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Events: Seminars - EBI Internal Seminars
Internal seminars are for staff only and usually take place from 16:00-17:00. There are drinks and nibbles afterwards.
| Event Category |
Seminars |
| Event Subcategory |
EBI Internal Seminars |
| Date |
30th Jun 2011 16:00 |
| Speaker |
Alvis Brazma EBI |
Abstract/
Additional Info |
I will begin with a very popular introduction into the central dogma of
molecular biology and functional genomics. Then I will briefly talk
about why and how the Microarray Team was created at EBI in late 90’s to
deal with new types of data at the time and how it evolved into the
Functional Genomics ‘multi-team’. Who is doing what, about our work on
ArrayExpress, Gene Expression Atlas and, most recently, on BioSample
Database as well as about our research. I will also briefly touch the
new challenges and the potential applications to biomedicine.
|
| Venue |
M203 (in the Cairns Pavilion) |
| Target Audience |
Although this talk is aimed at newcomers, everyone is welcome to attend. |
| Event Category |
Seminars |
| Event Subcategory |
EBI Internal Seminars |
| Date |
31st Mar 2011 16:00 |
| Speaker |
Peter Stoehr |
Abstract/
Additional Info |
As part of the induction process for new staff and fellows we are holding
another of our regular Introductory Seminars both to say welcome to newcomers and to provide insight on the work of the Institute (however this talk is open to all). The talk is normally about half an hour and will be followed by a Q&A session; there will also be some coffee and cake at the end.
|
| Venue |
M203 |
| Event Category |
Seminars |
| Event Subcategory |
EBI Internal Seminars |
| Date |
28th Mar 2011 11:30 to 28th Mar 2011 12:30 |
Abstract/
Additional Info |
The core of the NCRI INI's work is to enable researchers to share data and tools seamlessly for the benefit of scientific advancement and ultimately patients. This entails not only encouraging a willingness to publish and share such data, but also the promotion of its existence and the technical aspects required to make it easy to integrate the data with other resources. |
| Venue |
Courtyard Room, EBI Hinxton |
| Event Type |
Lecture |
| Host |
Victoria Wright, please mail Frank O'Donnell with questions
|
| Event Category |
Seminars |
| Event Subcategory |
EBI Internal Seminars |
| Date |
24th Sep 2010 12:00 to 24th Sep 2010 13:00 |
Abstract/
Additional Info |
Speaker: Guido Barbujani
Title: Human genome diversity: Frequently asked questions
Affiliation: University di Ferrara, Italy
Host: Chris Tyler-Smith
Abstract: Humans have large population sizes, yet they are genetically
less variable than other Primates. Many allele frequencies and
statistical descriptors of genome diversity form broad gradients,
tracing the main expansion from Africa, local migrations, and sometimes
adaptation. However, this continuous variation is discordant across loci
and seems mainly to reflect different blends of common and often
cosmopolitan alleles, rather than the presence of distinct gene pools in
different regions of the world. The elusive structure of human
populations is among the causes (although not the main one) of
difficulties in discovering the loci responsible for quantitative traits
and complex diseases. However, the rapidly growing body of data on our
genome diversity has already cast a new light on human population
history, and is revealing extensive biological relationships among all
members of our species. |
| Venue |
M203 |
| Event Category |
Seminars |
| Event Subcategory |
EBI Internal Seminars |
| Date |
15th Sep 2010 16:00 to 15th Sep 2010 16:00 |
Abstract/
Additional Info |
Jeff Barrett (WTSI)
The case of the missing heritability: clues so far and mysteries remaining
Genome wide association studies (GWAS) have identified
hundreds of genomic loci associated with complex diseases, but have
generally explained only a small fraction of the overall heritability of
these diseases. The question of where this "missing heritability" is
hiding is currently one of the most hotly debated topics in human
genetics. I'll show examples from existing GWAS and related work which
shed some light on missing heritability, and use these data to evaluate
proposed answers, including the "synthetic association" hypothesis. I'll
conclude with a round-up of open questions on the topic and how we might
answer them. |
| Venue |
M203 |
| Host |
Alex Bateman
|
| Event Category |
Seminars |
| Event Subcategory |
EBI Internal Seminars |
| Date |
30th Jul 2010 12:00 to 30th Jul 2010 13:00 |
Abstract/
Additional Info |
Speaker: Victor Velculescu
Affiliation: Associate Professor of Oncology, Director of Cancer
Genetics, Ludwig Center at Johns Hopkins, Co-Director of Cancer Biology,
Johns Hopkins Kimmel Cancer Center.
