvae and suitable resting sites). Daniel studied at the University of Nairobi, before proceeding to London and Bristol for Postgraduate studies, and was a Postdoctoral Fellow at Glasgow University (where he still holds an Honorary Research Fellowship).
Yasin is a Postdoctoral Fellow who works in Genome Informatics group. He is a physicist by training who now works in bioinformatics and statistical analysis of human genome sequencing projects.
Anna is a social scientist and registered genetic counsellor researching ethics and genomics at the Wellcome Sanger Institute.
Olivo is a Senior Informatics Fellow based in at the Mahidol-Oxford Research Unit (MORU) in Bangkok, whose main interest is the genomic epidemiology of Plasmodium, and its relationship to antimalarial resistance. A member of the Kwiatkowski lab, he divides his time between southeast Asia, the Wellcome Sanger Institute and Oxford University.
Georgina is currently a PhD student in the Genetic Epidemiology group at the Wellcome Sanger Institute and the International Health Research Group at the University of Cambridge, both led by Manjinder Sandhu. Her research focuses on the prevalence and distribution of cardiometabolic risk factors and disease in sub-Saharan Africa. She is also interested in the diagnosis of obesity and diabetes within African populations. Georgina has worked closely in collaboration with the Medical Research Council Uganda to set up and optimise a cross-sectional study on non-communicable diseases in a rural Ugandan cohort.
Zemin Ning is a Senior Scientific Manager. The group he leads, Sequence Assembly & Analysis, provides bioinformatics support for various sequencing projects at the Sanger Institute.
Alena Pance is a staff scientist in the Malaria Programme, where she works with Julian Rayner to develop a stem cell-based system to study the host component of malaria infection.
Alison is a Postdoctoral Research Fellow at the Environmental Futures Research Institute and the School of Environment at Griffith University, Australia, where she is working with Prof Hamish McCallum on Hendra virus disease dynamics in fruit bats.
Gareth worked in the Cell Surface Signalling Laboratory at the Wellcome Sanger Institute and was interested in understanding how muscles are formed in an embryo, from single cells to the beautiful array of multinucleate fibres that comprise each muscle. Gareth studied this in zebrafish embryos to understand better the role of cell surface proteins in cell fusion, a process intrinsic to muscle development.
Adam Reid is a Postdoctoral Fellow in the Parasite Genomics group led by Matt Berriman at the Wellcome Sanger Institute. He is interested in using comparative genomics and transcriptomics to understand host-parasite interactions.
Daniela is a PhD student in the Experimental Cancer Genetics team under the supervision of Dave Adams. She uses exome sequencing to search for alterations in the genomes of familial melanoma patients that predispose them to develop this disease.
Foad is a former clinical PhD student under the supervision of Allan Bradley. His research focussed on genetic and transcriptional variations following reprogramming of cells into induced pluripotent stem cells.
Alistair is a Principal Bioinformatician in Dave Adams’ group at the Wellcome Sanger Institute, uncovering cancer genes using mouse models.
Helena has recently moved from the Pathogen Genomics group to Zürich, where she now has a Marie Curie Fellowship at the Functional Genomics Center Zürich. She is still very interested in Chlamydial infections and is now studying relatives of Chlamydia which infect fish, which is a serious problem in farmed fish.
Aileen was a press officer in the Sanger Institute’s Media, PR and Communications Team.
Damian led a group of computational biologists in the Mouse Informatics Group who sought to make novel insights into gene function and human disease biology using the data emerging from the Mouse Genetics Project and Zebrafish Mutation Project.
Mark is a senior press officer in the Sanger Institute’s Media, PR and Communications Team.
Nick was trained as a wet lab molecular biologist is now a Senior Scientist directing a small research group within Pathogen Genomics at the Wellcome Sanger Institute. His research interests are the enteric bacteria including the Vibrio cholerae, the salmonellae, the yersiniae and shigellae and Chlamydia. The focus of his research is currently the global diversity of bacterial pathogens as well as trends in their long-term and short-term evolution with a view to understanding how this impacts on our understanding of human health. Nick has also spent a considerable amount of time developing the UK and Overseas Pathogen Genomics courses which have now reached 280 participants from 51 countries.