Title: "Integrated genomic analyses of human cancer"
Abstract: It is generally accepted that cancer is a disease caused by
accumulation of mutations in specific genes. These tumor-specific
mutations provide clues to the cellular processes underlying
tumorigenesis and have proven useful for diagnostic and therapeutic
purposes. To date, however, only a small fraction of the genes has been
analyzed and the number and type of alterations responsible for the
development of many tumor types are unknown. We have recently begun a
systematic study of the cancer genome through analysis of the majority
of protein coding genes in breast, colorectal, pancreatic and brain
cancers. These analyses have identified a wealth of new genes and
pathways that had not been previously linked to human cancer. These
studies define the genetic landscape of human cancers, provide new
targets for personalized intervention, and open fertile avenues for
basic research in tumor biology. |
| Venue |
M203 |
| Event Category |
Seminars |
| Event Subcategory |
EBI Internal Seminars |
| Date |
21st Jul 2010 16:00 to 21st Jul 2010 17:00 |
Abstract/
Additional Info |
WTSI Speaker: Nicole Soranzo
Title: Where to from GWAS in cardio-metabolic traits".
Abstract: Genome-wide association studies have contributed to the
discovery of a large number of genetic loci associated with complex
diseases and quantitative traits that are risk factors for disease.
However, future challenges will be to understand how these genetic
variants affect biological processes and what their possible clinical
utility is. I will describe some initial work in our group using GWAS
for gene discovery and how we are using these discoveries to further our
understanding of disease processes.
EBI Speaker: Julio Saez-Rodriguez
Title: "Comparative logical models of signaling networks in normal and
transformed hepatocytes"
Abstract: Protein interaction networks (PINs or interactomes), protein
signaling networks (PSNs) and gene regulatory networks have successfully
been used to classify drug-target interactions, identify master
transcriptional regulators and uncover new disease genes. Unfortunately,
PINs and PSNs are rarely cell-type specific and do not encode the
input-output relationships required for analyzing receptor-mediated
signaling cascades and the drugs that target them. Conversely,
traditional approaches to studying cell signaling do not make use of the
wealth of information that is now encoded in PINs and PSNs. Here we
describe a hybrid method to convert PSNs into logical models that can be
trained against data in which cells are exposed to-combinations of
ligands and drugs followed by multiplex biochemical measurement of
intracellular responses, and its implementation it in the toolboxes
CellNetOptimizer (Mol. Sys. Biol., 5:331, 2009) and DataRail
(Bioinformatics, 15(24):840, 2008). We apply the method to
distinguishing the topologies of immediate early signaling networks in
primary human hepatocytes and four hepatocellular carcinoma (HCC) cell
lines. We show that five distinct models cluster topologically into
normal and diseased sets, revealing three functional differences between
normal and diseased cells that involve activation of growth factor
receptors and intracellular kinase cascades. In a proof-of-principle
experiment we also infer a target for an I-kappa B kinase inhibitor
developed to treat arthritis and airway inflammation. |
| Venue |
M203 |
| Host |
Alex Bateman
|
| Event Category |
Seminars |
| Event Subcategory |
EBI Internal Seminars |
| Date |
30th Jun 2010 15:30 to 30th Jun 2010 16:30 |
| Speaker |
Natasha Karp |
Abstract/
Additional Info |
Quantitative proteomics, the detection of differential expressed
proteins between sample types, like other -omics introduces many
interesting biostatistical challenges that span three main areas. The
first are the classic experimental design issues, such as how many
samples to measure, or in the planning of what to randomise or
standardise to avoid variables influencing the data. The second
challenge arises from the high-throughput nature where we have a few
readings on many proteins. Finally, we have technological issues that
influence how the data should be processed and interpreted. In this talk
I am going to discuss two studies which consider two of the common
techniques used in proteomics, DiGE and iTRAQ, which highlight these
biostatistical challenges. |
| Venue |
C209/10 |
| Event Category |
Seminars |
| Event Subcategory |
EBI Internal Seminars |
| Date |
18th Jun 2010 14:00 to 18th Jun 2010 15:00 |
| Web Page |
Click here |
| Speaker |
Roy Ruddle University of Leeds, UK |
Abstract/
Additional Info |
This talk will be in three parts: (1) Summarising what we know
about how people navigate in a familiar information space (an
organisation’s intranet), (2) Explaining current research which is
applying “giga-pixel” (large, ultra-high resolution) displays for the
visualization of microscope slides (e.g., for the diagnosis of cancer
funded by the NHS, and EPSRC/Wellcome), and (3) Outlining how giga-pixel
displays could bring major benefits when bioinformatics data are being
analysed. |
| Venue |
M203 |
| Event Category |
Seminars |
| Event Subcategory |
EBI Internal Seminars |
| Date |
18th Jun 2010 12:00 to 18th Jun 2010 13:00 |
| Speaker |
Bartha-Maria Knoppers Universite de Montreal |
| Venue |
Auditorium |
| Event Category |
Seminars |
| Event Subcategory |
EBI Internal Seminars |
| Date |
16th Jun 2010 16:00 to 16th Jun 2010 17:00 |
| Speaker |
Karen Steel (WTSI) / Guy Cochrane (EBI) |
Abstract/
Additional Info |
WTSI Speaker: Karen Steel
Title: "The Mouse Genetics Programme: What has it told us about
deafness?"