Ana did her PhD in the Microbial Pathogenesis group under the supervision of Professor Gordon Dougan working with phages. She is currently at the European Bioinformatics Institute working in the European Nucleotide Archive project.
Valerie is an advanced research assistant phenotyper on the Mouse Genetics Project Phenotyping Team at the Wellcome Sanger Institute.
Peter is a visiting postdoctoral researcher at the Cancer Genome Project at the Wellcome Sanger Institute. The focus of his research is on cancer genomics, with a specific fascination on copy-number alterations in cancer genomes and on the subclonal architecture and life history of cancers.
Ana in a Postdoctoral researcher at the Departament of Twins Research and Genetics Epidemiology at the King’s College London where she works on the EuroBATS project.
Alan is a microbiologist by training with specific interests in the bacteria that inhabit the gastrointestinal and respiratory tracts of mammalian hosts, particularly in humans and mice. He currently works as a Staff Scientist at the Wellcome Sanger Institute, where he uses state of the art sequencing facilities to better characterise host-associated microbial communities and shed light on the roles these microbes play both in health and in diseases such Cystic Fibrosis, inflammatory bowel disease and infection with Salmonella spp. and Clostridium difficile.
Madushi was a PhD student at the Wellcome Sanger Institute. She worked under the supervision of Gavin Wright and Julian Rayner on the red blood cell invasion pathways of Plasmodium falciparum.
David Wedge is a Senior Staff Scientist in the Cancer Genome Project at the Wellcome Sanger Institute, working on heterogeneity and evolution within prostate and other cancers.
Wei Wei was a PhD student at Sichuan University, China. She joined the Human Evolution team at the Wellcome Sanger Institute as a visiting student in 2011. She is interested in studying human Y chromosome genetic variation.
Jacqui was a principal scientific manager and leader of the Mouse Genetics Project Phenotyping Team at the Wellcome Sanger Institute. Her research interests included extending our knowledge of gene function in order to better understand the process of development and maintenance of our bodies and to investigate what goes wrong when we are affected with debilitating diseases like diabetes, obesity, hearing and vision disorders, blood disorders or cardiovascular disease.
Simon worked in the Ensembl Genebuild team at the Institute, where he developed and ran pipelines for automated genome annotation. He had a particular interest in using next-generation sequencing transcriptome data (RNA-Seq) to improve automated annotation.
Caroline worked at the Wellcome Sanger Institute in Cambridge, where she managed the Deciphering Developmental Disorders project (www.ddduk.org), a UK-wide collaborative translational research study that aims to understand the genetic causes of severe developmental disorders. She was formerly Head of Science at the Foundation for Genomics and Population Health, where she remains a Fellow, and is also a member of the influential personal genomics blog GenomesUnzipped. She trained at the University of Cambridge, where she studied natural sciences followed by a PhD in biochemistry.
James was a senior bioinformatician in the Proteomic Mass Spectrometry team at the Wellcome Sanger Institute. He completed his PhD researching cross species proteomics at Manchester and Liverpool universities and joined the Institute in 2009. His work focused on label free protein quantification and analysis of MSe proteomics data, specifically new methods for proteomics tissue profiling and molecular pathology. Other research directions included the application of machine learning methods for the detection and validation of unexpected post translational modifications in mass spectrometry data, and using proteomics data as an annotation tool in genomics (proteogenomics).
Art is a postdoctoral fellow at the Sanger Institute, where he develops methods to identify mutations that cause genetic disorders. Before joining the Sanger Institute, he worked at an international firm of management consultants.
Yali is a senior staff scientist in the Human Evolution group at The Wellcome Sanger Institute. Her initial interest was in using variation on the Y chromosome to provide insights into aspects of human history and evolution. Now her work has extended to study patterns of variation throughout the entire human genome and to reveal further evolutionary insights, including medically-relevant ones.
Zenon was a postdoctoral fellow in The Sanger Institute Malaria Programme, under Julian Rayner, and he works on P. falciparum molecular genetics.