Abstract: The Mouse Genetics Programme (MGP) utilises the extensive set
of targeted ES cells from the EUCOMM/KOMP resource to generate around
200 new mouse mutant lines each year. The resulting mutants
(homozygotes if viable, heterozygotes if not) are screened for
indications of many different disease features including over 300
different parameters. We use an electrophysiological assessment of
hearing, the auditory brainstem response (ABR), to detect hearing
impairment. Over 250 lines have been screened so far, and several new
genes have been found to be associated with deafness. None of these
genes were predicted to be involved in deafness beforehand, emphasising
the value of carrying out broad-based phenotypic screening on all
mutants irrespective of prior assumptions about gene function.
EBI Speaker: Guy Cochrane
Title: "The European Nucleotide Archive: a comprehensive public domain
sequence resource"
Abstract: Nucleotide sequence data represent a foundation upon which
most life scientists have come to rely. Providing free and flexible
access to the body of public domain nucleotide sequences is central to
the EBI's
mission. The recently launched European Nucleotide Archive (ENA;
www.ebi.ac.uk/ena) captures and presents the world's primary public
domain nucleotide sequence data. The ENA brings together a number of
pre-existing and new sequence databases covering raw data, assembled
sequence and functional annotation, and presents their content in
unified submission and data retrieval interfaces. Amongst the new
features are a rapid comprehensive sequence similarity search, the
Sequence Read Archive (SRA) next generation sequence repository and
graphical browsing functionalities. In the talk, I will outline how ENA
can be used and discuss areas of the service that are currently
undergoing development. Finally, I will provide a glimpse further into
our thinking for the longer term future, including our response to the
challenge of ever growing data volumes and the provision of
organism-centric access to ENA data. |
| Venue |
M203 |
| Host |
Alex Bateman
|
| Event Category |
Seminars |
| Event Subcategory |
EBI Internal Seminars |
| Date |
15th Jun 2010 12:15 |
| Speaker |
Dr Phil Stephens WTSI |
Abstract/
Additional Info |
Cancer is driven by mutation. Using massively parallel sequencing
technology, we can now sequence the entire genome of cancer samples,
allowing the generation of comprehensive catalogues of somatic mutations
of all classes. The findings from our first handful of genomes
illustrate the potential for next-generation sequencing to provide
unprecedented insights into mutational processes, cellular repair
pathways and gene networks associated with cancer development. |
| Venue |
M203 |
| Event Category |
Seminars |
| Event Subcategory |
EBI Internal Seminars |
| Date |
19th May 2010 16:00 to 19th May 2010 17:00 |
Abstract/
Additional Info |
WTSI Speaker: Richard Durbin.
Title:"A framework for studying human genetic variation"
Abstract: The 1000 Genomes Project has now completed its pilot phase and
entered a production phase to sequence 1100 samples by the end of this
summer and ultimately 2500 samples. Looking beyond this we are entering
an era of genome-wide sequence based genetic studies. To support this I
believe we want a variation reference framework into which new
technology sequence data sets can be placed. My group has worked on
sequence mapping methods and more recently assembly methods, but also we
have begun to explore how we might begin to capture all or nearly all
the genetic diversity in a population, starting with population isolates
with reduced diversity.
Interestingly, the more that is known about a population's genetic
structure, the less data is needed to be collected from any one
individual to predict their genome sequence with very high accuracy.
EBI Speaker: Anton Enright.
Title: Prediction and Analysis of microRNA regulation in Animal Systems. |
| Venue |
M203 |
| Event Category |
Seminars |
| Event Subcategory |
EBI Internal Seminars |
| Date |
14th May 2010 12:00 to 14th May 2010 13:00 |
| Speaker |
Dr David Tuveson Cancer Research UK, Cambridge Research Institute |
Abstract/
Additional Info |
Dr David Tuveson
Title: Cancer Models and Medicine
AbstracT: Pancreatic Cancer and Melanoma are both highly lethal
malignancies with poor systemic therapeutic options. To investigate the
basic biological features of these malignancies and also pursue medical
applications, we generated M. musculus models of these cancers. With our
pancreatic cancer models, we have explored the basis of therapeutic
resistance and have translated our findings to a clinical trial. Also,
our melanoma model has revealed a potential mechanism for the resistance
to first generation Raf kinase inhibitors. These cancer models will
serve as a spring board for the discovery of new pathways pertinent to
the development, maintenance, and eradication of pancreatic cancer and
melanoma. |
| Venue |
M203 |
| Event Category |
Seminars |
| Event Subcategory |
EBI Internal Seminars |
| Date |
7th May 2010 12:00 to 7th May 2010 13:00 |
| Speaker |
Johannes Soeding University of Munich |
Abstract/
Additional Info |
In the main part of my talk, I will investigate the hypothesis
that protein domains, the structural and functional building blocks of
proteins, themselves evolved from smaller, preselected modular
fragments. We investigate this hypothesis using state-of-the-art protein
homology detection methods. Various examples of descendants of these
ancient modules underpin our hypothesis and serve to
illustrate the impact on the continuous vs. discrete nature of fold
space. As an example, we retrace the evolution of the class of outer
membrane beta barrels and show that the entire class descended from a
single beta-beta hairpin module through amplification and subsequent
diversification. In the second part, I will explain the idea of
context-specific alignment at the example of protein sequence searching
and genomic alignments. Finally, I will introduce our new sequence
search method HHblits, which is both faster and considerably more
sensitive than PSI-BLAST and HMMER3.0.
|
| Venue |
M203 |
| Event Category |
Seminars |
| Event Subcategory |
EBI Internal Seminars |
| Date |
30th Apr 2010 12:00 to 30th Apr 2010 13:00 |
Abstract/
Additional Info |
Speaker: Dave Evans - Sanger/EBI Seminar Series
Title/Topic: Genome-wide association studies in the Avon Longitudinal
Study of Parents and Children
Affiliation: University of Bristol
Host: Jeff Barrett
Abstract: The Avon Longitudinal Study of Parents and their Children
(ALSPAC) is a population-based birth cohort study consisting initially
of over 13000 women and their children recruited in the county of Avon,
UK in the early 1990s. Both mothers and children have been extensively
followed from the 8th gestational week onwards using a combination of
self-reported questionnaires, medical records and physical examinations.
Biological samples including DNA have been collected for 10121 of the
children from this cohort. This talk will discuss recent and soon to be
published research that has used the ALSPAC cohort including GWAS
studies of dentition, 2D:4D ratio, bone mineral density, lung function,
birth weight and intelligence, and outline some of the exciting
directions in which the cohort is going, including studies incorporating
gene expression, DNA methylation, and high resolution DNA sequencing.
|
| Venue |
M203 |
| Event Category |
Seminars |
| Event Subcategory |
EBI Internal Seminars |
| Date |
21st Apr 2010 16:00 to 21st Apr 2010 17:00 |
Abstract/
Additional Info |
Speaker: Gavin Wright - WTSI
Title/Topic: Working out ...... how to build muscle.
Abstract: Skeletal muscle is the most abundant tissue in our bodies. It
is composed of long multinucleate fibre-like cells which are created by
the fusion of precursor mononuclear myoblasts. Our current understanding
of how this remarkable process is regulated comes from research using
the fruit fly, Drosophila melanogaster in which two distinct myoblast
subtypes differentially express cell surface receptor proteins that
physically interact. In vertebrates, the functional equivalents of these
interacting receptors have not been identified and it therefore remains
unclear whether a similar regulatory mechanism is used.
In my talk, I will show that we have recently identified a vertebrate
cell surface receptor-ligand pair involved in myoblast recognition and
fusion. By using the experimental advantages afforded by the zebrafish
model, we have determined the biochemical and cellular mechanisms that
underlie this process. We conclude that vertebrates do not regulate
myoblast fusion by the deterministic specification of myoblast subtypes
as in Drosophila, but instead use dynamic local signaling events.
Speaker: Nick Goldman - EBI
Title/Topic: Abstract: I will show evidence from genomic analyses that a
little-regarded mechanism of strand switching during replication is
responsible for numerous mutations in the genomes of humans, other
primates and indeed a wide range of organisms. The result of these
events is the presence in the genome of short (up to 50bp) motif pairs
which are inverse complement to one-another, separated by just a few
bases. These events have occurred throughout the genome, and are still
occurring.
Consequences of this process include the generation of multiple
nucleotide changes in a single step, and the one-step generation of
sequence that will form RNA secondary structures (stems). The sequences
also seem to be maintained by the same process, meaning we now have a
neutral mechanism capable of generating and maintaining potentially
functional sequence. This has consequences for, amongst other things,
the generation of (RNA) function, the interpretation of apparent
compensatory evolution and the assessment of evolutionary divergence
between species. |
| Venue |
M203 |
| Host |
Janet Thornton
|
| Event Category |
Seminars |
| Event Subcategory |
EBI Internal Seminars |
| Date |
17th Mar 2010 16:00 to 17th Mar 2010 17:00 |
Abstract/
Additional Info |
Speaker: Seth Grant - SAC/EBI seminar
Affiliation: WTSI
Title: What has the brain done for the genome?
Abstract: Beneath the complexity of the human brain are molecular
principles shaped by evolution explaining the origins of the behavioural
repertoire. The role of the nervous system is to provide a repertoire of
behaviours allowing the animal to respond and adapt to changing
environments over the course of its life. Multiprotein complexes in the
postsynaptic terminal of synapses control adaptive and cognitive
processes in metazoan nervous systems. These multiprotein complexes are
organised into molecular networks that detect and respond to patterns of
neural activity. Combinations of proteins are use to build different
complexes and pathways producing great diversity. These complexes
evolved from an ancestral core set of proteins controlling adaptive
behaviours in unicellular organisms known as the protosynapse. Later
expansion in numbers and interactions resulted in more complex synapses
in invertebrates and vertebrates. The resultant combinatorial complexity
has contributed to the neuroanatomical, neurophysiological and
behavioural diversity of these species. Mutations in genes encoding the
complexes results in many human diseases of the nervous system. This
general mechanism of cognition provides a useful template for studying
evolution of behaviour in all animals and the basis of disease.
Speaker: Janet Thornton - SAC/EBI seminar
Affiliation: EBI
Title: Understanding the specificity of trans-membrane protein channels
Abstract: Trans-membrane channel proteins are responsible for the
transport of ions and molecules through biological membranes and are
pivotal for the physiology of the cell. Communication both within and
between cellular compartments is mediated in part by these channels.
Their specificity and selectivity to different ions or molecules depends
strongly on the shape, size and amino acid composition of the channel in
the protein. However to date it has proved difficult to understand and
predict this specificity. This is important since the malfunction of
these channels, through mutation or environmental factors, is implicated
in several of the most prevalent diseases (diabetes, myotonia,
Parkinson's disease, etc.).
As crystallisation protocols for membrane proteins become more
effective, there has been a steady stream of new protein structures for
these trans-membrane channel proteins. We have used these structures to
develop new approaches to predicting specificity from structure and
sequence. With new computational tools, we can compare and contrast the
geometry and chemistry of channels and calculate electrostatic profiles
along the channel. These profiles are remarkably conserved within
functional sub-families, yet differ between subfamilies with different
specificities. An overview of our current knowledge of these protein
channels through membranes will be presented, together with a detailed
analysis for the large aquaporin family and the potassium channel
proteins. |
| Venue |
M203 - Cairns Pavilion Shared Facilities |
| Host |
Matt Hurles
|
| Event Category |
Seminars |
| Event Subcategory |
EBI Internal Seminars |
| Date |
17th Feb 2010 16:00 to 17th Feb 2010 17:00 |
| Speaker |
Chris Tyler-Smith WTSI |
| Venue |
M2-03 |
|
